From dmitry.repchevski at bsc.es Sun Aug 3 12:34:48 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Sun, 03 Aug 2008 18:34:48 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> Message-ID: <4895DE28.7010102@bsc.es> Hello Martin, > What do you mean by "implement streaming"? I concluded that you meant > "sending binary data from (or to) a moby service". Is is correct? > yes it is. > This is again a SOAP-based specification, meaning another way how to make an > attachment (correct?). > XOP is the XML way to reference a binary attachment for XML using a reference to it. Even in theory it is not SOAP dependent, the only implementation I know (I may be wrong) is a MTOM that is for SOAP protocol. I couldn't find an implementation for straight XML (because we need a transport for it). > If the protocol for dereferencing is HTTP, we can use MIME type (content-type HTTP header) for > references data. > This is what XOP is about - the only problem is that it can not reference an external resource. It would be great to have something based on Servlet + XML + XOP on java, but I looked at JAX-RS (JSR-311) REST and there is nothing... I had an idea, but afraid it has a problem with an implementation. The idea is to use XML attachment (instead of binary one) and in those attachment put XInclude with a link to external document. Such document itself would be an XML with a binary attachment. So we would have: External resource represented by XML (moby ontology class like MobyImage) + a binary attachment with an image data itself. Then we have a main document with a MobyRef primitive that is encoded as an XML attachment where an attachment itself is an XInclude to the MobyImage. This way the document is assembled into a standard moby message automagically: The only problem is that XInclude works with a plain XML, I think... Cheers, Dmitry From dmitry.repchevski at bsc.es Sun Aug 3 12:48:05 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Sun, 03 Aug 2008 18:48:05 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: References: Message-ID: <4895E145.4060804@bsc.es> Hello Pieter, > ... I'd say pass-by-reference is practically the best solution to improve scalability in a pragmatic way. > This is what I am afraid of... :-( Even have to agree... Pragmatic way is not only to think about a "nice solution" but about an implementation also... So we have resources that could be temporal (like a result of some service execution) and permanent (pdb file). These results may be referenced by external links (using uri) or be internal ones (??? to the some local file). I just like to summarize things... Dmitry From martin.senger at gmail.com Sun Aug 3 22:54:36 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 4 Aug 2008 10:54:36 +0800 Subject: [MOBY-dev] data by reference - a request for comments In-Reply-To: References: <488B0123.3040608@bsc.es> <4d93f07c0807260452g3048765ev6f84be49dc8cf26d@mail.gmail.com> <4d93f07c0807271829v10ff50d5y2c6f83b279256fdb@mail.gmail.com> Message-ID: <4d93f07c0808031954v5e266c63kee2a1e1beac1bad1@mail.gmail.com> Hi all, Thank you for all comments and suggestions. Here is a summary. Before we consider it as an RFC we still need to answer few questions. [So this not yet a call to vote, but it is close to it, I hope. I would rather prefer Mark to make the call when the time is appropriate and the RFC clear.] ------- a) There is one change in the service registration (and, consequently, in the findService() response): A new property "allowingRefs" that contains a list of one or more protocols names (e.g. http or ftp). A service having this property non-empty is able both accepting references from clients and producing references in its responses. Commentary: I would leave it to the Mark/Eddie to specify how exactly this new property appears in the registration and in the findService. ------- b) A client asks for getting back references by including "acceptRefs" attribute in mobyData tag. The attribute lists one or more protocol names that the client can accept. For example: acceptRefs="http,ftp". A client can also send its input data by reference - but only to the services that has a non-empty property "allowingRefs". ------- c) A service can obey a request for references. Question: A service can obey or should obey? ------- d) The format of references: The references are expressed as an XInclude element, with the namespace http://www.w3.org/2001/XInclude. For example: Notice that in this example, there is a "text" - meaning that the references data are non-XML, non-escaped raw data. Such as (notice the non-escaped "greater-than" sign): >sp|Q25158|OPSC2_HEMSA Compound eye opsin BCRH2 OS=Hemigrapsus sanguineus PE=2 SV=1 MTNATGPQMAYYGAASMDFGYPEGVSIVDFVRPEIKPYVHQHWYNYPPVNPMWHYLLGVI YLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTNVPFFTYNCFSGGV WMFSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNGPKLTTGKAVVFALISWV IAIGCALPPFFGWGNYILEGILDSCSYDYLTQDFNTFSYNIFIFVFDYFLPAAIIVFSYV FIVKAIFAHEAAMRAQAKKMNVSTLRSNEADAQRAEIRIAKTALVNVSLWFICWTPYALI SLKGVMGDTSGITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCVHETET KSNDDSQSNSTVAQDKA Commentary, questions: i) I am not sure if we should use XInclude (as above) or rather XLink. Their differences are blurned for me. ii) If using XInclude, are we going to allow also the attribute "xpointer"? I hope not... ------- e) Location of references: The references may be placed inside any XML tag within a BioMoby message. Commentary: God bless those who are going to implement it... ------- f) Protocol and format of the referenced data: The protocol how to get data is specified in the "href" attribute of the "xi:include" tag. The format of referenced data depends where the "xi:include" tag is used: If it is used on any other tag than the primitive type, it has to be an XML complying with the BioMoby message specification, and the "xi:include" tag should have the parse="xml" attribute (or none at all). The same for primitive types when parse="xml" is used. For primitive types with parse="text", the referenced data may be encoded differently as they would in a regular BioMoby message. The new encoding can be specified in the "encoding" attribute of the "xi:include" tag, or - if the HTTP protocol is used - in the HTTP header "Content-type". Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Mon Aug 4 02:32:46 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 04 Aug 2008 08:32:46 +0200 Subject: [MOBY-dev] findService and the hierarchy In-Reply-To: <48899C0B.70408@mpiz-koeln.mpg.de> References: <487C9061.3030203@mpiz-koeln.mpg.de> <4d93f07c0807222009x7c108d25j52930dae4f9ddaf1@mail.gmail.com> <48899C0B.70408@mpiz-koeln.mpg.de> Message-ID: <4896A28E.1070204@mpiz-koeln.mpg.de> Martin Senger wrote: > I posted my results - now it is up to Eddie or Mark to draw > conclusion from that results... could any of you two state something about that ? Thanks Andreas Andreas Groscurth wrote: > i like to bring this up for discussion again ;-) > > thanks > > Martin Senger wrote: >>> In my opinion when searching for services consuming >>> Annotated_GO_Term via >>> the findService method i should also include the service which >>> consumes a >>> GO_Term datatype, as this is the parent datatype (per default >>> 'includeParentDatatype' is true).... >>> >>> >> >> I assume that by "I should also include" you actually meant "the >> registry >> response should also include". Is my understanding correct? >> >> If so, I am afraid that it is not the issue of the jMoby library but the >> registry itself. Eddie or Mark can confirm or reject this hypothesis. >> >> The BioMoby API allows to specify two XML tags when calling findService >> method: the >> >> X >> and >> X >> >> Where X can be either 1 or 0. >> >> The jMoby's findService() method sets these two tags according to the >> two >> boolean parameters that the method can get: >> >> boolean includeChildrenServiceTypes >> and >> boolean includeParentDataTypes >> >> I have tried to call the findService, with the Annotated_GO_Term input, >> using all combinations of these two tags (you can do it using the Moby >> command-line client with the optioins -nc and/or -np). The results are >> either no service or 713 services: >> >> expandObjects expandServices # of found services >> 1 1 713 >> 0 0 0 >> 1 0 713 >> 0 0 0 >> >> I have feeling that this is not a correct result. Could Eddie or Mark >> perhaps comment on it? >> >> [I vaguely remember that we had this conversation about these tags >> with Mark >> years(!) ago - but I do not recall what was the conclusion. I only, and >> again vaguely, remember to have this issue in my to-do list - which >> would >> indicate that something could be done in the jMoby library.] >> >> Cheers, >> Martin >> >> > > -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== From jmfernandez at cnio.es Mon Aug 4 06:53:58 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Mon, 04 Aug 2008 12:53:58 +0200 Subject: [MOBY-dev] data by reference - a request for comments In-Reply-To: <4d93f07c0808031954v5e266c63kee2a1e1beac1bad1@mail.gmail.com> References: <488B0123.3040608@bsc.es> <4d93f07c0807260452g3048765ev6f84be49dc8cf26d@mail.gmail.com> <4d93f07c0807271829v10ff50d5y2c6f83b279256fdb@mail.gmail.com> <4d93f07c0808031954v5e266c63kee2a1e1beac1bad1@mail.gmail.com> Message-ID: <4896DFC6.9040204@cnio.es> Hi everybody, here you are my "vacation" thoughts/comments about the different points, just inline: Martin Senger wrote: > Hi all, > > Thank you for all comments and suggestions. Here is a summary. Before > we consider it as an RFC we still need to answer few questions. > > [So this not yet a call to vote, but it is close to it, I hope. I > would rather prefer Mark to make the call when the time is appropriate > and the RFC clear.] > > ------- > a) There is one change in the service registration (and, consequently, > in the findService() response): A new property "allowingRefs" that > contains a list of one or more protocols names (e.g. http or ftp). A > service having this property non-empty is able both accepting > references from clients and producing references in its responses. > > Commentary: I would leave it to the Mark/Eddie to specify how exactly > this new property appears in the registration and in the findService. > I would split the proposed property in the two roles it plays: one for the acceptable reference types, and one for the possibly generated reference types. Many services will be able to accept reference types of http, ftp or other kinds, but I think they usually are only able to generate answers with fewer or different ones. > ------- > b) A client asks for getting back references by including "acceptRefs" > attribute in mobyData tag. The attribute lists one or more protocol > names that the client can accept. For example: acceptRefs="http,ftp". > A client can also send its input data by reference - but only to the > services that has a non-empty property "allowingRefs". > As all mobyData blocks are sent to the same service, I'd rather attach "acceptRefs" to mobyContent instead of mobyData, but it is only to avoid redundancy. > ------- > c) A service can obey a request for references. > > Question: A service can obey or should obey? > These are some scenarios: 1) A client cannot understand references, so the service's answers do not contain references. 2) A service cannot generate references, so the service's answers do not contain references. 3) A client tells what kind of references it understands, but it is not the same subset as the service is able to generate, so the service's answer do not contain references. 4) There is a common subset of reference types understood by both the client and the service, so the service's answer does contain references (if it is needed). Surely there are more interesting scenarios out there. > ------- > d) The format of references: The references are expressed as an > XInclude element, with the namespace > http://www.w3.org/2001/XInclude. For example: > > > > > > > > > > Notice that in this example, there is a "text" - meaning that the > references data are non-XML, non-escaped raw data. Such as (notice the > non-escaped "greater-than" sign): > >> sp|Q25158|OPSC2_HEMSA Compound eye opsin BCRH2 OS=Hemigrapsus sanguineus > PE=2 SV=1 > MTNATGPQMAYYGAASMDFGYPEGVSIVDFVRPEIKPYVHQHWYNYPPVNPMWHYLLGVI > YLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTNVPFFTYNCFSGGV > WMFSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNGPKLTTGKAVVFALISWV > IAIGCALPPFFGWGNYILEGILDSCSYDYLTQDFNTFSYNIFIFVFDYFLPAAIIVFSYV > FIVKAIFAHEAAMRAQAKKMNVSTLRSNEADAQRAEIRIAKTALVNVSLWFICWTPYALI > SLKGVMGDTSGITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCVHETET > KSNDDSQSNSTVAQDKA > > Commentary, questions: > > i) I am not sure if we should use XInclude (as > above) or rather XLink. Their differences are blurned for me. > XLink (2001) was superseded by XInclude (second revision in 2006). Next links points to the relationship between XInclude and XLink http://www.w3.org/TR/xinclude/#rel-xlink > ii) If using XInclude, are we going to allow also the attribute > "xpointer"? I hope not... > I would love that feature because it would allow referencing fragments of any XML content. The only problem is that there is (almost) no memory efficient implementation for XPath (used in "xpointer" feature) applied to disk stored XML content. Perhaps Saxon in Java side, but I don't know... > ------- > e) Location of references: The references may be placed inside any XML > tag within a BioMoby message. > > Commentary: God bless those who are going to implement it... > It would be very easy using "xpointer" feature from XInclude, and in that case the sentence would be again right: "God bless those who are going to implement it..." > ------- > f) Protocol and format of the referenced data: The protocol how to get > data is specified in the "href" attribute of the "xi:include" tag. > > The format of referenced data depends where the "xi:include" tag is > used: > > If it is used on any other tag than the primitive type, it has > to be an XML complying with the BioMoby message specification, and the > "xi:include" tag should have the parse="xml" attribute (or none at > all). The same for primitive types when parse="xml" is used. > > For primitive types with parse="text", the referenced data may be > encoded differently as they would in a regular BioMoby message. The > new encoding can be specified in the "encoding" attribute of the > "xi:include" tag, or - if the HTTP protocol is used - in the HTTP > header "Content-type". > > Cheers, > Martin > Nice holidays, Jos? Mar?a -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. 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From py at pingoured.fr Mon Aug 4 07:05:47 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Mon, 04 Aug 2008 13:05:47 +0200 Subject: [MOBY-dev] php client for biomoby services In-Reply-To: <488f3612.20d7720a.6190.1e4a@mx.google.com> References: <488EDE46.5070804@pingoured.fr> <488f3612.20d7720a.6190.1e4a@mx.google.com> Message-ID: <4896E28B.5060206@pingoured.fr> Edward Kawas wrote: > Just in case, you didn't get it working (I am sure that you did, but just in > case ...), I attached 2 php files that you can test with. > > The test client is in the file 'moby_php_test_service.php' and the > moby_soap_factory.php needs to be either in the same directory as the test > service or on your PHP include path. > > Thanks to Julian Tonti-Filippini for creating the PHP basis for the attached > examples! Thanks to him indeed, and thanks to you :) It is working here now. Thanks again, Regards, Pierre From martin.senger at gmail.com Mon Aug 4 22:21:57 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 5 Aug 2008 10:21:57 +0800 Subject: [MOBY-dev] data by reference - a request for comments In-Reply-To: <4896DFC6.9040204@cnio.es> References: <488B0123.3040608@bsc.es> <4d93f07c0807260452g3048765ev6f84be49dc8cf26d@mail.gmail.com> <4d93f07c0807271829v10ff50d5y2c6f83b279256fdb@mail.gmail.com> <4d93f07c0808031954v5e266c63kee2a1e1beac1bad1@mail.gmail.com> <4896DFC6.9040204@cnio.es> Message-ID: <4d93f07c0808041921q78a160e3qe6a4bed8ce9e29b1@mail.gmail.com> > I would split the proposed property in the two roles it plays: one for the > acceptable reference types, and one for the possibly generated reference > types. Many services will be able to accept reference types of http, ftp or > other kinds, but I think they usually are only able to generate answers with > fewer or different ones. I do not think that the situations will be drastically different for accepting and producing references - but I do not have any issue with it. I do not mind much how many new properties will be added to the central registry. As all mobyData blocks are sent to the same service, I'd rather attach > "acceptRefs" to mobyContent instead of mobyData, but it is only to avoid > redundancy. Again, no problem with me. These are some scenarios: My question was: if a service claims that it can produce a reference, and a client asks for it, should the service always produce a reference? I think that my question was obsolete already in the time of asking it. I am withdrawing my question, assuming the obvious answer for the above is "yes, it should". XLink (2001) was superseded by XInclude (second revision in 2006). Next > links points to the relationship between XInclude and XLink > > http://www.w3.org/TR/xinclude/#rel-xlink > Yes, I saw and read this link - but, as often with me when I read the w3 documents , I could not understand what is different, at all. I am glad, however, that XInclude is considered as a supersedor (I guess this word probably does not exist in Egnlish) of XLink. So we go with XInclude. I would love that feature because it would allow referencing fragments of > any XML content. The only problem is that there is (almost) no memory > efficient implementation for XPath (used in "xpointer" feature) applied to > disk stored XML content. This is exactly why I suggested not to allow it. I would prefer to stick to my guns on this issue. Many thanks for replying from the holidays. What about the others? Can we go ahead? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From dmitry.repchevski at bsc.es Tue Aug 5 04:54:29 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 05 Aug 2008 10:54:29 +0200 Subject: [MOBY-dev] data by reference - a request for comments In-Reply-To: <4d93f07c0808041921q78a160e3qe6a4bed8ce9e29b1@mail.gmail.com> References: <4d93f07c0808041921q78a160e3qe6a4bed8ce9e29b1@mail.gmail.com> Message-ID: <48981545.1010105@bsc.es> Hello Martin, > Yes, I saw and read this link - but, as often with me when I read the w3 > documents , I could not understand what is different, at all. I am glad, > however, that XInclude is considered as a supersedor (I guess this word > probably does not exist in Egnlish) of XLink. So we go with XInclude. > There is a big difference between two. XLink is a formalization of links inside XML. It doesn't specify the way of processing. For an XML parser it's nothing but a set of attributes with xlink namespace. Here is excerpt from XInclude specs: > XLink does not specify a specific processing model, but simply > facilitates the detection of links and recognition of associated > metadata by a higher level application. On the other hand, > XInclude specifies a media-type specific (XML into XML) > transformation. It defines a specific processing model for merging > information sets. XInclude processing occurs at a low level, often by > a generic XInclude processor which makes the resulting information set > available to higher level applications. Once you include XInclude into your XML it's up to a XML parser (in case it supports XInclude) to merge two XML (!) documents. XInclude can treat the embedded document as an "xml" or as a "text" (in this way it will be escaped). I wouldn't say that XInclude is "superior" to XLink - it's just for another purpose. You can not to reference things with XInclude, but only inject another resource (xml or text). You can put a reference using XLink, but in this way all the processing must be done by hand. Best regards, Dmitry From martin.senger at gmail.com Tue Aug 5 05:03:10 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 5 Aug 2008 17:03:10 +0800 Subject: [MOBY-dev] data by reference - a request for comments In-Reply-To: <48981545.1010105@bsc.es> References: <4d93f07c0808041921q78a160e3qe6a4bed8ce9e29b1@mail.gmail.com> <48981545.1010105@bsc.es> Message-ID: <4d93f07c0808050203l823c531v937537110e7990ef@mail.gmail.com> > Once you include XInclude into your XML it's up to a XML parser (in case it > supports XInclude) to merge two XML (!) documents. Yes, I understand it. And I hope (from reading some pages) that a parser could be said *not* to do the merging. Because that would prevent the main reason why we are going to have references , after all - which is the memory management. We should try if the current and obvious parsers can be instructed *not* to include XInclude automatically, but let us to do it... Anybody has tried it? Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Tue Aug 5 08:46:41 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 5 Aug 2008 05:46:41 -0700 Subject: [MOBY-dev] findService and the hierarchy In-Reply-To: <4896A28E.1070204@mpiz-koeln.mpg.de> References: <487C9061.3030203@mpiz-koeln.mpg.de> <4d93f07c0807222009x7c108d25j52930dae4f9ddaf1@mail.gmail.com> <48899C0B.70408@mpiz-koeln.mpg.de> <4896A28E.1070204@mpiz-koeln.mpg.de> Message-ID: <48984bd1.14b48c0a.3dff.ffffe18e@mx.google.com> Hi Andreas, I believe that the results are correct. There are no services in the default registry that consume Annotated_GO_Term. 1 service that consumes its parent (GO_Term) and 689 services that strictly consume Object. When you set the flag, includeParentDatatype, the behaviour is like doing a findservice for services that consume Annotated_GO_Term or any parent type up to and including Object with includeParentDatatype=false. Does this make sense? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth Sent: August-03-08 11:33 PM To: Core developer announcements Subject: Re: [MOBY-dev] findService and the hierarchy Martin Senger wrote: > I posted my results - now it is up to Eddie or Mark to draw > conclusion from that results... could any of you two state something about that ? Thanks Andreas Andreas Groscurth wrote: > i like to bring this up for discussion again ;-) > > thanks > > Martin Senger wrote: >>> In my opinion when searching for services consuming >>> Annotated_GO_Term via >>> the findService method i should also include the service which >>> consumes a >>> GO_Term datatype, as this is the parent datatype (per default >>> 'includeParentDatatype' is true).... >>> >>> >> >> I assume that by "I should also include" you actually meant "the >> registry >> response should also include". Is my understanding correct? >> >> If so, I am afraid that it is not the issue of the jMoby library but the >> registry itself. Eddie or Mark can confirm or reject this hypothesis. >> >> The BioMoby API allows to specify two XML tags when calling findService >> method: the >> >> X >> and >> X >> >> Where X can be either 1 or 0. >> >> The jMoby's findService() method sets these two tags according to the >> two >> boolean parameters that the method can get: >> >> boolean includeChildrenServiceTypes >> and >> boolean includeParentDataTypes >> >> I have tried to call the findService, with the Annotated_GO_Term input, >> using all combinations of these two tags (you can do it using the Moby >> command-line client with the optioins -nc and/or -np). The results are >> either no service or 713 services: >> >> expandObjects expandServices # of found services >> 1 1 713 >> 0 0 0 >> 1 0 713 >> 0 0 0 >> >> I have feeling that this is not a correct result. Could Eddie or Mark >> perhaps comment on it? >> >> [I vaguely remember that we had this conversation about these tags >> with Mark >> years(!) ago - but I do not recall what was the conclusion. I only, and >> again vaguely, remember to have this issue in my to-do list - which >> would >> indicate that something could be done in the jMoby library.] >> >> Cheers, >> Martin >> >> > > -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Tue Aug 5 09:06:56 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 05 Aug 2008 15:06:56 +0200 Subject: [MOBY-dev] findService and the hierarchy In-Reply-To: <48984bd1.14b48c0a.3dff.ffffe18e@mx.google.com> References: <487C9061.3030203@mpiz-koeln.mpg.de> <4d93f07c0807222009x7c108d25j52930dae4f9ddaf1@mail.gmail.com> <48899C0B.70408@mpiz-koeln.mpg.de> <4896A28E.1070204@mpiz-koeln.mpg.de> <48984bd1.14b48c0a.3dff.ffffe18e@mx.google.com> Message-ID: <48985070.6020804@mpiz-koeln.mpg.de> Hi, oh my god... i mixed inputs and outputs... yes there is no service which consumes Annotated_GO_Term... there are only services which returns it. So the find service call only checks for the inputs then ? Or is it possible to find a service which consumes an object with a specific namespace and returns an Annotated_GO_Term object or its parent? currently i ask for each output definition by its own. Sorry again for the confusion .... Andreas Edward Kawas wrote: > Hi Andreas, > > I believe that the results are correct. > > There are no services in the default registry that consume > Annotated_GO_Term. 1 service that consumes its parent (GO_Term) and 689 > services that strictly consume Object. > > When you set the flag, includeParentDatatype, the behaviour is like doing a > findservice for services that consume Annotated_GO_Term or any parent type > up to and including Object with includeParentDatatype=false. > > Does this make sense? > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth > Sent: August-03-08 11:33 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] findService and the hierarchy > > Martin Senger wrote: > > >> I posted my results - now it is up to Eddie or Mark to draw >> conclusion from that results... >> > > > could any of you two state something about that ? > > Thanks > Andreas > > Andreas Groscurth wrote: > >> i like to bring this up for discussion again ;-) >> >> thanks >> >> Martin Senger wrote: >> >>>> In my opinion when searching for services consuming >>>> Annotated_GO_Term via >>>> the findService method i should also include the service which >>>> consumes a >>>> GO_Term datatype, as this is the parent datatype (per default >>>> 'includeParentDatatype' is true).... >>>> >>>> >>>> >>> I assume that by "I should also include" you actually meant "the >>> registry >>> response should also include". Is my understanding correct? >>> >>> If so, I am afraid that it is not the issue of the jMoby library but the >>> registry itself. Eddie or Mark can confirm or reject this hypothesis. >>> >>> The BioMoby API allows to specify two XML tags when calling findService >>> method: the >>> >>> X >>> and >>> X >>> >>> Where X can be either 1 or 0. >>> >>> The jMoby's findService() method sets these two tags according to the >>> two >>> boolean parameters that the method can get: >>> >>> boolean includeChildrenServiceTypes >>> and >>> boolean includeParentDataTypes >>> >>> I have tried to call the findService, with the Annotated_GO_Term input, >>> using all combinations of these two tags (you can do it using the Moby >>> command-line client with the optioins -nc and/or -np). The results are >>> either no service or 713 services: >>> >>> expandObjects expandServices # of found services >>> 1 1 713 >>> 0 0 0 >>> 1 0 713 >>> 0 0 0 >>> >>> I have feeling that this is not a correct result. Could Eddie or Mark >>> perhaps comment on it? >>> >>> [I vaguely remember that we had this conversation about these tags >>> with Mark >>> years(!) ago - but I do not recall what was the conclusion. I only, and >>> again vaguely, remember to have this issue in my to-do list - which >>> would >>> indicate that something could be done in the jMoby library.] >>> >>> Cheers, >>> Martin >>> >>> >>> >> > > > -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== From edward.kawas at gmail.com Tue Aug 5 09:09:38 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 5 Aug 2008 06:09:38 -0700 Subject: [MOBY-dev] findService and the hierarchy In-Reply-To: <48985070.6020804@mpiz-koeln.mpg.de> References: <487C9061.3030203@mpiz-koeln.mpg.de> <4d93f07c0807222009x7c108d25j52930dae4f9ddaf1@mail.gmail.com> <48899C0B.70408@mpiz-koeln.mpg.de> <4896A28E.1070204@mpiz-koeln.mpg.de> <48984bd1.14b48c0a.3dff.ffffe18e@mx.google.com> <48985070.6020804@mpiz-koeln.mpg.de> Message-ID: <48985132.2a528c0a.468b.608f@mx.google.com> Currently, the flag only works on inputs. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth Sent: August-05-08 6:07 AM To: Core developer announcements Subject: Re: [MOBY-dev] findService and the hierarchy Hi, oh my god... i mixed inputs and outputs... yes there is no service which consumes Annotated_GO_Term... there are only services which returns it. So the find service call only checks for the inputs then ? Or is it possible to find a service which consumes an object with a specific namespace and returns an Annotated_GO_Term object or its parent? currently i ask for each output definition by its own. Sorry again for the confusion .... Andreas Edward Kawas wrote: > Hi Andreas, > > I believe that the results are correct. > > There are no services in the default registry that consume > Annotated_GO_Term. 1 service that consumes its parent (GO_Term) and 689 > services that strictly consume Object. > > When you set the flag, includeParentDatatype, the behaviour is like doing a > findservice for services that consume Annotated_GO_Term or any parent type > up to and including Object with includeParentDatatype=false. > > Does this make sense? > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth > Sent: August-03-08 11:33 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] findService and the hierarchy > > Martin Senger wrote: > > >> I posted my results - now it is up to Eddie or Mark to draw >> conclusion from that results... >> > > > could any of you two state something about that ? > > Thanks > Andreas > > Andreas Groscurth wrote: > >> i like to bring this up for discussion again ;-) >> >> thanks >> >> Martin Senger wrote: >> >>>> In my opinion when searching for services consuming >>>> Annotated_GO_Term via >>>> the findService method i should also include the service which >>>> consumes a >>>> GO_Term datatype, as this is the parent datatype (per default >>>> 'includeParentDatatype' is true).... >>>> >>>> >>>> >>> I assume that by "I should also include" you actually meant "the >>> registry >>> response should also include". Is my understanding correct? >>> >>> If so, I am afraid that it is not the issue of the jMoby library but the >>> registry itself. Eddie or Mark can confirm or reject this hypothesis. >>> >>> The BioMoby API allows to specify two XML tags when calling findService >>> method: the >>> >>> X >>> and >>> X >>> >>> Where X can be either 1 or 0. >>> >>> The jMoby's findService() method sets these two tags according to the >>> two >>> boolean parameters that the method can get: >>> >>> boolean includeChildrenServiceTypes >>> and >>> boolean includeParentDataTypes >>> >>> I have tried to call the findService, with the Annotated_GO_Term input, >>> using all combinations of these two tags (you can do it using the Moby >>> command-line client with the optioins -nc and/or -np). The results are >>> either no service or 713 services: >>> >>> expandObjects expandServices # of found services >>> 1 1 713 >>> 0 0 0 >>> 1 0 713 >>> 0 0 0 >>> >>> I have feeling that this is not a correct result. Could Eddie or Mark >>> perhaps comment on it? >>> >>> [I vaguely remember that we had this conversation about these tags >>> with Mark >>> years(!) ago - but I do not recall what was the conclusion. I only, and >>> again vaguely, remember to have this issue in my to-do list - which >>> would >>> indicate that something could be done in the jMoby library.] >>> >>> Cheers, >>> Martin >>> >>> >>> >> > > > -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Thu Aug 7 11:12:09 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 7 Aug 2008 08:12:09 -0700 Subject: [MOBY-dev] perl async services Message-ID: <489b10ce.1f538c0a.7a83.7c57@mx.google.com> Hi, I have a quick question to whomever has developed async services in perl using the MOBY::Async/WSRF modules. Is it true that there is a strict one dispatcher file to one service? For instance, the documentation for the module MOBY::Async has the following dispatcher.cgi example: dispatcher.cgi #!/usr/bin/perl BEGIN { @INC = ("/path/to/my/libs", @INC); } use strict; use SOAP::Transport::HTTP; use MOBY::Async::WSRF; use HelloWorld; my $server = new SOAP::Transport::HTTP::CGI; $server->serializer(WSRF::Serializer->new); $server->deserializer(WSRF::Deserializer->new); $server->on_action(sub{}); $server->dispatch_with({ $WSRF::Constants::MOBY.'#sayHello' => 'HelloWorld', $WSRF::Constants::MOBY.'#sayHello_submit' => 'HelloWorld', -> $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' => 'HelloWorld', -> $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourceP ropertiesRequest' => 'HelloWorld', -> $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' => 'HelloWorld', }); $server->handle(); Notice the lines prefixed with '->' hard code GetResourceProperty, etc map to a specific service. Is there any way around this? Thanks, Eddie From jmfernandez at cnio.es Thu Aug 7 12:48:31 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Thu, 07 Aug 2008 18:48:31 +0200 Subject: [MOBY-dev] perl async services In-Reply-To: <489b10ce.1f538c0a.7a83.7c57@mx.google.com> References: <489b10ce.1f538c0a.7a83.7c57@mx.google.com> Message-ID: <489B275F.50009@cnio.es> Hi Eddie, although the example shows only one service, you are not restricted to only one. About GetResourceProperty, GetMultipleResourceProperties and ImmediateResourceTermination, they are document/literal SOAP services based on WSRF specifications. If your service code is inheriting from MOBY::Async::SimpleServer, then you do not have to implement them, because MOBY::Async::SimpleServer takes care of them. The way MOBY::Async libraries work are the next: * They have been built on top of WSRF::Lite libraries, so they reuse as much routines as possible. That's the reason why Perl modules containing asynchronous services implementations must inherit from MOBY::Async::SimpleServer (typical 'use base qw(MOBY::Async::SimpleServer);' sentence). * Asynchronous services creators/coders only have to write the corresponding job routines as they were creating a synchronous MOBY service. All the job ticket generation, job management, job result status & storage, etc... work is handled either by WSRF::Lite or MOBY::Async::SimpleServer, and in most of cases only depends on job Id. As job routines are passed on job creation, they must be either functions passed by reference to the job creation statement or being anonymous functions assigned to a variable, used as input parameter for the job creation statement. For those of you interested on, the ticket, state, results, etc... information is stored in /tmp. This point should be more configurable, and we will fix it on September. I have attached an untested example of two asynchronous services using the same dispatcher and module. Best Regards from M?laga, Jos? Mar?a (on behalf Jos? Manuel and myself) Edward Kawas wrote: > Hi, > > I have a quick question to whomever has developed async services in perl > using the MOBY::Async/WSRF modules. Is it true that there is a strict one > dispatcher file to one service? > > For instance, the documentation for the module MOBY::Async has the following > dispatcher.cgi example: > > dispatcher.cgi > > #!/usr/bin/perl > BEGIN { @INC = ("/path/to/my/libs", @INC); } > use strict; > use SOAP::Transport::HTTP; > use MOBY::Async::WSRF; > use HelloWorld; > > my $server = new SOAP::Transport::HTTP::CGI; > $server->serializer(WSRF::Serializer->new); > $server->deserializer(WSRF::Deserializer->new); > $server->on_action(sub{}); > $server->dispatch_with({ > $WSRF::Constants::MOBY.'#sayHello' => 'HelloWorld', > $WSRF::Constants::MOBY.'#sayHello_submit' => 'HelloWorld', > -> > $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' => > 'HelloWorld', > -> > $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourceP > ropertiesRequest' => 'HelloWorld', > -> $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' > => 'HelloWorld', > }); > $server->handle(); > > Notice the lines prefixed with '->' hard code GetResourceProperty, etc map > to a specific service. Is there any way around this? > > Thanks, > > Eddie > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. -------------- next part -------------- A non-text attachment was scrubbed... Name: two-async-MOBY-test.cgi.pl Type: application/x-perl Size: 980 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TwoAsyncService.pm Type: application/x-perl Size: 2276 bytes Desc: not available URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: two-async-MOBY-test.cgi URL: From edward.kawas at gmail.com Thu Aug 7 13:14:12 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 7 Aug 2008 10:14:12 -0700 Subject: [MOBY-dev] perl async services In-Reply-To: <489B275F.50009@cnio.es> References: <489b10ce.1f538c0a.7a83.7c57@mx.google.com> <489B275F.50009@cnio.es> Message-ID: <489b2d6a.02578c0a.485f.ffffc011@mx.google.com> Thanks for the quick response! So your example have both service implementations inside of one file. Is it possible to have more than one service referenced in the dispatcher without have the implementations in the same package? i.e. ('->' shows what I mean): $server->dispatch_with({ -> $WSRF::Constants::MOBY.'#serviceOne' => 'OneAsyncService', -> $WSRF::Constants::MOBY.'#serviceOne_submit' => 'OneAsyncService', $WSRF::Constants::MOBY.'#serviceTwo' => 'TwoAsyncService', $WSRF::Constants::MOBY.'#serviceTwo_submit' => 'TwoAsyncService', $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' => 'TwoAsyncService', $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourceP ropertiesRequest' => 'TwoAsyncService', $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' => 'TwoAsyncService', }); Thanks again, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jos? Mar?a Fern?ndez Gonz?lez Sent: August-07-08 9:49 AM To: Core developer announcements Subject: Re: [MOBY-dev] perl async services Hi Eddie, although the example shows only one service, you are not restricted to only one. About GetResourceProperty, GetMultipleResourceProperties and ImmediateResourceTermination, they are document/literal SOAP services based on WSRF specifications. If your service code is inheriting from MOBY::Async::SimpleServer, then you do not have to implement them, because MOBY::Async::SimpleServer takes care of them. The way MOBY::Async libraries work are the next: * They have been built on top of WSRF::Lite libraries, so they reuse as much routines as possible. That's the reason why Perl modules containing asynchronous services implementations must inherit from MOBY::Async::SimpleServer (typical 'use base qw(MOBY::Async::SimpleServer);' sentence). * Asynchronous services creators/coders only have to write the corresponding job routines as they were creating a synchronous MOBY service. All the job ticket generation, job management, job result status & storage, etc... work is handled either by WSRF::Lite or MOBY::Async::SimpleServer, and in most of cases only depends on job Id. As job routines are passed on job creation, they must be either functions passed by reference to the job creation statement or being anonymous functions assigned to a variable, used as input parameter for the job creation statement. For those of you interested on, the ticket, state, results, etc... information is stored in /tmp. This point should be more configurable, and we will fix it on September. I have attached an untested example of two asynchronous services using the same dispatcher and module. Best Regards from M?laga, Jos? Mar?a (on behalf Jos? Manuel and myself) Edward Kawas wrote: > Hi, > > I have a quick question to whomever has developed async services in > perl using the MOBY::Async/WSRF modules. Is it true that there is a > strict one dispatcher file to one service? > > For instance, the documentation for the module MOBY::Async has the > following dispatcher.cgi example: > > dispatcher.cgi > > #!/usr/bin/perl > BEGIN { @INC = ("/path/to/my/libs", @INC); } > use strict; > use SOAP::Transport::HTTP; > use MOBY::Async::WSRF; > use HelloWorld; > > my $server = new SOAP::Transport::HTTP::CGI; > $server->serializer(WSRF::Serializer->new); > $server->deserializer(WSRF::Deserializer->new); > $server->on_action(sub{}); > $server->dispatch_with({ > $WSRF::Constants::MOBY.'#sayHello' => 'HelloWorld', > $WSRF::Constants::MOBY.'#sayHello_submit' => 'HelloWorld', > -> > $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyReque > st' => 'HelloWorld', > -> > $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleRes > ourceP > ropertiesRequest' => 'HelloWorld', > -> $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' > => 'HelloWorld', > }); > $server->handle(); > > Notice the lines prefixed with '->' hard code GetResourceProperty, etc > map to a specific service. Is there any way around this? > > Thanks, > > Eddie > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From r.ranzinger at dkfz-heidelberg.de Fri Aug 8 05:30:15 2008 From: r.ranzinger at dkfz-heidelberg.de (=?ISO-8859-15?Q?Ren=E9_Ranzinger?=) Date: Fri, 08 Aug 2008 11:30:15 +0200 Subject: [MOBY-dev] Problems with service registration using dashboard Message-ID: <489C1227.6010808@dkfz-heidelberg.de> HI, the last two day's I tried to register some new moby services with the dashboard (I used dashboard for registration several times before). During the registration an error window pops up with this message : ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: org.xml.sax.SAXParseException: Invalid byte 1 of 1-byte UTF-8 sequence. Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException Fault actor: null When calling: http://moby.ucalgary.ca/moby/MOBY-Central.pl =========== The service does not occur in the service list and if I do a update of the service list I get this error : Error creating input stream: java.io.IOException: Server returned HTTP response code: 500 for URL: http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances The last error disappear after some time, so that a update is possible, but still the service is not in the list. I tried two instances of Dashboard at two different computers and operation systems. I also tried to register via the stored registration XML : mobygetGlycomeIdByCarbohydrateRetrievalwww.glycome-db.orghttp://www.glycome-db.org/moby/getGlycomeIdByCarbohydrater.ranzinger at dkfz.de0 GlycomicsObject GlycomicsObject Does anyone have an idea whats the problem? Ren? From martin.senger at gmail.com Fri Aug 8 05:37:28 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 8 Aug 2008 17:37:28 +0800 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <489C1227.6010808@dkfz-heidelberg.de> References: <489C1227.6010808@dkfz-heidelberg.de> Message-ID: <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> > Fault string: org.xml.sax.SAXParseException: Invalid byte 1 of 1-byte > UTF-8 sequence. This may be because of the non-ascii characters in your service description. It should not be like that - but if you remove letters with the German accents, it will pass. We (developers) should look at it on which layer the problem occurs - but for you, this is the fastest workaround for now. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Fri Aug 8 06:14:10 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 08 Aug 2008 12:14:10 +0200 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> Message-ID: <489C1C72.5000402@mpiz-koeln.mpg.de> i confirm that this comes from an non-ascii character. I registered a service which has some german accents (ae, oe etc) and i got some errors during registration. ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: java.io.UTFDataFormatException: Invalid byte 2 of 3-byte UTF-8 sequence. Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException Fault actor: null When calling: http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl =========== it seems to register, because registering it does not work (you have to unregister first). But loading the services also fail due to this service. So as martin said, for this time avoid any german specific character. Best Andreas Martin Senger wrote: >> Fault string: org.xml.sax.SAXParseException: Invalid byte 1 of 1-byte >> UTF-8 sequence. >> > > > This may be because of the non-ascii characters in your service description. > It should not be like that - but if you remove letters with the German > accents, it will pass. We (developers) should look at it on which layer the > problem occurs - but for you, this is the fastest workaround for now. > > Martin > > -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== From jmfernandez at cnio.es Fri Aug 8 06:19:35 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Fri, 08 Aug 2008 12:19:35 +0200 Subject: [MOBY-dev] perl async services In-Reply-To: <489b2d6a.02578c0a.485f.ffffc011@mx.google.com> References: <489b10ce.1f538c0a.7a83.7c57@mx.google.com> <489B275F.50009@cnio.es> <489b2d6a.02578c0a.485f.ffffc011@mx.google.com> Message-ID: <489C1DB7.9040803@cnio.es> Now I see what you mean. Yes, it should be possible in the way you have explained because both of them should be inheriting from MOBY::Async::SimpleServer. Perhaps one of the cleaner ways to specify that is: $server->dispatch_with({ $WSRF::Constants::MOBY.'#serviceOne' => 'OneAsyncService', $WSRF::Constants::MOBY.'#serviceOne_submit' => 'OneAsyncService', $WSRF::Constants::MOBY.'#serviceTwo' => 'TwoAsyncService', $WSRF::Constants::MOBY.'#serviceTwo_submit' => 'TwoAsyncService', $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' => 'MOBY::Async::SimpleServer', $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourcePropertiesRequest' => 'MOBY::Async::SimpleServer', $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' => 'MOBY::Async::SimpleServer', }); Best Regards, Jos? Mar?a Edward Kawas wrote: > Thanks for the quick response! So your example have both service > implementations inside of one file. Is it possible to have more than one > service referenced in the dispatcher without have the implementations in the > same package? > > i.e. ('->' shows what I mean): > > $server->dispatch_with({ > -> $WSRF::Constants::MOBY.'#serviceOne' => 'OneAsyncService', > -> $WSRF::Constants::MOBY.'#serviceOne_submit' => 'OneAsyncService', > $WSRF::Constants::MOBY.'#serviceTwo' => 'TwoAsyncService', > $WSRF::Constants::MOBY.'#serviceTwo_submit' => 'TwoAsyncService', > > $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' => > 'TwoAsyncService', > > $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourceP > ropertiesRequest' => 'TwoAsyncService', > > $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' => > 'TwoAsyncService', > }); > > Thanks again, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jos? Mar?a > Fern?ndez Gonz?lez > Sent: August-07-08 9:49 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] perl async services > > Hi Eddie, > although the example shows only one service, you are not restricted > to only one. About GetResourceProperty, GetMultipleResourceProperties and > ImmediateResourceTermination, they are document/literal SOAP services based > on WSRF specifications. If your service code is inheriting from > MOBY::Async::SimpleServer, then you do not have to implement them, because > MOBY::Async::SimpleServer takes care of them. > > The way MOBY::Async libraries work are the next: > > * They have been built on top of WSRF::Lite libraries, so they reuse > as much > routines as possible. That's the reason why Perl modules containing > asynchronous services implementations must inherit from > MOBY::Async::SimpleServer (typical 'use base qw(MOBY::Async::SimpleServer);' > > sentence). > > * Asynchronous services creators/coders only have to write the > corresponding > job routines as they were creating a synchronous MOBY service. All the job > ticket generation, job management, job result status & storage, etc... work > is handled either by WSRF::Lite or MOBY::Async::SimpleServer, and in most of > cases only depends on job Id. As job routines are passed on job creation, > they must be either functions passed by reference to the job creation > statement or being anonymous functions assigned to a variable, used as input > parameter for the job creation statement. > > For those of you interested on, the ticket, state, results, etc... > information is stored in /tmp. This point should be more configurable, and > we will fix it on September. > > I have attached an untested example of two asynchronous services > using the same dispatcher and module. > > Best Regards from M?laga, > Jos? Mar?a (on behalf Jos? Manuel and myself) > > Edward Kawas wrote: >> Hi, >> >> I have a quick question to whomever has developed async services in >> perl using the MOBY::Async/WSRF modules. Is it true that there is a >> strict one dispatcher file to one service? >> >> For instance, the documentation for the module MOBY::Async has the >> following dispatcher.cgi example: >> >> dispatcher.cgi >> >> #!/usr/bin/perl >> BEGIN { @INC = ("/path/to/my/libs", @INC); } >> use strict; >> use SOAP::Transport::HTTP; >> use MOBY::Async::WSRF; >> use HelloWorld; >> >> my $server = new SOAP::Transport::HTTP::CGI; >> $server->serializer(WSRF::Serializer->new); >> $server->deserializer(WSRF::Deserializer->new); >> $server->on_action(sub{}); >> $server->dispatch_with({ >> $WSRF::Constants::MOBY.'#sayHello' => 'HelloWorld', >> $WSRF::Constants::MOBY.'#sayHello_submit' => 'HelloWorld', >> -> >> $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyReque >> st' => 'HelloWorld', >> -> >> $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleRes >> ourceP >> ropertiesRequest' => 'HelloWorld', >> -> $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' >> => 'HelloWorld', >> }); >> $server->handle(); >> >> Notice the lines prefixed with '->' hard code GetResourceProperty, etc >> map to a specific service. Is there any way around this? >> >> Thanks, >> >> Eddie >> >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > -- > "There is no reason why anybody would want a computer in their home" - > Ken Olson, founder of DEC 1977 > "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever > outgrow a 20Mb hard drive." - ??? > > "Premature optimization is the root of all evil." - Donald Knuth > > Jos? Mar?a Fern?ndez Gonz?lez > Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) > e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 > Unidad del Instituto Nacional de Bioinform?tica > Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing > Centro Nacional de Investigaciones Oncol?gicas > C.P.: 28029 Zip Code: 28029 > C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) > > > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los > ficheros adjuntos, pueden contener informaci?n protegida para el uso > exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o > cualquier otro tipo de transmisi?n por parte de otra persona que no sea el > destinatario. Si usted recibe por error este correo, se ruega comunicarlo al > remitente y borrar el mensaje recibido. > **CONFIDENTIALITY NOTICE** This email communication and any attachments may > contain confidential and privileged information for the sole use of the > designated recipient named above. Distribution, reproduction or any other > use of this transmission by any party other than the intended recipient is > prohibited. If you are not the intended recipient please contact the sender > and delete all copies. > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From py at pingoured.fr Fri Aug 8 08:52:51 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Fri, 08 Aug 2008 14:52:51 +0200 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <489C1C72.5000402@mpiz-koeln.mpg.de> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> <489C1C72.5000402@mpiz-koeln.mpg.de> Message-ID: <489C41A3.2010909@pingoured.fr> Andreas Groscurth wrote: > i confirm that this comes from an non-ascii character. > I registered a service which has some german accents (ae, oe etc) and i > got some errors during registration. > > ===ERROR=== > Fault details: > [stackTrace: null] > [hostname: null] > Fault string: java.io.UTFDataFormatException: Invalid byte 2 of 3-byte > UTF-8 sequence. > Fault code: > {http://schemas.xmlsoap.org/soap/envelope/}Server.userException > Fault actor: null > When calling: > http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl > =========== > > it seems to register, because registering it does not work (you have to > unregister first). But loading the services also fail due to this service. > > So as martin said, for this time avoid any german specific character. We are here facing the same problem, we can not register our service (well we do register it) but we can not load the list of services so we can not work with the dashboard on our service... (to bad it is friday afternoon :D !) Is there something we can do exempt waiting ? (We will generate the skeleton by hand, so there no problem for our work ;)) Thanks, Regards, Pierre From martin.senger at gmail.com Fri Aug 8 09:57:09 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 8 Aug 2008 21:57:09 +0800 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <489C41A3.2010909@pingoured.fr> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> <489C1C72.5000402@mpiz-koeln.mpg.de> <489C41A3.2010909@pingoured.fr> Message-ID: <4d93f07c0808080657u192935fat3027094ea576859a@mail.gmail.com> > Is there something we can do exempt waiting ? I am trying to find a work-around, or a fix. So far, let me just tell how I see where is the problem (which is not that much useful for you, I understand...): The registry is sending wrong XML. [Another question is why it has the wrong data, in the first place - but that's less important now.] The wrong data (coming from registry) are for the a service from authority www.glycome-db.org. The data has a German U with umlaut (?) - but it is coded as three characters 0xEF 0xBF 0xBD - which is not UTF-8 code of such character. Actually, it is no UNICODE code at all. This umlaut character should be coded as two characters 0x6C 0xC3. The best would be if Eddie can fix manually the database - because it is otherwise hard to fix it in Java (like in Dashboard) because the encoding is done in very low level, long before our Java code gets control. So I would rather ask Eddie to fix it - and only when he says he cannot, I will try to come with a Java-based fix. [But I am leaving for Europe in about 7 hours, so I may be out of the loop for a while if this is not responded soon.] Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Fri Aug 8 10:10:03 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 8 Aug 2008 07:10:03 -0700 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <4d93f07c0808080657u192935fat3027094ea576859a@mail.gmail.com> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> <489C1C72.5000402@mpiz-koeln.mpg.de> <489C41A3.2010909@pingoured.fr> <4d93f07c0808080657u192935fat3027094ea576859a@mail.gmail.com> Message-ID: <489c53c9.2a528c0a.69e3.ffffdc0c@mx.google.com> I updated the 2 services. Did this fix the problem? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: August-08-08 6:57 AM To: Core developer announcements Subject: Re: [MOBY-dev] Problems with service registration using dashboard > Is there something we can do exempt waiting ? I am trying to find a work-around, or a fix. So far, let me just tell how I see where is the problem (which is not that much useful for you, I understand...): The registry is sending wrong XML. [Another question is why it has the wrong data, in the first place - but that's less important now.] The wrong data (coming from registry) are for the a service from authority www.glycome-db.org. The data has a German U with umlaut (?) - but it is coded as three characters 0xEF 0xBF 0xBD - which is not UTF-8 code of such character. Actually, it is no UNICODE code at all. This umlaut character should be coded as two characters 0x6C 0xC3. The best would be if Eddie can fix manually the database - because it is otherwise hard to fix it in Java (like in Dashboard) because the encoding is done in very low level, long before our Java code gets control. So I would rather ask Eddie to fix it - and only when he says he cannot, I will try to come with a Java-based fix. [But I am leaving for Europe in about 7 hours, so I may be out of the loop for a while if this is not responded soon.] Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From martin.senger at gmail.com Fri Aug 8 10:17:50 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 8 Aug 2008 22:17:50 +0800 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <489c53c9.2a528c0a.69e3.ffffdc0c@mx.google.com> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> <489C1C72.5000402@mpiz-koeln.mpg.de> <489C41A3.2010909@pingoured.fr> <4d93f07c0808080657u192935fat3027094ea576859a@mail.gmail.com> <489c53c9.2a528c0a.69e3.ffffdc0c@mx.google.com> Message-ID: <4d93f07c0808080717r6753e469jc640aa8abbae7403@mail.gmail.com> > I updated the 2 services. Did this fix the problem? > Yes! Thanks. When do you want to start discussion how to fix it in order not to happen again :-) ? Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Fri Aug 8 10:20:15 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 8 Aug 2008 07:20:15 -0700 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <4d93f07c0808080717r6753e469jc640aa8abbae7403@mail.gmail.com> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> <489C1C72.5000402@mpiz-koeln.mpg.de> <489C41A3.2010909@pingoured.fr> <4d93f07c0808080657u192935fat3027094ea576859a@mail.gmail.com> <489c53c9.2a528c0a.69e3.ffffdc0c@mx.google.com> <4d93f07c0808080717r6753e469jc640aa8abbae7403@mail.gmail.com> Message-ID: <489c562c.27b38c0a.19a0.7d10@mx.google.com> Great! We can start it next week. Let's think of some solutions and then post them to the list! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: August-08-08 7:18 AM To: Core developer announcements Subject: Re: [MOBY-dev] Problems with service registration using dashboard > I updated the 2 services. Did this fix the problem? > Yes! Thanks. When do you want to start discussion how to fix it in order not to happen again :-) ? Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From martin.senger at gmail.com Fri Aug 8 10:32:19 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 8 Aug 2008 22:32:19 +0800 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <489c562c.27b38c0a.19a0.7d10@mx.google.com> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> <489C1C72.5000402@mpiz-koeln.mpg.de> <489C41A3.2010909@pingoured.fr> <4d93f07c0808080657u192935fat3027094ea576859a@mail.gmail.com> <489c53c9.2a528c0a.69e3.ffffdc0c@mx.google.com> <4d93f07c0808080717r6753e469jc640aa8abbae7403@mail.gmail.com> <489c562c.27b38c0a.19a0.7d10@mx.google.com> Message-ID: <4d93f07c0808080732m5af1d1c3nd56e684887ef757@mail.gmail.com> > We can start it next week. Okay, but... > Let's think of some solutions ...there is no special solution needed I think. You just must make sure that the XML data coming to the registry are really coded as UTF-8 - and if not (like it was, I assume, with the Rene's service) you have to refuse them to be registered. Or, the data from Rene's was, indeed, correct, but you read and saved them wrongly. Just a remark: When I said that the Rene's data were (probably) wrong, I am not suggesting that Rene made a mistake, it was probably my Java code in CentralImpl that created the XML with a wrong encoding. But I need you to be more careful at the registry side - once you reject such data on arrival, I will be definitely notified and learn about this situation and can fix it. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Mon Aug 11 09:14:18 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 11 Aug 2008 06:14:18 -0700 Subject: [MOBY-dev] perl async services In-Reply-To: <489C1DB7.9040803@cnio.es> References: <489b10ce.1f538c0a.7a83.7c57@mx.google.com> <489B275F.50009@cnio.es> <489b2d6a.02578c0a.485f.ffffc011@mx.google.com> <489C1DB7.9040803@cnio.es> Message-ID: <48a03b3a.27b38c0a.19af.ffffc634@mx.google.com> Excellent! Thanks. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jos? Mar?a Fern?ndez Gonz?lez Sent: August-08-08 3:20 AM To: Core developer announcements Subject: Re: [MOBY-dev] perl async services Now I see what you mean. Yes, it should be possible in the way you have explained because both of them should be inheriting from MOBY::Async::SimpleServer. Perhaps one of the cleaner ways to specify that is: $server->dispatch_with({ $WSRF::Constants::MOBY.'#serviceOne' => 'OneAsyncService', $WSRF::Constants::MOBY.'#serviceOne_submit' => 'OneAsyncService', $WSRF::Constants::MOBY.'#serviceTwo' => 'TwoAsyncService', $WSRF::Constants::MOBY.'#serviceTwo_submit' => 'TwoAsyncService', $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' => 'MOBY::Async::SimpleServer', $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourceP ropertiesRequest' => 'MOBY::Async::SimpleServer', $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' => 'MOBY::Async::SimpleServer', }); Best Regards, Jos? Mar?a Edward Kawas wrote: > Thanks for the quick response! So your example have both service > implementations inside of one file. Is it possible to have more than one > service referenced in the dispatcher without have the implementations in the > same package? > > i.e. ('->' shows what I mean): > > $server->dispatch_with({ > -> $WSRF::Constants::MOBY.'#serviceOne' => 'OneAsyncService', > -> $WSRF::Constants::MOBY.'#serviceOne_submit' => 'OneAsyncService', > $WSRF::Constants::MOBY.'#serviceTwo' => 'TwoAsyncService', > $WSRF::Constants::MOBY.'#serviceTwo_submit' => 'TwoAsyncService', > > $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' => > 'TwoAsyncService', > > $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourceP > ropertiesRequest' => 'TwoAsyncService', > > $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' => > 'TwoAsyncService', > }); > > Thanks again, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jos? Mar?a > Fern?ndez Gonz?lez > Sent: August-07-08 9:49 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] perl async services > > Hi Eddie, > although the example shows only one service, you are not restricted > to only one. About GetResourceProperty, GetMultipleResourceProperties and > ImmediateResourceTermination, they are document/literal SOAP services based > on WSRF specifications. If your service code is inheriting from > MOBY::Async::SimpleServer, then you do not have to implement them, because > MOBY::Async::SimpleServer takes care of them. > > The way MOBY::Async libraries work are the next: > > * They have been built on top of WSRF::Lite libraries, so they reuse > as much > routines as possible. That's the reason why Perl modules containing > asynchronous services implementations must inherit from > MOBY::Async::SimpleServer (typical 'use base qw(MOBY::Async::SimpleServer);' > > sentence). > > * Asynchronous services creators/coders only have to write the > corresponding > job routines as they were creating a synchronous MOBY service. All the job > ticket generation, job management, job result status & storage, etc... work > is handled either by WSRF::Lite or MOBY::Async::SimpleServer, and in most of > cases only depends on job Id. As job routines are passed on job creation, > they must be either functions passed by reference to the job creation > statement or being anonymous functions assigned to a variable, used as input > parameter for the job creation statement. > > For those of you interested on, the ticket, state, results, etc... > information is stored in /tmp. This point should be more configurable, and > we will fix it on September. > > I have attached an untested example of two asynchronous services > using the same dispatcher and module. > > Best Regards from M?laga, > Jos? Mar?a (on behalf Jos? Manuel and myself) > > Edward Kawas wrote: >> Hi, >> >> I have a quick question to whomever has developed async services in >> perl using the MOBY::Async/WSRF modules. Is it true that there is a >> strict one dispatcher file to one service? >> >> For instance, the documentation for the module MOBY::Async has the >> following dispatcher.cgi example: >> >> dispatcher.cgi >> >> #!/usr/bin/perl >> BEGIN { @INC = ("/path/to/my/libs", @INC); } >> use strict; >> use SOAP::Transport::HTTP; >> use MOBY::Async::WSRF; >> use HelloWorld; >> >> my $server = new SOAP::Transport::HTTP::CGI; >> $server->serializer(WSRF::Serializer->new); >> $server->deserializer(WSRF::Deserializer->new); >> $server->on_action(sub{}); >> $server->dispatch_with({ >> $WSRF::Constants::MOBY.'#sayHello' => 'HelloWorld', >> $WSRF::Constants::MOBY.'#sayHello_submit' => 'HelloWorld', >> -> >> $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyReque >> st' => 'HelloWorld', >> -> >> $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleRes >> ourceP >> ropertiesRequest' => 'HelloWorld', >> -> $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' >> => 'HelloWorld', >> }); >> $server->handle(); >> >> Notice the lines prefixed with '->' hard code GetResourceProperty, etc >> map to a specific service. Is there any way around this? >> >> Thanks, >> >> Eddie >> >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > -- > "There is no reason why anybody would want a computer in their home" - > Ken Olson, founder of DEC 1977 > "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever > outgrow a 20Mb hard drive." - ??? > > "Premature optimization is the root of all evil." - Donald Knuth > > Jos? Mar?a Fern?ndez Gonz?lez > Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) > e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 > Unidad del Instituto Nacional de Bioinform?tica > Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing > Centro Nacional de Investigaciones Oncol?gicas > C.P.: 28029 Zip Code: 28029 > C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) > > > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los > ficheros adjuntos, pueden contener informaci?n protegida para el uso > exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o > cualquier otro tipo de transmisi?n por parte de otra persona que no sea el > destinatario. Si usted recibe por error este correo, se ruega comunicarlo al > remitente y borrar el mensaje recibido. > **CONFIDENTIALITY NOTICE** This email communication and any attachments may > contain confidential and privileged information for the sole use of the > designated recipient named above. Distribution, reproduction or any other > use of this transmission by any party other than the intended recipient is > prohibited. If you are not the intended recipient please contact the sender > and delete all copies. > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From serr at ac.uma.es Tue Aug 12 05:04:24 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Tue, 12 Aug 2008 11:04:24 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <4895DE28.7010102@bsc.es> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> <4895DE28.7010102@bsc.es> Message-ID: <48A15218.10104@ac.uma.es> Hello Dmitry and others. Just a small question. What is the advantage of have a reference to a binary data in the atachments? Couldn't we got the same behaviour by adding the reference in the current moby XML structure? Could you explain me please? Best regards Sergio Dmitry Repchevsky wrote: > Hello Martin, > >> What do you mean by "implement streaming"? I concluded that you meant >> "sending binary data from (or to) a moby service". Is is correct? >> > yes it is. >> This is again a SOAP-based specification, meaning another way how to >> make an >> attachment (correct?). >> > XOP is the XML way to reference a binary attachment for XML using a > reference to it. > Even in theory it is not SOAP dependent, the only implementation I > know (I may be wrong) is a MTOM that is for SOAP protocol. > I couldn't find an implementation for straight XML (because we need a > transport for it). > >> If the protocol for dereferencing is HTTP, we can use MIME type >> (content-type HTTP header) for >> references data. >> > This is what XOP is about - the only problem is that it can not > reference an external resource. > > It would be great to have something based on Servlet + XML + XOP on > java, but I looked at JAX-RS (JSR-311) REST and there is nothing... > > I had an idea, but afraid it has a problem with an implementation. > > The idea is to use XML attachment (instead of binary one) and in those > attachment put XInclude with a link to external document. > Such document itself would be an XML with a binary attachment. > > So we would have: > > External resource represented by XML (moby ontology class like > MobyImage) + a binary attachment with an image data itself. > Then we have a main document with a MobyRef primitive that is encoded > as an XML attachment where an attachment itself is an XInclude to the > MobyImage. > This way the document is assembled into a standard moby message > automagically: > > The only problem is that XInclude works with a plain XML, I think... > > Cheers, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From serr at ac.uma.es Tue Aug 12 05:24:18 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Tue, 12 Aug 2008 11:24:18 +0200 Subject: [MOBY-dev] data by reference - a request for comments In-Reply-To: <4d93f07c0808041921q78a160e3qe6a4bed8ce9e29b1@mail.gmail.com> References: <488B0123.3040608@bsc.es> <4d93f07c0807260452g3048765ev6f84be49dc8cf26d@mail.gmail.com> <4d93f07c0807271829v10ff50d5y2c6f83b279256fdb@mail.gmail.com> <4d93f07c0808031954v5e266c63kee2a1e1beac1bad1@mail.gmail.com> <4896DFC6.9040204@cnio.es> <4d93f07c0808041921q78a160e3qe6a4bed8ce9e29b1@mail.gmail.com> Message-ID: <48A156C2.6080509@ac.uma.es> Hello all, Just an small contribution Martin Senger wrote: >> I would split the proposed property in the two roles it plays: one for the >> acceptable reference types, and one for the possibly generated reference >> types. Many services will be able to accept reference types of http, ftp or >> other kinds, but I think they usually are only able to generate answers with >> fewer or different ones. >> > > > I do not think that the situations will be drastically different for > accepting and producing references - but I do not have any issue with it. I > do not mind much how many new properties will be added to the central > registry. > > Maybe it can be a protocol between the service and the client, the second sent the references that is able to handle and if they are agree use one of them for the comunication if not is always possible to return the results without use references. If the client sent a reference (got from other service for example ) that the service can not handle it, an error or info notification can be returned to inform about that. In this case the client can resent the request without using references. In this case I think is not needed to register the references that the service can handle in the central registry, but could be a good idea for searching compatible services with your data. > As all mobyData blocks are sent to the same service, I'd rather attach > Could be possible to use mirrors and separated the mobydata to sent them to different mirror servers? > >> "acceptRefs" to mobyContent instead of mobyData, but it is only to avoid >> redundancy. >> > > > Again, no problem with me. > > These are some scenarios: > > > My question was: if a service claims that it can produce a reference, and a > client asks for it, should the service always produce a reference? I think > that my question was obsolete already in the time of asking it. I am > withdrawing my question, assuming the obvious answer for the above is "yes, > it should". > Maybe we can use some kind of algorithm to see if is will be good to use references; for small data couldn't be useful. Could also be defined for the client, specifying the max size that wants to receive (in total or by object) > XLink (2001) was superseded by XInclude (second revision in 2006). Next > >> links points to the relationship between XInclude and XLink >> >> http://www.w3.org/TR/xinclude/#rel-xlink >> >> > > Yes, I saw and read this link - but, as often with me when I read the w3 > documents , I could not understand what is different, at all. I am glad, > however, that XInclude is considered as a supersedor (I guess this word > probably does not exist in Egnlish) of XLink. So we go with XInclude. > > I would love that feature because it would allow referencing fragments of > >> any XML content. The only problem is that there is (almost) no memory >> efficient implementation for XPath (used in "xpointer" feature) applied to >> disk stored XML content. >> > > > This is exactly why I suggested not to allow it. I would prefer to stick to > my guns on this issue. > > Many thanks for replying from the holidays. What about the others? Can we go > ahead? > > Cheers, > Martin > > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From dmitry.repchevski at bsc.es Tue Aug 12 05:25:30 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 12 Aug 2008 11:25:30 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A15218.10104@ac.uma.es> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> <4895DE28.7010102@bsc.es> <48A15218.10104@ac.uma.es> Message-ID: <48A1570A.9080304@bsc.es> Hello, Sergio, > What is the advantage of have a reference to a binary data in the > atachments? Couldn't we got the same behaviour by adding the reference > in the current moby XML structure? Yes we could... The difference is that in the case of attachment, logically your data are in the same XML document. In case of using some external reference they couldn't be parsed using standard XML library and have to be parsed by "moby" framework. The same amount of work is needed by the service developer. If I use a standard way - I just construct my message and send it. The resource itself is a part of XML infoset. Then I put some structure into an XML that have some external meaning, I have to publish my resource somehow (for example through the servlet). The latter means that we are moving farther away from web services and SOAP. The main idea of web services is that we don't need any additional framework for the interoperability... At this moment this is not the case and maybe should never be an objective, but IMHO I'd like at least to move in this direction... Best regards, Dmitry Sergio Ramirez Ramirez wrote: > Hello Dmitry and others. > > Just a small question. > > What is the advantage of have a reference to a binary data in the > atachments? Couldn't we got the same behaviour by adding the reference > in the current moby XML structure? > > Could you explain me please? > > Best regards > Sergio > > Dmitry Repchevsky wrote: >> Hello Martin, >> >>> What do you mean by "implement streaming"? I concluded that you meant >>> "sending binary data from (or to) a moby service". Is is correct? >>> >> yes it is. >>> This is again a SOAP-based specification, meaning another way how to >>> make an >>> attachment (correct?). >>> >> XOP is the XML way to reference a binary attachment for XML using a >> reference to it. >> Even in theory it is not SOAP dependent, the only implementation I >> know (I may be wrong) is a MTOM that is for SOAP protocol. >> I couldn't find an implementation for straight XML (because we need a >> transport for it). >> >>> If the protocol for dereferencing is HTTP, we can use MIME type >>> (content-type HTTP header) for >>> references data. >>> >> This is what XOP is about - the only problem is that it can not >> reference an external resource. >> >> It would be great to have something based on Servlet + XML + XOP on >> java, but I looked at JAX-RS (JSR-311) REST and there is nothing... >> >> I had an idea, but afraid it has a problem with an implementation. >> >> The idea is to use XML attachment (instead of binary one) and in >> those attachment put XInclude with a link to external document. >> Such document itself would be an XML with a binary attachment. >> >> So we would have: >> >> External resource represented by XML (moby ontology class like >> MobyImage) + a binary attachment with an image data itself. >> Then we have a main document with a MobyRef primitive that is encoded >> as an XML attachment where an attachment itself is an XInclude to the >> MobyImage. >> This way the document is assembled into a standard moby message >> automagically: >> >> The only problem is that XInclude works with a plain XML, I think... >> >> Cheers, >> >> Dmitry >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > From martin.senger at gmail.com Tue Aug 12 05:36:34 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 12 Aug 2008 10:36:34 +0100 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A1570A.9080304@bsc.es> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> <4895DE28.7010102@bsc.es> <48A15218.10104@ac.uma.es> <48A1570A.9080304@bsc.es> Message-ID: <4d93f07c0808120236o34ab776eq7f2116f1ead20ec5@mail.gmail.com> My opinions: In case of using some external reference they couldn't be parsed using > standard XML library and have to be parsed by "moby" framework. That's exactly what I (we?) want - to have control over how to treat the referenced data. Additionally, we want to be able to use existing external references, at least in cases when the service provider wishes so (which may not be case always; e.g. for NCBI records, it would be harmful to let clients to resolve the NCBI's references too fast - as Pieter and Mark have already pointed out). > The latter means that we are moving farther away from web services and > SOAP. > That is what I hope for :-) Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From serr at ac.uma.es Tue Aug 12 05:49:17 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Tue, 12 Aug 2008 11:49:17 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <4d93f07c0808120236o34ab776eq7f2116f1ead20ec5@mail.gmail.com> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> <4895DE28.7010102@bsc.es> <48A15218.10104@ac.uma.es> <48A1570A.9080304@bsc.es> <4d93f07c0808120236o34ab776eq7f2116f1ead20ec5@mail.gmail.com> Message-ID: <48A15C9D.9030703@ac.uma.es> Hello Martin, Until I know the libraries are able to handle XInclude in both ways, if I want they understand the XInclude information and complete the xml with the contents of the reference; but this option can be desactivated and the reference handled by hand. Martin Senger wrote: > My opinions: > > In case of using some external reference they couldn't be parsed > using standard XML library and have to be parsed by "moby" framework. > > > That's exactly what I (we?) want - to have control over how to treat > the referenced data. Additionally, we want to be able to use existing > external references, at least in cases when the service provider > wishes so (which may not be case always; e.g. for NCBI records, it > would be harmful to let clients to resolve the NCBI's references too > fast - as Pieter and Mark have already pointed out). > > > > The latter means that we are moving farther away from web services > and SOAP. > > > That is what I hope for :-) > > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > ,m.senger at cgiar.org > > skype: martinsenger -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From martin.senger at gmail.com Tue Aug 12 05:53:46 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 12 Aug 2008 10:53:46 +0100 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A15C9D.9030703@ac.uma.es> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> <4895DE28.7010102@bsc.es> <48A15218.10104@ac.uma.es> <48A1570A.9080304@bsc.es> <4d93f07c0808120236o34ab776eq7f2116f1ead20ec5@mail.gmail.com> <48A15C9D.9030703@ac.uma.es> Message-ID: <4d93f07c0808120253n56fb287k34d49ae6c8171e1c@mail.gmail.com> > Until I know the libraries are able to handle XInclude in both ways, if I > want they understand the XInclude information and complete the xml with the > contents of the reference; but this option can be desactivated and the > reference handled by hand. > Sorry, I am not sure that I understood what you just said. Could you perhaps re-phrase it for me. Sorry... and thanks. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From serr at ac.uma.es Tue Aug 12 05:53:48 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Tue, 12 Aug 2008 11:53:48 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A1570A.9080304@bsc.es> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> <4895DE28.7010102@bsc.es> <48A15218.10104@ac.uma.es> <48A1570A.9080304@bsc.es> Message-ID: <48A15DAC.6000307@ac.uma.es> but the atachment is a reference that you have to handle in the same way as if it were in the XML schema, you only change the location. Is this correct? Dmitry Repchevsky wrote: > Hello, Sergio, > >> What is the advantage of have a reference to a binary data in the >> atachments? Couldn't we got the same behaviour by adding the >> reference in the current moby XML structure? > Yes we could... The difference is that in the case of attachment, > logically your data are in the same XML document. > In case of using some external reference they couldn't be parsed using > standard XML library and have to be parsed by "moby" framework. > The same amount of work is needed by the service developer. If I use a > standard way - I just construct my message and send it. The resource > itself is a part of XML infoset. > Then I put some structure into an XML that have some external meaning, > I have to publish my resource somehow (for example through the servlet). > The latter means that we are moving farther away from web services and > SOAP. > > The main idea of web services is that we don't need any additional > framework for the interoperability... > At this moment this is not the case and maybe should never be an > objective, but IMHO I'd like at least to move in this direction... > > Best regards, > Dmitry > > Sergio Ramirez Ramirez wrote: >> Hello Dmitry and others. >> >> Just a small question. >> >> What is the advantage of have a reference to a binary data in the >> atachments? Couldn't we got the same behaviour by adding the >> reference in the current moby XML structure? >> >> Could you explain me please? >> >> Best regards >> Sergio >> >> Dmitry Repchevsky wrote: >>> Hello Martin, >>> >>>> What do you mean by "implement streaming"? I concluded that you meant >>>> "sending binary data from (or to) a moby service". Is is correct? >>>> >>> yes it is. >>>> This is again a SOAP-based specification, meaning another way how >>>> to make an >>>> attachment (correct?). >>>> >>> XOP is the XML way to reference a binary attachment for XML using a >>> reference to it. >>> Even in theory it is not SOAP dependent, the only implementation I >>> know (I may be wrong) is a MTOM that is for SOAP protocol. >>> I couldn't find an implementation for straight XML (because we need >>> a transport for it). >>> >>>> If the protocol for dereferencing is HTTP, we can use MIME type >>>> (content-type HTTP header) for >>>> references data. >>>> >>> This is what XOP is about - the only problem is that it can not >>> reference an external resource. >>> >>> It would be great to have something based on Servlet + XML + XOP on >>> java, but I looked at JAX-RS (JSR-311) REST and there is nothing... >>> >>> I had an idea, but afraid it has a problem with an implementation. >>> >>> The idea is to use XML attachment (instead of binary one) and in >>> those attachment put XInclude with a link to external document. >>> Such document itself would be an XML with a binary attachment. >>> >>> So we would have: >>> >>> External resource represented by XML (moby ontology class like >>> MobyImage) + a binary attachment with an image data itself. >>> Then we have a main document with a MobyRef primitive that is >>> encoded as an XML attachment where an attachment itself is an >>> XInclude to the MobyImage. >>> This way the document is assembled into a standard moby message >>> automagically: >>> >>> The only problem is that XInclude works with a plain XML, I think... >>> >>> Cheers, >>> >>> Dmitry >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From dmitry.repchevski at bsc.es Tue Aug 12 06:02:39 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 12 Aug 2008 12:02:39 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A15DAC.6000307@ac.uma.es> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> <4895DE28.7010102@bsc.es> <48A15218.10104@ac.uma.es> <48A1570A.9080304@bsc.es> <48A15DAC.6000307@ac.uma.es> Message-ID: <48A15FBF.4000009@bsc.es> Hello Sergio, > but the atachment is a reference that you have to handle in the same > way as if it were in the XML schema, you only change the location. Is > this correct? XOP/MTOM doesn't affect the XML Schema. It uses XOP:Include to reference the binary data. Unfortunately, XOP specification doesn't reuse XInclude so the only reference you can have is to the mime attachment into the same multimime message... Dmitry Sergio Ramirez Ramirez wrote: > but the atachment is a reference that you have to handle in the same > way as if it were in the XML schema, you only change the location. Is > this correct? > > Dmitry Repchevsky wrote: >> Hello, Sergio, >> >>> What is the advantage of have a reference to a binary data in the >>> atachments? Couldn't we got the same behaviour by adding the >>> reference in the current moby XML structure? >> Yes we could... The difference is that in the case of attachment, >> logically your data are in the same XML document. >> In case of using some external reference they couldn't be parsed >> using standard XML library and have to be parsed by "moby" framework. >> The same amount of work is needed by the service developer. If I use >> a standard way - I just construct my message and send it. The >> resource itself is a part of XML infoset. >> Then I put some structure into an XML that have some external >> meaning, I have to publish my resource somehow (for example through >> the servlet). >> The latter means that we are moving farther away from web services >> and SOAP. >> >> The main idea of web services is that we don't need any additional >> framework for the interoperability... >> At this moment this is not the case and maybe should never be an >> objective, but IMHO I'd like at least to move in this direction... >> >> Best regards, >> Dmitry >> >> Sergio Ramirez Ramirez wrote: >>> Hello Dmitry and others. >>> >>> Just a small question. >>> >>> What is the advantage of have a reference to a binary data in the >>> atachments? Couldn't we got the same behaviour by adding the >>> reference in the current moby XML structure? >>> >>> Could you explain me please? >>> >>> Best regards >>> Sergio >>> >>> Dmitry Repchevsky wrote: >>>> Hello Martin, >>>> >>>>> What do you mean by "implement streaming"? I concluded that you meant >>>>> "sending binary data from (or to) a moby service". Is is correct? >>>>> >>>> yes it is. >>>>> This is again a SOAP-based specification, meaning another way how >>>>> to make an >>>>> attachment (correct?). >>>>> >>>> XOP is the XML way to reference a binary attachment for XML using a >>>> reference to it. >>>> Even in theory it is not SOAP dependent, the only implementation I >>>> know (I may be wrong) is a MTOM that is for SOAP protocol. >>>> I couldn't find an implementation for straight XML (because we need >>>> a transport for it). >>>> >>>>> If the protocol for dereferencing is HTTP, we can use MIME type >>>>> (content-type HTTP header) for >>>>> references data. >>>>> >>>> This is what XOP is about - the only problem is that it can not >>>> reference an external resource. >>>> >>>> It would be great to have something based on Servlet + XML + XOP on >>>> java, but I looked at JAX-RS (JSR-311) REST and there is nothing... >>>> >>>> I had an idea, but afraid it has a problem with an implementation. >>>> >>>> The idea is to use XML attachment (instead of binary one) and in >>>> those attachment put XInclude with a link to external document. >>>> Such document itself would be an XML with a binary attachment. >>>> >>>> So we would have: >>>> >>>> External resource represented by XML (moby ontology class like >>>> MobyImage) + a binary attachment with an image data itself. >>>> Then we have a main document with a MobyRef primitive that is >>>> encoded as an XML attachment where an attachment itself is an >>>> XInclude to the MobyImage. >>>> This way the document is assembled into a standard moby message >>>> automagically: >>>> >>>> The only problem is that XInclude works with a plain XML, I think... >>>> >>>> Cheers, >>>> >>>> Dmitry >>>> _______________________________________________ >>>> MOBY-dev mailing list >>>> MOBY-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>> >>> >> > From serr at ac.uma.es Tue Aug 12 06:04:29 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Tue, 12 Aug 2008 12:04:29 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <4d93f07c0808120253n56fb287k34d49ae6c8171e1c@mail.gmail.com> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> <4895DE28.7010102@bsc.es> <48A15218.10104@ac.uma.es> <48A1570A.9080304@bsc.es> <4d93f07c0808120236o34ab776eq7f2116f1ead20ec5@mail.gmail.com> <48A15C9D.9030703@ac.uma.es> <4d93f07c0808120253n56fb287k34d49ae6c8171e1c@mail.gmail.com> Message-ID: <48A1602D.9090804@ac.uma.es> Sorry for my bad English :-[ I mean that if you want "to have control over how to treat the referenced data" Xinclude allows this possibility, but at the same time offers the possibility of handle them automatically. Yo have the both behavior, is someones doesn't need to handled them by hand Martin Senger wrote: > > Until I know the libraries are able to handle XInclude in both > ways, if I want they understand the XInclude information and > complete the xml with the contents of the reference; but this > option can be desactivated and the reference handled by hand. > > > Sorry, I am not sure that I understood what you just said. Could you > perhaps re-phrase it for me. Sorry... and thanks. > > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > ,m.senger at cgiar.org > > skype: martinsenger -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From martin.senger at gmail.com Tue Aug 12 06:14:21 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 12 Aug 2008 11:14:21 +0100 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A1602D.9090804@ac.uma.es> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> <4895DE28.7010102@bsc.es> <48A15218.10104@ac.uma.es> <48A1570A.9080304@bsc.es> <4d93f07c0808120236o34ab776eq7f2116f1ead20ec5@mail.gmail.com> <48A15C9D.9030703@ac.uma.es> <4d93f07c0808120253n56fb287k34d49ae6c8171e1c@mail.gmail.com> <48A1602D.9090804@ac.uma.es> Message-ID: <4d93f07c0808120314o30b00cd6hfb9cedc2614dcb35@mail.gmail.com> > I mean that if you want "to have control over how to treat the referenced > data" Xinclude allows this possibility, but at the same time offers the > possibility of handle them automatically. > > Yo have the both behavior, is someones doesn't need to handled them by hand Exactly my point! Thanks. That's why I want to use XInclude and not the attachements. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From dmitry.repchevski at bsc.es Tue Aug 12 06:15:29 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 12 Aug 2008 12:15:29 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A1602D.9090804@ac.uma.es> References: <48A1602D.9090804@ac.uma.es> Message-ID: <48A162C1.3070207@bsc.es> > I mean that if you want "to have control over how to treat the > referenced data" Xinclude allows this possibility, but at the same time > offers the possibility of handle them automatically. I am afraid the only way to make it work is to have it always switched off... By the way, what is your opinion about FastInfoset??? Could it be used with XInclude? I mean that it compresses data very well (it transforms XML schema into ASN.1 and use BER encoding If I have some ontology class with binary data (base64binary) and send this "Moby Object" as an XML, but using FastInfoset... for the traffic if would be virtually the same as it was "plain" binary stream. I mean that we can have say "BinaryImage" ontology object that is using "binary" primitive type. Then instead of making an url into "http://mysite.com/image.jpg" we make a reference into "http://mysite.com/image.xml" The latter could be included and processed automatically by XInclude, but if we enable FastInfoset for it - it will be sent as a binary data over a network... Just a few thoughts... Best wishes, Dmitry From serr at ac.uma.es Tue Aug 12 06:50:42 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Tue, 12 Aug 2008 12:50:42 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A162C1.3070207@bsc.es> References: <48A1602D.9090804@ac.uma.es> <48A162C1.3070207@bsc.es> Message-ID: <48A16B02.1000102@ac.uma.es> About FastInfoSet it compress XML schema in binary data, is this correct? So the idea can be to compress the XML using this system to reduce the bandwidth used, correct? But I cannot see the relation with xml include. Dmitry Repchevsky wrote: > >> I mean that if you want "to have control over how to treat the >> referenced data" Xinclude allows this possibility, but at the same >> time offers the possibility of handle them automatically. > I am afraid the only way to make it work is to have it always switched > off... > > By the way, what is your opinion about FastInfoset??? > Could it be used with XInclude? > > I mean that it compresses data very well (it transforms XML schema > into ASN.1 and use BER encoding > If I have some ontology class with binary data (base64binary) and send > this "Moby Object" as an XML, but using FastInfoset... for the traffic > if would be virtually the same as it was "plain" binary stream. > > I mean that we can have say "BinaryImage" ontology object that is > using "binary" primitive type. > Then instead of making an url into "http://mysite.com/image.jpg" > we make a reference into "http://mysite.com/image.xml" > > The latter could be included and processed automatically by XInclude, > but if we enable FastInfoset for it - it will be sent as a binary data > over a network... > > Just a few thoughts... > > Best wishes, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From dmitry.repchevski at bsc.es Tue Aug 12 07:00:20 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 12 Aug 2008 13:00:20 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A16B02.1000102@ac.uma.es> References: <48A1602D.9090804@ac.uma.es> <48A162C1.3070207@bsc.es> <48A16B02.1000102@ac.uma.es> Message-ID: <48A16D44.3090204@bsc.es> Hello, > About FastInfoSet it compress XML schema in binary data, is this correct? It's better to say that it compress (transform) entire XML infoset. (while XOP is extract binary infoset and then again assemble then into one) > So the idea can be to compress the XML using this system to reduce the > bandwidth used, correct? Yes it is. > But I cannot see the relation with xml include. It's easy - XInclude can not handle not textual data - only XML/plain-text To use "disabled" XInclude to pass a reference into a custom parser is not better than using XLink... On the other hand it is possible to use XInclude to include fastinfoset encoded XML automatically. Another advantage would be to reference not to "some" resource, but to the entire "ontology" object that can be included into the place where it should be... This way you don't even need to change a message itself: you pass your image by "value" (with XOP/MTOM attachment) or by XInclude reference where it is encoded by fastinfoset. The final XML is the same! Parser just assembles such a message... Dmitry Sergio Ramirez Ramirez wrote: > About FastInfoSet it compress XML schema in binary data, is this correct? > > So the idea can be to compress the XML using this system to reduce the > bandwidth used, correct? > > But I cannot see the relation with xml include. > > Dmitry Repchevsky wrote: >> >>> I mean that if you want "to have control over how to treat the >>> referenced data" Xinclude allows this possibility, but at the same >>> time offers the possibility of handle them automatically. >> I am afraid the only way to make it work is to have it always >> switched off... >> >> By the way, what is your opinion about FastInfoset??? >> Could it be used with XInclude? >> >> I mean that it compresses data very well (it transforms XML schema >> into ASN.1 and use BER encoding >> If I have some ontology class with binary data (base64binary) and >> send this "Moby Object" as an XML, but using FastInfoset... for the >> traffic if would be virtually the same as it was "plain" binary stream. >> >> I mean that we can have say "BinaryImage" ontology object that is >> using "binary" primitive type. >> Then instead of making an url into "http://mysite.com/image.jpg" >> we make a reference into "http://mysite.com/image.xml" >> >> The latter could be included and processed automatically by XInclude, >> but if we enable FastInfoset for it - it will be sent as a binary >> data over a network... >> >> Just a few thoughts... >> >> Best wishes, >> >> Dmitry >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > From serr at ac.uma.es Tue Aug 12 07:27:43 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Tue, 12 Aug 2008 13:27:43 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A16D44.3090204@bsc.es> References: <48A1602D.9090804@ac.uma.es> <48A162C1.3070207@bsc.es> <48A16B02.1000102@ac.uma.es> <48A16D44.3090204@bsc.es> Message-ID: <48A173AF.5030400@ac.uma.es> So with FastInfoSet can be handled binary data using XInclude, is a good idea instead to use base64 in the other hand, "To use disabled XInclude to pass a reference into a custom parser" is useful for example if you don't want to handle the reference just to sent it to another service, if it is always on don't left you this possibility Dmitry Repchevsky wrote: > Hello, > >> About FastInfoSet it compress XML schema in binary data, is this >> correct? > It's better to say that it compress (transform) entire XML infoset. > (while XOP is extract binary infoset and then again assemble then into > one) > >> So the idea can be to compress the XML using this system to reduce >> the bandwidth used, correct? > Yes it is. > >> But I cannot see the relation with xml include. > It's easy - XInclude can not handle not textual data - only > XML/plain-text > To use "disabled" XInclude to pass a reference into a custom parser is > not better than using XLink... > > On the other hand it is possible to use XInclude to include > fastinfoset encoded XML automatically. > Another advantage would be to reference not to "some" resource, but to > the entire "ontology" object that can be included into the place where > it should be... > This way you don't even need to change a message itself: you pass your > image by "value" (with XOP/MTOM attachment) or by XInclude reference > where it is encoded by fastinfoset. > The final XML is the same! Parser just assembles such a message... > > Dmitry > > Sergio Ramirez Ramirez wrote: >> About FastInfoSet it compress XML schema in binary data, is this >> correct? >> >> So the idea can be to compress the XML using this system to reduce >> the bandwidth used, correct? >> >> But I cannot see the relation with xml include. >> >> Dmitry Repchevsky wrote: >>> >>>> I mean that if you want "to have control over how to treat the >>>> referenced data" Xinclude allows this possibility, but at the same >>>> time offers the possibility of handle them automatically. >>> I am afraid the only way to make it work is to have it always >>> switched off... >>> >>> By the way, what is your opinion about FastInfoset??? >>> Could it be used with XInclude? >>> >>> I mean that it compresses data very well (it transforms XML schema >>> into ASN.1 and use BER encoding >>> If I have some ontology class with binary data (base64binary) and >>> send this "Moby Object" as an XML, but using FastInfoset... for the >>> traffic if would be virtually the same as it was "plain" binary stream. >>> >>> I mean that we can have say "BinaryImage" ontology object that is >>> using "binary" primitive type. >>> Then instead of making an url into "http://mysite.com/image.jpg" >>> we make a reference into "http://mysite.com/image.xml" >>> >>> The latter could be included and processed automatically by >>> XInclude, but if we enable FastInfoset for it - it will be sent as a >>> binary data over a network... >>> >>> Just a few thoughts... >>> >>> Best wishes, >>> >>> Dmitry >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From py at pingoured.fr Tue Aug 19 04:00:23 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Tue, 19 Aug 2008 10:00:23 +0200 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <489c53c9.2a528c0a.69e3.ffffdc0c@mx.google.com> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> <489C1C72.5000402@mpiz-koeln.mpg.de> <489C41A3.2010909@pingoured.fr> <4d93f07c0808080657u192935fat3027094ea576859a@mail.gmail.com> <489c53c9.2a528c0a.69e3.ffffdc0c@mx.google.com> Message-ID: <48AA7D97.2010606@pingoured.fr> Edward Kawas wrote: > I updated the 2 services. Did this fix the problem? > Hi all, For our case we are still facing this error. While updating the list of services, or registering a new service or even generated the skeleton of our service via dashboard, we end with the error below. We updated our jMoby with the latest cvs version. Any hints ? Thanks, Regards, Pierre generate-services: [Service(s)] Using filter for authorities: 'avilin05.avignon.inra.fr' [Service(s)] Using filter for services: '^Solstis_getDatasetTypeFromExp$' [Service(s)] Generating services into '/home/pierrey/workspace/jMoby/generated/skeletons'... [Service(s)] Reading service names... [Service(s)] ===ERROR=== [Service(s)] ===ERROR=== [Service(s)] Fault details: [Service(s)] [stackTrace: null] [Service(s)] [hostname: null] [Service(s)] Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte UTF-8 sequence. [Service(s)] Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException [Service(s)] Fault actor: null [Service(s)] When calling: [Service(s)] http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl [Service(s)] =========== [Service(s)] =========== BUILD FAILED /home/pierrey/workspace/jMoby/xmls/mosesBuild.xml:209: Java returned: 1 Total time: 38 seconds From jmrodriguez at cnio.es Tue Aug 19 04:31:16 2008 From: jmrodriguez at cnio.es (jmrodriguez) Date: Tue, 19 Aug 2008 10:31:16 +0200 Subject: [MOBY-dev] php client for biomoby services In-Reply-To: <488f3612.20d7720a.6190.1e4a@mx.google.com> References: <488EDE46.5070804@pingoured.fr> <488f3612.20d7720a.6190.1e4a@mx.google.com> Message-ID: <48AA84D4.1080104@cnio.es> Hi, Talking about PHP client for web services. Have you checked the Web Services Framework WS02? http://wso2.org/projects/wsf/php I have recently discovered this framework and it looks nice. J Edward Kawas wrote: > Just in case, you didn't get it working (I am sure that you did, but just in > case ...), I attached 2 php files that you can test with. > > The test client is in the file 'moby_php_test_service.php' and the > moby_soap_factory.php needs to be either in the same directory as the test > service or on your PHP include path. > > Thanks to Julian Tonti-Filippini for creating the PHP basis for the attached > examples! > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon > Sent: July-29-08 2:09 AM > To: MOBY-dev at lists.open-bio.org > Subject: [MOBY-dev] php client for biomoby services > > Dear list, > > We have been trying to make a php client for a simple biomoby web > service that we developed few days ago. > We are facing a problem in the creation of the input XML. We think that > using php soap library we create soap XML and not moby XML. Which > obviously returns an error. > > Has anyone of you ever try to make a simple client in php or just even > call a bioMoby service via php ? > > Below is the input that is sent to our service and the XML retrieve from > that service > > Thanks for your help, > Best regards, > > Pierre > > > input: > > xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/" > xmlns:ns1="http://avilin05.avignon.inra.fr" > xmlns:xsd="http://www.w3.org/2001/XMLSchema" > xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" > xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/" > SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"> :Body> xsi:type="xsd:string">a:1:{s:12:"Solstis_User";a:3:{s:8:"userName";s:4:"test > ";s:8:"password";s:4:"test";s:5:"email";s:12:"test at test.fr";}} olstis_getProject> > > output: > xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" > xmlns:xsd="http://www.w3.org/2001/XMLSchema" > xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> stis_getProjectResponse > soapenv:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/" > xmlns:ns1="http://avilin05.avignon.inra.fr"> xsi:type="xsd:string"><?xml version="1.0" > encoding="UTF-8"?> > <moby:MOBY xmlns:moby="http://www.biomoby.org/moby"> > <moby:mobyContent> > <moby:serviceNotes> > <moby:mobyException moby:severity="error"> > <moby:exceptionCode>600</moby:exceptionCode> > <moby:exceptionMessage>AN ERROR OCCURED DURING THE > SERVICE EXECUTION: Error in the XML input. > SystemID: null > Line (perhaps): 1 > Column: 1</moby:exceptionMessage> > </moby:mobyException> > </moby:serviceNotes> > </moby:mobyContent> > </moby:MOBY> > > < > /soapenv:Envelope> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > ------------------------------------------------------------------------ > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Have you tried CARGO? http://cargo2.bioinfo.cnio.es/ ********************* Jos? Manuel Rodr?guez Carrasco e-mail: jmrodriguez at cnio.es Tlfn: (+34) 91 732 80 00 ext: 2256 Fax: (+34) 91 224 69 76 Bioinformatic Unit Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code: 28029 Address: C/. Melchor Fern?ndez Almagro n? 3, Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From martin.senger at gmail.com Tue Aug 19 05:51:23 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 19 Aug 2008 10:51:23 +0100 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <48AA7D97.2010606@pingoured.fr> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> <489C1C72.5000402@mpiz-koeln.mpg.de> <489C41A3.2010909@pingoured.fr> <4d93f07c0808080657u192935fat3027094ea576859a@mail.gmail.com> <489c53c9.2a528c0a.69e3.ffffdc0c@mx.google.com> <48AA7D97.2010606@pingoured.fr> Message-ID: <4d93f07c0808190251n6fe2317em2318ab96e4eeda86@mail.gmail.com> > For our case we are still facing this error. I do not face the error in my local copy of jMoby. Therefore, I think that your - and perhaps other users, as well - problem is in the cache (that the cache still has the old version of the services). I suggest you to remove the cache (you can do it manually by removing the whole cache directory, or by using "reload" in the dashboard, or by using the command-line: "build/run/run-cache-client -fill -cachedir=your-cache-dir"). Does it help? Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From py at pingoured.fr Tue Aug 19 08:58:28 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Tue, 19 Aug 2008 14:58:28 +0200 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <4d93f07c0808190251n6fe2317em2318ab96e4eeda86@mail.gmail.com> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> <489C1C72.5000402@mpiz-koeln.mpg.de> <489C41A3.2010909@pingoured.fr> <4d93f07c0808080657u192935fat3027094ea576859a@mail.gmail.com> <489c53c9.2a528c0a.69e3.ffffdc0c@mx.google.com> <48AA7D97.2010606@pingoured.fr> <4d93f07c0808190251n6fe2317em2318ab96e4eeda86@mail.gmail.com> Message-ID: <48AAC374.7040001@pingoured.fr> Martin Senger wrote: >> For our case we are still facing this error. > > > I do not face the error in my local copy of jMoby. Therefore, I think that > your - and perhaps other users, as well - problem is in the cache (that the > cache still has the old version of the services). I suggest you to remove > the cache (you can do it manually by removing the whole cache directory, or > by using "reload" in the dashboard, or by using the command-line: > "build/run/run-cache-client -fill -cachedir=your-cache-dir"). > > Does it help? We tried by unchecking the box "Use local cache" it crashed again, so we remove the cache folder and it seems to be working again. Thanks for your help, Regards, Pierre From markw at illuminae.com Tue Aug 19 16:07:25 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 19 Aug 2008 13:07:25 -0700 Subject: [MOBY-dev] a request: In preparation for the Moby Annotation Jamboree... Message-ID: Hello all Mobyers! We're putting together the last pieces of cyber-infrastructure to run the Moby Service annotation jamboree, but we need your help! This jamboree, while being useful to us, is actually part of an experiment being run by my grad student Ben Good, who is studying community annotation and ontology-building. He needs to be sure that he gets a concentration of annotations around services that are actively being used by the community in order to have the statistical power to measure improvement in discoverability as a result of these annotations. As such, we are requesting that anyone who is willing to share their workflows please do so, and we will "skew" the annotation jamboree to emphasize those services. If you are willing to share, please either send your workflow to the mailing list, or directly to me, or BETTER YET, consider adding it to the myExperiment repository (http://myexperiment.org) and tagging it "moby" to make it easy to find :-) If I could collect these within the next 2 weeks that would be PERFECTO! Thanks everyone! Mark From M.Roos1 at uva.nl Tue Aug 19 16:36:55 2008 From: M.Roos1 at uva.nl (Marco Roos) Date: Tue, 19 Aug 2008 22:36:55 +0200 Subject: [MOBY-dev] Is creating Web services a nightmare or a treat? In-Reply-To: <48980CFC.5070803@uva.nl> References: <48980CFC.5070803@uva.nl> Message-ID: <48AB2EE7.3020702@uva.nl> [My apologies if you receive this e-mail more than once] Dear all, Some time ago I sent a call to Web service creators on the Taverna users list to participate in a Web service creation survey (see below). This e-mail is a reminder and an extension of addressees. I would very much appreciate your contribution or your help in spreading this e-mail to more Web service creators, in particular creators of Web services for (bioinformatics) applications. The purpose of the survey is to learn from each other where bottlenecks lie, and help us give advice to relative newbies to creating Web services. The limited number of responders so far has already produced some interesting insights (that I won't share with you yet to prevent any bias). I would appreciate it very much if you could take a few minutes to fill out the survey by following this link: http://www.surveymonkey.com/s.aspx?sm=xez63l87nw2CBV_2f1ntC_2fkg_3d_3d. Shortly after the 5th of September I will post results of the survey back to the Taverna users mailing list. Thank you very much for your help! Marco. Marco Roos wrote: > Dear user and Web service developer, > > I have been invited by the Netherlands BioInformatics Centre (NBIC) to > join a discussion about pitfalls and issues regarding the creation of > Bioinformatics Web services. If you have experience with this, would > you share your experience by answering my questions below? I hope you > agree that this could be useful for users and developers of web services. > > My basic questions are: > > 1. What is your favourite type of Web service (e.g. a 'standard' > SOAP-based wsdl, BioMoby, SoapLab, REST-based, etc.)? > 2. What is your favourite editor or framework? > 3. How much time did it take you to master the necessary skills? > How steep was the learning curve? > 4. How much time does it take you now to create a Web service? > (excluding the time it takes to write the content of the service) > 5. Did you have any issues with creating services for use in Taverna? > > Please include the reason behind your answers. > > Many thanks! > Marco. > -- Marco Roos Adaptive Information Disclosure Faculty of Science University of Amsterdam Kruislaan 403, room F1.02 1098 SJ Amsterdam tel. +31 (0) 20 525 7522 Social communities: Professional: LinkedIn , myExperiment and LifeScience at IvI groups on facebook Personal: Hyves From py at pingoured.fr Wed Aug 20 07:50:16 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 20 Aug 2008 13:50:16 +0200 Subject: [MOBY-dev] Register service from xml Message-ID: <48AC04F8.9010708@pingoured.fr> Dear list, We are now busy to register several data types and services if possible in one go. We have looked at http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/API/org/biomoby/registry/Central/Registry.html#registerObjectClass(java.lang.String) but we have not been able to find the correct way to use/implement these functions. We also looked at the ./build/run/run-cmdline-client -help but from that it seems that it does not accept xml as input to register data type, services or any other moby object. Did we miss something ? Thanks in advance, Best regards, Pierre From martin.senger at gmail.com Wed Aug 20 08:35:55 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 20 Aug 2008 13:35:55 +0100 Subject: [MOBY-dev] Register service from xml In-Reply-To: <48AC04F8.9010708@pingoured.fr> References: <48AC04F8.9010708@pingoured.fr> Message-ID: <4d93f07c0808200535p3e4530dwf2e6974cd3b1c8df@mail.gmail.com> > We also looked at the > ./build/run/run-cmdline-client -help > but from that it seems that it does not accept xml as input to register > data type, services or any other moby object. It does, actually. There is a parameter -call which can have two arguments. The first one (mandatory) is a method name (e.g. registerObjectClass for regisytering a data type), the second one (optional) is either directly XML, or a file name containing the XML. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From py at pingoured.fr Thu Aug 21 04:07:12 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Thu, 21 Aug 2008 10:07:12 +0200 Subject: [MOBY-dev] Register service from xml In-Reply-To: <4d93f07c0808200535p3e4530dwf2e6974cd3b1c8df@mail.gmail.com> References: <48AC04F8.9010708@pingoured.fr> <4d93f07c0808200535p3e4530dwf2e6974cd3b1c8df@mail.gmail.com> Message-ID: <48AD2230.1090301@pingoured.fr> Martin Senger wrote: >> We also looked at the >> ./build/run/run-cmdline-client -help >> but from that it seems that it does not accept xml as input to register >> data type, services or any other moby object. > > > It does, actually. There is a parameter -call which can have two arguments. > The first one (mandatory) is a method name (e.g. registerObjectClass for > registering a data type), the second one (optional) is either directly XML, > or a file name containing the XML. Ok we made a small python script that parse our xml file and run this command to register our objects or services. Thanks for your help, Regards, Pierre From jmfernandez at cnio.es Thu Aug 21 10:29:02 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Thu, 21 Aug 2008 16:29:02 +0200 Subject: [MOBY-dev] [MOBY-l] a request: In preparation for the Moby Annotation Jamboree... In-Reply-To: References: Message-ID: <48AD7BAE.7060903@cnio.es> Hi Mark (and everybody), we (as INB) have developed our own workflow repository and web workflow enactor, called IWWE&M. Its graphical GUI is available at: http://ubio.bioinfo.cnio.es/biotools/IWWEM/workflowmanager.html A programmatic list of the available workflows can be fetched with: http://ubio.bioinfo.cnio.es/biotools/IWWEM/cgi-bin/workflowmanager and a programmatic list of the not yet erased enactions can be fetched with: http://ubio.bioinfo.cnio.es/biotools/IWWEM/cgi-bin/workflowmanager?id=enaction: Could you take into account our workflows, please? Best Regards, Jos? Mar?a (on behalf of INB) Mark Wilkinson wrote: > Hello all Mobyers! > > We're putting together the last pieces of cyber-infrastructure to run > the Moby Service annotation jamboree, but we need your help! > > This jamboree, while being useful to us, is actually part of an > experiment being run by my grad student Ben Good, who is studying > community annotation and ontology-building. He needs to be sure that he > gets a concentration of annotations around services that are actively > being used by the community in order to have the statistical power to > measure improvement in discoverability as a result of these > annotations. As such, we are requesting that anyone who is willing to > share their workflows please do so, and we will "skew" the annotation > jamboree to emphasize those services. > > If you are willing to share, please either send your workflow to the > mailing list, or directly to me, or BETTER YET, consider adding it to > the myExperiment repository (http://myexperiment.org) and tagging it > "moby" to make it easy to find :-) > > If I could collect these within the next 2 weeks that would be PERFECTO! > > Thanks everyone! > > Mark > > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l > -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From py at pingoured.fr Wed Aug 27 09:27:41 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 27 Aug 2008 15:27:41 +0200 Subject: [MOBY-dev] call to a service in a service Message-ID: <48B5564D.3060803@pingoured.fr> Dear list, We are at the moment trying to call one of our web service inside another of our web service (in Java). We found some documentation using the call function from org.apache.axis.client. We also found some code from Taverna's plugin, but it is not clear for us if there is at this point any class in BioMoby that would allow us to run our services from an BioMoby object directly ? Is there also a method to convert a Moby object to a Moby XML (string not object) to generate the whole XML piece that could be used to call the service afterward ? We are a bit wondering what is the standard way to process this (if there is any) ? Thanks for your help, Best regards, Pierre From edward.kawas at gmail.com Wed Aug 27 09:49:41 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 27 Aug 2008 06:49:41 -0700 Subject: [MOBY-dev] call to a service in a service In-Reply-To: <48B5564D.3060803@pingoured.fr> References: <48B5564D.3060803@pingoured.fr> Message-ID: <48b55b75.0fba720a.2474.62c8@mx.google.com> Hi Pierre, Are you using MoSeS? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon Sent: August-27-08 6:28 AM To: MOBY-dev at lists.open-bio.org Subject: [MOBY-dev] call to a service in a service Dear list, We are at the moment trying to call one of our web service inside another of our web service (in Java). We found some documentation using the call function from org.apache.axis.client. We also found some code from Taverna's plugin, but it is not clear for us if there is at this point any class in BioMoby that would allow us to run our services from an BioMoby object directly ? Is there also a method to convert a Moby object to a Moby XML (string not object) to generate the whole XML piece that could be used to call the service afterward ? We are a bit wondering what is the standard way to process this (if there is any) ? Thanks for your help, Best regards, Pierre _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From py at pingoured.fr Wed Aug 27 10:03:59 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 27 Aug 2008 16:03:59 +0200 Subject: [MOBY-dev] call to a service in a service In-Reply-To: <48b55b75.0fba720a.2474.62c8@mx.google.com> References: <48B5564D.3060803@pingoured.fr> <48b55b75.0fba720a.2474.62c8@mx.google.com> Message-ID: <48B55ECF.6040209@pingoured.fr> Edward Kawas wrote: > Hi Pierre, > > Are you using MoSeS? Hi Edward, Yes we used it to generate the skeleton but we need in the "processit" method to call two of our web service with an ID that the grab from the first part of the service. Let me rephrase that: User -> send an ID Service1 -> get the request -> perform a sql query -> call service 2 and service3 with the results of this query (a different ID) -> assemble results from service2 and 3 -> return data to the user. NB The object return by service2 and service3 are part of the objet returned by service1, we designed them in that purpose. Thanks for the quick reply Best regards, Pierre From edward.kawas at gmail.com Wed Aug 27 10:25:46 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 27 Aug 2008 07:25:46 -0700 Subject: [MOBY-dev] call to a service in a service In-Reply-To: <48B55ECF.6040209@pingoured.fr> References: <48B5564D.3060803@pingoured.fr> <48b55b75.0fba720a.2474.62c8@mx.google.com> <48B55ECF.6040209@pingoured.fr> Message-ID: <48b563eb.1f538c0a.6e3a.ffffd52a@mx.google.com> Okay, the reason that I asked was to see whether or not you had access to the classes: MobyPackage & MobyJob. Here is how you could create the XML for sending to a service: // get the following values somewhere String id, ns = ...; String result = ...; // the dnasequence that I retrieved MobyPackage result = new MobyPackage() MobyJob j = new MobyJob(); j.setId("myQueryId"); DNASequence output_data_type = new DNASequence(); output_data_type.setId(id); output_data_type.setNamespace(ns); output_data_type.set_content(result); j.setData(output_data_type,"sequence"); result.addJob(j); String xml = result.toXML(); // used below Here is how you could call the service: String endpoint = ""; // the url to the service String service = ""; // the service name String serviceOutput = new CentralImpl(endpoint,"http://biomoby.org/").call(service,xml) Now, to parse the serviceOutput, you could use MobyPackage.createFromXML(serviceOutput) The import statements that you would need are org.biomoby.client.CentralImpl, org.biomoby.shared.datatypes.*, org.biomoby.shared.parser.MobyJob, org.biomoby.shared.parser.MobyPackage Does this make sense? If you need any clarifications, let me know. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon Sent: August-27-08 7:04 AM To: Core developer announcements Subject: Re: [MOBY-dev] call to a service in a service Edward Kawas wrote: > Hi Pierre, > > Are you using MoSeS? Hi Edward, Yes we used it to generate the skeleton but we need in the "processit" method to call two of our web service with an ID that the grab from the first part of the service. Let me rephrase that: User -> send an ID Service1 -> get the request -> perform a sql query -> call service 2 and service3 with the results of this query (a different ID) -> assemble results from service2 and 3 -> return data to the user. NB The object return by service2 and service3 are part of the objet returned by service1, we designed them in that purpose. Thanks for the quick reply Best regards, Pierre _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From py at pingoured.fr Wed Aug 27 11:02:10 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 27 Aug 2008 17:02:10 +0200 Subject: [MOBY-dev] call to a service in a service In-Reply-To: <48b563eb.1f538c0a.6e3a.ffffd52a@mx.google.com> References: <48B5564D.3060803@pingoured.fr> <48b55b75.0fba720a.2474.62c8@mx.google.com> <48B55ECF.6040209@pingoured.fr> <48b563eb.1f538c0a.6e3a.ffffd52a@mx.google.com> Message-ID: <48B56C72.4090402@pingoured.fr> Edward Kawas wrote: > Okay, the reason that I asked was to see whether or not you had access to > the classes: MobyPackage & MobyJob. > > > Does this make sense? If you need any clarifications, let me know. > We made it working ! Thanks a lot Edward, Best regards, Pierre From jerzyo at genesilico.pl Wed Aug 27 11:28:50 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Wed, 27 Aug 2008 17:28:50 +0200 Subject: [MOBY-dev] jMoby import problems Message-ID: <48B572B2.3030406@genesilico.pl> Hi I wanted to test jmoby and I am trying to run the simplest code possible: import org.biomoby.client.*; import org.biomoby.shared.*; import org.biomoby.shared.data.*; public class mytestcode01{ public static void main(String args[]){ System.out.println ("Hello, World!"); String aaa= new String(); try{ org.biomoby.client.CentralDigestCachedImpl myClient= new org.biomoby.client.CentralDigestCachedImpl(); } catch (Exception e){ System.err.println("Caught Exception: " + e.getMessage()); } } } My system is ubuntu 8.0 So I - downloaded java, ant and tomcat5.5 - compiled everything with ant, set some classpaths: $ echo $CLASSPATH :/home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main:/home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/:/usr/share/tomcat5.5/bin/commons-logging-api.jar And I get: javac mytestcode01.java /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:36: package org.apache.axis does not exist import org.apache.axis.AxisFault; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:37: package org.apache.axis.client does not exist import org.apache.axis.client.Call; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:38: package org.apache.axis.client does not exist import org.apache.axis.client.Service; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:39: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.DefaultHttpMethodRetryHandler; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:40: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.Header; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:41: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.HttpClient; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:42: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.HttpException; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:43: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.HttpStatus; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:44: package org.apache.commons.httpclient.methods does not exist import org.apache.commons.httpclient.methods.HeadMethod; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:45: package org.apache.commons.httpclient.params does not exist import org.apache.commons.httpclient.params.HttpMethodParams; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:2087: cannot find symbol symbol : class AxisFault location: class org.biomoby.client.CentralImpl public static String formatFault (AxisFault e, String endpoint, QName method) { ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:2096: cannot find symbol symbol : class AxisFault location: class org.biomoby.client.CentralImpl public static void formatFault (AxisFault e, PrintStream out, ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java:14: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java:15: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java:16: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFReader; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java:17: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ResIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java:18: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Resource; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java:19: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Statement; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java:20: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.StmtIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java:21: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDF; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java:22: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDFS; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:23: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:24: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:25: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFNode; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:26: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFReader; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:27: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ResIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:28: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Resource; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:29: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Statement; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:30: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.StmtIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:31: package com.hp.hpl.jena.shared does not exist import com.hp.hpl.jena.shared.JenaException; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:32: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDF; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:33: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDFS; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:34: package com.ibm.lsid does not exist import com.ibm.lsid.LSID; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:176: cannot find symbol symbol : class Model location: class org.biomoby.shared.extended.ServiceInstanceParser public MobyService[] getMobyServicesFromRDF(Model model) throws MobyException { ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:192: cannot find symbol symbol : class Model location: class org.biomoby.shared.extended.ServiceInstanceParser private boolean processModel(ArrayList list, Model model) { ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java:12: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java:13: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java:14: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFNode; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java:15: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFReader; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java:16: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ResIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java:17: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Resource; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java:18: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDFS; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/Utils.java:27: package org.apache.commons.io does not exist import org.apache.commons.io.FileUtils; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/Utils.java:28: package org.apache.commons.io does not exist import org.apache.commons.io.IOUtils; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java:12: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java:13: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java:14: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFNode; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java:15: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFReader; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java:16: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ResIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java:17: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Resource; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java:18: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDFS; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/DC_PROTEGE.java:4: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.*; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/DC_PROTEGE.java:18: cannot find symbol symbol : class Model location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE private static Model m_model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/DC_PROTEGE.java:19: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE public static final Property publisher; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/DC_PROTEGE.java:21: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE public static final Property creator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/DC_PROTEGE.java:22: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE public static final Property format; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/DC_PROTEGE.java:23: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE public static final Property identifier; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:2: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:3: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:4: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Property; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:21: cannot find symbol symbol : class Model location: class org.biomoby.client.rdf.vocabulary.Predicates private final static Model _model = ModelFactory.createDefaultModel();; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:22: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property category = _model.getProperty(uri + "category"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:23: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property isa = _model.getProperty(uri + "isa"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:24: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property has = _model.getProperty(uri + "has"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:25: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property hasa = _model.getProperty(uri + "hasa"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:26: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property articleName = _model.getProperty(uri + "articleName"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:27: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property article_name = _model.getProperty(uri + "article_name"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:28: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property namespace_type = _model.getProperty(uri + "namespaceType"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:29: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property object_type = _model.getProperty(uri + "objectType"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:30: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property input = _model.getProperty(uri + "input"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:31: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property output = _model.getProperty(uri + "output"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:32: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property consumes = _model.getProperty(uri + "consumes"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:33: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property produces = _model.getProperty(uri + "produces"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:34: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property performs_task = _model.getProperty(uri + "performs_task"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:35: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property comment = _model.getProperty(uri + "comment"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:36: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property label = _model.getProperty(uri + "label"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:37: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property default_value = _model.getProperty(uri + "default_value"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:38: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property datatype = _model.getProperty(uri + "datatype"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:39: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property max = _model.getProperty(uri + "max"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:40: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property min = _model.getProperty(uri + "min"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:41: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property enumeration = _model.getProperty(uri + "enum"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:42: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property SignatureURL = _model.getProperty(uri + "SignatureURL"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:43: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property authoritative = _model.getProperty(uri + "authoritative"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:44: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property ofType = _model.getProperty(uri + "ofType"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:46: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property Simple = _model.getProperty(uri + "Simple"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:47: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property Secondary = _model.getProperty(uri + "Secondary"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:48: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property Collection = _model.getProperty(uri + "Collection"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:50: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property sampleInputData = _model.getProperty(uri + "sampleInputData"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:51: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property sampleOutputData = _model.getProperty(uri + "sampleOutputData"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:52: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property approvedBy = _model.getProperty(uri + "approvedBy"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:53: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property StructuralComponent = _model.getProperty(uri + "StructuralComponent"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:54: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property DataComponent = _model.getProperty(uri + "DataComponent"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:55: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property MobyMessageComponent = _model.getProperty(uri + "MobyMessageComponent"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:56: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property MobyThing = _model.getProperty(uri + "MobyThing"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:57: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property inNamespaces = _model.getProperty(uri + "inNamespaces"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:58: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property componentName = _model.getProperty(uri + "componentName"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/FetaVocabulary.java:4: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.*; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/FetaVocabulary.java:18: cannot find symbol symbol : class Model location: class org.biomoby.client.rdf.vocabulary.FetaVocabulary private static Model m_model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/FetaVocabulary.java:19: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.FetaVocabulary public static Property operationType; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/FetaVocabulary.java:20: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.FetaVocabulary public static final Property inNamespaces; ^ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 errors I guess I need to install something or set some classpaths. Please help Jerzy Orlowski From edward.kawas at gmail.com Wed Aug 27 11:53:49 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 27 Aug 2008 08:53:49 -0700 Subject: [MOBY-dev] jMoby import problems In-Reply-To: <48B572B2.3030406@genesilico.pl> References: <48B572B2.3030406@genesilico.pl> Message-ID: <48b5788e.1ed7720a.0ad5.ffffc1be@mx.google.com> Have you taken a look at: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/EclipseAndJMoby. html It might be useful for you. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jerzy Orlowski Sent: August-27-08 8:29 AM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] jMoby import problems Hi I wanted to test jmoby and I am trying to run the simplest code possible: import org.biomoby.client.*; import org.biomoby.shared.*; import org.biomoby.shared.data.*; public class mytestcode01{ public static void main(String args[]){ System.out.println ("Hello, World!"); String aaa= new String(); try{ org.biomoby.client.CentralDigestCachedImpl myClient= new org.biomoby.client.CentralDigestCachedImpl(); } catch (Exception e){ System.err.println("Caught Exception: " + e.getMessage()); } } } My system is ubuntu 8.0 So I - downloaded java, ant and tomcat5.5 - compiled everything with ant, set some classpaths: $ echo $CLASSPATH :/home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main:/home/jerzyo/ projects/workflows/jmoby/moby-live/Java/src/main/:/usr/share/tomcat5.5/bin/c ommons-logging-api.jar And I get: javac mytestcode01.java /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:36: package org.apache.axis does not exist import org.apache.axis.AxisFault; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:37: package org.apache.axis.client does not exist import org.apache.axis.client.Call; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:38: package org.apache.axis.client does not exist import org.apache.axis.client.Service; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:39: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.DefaultHttpMethodRetryHandler; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:40: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.Header; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:41: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.HttpClient; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:42: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.HttpException; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:43: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.HttpStatus; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:44: package org.apache.commons.httpclient.methods does not exist import org.apache.commons.httpclient.methods.HeadMethod; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:45: package org.apache.commons.httpclient.params does not exist import org.apache.commons.httpclient.params.HttpMethodParams; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:2087: cannot find symbol symbol : class AxisFault location: class org.biomoby.client.CentralImpl public static String formatFault (AxisFault e, String endpoint, QName method) { ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:2096: cannot find symbol symbol : class AxisFault location: class org.biomoby.client.CentralImpl public static void formatFault (AxisFault e, PrintStream out, ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/DataTypeParser.java:14: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/DataTypeParser.java:15: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/DataTypeParser.java:16: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFReader; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/DataTypeParser.java:17: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ResIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/DataTypeParser.java:18: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Resource; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/DataTypeParser.java:19: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Statement; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/DataTypeParser.java:20: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.StmtIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/DataTypeParser.java:21: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDF; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/DataTypeParser.java:22: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDFS; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:23: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:24: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:25: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFNode; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:26: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFReader; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:27: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ResIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:28: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Resource; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:29: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Statement; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:30: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.StmtIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:31: package com.hp.hpl.jena.shared does not exist import com.hp.hpl.jena.shared.JenaException; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:32: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDF; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:33: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDFS; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:34: package com.ibm.lsid does not exist import com.ibm.lsid.LSID; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:176: cannot find symbol symbol : class Model location: class org.biomoby.shared.extended.ServiceInstanceParser public MobyService[] getMobyServicesFromRDF(Model model) throws MobyException { ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:192: cannot find symbol symbol : class Model location: class org.biomoby.shared.extended.ServiceInstanceParser private boolean processModel(ArrayList list, Model model) { ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceTypeParser.java:12: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceTypeParser.java:13: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceTypeParser.java:14: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFNode; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceTypeParser.java:15: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFReader; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceTypeParser.java:16: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ResIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceTypeParser.java:17: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Resource; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceTypeParser.java:18: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDFS; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/Utils.java:27: package org.apache.commons.io does not exist import org.apache.commons.io.FileUtils; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/Utils.java:28: package org.apache.commons.io does not exist import org.apache.commons.io.IOUtils; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/NamespaceParser.java:12: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/NamespaceParser.java:13: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/NamespaceParser.java:14: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFNode; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/NamespaceParser.java:15: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFReader; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/NamespaceParser.java:16: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ResIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/NamespaceParser.java:17: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Resource; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/NamespaceParser.java:18: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDFS; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/DC_PROTEGE.java:4: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.*; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/DC_PROTEGE.java:18: cannot find symbol symbol : class Model location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE private static Model m_model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/DC_PROTEGE.java:19: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE public static final Property publisher; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/DC_PROTEGE.java:21: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE public static final Property creator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/DC_PROTEGE.java:22: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE public static final Property format; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/DC_PROTEGE.java:23: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE public static final Property identifier; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:2: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:3: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:4: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Property; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:21: cannot find symbol symbol : class Model location: class org.biomoby.client.rdf.vocabulary.Predicates private final static Model _model = ModelFactory.createDefaultModel();; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:22: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property category = _model.getProperty(uri + "category"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:23: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property isa = _model.getProperty(uri + "isa"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:24: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property has = _model.getProperty(uri + "has"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:25: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property hasa = _model.getProperty(uri + "hasa"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:26: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property articleName = _model.getProperty(uri + "articleName"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:27: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property article_name = _model.getProperty(uri + "article_name"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:28: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property namespace_type = _model.getProperty(uri + "namespaceType"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:29: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property object_type = _model.getProperty(uri + "objectType"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:30: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property input = _model.getProperty(uri + "input"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:31: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property output = _model.getProperty(uri + "output"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:32: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property consumes = _model.getProperty(uri + "consumes"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:33: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property produces = _model.getProperty(uri + "produces"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:34: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property performs_task = _model.getProperty(uri + "performs_task"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:35: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property comment = _model.getProperty(uri + "comment"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:36: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property label = _model.getProperty(uri + "label"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:37: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property default_value = _model.getProperty(uri + "default_value"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:38: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property datatype = _model.getProperty(uri + "datatype"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:39: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property max = _model.getProperty(uri + "max"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:40: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property min = _model.getProperty(uri + "min"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:41: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property enumeration = _model.getProperty(uri + "enum"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:42: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property SignatureURL = _model.getProperty(uri + "SignatureURL"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:43: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property authoritative = _model.getProperty(uri + "authoritative"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:44: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property ofType = _model.getProperty(uri + "ofType"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:46: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property Simple = _model.getProperty(uri + "Simple"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:47: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property Secondary = _model.getProperty(uri + "Secondary"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:48: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property Collection = _model.getProperty(uri + "Collection"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:50: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property sampleInputData = _model.getProperty(uri + "sampleInputData"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:51: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property sampleOutputData = _model.getProperty(uri + "sampleOutputData"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:52: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property approvedBy = _model.getProperty(uri + "approvedBy"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:53: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property StructuralComponent = _model.getProperty(uri + "StructuralComponent"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:54: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property DataComponent = _model.getProperty(uri + "DataComponent"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:55: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property MobyMessageComponent = _model.getProperty(uri + "MobyMessageComponent"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:56: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property MobyThing = _model.getProperty(uri + "MobyThing"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:57: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property inNamespaces = _model.getProperty(uri + "inNamespaces"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:58: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property componentName = _model.getProperty(uri + "componentName"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/FetaVocabulary.java:4: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.*; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/FetaVocabulary.java:18: cannot find symbol symbol : class Model location: class org.biomoby.client.rdf.vocabulary.FetaVocabulary private static Model m_model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/FetaVocabulary.java:19: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.FetaVocabulary public static Property operationType; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/FetaVocabulary.java:20: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.FetaVocabulary public static final Property inNamespaces; ^ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 errors I guess I need to install something or set some classpaths. Please help Jerzy Orlowski _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From martin.senger at gmail.com Wed Aug 27 11:59:24 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 27 Aug 2008 16:59:24 +0100 Subject: [MOBY-dev] jMoby import problems In-Reply-To: <48B572B2.3030406@genesilico.pl> References: <48B572B2.3030406@genesilico.pl> Message-ID: <4d93f07c0808270859h3f0ba8b9xf9ae2dd6c0a2bfc5@mail.gmail.com> > - compiled everything with ant, set some classpaths: The problem seems to be in setting the CLASSPATH. You should not set it manually. Better is to extend the Ant's build.xml for other tasks you intend to do. You can look into build/run/*.sh scripts to see what the full CLASSPATH should look like. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From jerzyo at genesilico.pl Wed Aug 27 12:22:12 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Wed, 27 Aug 2008 18:22:12 +0200 Subject: [MOBY-dev] MOBY-dev Digest, Vol 68, Issue 10 In-Reply-To: References: Message-ID: <48B57F34.8060008@genesilico.pl> But I am not on Windows, and I have never used Eclipse. Anyway, I managed to do something with my error 1. When I installed maven (sudo apt-get install maven2) the code compiles but does not execute: java mytestcode01.java Exception in thread "main" java.lang.NoClassDefFoundError: mytestcode01/java Caused by: java.lang.ClassNotFoundException: mytestcode01.java at java.net.URLClassLoader$1.run(URLClassLoader.java:200) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:188) at java.lang.ClassLoader.loadClass(ClassLoader.java:306) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276) at java.lang.ClassLoader.loadClass(ClassLoader.java:251) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:31 2. When I removed maven (apt-get remove maven2) and added all jars from ~/.m2/repository to my classpath, the code compiles and executes without errors. I think I made a kind of hack, but I do not even know what the ~/.m2/repository is for Any ideas? Jerzy moby-dev-request at lists.open-bio.org wrote: > Send MOBY-dev mailing list submissions to > moby-dev at lists.open-bio.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/moby-dev > or, via email, send a message with subject or body 'help' to > moby-dev-request at lists.open-bio.org > > You can reach the person managing the list at > moby-dev-owner at lists.open-bio.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of MOBY-dev digest..." > > > Today's Topics: > > 1. Re: jMoby import problems (Edward Kawas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 27 Aug 2008 08:53:49 -0700 > From: "Edward Kawas" > Subject: Re: [MOBY-dev] jMoby import problems > To: "'Core developer announcements'" > Message-ID: <48b5788e.1ed7720a.0ad5.ffffc1be at mx.google.com> > Content-Type: text/plain; charset="us-ascii" > > Have you taken a look at: > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/EclipseAndJMoby. > html > > It might be useful for you. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jerzy Orlowski > Sent: August-27-08 8:29 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] jMoby import problems > > Hi > > I wanted to test jmoby and I am trying to run the simplest code possible: > > import org.biomoby.client.*; > import org.biomoby.shared.*; > import org.biomoby.shared.data.*; > > public class mytestcode01{ > public static void main(String args[]){ > System.out.println ("Hello, World!"); > String aaa= new String(); > > try{ > org.biomoby.client.CentralDigestCachedImpl myClient= new > org.biomoby.client.CentralDigestCachedImpl(); > } > catch (Exception e){ > System.err.println("Caught Exception: " + e.getMessage()); > > } > } > } > > My system is ubuntu 8.0 > > So I > - downloaded java, ant and tomcat5.5 > - compiled everything with ant, set some classpaths: > $ echo $CLASSPATH > :/home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main:/home/jerzyo/ > projects/workflows/jmoby/moby-live/Java/src/main/:/usr/share/tomcat5.5/bin/c > ommons-logging-api.jar > > And I get: > > > > > > > javac mytestcode01.java > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:36: > package org.apache.axis does not exist > import org.apache.axis.AxisFault; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:37: > package org.apache.axis.client does not exist > import org.apache.axis.client.Call; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:38: > package org.apache.axis.client does not exist > import org.apache.axis.client.Service; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:39: > package org.apache.commons.httpclient does not exist > import org.apache.commons.httpclient.DefaultHttpMethodRetryHandler; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:40: > package org.apache.commons.httpclient does not exist > import org.apache.commons.httpclient.Header; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:41: > package org.apache.commons.httpclient does not exist > import org.apache.commons.httpclient.HttpClient; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:42: > package org.apache.commons.httpclient does not exist > import org.apache.commons.httpclient.HttpException; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:43: > package org.apache.commons.httpclient does not exist > import org.apache.commons.httpclient.HttpStatus; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:44: > package org.apache.commons.httpclient.methods does not exist > import org.apache.commons.httpclient.methods.HeadMethod; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:45: > package org.apache.commons.httpclient.params does not exist > import org.apache.commons.httpclient.params.HttpMethodParams; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:2087: > cannot find symbol > symbol : class AxisFault > location: class org.biomoby.client.CentralImpl > public static String formatFault (AxisFault e, String endpoint, > QName method) { > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:2096: > cannot find symbol > symbol : class AxisFault > location: class org.biomoby.client.CentralImpl > public static void formatFault (AxisFault e, PrintStream out, > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/DataTypeParser.java:14: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Model; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/DataTypeParser.java:15: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.ModelFactory; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/DataTypeParser.java:16: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.RDFReader; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/DataTypeParser.java:17: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.ResIterator; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/DataTypeParser.java:18: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Resource; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/DataTypeParser.java:19: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Statement; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/DataTypeParser.java:20: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.StmtIterator; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/DataTypeParser.java:21: > package com.hp.hpl.jena.vocabulary does not exist > import com.hp.hpl.jena.vocabulary.RDF; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/DataTypeParser.java:22: > package com.hp.hpl.jena.vocabulary does not exist > import com.hp.hpl.jena.vocabulary.RDFS; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:23: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Model; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:24: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.ModelFactory; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:25: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.RDFNode; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:26: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.RDFReader; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:27: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.ResIterator; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:28: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Resource; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:29: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Statement; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:30: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.StmtIterator; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:31: > package com.hp.hpl.jena.shared does not exist > import com.hp.hpl.jena.shared.JenaException; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:32: > package com.hp.hpl.jena.vocabulary does not exist > import com.hp.hpl.jena.vocabulary.RDF; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:33: > package com.hp.hpl.jena.vocabulary does not exist > import com.hp.hpl.jena.vocabulary.RDFS; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:34: > package com.ibm.lsid does not exist > import com.ibm.lsid.LSID; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:176: > cannot find symbol > symbol : class Model > location: class org.biomoby.shared.extended.ServiceInstanceParser > public MobyService[] getMobyServicesFromRDF(Model model) throws > MobyException { > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:192: > cannot find symbol > symbol : class Model > location: class org.biomoby.shared.extended.ServiceInstanceParser > private boolean processModel(ArrayList list, Model > model) { > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceTypeParser.java:12: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Model; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceTypeParser.java:13: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.ModelFactory; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceTypeParser.java:14: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.RDFNode; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceTypeParser.java:15: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.RDFReader; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceTypeParser.java:16: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.ResIterator; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceTypeParser.java:17: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Resource; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceTypeParser.java:18: > package com.hp.hpl.jena.vocabulary does not exist > import com.hp.hpl.jena.vocabulary.RDFS; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/Utils.java:27: > package org.apache.commons.io does not exist > import org.apache.commons.io.FileUtils; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/Utils.java:28: > package org.apache.commons.io does not exist > import org.apache.commons.io.IOUtils; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/NamespaceParser.java:12: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Model; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/NamespaceParser.java:13: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.ModelFactory; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/NamespaceParser.java:14: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.RDFNode; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/NamespaceParser.java:15: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.RDFReader; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/NamespaceParser.java:16: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.ResIterator; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/NamespaceParser.java:17: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Resource; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/NamespaceParser.java:18: > package com.hp.hpl.jena.vocabulary does not exist > import com.hp.hpl.jena.vocabulary.RDFS; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/DC_PROTEGE.java:4: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.*; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/DC_PROTEGE.java:18: > cannot find symbol > symbol : class Model > location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE > private static Model m_model; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/DC_PROTEGE.java:19: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE > public static final Property publisher; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/DC_PROTEGE.java:21: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE > public static final Property creator; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/DC_PROTEGE.java:22: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE > public static final Property format; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/DC_PROTEGE.java:23: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE > public static final Property identifier; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:2: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Model; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:3: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.ModelFactory; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:4: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Property; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:21: > cannot find symbol > symbol : class Model > location: class org.biomoby.client.rdf.vocabulary.Predicates > private final static Model _model = ModelFactory.createDefaultModel();; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:22: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property category = _model.getProperty(uri + > "category"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:23: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property isa = _model.getProperty(uri + "isa"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:24: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property has = _model.getProperty(uri + "has"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:25: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property hasa = _model.getProperty(uri + "hasa"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:26: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property articleName = _model.getProperty(uri + > "articleName"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:27: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property article_name = _model.getProperty(uri + > "article_name"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:28: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property namespace_type = _model.getProperty(uri > + "namespaceType"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:29: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property object_type = _model.getProperty(uri + > "objectType"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:30: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property input = _model.getProperty(uri + "input"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:31: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property output = _model.getProperty(uri + > "output"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:32: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property consumes = _model.getProperty(uri + > "consumes"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:33: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property produces = _model.getProperty(uri + > "produces"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:34: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property performs_task = _model.getProperty(uri > + "performs_task"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:35: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property comment = _model.getProperty(uri + > "comment"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:36: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property label = _model.getProperty(uri + "label"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:37: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property default_value = _model.getProperty(uri > + "default_value"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:38: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property datatype = _model.getProperty(uri + > "datatype"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:39: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property max = _model.getProperty(uri + "max"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:40: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property min = _model.getProperty(uri + "min"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:41: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property enumeration = _model.getProperty(uri + > "enum"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:42: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property SignatureURL = _model.getProperty(uri + > "SignatureURL"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:43: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property authoritative = _model.getProperty(uri > + "authoritative"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:44: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property ofType = _model.getProperty(uri + > "ofType"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:46: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property Simple = _model.getProperty(uri + > "Simple"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:47: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property Secondary = _model.getProperty(uri + > "Secondary"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:48: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property Collection = _model.getProperty(uri + > "Collection"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:50: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property sampleInputData = > _model.getProperty(uri + "sampleInputData"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:51: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property sampleOutputData = > _model.getProperty(uri + "sampleOutputData"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:52: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property approvedBy = _model.getProperty(uri + > "approvedBy"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:53: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property StructuralComponent = > _model.getProperty(uri + "StructuralComponent"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:54: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property DataComponent = _model.getProperty(uri > + "DataComponent"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:55: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property MobyMessageComponent = > _model.getProperty(uri + "MobyMessageComponent"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:56: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property MobyThing = _model.getProperty(uri + > "MobyThing"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:57: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property inNamespaces = _model.getProperty(uri + > "inNamespaces"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:58: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property componentName = _model.getProperty(uri > + "componentName"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/FetaVocabulary.java:4: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.*; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/FetaVocabulary.java:18: > cannot find symbol > symbol : class Model > location: class org.biomoby.client.rdf.vocabulary.FetaVocabulary > private static Model m_model; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/FetaVocabulary.java:19: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.FetaVocabulary > public static Property operationType; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/FetaVocabulary.java:20: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.FetaVocabulary > public static final Property inNamespaces; > ^ > Note: Some input files use unchecked or unsafe operations. > Note: Recompile with -Xlint:unchecked for details. > 100 errors > > > > I guess I need to install something or set some classpaths. > Please help > > Jerzy Orlowski > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > > ------------------------------ > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > End of MOBY-dev Digest, Vol 68, Issue 10 > **************************************** > > > > From martin.senger at gmail.com Wed Aug 27 12:32:32 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 27 Aug 2008 17:32:32 +0100 Subject: [MOBY-dev] MOBY-dev Digest, Vol 68, Issue 10 In-Reply-To: <48B57F34.8060008@genesilico.pl> References: <48B57F34.8060008@genesilico.pl> Message-ID: <4d93f07c0808270932o719b2f0dxf09d31afdb699b60@mail.gmail.com> > 1. When I installed maven You do not need maven in order to use jMoby. added all jars from ~/.m2/repository to my classpath That's what I was suggesting you; that's what you see in the build/run/run* scripts. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From jerzyo at genesilico.pl Wed Aug 27 12:49:34 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Wed, 27 Aug 2008 18:49:34 +0200 Subject: [MOBY-dev] jMoby import problems In-Reply-To: References: Message-ID: <48B5859E.9010209@genesilico.pl> Thanks a lot, sourcing build/run/run.me.sh solves the problem. Jerzy moby-dev-request at lists.open-bio.org wrote: > Date: Wed, 27 Aug 2008 16:59:24 +0100 > From: "Martin Senger" > Subject: Re: [MOBY-dev] jMoby import problems > To: "Core developer announcements" > Message-ID: > <4d93f07c0808270859h3f0ba8b9xf9ae2dd6c0a2bfc5 at mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > >> - compiled everything with ant, set some classpaths: >> > > > The problem seems to be in setting the CLASSPATH. You should not set it > manually. Better is to extend the Ant's build.xml for other tasks you intend > to do. You can look into build/run/*.sh scripts to see what the full > CLASSPATH should look like. > > Cheers, > Martin > > From martin.senger at gmail.com Fri Aug 1 00:03:03 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 1 Aug 2008 08:03:03 +0800 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48918170.2060300@bsc.es> References: <48918170.2060300@bsc.es> Message-ID: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> > the correct way to implement streaming What do you mean by "implement streaming"? I concluded that you meant "sending binary data from (or to) a moby service". Is is correct? > would be using XOP/MTOM specifications This is again a SOAP-based specification, meaning another way how to make an attachment (correct?). I have feeling that our current proposal about the data-by-reference (that I am going to summarize in the next few hours) has a reasonable tools for getting binary data - if sent as a reference. If the protocol for dereferencing is HTTP, we can use MIME type (content-type HTTP header) for references data. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From pieter.neerincx at gmail.com Fri Aug 1 01:45:33 2008 From: pieter.neerincx at gmail.com (Pieter Neerincx) Date: Fri, 1 Aug 2008 03:45:33 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> References: <48918170.2060300@bsc.es> <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> Message-ID: Hi, On 01 Aug 2008, at 02:03, Martin Senger wrote: >> the correct way to implement streaming > > > What do you mean by "implement streaming"? I concluded that you meant > "sending binary data from (or to) a moby service". Is is correct? > > >> would be using XOP/MTOM specifications > > > This is again a SOAP-based specification, meaning another way how to > make an > attachment (correct?). Well theoretically an attachment would be ideal. It makes sure the attachment can be parsed separately to provide scalability. Furthermore, you always keep the data "together". With "external" references the data is separated and has to go over the wire in two different sessions. This way data might get lost. If the first session uses SOAP over HTTP with a reference to data available only over FTP and my client or service doesn't talk FTP, I received only half of the package. With an attachment it either arrives completely or it doesn't arrive at all. So, theoretically I'd love attachment support for BioMoby services, but my previous questions remained unanswered: 1. Is there any Perl support for such XOP/MTOM attachments. I mean a module that actually *works* in contrast to the MIME-tools package. 2. Do XOP/MTOM attachments scale beyond the reach of the casual firewall? Most firewalls block MIME/DIME attachments over 5 MB in size. Attachments ain't going to improve scalability of BioMoby services if 99% of our users scale to a max of 5 MB. Martin, if you are at the EBI right now, you might ask for some advise at the external services group. I know they are one of the few smart guys who managed to get their SOAP services working with MIME attachments and hit the firewall limits. It was at ISMB in Fortaleza 2006 when I talked to them about these issues, so the situation might have improved by now... Still, even if we wouldn't need it for scalability, pass-by-reference would be very handy so you can reference existing data from others (like a reference to a UniProt record on a EBI server.) So unless the issues above are resolved, attachments are theoretically maybe a nicer solution, but I'd say pass-by-reference is practically the best solution to improve scalability in a pragmatic way. Cheers, Pi > I have feeling that our current proposal about the data-by-reference > (that I > am going to summarize in the next few hours) has a reasonable tools > for > getting binary data - if sent as a reference. If the protocol for > dereferencing is HTTP, we can use MIME type (content-type HTTP > header) for > references data. > > Martin > > -- > Martin Senger > email: martin.senger at gmail.com,m.senger at cgiar.org > skype: martinsenger > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: +31 (0)317-483 060 mobile: +31 (0)6-143 66 783 e-mail: pieter.neerincx at gmail.com skype: pieter.online ------------------------------------------------------------- From dmitry.repchevski at bsc.es Sun Aug 3 16:34:48 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Sun, 03 Aug 2008 18:34:48 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> Message-ID: <4895DE28.7010102@bsc.es> Hello Martin, > What do you mean by "implement streaming"? I concluded that you meant > "sending binary data from (or to) a moby service". Is is correct? > yes it is. > This is again a SOAP-based specification, meaning another way how to make an > attachment (correct?). > XOP is the XML way to reference a binary attachment for XML using a reference to it. Even in theory it is not SOAP dependent, the only implementation I know (I may be wrong) is a MTOM that is for SOAP protocol. I couldn't find an implementation for straight XML (because we need a transport for it). > If the protocol for dereferencing is HTTP, we can use MIME type (content-type HTTP header) for > references data. > This is what XOP is about - the only problem is that it can not reference an external resource. It would be great to have something based on Servlet + XML + XOP on java, but I looked at JAX-RS (JSR-311) REST and there is nothing... I had an idea, but afraid it has a problem with an implementation. The idea is to use XML attachment (instead of binary one) and in those attachment put XInclude with a link to external document. Such document itself would be an XML with a binary attachment. So we would have: External resource represented by XML (moby ontology class like MobyImage) + a binary attachment with an image data itself. Then we have a main document with a MobyRef primitive that is encoded as an XML attachment where an attachment itself is an XInclude to the MobyImage. This way the document is assembled into a standard moby message automagically: The only problem is that XInclude works with a plain XML, I think... Cheers, Dmitry From dmitry.repchevski at bsc.es Sun Aug 3 16:48:05 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Sun, 03 Aug 2008 18:48:05 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: References: Message-ID: <4895E145.4060804@bsc.es> Hello Pieter, > ... I'd say pass-by-reference is practically the best solution to improve scalability in a pragmatic way. > This is what I am afraid of... :-( Even have to agree... Pragmatic way is not only to think about a "nice solution" but about an implementation also... So we have resources that could be temporal (like a result of some service execution) and permanent (pdb file). These results may be referenced by external links (using uri) or be internal ones (??? to the some local file). I just like to summarize things... Dmitry From martin.senger at gmail.com Mon Aug 4 02:54:36 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 4 Aug 2008 10:54:36 +0800 Subject: [MOBY-dev] data by reference - a request for comments In-Reply-To: References: <488B0123.3040608@bsc.es> <4d93f07c0807260452g3048765ev6f84be49dc8cf26d@mail.gmail.com> <4d93f07c0807271829v10ff50d5y2c6f83b279256fdb@mail.gmail.com> Message-ID: <4d93f07c0808031954v5e266c63kee2a1e1beac1bad1@mail.gmail.com> Hi all, Thank you for all comments and suggestions. Here is a summary. Before we consider it as an RFC we still need to answer few questions. [So this not yet a call to vote, but it is close to it, I hope. I would rather prefer Mark to make the call when the time is appropriate and the RFC clear.] ------- a) There is one change in the service registration (and, consequently, in the findService() response): A new property "allowingRefs" that contains a list of one or more protocols names (e.g. http or ftp). A service having this property non-empty is able both accepting references from clients and producing references in its responses. Commentary: I would leave it to the Mark/Eddie to specify how exactly this new property appears in the registration and in the findService. ------- b) A client asks for getting back references by including "acceptRefs" attribute in mobyData tag. The attribute lists one or more protocol names that the client can accept. For example: acceptRefs="http,ftp". A client can also send its input data by reference - but only to the services that has a non-empty property "allowingRefs". ------- c) A service can obey a request for references. Question: A service can obey or should obey? ------- d) The format of references: The references are expressed as an XInclude element, with the namespace http://www.w3.org/2001/XInclude. For example: Notice that in this example, there is a "text" - meaning that the references data are non-XML, non-escaped raw data. Such as (notice the non-escaped "greater-than" sign): >sp|Q25158|OPSC2_HEMSA Compound eye opsin BCRH2 OS=Hemigrapsus sanguineus PE=2 SV=1 MTNATGPQMAYYGAASMDFGYPEGVSIVDFVRPEIKPYVHQHWYNYPPVNPMWHYLLGVI YLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTNVPFFTYNCFSGGV WMFSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNGPKLTTGKAVVFALISWV IAIGCALPPFFGWGNYILEGILDSCSYDYLTQDFNTFSYNIFIFVFDYFLPAAIIVFSYV FIVKAIFAHEAAMRAQAKKMNVSTLRSNEADAQRAEIRIAKTALVNVSLWFICWTPYALI SLKGVMGDTSGITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCVHETET KSNDDSQSNSTVAQDKA Commentary, questions: i) I am not sure if we should use XInclude (as above) or rather XLink. Their differences are blurned for me. ii) If using XInclude, are we going to allow also the attribute "xpointer"? I hope not... ------- e) Location of references: The references may be placed inside any XML tag within a BioMoby message. Commentary: God bless those who are going to implement it... ------- f) Protocol and format of the referenced data: The protocol how to get data is specified in the "href" attribute of the "xi:include" tag. The format of referenced data depends where the "xi:include" tag is used: If it is used on any other tag than the primitive type, it has to be an XML complying with the BioMoby message specification, and the "xi:include" tag should have the parse="xml" attribute (or none at all). The same for primitive types when parse="xml" is used. For primitive types with parse="text", the referenced data may be encoded differently as they would in a regular BioMoby message. The new encoding can be specified in the "encoding" attribute of the "xi:include" tag, or - if the HTTP protocol is used - in the HTTP header "Content-type". Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Mon Aug 4 06:32:46 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 04 Aug 2008 08:32:46 +0200 Subject: [MOBY-dev] findService and the hierarchy In-Reply-To: <48899C0B.70408@mpiz-koeln.mpg.de> References: <487C9061.3030203@mpiz-koeln.mpg.de> <4d93f07c0807222009x7c108d25j52930dae4f9ddaf1@mail.gmail.com> <48899C0B.70408@mpiz-koeln.mpg.de> Message-ID: <4896A28E.1070204@mpiz-koeln.mpg.de> Martin Senger wrote: > I posted my results - now it is up to Eddie or Mark to draw > conclusion from that results... could any of you two state something about that ? Thanks Andreas Andreas Groscurth wrote: > i like to bring this up for discussion again ;-) > > thanks > > Martin Senger wrote: >>> In my opinion when searching for services consuming >>> Annotated_GO_Term via >>> the findService method i should also include the service which >>> consumes a >>> GO_Term datatype, as this is the parent datatype (per default >>> 'includeParentDatatype' is true).... >>> >>> >> >> I assume that by "I should also include" you actually meant "the >> registry >> response should also include". Is my understanding correct? >> >> If so, I am afraid that it is not the issue of the jMoby library but the >> registry itself. Eddie or Mark can confirm or reject this hypothesis. >> >> The BioMoby API allows to specify two XML tags when calling findService >> method: the >> >> X >> and >> X >> >> Where X can be either 1 or 0. >> >> The jMoby's findService() method sets these two tags according to the >> two >> boolean parameters that the method can get: >> >> boolean includeChildrenServiceTypes >> and >> boolean includeParentDataTypes >> >> I have tried to call the findService, with the Annotated_GO_Term input, >> using all combinations of these two tags (you can do it using the Moby >> command-line client with the optioins -nc and/or -np). The results are >> either no service or 713 services: >> >> expandObjects expandServices # of found services >> 1 1 713 >> 0 0 0 >> 1 0 713 >> 0 0 0 >> >> I have feeling that this is not a correct result. Could Eddie or Mark >> perhaps comment on it? >> >> [I vaguely remember that we had this conversation about these tags >> with Mark >> years(!) ago - but I do not recall what was the conclusion. I only, and >> again vaguely, remember to have this issue in my to-do list - which >> would >> indicate that something could be done in the jMoby library.] >> >> Cheers, >> Martin >> >> > > -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== From jmfernandez at cnio.es Mon Aug 4 10:53:58 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Mon, 04 Aug 2008 12:53:58 +0200 Subject: [MOBY-dev] data by reference - a request for comments In-Reply-To: <4d93f07c0808031954v5e266c63kee2a1e1beac1bad1@mail.gmail.com> References: <488B0123.3040608@bsc.es> <4d93f07c0807260452g3048765ev6f84be49dc8cf26d@mail.gmail.com> <4d93f07c0807271829v10ff50d5y2c6f83b279256fdb@mail.gmail.com> <4d93f07c0808031954v5e266c63kee2a1e1beac1bad1@mail.gmail.com> Message-ID: <4896DFC6.9040204@cnio.es> Hi everybody, here you are my "vacation" thoughts/comments about the different points, just inline: Martin Senger wrote: > Hi all, > > Thank you for all comments and suggestions. Here is a summary. Before > we consider it as an RFC we still need to answer few questions. > > [So this not yet a call to vote, but it is close to it, I hope. I > would rather prefer Mark to make the call when the time is appropriate > and the RFC clear.] > > ------- > a) There is one change in the service registration (and, consequently, > in the findService() response): A new property "allowingRefs" that > contains a list of one or more protocols names (e.g. http or ftp). A > service having this property non-empty is able both accepting > references from clients and producing references in its responses. > > Commentary: I would leave it to the Mark/Eddie to specify how exactly > this new property appears in the registration and in the findService. > I would split the proposed property in the two roles it plays: one for the acceptable reference types, and one for the possibly generated reference types. Many services will be able to accept reference types of http, ftp or other kinds, but I think they usually are only able to generate answers with fewer or different ones. > ------- > b) A client asks for getting back references by including "acceptRefs" > attribute in mobyData tag. The attribute lists one or more protocol > names that the client can accept. For example: acceptRefs="http,ftp". > A client can also send its input data by reference - but only to the > services that has a non-empty property "allowingRefs". > As all mobyData blocks are sent to the same service, I'd rather attach "acceptRefs" to mobyContent instead of mobyData, but it is only to avoid redundancy. > ------- > c) A service can obey a request for references. > > Question: A service can obey or should obey? > These are some scenarios: 1) A client cannot understand references, so the service's answers do not contain references. 2) A service cannot generate references, so the service's answers do not contain references. 3) A client tells what kind of references it understands, but it is not the same subset as the service is able to generate, so the service's answer do not contain references. 4) There is a common subset of reference types understood by both the client and the service, so the service's answer does contain references (if it is needed). Surely there are more interesting scenarios out there. > ------- > d) The format of references: The references are expressed as an > XInclude element, with the namespace > http://www.w3.org/2001/XInclude. For example: > > > > > > > > > > Notice that in this example, there is a "text" - meaning that the > references data are non-XML, non-escaped raw data. Such as (notice the > non-escaped "greater-than" sign): > >> sp|Q25158|OPSC2_HEMSA Compound eye opsin BCRH2 OS=Hemigrapsus sanguineus > PE=2 SV=1 > MTNATGPQMAYYGAASMDFGYPEGVSIVDFVRPEIKPYVHQHWYNYPPVNPMWHYLLGVI > YLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTNVPFFTYNCFSGGV > WMFSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNGPKLTTGKAVVFALISWV > IAIGCALPPFFGWGNYILEGILDSCSYDYLTQDFNTFSYNIFIFVFDYFLPAAIIVFSYV > FIVKAIFAHEAAMRAQAKKMNVSTLRSNEADAQRAEIRIAKTALVNVSLWFICWTPYALI > SLKGVMGDTSGITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCVHETET > KSNDDSQSNSTVAQDKA > > Commentary, questions: > > i) I am not sure if we should use XInclude (as > above) or rather XLink. Their differences are blurned for me. > XLink (2001) was superseded by XInclude (second revision in 2006). Next links points to the relationship between XInclude and XLink http://www.w3.org/TR/xinclude/#rel-xlink > ii) If using XInclude, are we going to allow also the attribute > "xpointer"? I hope not... > I would love that feature because it would allow referencing fragments of any XML content. The only problem is that there is (almost) no memory efficient implementation for XPath (used in "xpointer" feature) applied to disk stored XML content. Perhaps Saxon in Java side, but I don't know... > ------- > e) Location of references: The references may be placed inside any XML > tag within a BioMoby message. > > Commentary: God bless those who are going to implement it... > It would be very easy using "xpointer" feature from XInclude, and in that case the sentence would be again right: "God bless those who are going to implement it..." > ------- > f) Protocol and format of the referenced data: The protocol how to get > data is specified in the "href" attribute of the "xi:include" tag. > > The format of referenced data depends where the "xi:include" tag is > used: > > If it is used on any other tag than the primitive type, it has > to be an XML complying with the BioMoby message specification, and the > "xi:include" tag should have the parse="xml" attribute (or none at > all). The same for primitive types when parse="xml" is used. > > For primitive types with parse="text", the referenced data may be > encoded differently as they would in a regular BioMoby message. The > new encoding can be specified in the "encoding" attribute of the > "xi:include" tag, or - if the HTTP protocol is used - in the HTTP > header "Content-type". > > Cheers, > Martin > Nice holidays, Jos? Mar?a -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. 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From py at pingoured.fr Mon Aug 4 11:05:47 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Mon, 04 Aug 2008 13:05:47 +0200 Subject: [MOBY-dev] php client for biomoby services In-Reply-To: <488f3612.20d7720a.6190.1e4a@mx.google.com> References: <488EDE46.5070804@pingoured.fr> <488f3612.20d7720a.6190.1e4a@mx.google.com> Message-ID: <4896E28B.5060206@pingoured.fr> Edward Kawas wrote: > Just in case, you didn't get it working (I am sure that you did, but just in > case ...), I attached 2 php files that you can test with. > > The test client is in the file 'moby_php_test_service.php' and the > moby_soap_factory.php needs to be either in the same directory as the test > service or on your PHP include path. > > Thanks to Julian Tonti-Filippini for creating the PHP basis for the attached > examples! Thanks to him indeed, and thanks to you :) It is working here now. Thanks again, Regards, Pierre From martin.senger at gmail.com Tue Aug 5 02:21:57 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 5 Aug 2008 10:21:57 +0800 Subject: [MOBY-dev] data by reference - a request for comments In-Reply-To: <4896DFC6.9040204@cnio.es> References: <488B0123.3040608@bsc.es> <4d93f07c0807260452g3048765ev6f84be49dc8cf26d@mail.gmail.com> <4d93f07c0807271829v10ff50d5y2c6f83b279256fdb@mail.gmail.com> <4d93f07c0808031954v5e266c63kee2a1e1beac1bad1@mail.gmail.com> <4896DFC6.9040204@cnio.es> Message-ID: <4d93f07c0808041921q78a160e3qe6a4bed8ce9e29b1@mail.gmail.com> > I would split the proposed property in the two roles it plays: one for the > acceptable reference types, and one for the possibly generated reference > types. Many services will be able to accept reference types of http, ftp or > other kinds, but I think they usually are only able to generate answers with > fewer or different ones. I do not think that the situations will be drastically different for accepting and producing references - but I do not have any issue with it. I do not mind much how many new properties will be added to the central registry. As all mobyData blocks are sent to the same service, I'd rather attach > "acceptRefs" to mobyContent instead of mobyData, but it is only to avoid > redundancy. Again, no problem with me. These are some scenarios: My question was: if a service claims that it can produce a reference, and a client asks for it, should the service always produce a reference? I think that my question was obsolete already in the time of asking it. I am withdrawing my question, assuming the obvious answer for the above is "yes, it should". XLink (2001) was superseded by XInclude (second revision in 2006). Next > links points to the relationship between XInclude and XLink > > http://www.w3.org/TR/xinclude/#rel-xlink > Yes, I saw and read this link - but, as often with me when I read the w3 documents , I could not understand what is different, at all. I am glad, however, that XInclude is considered as a supersedor (I guess this word probably does not exist in Egnlish) of XLink. So we go with XInclude. I would love that feature because it would allow referencing fragments of > any XML content. The only problem is that there is (almost) no memory > efficient implementation for XPath (used in "xpointer" feature) applied to > disk stored XML content. This is exactly why I suggested not to allow it. I would prefer to stick to my guns on this issue. Many thanks for replying from the holidays. What about the others? Can we go ahead? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From dmitry.repchevski at bsc.es Tue Aug 5 08:54:29 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 05 Aug 2008 10:54:29 +0200 Subject: [MOBY-dev] data by reference - a request for comments In-Reply-To: <4d93f07c0808041921q78a160e3qe6a4bed8ce9e29b1@mail.gmail.com> References: <4d93f07c0808041921q78a160e3qe6a4bed8ce9e29b1@mail.gmail.com> Message-ID: <48981545.1010105@bsc.es> Hello Martin, > Yes, I saw and read this link - but, as often with me when I read the w3 > documents , I could not understand what is different, at all. I am glad, > however, that XInclude is considered as a supersedor (I guess this word > probably does not exist in Egnlish) of XLink. So we go with XInclude. > There is a big difference between two. XLink is a formalization of links inside XML. It doesn't specify the way of processing. For an XML parser it's nothing but a set of attributes with xlink namespace. Here is excerpt from XInclude specs: > XLink does not specify a specific processing model, but simply > facilitates the detection of links and recognition of associated > metadata by a higher level application. On the other hand, > XInclude specifies a media-type specific (XML into XML) > transformation. It defines a specific processing model for merging > information sets. XInclude processing occurs at a low level, often by > a generic XInclude processor which makes the resulting information set > available to higher level applications. Once you include XInclude into your XML it's up to a XML parser (in case it supports XInclude) to merge two XML (!) documents. XInclude can treat the embedded document as an "xml" or as a "text" (in this way it will be escaped). I wouldn't say that XInclude is "superior" to XLink - it's just for another purpose. You can not to reference things with XInclude, but only inject another resource (xml or text). You can put a reference using XLink, but in this way all the processing must be done by hand. Best regards, Dmitry From martin.senger at gmail.com Tue Aug 5 09:03:10 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 5 Aug 2008 17:03:10 +0800 Subject: [MOBY-dev] data by reference - a request for comments In-Reply-To: <48981545.1010105@bsc.es> References: <4d93f07c0808041921q78a160e3qe6a4bed8ce9e29b1@mail.gmail.com> <48981545.1010105@bsc.es> Message-ID: <4d93f07c0808050203l823c531v937537110e7990ef@mail.gmail.com> > Once you include XInclude into your XML it's up to a XML parser (in case it > supports XInclude) to merge two XML (!) documents. Yes, I understand it. And I hope (from reading some pages) that a parser could be said *not* to do the merging. Because that would prevent the main reason why we are going to have references , after all - which is the memory management. We should try if the current and obvious parsers can be instructed *not* to include XInclude automatically, but let us to do it... Anybody has tried it? Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Tue Aug 5 12:46:41 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 5 Aug 2008 05:46:41 -0700 Subject: [MOBY-dev] findService and the hierarchy In-Reply-To: <4896A28E.1070204@mpiz-koeln.mpg.de> References: <487C9061.3030203@mpiz-koeln.mpg.de> <4d93f07c0807222009x7c108d25j52930dae4f9ddaf1@mail.gmail.com> <48899C0B.70408@mpiz-koeln.mpg.de> <4896A28E.1070204@mpiz-koeln.mpg.de> Message-ID: <48984bd1.14b48c0a.3dff.ffffe18e@mx.google.com> Hi Andreas, I believe that the results are correct. There are no services in the default registry that consume Annotated_GO_Term. 1 service that consumes its parent (GO_Term) and 689 services that strictly consume Object. When you set the flag, includeParentDatatype, the behaviour is like doing a findservice for services that consume Annotated_GO_Term or any parent type up to and including Object with includeParentDatatype=false. Does this make sense? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth Sent: August-03-08 11:33 PM To: Core developer announcements Subject: Re: [MOBY-dev] findService and the hierarchy Martin Senger wrote: > I posted my results - now it is up to Eddie or Mark to draw > conclusion from that results... could any of you two state something about that ? Thanks Andreas Andreas Groscurth wrote: > i like to bring this up for discussion again ;-) > > thanks > > Martin Senger wrote: >>> In my opinion when searching for services consuming >>> Annotated_GO_Term via >>> the findService method i should also include the service which >>> consumes a >>> GO_Term datatype, as this is the parent datatype (per default >>> 'includeParentDatatype' is true).... >>> >>> >> >> I assume that by "I should also include" you actually meant "the >> registry >> response should also include". Is my understanding correct? >> >> If so, I am afraid that it is not the issue of the jMoby library but the >> registry itself. Eddie or Mark can confirm or reject this hypothesis. >> >> The BioMoby API allows to specify two XML tags when calling findService >> method: the >> >> X >> and >> X >> >> Where X can be either 1 or 0. >> >> The jMoby's findService() method sets these two tags according to the >> two >> boolean parameters that the method can get: >> >> boolean includeChildrenServiceTypes >> and >> boolean includeParentDataTypes >> >> I have tried to call the findService, with the Annotated_GO_Term input, >> using all combinations of these two tags (you can do it using the Moby >> command-line client with the optioins -nc and/or -np). The results are >> either no service or 713 services: >> >> expandObjects expandServices # of found services >> 1 1 713 >> 0 0 0 >> 1 0 713 >> 0 0 0 >> >> I have feeling that this is not a correct result. Could Eddie or Mark >> perhaps comment on it? >> >> [I vaguely remember that we had this conversation about these tags >> with Mark >> years(!) ago - but I do not recall what was the conclusion. I only, and >> again vaguely, remember to have this issue in my to-do list - which >> would >> indicate that something could be done in the jMoby library.] >> >> Cheers, >> Martin >> >> > > -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Tue Aug 5 13:06:56 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 05 Aug 2008 15:06:56 +0200 Subject: [MOBY-dev] findService and the hierarchy In-Reply-To: <48984bd1.14b48c0a.3dff.ffffe18e@mx.google.com> References: <487C9061.3030203@mpiz-koeln.mpg.de> <4d93f07c0807222009x7c108d25j52930dae4f9ddaf1@mail.gmail.com> <48899C0B.70408@mpiz-koeln.mpg.de> <4896A28E.1070204@mpiz-koeln.mpg.de> <48984bd1.14b48c0a.3dff.ffffe18e@mx.google.com> Message-ID: <48985070.6020804@mpiz-koeln.mpg.de> Hi, oh my god... i mixed inputs and outputs... yes there is no service which consumes Annotated_GO_Term... there are only services which returns it. So the find service call only checks for the inputs then ? Or is it possible to find a service which consumes an object with a specific namespace and returns an Annotated_GO_Term object or its parent? currently i ask for each output definition by its own. Sorry again for the confusion .... Andreas Edward Kawas wrote: > Hi Andreas, > > I believe that the results are correct. > > There are no services in the default registry that consume > Annotated_GO_Term. 1 service that consumes its parent (GO_Term) and 689 > services that strictly consume Object. > > When you set the flag, includeParentDatatype, the behaviour is like doing a > findservice for services that consume Annotated_GO_Term or any parent type > up to and including Object with includeParentDatatype=false. > > Does this make sense? > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth > Sent: August-03-08 11:33 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] findService and the hierarchy > > Martin Senger wrote: > > >> I posted my results - now it is up to Eddie or Mark to draw >> conclusion from that results... >> > > > could any of you two state something about that ? > > Thanks > Andreas > > Andreas Groscurth wrote: > >> i like to bring this up for discussion again ;-) >> >> thanks >> >> Martin Senger wrote: >> >>>> In my opinion when searching for services consuming >>>> Annotated_GO_Term via >>>> the findService method i should also include the service which >>>> consumes a >>>> GO_Term datatype, as this is the parent datatype (per default >>>> 'includeParentDatatype' is true).... >>>> >>>> >>>> >>> I assume that by "I should also include" you actually meant "the >>> registry >>> response should also include". Is my understanding correct? >>> >>> If so, I am afraid that it is not the issue of the jMoby library but the >>> registry itself. Eddie or Mark can confirm or reject this hypothesis. >>> >>> The BioMoby API allows to specify two XML tags when calling findService >>> method: the >>> >>> X >>> and >>> X >>> >>> Where X can be either 1 or 0. >>> >>> The jMoby's findService() method sets these two tags according to the >>> two >>> boolean parameters that the method can get: >>> >>> boolean includeChildrenServiceTypes >>> and >>> boolean includeParentDataTypes >>> >>> I have tried to call the findService, with the Annotated_GO_Term input, >>> using all combinations of these two tags (you can do it using the Moby >>> command-line client with the optioins -nc and/or -np). The results are >>> either no service or 713 services: >>> >>> expandObjects expandServices # of found services >>> 1 1 713 >>> 0 0 0 >>> 1 0 713 >>> 0 0 0 >>> >>> I have feeling that this is not a correct result. Could Eddie or Mark >>> perhaps comment on it? >>> >>> [I vaguely remember that we had this conversation about these tags >>> with Mark >>> years(!) ago - but I do not recall what was the conclusion. I only, and >>> again vaguely, remember to have this issue in my to-do list - which >>> would >>> indicate that something could be done in the jMoby library.] >>> >>> Cheers, >>> Martin >>> >>> >>> >> > > > -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== From edward.kawas at gmail.com Tue Aug 5 13:09:38 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 5 Aug 2008 06:09:38 -0700 Subject: [MOBY-dev] findService and the hierarchy In-Reply-To: <48985070.6020804@mpiz-koeln.mpg.de> References: <487C9061.3030203@mpiz-koeln.mpg.de> <4d93f07c0807222009x7c108d25j52930dae4f9ddaf1@mail.gmail.com> <48899C0B.70408@mpiz-koeln.mpg.de> <4896A28E.1070204@mpiz-koeln.mpg.de> <48984bd1.14b48c0a.3dff.ffffe18e@mx.google.com> <48985070.6020804@mpiz-koeln.mpg.de> Message-ID: <48985132.2a528c0a.468b.608f@mx.google.com> Currently, the flag only works on inputs. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth Sent: August-05-08 6:07 AM To: Core developer announcements Subject: Re: [MOBY-dev] findService and the hierarchy Hi, oh my god... i mixed inputs and outputs... yes there is no service which consumes Annotated_GO_Term... there are only services which returns it. So the find service call only checks for the inputs then ? Or is it possible to find a service which consumes an object with a specific namespace and returns an Annotated_GO_Term object or its parent? currently i ask for each output definition by its own. Sorry again for the confusion .... Andreas Edward Kawas wrote: > Hi Andreas, > > I believe that the results are correct. > > There are no services in the default registry that consume > Annotated_GO_Term. 1 service that consumes its parent (GO_Term) and 689 > services that strictly consume Object. > > When you set the flag, includeParentDatatype, the behaviour is like doing a > findservice for services that consume Annotated_GO_Term or any parent type > up to and including Object with includeParentDatatype=false. > > Does this make sense? > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth > Sent: August-03-08 11:33 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] findService and the hierarchy > > Martin Senger wrote: > > >> I posted my results - now it is up to Eddie or Mark to draw >> conclusion from that results... >> > > > could any of you two state something about that ? > > Thanks > Andreas > > Andreas Groscurth wrote: > >> i like to bring this up for discussion again ;-) >> >> thanks >> >> Martin Senger wrote: >> >>>> In my opinion when searching for services consuming >>>> Annotated_GO_Term via >>>> the findService method i should also include the service which >>>> consumes a >>>> GO_Term datatype, as this is the parent datatype (per default >>>> 'includeParentDatatype' is true).... >>>> >>>> >>>> >>> I assume that by "I should also include" you actually meant "the >>> registry >>> response should also include". Is my understanding correct? >>> >>> If so, I am afraid that it is not the issue of the jMoby library but the >>> registry itself. Eddie or Mark can confirm or reject this hypothesis. >>> >>> The BioMoby API allows to specify two XML tags when calling findService >>> method: the >>> >>> X >>> and >>> X >>> >>> Where X can be either 1 or 0. >>> >>> The jMoby's findService() method sets these two tags according to the >>> two >>> boolean parameters that the method can get: >>> >>> boolean includeChildrenServiceTypes >>> and >>> boolean includeParentDataTypes >>> >>> I have tried to call the findService, with the Annotated_GO_Term input, >>> using all combinations of these two tags (you can do it using the Moby >>> command-line client with the optioins -nc and/or -np). The results are >>> either no service or 713 services: >>> >>> expandObjects expandServices # of found services >>> 1 1 713 >>> 0 0 0 >>> 1 0 713 >>> 0 0 0 >>> >>> I have feeling that this is not a correct result. Could Eddie or Mark >>> perhaps comment on it? >>> >>> [I vaguely remember that we had this conversation about these tags >>> with Mark >>> years(!) ago - but I do not recall what was the conclusion. I only, and >>> again vaguely, remember to have this issue in my to-do list - which >>> would >>> indicate that something could be done in the jMoby library.] >>> >>> Cheers, >>> Martin >>> >>> >>> >> > > > -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Thu Aug 7 15:12:09 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 7 Aug 2008 08:12:09 -0700 Subject: [MOBY-dev] perl async services Message-ID: <489b10ce.1f538c0a.7a83.7c57@mx.google.com> Hi, I have a quick question to whomever has developed async services in perl using the MOBY::Async/WSRF modules. Is it true that there is a strict one dispatcher file to one service? For instance, the documentation for the module MOBY::Async has the following dispatcher.cgi example: dispatcher.cgi #!/usr/bin/perl BEGIN { @INC = ("/path/to/my/libs", @INC); } use strict; use SOAP::Transport::HTTP; use MOBY::Async::WSRF; use HelloWorld; my $server = new SOAP::Transport::HTTP::CGI; $server->serializer(WSRF::Serializer->new); $server->deserializer(WSRF::Deserializer->new); $server->on_action(sub{}); $server->dispatch_with({ $WSRF::Constants::MOBY.'#sayHello' => 'HelloWorld', $WSRF::Constants::MOBY.'#sayHello_submit' => 'HelloWorld', -> $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' => 'HelloWorld', -> $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourceP ropertiesRequest' => 'HelloWorld', -> $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' => 'HelloWorld', }); $server->handle(); Notice the lines prefixed with '->' hard code GetResourceProperty, etc map to a specific service. Is there any way around this? Thanks, Eddie From jmfernandez at cnio.es Thu Aug 7 16:48:31 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Thu, 07 Aug 2008 18:48:31 +0200 Subject: [MOBY-dev] perl async services In-Reply-To: <489b10ce.1f538c0a.7a83.7c57@mx.google.com> References: <489b10ce.1f538c0a.7a83.7c57@mx.google.com> Message-ID: <489B275F.50009@cnio.es> Hi Eddie, although the example shows only one service, you are not restricted to only one. About GetResourceProperty, GetMultipleResourceProperties and ImmediateResourceTermination, they are document/literal SOAP services based on WSRF specifications. If your service code is inheriting from MOBY::Async::SimpleServer, then you do not have to implement them, because MOBY::Async::SimpleServer takes care of them. The way MOBY::Async libraries work are the next: * They have been built on top of WSRF::Lite libraries, so they reuse as much routines as possible. That's the reason why Perl modules containing asynchronous services implementations must inherit from MOBY::Async::SimpleServer (typical 'use base qw(MOBY::Async::SimpleServer);' sentence). * Asynchronous services creators/coders only have to write the corresponding job routines as they were creating a synchronous MOBY service. All the job ticket generation, job management, job result status & storage, etc... work is handled either by WSRF::Lite or MOBY::Async::SimpleServer, and in most of cases only depends on job Id. As job routines are passed on job creation, they must be either functions passed by reference to the job creation statement or being anonymous functions assigned to a variable, used as input parameter for the job creation statement. For those of you interested on, the ticket, state, results, etc... information is stored in /tmp. This point should be more configurable, and we will fix it on September. I have attached an untested example of two asynchronous services using the same dispatcher and module. Best Regards from M?laga, Jos? Mar?a (on behalf Jos? Manuel and myself) Edward Kawas wrote: > Hi, > > I have a quick question to whomever has developed async services in perl > using the MOBY::Async/WSRF modules. Is it true that there is a strict one > dispatcher file to one service? > > For instance, the documentation for the module MOBY::Async has the following > dispatcher.cgi example: > > dispatcher.cgi > > #!/usr/bin/perl > BEGIN { @INC = ("/path/to/my/libs", @INC); } > use strict; > use SOAP::Transport::HTTP; > use MOBY::Async::WSRF; > use HelloWorld; > > my $server = new SOAP::Transport::HTTP::CGI; > $server->serializer(WSRF::Serializer->new); > $server->deserializer(WSRF::Deserializer->new); > $server->on_action(sub{}); > $server->dispatch_with({ > $WSRF::Constants::MOBY.'#sayHello' => 'HelloWorld', > $WSRF::Constants::MOBY.'#sayHello_submit' => 'HelloWorld', > -> > $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' => > 'HelloWorld', > -> > $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourceP > ropertiesRequest' => 'HelloWorld', > -> $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' > => 'HelloWorld', > }); > $server->handle(); > > Notice the lines prefixed with '->' hard code GetResourceProperty, etc map > to a specific service. Is there any way around this? > > Thanks, > > Eddie > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. -------------- next part -------------- A non-text attachment was scrubbed... Name: two-async-MOBY-test.cgi.pl Type: application/x-perl Size: 980 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TwoAsyncService.pm Type: application/x-perl Size: 2276 bytes Desc: not available URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: two-async-MOBY-test.cgi URL: From edward.kawas at gmail.com Thu Aug 7 17:14:12 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 7 Aug 2008 10:14:12 -0700 Subject: [MOBY-dev] perl async services In-Reply-To: <489B275F.50009@cnio.es> References: <489b10ce.1f538c0a.7a83.7c57@mx.google.com> <489B275F.50009@cnio.es> Message-ID: <489b2d6a.02578c0a.485f.ffffc011@mx.google.com> Thanks for the quick response! So your example have both service implementations inside of one file. Is it possible to have more than one service referenced in the dispatcher without have the implementations in the same package? i.e. ('->' shows what I mean): $server->dispatch_with({ -> $WSRF::Constants::MOBY.'#serviceOne' => 'OneAsyncService', -> $WSRF::Constants::MOBY.'#serviceOne_submit' => 'OneAsyncService', $WSRF::Constants::MOBY.'#serviceTwo' => 'TwoAsyncService', $WSRF::Constants::MOBY.'#serviceTwo_submit' => 'TwoAsyncService', $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' => 'TwoAsyncService', $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourceP ropertiesRequest' => 'TwoAsyncService', $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' => 'TwoAsyncService', }); Thanks again, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jos? Mar?a Fern?ndez Gonz?lez Sent: August-07-08 9:49 AM To: Core developer announcements Subject: Re: [MOBY-dev] perl async services Hi Eddie, although the example shows only one service, you are not restricted to only one. About GetResourceProperty, GetMultipleResourceProperties and ImmediateResourceTermination, they are document/literal SOAP services based on WSRF specifications. If your service code is inheriting from MOBY::Async::SimpleServer, then you do not have to implement them, because MOBY::Async::SimpleServer takes care of them. The way MOBY::Async libraries work are the next: * They have been built on top of WSRF::Lite libraries, so they reuse as much routines as possible. That's the reason why Perl modules containing asynchronous services implementations must inherit from MOBY::Async::SimpleServer (typical 'use base qw(MOBY::Async::SimpleServer);' sentence). * Asynchronous services creators/coders only have to write the corresponding job routines as they were creating a synchronous MOBY service. All the job ticket generation, job management, job result status & storage, etc... work is handled either by WSRF::Lite or MOBY::Async::SimpleServer, and in most of cases only depends on job Id. As job routines are passed on job creation, they must be either functions passed by reference to the job creation statement or being anonymous functions assigned to a variable, used as input parameter for the job creation statement. For those of you interested on, the ticket, state, results, etc... information is stored in /tmp. This point should be more configurable, and we will fix it on September. I have attached an untested example of two asynchronous services using the same dispatcher and module. Best Regards from M?laga, Jos? Mar?a (on behalf Jos? Manuel and myself) Edward Kawas wrote: > Hi, > > I have a quick question to whomever has developed async services in > perl using the MOBY::Async/WSRF modules. Is it true that there is a > strict one dispatcher file to one service? > > For instance, the documentation for the module MOBY::Async has the > following dispatcher.cgi example: > > dispatcher.cgi > > #!/usr/bin/perl > BEGIN { @INC = ("/path/to/my/libs", @INC); } > use strict; > use SOAP::Transport::HTTP; > use MOBY::Async::WSRF; > use HelloWorld; > > my $server = new SOAP::Transport::HTTP::CGI; > $server->serializer(WSRF::Serializer->new); > $server->deserializer(WSRF::Deserializer->new); > $server->on_action(sub{}); > $server->dispatch_with({ > $WSRF::Constants::MOBY.'#sayHello' => 'HelloWorld', > $WSRF::Constants::MOBY.'#sayHello_submit' => 'HelloWorld', > -> > $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyReque > st' => 'HelloWorld', > -> > $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleRes > ourceP > ropertiesRequest' => 'HelloWorld', > -> $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' > => 'HelloWorld', > }); > $server->handle(); > > Notice the lines prefixed with '->' hard code GetResourceProperty, etc > map to a specific service. Is there any way around this? > > Thanks, > > Eddie > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From r.ranzinger at dkfz-heidelberg.de Fri Aug 8 09:30:15 2008 From: r.ranzinger at dkfz-heidelberg.de (=?ISO-8859-15?Q?Ren=E9_Ranzinger?=) Date: Fri, 08 Aug 2008 11:30:15 +0200 Subject: [MOBY-dev] Problems with service registration using dashboard Message-ID: <489C1227.6010808@dkfz-heidelberg.de> HI, the last two day's I tried to register some new moby services with the dashboard (I used dashboard for registration several times before). During the registration an error window pops up with this message : ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: org.xml.sax.SAXParseException: Invalid byte 1 of 1-byte UTF-8 sequence. Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException Fault actor: null When calling: http://moby.ucalgary.ca/moby/MOBY-Central.pl =========== The service does not occur in the service list and if I do a update of the service list I get this error : Error creating input stream: java.io.IOException: Server returned HTTP response code: 500 for URL: http://moby.ucalgary.ca/RESOURCES/MOBY-S/ServiceInstances The last error disappear after some time, so that a update is possible, but still the service is not in the list. I tried two instances of Dashboard at two different computers and operation systems. I also tried to register via the stored registration XML : mobygetGlycomeIdByCarbohydrateRetrievalwww.glycome-db.orghttp://www.glycome-db.org/moby/getGlycomeIdByCarbohydrater.ranzinger at dkfz.de0 GlycomicsObject GlycomicsObject Does anyone have an idea whats the problem? Ren? From martin.senger at gmail.com Fri Aug 8 09:37:28 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 8 Aug 2008 17:37:28 +0800 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <489C1227.6010808@dkfz-heidelberg.de> References: <489C1227.6010808@dkfz-heidelberg.de> Message-ID: <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> > Fault string: org.xml.sax.SAXParseException: Invalid byte 1 of 1-byte > UTF-8 sequence. This may be because of the non-ascii characters in your service description. It should not be like that - but if you remove letters with the German accents, it will pass. We (developers) should look at it on which layer the problem occurs - but for you, this is the fastest workaround for now. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Fri Aug 8 10:14:10 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 08 Aug 2008 12:14:10 +0200 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> Message-ID: <489C1C72.5000402@mpiz-koeln.mpg.de> i confirm that this comes from an non-ascii character. I registered a service which has some german accents (ae, oe etc) and i got some errors during registration. ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: java.io.UTFDataFormatException: Invalid byte 2 of 3-byte UTF-8 sequence. Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException Fault actor: null When calling: http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl =========== it seems to register, because registering it does not work (you have to unregister first). But loading the services also fail due to this service. So as martin said, for this time avoid any german specific character. Best Andreas Martin Senger wrote: >> Fault string: org.xml.sax.SAXParseException: Invalid byte 1 of 1-byte >> UTF-8 sequence. >> > > > This may be because of the non-ascii characters in your service description. > It should not be like that - but if you remove letters with the German > accents, it will pass. We (developers) should look at it on which layer the > problem occurs - but for you, this is the fastest workaround for now. > > Martin > > -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== From jmfernandez at cnio.es Fri Aug 8 10:19:35 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Fri, 08 Aug 2008 12:19:35 +0200 Subject: [MOBY-dev] perl async services In-Reply-To: <489b2d6a.02578c0a.485f.ffffc011@mx.google.com> References: <489b10ce.1f538c0a.7a83.7c57@mx.google.com> <489B275F.50009@cnio.es> <489b2d6a.02578c0a.485f.ffffc011@mx.google.com> Message-ID: <489C1DB7.9040803@cnio.es> Now I see what you mean. Yes, it should be possible in the way you have explained because both of them should be inheriting from MOBY::Async::SimpleServer. Perhaps one of the cleaner ways to specify that is: $server->dispatch_with({ $WSRF::Constants::MOBY.'#serviceOne' => 'OneAsyncService', $WSRF::Constants::MOBY.'#serviceOne_submit' => 'OneAsyncService', $WSRF::Constants::MOBY.'#serviceTwo' => 'TwoAsyncService', $WSRF::Constants::MOBY.'#serviceTwo_submit' => 'TwoAsyncService', $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' => 'MOBY::Async::SimpleServer', $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourcePropertiesRequest' => 'MOBY::Async::SimpleServer', $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' => 'MOBY::Async::SimpleServer', }); Best Regards, Jos? Mar?a Edward Kawas wrote: > Thanks for the quick response! So your example have both service > implementations inside of one file. Is it possible to have more than one > service referenced in the dispatcher without have the implementations in the > same package? > > i.e. ('->' shows what I mean): > > $server->dispatch_with({ > -> $WSRF::Constants::MOBY.'#serviceOne' => 'OneAsyncService', > -> $WSRF::Constants::MOBY.'#serviceOne_submit' => 'OneAsyncService', > $WSRF::Constants::MOBY.'#serviceTwo' => 'TwoAsyncService', > $WSRF::Constants::MOBY.'#serviceTwo_submit' => 'TwoAsyncService', > > $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' => > 'TwoAsyncService', > > $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourceP > ropertiesRequest' => 'TwoAsyncService', > > $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' => > 'TwoAsyncService', > }); > > Thanks again, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jos? Mar?a > Fern?ndez Gonz?lez > Sent: August-07-08 9:49 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] perl async services > > Hi Eddie, > although the example shows only one service, you are not restricted > to only one. About GetResourceProperty, GetMultipleResourceProperties and > ImmediateResourceTermination, they are document/literal SOAP services based > on WSRF specifications. If your service code is inheriting from > MOBY::Async::SimpleServer, then you do not have to implement them, because > MOBY::Async::SimpleServer takes care of them. > > The way MOBY::Async libraries work are the next: > > * They have been built on top of WSRF::Lite libraries, so they reuse > as much > routines as possible. That's the reason why Perl modules containing > asynchronous services implementations must inherit from > MOBY::Async::SimpleServer (typical 'use base qw(MOBY::Async::SimpleServer);' > > sentence). > > * Asynchronous services creators/coders only have to write the > corresponding > job routines as they were creating a synchronous MOBY service. All the job > ticket generation, job management, job result status & storage, etc... work > is handled either by WSRF::Lite or MOBY::Async::SimpleServer, and in most of > cases only depends on job Id. As job routines are passed on job creation, > they must be either functions passed by reference to the job creation > statement or being anonymous functions assigned to a variable, used as input > parameter for the job creation statement. > > For those of you interested on, the ticket, state, results, etc... > information is stored in /tmp. This point should be more configurable, and > we will fix it on September. > > I have attached an untested example of two asynchronous services > using the same dispatcher and module. > > Best Regards from M?laga, > Jos? Mar?a (on behalf Jos? Manuel and myself) > > Edward Kawas wrote: >> Hi, >> >> I have a quick question to whomever has developed async services in >> perl using the MOBY::Async/WSRF modules. Is it true that there is a >> strict one dispatcher file to one service? >> >> For instance, the documentation for the module MOBY::Async has the >> following dispatcher.cgi example: >> >> dispatcher.cgi >> >> #!/usr/bin/perl >> BEGIN { @INC = ("/path/to/my/libs", @INC); } >> use strict; >> use SOAP::Transport::HTTP; >> use MOBY::Async::WSRF; >> use HelloWorld; >> >> my $server = new SOAP::Transport::HTTP::CGI; >> $server->serializer(WSRF::Serializer->new); >> $server->deserializer(WSRF::Deserializer->new); >> $server->on_action(sub{}); >> $server->dispatch_with({ >> $WSRF::Constants::MOBY.'#sayHello' => 'HelloWorld', >> $WSRF::Constants::MOBY.'#sayHello_submit' => 'HelloWorld', >> -> >> $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyReque >> st' => 'HelloWorld', >> -> >> $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleRes >> ourceP >> ropertiesRequest' => 'HelloWorld', >> -> $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' >> => 'HelloWorld', >> }); >> $server->handle(); >> >> Notice the lines prefixed with '->' hard code GetResourceProperty, etc >> map to a specific service. Is there any way around this? >> >> Thanks, >> >> Eddie >> >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > -- > "There is no reason why anybody would want a computer in their home" - > Ken Olson, founder of DEC 1977 > "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever > outgrow a 20Mb hard drive." - ??? > > "Premature optimization is the root of all evil." - Donald Knuth > > Jos? Mar?a Fern?ndez Gonz?lez > Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) > e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 > Unidad del Instituto Nacional de Bioinform?tica > Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing > Centro Nacional de Investigaciones Oncol?gicas > C.P.: 28029 Zip Code: 28029 > C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) > > > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los > ficheros adjuntos, pueden contener informaci?n protegida para el uso > exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o > cualquier otro tipo de transmisi?n por parte de otra persona que no sea el > destinatario. Si usted recibe por error este correo, se ruega comunicarlo al > remitente y borrar el mensaje recibido. > **CONFIDENTIALITY NOTICE** This email communication and any attachments may > contain confidential and privileged information for the sole use of the > designated recipient named above. Distribution, reproduction or any other > use of this transmission by any party other than the intended recipient is > prohibited. If you are not the intended recipient please contact the sender > and delete all copies. > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From py at pingoured.fr Fri Aug 8 12:52:51 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Fri, 08 Aug 2008 14:52:51 +0200 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <489C1C72.5000402@mpiz-koeln.mpg.de> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> <489C1C72.5000402@mpiz-koeln.mpg.de> Message-ID: <489C41A3.2010909@pingoured.fr> Andreas Groscurth wrote: > i confirm that this comes from an non-ascii character. > I registered a service which has some german accents (ae, oe etc) and i > got some errors during registration. > > ===ERROR=== > Fault details: > [stackTrace: null] > [hostname: null] > Fault string: java.io.UTFDataFormatException: Invalid byte 2 of 3-byte > UTF-8 sequence. > Fault code: > {http://schemas.xmlsoap.org/soap/envelope/}Server.userException > Fault actor: null > When calling: > http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl > =========== > > it seems to register, because registering it does not work (you have to > unregister first). But loading the services also fail due to this service. > > So as martin said, for this time avoid any german specific character. We are here facing the same problem, we can not register our service (well we do register it) but we can not load the list of services so we can not work with the dashboard on our service... (to bad it is friday afternoon :D !) Is there something we can do exempt waiting ? (We will generate the skeleton by hand, so there no problem for our work ;)) Thanks, Regards, Pierre From martin.senger at gmail.com Fri Aug 8 13:57:09 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 8 Aug 2008 21:57:09 +0800 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <489C41A3.2010909@pingoured.fr> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> <489C1C72.5000402@mpiz-koeln.mpg.de> <489C41A3.2010909@pingoured.fr> Message-ID: <4d93f07c0808080657u192935fat3027094ea576859a@mail.gmail.com> > Is there something we can do exempt waiting ? I am trying to find a work-around, or a fix. So far, let me just tell how I see where is the problem (which is not that much useful for you, I understand...): The registry is sending wrong XML. [Another question is why it has the wrong data, in the first place - but that's less important now.] The wrong data (coming from registry) are for the a service from authority www.glycome-db.org. The data has a German U with umlaut (?) - but it is coded as three characters 0xEF 0xBF 0xBD - which is not UTF-8 code of such character. Actually, it is no UNICODE code at all. This umlaut character should be coded as two characters 0x6C 0xC3. The best would be if Eddie can fix manually the database - because it is otherwise hard to fix it in Java (like in Dashboard) because the encoding is done in very low level, long before our Java code gets control. So I would rather ask Eddie to fix it - and only when he says he cannot, I will try to come with a Java-based fix. [But I am leaving for Europe in about 7 hours, so I may be out of the loop for a while if this is not responded soon.] Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Fri Aug 8 14:10:03 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 8 Aug 2008 07:10:03 -0700 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <4d93f07c0808080657u192935fat3027094ea576859a@mail.gmail.com> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> <489C1C72.5000402@mpiz-koeln.mpg.de> <489C41A3.2010909@pingoured.fr> <4d93f07c0808080657u192935fat3027094ea576859a@mail.gmail.com> Message-ID: <489c53c9.2a528c0a.69e3.ffffdc0c@mx.google.com> I updated the 2 services. Did this fix the problem? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: August-08-08 6:57 AM To: Core developer announcements Subject: Re: [MOBY-dev] Problems with service registration using dashboard > Is there something we can do exempt waiting ? I am trying to find a work-around, or a fix. So far, let me just tell how I see where is the problem (which is not that much useful for you, I understand...): The registry is sending wrong XML. [Another question is why it has the wrong data, in the first place - but that's less important now.] The wrong data (coming from registry) are for the a service from authority www.glycome-db.org. The data has a German U with umlaut (?) - but it is coded as three characters 0xEF 0xBF 0xBD - which is not UTF-8 code of such character. Actually, it is no UNICODE code at all. This umlaut character should be coded as two characters 0x6C 0xC3. The best would be if Eddie can fix manually the database - because it is otherwise hard to fix it in Java (like in Dashboard) because the encoding is done in very low level, long before our Java code gets control. So I would rather ask Eddie to fix it - and only when he says he cannot, I will try to come with a Java-based fix. [But I am leaving for Europe in about 7 hours, so I may be out of the loop for a while if this is not responded soon.] Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From martin.senger at gmail.com Fri Aug 8 14:17:50 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 8 Aug 2008 22:17:50 +0800 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <489c53c9.2a528c0a.69e3.ffffdc0c@mx.google.com> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> <489C1C72.5000402@mpiz-koeln.mpg.de> <489C41A3.2010909@pingoured.fr> <4d93f07c0808080657u192935fat3027094ea576859a@mail.gmail.com> <489c53c9.2a528c0a.69e3.ffffdc0c@mx.google.com> Message-ID: <4d93f07c0808080717r6753e469jc640aa8abbae7403@mail.gmail.com> > I updated the 2 services. Did this fix the problem? > Yes! Thanks. When do you want to start discussion how to fix it in order not to happen again :-) ? Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Fri Aug 8 14:20:15 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 8 Aug 2008 07:20:15 -0700 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <4d93f07c0808080717r6753e469jc640aa8abbae7403@mail.gmail.com> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> <489C1C72.5000402@mpiz-koeln.mpg.de> <489C41A3.2010909@pingoured.fr> <4d93f07c0808080657u192935fat3027094ea576859a@mail.gmail.com> <489c53c9.2a528c0a.69e3.ffffdc0c@mx.google.com> <4d93f07c0808080717r6753e469jc640aa8abbae7403@mail.gmail.com> Message-ID: <489c562c.27b38c0a.19a0.7d10@mx.google.com> Great! We can start it next week. Let's think of some solutions and then post them to the list! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: August-08-08 7:18 AM To: Core developer announcements Subject: Re: [MOBY-dev] Problems with service registration using dashboard > I updated the 2 services. Did this fix the problem? > Yes! Thanks. When do you want to start discussion how to fix it in order not to happen again :-) ? Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From martin.senger at gmail.com Fri Aug 8 14:32:19 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 8 Aug 2008 22:32:19 +0800 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <489c562c.27b38c0a.19a0.7d10@mx.google.com> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> <489C1C72.5000402@mpiz-koeln.mpg.de> <489C41A3.2010909@pingoured.fr> <4d93f07c0808080657u192935fat3027094ea576859a@mail.gmail.com> <489c53c9.2a528c0a.69e3.ffffdc0c@mx.google.com> <4d93f07c0808080717r6753e469jc640aa8abbae7403@mail.gmail.com> <489c562c.27b38c0a.19a0.7d10@mx.google.com> Message-ID: <4d93f07c0808080732m5af1d1c3nd56e684887ef757@mail.gmail.com> > We can start it next week. Okay, but... > Let's think of some solutions ...there is no special solution needed I think. You just must make sure that the XML data coming to the registry are really coded as UTF-8 - and if not (like it was, I assume, with the Rene's service) you have to refuse them to be registered. Or, the data from Rene's was, indeed, correct, but you read and saved them wrongly. Just a remark: When I said that the Rene's data were (probably) wrong, I am not suggesting that Rene made a mistake, it was probably my Java code in CentralImpl that created the XML with a wrong encoding. But I need you to be more careful at the registry side - once you reject such data on arrival, I will be definitely notified and learn about this situation and can fix it. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Mon Aug 11 13:14:18 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 11 Aug 2008 06:14:18 -0700 Subject: [MOBY-dev] perl async services In-Reply-To: <489C1DB7.9040803@cnio.es> References: <489b10ce.1f538c0a.7a83.7c57@mx.google.com> <489B275F.50009@cnio.es> <489b2d6a.02578c0a.485f.ffffc011@mx.google.com> <489C1DB7.9040803@cnio.es> Message-ID: <48a03b3a.27b38c0a.19af.ffffc634@mx.google.com> Excellent! Thanks. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jos? Mar?a Fern?ndez Gonz?lez Sent: August-08-08 3:20 AM To: Core developer announcements Subject: Re: [MOBY-dev] perl async services Now I see what you mean. Yes, it should be possible in the way you have explained because both of them should be inheriting from MOBY::Async::SimpleServer. Perhaps one of the cleaner ways to specify that is: $server->dispatch_with({ $WSRF::Constants::MOBY.'#serviceOne' => 'OneAsyncService', $WSRF::Constants::MOBY.'#serviceOne_submit' => 'OneAsyncService', $WSRF::Constants::MOBY.'#serviceTwo' => 'TwoAsyncService', $WSRF::Constants::MOBY.'#serviceTwo_submit' => 'TwoAsyncService', $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' => 'MOBY::Async::SimpleServer', $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourceP ropertiesRequest' => 'MOBY::Async::SimpleServer', $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' => 'MOBY::Async::SimpleServer', }); Best Regards, Jos? Mar?a Edward Kawas wrote: > Thanks for the quick response! So your example have both service > implementations inside of one file. Is it possible to have more than one > service referenced in the dispatcher without have the implementations in the > same package? > > i.e. ('->' shows what I mean): > > $server->dispatch_with({ > -> $WSRF::Constants::MOBY.'#serviceOne' => 'OneAsyncService', > -> $WSRF::Constants::MOBY.'#serviceOne_submit' => 'OneAsyncService', > $WSRF::Constants::MOBY.'#serviceTwo' => 'TwoAsyncService', > $WSRF::Constants::MOBY.'#serviceTwo_submit' => 'TwoAsyncService', > > $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' => > 'TwoAsyncService', > > $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourceP > ropertiesRequest' => 'TwoAsyncService', > > $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' => > 'TwoAsyncService', > }); > > Thanks again, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jos? Mar?a > Fern?ndez Gonz?lez > Sent: August-07-08 9:49 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] perl async services > > Hi Eddie, > although the example shows only one service, you are not restricted > to only one. About GetResourceProperty, GetMultipleResourceProperties and > ImmediateResourceTermination, they are document/literal SOAP services based > on WSRF specifications. If your service code is inheriting from > MOBY::Async::SimpleServer, then you do not have to implement them, because > MOBY::Async::SimpleServer takes care of them. > > The way MOBY::Async libraries work are the next: > > * They have been built on top of WSRF::Lite libraries, so they reuse > as much > routines as possible. That's the reason why Perl modules containing > asynchronous services implementations must inherit from > MOBY::Async::SimpleServer (typical 'use base qw(MOBY::Async::SimpleServer);' > > sentence). > > * Asynchronous services creators/coders only have to write the > corresponding > job routines as they were creating a synchronous MOBY service. All the job > ticket generation, job management, job result status & storage, etc... work > is handled either by WSRF::Lite or MOBY::Async::SimpleServer, and in most of > cases only depends on job Id. As job routines are passed on job creation, > they must be either functions passed by reference to the job creation > statement or being anonymous functions assigned to a variable, used as input > parameter for the job creation statement. > > For those of you interested on, the ticket, state, results, etc... > information is stored in /tmp. This point should be more configurable, and > we will fix it on September. > > I have attached an untested example of two asynchronous services > using the same dispatcher and module. > > Best Regards from M?laga, > Jos? Mar?a (on behalf Jos? Manuel and myself) > > Edward Kawas wrote: >> Hi, >> >> I have a quick question to whomever has developed async services in >> perl using the MOBY::Async/WSRF modules. Is it true that there is a >> strict one dispatcher file to one service? >> >> For instance, the documentation for the module MOBY::Async has the >> following dispatcher.cgi example: >> >> dispatcher.cgi >> >> #!/usr/bin/perl >> BEGIN { @INC = ("/path/to/my/libs", @INC); } >> use strict; >> use SOAP::Transport::HTTP; >> use MOBY::Async::WSRF; >> use HelloWorld; >> >> my $server = new SOAP::Transport::HTTP::CGI; >> $server->serializer(WSRF::Serializer->new); >> $server->deserializer(WSRF::Deserializer->new); >> $server->on_action(sub{}); >> $server->dispatch_with({ >> $WSRF::Constants::MOBY.'#sayHello' => 'HelloWorld', >> $WSRF::Constants::MOBY.'#sayHello_submit' => 'HelloWorld', >> -> >> $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyReque >> st' => 'HelloWorld', >> -> >> $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleRes >> ourceP >> ropertiesRequest' => 'HelloWorld', >> -> $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' >> => 'HelloWorld', >> }); >> $server->handle(); >> >> Notice the lines prefixed with '->' hard code GetResourceProperty, etc >> map to a specific service. Is there any way around this? >> >> Thanks, >> >> Eddie >> >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > -- > "There is no reason why anybody would want a computer in their home" - > Ken Olson, founder of DEC 1977 > "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever > outgrow a 20Mb hard drive." - ??? > > "Premature optimization is the root of all evil." - Donald Knuth > > Jos? Mar?a Fern?ndez Gonz?lez > Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) > e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 > Unidad del Instituto Nacional de Bioinform?tica > Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing > Centro Nacional de Investigaciones Oncol?gicas > C.P.: 28029 Zip Code: 28029 > C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) > > > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los > ficheros adjuntos, pueden contener informaci?n protegida para el uso > exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o > cualquier otro tipo de transmisi?n por parte de otra persona que no sea el > destinatario. Si usted recibe por error este correo, se ruega comunicarlo al > remitente y borrar el mensaje recibido. > **CONFIDENTIALITY NOTICE** This email communication and any attachments may > contain confidential and privileged information for the sole use of the > designated recipient named above. Distribution, reproduction or any other > use of this transmission by any party other than the intended recipient is > prohibited. If you are not the intended recipient please contact the sender > and delete all copies. > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From serr at ac.uma.es Tue Aug 12 09:04:24 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Tue, 12 Aug 2008 11:04:24 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <4895DE28.7010102@bsc.es> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> <4895DE28.7010102@bsc.es> Message-ID: <48A15218.10104@ac.uma.es> Hello Dmitry and others. Just a small question. What is the advantage of have a reference to a binary data in the atachments? Couldn't we got the same behaviour by adding the reference in the current moby XML structure? Could you explain me please? Best regards Sergio Dmitry Repchevsky wrote: > Hello Martin, > >> What do you mean by "implement streaming"? I concluded that you meant >> "sending binary data from (or to) a moby service". Is is correct? >> > yes it is. >> This is again a SOAP-based specification, meaning another way how to >> make an >> attachment (correct?). >> > XOP is the XML way to reference a binary attachment for XML using a > reference to it. > Even in theory it is not SOAP dependent, the only implementation I > know (I may be wrong) is a MTOM that is for SOAP protocol. > I couldn't find an implementation for straight XML (because we need a > transport for it). > >> If the protocol for dereferencing is HTTP, we can use MIME type >> (content-type HTTP header) for >> references data. >> > This is what XOP is about - the only problem is that it can not > reference an external resource. > > It would be great to have something based on Servlet + XML + XOP on > java, but I looked at JAX-RS (JSR-311) REST and there is nothing... > > I had an idea, but afraid it has a problem with an implementation. > > The idea is to use XML attachment (instead of binary one) and in those > attachment put XInclude with a link to external document. > Such document itself would be an XML with a binary attachment. > > So we would have: > > External resource represented by XML (moby ontology class like > MobyImage) + a binary attachment with an image data itself. > Then we have a main document with a MobyRef primitive that is encoded > as an XML attachment where an attachment itself is an XInclude to the > MobyImage. > This way the document is assembled into a standard moby message > automagically: > > The only problem is that XInclude works with a plain XML, I think... > > Cheers, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From serr at ac.uma.es Tue Aug 12 09:24:18 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Tue, 12 Aug 2008 11:24:18 +0200 Subject: [MOBY-dev] data by reference - a request for comments In-Reply-To: <4d93f07c0808041921q78a160e3qe6a4bed8ce9e29b1@mail.gmail.com> References: <488B0123.3040608@bsc.es> <4d93f07c0807260452g3048765ev6f84be49dc8cf26d@mail.gmail.com> <4d93f07c0807271829v10ff50d5y2c6f83b279256fdb@mail.gmail.com> <4d93f07c0808031954v5e266c63kee2a1e1beac1bad1@mail.gmail.com> <4896DFC6.9040204@cnio.es> <4d93f07c0808041921q78a160e3qe6a4bed8ce9e29b1@mail.gmail.com> Message-ID: <48A156C2.6080509@ac.uma.es> Hello all, Just an small contribution Martin Senger wrote: >> I would split the proposed property in the two roles it plays: one for the >> acceptable reference types, and one for the possibly generated reference >> types. Many services will be able to accept reference types of http, ftp or >> other kinds, but I think they usually are only able to generate answers with >> fewer or different ones. >> > > > I do not think that the situations will be drastically different for > accepting and producing references - but I do not have any issue with it. I > do not mind much how many new properties will be added to the central > registry. > > Maybe it can be a protocol between the service and the client, the second sent the references that is able to handle and if they are agree use one of them for the comunication if not is always possible to return the results without use references. If the client sent a reference (got from other service for example ) that the service can not handle it, an error or info notification can be returned to inform about that. In this case the client can resent the request without using references. In this case I think is not needed to register the references that the service can handle in the central registry, but could be a good idea for searching compatible services with your data. > As all mobyData blocks are sent to the same service, I'd rather attach > Could be possible to use mirrors and separated the mobydata to sent them to different mirror servers? > >> "acceptRefs" to mobyContent instead of mobyData, but it is only to avoid >> redundancy. >> > > > Again, no problem with me. > > These are some scenarios: > > > My question was: if a service claims that it can produce a reference, and a > client asks for it, should the service always produce a reference? I think > that my question was obsolete already in the time of asking it. I am > withdrawing my question, assuming the obvious answer for the above is "yes, > it should". > Maybe we can use some kind of algorithm to see if is will be good to use references; for small data couldn't be useful. Could also be defined for the client, specifying the max size that wants to receive (in total or by object) > XLink (2001) was superseded by XInclude (second revision in 2006). Next > >> links points to the relationship between XInclude and XLink >> >> http://www.w3.org/TR/xinclude/#rel-xlink >> >> > > Yes, I saw and read this link - but, as often with me when I read the w3 > documents , I could not understand what is different, at all. I am glad, > however, that XInclude is considered as a supersedor (I guess this word > probably does not exist in Egnlish) of XLink. So we go with XInclude. > > I would love that feature because it would allow referencing fragments of > >> any XML content. The only problem is that there is (almost) no memory >> efficient implementation for XPath (used in "xpointer" feature) applied to >> disk stored XML content. >> > > > This is exactly why I suggested not to allow it. I would prefer to stick to > my guns on this issue. > > Many thanks for replying from the holidays. What about the others? Can we go > ahead? > > Cheers, > Martin > > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From dmitry.repchevski at bsc.es Tue Aug 12 09:25:30 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 12 Aug 2008 11:25:30 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A15218.10104@ac.uma.es> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> <4895DE28.7010102@bsc.es> <48A15218.10104@ac.uma.es> Message-ID: <48A1570A.9080304@bsc.es> Hello, Sergio, > What is the advantage of have a reference to a binary data in the > atachments? Couldn't we got the same behaviour by adding the reference > in the current moby XML structure? Yes we could... The difference is that in the case of attachment, logically your data are in the same XML document. In case of using some external reference they couldn't be parsed using standard XML library and have to be parsed by "moby" framework. The same amount of work is needed by the service developer. If I use a standard way - I just construct my message and send it. The resource itself is a part of XML infoset. Then I put some structure into an XML that have some external meaning, I have to publish my resource somehow (for example through the servlet). The latter means that we are moving farther away from web services and SOAP. The main idea of web services is that we don't need any additional framework for the interoperability... At this moment this is not the case and maybe should never be an objective, but IMHO I'd like at least to move in this direction... Best regards, Dmitry Sergio Ramirez Ramirez wrote: > Hello Dmitry and others. > > Just a small question. > > What is the advantage of have a reference to a binary data in the > atachments? Couldn't we got the same behaviour by adding the reference > in the current moby XML structure? > > Could you explain me please? > > Best regards > Sergio > > Dmitry Repchevsky wrote: >> Hello Martin, >> >>> What do you mean by "implement streaming"? I concluded that you meant >>> "sending binary data from (or to) a moby service". Is is correct? >>> >> yes it is. >>> This is again a SOAP-based specification, meaning another way how to >>> make an >>> attachment (correct?). >>> >> XOP is the XML way to reference a binary attachment for XML using a >> reference to it. >> Even in theory it is not SOAP dependent, the only implementation I >> know (I may be wrong) is a MTOM that is for SOAP protocol. >> I couldn't find an implementation for straight XML (because we need a >> transport for it). >> >>> If the protocol for dereferencing is HTTP, we can use MIME type >>> (content-type HTTP header) for >>> references data. >>> >> This is what XOP is about - the only problem is that it can not >> reference an external resource. >> >> It would be great to have something based on Servlet + XML + XOP on >> java, but I looked at JAX-RS (JSR-311) REST and there is nothing... >> >> I had an idea, but afraid it has a problem with an implementation. >> >> The idea is to use XML attachment (instead of binary one) and in >> those attachment put XInclude with a link to external document. >> Such document itself would be an XML with a binary attachment. >> >> So we would have: >> >> External resource represented by XML (moby ontology class like >> MobyImage) + a binary attachment with an image data itself. >> Then we have a main document with a MobyRef primitive that is encoded >> as an XML attachment where an attachment itself is an XInclude to the >> MobyImage. >> This way the document is assembled into a standard moby message >> automagically: >> >> The only problem is that XInclude works with a plain XML, I think... >> >> Cheers, >> >> Dmitry >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > From martin.senger at gmail.com Tue Aug 12 09:36:34 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 12 Aug 2008 10:36:34 +0100 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A1570A.9080304@bsc.es> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> <4895DE28.7010102@bsc.es> <48A15218.10104@ac.uma.es> <48A1570A.9080304@bsc.es> Message-ID: <4d93f07c0808120236o34ab776eq7f2116f1ead20ec5@mail.gmail.com> My opinions: In case of using some external reference they couldn't be parsed using > standard XML library and have to be parsed by "moby" framework. That's exactly what I (we?) want - to have control over how to treat the referenced data. Additionally, we want to be able to use existing external references, at least in cases when the service provider wishes so (which may not be case always; e.g. for NCBI records, it would be harmful to let clients to resolve the NCBI's references too fast - as Pieter and Mark have already pointed out). > The latter means that we are moving farther away from web services and > SOAP. > That is what I hope for :-) Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From serr at ac.uma.es Tue Aug 12 09:49:17 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Tue, 12 Aug 2008 11:49:17 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <4d93f07c0808120236o34ab776eq7f2116f1ead20ec5@mail.gmail.com> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> <4895DE28.7010102@bsc.es> <48A15218.10104@ac.uma.es> <48A1570A.9080304@bsc.es> <4d93f07c0808120236o34ab776eq7f2116f1ead20ec5@mail.gmail.com> Message-ID: <48A15C9D.9030703@ac.uma.es> Hello Martin, Until I know the libraries are able to handle XInclude in both ways, if I want they understand the XInclude information and complete the xml with the contents of the reference; but this option can be desactivated and the reference handled by hand. Martin Senger wrote: > My opinions: > > In case of using some external reference they couldn't be parsed > using standard XML library and have to be parsed by "moby" framework. > > > That's exactly what I (we?) want - to have control over how to treat > the referenced data. Additionally, we want to be able to use existing > external references, at least in cases when the service provider > wishes so (which may not be case always; e.g. for NCBI records, it > would be harmful to let clients to resolve the NCBI's references too > fast - as Pieter and Mark have already pointed out). > > > > The latter means that we are moving farther away from web services > and SOAP. > > > That is what I hope for :-) > > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > ,m.senger at cgiar.org > > skype: martinsenger -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From martin.senger at gmail.com Tue Aug 12 09:53:46 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 12 Aug 2008 10:53:46 +0100 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A15C9D.9030703@ac.uma.es> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> <4895DE28.7010102@bsc.es> <48A15218.10104@ac.uma.es> <48A1570A.9080304@bsc.es> <4d93f07c0808120236o34ab776eq7f2116f1ead20ec5@mail.gmail.com> <48A15C9D.9030703@ac.uma.es> Message-ID: <4d93f07c0808120253n56fb287k34d49ae6c8171e1c@mail.gmail.com> > Until I know the libraries are able to handle XInclude in both ways, if I > want they understand the XInclude information and complete the xml with the > contents of the reference; but this option can be desactivated and the > reference handled by hand. > Sorry, I am not sure that I understood what you just said. Could you perhaps re-phrase it for me. Sorry... and thanks. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From serr at ac.uma.es Tue Aug 12 09:53:48 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Tue, 12 Aug 2008 11:53:48 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A1570A.9080304@bsc.es> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> <4895DE28.7010102@bsc.es> <48A15218.10104@ac.uma.es> <48A1570A.9080304@bsc.es> Message-ID: <48A15DAC.6000307@ac.uma.es> but the atachment is a reference that you have to handle in the same way as if it were in the XML schema, you only change the location. Is this correct? Dmitry Repchevsky wrote: > Hello, Sergio, > >> What is the advantage of have a reference to a binary data in the >> atachments? Couldn't we got the same behaviour by adding the >> reference in the current moby XML structure? > Yes we could... The difference is that in the case of attachment, > logically your data are in the same XML document. > In case of using some external reference they couldn't be parsed using > standard XML library and have to be parsed by "moby" framework. > The same amount of work is needed by the service developer. If I use a > standard way - I just construct my message and send it. The resource > itself is a part of XML infoset. > Then I put some structure into an XML that have some external meaning, > I have to publish my resource somehow (for example through the servlet). > The latter means that we are moving farther away from web services and > SOAP. > > The main idea of web services is that we don't need any additional > framework for the interoperability... > At this moment this is not the case and maybe should never be an > objective, but IMHO I'd like at least to move in this direction... > > Best regards, > Dmitry > > Sergio Ramirez Ramirez wrote: >> Hello Dmitry and others. >> >> Just a small question. >> >> What is the advantage of have a reference to a binary data in the >> atachments? Couldn't we got the same behaviour by adding the >> reference in the current moby XML structure? >> >> Could you explain me please? >> >> Best regards >> Sergio >> >> Dmitry Repchevsky wrote: >>> Hello Martin, >>> >>>> What do you mean by "implement streaming"? I concluded that you meant >>>> "sending binary data from (or to) a moby service". Is is correct? >>>> >>> yes it is. >>>> This is again a SOAP-based specification, meaning another way how >>>> to make an >>>> attachment (correct?). >>>> >>> XOP is the XML way to reference a binary attachment for XML using a >>> reference to it. >>> Even in theory it is not SOAP dependent, the only implementation I >>> know (I may be wrong) is a MTOM that is for SOAP protocol. >>> I couldn't find an implementation for straight XML (because we need >>> a transport for it). >>> >>>> If the protocol for dereferencing is HTTP, we can use MIME type >>>> (content-type HTTP header) for >>>> references data. >>>> >>> This is what XOP is about - the only problem is that it can not >>> reference an external resource. >>> >>> It would be great to have something based on Servlet + XML + XOP on >>> java, but I looked at JAX-RS (JSR-311) REST and there is nothing... >>> >>> I had an idea, but afraid it has a problem with an implementation. >>> >>> The idea is to use XML attachment (instead of binary one) and in >>> those attachment put XInclude with a link to external document. >>> Such document itself would be an XML with a binary attachment. >>> >>> So we would have: >>> >>> External resource represented by XML (moby ontology class like >>> MobyImage) + a binary attachment with an image data itself. >>> Then we have a main document with a MobyRef primitive that is >>> encoded as an XML attachment where an attachment itself is an >>> XInclude to the MobyImage. >>> This way the document is assembled into a standard moby message >>> automagically: >>> >>> The only problem is that XInclude works with a plain XML, I think... >>> >>> Cheers, >>> >>> Dmitry >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From dmitry.repchevski at bsc.es Tue Aug 12 10:02:39 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 12 Aug 2008 12:02:39 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A15DAC.6000307@ac.uma.es> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> <4895DE28.7010102@bsc.es> <48A15218.10104@ac.uma.es> <48A1570A.9080304@bsc.es> <48A15DAC.6000307@ac.uma.es> Message-ID: <48A15FBF.4000009@bsc.es> Hello Sergio, > but the atachment is a reference that you have to handle in the same > way as if it were in the XML schema, you only change the location. Is > this correct? XOP/MTOM doesn't affect the XML Schema. It uses XOP:Include to reference the binary data. Unfortunately, XOP specification doesn't reuse XInclude so the only reference you can have is to the mime attachment into the same multimime message... Dmitry Sergio Ramirez Ramirez wrote: > but the atachment is a reference that you have to handle in the same > way as if it were in the XML schema, you only change the location. Is > this correct? > > Dmitry Repchevsky wrote: >> Hello, Sergio, >> >>> What is the advantage of have a reference to a binary data in the >>> atachments? Couldn't we got the same behaviour by adding the >>> reference in the current moby XML structure? >> Yes we could... The difference is that in the case of attachment, >> logically your data are in the same XML document. >> In case of using some external reference they couldn't be parsed >> using standard XML library and have to be parsed by "moby" framework. >> The same amount of work is needed by the service developer. If I use >> a standard way - I just construct my message and send it. The >> resource itself is a part of XML infoset. >> Then I put some structure into an XML that have some external >> meaning, I have to publish my resource somehow (for example through >> the servlet). >> The latter means that we are moving farther away from web services >> and SOAP. >> >> The main idea of web services is that we don't need any additional >> framework for the interoperability... >> At this moment this is not the case and maybe should never be an >> objective, but IMHO I'd like at least to move in this direction... >> >> Best regards, >> Dmitry >> >> Sergio Ramirez Ramirez wrote: >>> Hello Dmitry and others. >>> >>> Just a small question. >>> >>> What is the advantage of have a reference to a binary data in the >>> atachments? Couldn't we got the same behaviour by adding the >>> reference in the current moby XML structure? >>> >>> Could you explain me please? >>> >>> Best regards >>> Sergio >>> >>> Dmitry Repchevsky wrote: >>>> Hello Martin, >>>> >>>>> What do you mean by "implement streaming"? I concluded that you meant >>>>> "sending binary data from (or to) a moby service". Is is correct? >>>>> >>>> yes it is. >>>>> This is again a SOAP-based specification, meaning another way how >>>>> to make an >>>>> attachment (correct?). >>>>> >>>> XOP is the XML way to reference a binary attachment for XML using a >>>> reference to it. >>>> Even in theory it is not SOAP dependent, the only implementation I >>>> know (I may be wrong) is a MTOM that is for SOAP protocol. >>>> I couldn't find an implementation for straight XML (because we need >>>> a transport for it). >>>> >>>>> If the protocol for dereferencing is HTTP, we can use MIME type >>>>> (content-type HTTP header) for >>>>> references data. >>>>> >>>> This is what XOP is about - the only problem is that it can not >>>> reference an external resource. >>>> >>>> It would be great to have something based on Servlet + XML + XOP on >>>> java, but I looked at JAX-RS (JSR-311) REST and there is nothing... >>>> >>>> I had an idea, but afraid it has a problem with an implementation. >>>> >>>> The idea is to use XML attachment (instead of binary one) and in >>>> those attachment put XInclude with a link to external document. >>>> Such document itself would be an XML with a binary attachment. >>>> >>>> So we would have: >>>> >>>> External resource represented by XML (moby ontology class like >>>> MobyImage) + a binary attachment with an image data itself. >>>> Then we have a main document with a MobyRef primitive that is >>>> encoded as an XML attachment where an attachment itself is an >>>> XInclude to the MobyImage. >>>> This way the document is assembled into a standard moby message >>>> automagically: >>>> >>>> The only problem is that XInclude works with a plain XML, I think... >>>> >>>> Cheers, >>>> >>>> Dmitry >>>> _______________________________________________ >>>> MOBY-dev mailing list >>>> MOBY-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>> >>> >> > From serr at ac.uma.es Tue Aug 12 10:04:29 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Tue, 12 Aug 2008 12:04:29 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <4d93f07c0808120253n56fb287k34d49ae6c8171e1c@mail.gmail.com> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> <4895DE28.7010102@bsc.es> <48A15218.10104@ac.uma.es> <48A1570A.9080304@bsc.es> <4d93f07c0808120236o34ab776eq7f2116f1ead20ec5@mail.gmail.com> <48A15C9D.9030703@ac.uma.es> <4d93f07c0808120253n56fb287k34d49ae6c8171e1c@mail.gmail.com> Message-ID: <48A1602D.9090804@ac.uma.es> Sorry for my bad English :-[ I mean that if you want "to have control over how to treat the referenced data" Xinclude allows this possibility, but at the same time offers the possibility of handle them automatically. Yo have the both behavior, is someones doesn't need to handled them by hand Martin Senger wrote: > > Until I know the libraries are able to handle XInclude in both > ways, if I want they understand the XInclude information and > complete the xml with the contents of the reference; but this > option can be desactivated and the reference handled by hand. > > > Sorry, I am not sure that I understood what you just said. Could you > perhaps re-phrase it for me. Sorry... and thanks. > > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > ,m.senger at cgiar.org > > skype: martinsenger -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From martin.senger at gmail.com Tue Aug 12 10:14:21 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 12 Aug 2008 11:14:21 +0100 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A1602D.9090804@ac.uma.es> References: <4d93f07c0807311703t5a361e9fmb4e44f8bb2663e87@mail.gmail.com> <4895DE28.7010102@bsc.es> <48A15218.10104@ac.uma.es> <48A1570A.9080304@bsc.es> <4d93f07c0808120236o34ab776eq7f2116f1ead20ec5@mail.gmail.com> <48A15C9D.9030703@ac.uma.es> <4d93f07c0808120253n56fb287k34d49ae6c8171e1c@mail.gmail.com> <48A1602D.9090804@ac.uma.es> Message-ID: <4d93f07c0808120314o30b00cd6hfb9cedc2614dcb35@mail.gmail.com> > I mean that if you want "to have control over how to treat the referenced > data" Xinclude allows this possibility, but at the same time offers the > possibility of handle them automatically. > > Yo have the both behavior, is someones doesn't need to handled them by hand Exactly my point! Thanks. That's why I want to use XInclude and not the attachements. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From dmitry.repchevski at bsc.es Tue Aug 12 10:15:29 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 12 Aug 2008 12:15:29 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A1602D.9090804@ac.uma.es> References: <48A1602D.9090804@ac.uma.es> Message-ID: <48A162C1.3070207@bsc.es> > I mean that if you want "to have control over how to treat the > referenced data" Xinclude allows this possibility, but at the same time > offers the possibility of handle them automatically. I am afraid the only way to make it work is to have it always switched off... By the way, what is your opinion about FastInfoset??? Could it be used with XInclude? I mean that it compresses data very well (it transforms XML schema into ASN.1 and use BER encoding If I have some ontology class with binary data (base64binary) and send this "Moby Object" as an XML, but using FastInfoset... for the traffic if would be virtually the same as it was "plain" binary stream. I mean that we can have say "BinaryImage" ontology object that is using "binary" primitive type. Then instead of making an url into "http://mysite.com/image.jpg" we make a reference into "http://mysite.com/image.xml" The latter could be included and processed automatically by XInclude, but if we enable FastInfoset for it - it will be sent as a binary data over a network... Just a few thoughts... Best wishes, Dmitry From serr at ac.uma.es Tue Aug 12 10:50:42 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Tue, 12 Aug 2008 12:50:42 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A162C1.3070207@bsc.es> References: <48A1602D.9090804@ac.uma.es> <48A162C1.3070207@bsc.es> Message-ID: <48A16B02.1000102@ac.uma.es> About FastInfoSet it compress XML schema in binary data, is this correct? So the idea can be to compress the XML using this system to reduce the bandwidth used, correct? But I cannot see the relation with xml include. Dmitry Repchevsky wrote: > >> I mean that if you want "to have control over how to treat the >> referenced data" Xinclude allows this possibility, but at the same >> time offers the possibility of handle them automatically. > I am afraid the only way to make it work is to have it always switched > off... > > By the way, what is your opinion about FastInfoset??? > Could it be used with XInclude? > > I mean that it compresses data very well (it transforms XML schema > into ASN.1 and use BER encoding > If I have some ontology class with binary data (base64binary) and send > this "Moby Object" as an XML, but using FastInfoset... for the traffic > if would be virtually the same as it was "plain" binary stream. > > I mean that we can have say "BinaryImage" ontology object that is > using "binary" primitive type. > Then instead of making an url into "http://mysite.com/image.jpg" > we make a reference into "http://mysite.com/image.xml" > > The latter could be included and processed automatically by XInclude, > but if we enable FastInfoset for it - it will be sent as a binary data > over a network... > > Just a few thoughts... > > Best wishes, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From dmitry.repchevski at bsc.es Tue Aug 12 11:00:20 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 12 Aug 2008 13:00:20 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A16B02.1000102@ac.uma.es> References: <48A1602D.9090804@ac.uma.es> <48A162C1.3070207@bsc.es> <48A16B02.1000102@ac.uma.es> Message-ID: <48A16D44.3090204@bsc.es> Hello, > About FastInfoSet it compress XML schema in binary data, is this correct? It's better to say that it compress (transform) entire XML infoset. (while XOP is extract binary infoset and then again assemble then into one) > So the idea can be to compress the XML using this system to reduce the > bandwidth used, correct? Yes it is. > But I cannot see the relation with xml include. It's easy - XInclude can not handle not textual data - only XML/plain-text To use "disabled" XInclude to pass a reference into a custom parser is not better than using XLink... On the other hand it is possible to use XInclude to include fastinfoset encoded XML automatically. Another advantage would be to reference not to "some" resource, but to the entire "ontology" object that can be included into the place where it should be... This way you don't even need to change a message itself: you pass your image by "value" (with XOP/MTOM attachment) or by XInclude reference where it is encoded by fastinfoset. The final XML is the same! Parser just assembles such a message... Dmitry Sergio Ramirez Ramirez wrote: > About FastInfoSet it compress XML schema in binary data, is this correct? > > So the idea can be to compress the XML using this system to reduce the > bandwidth used, correct? > > But I cannot see the relation with xml include. > > Dmitry Repchevsky wrote: >> >>> I mean that if you want "to have control over how to treat the >>> referenced data" Xinclude allows this possibility, but at the same >>> time offers the possibility of handle them automatically. >> I am afraid the only way to make it work is to have it always >> switched off... >> >> By the way, what is your opinion about FastInfoset??? >> Could it be used with XInclude? >> >> I mean that it compresses data very well (it transforms XML schema >> into ASN.1 and use BER encoding >> If I have some ontology class with binary data (base64binary) and >> send this "Moby Object" as an XML, but using FastInfoset... for the >> traffic if would be virtually the same as it was "plain" binary stream. >> >> I mean that we can have say "BinaryImage" ontology object that is >> using "binary" primitive type. >> Then instead of making an url into "http://mysite.com/image.jpg" >> we make a reference into "http://mysite.com/image.xml" >> >> The latter could be included and processed automatically by XInclude, >> but if we enable FastInfoset for it - it will be sent as a binary >> data over a network... >> >> Just a few thoughts... >> >> Best wishes, >> >> Dmitry >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > From serr at ac.uma.es Tue Aug 12 11:27:43 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Tue, 12 Aug 2008 13:27:43 +0200 Subject: [MOBY-dev] Binary data streaming In-Reply-To: <48A16D44.3090204@bsc.es> References: <48A1602D.9090804@ac.uma.es> <48A162C1.3070207@bsc.es> <48A16B02.1000102@ac.uma.es> <48A16D44.3090204@bsc.es> Message-ID: <48A173AF.5030400@ac.uma.es> So with FastInfoSet can be handled binary data using XInclude, is a good idea instead to use base64 in the other hand, "To use disabled XInclude to pass a reference into a custom parser" is useful for example if you don't want to handle the reference just to sent it to another service, if it is always on don't left you this possibility Dmitry Repchevsky wrote: > Hello, > >> About FastInfoSet it compress XML schema in binary data, is this >> correct? > It's better to say that it compress (transform) entire XML infoset. > (while XOP is extract binary infoset and then again assemble then into > one) > >> So the idea can be to compress the XML using this system to reduce >> the bandwidth used, correct? > Yes it is. > >> But I cannot see the relation with xml include. > It's easy - XInclude can not handle not textual data - only > XML/plain-text > To use "disabled" XInclude to pass a reference into a custom parser is > not better than using XLink... > > On the other hand it is possible to use XInclude to include > fastinfoset encoded XML automatically. > Another advantage would be to reference not to "some" resource, but to > the entire "ontology" object that can be included into the place where > it should be... > This way you don't even need to change a message itself: you pass your > image by "value" (with XOP/MTOM attachment) or by XInclude reference > where it is encoded by fastinfoset. > The final XML is the same! Parser just assembles such a message... > > Dmitry > > Sergio Ramirez Ramirez wrote: >> About FastInfoSet it compress XML schema in binary data, is this >> correct? >> >> So the idea can be to compress the XML using this system to reduce >> the bandwidth used, correct? >> >> But I cannot see the relation with xml include. >> >> Dmitry Repchevsky wrote: >>> >>>> I mean that if you want "to have control over how to treat the >>>> referenced data" Xinclude allows this possibility, but at the same >>>> time offers the possibility of handle them automatically. >>> I am afraid the only way to make it work is to have it always >>> switched off... >>> >>> By the way, what is your opinion about FastInfoset??? >>> Could it be used with XInclude? >>> >>> I mean that it compresses data very well (it transforms XML schema >>> into ASN.1 and use BER encoding >>> If I have some ontology class with binary data (base64binary) and >>> send this "Moby Object" as an XML, but using FastInfoset... for the >>> traffic if would be virtually the same as it was "plain" binary stream. >>> >>> I mean that we can have say "BinaryImage" ontology object that is >>> using "binary" primitive type. >>> Then instead of making an url into "http://mysite.com/image.jpg" >>> we make a reference into "http://mysite.com/image.xml" >>> >>> The latter could be included and processed automatically by >>> XInclude, but if we enable FastInfoset for it - it will be sent as a >>> binary data over a network... >>> >>> Just a few thoughts... >>> >>> Best wishes, >>> >>> Dmitry >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From py at pingoured.fr Tue Aug 19 08:00:23 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Tue, 19 Aug 2008 10:00:23 +0200 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <489c53c9.2a528c0a.69e3.ffffdc0c@mx.google.com> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> <489C1C72.5000402@mpiz-koeln.mpg.de> <489C41A3.2010909@pingoured.fr> <4d93f07c0808080657u192935fat3027094ea576859a@mail.gmail.com> <489c53c9.2a528c0a.69e3.ffffdc0c@mx.google.com> Message-ID: <48AA7D97.2010606@pingoured.fr> Edward Kawas wrote: > I updated the 2 services. Did this fix the problem? > Hi all, For our case we are still facing this error. While updating the list of services, or registering a new service or even generated the skeleton of our service via dashboard, we end with the error below. We updated our jMoby with the latest cvs version. Any hints ? Thanks, Regards, Pierre generate-services: [Service(s)] Using filter for authorities: 'avilin05.avignon.inra.fr' [Service(s)] Using filter for services: '^Solstis_getDatasetTypeFromExp$' [Service(s)] Generating services into '/home/pierrey/workspace/jMoby/generated/skeletons'... [Service(s)] Reading service names... [Service(s)] ===ERROR=== [Service(s)] ===ERROR=== [Service(s)] Fault details: [Service(s)] [stackTrace: null] [Service(s)] [hostname: null] [Service(s)] Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte UTF-8 sequence. [Service(s)] Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException [Service(s)] Fault actor: null [Service(s)] When calling: [Service(s)] http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl [Service(s)] =========== [Service(s)] =========== BUILD FAILED /home/pierrey/workspace/jMoby/xmls/mosesBuild.xml:209: Java returned: 1 Total time: 38 seconds From jmrodriguez at cnio.es Tue Aug 19 08:31:16 2008 From: jmrodriguez at cnio.es (jmrodriguez) Date: Tue, 19 Aug 2008 10:31:16 +0200 Subject: [MOBY-dev] php client for biomoby services In-Reply-To: <488f3612.20d7720a.6190.1e4a@mx.google.com> References: <488EDE46.5070804@pingoured.fr> <488f3612.20d7720a.6190.1e4a@mx.google.com> Message-ID: <48AA84D4.1080104@cnio.es> Hi, Talking about PHP client for web services. Have you checked the Web Services Framework WS02? http://wso2.org/projects/wsf/php I have recently discovered this framework and it looks nice. J Edward Kawas wrote: > Just in case, you didn't get it working (I am sure that you did, but just in > case ...), I attached 2 php files that you can test with. > > The test client is in the file 'moby_php_test_service.php' and the > moby_soap_factory.php needs to be either in the same directory as the test > service or on your PHP include path. > > Thanks to Julian Tonti-Filippini for creating the PHP basis for the attached > examples! > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon > Sent: July-29-08 2:09 AM > To: MOBY-dev at lists.open-bio.org > Subject: [MOBY-dev] php client for biomoby services > > Dear list, > > We have been trying to make a php client for a simple biomoby web > service that we developed few days ago. > We are facing a problem in the creation of the input XML. We think that > using php soap library we create soap XML and not moby XML. Which > obviously returns an error. > > Has anyone of you ever try to make a simple client in php or just even > call a bioMoby service via php ? > > Below is the input that is sent to our service and the XML retrieve from > that service > > Thanks for your help, > Best regards, > > Pierre > > > input: > > xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/" > xmlns:ns1="http://avilin05.avignon.inra.fr" > xmlns:xsd="http://www.w3.org/2001/XMLSchema" > xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" > xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/" > SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"> :Body> xsi:type="xsd:string">a:1:{s:12:"Solstis_User";a:3:{s:8:"userName";s:4:"test > ";s:8:"password";s:4:"test";s:5:"email";s:12:"test at test.fr";}} olstis_getProject> > > output: > xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" > xmlns:xsd="http://www.w3.org/2001/XMLSchema" > xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> stis_getProjectResponse > soapenv:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/" > xmlns:ns1="http://avilin05.avignon.inra.fr"> xsi:type="xsd:string"><?xml version="1.0" > encoding="UTF-8"?> > <moby:MOBY xmlns:moby="http://www.biomoby.org/moby"> > <moby:mobyContent> > <moby:serviceNotes> > <moby:mobyException moby:severity="error"> > <moby:exceptionCode>600</moby:exceptionCode> > <moby:exceptionMessage>AN ERROR OCCURED DURING THE > SERVICE EXECUTION: Error in the XML input. > SystemID: null > Line (perhaps): 1 > Column: 1</moby:exceptionMessage> > </moby:mobyException> > </moby:serviceNotes> > </moby:mobyContent> > </moby:MOBY> > > < > /soapenv:Envelope> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > ------------------------------------------------------------------------ > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Have you tried CARGO? http://cargo2.bioinfo.cnio.es/ ********************* Jos? Manuel Rodr?guez Carrasco e-mail: jmrodriguez at cnio.es Tlfn: (+34) 91 732 80 00 ext: 2256 Fax: (+34) 91 224 69 76 Bioinformatic Unit Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code: 28029 Address: C/. Melchor Fern?ndez Almagro n? 3, Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From martin.senger at gmail.com Tue Aug 19 09:51:23 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 19 Aug 2008 10:51:23 +0100 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <48AA7D97.2010606@pingoured.fr> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> <489C1C72.5000402@mpiz-koeln.mpg.de> <489C41A3.2010909@pingoured.fr> <4d93f07c0808080657u192935fat3027094ea576859a@mail.gmail.com> <489c53c9.2a528c0a.69e3.ffffdc0c@mx.google.com> <48AA7D97.2010606@pingoured.fr> Message-ID: <4d93f07c0808190251n6fe2317em2318ab96e4eeda86@mail.gmail.com> > For our case we are still facing this error. I do not face the error in my local copy of jMoby. Therefore, I think that your - and perhaps other users, as well - problem is in the cache (that the cache still has the old version of the services). I suggest you to remove the cache (you can do it manually by removing the whole cache directory, or by using "reload" in the dashboard, or by using the command-line: "build/run/run-cache-client -fill -cachedir=your-cache-dir"). Does it help? Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From py at pingoured.fr Tue Aug 19 12:58:28 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Tue, 19 Aug 2008 14:58:28 +0200 Subject: [MOBY-dev] Problems with service registration using dashboard In-Reply-To: <4d93f07c0808190251n6fe2317em2318ab96e4eeda86@mail.gmail.com> References: <489C1227.6010808@dkfz-heidelberg.de> <4d93f07c0808080237l2790a015w882a37cd8e406@mail.gmail.com> <489C1C72.5000402@mpiz-koeln.mpg.de> <489C41A3.2010909@pingoured.fr> <4d93f07c0808080657u192935fat3027094ea576859a@mail.gmail.com> <489c53c9.2a528c0a.69e3.ffffdc0c@mx.google.com> <48AA7D97.2010606@pingoured.fr> <4d93f07c0808190251n6fe2317em2318ab96e4eeda86@mail.gmail.com> Message-ID: <48AAC374.7040001@pingoured.fr> Martin Senger wrote: >> For our case we are still facing this error. > > > I do not face the error in my local copy of jMoby. Therefore, I think that > your - and perhaps other users, as well - problem is in the cache (that the > cache still has the old version of the services). I suggest you to remove > the cache (you can do it manually by removing the whole cache directory, or > by using "reload" in the dashboard, or by using the command-line: > "build/run/run-cache-client -fill -cachedir=your-cache-dir"). > > Does it help? We tried by unchecking the box "Use local cache" it crashed again, so we remove the cache folder and it seems to be working again. Thanks for your help, Regards, Pierre From markw at illuminae.com Tue Aug 19 20:07:25 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 19 Aug 2008 13:07:25 -0700 Subject: [MOBY-dev] a request: In preparation for the Moby Annotation Jamboree... Message-ID: Hello all Mobyers! We're putting together the last pieces of cyber-infrastructure to run the Moby Service annotation jamboree, but we need your help! This jamboree, while being useful to us, is actually part of an experiment being run by my grad student Ben Good, who is studying community annotation and ontology-building. He needs to be sure that he gets a concentration of annotations around services that are actively being used by the community in order to have the statistical power to measure improvement in discoverability as a result of these annotations. As such, we are requesting that anyone who is willing to share their workflows please do so, and we will "skew" the annotation jamboree to emphasize those services. If you are willing to share, please either send your workflow to the mailing list, or directly to me, or BETTER YET, consider adding it to the myExperiment repository (http://myexperiment.org) and tagging it "moby" to make it easy to find :-) If I could collect these within the next 2 weeks that would be PERFECTO! Thanks everyone! Mark From M.Roos1 at uva.nl Tue Aug 19 20:36:55 2008 From: M.Roos1 at uva.nl (Marco Roos) Date: Tue, 19 Aug 2008 22:36:55 +0200 Subject: [MOBY-dev] Is creating Web services a nightmare or a treat? In-Reply-To: <48980CFC.5070803@uva.nl> References: <48980CFC.5070803@uva.nl> Message-ID: <48AB2EE7.3020702@uva.nl> [My apologies if you receive this e-mail more than once] Dear all, Some time ago I sent a call to Web service creators on the Taverna users list to participate in a Web service creation survey (see below). This e-mail is a reminder and an extension of addressees. I would very much appreciate your contribution or your help in spreading this e-mail to more Web service creators, in particular creators of Web services for (bioinformatics) applications. The purpose of the survey is to learn from each other where bottlenecks lie, and help us give advice to relative newbies to creating Web services. The limited number of responders so far has already produced some interesting insights (that I won't share with you yet to prevent any bias). I would appreciate it very much if you could take a few minutes to fill out the survey by following this link: http://www.surveymonkey.com/s.aspx?sm=xez63l87nw2CBV_2f1ntC_2fkg_3d_3d. Shortly after the 5th of September I will post results of the survey back to the Taverna users mailing list. Thank you very much for your help! Marco. Marco Roos wrote: > Dear user and Web service developer, > > I have been invited by the Netherlands BioInformatics Centre (NBIC) to > join a discussion about pitfalls and issues regarding the creation of > Bioinformatics Web services. If you have experience with this, would > you share your experience by answering my questions below? I hope you > agree that this could be useful for users and developers of web services. > > My basic questions are: > > 1. What is your favourite type of Web service (e.g. a 'standard' > SOAP-based wsdl, BioMoby, SoapLab, REST-based, etc.)? > 2. What is your favourite editor or framework? > 3. How much time did it take you to master the necessary skills? > How steep was the learning curve? > 4. How much time does it take you now to create a Web service? > (excluding the time it takes to write the content of the service) > 5. Did you have any issues with creating services for use in Taverna? > > Please include the reason behind your answers. > > Many thanks! > Marco. > -- Marco Roos Adaptive Information Disclosure Faculty of Science University of Amsterdam Kruislaan 403, room F1.02 1098 SJ Amsterdam tel. +31 (0) 20 525 7522 Social communities: Professional: LinkedIn , myExperiment and LifeScience at IvI groups on facebook Personal: Hyves From py at pingoured.fr Wed Aug 20 11:50:16 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 20 Aug 2008 13:50:16 +0200 Subject: [MOBY-dev] Register service from xml Message-ID: <48AC04F8.9010708@pingoured.fr> Dear list, We are now busy to register several data types and services if possible in one go. We have looked at http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/API/org/biomoby/registry/Central/Registry.html#registerObjectClass(java.lang.String) but we have not been able to find the correct way to use/implement these functions. We also looked at the ./build/run/run-cmdline-client -help but from that it seems that it does not accept xml as input to register data type, services or any other moby object. Did we miss something ? Thanks in advance, Best regards, Pierre From martin.senger at gmail.com Wed Aug 20 12:35:55 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 20 Aug 2008 13:35:55 +0100 Subject: [MOBY-dev] Register service from xml In-Reply-To: <48AC04F8.9010708@pingoured.fr> References: <48AC04F8.9010708@pingoured.fr> Message-ID: <4d93f07c0808200535p3e4530dwf2e6974cd3b1c8df@mail.gmail.com> > We also looked at the > ./build/run/run-cmdline-client -help > but from that it seems that it does not accept xml as input to register > data type, services or any other moby object. It does, actually. There is a parameter -call which can have two arguments. The first one (mandatory) is a method name (e.g. registerObjectClass for regisytering a data type), the second one (optional) is either directly XML, or a file name containing the XML. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From py at pingoured.fr Thu Aug 21 08:07:12 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Thu, 21 Aug 2008 10:07:12 +0200 Subject: [MOBY-dev] Register service from xml In-Reply-To: <4d93f07c0808200535p3e4530dwf2e6974cd3b1c8df@mail.gmail.com> References: <48AC04F8.9010708@pingoured.fr> <4d93f07c0808200535p3e4530dwf2e6974cd3b1c8df@mail.gmail.com> Message-ID: <48AD2230.1090301@pingoured.fr> Martin Senger wrote: >> We also looked at the >> ./build/run/run-cmdline-client -help >> but from that it seems that it does not accept xml as input to register >> data type, services or any other moby object. > > > It does, actually. There is a parameter -call which can have two arguments. > The first one (mandatory) is a method name (e.g. registerObjectClass for > registering a data type), the second one (optional) is either directly XML, > or a file name containing the XML. Ok we made a small python script that parse our xml file and run this command to register our objects or services. Thanks for your help, Regards, Pierre From jmfernandez at cnio.es Thu Aug 21 14:29:02 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Thu, 21 Aug 2008 16:29:02 +0200 Subject: [MOBY-dev] [MOBY-l] a request: In preparation for the Moby Annotation Jamboree... In-Reply-To: References: Message-ID: <48AD7BAE.7060903@cnio.es> Hi Mark (and everybody), we (as INB) have developed our own workflow repository and web workflow enactor, called IWWE&M. Its graphical GUI is available at: http://ubio.bioinfo.cnio.es/biotools/IWWEM/workflowmanager.html A programmatic list of the available workflows can be fetched with: http://ubio.bioinfo.cnio.es/biotools/IWWEM/cgi-bin/workflowmanager and a programmatic list of the not yet erased enactions can be fetched with: http://ubio.bioinfo.cnio.es/biotools/IWWEM/cgi-bin/workflowmanager?id=enaction: Could you take into account our workflows, please? Best Regards, Jos? Mar?a (on behalf of INB) Mark Wilkinson wrote: > Hello all Mobyers! > > We're putting together the last pieces of cyber-infrastructure to run > the Moby Service annotation jamboree, but we need your help! > > This jamboree, while being useful to us, is actually part of an > experiment being run by my grad student Ben Good, who is studying > community annotation and ontology-building. He needs to be sure that he > gets a concentration of annotations around services that are actively > being used by the community in order to have the statistical power to > measure improvement in discoverability as a result of these > annotations. As such, we are requesting that anyone who is willing to > share their workflows please do so, and we will "skew" the annotation > jamboree to emphasize those services. > > If you are willing to share, please either send your workflow to the > mailing list, or directly to me, or BETTER YET, consider adding it to > the myExperiment repository (http://myexperiment.org) and tagging it > "moby" to make it easy to find :-) > > If I could collect these within the next 2 weeks that would be PERFECTO! > > Thanks everyone! > > Mark > > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l > -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From py at pingoured.fr Wed Aug 27 13:27:41 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 27 Aug 2008 15:27:41 +0200 Subject: [MOBY-dev] call to a service in a service Message-ID: <48B5564D.3060803@pingoured.fr> Dear list, We are at the moment trying to call one of our web service inside another of our web service (in Java). We found some documentation using the call function from org.apache.axis.client. We also found some code from Taverna's plugin, but it is not clear for us if there is at this point any class in BioMoby that would allow us to run our services from an BioMoby object directly ? Is there also a method to convert a Moby object to a Moby XML (string not object) to generate the whole XML piece that could be used to call the service afterward ? We are a bit wondering what is the standard way to process this (if there is any) ? Thanks for your help, Best regards, Pierre From edward.kawas at gmail.com Wed Aug 27 13:49:41 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 27 Aug 2008 06:49:41 -0700 Subject: [MOBY-dev] call to a service in a service In-Reply-To: <48B5564D.3060803@pingoured.fr> References: <48B5564D.3060803@pingoured.fr> Message-ID: <48b55b75.0fba720a.2474.62c8@mx.google.com> Hi Pierre, Are you using MoSeS? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon Sent: August-27-08 6:28 AM To: MOBY-dev at lists.open-bio.org Subject: [MOBY-dev] call to a service in a service Dear list, We are at the moment trying to call one of our web service inside another of our web service (in Java). We found some documentation using the call function from org.apache.axis.client. We also found some code from Taverna's plugin, but it is not clear for us if there is at this point any class in BioMoby that would allow us to run our services from an BioMoby object directly ? Is there also a method to convert a Moby object to a Moby XML (string not object) to generate the whole XML piece that could be used to call the service afterward ? We are a bit wondering what is the standard way to process this (if there is any) ? Thanks for your help, Best regards, Pierre _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From py at pingoured.fr Wed Aug 27 14:03:59 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 27 Aug 2008 16:03:59 +0200 Subject: [MOBY-dev] call to a service in a service In-Reply-To: <48b55b75.0fba720a.2474.62c8@mx.google.com> References: <48B5564D.3060803@pingoured.fr> <48b55b75.0fba720a.2474.62c8@mx.google.com> Message-ID: <48B55ECF.6040209@pingoured.fr> Edward Kawas wrote: > Hi Pierre, > > Are you using MoSeS? Hi Edward, Yes we used it to generate the skeleton but we need in the "processit" method to call two of our web service with an ID that the grab from the first part of the service. Let me rephrase that: User -> send an ID Service1 -> get the request -> perform a sql query -> call service 2 and service3 with the results of this query (a different ID) -> assemble results from service2 and 3 -> return data to the user. NB The object return by service2 and service3 are part of the objet returned by service1, we designed them in that purpose. Thanks for the quick reply Best regards, Pierre From edward.kawas at gmail.com Wed Aug 27 14:25:46 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 27 Aug 2008 07:25:46 -0700 Subject: [MOBY-dev] call to a service in a service In-Reply-To: <48B55ECF.6040209@pingoured.fr> References: <48B5564D.3060803@pingoured.fr> <48b55b75.0fba720a.2474.62c8@mx.google.com> <48B55ECF.6040209@pingoured.fr> Message-ID: <48b563eb.1f538c0a.6e3a.ffffd52a@mx.google.com> Okay, the reason that I asked was to see whether or not you had access to the classes: MobyPackage & MobyJob. Here is how you could create the XML for sending to a service: // get the following values somewhere String id, ns = ...; String result = ...; // the dnasequence that I retrieved MobyPackage result = new MobyPackage() MobyJob j = new MobyJob(); j.setId("myQueryId"); DNASequence output_data_type = new DNASequence(); output_data_type.setId(id); output_data_type.setNamespace(ns); output_data_type.set_content(result); j.setData(output_data_type,"sequence"); result.addJob(j); String xml = result.toXML(); // used below Here is how you could call the service: String endpoint = ""; // the url to the service String service = ""; // the service name String serviceOutput = new CentralImpl(endpoint,"http://biomoby.org/").call(service,xml) Now, to parse the serviceOutput, you could use MobyPackage.createFromXML(serviceOutput) The import statements that you would need are org.biomoby.client.CentralImpl, org.biomoby.shared.datatypes.*, org.biomoby.shared.parser.MobyJob, org.biomoby.shared.parser.MobyPackage Does this make sense? If you need any clarifications, let me know. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon Sent: August-27-08 7:04 AM To: Core developer announcements Subject: Re: [MOBY-dev] call to a service in a service Edward Kawas wrote: > Hi Pierre, > > Are you using MoSeS? Hi Edward, Yes we used it to generate the skeleton but we need in the "processit" method to call two of our web service with an ID that the grab from the first part of the service. Let me rephrase that: User -> send an ID Service1 -> get the request -> perform a sql query -> call service 2 and service3 with the results of this query (a different ID) -> assemble results from service2 and 3 -> return data to the user. NB The object return by service2 and service3 are part of the objet returned by service1, we designed them in that purpose. Thanks for the quick reply Best regards, Pierre _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From py at pingoured.fr Wed Aug 27 15:02:10 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 27 Aug 2008 17:02:10 +0200 Subject: [MOBY-dev] call to a service in a service In-Reply-To: <48b563eb.1f538c0a.6e3a.ffffd52a@mx.google.com> References: <48B5564D.3060803@pingoured.fr> <48b55b75.0fba720a.2474.62c8@mx.google.com> <48B55ECF.6040209@pingoured.fr> <48b563eb.1f538c0a.6e3a.ffffd52a@mx.google.com> Message-ID: <48B56C72.4090402@pingoured.fr> Edward Kawas wrote: > Okay, the reason that I asked was to see whether or not you had access to > the classes: MobyPackage & MobyJob. > > > Does this make sense? If you need any clarifications, let me know. > We made it working ! Thanks a lot Edward, Best regards, Pierre From jerzyo at genesilico.pl Wed Aug 27 15:28:50 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Wed, 27 Aug 2008 17:28:50 +0200 Subject: [MOBY-dev] jMoby import problems Message-ID: <48B572B2.3030406@genesilico.pl> Hi I wanted to test jmoby and I am trying to run the simplest code possible: import org.biomoby.client.*; import org.biomoby.shared.*; import org.biomoby.shared.data.*; public class mytestcode01{ public static void main(String args[]){ System.out.println ("Hello, World!"); String aaa= new String(); try{ org.biomoby.client.CentralDigestCachedImpl myClient= new org.biomoby.client.CentralDigestCachedImpl(); } catch (Exception e){ System.err.println("Caught Exception: " + e.getMessage()); } } } My system is ubuntu 8.0 So I - downloaded java, ant and tomcat5.5 - compiled everything with ant, set some classpaths: $ echo $CLASSPATH :/home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main:/home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/:/usr/share/tomcat5.5/bin/commons-logging-api.jar And I get: javac mytestcode01.java /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:36: package org.apache.axis does not exist import org.apache.axis.AxisFault; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:37: package org.apache.axis.client does not exist import org.apache.axis.client.Call; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:38: package org.apache.axis.client does not exist import org.apache.axis.client.Service; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:39: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.DefaultHttpMethodRetryHandler; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:40: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.Header; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:41: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.HttpClient; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:42: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.HttpException; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:43: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.HttpStatus; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:44: package org.apache.commons.httpclient.methods does not exist import org.apache.commons.httpclient.methods.HeadMethod; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:45: package org.apache.commons.httpclient.params does not exist import org.apache.commons.httpclient.params.HttpMethodParams; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:2087: cannot find symbol symbol : class AxisFault location: class org.biomoby.client.CentralImpl public static String formatFault (AxisFault e, String endpoint, QName method) { ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java:2096: cannot find symbol symbol : class AxisFault location: class org.biomoby.client.CentralImpl public static void formatFault (AxisFault e, PrintStream out, ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java:14: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java:15: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java:16: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFReader; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java:17: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ResIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java:18: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Resource; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java:19: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Statement; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java:20: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.StmtIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java:21: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDF; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java:22: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDFS; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:23: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:24: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:25: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFNode; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:26: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFReader; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:27: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ResIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:28: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Resource; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:29: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Statement; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:30: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.StmtIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:31: package com.hp.hpl.jena.shared does not exist import com.hp.hpl.jena.shared.JenaException; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:32: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDF; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:33: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDFS; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:34: package com.ibm.lsid does not exist import com.ibm.lsid.LSID; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:176: cannot find symbol symbol : class Model location: class org.biomoby.shared.extended.ServiceInstanceParser public MobyService[] getMobyServicesFromRDF(Model model) throws MobyException { ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java:192: cannot find symbol symbol : class Model location: class org.biomoby.shared.extended.ServiceInstanceParser private boolean processModel(ArrayList list, Model model) { ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java:12: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java:13: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java:14: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFNode; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java:15: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFReader; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java:16: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ResIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java:17: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Resource; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java:18: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDFS; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/Utils.java:27: package org.apache.commons.io does not exist import org.apache.commons.io.FileUtils; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/Utils.java:28: package org.apache.commons.io does not exist import org.apache.commons.io.IOUtils; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java:12: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java:13: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java:14: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFNode; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java:15: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFReader; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java:16: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ResIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java:17: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Resource; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java:18: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDFS; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/DC_PROTEGE.java:4: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.*; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/DC_PROTEGE.java:18: cannot find symbol symbol : class Model location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE private static Model m_model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/DC_PROTEGE.java:19: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE public static final Property publisher; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/DC_PROTEGE.java:21: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE public static final Property creator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/DC_PROTEGE.java:22: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE public static final Property format; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/DC_PROTEGE.java:23: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE public static final Property identifier; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:2: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:3: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:4: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Property; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:21: cannot find symbol symbol : class Model location: class org.biomoby.client.rdf.vocabulary.Predicates private final static Model _model = ModelFactory.createDefaultModel();; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:22: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property category = _model.getProperty(uri + "category"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:23: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property isa = _model.getProperty(uri + "isa"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:24: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property has = _model.getProperty(uri + "has"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:25: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property hasa = _model.getProperty(uri + "hasa"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:26: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property articleName = _model.getProperty(uri + "articleName"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:27: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property article_name = _model.getProperty(uri + "article_name"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:28: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property namespace_type = _model.getProperty(uri + "namespaceType"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:29: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property object_type = _model.getProperty(uri + "objectType"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:30: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property input = _model.getProperty(uri + "input"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:31: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property output = _model.getProperty(uri + "output"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:32: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property consumes = _model.getProperty(uri + "consumes"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:33: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property produces = _model.getProperty(uri + "produces"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:34: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property performs_task = _model.getProperty(uri + "performs_task"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:35: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property comment = _model.getProperty(uri + "comment"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:36: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property label = _model.getProperty(uri + "label"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:37: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property default_value = _model.getProperty(uri + "default_value"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:38: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property datatype = _model.getProperty(uri + "datatype"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:39: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property max = _model.getProperty(uri + "max"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:40: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property min = _model.getProperty(uri + "min"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:41: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property enumeration = _model.getProperty(uri + "enum"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:42: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property SignatureURL = _model.getProperty(uri + "SignatureURL"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:43: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property authoritative = _model.getProperty(uri + "authoritative"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:44: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property ofType = _model.getProperty(uri + "ofType"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:46: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property Simple = _model.getProperty(uri + "Simple"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:47: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property Secondary = _model.getProperty(uri + "Secondary"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:48: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property Collection = _model.getProperty(uri + "Collection"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:50: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property sampleInputData = _model.getProperty(uri + "sampleInputData"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:51: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property sampleOutputData = _model.getProperty(uri + "sampleOutputData"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:52: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property approvedBy = _model.getProperty(uri + "approvedBy"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:53: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property StructuralComponent = _model.getProperty(uri + "StructuralComponent"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:54: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property DataComponent = _model.getProperty(uri + "DataComponent"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:55: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property MobyMessageComponent = _model.getProperty(uri + "MobyMessageComponent"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:56: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property MobyThing = _model.getProperty(uri + "MobyThing"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:57: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property inNamespaces = _model.getProperty(uri + "inNamespaces"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java:58: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property componentName = _model.getProperty(uri + "componentName"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/FetaVocabulary.java:4: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.*; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/FetaVocabulary.java:18: cannot find symbol symbol : class Model location: class org.biomoby.client.rdf.vocabulary.FetaVocabulary private static Model m_model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/FetaVocabulary.java:19: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.FetaVocabulary public static Property operationType; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/FetaVocabulary.java:20: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.FetaVocabulary public static final Property inNamespaces; ^ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 errors I guess I need to install something or set some classpaths. Please help Jerzy Orlowski From edward.kawas at gmail.com Wed Aug 27 15:53:49 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 27 Aug 2008 08:53:49 -0700 Subject: [MOBY-dev] jMoby import problems In-Reply-To: <48B572B2.3030406@genesilico.pl> References: <48B572B2.3030406@genesilico.pl> Message-ID: <48b5788e.1ed7720a.0ad5.ffffc1be@mx.google.com> Have you taken a look at: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/EclipseAndJMoby. html It might be useful for you. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jerzy Orlowski Sent: August-27-08 8:29 AM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] jMoby import problems Hi I wanted to test jmoby and I am trying to run the simplest code possible: import org.biomoby.client.*; import org.biomoby.shared.*; import org.biomoby.shared.data.*; public class mytestcode01{ public static void main(String args[]){ System.out.println ("Hello, World!"); String aaa= new String(); try{ org.biomoby.client.CentralDigestCachedImpl myClient= new org.biomoby.client.CentralDigestCachedImpl(); } catch (Exception e){ System.err.println("Caught Exception: " + e.getMessage()); } } } My system is ubuntu 8.0 So I - downloaded java, ant and tomcat5.5 - compiled everything with ant, set some classpaths: $ echo $CLASSPATH :/home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main:/home/jerzyo/ projects/workflows/jmoby/moby-live/Java/src/main/:/usr/share/tomcat5.5/bin/c ommons-logging-api.jar And I get: javac mytestcode01.java /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:36: package org.apache.axis does not exist import org.apache.axis.AxisFault; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:37: package org.apache.axis.client does not exist import org.apache.axis.client.Call; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:38: package org.apache.axis.client does not exist import org.apache.axis.client.Service; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:39: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.DefaultHttpMethodRetryHandler; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:40: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.Header; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:41: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.HttpClient; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:42: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.HttpException; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:43: package org.apache.commons.httpclient does not exist import org.apache.commons.httpclient.HttpStatus; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:44: package org.apache.commons.httpclient.methods does not exist import org.apache.commons.httpclient.methods.HeadMethod; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:45: package org.apache.commons.httpclient.params does not exist import org.apache.commons.httpclient.params.HttpMethodParams; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:2087: cannot find symbol symbol : class AxisFault location: class org.biomoby.client.CentralImpl public static String formatFault (AxisFault e, String endpoint, QName method) { ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/CentralImpl.java:2096: cannot find symbol symbol : class AxisFault location: class org.biomoby.client.CentralImpl public static void formatFault (AxisFault e, PrintStream out, ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/DataTypeParser.java:14: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/DataTypeParser.java:15: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/DataTypeParser.java:16: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFReader; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/DataTypeParser.java:17: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ResIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/DataTypeParser.java:18: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Resource; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/DataTypeParser.java:19: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Statement; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/DataTypeParser.java:20: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.StmtIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/DataTypeParser.java:21: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDF; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/DataTypeParser.java:22: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDFS; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:23: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:24: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:25: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFNode; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:26: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFReader; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:27: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ResIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:28: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Resource; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:29: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Statement; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:30: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.StmtIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:31: package com.hp.hpl.jena.shared does not exist import com.hp.hpl.jena.shared.JenaException; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:32: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDF; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:33: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDFS; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:34: package com.ibm.lsid does not exist import com.ibm.lsid.LSID; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:176: cannot find symbol symbol : class Model location: class org.biomoby.shared.extended.ServiceInstanceParser public MobyService[] getMobyServicesFromRDF(Model model) throws MobyException { ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceInstanceParser.java:192: cannot find symbol symbol : class Model location: class org.biomoby.shared.extended.ServiceInstanceParser private boolean processModel(ArrayList list, Model model) { ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceTypeParser.java:12: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceTypeParser.java:13: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceTypeParser.java:14: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFNode; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceTypeParser.java:15: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFReader; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceTypeParser.java:16: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ResIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceTypeParser.java:17: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Resource; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/ServiceTypeParser.java:18: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDFS; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/Utils.java:27: package org.apache.commons.io does not exist import org.apache.commons.io.FileUtils; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/Utils.java:28: package org.apache.commons.io does not exist import org.apache.commons.io.IOUtils; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/NamespaceParser.java:12: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/NamespaceParser.java:13: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/NamespaceParser.java:14: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFNode; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/NamespaceParser.java:15: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.RDFReader; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/NamespaceParser.java:16: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ResIterator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/NamespaceParser.java:17: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Resource; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh ared/extended/NamespaceParser.java:18: package com.hp.hpl.jena.vocabulary does not exist import com.hp.hpl.jena.vocabulary.RDFS; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/DC_PROTEGE.java:4: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.*; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/DC_PROTEGE.java:18: cannot find symbol symbol : class Model location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE private static Model m_model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/DC_PROTEGE.java:19: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE public static final Property publisher; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/DC_PROTEGE.java:21: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE public static final Property creator; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/DC_PROTEGE.java:22: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE public static final Property format; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/DC_PROTEGE.java:23: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE public static final Property identifier; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:2: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:3: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.ModelFactory; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:4: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.Property; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:21: cannot find symbol symbol : class Model location: class org.biomoby.client.rdf.vocabulary.Predicates private final static Model _model = ModelFactory.createDefaultModel();; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:22: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property category = _model.getProperty(uri + "category"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:23: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property isa = _model.getProperty(uri + "isa"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:24: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property has = _model.getProperty(uri + "has"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:25: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property hasa = _model.getProperty(uri + "hasa"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:26: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property articleName = _model.getProperty(uri + "articleName"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:27: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property article_name = _model.getProperty(uri + "article_name"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:28: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property namespace_type = _model.getProperty(uri + "namespaceType"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:29: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property object_type = _model.getProperty(uri + "objectType"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:30: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property input = _model.getProperty(uri + "input"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:31: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property output = _model.getProperty(uri + "output"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:32: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property consumes = _model.getProperty(uri + "consumes"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:33: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property produces = _model.getProperty(uri + "produces"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:34: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property performs_task = _model.getProperty(uri + "performs_task"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:35: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property comment = _model.getProperty(uri + "comment"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:36: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property label = _model.getProperty(uri + "label"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:37: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property default_value = _model.getProperty(uri + "default_value"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:38: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property datatype = _model.getProperty(uri + "datatype"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:39: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property max = _model.getProperty(uri + "max"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:40: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property min = _model.getProperty(uri + "min"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:41: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property enumeration = _model.getProperty(uri + "enum"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:42: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property SignatureURL = _model.getProperty(uri + "SignatureURL"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:43: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property authoritative = _model.getProperty(uri + "authoritative"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:44: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property ofType = _model.getProperty(uri + "ofType"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:46: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property Simple = _model.getProperty(uri + "Simple"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:47: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property Secondary = _model.getProperty(uri + "Secondary"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:48: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property Collection = _model.getProperty(uri + "Collection"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:50: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property sampleInputData = _model.getProperty(uri + "sampleInputData"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:51: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property sampleOutputData = _model.getProperty(uri + "sampleOutputData"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:52: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property approvedBy = _model.getProperty(uri + "approvedBy"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:53: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property StructuralComponent = _model.getProperty(uri + "StructuralComponent"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:54: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property DataComponent = _model.getProperty(uri + "DataComponent"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:55: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property MobyMessageComponent = _model.getProperty(uri + "MobyMessageComponent"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:56: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property MobyThing = _model.getProperty(uri + "MobyThing"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:57: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property inNamespaces = _model.getProperty(uri + "inNamespaces"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/Predicates.java:58: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.Predicates public static final Property componentName = _model.getProperty(uri + "componentName"); ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/FetaVocabulary.java:4: package com.hp.hpl.jena.rdf.model does not exist import com.hp.hpl.jena.rdf.model.*; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/FetaVocabulary.java:18: cannot find symbol symbol : class Model location: class org.biomoby.client.rdf.vocabulary.FetaVocabulary private static Model m_model; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/FetaVocabulary.java:19: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.FetaVocabulary public static Property operationType; ^ /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl ient/rdf/vocabulary/FetaVocabulary.java:20: cannot find symbol symbol : class Property location: class org.biomoby.client.rdf.vocabulary.FetaVocabulary public static final Property inNamespaces; ^ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 errors I guess I need to install something or set some classpaths. Please help Jerzy Orlowski _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From martin.senger at gmail.com Wed Aug 27 15:59:24 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 27 Aug 2008 16:59:24 +0100 Subject: [MOBY-dev] jMoby import problems In-Reply-To: <48B572B2.3030406@genesilico.pl> References: <48B572B2.3030406@genesilico.pl> Message-ID: <4d93f07c0808270859h3f0ba8b9xf9ae2dd6c0a2bfc5@mail.gmail.com> > - compiled everything with ant, set some classpaths: The problem seems to be in setting the CLASSPATH. You should not set it manually. Better is to extend the Ant's build.xml for other tasks you intend to do. You can look into build/run/*.sh scripts to see what the full CLASSPATH should look like. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From jerzyo at genesilico.pl Wed Aug 27 16:22:12 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Wed, 27 Aug 2008 18:22:12 +0200 Subject: [MOBY-dev] MOBY-dev Digest, Vol 68, Issue 10 In-Reply-To: References: Message-ID: <48B57F34.8060008@genesilico.pl> But I am not on Windows, and I have never used Eclipse. Anyway, I managed to do something with my error 1. When I installed maven (sudo apt-get install maven2) the code compiles but does not execute: java mytestcode01.java Exception in thread "main" java.lang.NoClassDefFoundError: mytestcode01/java Caused by: java.lang.ClassNotFoundException: mytestcode01.java at java.net.URLClassLoader$1.run(URLClassLoader.java:200) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:188) at java.lang.ClassLoader.loadClass(ClassLoader.java:306) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276) at java.lang.ClassLoader.loadClass(ClassLoader.java:251) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:31 2. When I removed maven (apt-get remove maven2) and added all jars from ~/.m2/repository to my classpath, the code compiles and executes without errors. I think I made a kind of hack, but I do not even know what the ~/.m2/repository is for Any ideas? Jerzy moby-dev-request at lists.open-bio.org wrote: > Send MOBY-dev mailing list submissions to > moby-dev at lists.open-bio.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/moby-dev > or, via email, send a message with subject or body 'help' to > moby-dev-request at lists.open-bio.org > > You can reach the person managing the list at > moby-dev-owner at lists.open-bio.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of MOBY-dev digest..." > > > Today's Topics: > > 1. Re: jMoby import problems (Edward Kawas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 27 Aug 2008 08:53:49 -0700 > From: "Edward Kawas" > Subject: Re: [MOBY-dev] jMoby import problems > To: "'Core developer announcements'" > Message-ID: <48b5788e.1ed7720a.0ad5.ffffc1be at mx.google.com> > Content-Type: text/plain; charset="us-ascii" > > Have you taken a look at: > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/EclipseAndJMoby. > html > > It might be useful for you. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jerzy Orlowski > Sent: August-27-08 8:29 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] jMoby import problems > > Hi > > I wanted to test jmoby and I am trying to run the simplest code possible: > > import org.biomoby.client.*; > import org.biomoby.shared.*; > import org.biomoby.shared.data.*; > > public class mytestcode01{ > public static void main(String args[]){ > System.out.println ("Hello, World!"); > String aaa= new String(); > > try{ > org.biomoby.client.CentralDigestCachedImpl myClient= new > org.biomoby.client.CentralDigestCachedImpl(); > } > catch (Exception e){ > System.err.println("Caught Exception: " + e.getMessage()); > > } > } > } > > My system is ubuntu 8.0 > > So I > - downloaded java, ant and tomcat5.5 > - compiled everything with ant, set some classpaths: > $ echo $CLASSPATH > :/home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main:/home/jerzyo/ > projects/workflows/jmoby/moby-live/Java/src/main/:/usr/share/tomcat5.5/bin/c > ommons-logging-api.jar > > And I get: > > > > > > > javac mytestcode01.java > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:36: > package org.apache.axis does not exist > import org.apache.axis.AxisFault; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:37: > package org.apache.axis.client does not exist > import org.apache.axis.client.Call; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:38: > package org.apache.axis.client does not exist > import org.apache.axis.client.Service; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:39: > package org.apache.commons.httpclient does not exist > import org.apache.commons.httpclient.DefaultHttpMethodRetryHandler; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:40: > package org.apache.commons.httpclient does not exist > import org.apache.commons.httpclient.Header; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:41: > package org.apache.commons.httpclient does not exist > import org.apache.commons.httpclient.HttpClient; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:42: > package org.apache.commons.httpclient does not exist > import org.apache.commons.httpclient.HttpException; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:43: > package org.apache.commons.httpclient does not exist > import org.apache.commons.httpclient.HttpStatus; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:44: > package org.apache.commons.httpclient.methods does not exist > import org.apache.commons.httpclient.methods.HeadMethod; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:45: > package org.apache.commons.httpclient.params does not exist > import org.apache.commons.httpclient.params.HttpMethodParams; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:2087: > cannot find symbol > symbol : class AxisFault > location: class org.biomoby.client.CentralImpl > public static String formatFault (AxisFault e, String endpoint, > QName method) { > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/CentralImpl.java:2096: > cannot find symbol > symbol : class AxisFault > location: class org.biomoby.client.CentralImpl > public static void formatFault (AxisFault e, PrintStream out, > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/DataTypeParser.java:14: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Model; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/DataTypeParser.java:15: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.ModelFactory; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/DataTypeParser.java:16: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.RDFReader; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/DataTypeParser.java:17: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.ResIterator; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/DataTypeParser.java:18: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Resource; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/DataTypeParser.java:19: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Statement; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/DataTypeParser.java:20: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.StmtIterator; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/DataTypeParser.java:21: > package com.hp.hpl.jena.vocabulary does not exist > import com.hp.hpl.jena.vocabulary.RDF; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/DataTypeParser.java:22: > package com.hp.hpl.jena.vocabulary does not exist > import com.hp.hpl.jena.vocabulary.RDFS; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:23: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Model; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:24: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.ModelFactory; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:25: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.RDFNode; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:26: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.RDFReader; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:27: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.ResIterator; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:28: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Resource; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:29: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Statement; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:30: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.StmtIterator; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:31: > package com.hp.hpl.jena.shared does not exist > import com.hp.hpl.jena.shared.JenaException; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:32: > package com.hp.hpl.jena.vocabulary does not exist > import com.hp.hpl.jena.vocabulary.RDF; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:33: > package com.hp.hpl.jena.vocabulary does not exist > import com.hp.hpl.jena.vocabulary.RDFS; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:34: > package com.ibm.lsid does not exist > import com.ibm.lsid.LSID; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:176: > cannot find symbol > symbol : class Model > location: class org.biomoby.shared.extended.ServiceInstanceParser > public MobyService[] getMobyServicesFromRDF(Model model) throws > MobyException { > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceInstanceParser.java:192: > cannot find symbol > symbol : class Model > location: class org.biomoby.shared.extended.ServiceInstanceParser > private boolean processModel(ArrayList list, Model > model) { > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceTypeParser.java:12: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Model; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceTypeParser.java:13: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.ModelFactory; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceTypeParser.java:14: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.RDFNode; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceTypeParser.java:15: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.RDFReader; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceTypeParser.java:16: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.ResIterator; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceTypeParser.java:17: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Resource; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/ServiceTypeParser.java:18: > package com.hp.hpl.jena.vocabulary does not exist > import com.hp.hpl.jena.vocabulary.RDFS; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/Utils.java:27: > package org.apache.commons.io does not exist > import org.apache.commons.io.FileUtils; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/Utils.java:28: > package org.apache.commons.io does not exist > import org.apache.commons.io.IOUtils; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/NamespaceParser.java:12: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Model; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/NamespaceParser.java:13: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.ModelFactory; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/NamespaceParser.java:14: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.RDFNode; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/NamespaceParser.java:15: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.RDFReader; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/NamespaceParser.java:16: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.ResIterator; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/NamespaceParser.java:17: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Resource; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/sh > ared/extended/NamespaceParser.java:18: > package com.hp.hpl.jena.vocabulary does not exist > import com.hp.hpl.jena.vocabulary.RDFS; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/DC_PROTEGE.java:4: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.*; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/DC_PROTEGE.java:18: > cannot find symbol > symbol : class Model > location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE > private static Model m_model; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/DC_PROTEGE.java:19: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE > public static final Property publisher; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/DC_PROTEGE.java:21: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE > public static final Property creator; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/DC_PROTEGE.java:22: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE > public static final Property format; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/DC_PROTEGE.java:23: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.DC_PROTEGE > public static final Property identifier; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:2: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Model; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:3: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.ModelFactory; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:4: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.Property; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:21: > cannot find symbol > symbol : class Model > location: class org.biomoby.client.rdf.vocabulary.Predicates > private final static Model _model = ModelFactory.createDefaultModel();; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:22: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property category = _model.getProperty(uri + > "category"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:23: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property isa = _model.getProperty(uri + "isa"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:24: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property has = _model.getProperty(uri + "has"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:25: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property hasa = _model.getProperty(uri + "hasa"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:26: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property articleName = _model.getProperty(uri + > "articleName"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:27: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property article_name = _model.getProperty(uri + > "article_name"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:28: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property namespace_type = _model.getProperty(uri > + "namespaceType"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:29: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property object_type = _model.getProperty(uri + > "objectType"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:30: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property input = _model.getProperty(uri + "input"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:31: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property output = _model.getProperty(uri + > "output"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:32: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property consumes = _model.getProperty(uri + > "consumes"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:33: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property produces = _model.getProperty(uri + > "produces"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:34: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property performs_task = _model.getProperty(uri > + "performs_task"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:35: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property comment = _model.getProperty(uri + > "comment"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:36: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property label = _model.getProperty(uri + "label"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:37: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property default_value = _model.getProperty(uri > + "default_value"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:38: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property datatype = _model.getProperty(uri + > "datatype"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:39: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property max = _model.getProperty(uri + "max"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:40: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property min = _model.getProperty(uri + "min"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:41: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property enumeration = _model.getProperty(uri + > "enum"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:42: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property SignatureURL = _model.getProperty(uri + > "SignatureURL"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:43: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property authoritative = _model.getProperty(uri > + "authoritative"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:44: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property ofType = _model.getProperty(uri + > "ofType"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:46: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property Simple = _model.getProperty(uri + > "Simple"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:47: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property Secondary = _model.getProperty(uri + > "Secondary"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:48: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property Collection = _model.getProperty(uri + > "Collection"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:50: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property sampleInputData = > _model.getProperty(uri + "sampleInputData"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:51: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property sampleOutputData = > _model.getProperty(uri + "sampleOutputData"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:52: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property approvedBy = _model.getProperty(uri + > "approvedBy"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:53: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property StructuralComponent = > _model.getProperty(uri + "StructuralComponent"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:54: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property DataComponent = _model.getProperty(uri > + "DataComponent"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:55: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property MobyMessageComponent = > _model.getProperty(uri + "MobyMessageComponent"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:56: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property MobyThing = _model.getProperty(uri + > "MobyThing"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:57: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property inNamespaces = _model.getProperty(uri + > "inNamespaces"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/Predicates.java:58: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.Predicates > public static final Property componentName = _model.getProperty(uri > + "componentName"); > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/FetaVocabulary.java:4: > package com.hp.hpl.jena.rdf.model does not exist > import com.hp.hpl.jena.rdf.model.*; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/FetaVocabulary.java:18: > cannot find symbol > symbol : class Model > location: class org.biomoby.client.rdf.vocabulary.FetaVocabulary > private static Model m_model; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/FetaVocabulary.java:19: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.FetaVocabulary > public static Property operationType; > ^ > /home/jerzyo/projects/workflows/jmoby/moby-live/Java/src/main/org/biomoby/cl > ient/rdf/vocabulary/FetaVocabulary.java:20: > cannot find symbol > symbol : class Property > location: class org.biomoby.client.rdf.vocabulary.FetaVocabulary > public static final Property inNamespaces; > ^ > Note: Some input files use unchecked or unsafe operations. > Note: Recompile with -Xlint:unchecked for details. > 100 errors > > > > I guess I need to install something or set some classpaths. > Please help > > Jerzy Orlowski > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > > ------------------------------ > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > End of MOBY-dev Digest, Vol 68, Issue 10 > **************************************** > > > > From martin.senger at gmail.com Wed Aug 27 16:32:32 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 27 Aug 2008 17:32:32 +0100 Subject: [MOBY-dev] MOBY-dev Digest, Vol 68, Issue 10 In-Reply-To: <48B57F34.8060008@genesilico.pl> References: <48B57F34.8060008@genesilico.pl> Message-ID: <4d93f07c0808270932o719b2f0dxf09d31afdb699b60@mail.gmail.com> > 1. When I installed maven You do not need maven in order to use jMoby. added all jars from ~/.m2/repository to my classpath That's what I was suggesting you; that's what you see in the build/run/run* scripts. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From jerzyo at genesilico.pl Wed Aug 27 16:49:34 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Wed, 27 Aug 2008 18:49:34 +0200 Subject: [MOBY-dev] jMoby import problems In-Reply-To: References: Message-ID: <48B5859E.9010209@genesilico.pl> Thanks a lot, sourcing build/run/run.me.sh solves the problem. Jerzy moby-dev-request at lists.open-bio.org wrote: > Date: Wed, 27 Aug 2008 16:59:24 +0100 > From: "Martin Senger" > Subject: Re: [MOBY-dev] jMoby import problems > To: "Core developer announcements" > Message-ID: > <4d93f07c0808270859h3f0ba8b9xf9ae2dd6c0a2bfc5 at mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > >> - compiled everything with ant, set some classpaths: >> > > > The problem seems to be in setting the CLASSPATH. You should not set it > manually. Better is to extend the Ant's build.xml for other tasks you intend > to do. You can look into build/run/*.sh scripts to see what the full > CLASSPATH should look like. > > Cheers, > Martin > >