From Pieter.Neerincx at wur.nl Tue May 8 14:53:20 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Tue, 8 May 2007 20:53:20 +0200 Subject: [MOBY-dev] Valid boolean values for primitives and secondary parmeters In-Reply-To: References: Message-ID: <5AE74DCB-BD91-495F-8961-C25361B6F83B@wur.nl> Hi Mobifiers, Currently the BioMOBY specification does not explicitly list what values can be used for boolean primaries and secondaries. However for optimal interoperability services need to know what values they can expect from a client or the other way around clients need to be able to figure out what input a service needs. Hereby I propose we stick to the XML Schema specification for valid boolean values. From the XML Schema spec (http://www.w3.org/TR/xmlschema-2/#dt- boolean): "An instance of a datatype that is defined as boolean can have the following legal literals {true, false, 1, 0}." This would mean that clients are not allowed to send anything besides {true, false, 1, 0} as booleans and services must understand {true, false, 1, 0}. Hence frequently used booleans as T, F, t, f, True, False or biology specific booleans like male, female, M, F, XX, XY, etc. will be value non-grata in mobi-lingua. Any additional suggestions or objections? Cheers, Pi ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From gordonp at ucalgary.ca Tue May 8 15:05:31 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 08 May 2007 13:05:31 -0600 Subject: [MOBY-dev] Valid boolean values for primitives and secondary parmeters In-Reply-To: <5AE74DCB-BD91-495F-8961-C25361B6F83B@wur.nl> References: <5AE74DCB-BD91-495F-8961-C25361B6F83B@wur.nl> Message-ID: <4640C9FB.40502@ucalgary.ca> I agree. I think we had this conversation a couple of years ago! Time to put it in the spec... > Hi Mobifiers, > > Currently the BioMOBY specification does not explicitly list what > values can be used for boolean primaries and secondaries. However for > optimal interoperability services need to know what values they can > expect from a client or the other way around clients need to be able > to figure out what input a service needs. Hereby I propose we stick > to the XML Schema specification for valid boolean values. > > From the XML Schema spec (http://www.w3.org/TR/xmlschema-2/#dt- > boolean): > "An instance of a datatype that is defined as boolean can have the > following legal literals {true, false, 1, 0}." > > This would mean that clients are not allowed to send anything besides > {true, false, 1, 0} as booleans and services must understand {true, > false, 1, 0}. Hence frequently used booleans as T, F, t, f, True, > False or biology specific booleans like male, female, M, F, XX, XY, > etc. will be value non-grata in mobi-lingua. > > Any additional suggestions or objections? > > Cheers, > > Pi > > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 060 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From darin.london at duke.edu Thu May 10 12:17:40 2007 From: darin.london at duke.edu (darin.london at duke.edu) Date: Thu, 10 May 2007 12:17:40 -0400 Subject: [MOBY-dev] BOSC 2007 Second Call For Papers Message-ID: <200705101617.l4AGHeOl002544@tenero.duhs.duke.edu> The BOSC Organizing Committee are proud to announce BOSC 2007, occurring in Vienna, Austria on July 19th, 20th. The conference this year promises to be exciting, as the BOSC developers attempt to define and solve currently intractable problems in Bioinformatics. Please refer to the following website for complete information, and requests for submissions. Thank you, and we hope to see you in Vienna. http://open-bio.org/wiki/BOSC_2007 The BOSC organizing Committee Please pass this email on to anyone that would be interested. From darin.london at duke.edu Mon May 14 10:44:58 2007 From: darin.london at duke.edu (darin.london at duke.edu) Date: Mon, 14 May 2007 10:44:58 -0400 Subject: [MOBY-dev] BOSC 2007 Abstract Submission Deadline Extended Message-ID: <200705141444.l4EEiw9G027027@tenero.duhs.duke.edu> Due to technical difficulties in sending out the 2nd call for papers, the BOSC organizers are extending the deadline for abstract submissions to Monday May 21st. The announcement day will remain the same so that it remains before the Early Discount Date. http://open-bio.org/wiki/BOSC_2007 The BOSC organizing Committee Please pass this email on to anyone that would be interested. From ivanp at mmb.pcb.ub.es Tue May 15 14:38:49 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Tue, 15 May 2007 20:38:49 +0200 Subject: [MOBY-dev] XML elements into serviceNote get scaped Message-ID: <4649FE39.8070901@mmb.pcb.ub.es> Hi, I'm working with jMoby and MoSeS. As part of the moby specification, when a problem executing the service is encountered a mobyException must be launched: as many as needed XML elements must appear in the serviceNotes element in the response message. The problem is that the symbols < and > get scaped for all those elements inside serviceNotes; something like this: <moby:mobyException severity="2" > <moby:exceptionCode>201</moby:exceptionCode> <moby:exceptionMessage>Method is empty or is not a valid method name, applying default method: Atom_CyclohexaneWaterEnergyLomize Valid methods: Atom_OctanolWaterEnergyEisenbergMcLachlan ... </moby:mobyException> ... Is this a bug? or am I doing something bad? Thanks, -- ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ From martin.senger at gmail.com Tue May 15 15:19:23 2007 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 15 May 2007 20:19:23 +0100 Subject: [MOBY-dev] XML elements into serviceNote get scaped In-Reply-To: <4649FE39.8070901@mmb.pcb.ub.es> References: <4649FE39.8070901@mmb.pcb.ub.es> Message-ID: <4d93f07c0705151219o37fde9f3ha62d1db2703428f3@mail.gmail.com> > Is this a bug? or am I doing something bad? Is there a way I can reproduce this behaviour? How did you get this output - in the Dashboard, or somewhere else? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ivanp at mmb.pcb.ub.es Tue May 15 15:38:09 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Tue, 15 May 2007 21:38:09 +0200 Subject: [MOBY-dev] XML elements into serviceNote get scaped In-Reply-To: <4d93f07c0705151219o37fde9f3ha62d1db2703428f3@mail.gmail.com> References: <4649FE39.8070901@mmb.pcb.ub.es> <4d93f07c0705151219o37fde9f3ha62d1db2703428f3@mail.gmail.com> Message-ID: <464A0C21.6070305@mmb.pcb.ub.es> Hi, I get this behaviour in Dashboard & java command line client. The service that produced it is not in production yet (so it's not in a public server), but you can reproduce it with another one. For example: MOBY_SERVER=http://moby-dev.inab.org/cgi-bin/MOBY-Central.pl MOBY_URI=http://moby-dev.inab.org/MOBY/Central serviceName: getActiveSiteInterfaceFromPDBId and as input: I've suffered these problems in the past with Java XML... Perhaps is related to the way the children nodes of serviceNotes elements are created. Make sure you're adding Node objects and no String objects... I don't remember exactly what the problem was, but it was related to this kind of things. Regards, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Martin Senger escribi?: >> Is this a bug? or am I doing something bad? >> > > > Is there a way I can reproduce this behaviour? How did you get this output - > in the Dashboard, or somewhere else? > > Martin > > > From martin.senger at gmail.com Tue May 15 17:47:43 2007 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 15 May 2007 22:47:43 +0100 Subject: [MOBY-dev] XML elements into serviceNote get scaped In-Reply-To: <464A0C21.6070305@mmb.pcb.ub.es> References: <4649FE39.8070901@mmb.pcb.ub.es> <4d93f07c0705151219o37fde9f3ha62d1db2703428f3@mail.gmail.com> <464A0C21.6070305@mmb.pcb.ub.es> Message-ID: <4d93f07c0705151447y4354b110g80a3ea0de2e620ae@mail.gmail.com> > I've suffered these problems in the past with Java XML... Yes, me too. And so far I always found that the problem was on the service side. As it is here (see below). Was this service generated by Moses? Because if yes then it is also my problem :-) The XML returned by the service in question is wrongly escaped. This is what is on -the-wire: ... <?xml version="1.0" encoding="UTF-8"?> <moby:MOBY xmlns:moby="http://www.biomoby.org/moby"> <moby:mobyContent> <moby:serviceNotes>&lt;moby:mobyException severity="2" &gt; ... The beginning is as it should be: <moby:MOBY... But the service notes are double-escaped - because the ampersand which is the part of the construct "<" is again escaped so we get wrongly " >&lt;moby:mobyException". And this is what the service sent over the network (I caught it using a TCP monitor, not the Dashboard or other tool that may already fiddle with the raw data). Regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ivanp at mmb.pcb.ub.es Tue May 15 18:07:54 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Wed, 16 May 2007 00:07:54 +0200 Subject: [MOBY-dev] XML elements into serviceNote get scaped In-Reply-To: <4d93f07c0705151447y4354b110g80a3ea0de2e620ae@mail.gmail.com> References: <4649FE39.8070901@mmb.pcb.ub.es><4d93f07c0705151219o37fde9f3ha62 d1db2703428f3@mail.gmail.com><464A0C21.6070305@mmb.pcb.ub.es> <4d93f07c0705151447y4354b110g80a3ea0de2e620ae@mail.gmail.com> Message-ID: <464A2F3A.1080708@mmb.pcb.ub.es> Hi Martin, All my services are MoSeS generated. I don't deal directly with any XML at all... Tomorrow I can perform more tests on different services, but my intuition is that there is a problem in MoSeS... The strange thing is that I didn't realize about it before...Have you performed any test with any other service provider? Cheers, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Martin Senger escribi?: >> I've suffered these problems in the past with Java XML... >> > > > Yes, me too. And so far I always found that the problem was on the service > side. As it is here (see below). Was this service generated by Moses? > Because if yes then it is also my problem :-) > > The XML returned by the service in question is wrongly escaped. This is what > is on -the-wire: > > ... > <?xml version="1.0" > encoding="UTF-8"?> > <moby:MOBY xmlns:moby="http://www.biomoby.org/moby"> > <moby:mobyContent> > <moby:serviceNotes>&lt;moby:mobyException > severity="2" &gt; > ... > > The beginning is as it should be: <moby:MOBY... > > But the service notes are double-escaped - because the ampersand which is > the part of the construct "<" is again escaped so we get wrongly " > >&lt;moby:mobyException". And this is what the service sent over the > network (I caught it using a TCP monitor, not the Dashboard or other tool > that may already fiddle with the raw data). > > Regards, > Martin > > > From gordonp at ucalgary.ca Tue May 15 18:15:26 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 15 May 2007 16:15:26 -0600 Subject: [MOBY-dev] XML elements into serviceNote get scaped In-Reply-To: <464A2F3A.1080708@mmb.pcb.ub.es> References: <4649FE39.8070901@mmb.pcb.ub.es><4d93f07c0705151219o37fde9f3ha62 d1db2703428f3@mail.gmail.com><464A0C21.6070305@mmb.pcb.ub.es> <4d93f07c0705151447y4354b110g80a3ea0de2e620ae@mail.gmail.com> <464A2F3A.1080708@mmb.pcb.ub.es> Message-ID: <464A30FE.1050606@ucalgary.ca> I have noticed this problem before too with some services, but did not know how those services were built...this leads me to believe it probably is a latent bug in MoSeS. > Hi Martin, > > All my services are MoSeS generated. I don't deal directly with any XML > at all... Tomorrow I can perform more tests on different services, but > my intuition is that there is a problem in MoSeS... The strange thing is > that I didn't realize about it before...Have you performed any test with > any other service provider? > > Cheers, > > ------------------------------------------------ > Iv?n P?rraga Garc?a > Computer Scientist > Molecular Modelling & Bioinformatics Unit > INB - Instituto Nacional de Bioinform?tica > Josep Samitier 1-5 > 08028 Barcelona > Spain > tel.: +34 93 403 71 55 > fax.: +34 93 403 71 57 > e-mail: ivanp at mmb.pcb.ub.es > group page: http://mmb.pcb.ub.es > pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc > ------------------------------------------------ > > > > Martin Senger escribi?: > >>> I've suffered these problems in the past with Java XML... >>> >>> >> Yes, me too. And so far I always found that the problem was on the service >> side. As it is here (see below). Was this service generated by Moses? >> Because if yes then it is also my problem :-) >> >> The XML returned by the service in question is wrongly escaped. This is what >> is on -the-wire: >> >> ... >> <?xml version="1.0" >> encoding="UTF-8"?> >> <moby:MOBY xmlns:moby="http://www.biomoby.org/moby"> >> <moby:mobyContent> >> <moby:serviceNotes>&lt;moby:mobyException >> severity="2" &gt; >> ... >> >> The beginning is as it should be: <moby:MOBY... >> >> But the service notes are double-escaped - because the ampersand which is >> the part of the construct "<" is again escaped so we get wrongly " >> >&lt;moby:mobyException". And this is what the service sent over the >> network (I caught it using a TCP monitor, not the Dashboard or other tool >> that may already fiddle with the raw data). >> >> Regards, >> Martin >> >> >> >> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,464a2e0121086797816178! > > > > From martin.senger at gmail.com Tue May 15 18:17:49 2007 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 15 May 2007 23:17:49 +0100 Subject: [MOBY-dev] XML elements into serviceNote get scaped In-Reply-To: <464A2F3A.1080708@mmb.pcb.ub.es> References: <4649FE39.8070901@mmb.pcb.ub.es> <464A0C21.6070305@mmb.pcb.ub.es> <4d93f07c0705151447y4354b110g80a3ea0de2e620ae@mail.gmail.com> <464A2F3A.1080708@mmb.pcb.ub.es> Message-ID: <4d93f07c0705151517m256c7560le37265b41dfe9760@mail.gmail.com> > All my services are MoSeS generated. Okay, I will look at it. (But I have a timing problem, heading on Thursday for a meeting in Italy for couple of days; I will try my best to solve it before that.) Have you performed any test with > any other service provider? I did, but it is a long time ago. I have not touched jMoby recently. [ But I will do it now, and I will use this opportunity to fix the long-ago reported bug with the full format of the calendar day :-) ] Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ivanp at mmb.pcb.ub.es Tue May 15 19:09:11 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Wed, 16 May 2007 01:09:11 +0200 Subject: [MOBY-dev] XML elements into serviceNote get scaped In-Reply-To: <4d93f07c0705151517m256c7560le37265b41dfe9760@mail.gmail.com> References: <4649FE39.8070901@mmb.pcb.ub.es> <464A0C21.6070305@mmb.pcb.ub.es><4d93f07c0705151447y4354b110g80a3ea0de2e620 ae@mail.gmail.com><464A2F3A.1080708@mmb.pcb.ub.es> <4d93f07c0705151517m256c7560le37265b41dfe9760@mail.gmail.com> Message-ID: <464A3D97.1000303@mmb.pcb.ub.es> > > Okay, I will look at it. (But I have a timing problem, heading on Thursday > for a meeting in Italy for couple of days; I will try my best to solve it > before that.) Thanks and don't worry, I'll survive if it's not fixed in the next days :-P > to fix the long-ago > reported bug with the full format of the calendar day I had forgotten about it :-P Thanks! Cheers, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Martin Senger escribi?: >> All my services are MoSeS generated. >> > > > Okay, I will look at it. (But I have a timing problem, heading on Thursday > for a meeting in Italy for couple of days; I will try my best to solve it > before that.) > > Have you performed any test with > >> any other service provider? >> > > > I did, but it is a long time ago. I have not touched jMoby recently. [ But > I will do it now, and I will use this opportunity to fix the long-ago > reported bug with the full format of the calendar day :-) ] > > Cheers, > Martin > > From ivanp at mmb.pcb.ub.es Thu May 17 12:07:53 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Thu, 17 May 2007 18:07:53 +0200 Subject: [MOBY-dev] Conceptual doubt about datatypes representation in resquests/responses Message-ID: <464C7DD9.6080003@mmb.pcb.ub.es> Hi, I have a conceptual doubt and I've not been able to find an answer reviewing the documentation. Let's say that we have a datatype dat with three articleNames art1, art2, ar3 and a service whose return object is this datatype. In the response object, is mandatory that for the object dat to have the XML tags for all the article names even in any of them is empty? I mean this (imagine proper XML representation): anything1 --- anything1 Both of these representations are equivalent and valid? or only the first one? Thanks, -- ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ From gordonp at ucalgary.ca Thu May 17 12:13:37 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 17 May 2007 10:13:37 -0600 Subject: [MOBY-dev] Conceptual doubt about datatypes representation in resquests/responses In-Reply-To: <464C7DD9.6080003@mmb.pcb.ub.es> References: <464C7DD9.6080003@mmb.pcb.ub.es> Message-ID: <464C7F31.5070507@ucalgary.ca> Only the first one. Just like in an OO language, where every instance of an object has a "place" for a member, even if the value is null (or empty tag, in the case of MOBY). > Hi, > > I have a conceptual doubt and I've not been able to find an answer > reviewing the documentation. Let's say that we have a datatype dat with > three articleNames art1, art2, ar3 and a service whose return object is > this datatype. In the response object, is mandatory that for the object > dat to have the XML tags for all the article names even in any of them > is empty? > > I mean this (imagine proper XML representation): > > > > anything1 > > > > > > --- > > > > anything1 > > > > > Both of these representations are equivalent and valid? or only the > first one? > > Thanks, > > From ivanp at mmb.pcb.ub.es Thu May 17 12:23:35 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Thu, 17 May 2007 18:23:35 +0200 Subject: [MOBY-dev] Conceptual doubt about datatypes representation inresquests/responses In-Reply-To: <464C7F31.5070507@ucalgary.ca> References: <464C7DD9.6080003@mmb.pcb.ub.es> <464C7F31.5070507@ucalgary.ca> Message-ID: <464C8187.7070409@mmb.pcb.ub.es> Ok, that is what I thought. Then I'd like to suggest a little improvement in the Java MoSeS generated services: if an article name is not explicitly setted, it would be nice to obtain the datatype like it has to be; currently if you omit to set an attribute there is no XML tag for it in the response. Thanks, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Paul Gordon escribi?: > Only the first one. Just like in an OO language, where every instance > of an object has a "place" for a member, even if the value is null (or > empty tag, in the case of MOBY). > >> Hi, >> >> I have a conceptual doubt and I've not been able to find an answer >> reviewing the documentation. Let's say that we have a datatype dat with >> three articleNames art1, art2, ar3 and a service whose return object is >> this datatype. In the response object, is mandatory that for the object >> dat to have the XML tags for all the article names even in any of them >> is empty? >> >> I mean this (imagine proper XML representation): >> >> >> >> anything1 >> >> >> >> >> >> --- >> >> >> >> anything1 >> >> >> >> >> Both of these representations are equivalent and valid? or only the >> first one? >> >> Thanks, >> >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From ivanp at mmb.pcb.ub.es Fri May 18 06:39:42 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Fri, 18 May 2007 12:39:42 +0200 Subject: [MOBY-dev] hierarchy and castings in Moby Message-ID: <464D826E.1050608@mmb.pcb.ub.es> Hi, Another philosophical question about moby... Unfortunately moby does not support the concept of templates (in the C++ sense), so there is a no clear way to build container objects (let's say an array or a hash map, for example). A solution could be the concept of generics (like in Java prior to version 1.5), where you define a container as containing the most generic type of object in the hierarchy (the Object "class") and then the container can hold any kind of contents. Afterwards, if you want to emphasize what is the content of a container you can specialize by subclassing. Not sure if I explain myself, I mean something like this: The root container Map ../.. Object MapEntry Integer String String The content: MapEntry ../.. Object Object Object and then an specialized container: ResidueFloatMap ../.. . This is only a semantic inheritance]]> Map Because of inheritance, the ResidueFloatMap, will contain MapEntry objects, but the programmer (by convention) must guarantee if using this datatype that the contents of the MapEntry must be Residue and Float respectively. I think this should work because, obviously, any moby class inherits of the root Object, isn't it? Ok, my question is if this approach is right. I had the impression that it should be, but I'm having some parsing problems with the MoSeS - jMoby and I'm not sure if is because of this approach or it it is a bug. An additional question (I couldn't check it because of these previous problems): to have this solution working, I would need to perform casting conversion in the source of the services that receive an specialized container, something like this (excuse my pseudo-code): ResidueFloatMap map = ... Entry[] entries = map.getMoby_Entries(); Residue residue = ((Residue)(entries[0].getMoby_key())); Is this right/possible? If not, any way to do it? Thanks, -- ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ From martin.senger at gmail.com Fri May 18 08:26:29 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 18 May 2007 13:26:29 +0100 Subject: [MOBY-dev] Conceptual doubt about datatypes representation inresquests/responses In-Reply-To: <464C8187.7070409@mmb.pcb.ub.es> References: <464C7DD9.6080003@mmb.pcb.ub.es> <464C7F31.5070507@ucalgary.ca> <464C8187.7070409@mmb.pcb.ub.es> Message-ID: <4d93f07c0705180526r568651f7qb54d2a1905c418e4@mail.gmail.com> > Ok, that is what I thought. Then I'd like to suggest a little > improvement in the Java MoSeS generated services: if an article name is > not explicitly setted, it would be nice to obtain the datatype like it > has to be; currently if you omit to set an attribute there is no XML tag > for it in the response. That's because I have a different view that Paul expressed :-) When I was doing my research of the moby API documentation I concluded that no data means no data. Why should I send them at all? What are the pros and cons? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Fri May 18 08:36:18 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 18 May 2007 13:36:18 +0100 Subject: [MOBY-dev] hierarchy and castings in Moby In-Reply-To: <464D826E.1050608@mmb.pcb.ub.es> References: <464D826E.1050608@mmb.pcb.ub.es> Message-ID: <4d93f07c0705180536qc2c8a23ue5100ab05b40a1ea@mail.gmail.com> You are asking actually two questions (both related): 1) Is it possible to register a different type for an existing member article in an inherited data type? (Assuming that the new different type is a sub-class of the existing one). 2) Is it possible to send data where an article member is actually a subclass of the registered one. The latter question (2) was recently (last month) discussed between Mark, Eddie, Paul and me - and I believe most of us expressed willingness to change our parsers (including the MoSeS parser) to support it. But the decision to allow this kind of data will take place in the Vancouver meeting this June. I am not aware about any discussion of the former question (1). In order to do so would require changes in the moby registry I guess. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ivanp at mmb.pcb.ub.es Fri May 18 09:34:23 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Fri, 18 May 2007 15:34:23 +0200 Subject: [MOBY-dev] Conceptual doubt about datatypes representationinresquests/responses In-Reply-To: <4d93f07c0705180526r568651f7qb54d2a1905c418e4@mail.gmail.com> References: <464C7DD9.6080003@mmb.pcb.ub.es> <464C7F31.5070507@ucalgary.ca><464C8187.7070409@mmb.pcb.ub.es> <4d93f07c0705180526r568651f7qb54d2a1905c418e4@mail.gmail.com> Message-ID: <464DAB5F.2000702@mmb.pcb.ub.es> Hi, I prefer your approach Martin, although I saw some examples that made me think that the behavior stated by Paul was the expected one. Sincerely, I don't see the need to send no necessary data. At the end, an empty XML tag or a non-existent one will produce a "null" value, when trying to retrieve it, won't it? Furthermore, I have some of my services in mind with "HAS" relations and a big amount of instances related to a container and these instances have only relevant values for half of the attributes. This situation produces a big amount of unnecessary data transfer over the net... If I could vote, no doubt I would agree with Martin (I don't see exactly what is the advantage of the other approach). Cheers, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Martin Senger escribi?: >> Ok, that is what I thought. Then I'd like to suggest a little >> improvement in the Java MoSeS generated services: if an article name is >> not explicitly setted, it would be nice to obtain the datatype like it >> has to be; currently if you omit to set an attribute there is no XML tag >> for it in the response. >> > > > That's because I have a different view that Paul expressed :-) When I was > doing my research of the moby API documentation I concluded that no data > means no data. Why should I send them at all? What are the pros and cons? > > Martin > > > From ivanp at mmb.pcb.ub.es Fri May 18 09:42:41 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Fri, 18 May 2007 15:42:41 +0200 Subject: [MOBY-dev] hierarchy and castings in Moby In-Reply-To: <4d93f07c0705180536qc2c8a23ue5100ab05b40a1ea@mail.gmail.com> References: <464D826E.1050608@mmb.pcb.ub.es> <4d93f07c0705180536qc2c8a23ue5100ab05b40a1ea@mail.gmail.com> Message-ID: <464DAD51.4070804@mmb.pcb.ub.es> Yes, you caught exactly what I meant. To have feature 1 would be great because it would be a nice way to implement the concept of "template" or "generics", but as you say, perhaps it has more deep implications in the Moby architecture. However in my modest opinion, a way to handle generic datatypes should be addressed to allow versatile services. Before sending the e-mail I was assuming "2" to be right, but MobyParser in jMoby MoSeS didn't agree with me I think ;-) Thanks, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Martin Senger escribi?: > You are asking actually two questions (both related): > > 1) Is it possible to register a different type for an existing member > article in an inherited data type? (Assuming that the new different type is > a sub-class of the existing one). > > 2) Is it possible to send data where an article member is actually a > subclass of the registered one. > > The latter question (2) was recently (last month) discussed between Mark, > Eddie, Paul and me - and I believe most of us expressed willingness to > change our parsers (including the MoSeS parser) to support it. But the > decision to allow this kind of data will take place in the Vancouver meeting > this June. > > I am not aware about any discussion of the former question (1). In order to > do so would require changes in the moby registry I guess. > > Martin > > From markw at illuminae.com Fri May 18 10:36:23 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 18 May 2007 07:36:23 -0700 Subject: [MOBY-dev] hierarchy and castings in Moby In-Reply-To: <4d93f07c0705180536qc2c8a23ue5100ab05b40a1ea@mail.gmail.com> References: <464D826E.1050608@mmb.pcb.ub.es> <4d93f07c0705180536qc2c8a23ue5100ab05b40a1ea@mail.gmail.com> Message-ID: > 1) Is it possible to register a different type for an existing member > article in an inherited data type? (Assuming that the new different type > is a sub-class of the existing one). As Martin says, this would require changes to the API and registry > 2) Is it possible to send data where an article member is actually a > subclass of the registered one. Again, Martin is correct that there was an "inside conversation" a few weeks ago after we discovered that Paul's parser already supported this behaviour. Mine (CommonSubs.pm) does not, and Martin's doesn't either at the moment (I beleive?). However, it does make sense to support this, and I changed the wording of the Moby 1.0 manuscript to suggest that we would support this in the near future, so I suspect that we'll make the final decision at the June meeting. Once this is supported, it would make sense to think about what you suggest above... though we have then reinvented RDF/OWL :-) M From markw at illuminae.com Fri May 18 10:57:04 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 18 May 2007 07:57:04 -0700 Subject: [MOBY-dev] Conceptual doubt about datatypes representationinresquests/responses In-Reply-To: <464DAB5F.2000702@mmb.pcb.ub.es> References: <464C7DD9.6080003@mmb.pcb.ub.es> <464C7F31.5070507@ucalgary.ca> <464C8187.7070409@mmb.pcb.ub.es> <4d93f07c0705180526r568651f7qb54d2a1905c418e4@mail.gmail.com> <464DAB5F.2000702@mmb.pcb.ub.es> Message-ID: On Fri, 18 May 2007 06:34:23 -0700, Iv?n P?rraga Garc?a wrote: > I prefer your approach Martin, although I saw some examples that made me > think that the behavior stated by Paul was the expected one. I feel like we have had this discussion before, but I can't find any reference to it in the mailing list archives... My parser (CommonSubs.pm) assumes that all declared has/has-a components exist in the XML, and we explicitly state that this is the case in the 1.0 manuscript as one of the advantges that Moby has over RDF; however, the API docs don't clearly say one way or the other... So... At a minimum it needs more discussion... M From martin.senger at gmail.com Sun May 20 12:06:42 2007 From: martin.senger at gmail.com (Martin Senger) Date: Sun, 20 May 2007 17:06:42 +0100 Subject: [MOBY-dev] planned changes in how to build jMoby Message-ID: <4d93f07c0705200906y8f3e97fo921e46303f6fefd3@mail.gmail.com> Dear developers, Some times ago I indicated that I would like to start using Maven for jMoby dependencies - but not a full Maven, only its major features (dependencies mechanism and repositories of libraries), using Maven from the current Ant. The major difference for the jMoby user and developers will be that jMoby CVS package will not anymore include Ant itself. Which means that each developer has to install it separately on her machine. I wonder if this is acceptable for you. Are there any objections? The details about this Ant-Maven marriage can be found in one article ( http://pantheon.generationcp.org/UsingMaven.html) that I wrote for another project but I will make a similar article tailored for the jMoby before I commit changes. [At the moment of writing this email the link above is not accessible but it is only temporarily.] Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Sun May 20 20:57:05 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 21 May 2007 01:57:05 +0100 Subject: [MOBY-dev] Dashboard and date types In-Reply-To: <4614FCE8.70904@mmb.pcb.ub.es> References: <4614FCE8.70904@mmb.pcb.ub.es> Message-ID: <4d93f07c0705201757y656fd6danfe60fb26bd81193d@mail.gmail.com> I have fixed the bug reported by Ivan about the wrong format of date/time strings produced by jMoby classes. The format, indeed, did not conform with the http://www.w3.org/TR/NOTE-datetime standard as required by Biomoby API). But doing it I found some unanswered questions. Perhaps mainly for Paul, but because the bug was reported here, I am discussing it also here. The problem was caused mainly by the fact that the java class SimpleDateFormat (a class that is usually used for creating formatted strings from the Date objects) produces strings that are not compatible with the "http://www.w3.org/TR/NOTE-datetime" standard. Or, at least, I have not found a way how to do it (which is the first question: can it be done? how?). The lines: SimpleDateFormat sdf = new SimpleDateFormat (MobyDateTime.FULL_FORMAT); System.out.println (sdf.format (new Date())); produces "2007-05-21T00:40:35+0100" which does not comply with he mentioned standard (the result that complies should be: "2007-05-21T00:40:35+01:00"). But because of using SimpleDateFormat is otherwise very convenient, I have added a hack into MobyDateTime class that accepts even this non-standard format and converts it into a good one (by adding a colon separator). Here is the second question: is there a better place or way to replace this hack? Last, and actually the main question, is that I suspect a bug in the method MobyDataDateTime.getString(calendar). When I feed it with the calendar created from the string "2007-05-21T00:40:35+01:00" I will get a string "2007-05-21T02:40:35Z". The method removed timezone (and replaced it with a single Z letter, which is correct) but the time - that should be now in GMT - is now bigger by two hours when I expected decrease by one hour (moving from my BST time which is +01 to the GMT). Is this a bug or my misinterpretation of the times? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From jmfernandez at cnio.es Mon May 21 03:05:53 2007 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Mon, 21 May 2007 09:05:53 +0200 Subject: [MOBY-dev] Dashboard and date types In-Reply-To: <4d93f07c0705201757y656fd6danfe60fb26bd81193d@mail.gmail.com> References: <4614FCE8.70904@mmb.pcb.ub.es> <4d93f07c0705201757y656fd6danfe60fb26bd81193d@mail.gmail.com> Message-ID: <465144D1.7070706@cnio.es> Hi Martin, have you taken into account that daylight saving is currently in effect? GMT and UTC are not the same in that case, because most (if not all) GMT countries followed the daylight saving change. But it could be a Java bug, because the standard says that +01:00 is a shift from UTC. In that case, you could validate that behavior using alternate Date and Time clases from http://joda-time.sourceforge.net/. Best Regards, Jos? Mar?a Martin Senger wrote: > I have fixed the bug reported by Ivan about the wrong format of date/time > strings produced by jMoby classes. The format, indeed, did not conform with > the http://www.w3.org/TR/NOTE-datetime standard as required by Biomoby API). > > But doing it I found some unanswered questions. Perhaps mainly for Paul, but > because the bug was reported here, I am discussing it also here. > > The problem was caused mainly by the fact that the java class > SimpleDateFormat (a class that is usually used for creating formatted > strings from the Date objects) produces strings that are not compatible with > the "http://www.w3.org/TR/NOTE-datetime" standard. Or, at least, I have not > found a way how to do it (which is the first question: can it be done? > how?). The lines: > > SimpleDateFormat sdf = new SimpleDateFormat (MobyDateTime.FULL_FORMAT); > System.out.println (sdf.format (new Date())); > > produces "2007-05-21T00:40:35+0100" which does not comply with he mentioned > standard (the result that complies should be: "2007-05-21T00:40:35+01:00"). > > But because of using SimpleDateFormat is otherwise very convenient, I have > added a hack into MobyDateTime class that accepts even this non-standard > format and converts it into a good one (by adding a colon separator). Here > is the second question: is there a better place or way to replace this hack? > > Last, and actually the main question, is that I suspect a bug in the method > MobyDataDateTime.getString(calendar). When I feed it with the calendar > created from the string "2007-05-21T00:40:35+01:00" I will get a string > "2007-05-21T02:40:35Z". The method removed timezone (and replaced it with a > single Z letter, which is correct) but the time - that should be now in GMT > - is now bigger by two hours when I expected decrease by one hour (moving > from my BST time which is +01 to the GMT). Is this a bug or my > misinterpretation of the times? > > Cheers, > Martin > -- Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 2256) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Biolog?a Estructural y Bioinform?tica Structural Biology and Bioinformatics 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. 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From martin.senger at gmail.com Mon May 21 04:01:33 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 21 May 2007 09:01:33 +0100 Subject: [MOBY-dev] Dashboard and date types In-Reply-To: <465144D1.7070706@cnio.es> References: <4614FCE8.70904@mmb.pcb.ub.es> <4d93f07c0705201757y656fd6danfe60fb26bd81193d@mail.gmail.com> <465144D1.7070706@cnio.es> Message-ID: <4d93f07c0705210101q11e43c79g36abdc2986346e8c@mail.gmail.com> HI, have you taken into account that daylight saving is currently in effect? No, but I thought about it. Then I let the thinking to Paul (after all, I am using his method to convert a calendar to a string :-)). GMT > and UTC are not the same in that case Well, I always thought that GMT and UTC are the same, no matter what daylight saving time is used. And the wikipedia confirms that: For most practical and legal-trade purposes, the fractional difference > between UTC and UT (or GMT) is inconsequentially small, and for this reason > UTC is colloquially called GMT sometimes, even if this is not technically > correct. > But it could be a Java bug, because the standard says that +01:00 is a shift > from UTC. In that case, you could validate that behavior using alternate > Date > and Time clases from http://joda-time.sourceforge.net/. I would prefer to use standard Java functions. So far. I have not heard about any related java bug (there are some bugs regarding the three-letters abbreviations of time zones but it is not our case). Let's wait for Paul's opinion. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ivanp at mmb.pcb.ub.es Mon May 21 06:13:22 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Mon, 21 May 2007 12:13:22 +0200 Subject: [MOBY-dev] planned changes in how to build jMoby In-Reply-To: <4d93f07c0705200906y8f3e97fo921e46303f6fefd3@mail.gmail.com> References: <4d93f07c0705200906y8f3e97fo921e46303f6fefd3@mail.gmail.com> Message-ID: <465170C2.70501@mmb.pcb.ub.es> Hi, I have no previous experience in Maven but I think this could be a good moment to start. In my case there is no problem in externalizing ANT from jMoby. In my case, ANT is installed in my systems as a common tool for my own projects. My vote is positive. Cheers, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Martin Senger escribi?: > Dear developers, > > Some times ago I indicated that I would like to start using Maven for jMoby > dependencies - but not a full Maven, only its major features (dependencies > mechanism and repositories of libraries), using Maven from the current Ant. > The major difference for the jMoby user and developers will be that jMoby > CVS package will not anymore include Ant itself. Which means that each > developer has to install it separately on her machine. I wonder if this is > acceptable for you. Are there any objections? > > The details about this Ant-Maven marriage can be found in one article ( > http://pantheon.generationcp.org/UsingMaven.html) that I wrote for another > project but I will make a similar article tailored for the jMoby before I > commit changes. [At the moment of writing this email the link above is not > accessible but it is only temporarily.] > > Cheers, > Martin > > From martin.senger at gmail.com Sun May 27 15:28:32 2007 From: martin.senger at gmail.com (Martin Senger) Date: Sun, 27 May 2007 20:28:32 +0100 Subject: [MOBY-dev] an easy way to see the input/output size whenusingjMoby? In-Reply-To: <4626432F.5030109@mmb.pcb.ub.es> References: <462637AE.6080303@mmb.pcb.ub.es> <000901c781d1$6c61b880$6800a8c0@notebook> <4626432F.5030109@mmb.pcb.ub.es> Message-ID: <4d93f07c0705271228p23fbfebcy65efaf00e3bcc00c@mail.gmail.com> > However, the best would be to have a realistic size in bytes but it's > not a real need. To comply with the Ivan's request, I have added few new methods to the BaseService (the class that is used by all Moses-based services): * getHTTPHeaders() will allow the service to inspect what headers were used to deliver a request * getRequestLength() is only a convenient method extracting one particular header from the HTTP headers * getServletRequest() accessing all the richness of the servlet context. Together with already existing method getCallerAddr() you can, for example, have in your service the following code: log.info ("Request length: " + getRequestLength()); log.info ("Request from: " + getCallerAddr()); log.debug ("Request URL: " + getServletRequest().getRequestURL()); log.debug ("Request headers: " + getHTTPHeaders().toString()); In the src/samples, there is a new testing service (registered in the usual Central registry) TestServiceNotes that prints similar things in the service notes. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Sun May 27 19:34:47 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 28 May 2007 00:34:47 +0100 Subject: [MOBY-dev] looking for documentation on asynchronous service... Message-ID: <4d93f07c0705271634q26feff7bne54e1b21aba43ea6@mail.gmail.com> ...(the proposal we agreed on sometimes ago) - but the biomoby.org pages seem to be even more obfuscated that they were when I looked there the last time. Could anybody help me please? [And could anybody help to make the biomoby pages readable and useful? Well, this was a joke... We all know that it is next to impossible.] Thanks, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ivanp at mmb.pcb.ub.es Sun May 27 20:12:29 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Mon, 28 May 2007 02:12:29 +0200 Subject: [MOBY-dev] an easy way to see the input/output sizewhenusingjMoby? In-Reply-To: <4d93f07c0705271228p23fbfebcy65efaf00e3bcc00c@mail.gmail.com> References: <462637AE.6080303@mmb.pcb.ub.es><000901c781d1$6c61b880$6800a8c0@ notebook><4626432F.5030109@mmb.pcb.ub.es> <4d93f07c0705271228p23fbfebcy65efaf00e3bcc00c@mail.gmail.com> Message-ID: <465A1E6D.70902@mmb.pcb.ub.es> Thanks a lot for your help Martin. Tomorrow I'll change my logging system to use the new features. Cheers, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Martin Senger escribi?: >> However, the best would be to have a realistic size in bytes but it's >> not a real need. >> > > > To comply with the Ivan's request, I have added few new methods to the > BaseService (the class that is used by all Moses-based services): > > * getHTTPHeaders() will allow the service to inspect what headers were used > to deliver a request > > * getRequestLength() is only a convenient method extracting one particular > header from the HTTP headers > > * getServletRequest() accessing all the richness of the servlet context. > > Together with already existing method getCallerAddr() you can, for example, > have in your service the following code: > > log.info ("Request length: " + getRequestLength()); > log.info ("Request from: " + getCallerAddr()); > log.debug ("Request URL: " + getServletRequest().getRequestURL()); > log.debug ("Request headers: " + getHTTPHeaders().toString()); > > In the src/samples, there is a new testing service (registered in the usual > Central registry) TestServiceNotes that prints similar things in the service > notes. > > Cheers, > Martin > > From johan at ac.uma.es Mon May 28 03:12:16 2007 From: johan at ac.uma.es (Johan Karlsson) Date: Mon, 28 May 2007 09:12:16 +0200 Subject: [MOBY-dev] looking for documentation on asynchronous service... In-Reply-To: <4d93f07c0705271634q26feff7bne54e1b21aba43ea6@mail.gmail.com> References: <4d93f07c0705271634q26feff7bne54e1b21aba43ea6@mail.gmail.com> Message-ID: <465A80D0.7080602@ac.uma.es> Hi Martin (and others), Here is a link to the pdf of the accepted proposal. http://chirimoyo.ac.uma.es/asynchronysm/BioMOBY_Asynchronous_Service_Call_Proposal_WSRF_v2.3.pdf Kind regards, Johan Martin Senger wrote: > ...(the proposal we agreed on sometimes ago) - but the biomoby.org pages > seem to be even more obfuscated that they were when I looked there the last > time. Could anybody help me please? > > [And could anybody help to make the biomoby pages readable and useful? Well, > this was a joke... We all know that it is next to impossible.] > > Thanks, > Martin > > -- Johan Karlsson 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 From ivanp at mmb.pcb.ub.es Mon May 28 06:36:55 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Mon, 28 May 2007 12:36:55 +0200 Subject: [MOBY-dev] java.lang.NoSuchMethodError launched when MobyException raised Message-ID: <465AB0C7.2070905@mmb.pcb.ub.es> Hi, Is it possible that the return value of the method ServiceException.toXML() has changed from String to Node (or any other XML representation) and this has not been taking into account in some other parts of jMoby? Perhaps I'm doing something bad, but when I invoke a service with an incorrect ouput instead of the proper MobyException (or any other situtation which provokes the raise of a MobyException) a Java exception is launched. Here it is an example error stack: {http://xml.apache.org/axis/}stackTrace: java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.jboss.webservice.server.InvokerProviderJSE.invokeServiceEndpoint(InvokerProviderJSE.java:154) at org.jboss.webservice.server.InvokerProvider.invokeMethod(InvokerProvider.java:305) at org.jboss.axis.providers.java.RPCProvider.invokeTarget(RPCProvider.java:176) at org.jboss.webservice.server.InvokerProviderJSE.invokeTarget(InvokerProviderJSE.java:93) at org.jboss.axis.providers.java.RPCProvider.processMessage(RPCProvider.java:121) at org.jboss.axis.providers.java.JavaProvider.invoke(JavaProvider.java:358) at org.jboss.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:73) at org.jboss.axis.SimpleChain.doVisiting(SimpleChain.java:160) at org.jboss.axis.SimpleChain.invoke(SimpleChain.java:123) at org.jboss.axis.handlers.soap.SOAPService.invoke(SOAPService.java:560) at org.jboss.webservice.server.ServerEngine.invokeInternal(ServerEngine.java:200) at org.jboss.webservice.server.ServerEngine.invoke(ServerEngine.java:89) at org.jboss.axis.transport.http.AxisServlet.doPost(AxisServlet.java:911) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.jboss.axis.transport.http.AxisServletBase.service(AxisServletBase.java:370) at javax.servlet.http.HttpServlet.service(HttpServlet.java:810) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) at org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.java:81) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178) at org.jboss.web.tomcat.security.CustomPrincipalValve.invoke(CustomPrincipalValve.java:39) at org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssociationValve.java:159) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:407) at org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java:59) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:856) at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processConnection(Http11Protocol.java:744) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527) at org.apache.tomcat.util.net.MasterSlaveWorkerThread.run(MasterSlaveWorkerThread.java:112) at java.lang.Thread.run(Thread.java:619) Caused by: java.lang.NoSuchMethodError: org.biomoby.shared.parser.ServiceException.toXML()Ljava/lang/String; at org.biomoby.shared.parser.MobyPackage.toXMLDocument(MobyPackage.java:235) at org.biomoby.shared.parser.MobyPackage.toXML(MobyPackage.java:213) at org.biomoby.service.BaseService.error(BaseService.java:330) at org.mmb.moby.webservice.plotFeatureAASequence.plotFeatureAASequenceSkel.plotFeatureAASequence(plotFeatureAASequenceSkel.java:72) ... 40 more Obviously I've recreated and deployed the jmoby.jar. Should I regenerate skeletons? I imagine (and hope) not. Regards, Iv?n From ivanp at mmb.pcb.ub.es Mon May 28 06:52:14 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Mon, 28 May 2007 12:52:14 +0200 Subject: [MOBY-dev] java.lang.NoSuchMethodError launched when MobyExceptionraised In-Reply-To: <465AB0C7.2070905@mmb.pcb.ub.es> References: <465AB0C7.2070905@mmb.pcb.ub.es> Message-ID: <465AB45E.5010504@mmb.pcb.ub.es> I meant: "... Perhaps I'm doing something bad, but when I invoke a service with an incorrect input, instead of the proper MobyException ..." instead of "... Perhaps I'm doing something bad, but when I invoke a service with an incorrect ouput instead of the proper MobyException..." Sorry, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Iv?n P?rraga Garc?a escribi?: > Hi, > > Is it possible that the return value of the method > ServiceException.toXML() has changed from String to Node (or any other > XML representation) and this has not been taking into account in some > other parts of jMoby? > > Perhaps I'm doing something bad, but when I invoke a service with an > incorrect ouput instead of the proper MobyException (or any other > situtation which provokes the raise of a MobyException) a Java exception > is launched. Here it is an example error stack: > > {http://xml.apache.org/axis/}stackTrace: > java.lang.reflect.InvocationTargetException > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > at java.lang.reflect.Method.invoke(Method.java:597) > at > org.jboss.webservice.server.InvokerProviderJSE.invokeServiceEndpoint(InvokerProviderJSE.java:154) > at > org.jboss.webservice.server.InvokerProvider.invokeMethod(InvokerProvider.java:305) > at > org.jboss.axis.providers.java.RPCProvider.invokeTarget(RPCProvider.java:176) > at > org.jboss.webservice.server.InvokerProviderJSE.invokeTarget(InvokerProviderJSE.java:93) > at > org.jboss.axis.providers.java.RPCProvider.processMessage(RPCProvider.java:121) > at > org.jboss.axis.providers.java.JavaProvider.invoke(JavaProvider.java:358) > at > org.jboss.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:73) > at org.jboss.axis.SimpleChain.doVisiting(SimpleChain.java:160) > at org.jboss.axis.SimpleChain.invoke(SimpleChain.java:123) > at org.jboss.axis.handlers.soap.SOAPService.invoke(SOAPService.java:560) > at > org.jboss.webservice.server.ServerEngine.invokeInternal(ServerEngine.java:200) > at org.jboss.webservice.server.ServerEngine.invoke(ServerEngine.java:89) > at > org.jboss.axis.transport.http.AxisServlet.doPost(AxisServlet.java:911) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) > at > org.jboss.axis.transport.http.AxisServletBase.service(AxisServletBase.java:370) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:810) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) > at > org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.java:81) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) > at > org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) > at > org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178) > at > org.jboss.web.tomcat.security.CustomPrincipalValve.invoke(CustomPrincipalValve.java:39) > at > org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssociationValve.java:159) > at > org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:407) > at > org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java:59) > at > org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126) > at > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105) > at > org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107) > at > org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148) > at > org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:856) > at > org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processConnection(Http11Protocol.java:744) > at > org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527) > at > org.apache.tomcat.util.net.MasterSlaveWorkerThread.run(MasterSlaveWorkerThread.java:112) > at java.lang.Thread.run(Thread.java:619) > Caused by: java.lang.NoSuchMethodError: > org.biomoby.shared.parser.ServiceException.toXML()Ljava/lang/String; > at > org.biomoby.shared.parser.MobyPackage.toXMLDocument(MobyPackage.java:235) > at org.biomoby.shared.parser.MobyPackage.toXML(MobyPackage.java:213) > at org.biomoby.service.BaseService.error(BaseService.java:330) > at > org.mmb.moby.webservice.plotFeatureAASequence.plotFeatureAASequenceSkel.plotFeatureAASequence(plotFeatureAASequenceSkel.java:72) > ... 40 more > > > Obviously I've recreated and deployed the jmoby.jar. Should I regenerate > skeletons? I imagine (and hope) not. > > Regards, > > Iv?n > _______________________________________________ > 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 Mon May 28 06:58:17 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 28 May 2007 11:58:17 +0100 Subject: [MOBY-dev] java.lang.NoSuchMethodError launched when MobyExceptionraised In-Reply-To: <465AB45E.5010504@mmb.pcb.ub.es> References: <465AB0C7.2070905@mmb.pcb.ub.es> <465AB45E.5010504@mmb.pcb.ub.es> Message-ID: <4d93f07c0705280358j5416408eyd5b6dc11df50e45f@mail.gmail.com> I am looking at it just now... Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Mon May 28 07:18:56 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 28 May 2007 12:18:56 +0100 Subject: [MOBY-dev] java.lang.NoSuchMethodError launched when MobyException raised In-Reply-To: <465AB0C7.2070905@mmb.pcb.ub.es> References: <465AB0C7.2070905@mmb.pcb.ub.es> Message-ID: <4d93f07c0705280418q4b22ebf2r8f37fef34e23f2a2@mail.gmail.com> Hi Ivan, Is it possible that the return value of the method > ServiceException.toXML() has changed from String to Node (or any other > XML representation) It is not only possible but it is a fact :-). You may recall a private message about it (to you and to Paul), from the last week. Simply speaking, the method signature is back where it was before Paul changed it sometimes ago. and this has not been taking into account in some > other parts of jMoby? I did my best to check this. Did I forgot anything? However, just now I have tried again, and I could not reproduce the behaviour you are reporting. I have raised a MobyException in the sample TestServiceNotes service (which is part of the jMoby), in the processIt() method, and I have got a reasonable output, without any Java exception: 700 Input date was 2007-05-20T10:54:59Z 600 AN ERROR OCCURED DURING THE SERVICE EXECUTION: Yes, this is bad... ... Obviously I've recreated and deployed the jmoby.jar. Should I regenerate > skeletons? I imagine (and hope) not. > No, that would not be necessary. But you need to restart your server I guess (or whatever is needed in JBoss to make it reload all classes. I am not sure how to continue now, how to help you (because definitely the cause of your troubles is in the change of jMoby, but at the moment I believe that the change itself was fixed correctly...). Any idea? Oh, now I think what may be the problem. You said that you "recreated jmoby.jar". But perhaps you have not clean the old classes first. Which would cause the problem. Please do: ./build-devsh clean compile ...and then create jmoby.jar and redeploy. It should fix it. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ivanp at mmb.pcb.ub.es Mon May 28 09:11:08 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Mon, 28 May 2007 15:11:08 +0200 Subject: [MOBY-dev] java.lang.NoSuchMethodError launched whenMobyException raised In-Reply-To: <4d93f07c0705280418q4b22ebf2r8f37fef34e23f2a2@mail.gmail.com> References: <465AB0C7.2070905@mmb.pcb.ub.es> <4d93f07c0705280418q4b22ebf2r8f37fef34e23f2a2@mail.gmail.com> Message-ID: <465AD4EC.9080902@mmb.pcb.ub.es> Thanks Martin, you were right. Sorry, for this newbie mistake, but I'm very used to my own build.xml's which check for these things and recompile if necessary before packing. Thanks for your help, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Martin Senger escribi?: > Hi Ivan, > > Is it possible that the return value of the method > >> ServiceException.toXML() has changed from String to Node (or any other >> XML representation) >> > > > It is not only possible but it is a fact :-). You may recall a private > message about it (to you and to Paul), from the last week. Simply speaking, > the method signature is back where it was before Paul changed it sometimes > ago. > > and this has not been taking into account in some > >> other parts of jMoby? >> > > > I did my best to check this. Did I forgot anything? However, just now I have > tried again, and I could not reproduce the behaviour you are reporting. I > have raised a MobyException in the sample TestServiceNotes service (which is > part of the jMoby), in the processIt() method, and I have got a reasonable > output, without any Java exception: > > > > > > moby:refQueryID="sip_1_"> > 700 > Input date was > 2007-05-20T10:54:59Z > > > 600 > AN ERROR OCCURED DURING THE SERVICE > EXECUTION: Yes, this is bad... > > ... > > Obviously I've recreated and deployed the jmoby.jar. Should I regenerate > >> skeletons? I imagine (and hope) not. >> >> > > No, that would not be necessary. But you need to restart your server I guess > (or whatever is needed in JBoss to make it reload all classes. > > I am not sure how to continue now, how to help you (because definitely the > cause of your troubles is in the change of jMoby, but at the moment I > believe that the change itself was fixed correctly...). Any idea? > > Oh, now I think what may be the problem. You said that you "recreated > jmoby.jar". But perhaps you have not clean the old classes first. Which > would cause the problem. Please do: > > ./build-devsh clean compile > > ...and then create jmoby.jar and redeploy. It should fix it. > > Martin > > From martin.senger at gmail.com Mon May 28 09:23:16 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 28 May 2007 14:23:16 +0100 Subject: [MOBY-dev] java.lang.NoSuchMethodError launched whenMobyException raised In-Reply-To: <465AD4EC.9080902@mmb.pcb.ub.es> References: <465AB0C7.2070905@mmb.pcb.ub.es> <4d93f07c0705280418q4b22ebf2r8f37fef34e23f2a2@mail.gmail.com> <465AD4EC.9080902@mmb.pcb.ub.es> Message-ID: <4d93f07c0705280623p78d02a1er83c74cb0288d3b1a@mail.gmail.com> > Sorry, for this newbie mistake C'mon... you are definitely not a newbie, and I do not think that you made any mistake. Does it mean that your services are now working? If so I am glad and I hope that I have not caused you too much of disturbance. but I'm very used to my own build.xml's > which check for these things and recompile if necessary before packing I do not know about such build.xml :-) Such build.xml would need to check all the internal Java classes dependencies to find that a class whose source code has not been changed should be recompiled because a source code of a class used by that class was changed. I am not aware of such feature in Ant - but if it exists I would be glad to add it there. Please tell us. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ivanp at mmb.pcb.ub.es Mon May 28 09:42:31 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Mon, 28 May 2007 15:42:31 +0200 Subject: [MOBY-dev] java.lang.NoSuchMethodError launchedwhenMobyException raised In-Reply-To: <4d93f07c0705280623p78d02a1er83c74cb0288d3b1a@mail.gmail.com> References: <465AB0C7.2070905@mmb.pcb.ub.es><4d93f07c0705280418q4b22ebf2r8f3 7fef34e23f2a2@mail.gmail.com><465AD4EC.9080902@mmb.pcb.ub.es> <4d93f07c0705280623p78d02a1er83c74cb0288d3b1a@mail.gmail.com> Message-ID: <465ADC47.8000109@mmb.pcb.ub.es> :-D Yes, you're right, this feature does not exist as long as I know. Obviously I wrote the e-mail without thinking very deeply what I was saying. In my head your class was calling directly this method which signature had been changed and so it had to have been changed also. I couldn't understand why a class whose source had been changed, was not being recompiled by ANT (but in fact, as you say, its was unchanged). By the way, my services working again, yes ;-) Thanks, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Martin Senger escribi?: >> Sorry, for this newbie mistake >> > > > C'mon... you are definitely not a newbie, and I do not think that you made > any mistake. Does it mean that your services are now working? If so I am > glad and I hope that I have not caused you too much of disturbance. > > but I'm very used to my own build.xml's > >> which check for these things and recompile if necessary before packing >> > > > I do not know about such build.xml :-) Such build.xml would need to check > all the internal Java classes dependencies to find that a class whose source > code has not been changed should be recompiled because a source code of a > class used by that class was changed. I am not aware of such feature in Ant > - but if it exists I would be glad to add it there. Please tell us. > > Cheers, > Martin > > From gordonp at ucalgary.ca Mon May 28 10:54:45 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 28 May 2007 08:54:45 -0600 Subject: [MOBY-dev] Dashboard and date types In-Reply-To: <4d93f07c0705210101q11e43c79g36abdc2986346e8c@mail.gmail.com> References: <4614FCE8.70904@mmb.pcb.ub.es> <4d93f07c0705201757y656fd6danfe60fb26bd81193d@mail.gmail.com> <465144D1.7070706@cnio.es> <4d93f07c0705210101q11e43c79g36abdc2986346e8c@mail.gmail.com> Message-ID: <465AED35.6010600@ucalgary.ca> The ISO8601 parsing code is pretty much ripped directly from a W3C library (and attributed in the comments), so I left the thinking to someone else too. :-) I'll have a look at this timezone issue in the next couple of days though. > HI, > > have you taken into account that daylight saving is currently in effect? > > > No, but I thought about it. Then I let the thinking to Paul (after all, I am > using his method to convert a calendar to a string :-)). > > GMT > From martin.senger at gmail.com Mon May 28 11:35:45 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 28 May 2007 16:35:45 +0100 Subject: [MOBY-dev] Dashboard and date types In-Reply-To: <465AED35.6010600@ucalgary.ca> References: <4614FCE8.70904@mmb.pcb.ub.es> <4d93f07c0705201757y656fd6danfe60fb26bd81193d@mail.gmail.com> <465144D1.7070706@cnio.es> <4d93f07c0705210101q11e43c79g36abdc2986346e8c@mail.gmail.com> <465AED35.6010600@ucalgary.ca> Message-ID: <4d93f07c0705280835l4e03bb4et1ab19b012ab20e3a@mail.gmail.com> > The ISO8601 parsing code is pretty much ripped directly from a W3C > library (and attributed in the comments), so I left the thinking to > someone else too. :-) > > I'll have a look at this timezone issue in the next couple of days though. Okay, glad to hear it. For me (us), it does not matter much that the method was ripped from someone else's code, the important is whether it is correct or not. Thanks for looking into it. This is just a reminder of my observations regarding this method: Last, and actually the main question, is that I suspect a bug in the method > MobyDataDateTime.getString(calendar). When I feed it with the calendar > created from the string "2007-05-21T00:40:35+01:00" I will get a string > "2007-05-21T02:40:35Z". The method removed timezone (and replaced it with a > single Z letter, which is correct) but the time - that should be now in GMT > - is now bigger by two hours when I expected decrease by one hour (moving > from my BST time which is +01 to the GMT). Is this a bug or my > misinterpretation of the times? > Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Mon May 28 17:22:56 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 28 May 2007 22:22:56 +0100 Subject: [MOBY-dev] looking for a functioning asynchronous service... Message-ID: <4d93f07c0705281422g5c195438tddb885de14d9fa2@mail.gmail.com> ...preferable one that does not take too long to finish. Any help here? If yes please let me know also some good input data for it. Many thanks. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Mon May 28 23:56:11 2007 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 29 May 2007 04:56:11 +0100 Subject: [MOBY-dev] few fixes in jMoby Message-ID: <4d93f07c0705282056lb746cc8t9de9d3a24d9bfd52@mail.gmail.com> Few fixes dealing with the fact that we do not have anymore just services with 'moby' category but also with 'moby-async' category. Until now (before this fix), the latter ones were not included in search results - not even in the Dashboard browser. Cheers, Martin ChangeLog -------------- 2007-05-29 Martin Senger * Fixed: on various place where a service was looking for, the used service pattern has now category empty (so not only services with the default 'moby' category are found). * Changed: the output list with names of found services (created by MobyCmdLineClient) contains now also service authority. * Added: MobyCmdLineClient has a new option -fc for finding services by category. -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Tue May 29 17:45:16 2007 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 29 May 2007 22:45:16 +0100 Subject: [MOBY-dev] is anything wrong with asynchrounous services? Message-ID: <4d93f07c0705291445l31af2064y60fd60981d3027ea@mail.gmail.com> I have just spent a day trying to implement the asynchronous services spec in jMoby. Thanks to an immediate help from Natalia, Johan, Romina, Ivan a probably others, I was able to call an asynchronous service and make some progress. The progress stopped, however, soon, and I am now wondering where is the problem. It can be in the asynchronous specification itself, or in the implementation of a service I was trying to call, or in my lack of knowledge of web services protocols. Please help me clarify the situation. The problem starts immediately at the beginning, with the first response, so we do not need to go and dive into the SOAP headers. Just as the spec says, the first step is that a client sends a request (submit) to an asynchronous service: "This message is identical to the BioMOBY XML to request synchronous service > execution. The only difference is that > the client sends the request to the servicename_submit SOAP method." > This went fine, in my case. The second step is that the service responds with a body that contains a WS-Addressing-based EndpointReference. The service I was using, indeed, did so. The problem is not with the contents of such response, but with its format (well, now I am already expressing my opinions, which I should not do...). It looks like this: http://inb.bsc.es/cgi-bin/mobyServices/asyncDispatcher.cgi 5627142941072148070044 The above is exactly what the biomoby spec for async. services says it should be. That's why I do not think that the problem is in the implementation. I believe that it is either in the spec or in my understanding (or better the lack of understanding). What I see is that this is not an RPC/Encoded response. This looks more like a document/literal response. And, indeed, the Axis toolkit I am using, refuses to parse such message complaining that there are some unexpected children elements. And it is true: in the RPC/Encoded style, the contents of the tag (or its child, I am not sure) should be a string without any (visible, not-encoded) XML. Like in any normal Biomoby response. Shortly, this response should look, XML-encoding-wise, like any other Biomoby response. Which it does not I think. So where is the problem? It is just me who do not fully understand the difference between RPC/Encoded and document/literal style? Even if so, I wonder if anybody can "convince" Axis to send a request as RPC/encoded (as the spec requires) and receive a response as document/literal. You may ask why this does not matter in the Eddie's AsyncClient? As I see it it is because Eddie creates there everything manually, so he is allowed to send a request one style and parse the response in another style. Which I feel is not a right way to do. Of course, I said already several times that I will be glad if someone explains that I see it in a wrong way. I really appreciate any answers, especially please soon answers - because the next weekend there is a small meeting of Java biomoby developers in Vancouver and we may discuss this issue there if we have some background explanations and opinions from you. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Tue May 29 19:59:06 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 29 May 2007 17:59:06 -0600 Subject: [MOBY-dev] Dashboard and date types In-Reply-To: <4d93f07c0705280835l4e03bb4et1ab19b012ab20e3a@mail.gmail.com> References: <4614FCE8.70904@mmb.pcb.ub.es> <4d93f07c0705201757y656fd6danfe60fb26bd81193d@mail.gmail.com> <465144D1.7070706@cnio.es> <4d93f07c0705210101q11e43c79g36abdc2986346e8c@mail.gmail.com> <465AED35.6010600@ucalgary.ca> <4d93f07c0705280835l4e03bb4et1ab19b012ab20e3a@mail.gmail.com> Message-ID: <465CBE4A.5020308@ucalgary.ca> After going crazy for hours trying to get SimpleDateFormat to work properly, I rolled my own formatter. I also now keep the timezone offset data, rather than converting to Zulu time (a.k.a. GMT). I have added some test cases too, so it definitely works for samples from Central European times (daylight and standard), Halifax (Canada) standard, and Newfoundland (which uses a half-hour zone). One minor point: "2007-05-21T00:40:35+01:00" is the time in London (i.e. ISO8601 does not store daylight data, so time zones flip offsets in autumn and spring relative to GMT) This should now be Case Closed! >> The ISO8601 parsing code is pretty much ripped directly from a W3C >> library (and attributed in the comments), so I left the thinking to >> someone else too. :-) >> >> I'll have a look at this timezone issue in the next couple of days though. >> > > > Okay, glad to hear it. For me (us), it does not matter much that the method > was ripped from someone else's code, the important is whether it is correct > or not. Thanks for looking into it. This is just a reminder of my > observations regarding this method: > > Last, and actually the main question, is that I suspect a bug in the method > >> MobyDataDateTime.getString(calendar). When I feed it with the calendar >> created from the string "2007-05-21T00:40:35+01:00" I will get a string >> "2007-05-21T02:40:35Z". The method removed timezone (and replaced it with a >> single Z letter, which is correct) but the time - that should be now in GMT >> - is now bigger by two hours when I expected decrease by one hour (moving >> from my BST time which is +01 to the GMT). Is this a bug or my >> misinterpretation of the times? >> >> > > Cheers, > Martin > > > From L.Barboza at cgiar.org Wed May 30 23:12:32 2007 From: L.Barboza at cgiar.org (Barboza, Lord Hendrix (IRRI)) Date: Thu, 31 May 2007 11:12:32 +0800 Subject: [MOBY-dev] help: local registry installation Message-ID: I have already got and installed the biomoby code in the server. Then running the "make test" give me this result: PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Central.....................ok t/Client-Central..............ok 22/0:7: parser error : Sequence ']]>' not allowed in content ]]>]]> ^ :7: parser error : internal error ]]>]]> ^ :7: parser error : Extra content at the end of the document ]]>]]> ^ at /usr/local/moby-live/Perl/blib/lib/MOBY/Client/Central.pm line 2107 t/Client-Central..............ok 23/0# Looks like your test died just after 23. t/Client-Central..............dubious Test returned status 255 (wstat 65280, 0xff00) after all the subtests completed successfully t/Client-CollectionArticle....ok t/Client-OntologyServer.......ok t/Client-Registration.........ok t/Client-SecondaryArticle.....ok t/Client-Service..............ok 2/0:7: parser error : Sequence ']]>' not allowed in content ]]>]]> ^ :7: parser error : internal error ]]>]]> ^ :7: parser error : Extra content at the end of the document ]]>]]> ^ at /usr/local/moby-live/Perl/blib/lib/MOBY/Client/Central.pm line 2107 # Looks like your test died just after 2. t/Client-Service..............dubious Test returned status 255 (wstat 65280, 0xff00) after all the subtests completed successfully t/Client-ServiceInstance......ok t/Client-SimpleArticle........ok t/CommonSubs..................ok t/Config......................skipped all skipped: Required only when you have your own local MOBY Central t/CrossReference..............ok t/Template....................ok Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------ ------- t/Client-Central.t 255 65280 23 0 0.00% ?? t/Client-Service.t 255 65280 2 0 0.00% ?? 1 test skipped. Failed 2/13 test scripts, 84.62% okay. 0/235 subtests failed, 100.00% okay. make: *** [test_dynamic] Error 255 lbarboza at cropwiki:/usr/local/moby-live/Perl$ -bash: syntax error near unexpected token `newline' I am using perl v5.8.4. pls help thanks Lord Hendrix A. Barbozax` Programmer - Web Services Crop Research Informatics Laboratory (CRIL) From maliha.aziz at asu.edu Thu May 31 03:15:28 2007 From: maliha.aziz at asu.edu (Maliha Aziz) Date: Thu, 31 May 2007 00:15:28 -0700 Subject: [MOBY-dev] dashboard error ! Message-ID: hi does anyone know why dashboard is giving me the following error as soon as it builds and the main screen comes up and it tires to populate its lists of services , datatypes etc the following is the text displayed on the screen ( window) An error happened when accessing a list of available services Check please values in text fields( in Registry Browser) specifying registry endpoint and namespace , and in the one specifying directory used as local cache. Then right-click in the data types area and select 'Reload'. the actual error is http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.plnull From martin.senger at gmail.com Thu May 31 12:15:18 2007 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 31 May 2007 17:15:18 +0100 Subject: [MOBY-dev] dashboard error ! In-Reply-To: References: Message-ID: <4d93f07c0705310915t44a66786yde17f3ceb61eb236@mail.gmail.com> > An error happened when accessing a list of available services > Check please values in text fields( in Registry Browser) specifying > registry > endpoint and namespace , and in the one specifying directory used as local > cache. So what are those values in your case? I am attaching (as an image) what I see in my dashboard. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger -------------- next part -------------- A non-text attachment was scrubbed... Name: browser-screen.png Type: image/png Size: 9221 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/moby-dev/attachments/20070531/3503ce67/attachment.png From markw at illuminae.com Thu May 31 12:06:16 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 31 May 2007 09:06:16 -0700 Subject: [MOBY-dev] help: local registry installation In-Reply-To: References: Message-ID: Never seen that error before... perhaps check that your LibXML C libraries are up-to-date? They are used by the XML::LibXML module that Moby uses for XML parsing. M On Wed, 30 May 2007 20:12:32 -0700, Barboza, Lord Hendrix (IRRI) wrote: > I have already got and installed the biomoby code in the server. Then > running the "make test" give me this result: > > > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > > t/Central.....................ok > > > t/Client-Central..............ok 22/0:7: parser error : Sequence ']]>' > not allowed in content > > ]]>]]> > > ^ > > :7: parser error : internal error > > ]]>]]> > > ^ > > :7: parser error : Extra content at the end of the document > > ]]>]]> > > ^ > > at /usr/local/moby-live/Perl/blib/lib/MOBY/Client/Central.pm line 2107 > > t/Client-Central..............ok 23/0# Looks like your test died just > after 23. > > t/Client-Central..............dubious > > > Test returned status 255 (wstat 65280, 0xff00) > > after all the subtests completed successfully > > t/Client-CollectionArticle....ok > > > t/Client-OntologyServer.......ok > > > t/Client-Registration.........ok > > > t/Client-SecondaryArticle.....ok > > > t/Client-Service..............ok 2/0:7: parser error : Sequence ']]>' > not allowed in content > > ]]>]]> > > ^ > > :7: parser error : internal error > > ]]>]]> > > ^ > > :7: parser error : Extra content at the end of the document > > ]]>]]> > > ^ > > at /usr/local/moby-live/Perl/blib/lib/MOBY/Client/Central.pm line 2107 > > # Looks like your test died just after 2. > > t/Client-Service..............dubious > > > Test returned status 255 (wstat 65280, 0xff00) > > after all the subtests completed successfully > > t/Client-ServiceInstance......ok > > > t/Client-SimpleArticle........ok > > > t/CommonSubs..................ok > > > t/Config......................skipped > > all skipped: Required only when you have your own local MOBY > Central > > t/CrossReference..............ok > > > t/Template....................ok > > > Failed Test Stat Wstat Total Fail Failed List of Failed > > ------------------------------------------------------------------------ > ------- > > t/Client-Central.t 255 65280 23 0 0.00% ?? > > t/Client-Service.t 255 65280 2 0 0.00% ?? > > 1 test skipped. > > Failed 2/13 test scripts, 84.62% okay. 0/235 subtests failed, 100.00% > okay. > > make: *** [test_dynamic] Error 255 > > lbarboza at cropwiki:/usr/local/moby-live/Perl$ > > -bash: syntax error near unexpected token `newline' > > > > I am using perl v5.8.4. pls help > > > thanks > > > Lord Hendrix A. Barbozax` > > Programmer - Web Services > > Crop Research Informatics Laboratory (CRIL) > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From Pieter.Neerincx at wur.nl Thu May 31 15:01:29 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 31 May 2007 21:01:29 +0200 Subject: [MOBY-dev] help: local registry installation In-Reply-To: References: Message-ID: Hi, I also didn't see this specific case before, but it looks like a double encoded CDATA section. We've had problems with double encoded stuff before due to the way some versions of SOAP::Lite were handling encoding/decoding. If you are running SOAP::Lite < 0.69 please upgrade to 0.69. If you are running something more recent please let us know. Might be a new S::L peculiarity in that case... Cheers, Pi On 31 May 2007, at 18:06, Mark Wilkinson wrote: > Never seen that error before... > > perhaps check that your LibXML C libraries are up-to-date? They > are used > by the XML::LibXML module that Moby uses for XML parsing. > > M > > > > On Wed, 30 May 2007 20:12:32 -0700, Barboza, Lord Hendrix (IRRI) > wrote: > >> I have already got and installed the biomoby code in the server. Then >> running the "make test" give me this result: >> >> >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >> >> t/Central.....................ok >> >> >> t/Client-Central..............ok 22/0:7: parser error : Sequence >> ']]>' >> not allowed in content >> >> ]]>]]> >> >> ^ >> >> :7: parser error : internal error >> >> ]]>]]> >> >> ^ >> >> :7: parser error : Extra content at the end of the document >> >> ]]>]]> >> >> ^ >> >> at /usr/local/moby-live/Perl/blib/lib/MOBY/Client/Central.pm line >> 2107 >> >> t/Client-Central..............ok 23/0# Looks like your test died just >> after 23. >> >> t/Client-Central..............dubious >> >> >> Test returned status 255 (wstat 65280, 0xff00) >> >> after all the subtests completed successfully >> >> t/Client-CollectionArticle....ok >> >> >> t/Client-OntologyServer.......ok >> >> >> t/Client-Registration.........ok >> >> >> t/Client-SecondaryArticle.....ok >> >> >> t/Client-Service..............ok 2/0:7: parser error : Sequence ']]>' >> not allowed in content >> >> ]]>]]> >> >> ^ >> >> :7: parser error : internal error >> >> ]]>]]> >> >> ^ >> >> :7: parser error : Extra content at the end of the document >> >> ]]>]]> >> >> ^ >> >> at /usr/local/moby-live/Perl/blib/lib/MOBY/Client/Central.pm line >> 2107 >> >> # Looks like your test died just after 2. >> >> t/Client-Service..............dubious >> >> >> Test returned status 255 (wstat 65280, 0xff00) >> >> after all the subtests completed successfully >> >> t/Client-ServiceInstance......ok >> >> >> t/Client-SimpleArticle........ok >> >> >> t/CommonSubs..................ok >> >> >> t/Config......................skipped >> >> all skipped: Required only when you have your own local MOBY >> Central >> >> t/CrossReference..............ok >> >> >> t/Template....................ok >> >> >> Failed Test Stat Wstat Total Fail Failed List of Failed >> >> --------------------------------------------------------------------- >> --- >> ------- >> >> t/Client-Central.t 255 65280 23 0 0.00% ?? >> >> t/Client-Service.t 255 65280 2 0 0.00% ?? >> >> 1 test skipped. >> >> Failed 2/13 test scripts, 84.62% okay. 0/235 subtests failed, 100.00% >> okay. >> >> make: *** [test_dynamic] Error 255 >> >> lbarboza at cropwiki:/usr/local/moby-live/Perl$ >> >> -bash: syntax error near unexpected token `newline' >> >> >> >> I am using perl v5.8.4. pls help >> >> >> thanks >> >> >> Lord Hendrix A. Barbozax` >> >> Programmer - Web Services >> >> Crop Research Informatics Laboratory (CRIL) >> >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the > addressee and > may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have > received this > communication in error, please notify the sender immediately by reply > e-mail and delete the original and all copies from your system. > > > _______________________________________________ > 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: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- From Pieter.Neerincx at wur.nl Tue May 8 18:53:20 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Tue, 8 May 2007 20:53:20 +0200 Subject: [MOBY-dev] Valid boolean values for primitives and secondary parmeters In-Reply-To: References: Message-ID: <5AE74DCB-BD91-495F-8961-C25361B6F83B@wur.nl> Hi Mobifiers, Currently the BioMOBY specification does not explicitly list what values can be used for boolean primaries and secondaries. However for optimal interoperability services need to know what values they can expect from a client or the other way around clients need to be able to figure out what input a service needs. Hereby I propose we stick to the XML Schema specification for valid boolean values. From the XML Schema spec (http://www.w3.org/TR/xmlschema-2/#dt- boolean): "An instance of a datatype that is defined as boolean can have the following legal literals {true, false, 1, 0}." This would mean that clients are not allowed to send anything besides {true, false, 1, 0} as booleans and services must understand {true, false, 1, 0}. Hence frequently used booleans as T, F, t, f, True, False or biology specific booleans like male, female, M, F, XX, XY, etc. will be value non-grata in mobi-lingua. Any additional suggestions or objections? Cheers, Pi ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From gordonp at ucalgary.ca Tue May 8 19:05:31 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 08 May 2007 13:05:31 -0600 Subject: [MOBY-dev] Valid boolean values for primitives and secondary parmeters In-Reply-To: <5AE74DCB-BD91-495F-8961-C25361B6F83B@wur.nl> References: <5AE74DCB-BD91-495F-8961-C25361B6F83B@wur.nl> Message-ID: <4640C9FB.40502@ucalgary.ca> I agree. I think we had this conversation a couple of years ago! Time to put it in the spec... > Hi Mobifiers, > > Currently the BioMOBY specification does not explicitly list what > values can be used for boolean primaries and secondaries. However for > optimal interoperability services need to know what values they can > expect from a client or the other way around clients need to be able > to figure out what input a service needs. Hereby I propose we stick > to the XML Schema specification for valid boolean values. > > From the XML Schema spec (http://www.w3.org/TR/xmlschema-2/#dt- > boolean): > "An instance of a datatype that is defined as boolean can have the > following legal literals {true, false, 1, 0}." > > This would mean that clients are not allowed to send anything besides > {true, false, 1, 0} as booleans and services must understand {true, > false, 1, 0}. Hence frequently used booleans as T, F, t, f, True, > False or biology specific booleans like male, female, M, F, XX, XY, > etc. will be value non-grata in mobi-lingua. > > Any additional suggestions or objections? > > Cheers, > > Pi > > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 060 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From darin.london at duke.edu Thu May 10 16:17:40 2007 From: darin.london at duke.edu (darin.london at duke.edu) Date: Thu, 10 May 2007 12:17:40 -0400 Subject: [MOBY-dev] BOSC 2007 Second Call For Papers Message-ID: <200705101617.l4AGHeOl002544@tenero.duhs.duke.edu> The BOSC Organizing Committee are proud to announce BOSC 2007, occurring in Vienna, Austria on July 19th, 20th. The conference this year promises to be exciting, as the BOSC developers attempt to define and solve currently intractable problems in Bioinformatics. Please refer to the following website for complete information, and requests for submissions. Thank you, and we hope to see you in Vienna. http://open-bio.org/wiki/BOSC_2007 The BOSC organizing Committee Please pass this email on to anyone that would be interested. From darin.london at duke.edu Mon May 14 14:44:58 2007 From: darin.london at duke.edu (darin.london at duke.edu) Date: Mon, 14 May 2007 10:44:58 -0400 Subject: [MOBY-dev] BOSC 2007 Abstract Submission Deadline Extended Message-ID: <200705141444.l4EEiw9G027027@tenero.duhs.duke.edu> Due to technical difficulties in sending out the 2nd call for papers, the BOSC organizers are extending the deadline for abstract submissions to Monday May 21st. The announcement day will remain the same so that it remains before the Early Discount Date. http://open-bio.org/wiki/BOSC_2007 The BOSC organizing Committee Please pass this email on to anyone that would be interested. From ivanp at mmb.pcb.ub.es Tue May 15 18:38:49 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Tue, 15 May 2007 20:38:49 +0200 Subject: [MOBY-dev] XML elements into serviceNote get scaped Message-ID: <4649FE39.8070901@mmb.pcb.ub.es> Hi, I'm working with jMoby and MoSeS. As part of the moby specification, when a problem executing the service is encountered a mobyException must be launched: as many as needed XML elements must appear in the serviceNotes element in the response message. The problem is that the symbols < and > get scaped for all those elements inside serviceNotes; something like this: <moby:mobyException severity="2" > <moby:exceptionCode>201</moby:exceptionCode> <moby:exceptionMessage>Method is empty or is not a valid method name, applying default method: Atom_CyclohexaneWaterEnergyLomize Valid methods: Atom_OctanolWaterEnergyEisenbergMcLachlan ... </moby:mobyException> ... Is this a bug? or am I doing something bad? Thanks, -- ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ From martin.senger at gmail.com Tue May 15 19:19:23 2007 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 15 May 2007 20:19:23 +0100 Subject: [MOBY-dev] XML elements into serviceNote get scaped In-Reply-To: <4649FE39.8070901@mmb.pcb.ub.es> References: <4649FE39.8070901@mmb.pcb.ub.es> Message-ID: <4d93f07c0705151219o37fde9f3ha62d1db2703428f3@mail.gmail.com> > Is this a bug? or am I doing something bad? Is there a way I can reproduce this behaviour? How did you get this output - in the Dashboard, or somewhere else? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ivanp at mmb.pcb.ub.es Tue May 15 19:38:09 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Tue, 15 May 2007 21:38:09 +0200 Subject: [MOBY-dev] XML elements into serviceNote get scaped In-Reply-To: <4d93f07c0705151219o37fde9f3ha62d1db2703428f3@mail.gmail.com> References: <4649FE39.8070901@mmb.pcb.ub.es> <4d93f07c0705151219o37fde9f3ha62d1db2703428f3@mail.gmail.com> Message-ID: <464A0C21.6070305@mmb.pcb.ub.es> Hi, I get this behaviour in Dashboard & java command line client. The service that produced it is not in production yet (so it's not in a public server), but you can reproduce it with another one. For example: MOBY_SERVER=http://moby-dev.inab.org/cgi-bin/MOBY-Central.pl MOBY_URI=http://moby-dev.inab.org/MOBY/Central serviceName: getActiveSiteInterfaceFromPDBId and as input: I've suffered these problems in the past with Java XML... Perhaps is related to the way the children nodes of serviceNotes elements are created. Make sure you're adding Node objects and no String objects... I don't remember exactly what the problem was, but it was related to this kind of things. Regards, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Martin Senger escribi?: >> Is this a bug? or am I doing something bad? >> > > > Is there a way I can reproduce this behaviour? How did you get this output - > in the Dashboard, or somewhere else? > > Martin > > > From martin.senger at gmail.com Tue May 15 21:47:43 2007 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 15 May 2007 22:47:43 +0100 Subject: [MOBY-dev] XML elements into serviceNote get scaped In-Reply-To: <464A0C21.6070305@mmb.pcb.ub.es> References: <4649FE39.8070901@mmb.pcb.ub.es> <4d93f07c0705151219o37fde9f3ha62d1db2703428f3@mail.gmail.com> <464A0C21.6070305@mmb.pcb.ub.es> Message-ID: <4d93f07c0705151447y4354b110g80a3ea0de2e620ae@mail.gmail.com> > I've suffered these problems in the past with Java XML... Yes, me too. And so far I always found that the problem was on the service side. As it is here (see below). Was this service generated by Moses? Because if yes then it is also my problem :-) The XML returned by the service in question is wrongly escaped. This is what is on -the-wire: ... <?xml version="1.0" encoding="UTF-8"?> <moby:MOBY xmlns:moby="http://www.biomoby.org/moby"> <moby:mobyContent> <moby:serviceNotes>&lt;moby:mobyException severity="2" &gt; ... The beginning is as it should be: <moby:MOBY... But the service notes are double-escaped - because the ampersand which is the part of the construct "<" is again escaped so we get wrongly " >&lt;moby:mobyException". And this is what the service sent over the network (I caught it using a TCP monitor, not the Dashboard or other tool that may already fiddle with the raw data). Regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ivanp at mmb.pcb.ub.es Tue May 15 22:07:54 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Wed, 16 May 2007 00:07:54 +0200 Subject: [MOBY-dev] XML elements into serviceNote get scaped In-Reply-To: <4d93f07c0705151447y4354b110g80a3ea0de2e620ae@mail.gmail.com> References: <4649FE39.8070901@mmb.pcb.ub.es><4d93f07c0705151219o37fde9f3ha62 d1db2703428f3@mail.gmail.com><464A0C21.6070305@mmb.pcb.ub.es> <4d93f07c0705151447y4354b110g80a3ea0de2e620ae@mail.gmail.com> Message-ID: <464A2F3A.1080708@mmb.pcb.ub.es> Hi Martin, All my services are MoSeS generated. I don't deal directly with any XML at all... Tomorrow I can perform more tests on different services, but my intuition is that there is a problem in MoSeS... The strange thing is that I didn't realize about it before...Have you performed any test with any other service provider? Cheers, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Martin Senger escribi?: >> I've suffered these problems in the past with Java XML... >> > > > Yes, me too. And so far I always found that the problem was on the service > side. As it is here (see below). Was this service generated by Moses? > Because if yes then it is also my problem :-) > > The XML returned by the service in question is wrongly escaped. This is what > is on -the-wire: > > ... > <?xml version="1.0" > encoding="UTF-8"?> > <moby:MOBY xmlns:moby="http://www.biomoby.org/moby"> > <moby:mobyContent> > <moby:serviceNotes>&lt;moby:mobyException > severity="2" &gt; > ... > > The beginning is as it should be: <moby:MOBY... > > But the service notes are double-escaped - because the ampersand which is > the part of the construct "<" is again escaped so we get wrongly " > >&lt;moby:mobyException". And this is what the service sent over the > network (I caught it using a TCP monitor, not the Dashboard or other tool > that may already fiddle with the raw data). > > Regards, > Martin > > > From gordonp at ucalgary.ca Tue May 15 22:15:26 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 15 May 2007 16:15:26 -0600 Subject: [MOBY-dev] XML elements into serviceNote get scaped In-Reply-To: <464A2F3A.1080708@mmb.pcb.ub.es> References: <4649FE39.8070901@mmb.pcb.ub.es><4d93f07c0705151219o37fde9f3ha62 d1db2703428f3@mail.gmail.com><464A0C21.6070305@mmb.pcb.ub.es> <4d93f07c0705151447y4354b110g80a3ea0de2e620ae@mail.gmail.com> <464A2F3A.1080708@mmb.pcb.ub.es> Message-ID: <464A30FE.1050606@ucalgary.ca> I have noticed this problem before too with some services, but did not know how those services were built...this leads me to believe it probably is a latent bug in MoSeS. > Hi Martin, > > All my services are MoSeS generated. I don't deal directly with any XML > at all... Tomorrow I can perform more tests on different services, but > my intuition is that there is a problem in MoSeS... The strange thing is > that I didn't realize about it before...Have you performed any test with > any other service provider? > > Cheers, > > ------------------------------------------------ > Iv?n P?rraga Garc?a > Computer Scientist > Molecular Modelling & Bioinformatics Unit > INB - Instituto Nacional de Bioinform?tica > Josep Samitier 1-5 > 08028 Barcelona > Spain > tel.: +34 93 403 71 55 > fax.: +34 93 403 71 57 > e-mail: ivanp at mmb.pcb.ub.es > group page: http://mmb.pcb.ub.es > pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc > ------------------------------------------------ > > > > Martin Senger escribi?: > >>> I've suffered these problems in the past with Java XML... >>> >>> >> Yes, me too. And so far I always found that the problem was on the service >> side. As it is here (see below). Was this service generated by Moses? >> Because if yes then it is also my problem :-) >> >> The XML returned by the service in question is wrongly escaped. This is what >> is on -the-wire: >> >> ... >> <?xml version="1.0" >> encoding="UTF-8"?> >> <moby:MOBY xmlns:moby="http://www.biomoby.org/moby"> >> <moby:mobyContent> >> <moby:serviceNotes>&lt;moby:mobyException >> severity="2" &gt; >> ... >> >> The beginning is as it should be: <moby:MOBY... >> >> But the service notes are double-escaped - because the ampersand which is >> the part of the construct "<" is again escaped so we get wrongly " >> >&lt;moby:mobyException". And this is what the service sent over the >> network (I caught it using a TCP monitor, not the Dashboard or other tool >> that may already fiddle with the raw data). >> >> Regards, >> Martin >> >> >> >> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,464a2e0121086797816178! > > > > From martin.senger at gmail.com Tue May 15 22:17:49 2007 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 15 May 2007 23:17:49 +0100 Subject: [MOBY-dev] XML elements into serviceNote get scaped In-Reply-To: <464A2F3A.1080708@mmb.pcb.ub.es> References: <4649FE39.8070901@mmb.pcb.ub.es> <464A0C21.6070305@mmb.pcb.ub.es> <4d93f07c0705151447y4354b110g80a3ea0de2e620ae@mail.gmail.com> <464A2F3A.1080708@mmb.pcb.ub.es> Message-ID: <4d93f07c0705151517m256c7560le37265b41dfe9760@mail.gmail.com> > All my services are MoSeS generated. Okay, I will look at it. (But I have a timing problem, heading on Thursday for a meeting in Italy for couple of days; I will try my best to solve it before that.) Have you performed any test with > any other service provider? I did, but it is a long time ago. I have not touched jMoby recently. [ But I will do it now, and I will use this opportunity to fix the long-ago reported bug with the full format of the calendar day :-) ] Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ivanp at mmb.pcb.ub.es Tue May 15 23:09:11 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Wed, 16 May 2007 01:09:11 +0200 Subject: [MOBY-dev] XML elements into serviceNote get scaped In-Reply-To: <4d93f07c0705151517m256c7560le37265b41dfe9760@mail.gmail.com> References: <4649FE39.8070901@mmb.pcb.ub.es> <464A0C21.6070305@mmb.pcb.ub.es><4d93f07c0705151447y4354b110g80a3ea0de2e620 ae@mail.gmail.com><464A2F3A.1080708@mmb.pcb.ub.es> <4d93f07c0705151517m256c7560le37265b41dfe9760@mail.gmail.com> Message-ID: <464A3D97.1000303@mmb.pcb.ub.es> > > Okay, I will look at it. (But I have a timing problem, heading on Thursday > for a meeting in Italy for couple of days; I will try my best to solve it > before that.) Thanks and don't worry, I'll survive if it's not fixed in the next days :-P > to fix the long-ago > reported bug with the full format of the calendar day I had forgotten about it :-P Thanks! Cheers, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Martin Senger escribi?: >> All my services are MoSeS generated. >> > > > Okay, I will look at it. (But I have a timing problem, heading on Thursday > for a meeting in Italy for couple of days; I will try my best to solve it > before that.) > > Have you performed any test with > >> any other service provider? >> > > > I did, but it is a long time ago. I have not touched jMoby recently. [ But > I will do it now, and I will use this opportunity to fix the long-ago > reported bug with the full format of the calendar day :-) ] > > Cheers, > Martin > > From ivanp at mmb.pcb.ub.es Thu May 17 16:07:53 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Thu, 17 May 2007 18:07:53 +0200 Subject: [MOBY-dev] Conceptual doubt about datatypes representation in resquests/responses Message-ID: <464C7DD9.6080003@mmb.pcb.ub.es> Hi, I have a conceptual doubt and I've not been able to find an answer reviewing the documentation. Let's say that we have a datatype dat with three articleNames art1, art2, ar3 and a service whose return object is this datatype. In the response object, is mandatory that for the object dat to have the XML tags for all the article names even in any of them is empty? I mean this (imagine proper XML representation): anything1 --- anything1 Both of these representations are equivalent and valid? or only the first one? Thanks, -- ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ From gordonp at ucalgary.ca Thu May 17 16:13:37 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 17 May 2007 10:13:37 -0600 Subject: [MOBY-dev] Conceptual doubt about datatypes representation in resquests/responses In-Reply-To: <464C7DD9.6080003@mmb.pcb.ub.es> References: <464C7DD9.6080003@mmb.pcb.ub.es> Message-ID: <464C7F31.5070507@ucalgary.ca> Only the first one. Just like in an OO language, where every instance of an object has a "place" for a member, even if the value is null (or empty tag, in the case of MOBY). > Hi, > > I have a conceptual doubt and I've not been able to find an answer > reviewing the documentation. Let's say that we have a datatype dat with > three articleNames art1, art2, ar3 and a service whose return object is > this datatype. In the response object, is mandatory that for the object > dat to have the XML tags for all the article names even in any of them > is empty? > > I mean this (imagine proper XML representation): > > > > anything1 > > > > > > --- > > > > anything1 > > > > > Both of these representations are equivalent and valid? or only the > first one? > > Thanks, > > From ivanp at mmb.pcb.ub.es Thu May 17 16:23:35 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Thu, 17 May 2007 18:23:35 +0200 Subject: [MOBY-dev] Conceptual doubt about datatypes representation inresquests/responses In-Reply-To: <464C7F31.5070507@ucalgary.ca> References: <464C7DD9.6080003@mmb.pcb.ub.es> <464C7F31.5070507@ucalgary.ca> Message-ID: <464C8187.7070409@mmb.pcb.ub.es> Ok, that is what I thought. Then I'd like to suggest a little improvement in the Java MoSeS generated services: if an article name is not explicitly setted, it would be nice to obtain the datatype like it has to be; currently if you omit to set an attribute there is no XML tag for it in the response. Thanks, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Paul Gordon escribi?: > Only the first one. Just like in an OO language, where every instance > of an object has a "place" for a member, even if the value is null (or > empty tag, in the case of MOBY). > >> Hi, >> >> I have a conceptual doubt and I've not been able to find an answer >> reviewing the documentation. Let's say that we have a datatype dat with >> three articleNames art1, art2, ar3 and a service whose return object is >> this datatype. In the response object, is mandatory that for the object >> dat to have the XML tags for all the article names even in any of them >> is empty? >> >> I mean this (imagine proper XML representation): >> >> >> >> anything1 >> >> >> >> >> >> --- >> >> >> >> anything1 >> >> >> >> >> Both of these representations are equivalent and valid? or only the >> first one? >> >> Thanks, >> >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From ivanp at mmb.pcb.ub.es Fri May 18 10:39:42 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Fri, 18 May 2007 12:39:42 +0200 Subject: [MOBY-dev] hierarchy and castings in Moby Message-ID: <464D826E.1050608@mmb.pcb.ub.es> Hi, Another philosophical question about moby... Unfortunately moby does not support the concept of templates (in the C++ sense), so there is a no clear way to build container objects (let's say an array or a hash map, for example). A solution could be the concept of generics (like in Java prior to version 1.5), where you define a container as containing the most generic type of object in the hierarchy (the Object "class") and then the container can hold any kind of contents. Afterwards, if you want to emphasize what is the content of a container you can specialize by subclassing. Not sure if I explain myself, I mean something like this: The root container Map ../.. Object MapEntry Integer String String The content: MapEntry ../.. Object Object Object and then an specialized container: ResidueFloatMap ../.. . This is only a semantic inheritance]]> Map Because of inheritance, the ResidueFloatMap, will contain MapEntry objects, but the programmer (by convention) must guarantee if using this datatype that the contents of the MapEntry must be Residue and Float respectively. I think this should work because, obviously, any moby class inherits of the root Object, isn't it? Ok, my question is if this approach is right. I had the impression that it should be, but I'm having some parsing problems with the MoSeS - jMoby and I'm not sure if is because of this approach or it it is a bug. An additional question (I couldn't check it because of these previous problems): to have this solution working, I would need to perform casting conversion in the source of the services that receive an specialized container, something like this (excuse my pseudo-code): ResidueFloatMap map = ... Entry[] entries = map.getMoby_Entries(); Residue residue = ((Residue)(entries[0].getMoby_key())); Is this right/possible? If not, any way to do it? Thanks, -- ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ From martin.senger at gmail.com Fri May 18 12:26:29 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 18 May 2007 13:26:29 +0100 Subject: [MOBY-dev] Conceptual doubt about datatypes representation inresquests/responses In-Reply-To: <464C8187.7070409@mmb.pcb.ub.es> References: <464C7DD9.6080003@mmb.pcb.ub.es> <464C7F31.5070507@ucalgary.ca> <464C8187.7070409@mmb.pcb.ub.es> Message-ID: <4d93f07c0705180526r568651f7qb54d2a1905c418e4@mail.gmail.com> > Ok, that is what I thought. Then I'd like to suggest a little > improvement in the Java MoSeS generated services: if an article name is > not explicitly setted, it would be nice to obtain the datatype like it > has to be; currently if you omit to set an attribute there is no XML tag > for it in the response. That's because I have a different view that Paul expressed :-) When I was doing my research of the moby API documentation I concluded that no data means no data. Why should I send them at all? What are the pros and cons? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Fri May 18 12:36:18 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 18 May 2007 13:36:18 +0100 Subject: [MOBY-dev] hierarchy and castings in Moby In-Reply-To: <464D826E.1050608@mmb.pcb.ub.es> References: <464D826E.1050608@mmb.pcb.ub.es> Message-ID: <4d93f07c0705180536qc2c8a23ue5100ab05b40a1ea@mail.gmail.com> You are asking actually two questions (both related): 1) Is it possible to register a different type for an existing member article in an inherited data type? (Assuming that the new different type is a sub-class of the existing one). 2) Is it possible to send data where an article member is actually a subclass of the registered one. The latter question (2) was recently (last month) discussed between Mark, Eddie, Paul and me - and I believe most of us expressed willingness to change our parsers (including the MoSeS parser) to support it. But the decision to allow this kind of data will take place in the Vancouver meeting this June. I am not aware about any discussion of the former question (1). In order to do so would require changes in the moby registry I guess. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ivanp at mmb.pcb.ub.es Fri May 18 13:34:23 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Fri, 18 May 2007 15:34:23 +0200 Subject: [MOBY-dev] Conceptual doubt about datatypes representationinresquests/responses In-Reply-To: <4d93f07c0705180526r568651f7qb54d2a1905c418e4@mail.gmail.com> References: <464C7DD9.6080003@mmb.pcb.ub.es> <464C7F31.5070507@ucalgary.ca><464C8187.7070409@mmb.pcb.ub.es> <4d93f07c0705180526r568651f7qb54d2a1905c418e4@mail.gmail.com> Message-ID: <464DAB5F.2000702@mmb.pcb.ub.es> Hi, I prefer your approach Martin, although I saw some examples that made me think that the behavior stated by Paul was the expected one. Sincerely, I don't see the need to send no necessary data. At the end, an empty XML tag or a non-existent one will produce a "null" value, when trying to retrieve it, won't it? Furthermore, I have some of my services in mind with "HAS" relations and a big amount of instances related to a container and these instances have only relevant values for half of the attributes. This situation produces a big amount of unnecessary data transfer over the net... If I could vote, no doubt I would agree with Martin (I don't see exactly what is the advantage of the other approach). Cheers, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Martin Senger escribi?: >> Ok, that is what I thought. Then I'd like to suggest a little >> improvement in the Java MoSeS generated services: if an article name is >> not explicitly setted, it would be nice to obtain the datatype like it >> has to be; currently if you omit to set an attribute there is no XML tag >> for it in the response. >> > > > That's because I have a different view that Paul expressed :-) When I was > doing my research of the moby API documentation I concluded that no data > means no data. Why should I send them at all? What are the pros and cons? > > Martin > > > From ivanp at mmb.pcb.ub.es Fri May 18 13:42:41 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Fri, 18 May 2007 15:42:41 +0200 Subject: [MOBY-dev] hierarchy and castings in Moby In-Reply-To: <4d93f07c0705180536qc2c8a23ue5100ab05b40a1ea@mail.gmail.com> References: <464D826E.1050608@mmb.pcb.ub.es> <4d93f07c0705180536qc2c8a23ue5100ab05b40a1ea@mail.gmail.com> Message-ID: <464DAD51.4070804@mmb.pcb.ub.es> Yes, you caught exactly what I meant. To have feature 1 would be great because it would be a nice way to implement the concept of "template" or "generics", but as you say, perhaps it has more deep implications in the Moby architecture. However in my modest opinion, a way to handle generic datatypes should be addressed to allow versatile services. Before sending the e-mail I was assuming "2" to be right, but MobyParser in jMoby MoSeS didn't agree with me I think ;-) Thanks, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Martin Senger escribi?: > You are asking actually two questions (both related): > > 1) Is it possible to register a different type for an existing member > article in an inherited data type? (Assuming that the new different type is > a sub-class of the existing one). > > 2) Is it possible to send data where an article member is actually a > subclass of the registered one. > > The latter question (2) was recently (last month) discussed between Mark, > Eddie, Paul and me - and I believe most of us expressed willingness to > change our parsers (including the MoSeS parser) to support it. But the > decision to allow this kind of data will take place in the Vancouver meeting > this June. > > I am not aware about any discussion of the former question (1). In order to > do so would require changes in the moby registry I guess. > > Martin > > From markw at illuminae.com Fri May 18 14:36:23 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 18 May 2007 07:36:23 -0700 Subject: [MOBY-dev] hierarchy and castings in Moby In-Reply-To: <4d93f07c0705180536qc2c8a23ue5100ab05b40a1ea@mail.gmail.com> References: <464D826E.1050608@mmb.pcb.ub.es> <4d93f07c0705180536qc2c8a23ue5100ab05b40a1ea@mail.gmail.com> Message-ID: > 1) Is it possible to register a different type for an existing member > article in an inherited data type? (Assuming that the new different type > is a sub-class of the existing one). As Martin says, this would require changes to the API and registry > 2) Is it possible to send data where an article member is actually a > subclass of the registered one. Again, Martin is correct that there was an "inside conversation" a few weeks ago after we discovered that Paul's parser already supported this behaviour. Mine (CommonSubs.pm) does not, and Martin's doesn't either at the moment (I beleive?). However, it does make sense to support this, and I changed the wording of the Moby 1.0 manuscript to suggest that we would support this in the near future, so I suspect that we'll make the final decision at the June meeting. Once this is supported, it would make sense to think about what you suggest above... though we have then reinvented RDF/OWL :-) M From markw at illuminae.com Fri May 18 14:57:04 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 18 May 2007 07:57:04 -0700 Subject: [MOBY-dev] Conceptual doubt about datatypes representationinresquests/responses In-Reply-To: <464DAB5F.2000702@mmb.pcb.ub.es> References: <464C7DD9.6080003@mmb.pcb.ub.es> <464C7F31.5070507@ucalgary.ca> <464C8187.7070409@mmb.pcb.ub.es> <4d93f07c0705180526r568651f7qb54d2a1905c418e4@mail.gmail.com> <464DAB5F.2000702@mmb.pcb.ub.es> Message-ID: On Fri, 18 May 2007 06:34:23 -0700, Iv?n P?rraga Garc?a wrote: > I prefer your approach Martin, although I saw some examples that made me > think that the behavior stated by Paul was the expected one. I feel like we have had this discussion before, but I can't find any reference to it in the mailing list archives... My parser (CommonSubs.pm) assumes that all declared has/has-a components exist in the XML, and we explicitly state that this is the case in the 1.0 manuscript as one of the advantges that Moby has over RDF; however, the API docs don't clearly say one way or the other... So... At a minimum it needs more discussion... M From martin.senger at gmail.com Sun May 20 16:06:42 2007 From: martin.senger at gmail.com (Martin Senger) Date: Sun, 20 May 2007 17:06:42 +0100 Subject: [MOBY-dev] planned changes in how to build jMoby Message-ID: <4d93f07c0705200906y8f3e97fo921e46303f6fefd3@mail.gmail.com> Dear developers, Some times ago I indicated that I would like to start using Maven for jMoby dependencies - but not a full Maven, only its major features (dependencies mechanism and repositories of libraries), using Maven from the current Ant. The major difference for the jMoby user and developers will be that jMoby CVS package will not anymore include Ant itself. Which means that each developer has to install it separately on her machine. I wonder if this is acceptable for you. Are there any objections? The details about this Ant-Maven marriage can be found in one article ( http://pantheon.generationcp.org/UsingMaven.html) that I wrote for another project but I will make a similar article tailored for the jMoby before I commit changes. [At the moment of writing this email the link above is not accessible but it is only temporarily.] Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Mon May 21 00:57:05 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 21 May 2007 01:57:05 +0100 Subject: [MOBY-dev] Dashboard and date types In-Reply-To: <4614FCE8.70904@mmb.pcb.ub.es> References: <4614FCE8.70904@mmb.pcb.ub.es> Message-ID: <4d93f07c0705201757y656fd6danfe60fb26bd81193d@mail.gmail.com> I have fixed the bug reported by Ivan about the wrong format of date/time strings produced by jMoby classes. The format, indeed, did not conform with the http://www.w3.org/TR/NOTE-datetime standard as required by Biomoby API). But doing it I found some unanswered questions. Perhaps mainly for Paul, but because the bug was reported here, I am discussing it also here. The problem was caused mainly by the fact that the java class SimpleDateFormat (a class that is usually used for creating formatted strings from the Date objects) produces strings that are not compatible with the "http://www.w3.org/TR/NOTE-datetime" standard. Or, at least, I have not found a way how to do it (which is the first question: can it be done? how?). The lines: SimpleDateFormat sdf = new SimpleDateFormat (MobyDateTime.FULL_FORMAT); System.out.println (sdf.format (new Date())); produces "2007-05-21T00:40:35+0100" which does not comply with he mentioned standard (the result that complies should be: "2007-05-21T00:40:35+01:00"). But because of using SimpleDateFormat is otherwise very convenient, I have added a hack into MobyDateTime class that accepts even this non-standard format and converts it into a good one (by adding a colon separator). Here is the second question: is there a better place or way to replace this hack? Last, and actually the main question, is that I suspect a bug in the method MobyDataDateTime.getString(calendar). When I feed it with the calendar created from the string "2007-05-21T00:40:35+01:00" I will get a string "2007-05-21T02:40:35Z". The method removed timezone (and replaced it with a single Z letter, which is correct) but the time - that should be now in GMT - is now bigger by two hours when I expected decrease by one hour (moving from my BST time which is +01 to the GMT). Is this a bug or my misinterpretation of the times? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From jmfernandez at cnio.es Mon May 21 07:05:53 2007 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Mon, 21 May 2007 09:05:53 +0200 Subject: [MOBY-dev] Dashboard and date types In-Reply-To: <4d93f07c0705201757y656fd6danfe60fb26bd81193d@mail.gmail.com> References: <4614FCE8.70904@mmb.pcb.ub.es> <4d93f07c0705201757y656fd6danfe60fb26bd81193d@mail.gmail.com> Message-ID: <465144D1.7070706@cnio.es> Hi Martin, have you taken into account that daylight saving is currently in effect? GMT and UTC are not the same in that case, because most (if not all) GMT countries followed the daylight saving change. But it could be a Java bug, because the standard says that +01:00 is a shift from UTC. In that case, you could validate that behavior using alternate Date and Time clases from http://joda-time.sourceforge.net/. Best Regards, Jos? Mar?a Martin Senger wrote: > I have fixed the bug reported by Ivan about the wrong format of date/time > strings produced by jMoby classes. The format, indeed, did not conform with > the http://www.w3.org/TR/NOTE-datetime standard as required by Biomoby API). > > But doing it I found some unanswered questions. Perhaps mainly for Paul, but > because the bug was reported here, I am discussing it also here. > > The problem was caused mainly by the fact that the java class > SimpleDateFormat (a class that is usually used for creating formatted > strings from the Date objects) produces strings that are not compatible with > the "http://www.w3.org/TR/NOTE-datetime" standard. Or, at least, I have not > found a way how to do it (which is the first question: can it be done? > how?). The lines: > > SimpleDateFormat sdf = new SimpleDateFormat (MobyDateTime.FULL_FORMAT); > System.out.println (sdf.format (new Date())); > > produces "2007-05-21T00:40:35+0100" which does not comply with he mentioned > standard (the result that complies should be: "2007-05-21T00:40:35+01:00"). > > But because of using SimpleDateFormat is otherwise very convenient, I have > added a hack into MobyDateTime class that accepts even this non-standard > format and converts it into a good one (by adding a colon separator). Here > is the second question: is there a better place or way to replace this hack? > > Last, and actually the main question, is that I suspect a bug in the method > MobyDataDateTime.getString(calendar). When I feed it with the calendar > created from the string "2007-05-21T00:40:35+01:00" I will get a string > "2007-05-21T02:40:35Z". The method removed timezone (and replaced it with a > single Z letter, which is correct) but the time - that should be now in GMT > - is now bigger by two hours when I expected decrease by one hour (moving > from my BST time which is +01 to the GMT). Is this a bug or my > misinterpretation of the times? > > Cheers, > Martin > -- Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 2256) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Biolog?a Estructural y Bioinform?tica Structural Biology and Bioinformatics 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. 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From martin.senger at gmail.com Mon May 21 08:01:33 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 21 May 2007 09:01:33 +0100 Subject: [MOBY-dev] Dashboard and date types In-Reply-To: <465144D1.7070706@cnio.es> References: <4614FCE8.70904@mmb.pcb.ub.es> <4d93f07c0705201757y656fd6danfe60fb26bd81193d@mail.gmail.com> <465144D1.7070706@cnio.es> Message-ID: <4d93f07c0705210101q11e43c79g36abdc2986346e8c@mail.gmail.com> HI, have you taken into account that daylight saving is currently in effect? No, but I thought about it. Then I let the thinking to Paul (after all, I am using his method to convert a calendar to a string :-)). GMT > and UTC are not the same in that case Well, I always thought that GMT and UTC are the same, no matter what daylight saving time is used. And the wikipedia confirms that: For most practical and legal-trade purposes, the fractional difference > between UTC and UT (or GMT) is inconsequentially small, and for this reason > UTC is colloquially called GMT sometimes, even if this is not technically > correct. > But it could be a Java bug, because the standard says that +01:00 is a shift > from UTC. In that case, you could validate that behavior using alternate > Date > and Time clases from http://joda-time.sourceforge.net/. I would prefer to use standard Java functions. So far. I have not heard about any related java bug (there are some bugs regarding the three-letters abbreviations of time zones but it is not our case). Let's wait for Paul's opinion. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ivanp at mmb.pcb.ub.es Mon May 21 10:13:22 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Mon, 21 May 2007 12:13:22 +0200 Subject: [MOBY-dev] planned changes in how to build jMoby In-Reply-To: <4d93f07c0705200906y8f3e97fo921e46303f6fefd3@mail.gmail.com> References: <4d93f07c0705200906y8f3e97fo921e46303f6fefd3@mail.gmail.com> Message-ID: <465170C2.70501@mmb.pcb.ub.es> Hi, I have no previous experience in Maven but I think this could be a good moment to start. In my case there is no problem in externalizing ANT from jMoby. In my case, ANT is installed in my systems as a common tool for my own projects. My vote is positive. Cheers, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Martin Senger escribi?: > Dear developers, > > Some times ago I indicated that I would like to start using Maven for jMoby > dependencies - but not a full Maven, only its major features (dependencies > mechanism and repositories of libraries), using Maven from the current Ant. > The major difference for the jMoby user and developers will be that jMoby > CVS package will not anymore include Ant itself. Which means that each > developer has to install it separately on her machine. I wonder if this is > acceptable for you. Are there any objections? > > The details about this Ant-Maven marriage can be found in one article ( > http://pantheon.generationcp.org/UsingMaven.html) that I wrote for another > project but I will make a similar article tailored for the jMoby before I > commit changes. [At the moment of writing this email the link above is not > accessible but it is only temporarily.] > > Cheers, > Martin > > From martin.senger at gmail.com Sun May 27 19:28:32 2007 From: martin.senger at gmail.com (Martin Senger) Date: Sun, 27 May 2007 20:28:32 +0100 Subject: [MOBY-dev] an easy way to see the input/output size whenusingjMoby? In-Reply-To: <4626432F.5030109@mmb.pcb.ub.es> References: <462637AE.6080303@mmb.pcb.ub.es> <000901c781d1$6c61b880$6800a8c0@notebook> <4626432F.5030109@mmb.pcb.ub.es> Message-ID: <4d93f07c0705271228p23fbfebcy65efaf00e3bcc00c@mail.gmail.com> > However, the best would be to have a realistic size in bytes but it's > not a real need. To comply with the Ivan's request, I have added few new methods to the BaseService (the class that is used by all Moses-based services): * getHTTPHeaders() will allow the service to inspect what headers were used to deliver a request * getRequestLength() is only a convenient method extracting one particular header from the HTTP headers * getServletRequest() accessing all the richness of the servlet context. Together with already existing method getCallerAddr() you can, for example, have in your service the following code: log.info ("Request length: " + getRequestLength()); log.info ("Request from: " + getCallerAddr()); log.debug ("Request URL: " + getServletRequest().getRequestURL()); log.debug ("Request headers: " + getHTTPHeaders().toString()); In the src/samples, there is a new testing service (registered in the usual Central registry) TestServiceNotes that prints similar things in the service notes. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Sun May 27 23:34:47 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 28 May 2007 00:34:47 +0100 Subject: [MOBY-dev] looking for documentation on asynchronous service... Message-ID: <4d93f07c0705271634q26feff7bne54e1b21aba43ea6@mail.gmail.com> ...(the proposal we agreed on sometimes ago) - but the biomoby.org pages seem to be even more obfuscated that they were when I looked there the last time. Could anybody help me please? [And could anybody help to make the biomoby pages readable and useful? Well, this was a joke... We all know that it is next to impossible.] Thanks, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ivanp at mmb.pcb.ub.es Mon May 28 00:12:29 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Mon, 28 May 2007 02:12:29 +0200 Subject: [MOBY-dev] an easy way to see the input/output sizewhenusingjMoby? In-Reply-To: <4d93f07c0705271228p23fbfebcy65efaf00e3bcc00c@mail.gmail.com> References: <462637AE.6080303@mmb.pcb.ub.es><000901c781d1$6c61b880$6800a8c0@ notebook><4626432F.5030109@mmb.pcb.ub.es> <4d93f07c0705271228p23fbfebcy65efaf00e3bcc00c@mail.gmail.com> Message-ID: <465A1E6D.70902@mmb.pcb.ub.es> Thanks a lot for your help Martin. Tomorrow I'll change my logging system to use the new features. Cheers, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Martin Senger escribi?: >> However, the best would be to have a realistic size in bytes but it's >> not a real need. >> > > > To comply with the Ivan's request, I have added few new methods to the > BaseService (the class that is used by all Moses-based services): > > * getHTTPHeaders() will allow the service to inspect what headers were used > to deliver a request > > * getRequestLength() is only a convenient method extracting one particular > header from the HTTP headers > > * getServletRequest() accessing all the richness of the servlet context. > > Together with already existing method getCallerAddr() you can, for example, > have in your service the following code: > > log.info ("Request length: " + getRequestLength()); > log.info ("Request from: " + getCallerAddr()); > log.debug ("Request URL: " + getServletRequest().getRequestURL()); > log.debug ("Request headers: " + getHTTPHeaders().toString()); > > In the src/samples, there is a new testing service (registered in the usual > Central registry) TestServiceNotes that prints similar things in the service > notes. > > Cheers, > Martin > > From johan at ac.uma.es Mon May 28 07:12:16 2007 From: johan at ac.uma.es (Johan Karlsson) Date: Mon, 28 May 2007 09:12:16 +0200 Subject: [MOBY-dev] looking for documentation on asynchronous service... In-Reply-To: <4d93f07c0705271634q26feff7bne54e1b21aba43ea6@mail.gmail.com> References: <4d93f07c0705271634q26feff7bne54e1b21aba43ea6@mail.gmail.com> Message-ID: <465A80D0.7080602@ac.uma.es> Hi Martin (and others), Here is a link to the pdf of the accepted proposal. http://chirimoyo.ac.uma.es/asynchronysm/BioMOBY_Asynchronous_Service_Call_Proposal_WSRF_v2.3.pdf Kind regards, Johan Martin Senger wrote: > ...(the proposal we agreed on sometimes ago) - but the biomoby.org pages > seem to be even more obfuscated that they were when I looked there the last > time. Could anybody help me please? > > [And could anybody help to make the biomoby pages readable and useful? Well, > this was a joke... We all know that it is next to impossible.] > > Thanks, > Martin > > -- Johan Karlsson 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 From ivanp at mmb.pcb.ub.es Mon May 28 10:36:55 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Mon, 28 May 2007 12:36:55 +0200 Subject: [MOBY-dev] java.lang.NoSuchMethodError launched when MobyException raised Message-ID: <465AB0C7.2070905@mmb.pcb.ub.es> Hi, Is it possible that the return value of the method ServiceException.toXML() has changed from String to Node (or any other XML representation) and this has not been taking into account in some other parts of jMoby? Perhaps I'm doing something bad, but when I invoke a service with an incorrect ouput instead of the proper MobyException (or any other situtation which provokes the raise of a MobyException) a Java exception is launched. Here it is an example error stack: {http://xml.apache.org/axis/}stackTrace: java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.jboss.webservice.server.InvokerProviderJSE.invokeServiceEndpoint(InvokerProviderJSE.java:154) at org.jboss.webservice.server.InvokerProvider.invokeMethod(InvokerProvider.java:305) at org.jboss.axis.providers.java.RPCProvider.invokeTarget(RPCProvider.java:176) at org.jboss.webservice.server.InvokerProviderJSE.invokeTarget(InvokerProviderJSE.java:93) at org.jboss.axis.providers.java.RPCProvider.processMessage(RPCProvider.java:121) at org.jboss.axis.providers.java.JavaProvider.invoke(JavaProvider.java:358) at org.jboss.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:73) at org.jboss.axis.SimpleChain.doVisiting(SimpleChain.java:160) at org.jboss.axis.SimpleChain.invoke(SimpleChain.java:123) at org.jboss.axis.handlers.soap.SOAPService.invoke(SOAPService.java:560) at org.jboss.webservice.server.ServerEngine.invokeInternal(ServerEngine.java:200) at org.jboss.webservice.server.ServerEngine.invoke(ServerEngine.java:89) at org.jboss.axis.transport.http.AxisServlet.doPost(AxisServlet.java:911) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.jboss.axis.transport.http.AxisServletBase.service(AxisServletBase.java:370) at javax.servlet.http.HttpServlet.service(HttpServlet.java:810) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) at org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.java:81) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178) at org.jboss.web.tomcat.security.CustomPrincipalValve.invoke(CustomPrincipalValve.java:39) at org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssociationValve.java:159) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:407) at org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java:59) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:856) at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processConnection(Http11Protocol.java:744) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527) at org.apache.tomcat.util.net.MasterSlaveWorkerThread.run(MasterSlaveWorkerThread.java:112) at java.lang.Thread.run(Thread.java:619) Caused by: java.lang.NoSuchMethodError: org.biomoby.shared.parser.ServiceException.toXML()Ljava/lang/String; at org.biomoby.shared.parser.MobyPackage.toXMLDocument(MobyPackage.java:235) at org.biomoby.shared.parser.MobyPackage.toXML(MobyPackage.java:213) at org.biomoby.service.BaseService.error(BaseService.java:330) at org.mmb.moby.webservice.plotFeatureAASequence.plotFeatureAASequenceSkel.plotFeatureAASequence(plotFeatureAASequenceSkel.java:72) ... 40 more Obviously I've recreated and deployed the jmoby.jar. Should I regenerate skeletons? I imagine (and hope) not. Regards, Iv?n From ivanp at mmb.pcb.ub.es Mon May 28 10:52:14 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Mon, 28 May 2007 12:52:14 +0200 Subject: [MOBY-dev] java.lang.NoSuchMethodError launched when MobyExceptionraised In-Reply-To: <465AB0C7.2070905@mmb.pcb.ub.es> References: <465AB0C7.2070905@mmb.pcb.ub.es> Message-ID: <465AB45E.5010504@mmb.pcb.ub.es> I meant: "... Perhaps I'm doing something bad, but when I invoke a service with an incorrect input, instead of the proper MobyException ..." instead of "... Perhaps I'm doing something bad, but when I invoke a service with an incorrect ouput instead of the proper MobyException..." Sorry, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Iv?n P?rraga Garc?a escribi?: > Hi, > > Is it possible that the return value of the method > ServiceException.toXML() has changed from String to Node (or any other > XML representation) and this has not been taking into account in some > other parts of jMoby? > > Perhaps I'm doing something bad, but when I invoke a service with an > incorrect ouput instead of the proper MobyException (or any other > situtation which provokes the raise of a MobyException) a Java exception > is launched. Here it is an example error stack: > > {http://xml.apache.org/axis/}stackTrace: > java.lang.reflect.InvocationTargetException > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > at java.lang.reflect.Method.invoke(Method.java:597) > at > org.jboss.webservice.server.InvokerProviderJSE.invokeServiceEndpoint(InvokerProviderJSE.java:154) > at > org.jboss.webservice.server.InvokerProvider.invokeMethod(InvokerProvider.java:305) > at > org.jboss.axis.providers.java.RPCProvider.invokeTarget(RPCProvider.java:176) > at > org.jboss.webservice.server.InvokerProviderJSE.invokeTarget(InvokerProviderJSE.java:93) > at > org.jboss.axis.providers.java.RPCProvider.processMessage(RPCProvider.java:121) > at > org.jboss.axis.providers.java.JavaProvider.invoke(JavaProvider.java:358) > at > org.jboss.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:73) > at org.jboss.axis.SimpleChain.doVisiting(SimpleChain.java:160) > at org.jboss.axis.SimpleChain.invoke(SimpleChain.java:123) > at org.jboss.axis.handlers.soap.SOAPService.invoke(SOAPService.java:560) > at > org.jboss.webservice.server.ServerEngine.invokeInternal(ServerEngine.java:200) > at org.jboss.webservice.server.ServerEngine.invoke(ServerEngine.java:89) > at > org.jboss.axis.transport.http.AxisServlet.doPost(AxisServlet.java:911) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) > at > org.jboss.axis.transport.http.AxisServletBase.service(AxisServletBase.java:370) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:810) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) > at > org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.java:81) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) > at > org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) > at > org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178) > at > org.jboss.web.tomcat.security.CustomPrincipalValve.invoke(CustomPrincipalValve.java:39) > at > org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssociationValve.java:159) > at > org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:407) > at > org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java:59) > at > org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126) > at > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105) > at > org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107) > at > org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148) > at > org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:856) > at > org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processConnection(Http11Protocol.java:744) > at > org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527) > at > org.apache.tomcat.util.net.MasterSlaveWorkerThread.run(MasterSlaveWorkerThread.java:112) > at java.lang.Thread.run(Thread.java:619) > Caused by: java.lang.NoSuchMethodError: > org.biomoby.shared.parser.ServiceException.toXML()Ljava/lang/String; > at > org.biomoby.shared.parser.MobyPackage.toXMLDocument(MobyPackage.java:235) > at org.biomoby.shared.parser.MobyPackage.toXML(MobyPackage.java:213) > at org.biomoby.service.BaseService.error(BaseService.java:330) > at > org.mmb.moby.webservice.plotFeatureAASequence.plotFeatureAASequenceSkel.plotFeatureAASequence(plotFeatureAASequenceSkel.java:72) > ... 40 more > > > Obviously I've recreated and deployed the jmoby.jar. Should I regenerate > skeletons? I imagine (and hope) not. > > Regards, > > Iv?n > _______________________________________________ > 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 Mon May 28 10:58:17 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 28 May 2007 11:58:17 +0100 Subject: [MOBY-dev] java.lang.NoSuchMethodError launched when MobyExceptionraised In-Reply-To: <465AB45E.5010504@mmb.pcb.ub.es> References: <465AB0C7.2070905@mmb.pcb.ub.es> <465AB45E.5010504@mmb.pcb.ub.es> Message-ID: <4d93f07c0705280358j5416408eyd5b6dc11df50e45f@mail.gmail.com> I am looking at it just now... Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Mon May 28 11:18:56 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 28 May 2007 12:18:56 +0100 Subject: [MOBY-dev] java.lang.NoSuchMethodError launched when MobyException raised In-Reply-To: <465AB0C7.2070905@mmb.pcb.ub.es> References: <465AB0C7.2070905@mmb.pcb.ub.es> Message-ID: <4d93f07c0705280418q4b22ebf2r8f37fef34e23f2a2@mail.gmail.com> Hi Ivan, Is it possible that the return value of the method > ServiceException.toXML() has changed from String to Node (or any other > XML representation) It is not only possible but it is a fact :-). You may recall a private message about it (to you and to Paul), from the last week. Simply speaking, the method signature is back where it was before Paul changed it sometimes ago. and this has not been taking into account in some > other parts of jMoby? I did my best to check this. Did I forgot anything? However, just now I have tried again, and I could not reproduce the behaviour you are reporting. I have raised a MobyException in the sample TestServiceNotes service (which is part of the jMoby), in the processIt() method, and I have got a reasonable output, without any Java exception: 700 Input date was 2007-05-20T10:54:59Z 600 AN ERROR OCCURED DURING THE SERVICE EXECUTION: Yes, this is bad... ... Obviously I've recreated and deployed the jmoby.jar. Should I regenerate > skeletons? I imagine (and hope) not. > No, that would not be necessary. But you need to restart your server I guess (or whatever is needed in JBoss to make it reload all classes. I am not sure how to continue now, how to help you (because definitely the cause of your troubles is in the change of jMoby, but at the moment I believe that the change itself was fixed correctly...). Any idea? Oh, now I think what may be the problem. You said that you "recreated jmoby.jar". But perhaps you have not clean the old classes first. Which would cause the problem. Please do: ./build-devsh clean compile ...and then create jmoby.jar and redeploy. It should fix it. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ivanp at mmb.pcb.ub.es Mon May 28 13:11:08 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Mon, 28 May 2007 15:11:08 +0200 Subject: [MOBY-dev] java.lang.NoSuchMethodError launched whenMobyException raised In-Reply-To: <4d93f07c0705280418q4b22ebf2r8f37fef34e23f2a2@mail.gmail.com> References: <465AB0C7.2070905@mmb.pcb.ub.es> <4d93f07c0705280418q4b22ebf2r8f37fef34e23f2a2@mail.gmail.com> Message-ID: <465AD4EC.9080902@mmb.pcb.ub.es> Thanks Martin, you were right. Sorry, for this newbie mistake, but I'm very used to my own build.xml's which check for these things and recompile if necessary before packing. Thanks for your help, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Martin Senger escribi?: > Hi Ivan, > > Is it possible that the return value of the method > >> ServiceException.toXML() has changed from String to Node (or any other >> XML representation) >> > > > It is not only possible but it is a fact :-). You may recall a private > message about it (to you and to Paul), from the last week. Simply speaking, > the method signature is back where it was before Paul changed it sometimes > ago. > > and this has not been taking into account in some > >> other parts of jMoby? >> > > > I did my best to check this. Did I forgot anything? However, just now I have > tried again, and I could not reproduce the behaviour you are reporting. I > have raised a MobyException in the sample TestServiceNotes service (which is > part of the jMoby), in the processIt() method, and I have got a reasonable > output, without any Java exception: > > > > > > moby:refQueryID="sip_1_"> > 700 > Input date was > 2007-05-20T10:54:59Z > > > 600 > AN ERROR OCCURED DURING THE SERVICE > EXECUTION: Yes, this is bad... > > ... > > Obviously I've recreated and deployed the jmoby.jar. Should I regenerate > >> skeletons? I imagine (and hope) not. >> >> > > No, that would not be necessary. But you need to restart your server I guess > (or whatever is needed in JBoss to make it reload all classes. > > I am not sure how to continue now, how to help you (because definitely the > cause of your troubles is in the change of jMoby, but at the moment I > believe that the change itself was fixed correctly...). Any idea? > > Oh, now I think what may be the problem. You said that you "recreated > jmoby.jar". But perhaps you have not clean the old classes first. Which > would cause the problem. Please do: > > ./build-devsh clean compile > > ...and then create jmoby.jar and redeploy. It should fix it. > > Martin > > From martin.senger at gmail.com Mon May 28 13:23:16 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 28 May 2007 14:23:16 +0100 Subject: [MOBY-dev] java.lang.NoSuchMethodError launched whenMobyException raised In-Reply-To: <465AD4EC.9080902@mmb.pcb.ub.es> References: <465AB0C7.2070905@mmb.pcb.ub.es> <4d93f07c0705280418q4b22ebf2r8f37fef34e23f2a2@mail.gmail.com> <465AD4EC.9080902@mmb.pcb.ub.es> Message-ID: <4d93f07c0705280623p78d02a1er83c74cb0288d3b1a@mail.gmail.com> > Sorry, for this newbie mistake C'mon... you are definitely not a newbie, and I do not think that you made any mistake. Does it mean that your services are now working? If so I am glad and I hope that I have not caused you too much of disturbance. but I'm very used to my own build.xml's > which check for these things and recompile if necessary before packing I do not know about such build.xml :-) Such build.xml would need to check all the internal Java classes dependencies to find that a class whose source code has not been changed should be recompiled because a source code of a class used by that class was changed. I am not aware of such feature in Ant - but if it exists I would be glad to add it there. Please tell us. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ivanp at mmb.pcb.ub.es Mon May 28 13:42:31 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Mon, 28 May 2007 15:42:31 +0200 Subject: [MOBY-dev] java.lang.NoSuchMethodError launchedwhenMobyException raised In-Reply-To: <4d93f07c0705280623p78d02a1er83c74cb0288d3b1a@mail.gmail.com> References: <465AB0C7.2070905@mmb.pcb.ub.es><4d93f07c0705280418q4b22ebf2r8f3 7fef34e23f2a2@mail.gmail.com><465AD4EC.9080902@mmb.pcb.ub.es> <4d93f07c0705280623p78d02a1er83c74cb0288d3b1a@mail.gmail.com> Message-ID: <465ADC47.8000109@mmb.pcb.ub.es> :-D Yes, you're right, this feature does not exist as long as I know. Obviously I wrote the e-mail without thinking very deeply what I was saying. In my head your class was calling directly this method which signature had been changed and so it had to have been changed also. I couldn't understand why a class whose source had been changed, was not being recompiled by ANT (but in fact, as you say, its was unchanged). By the way, my services working again, yes ;-) Thanks, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Martin Senger escribi?: >> Sorry, for this newbie mistake >> > > > C'mon... you are definitely not a newbie, and I do not think that you made > any mistake. Does it mean that your services are now working? If so I am > glad and I hope that I have not caused you too much of disturbance. > > but I'm very used to my own build.xml's > >> which check for these things and recompile if necessary before packing >> > > > I do not know about such build.xml :-) Such build.xml would need to check > all the internal Java classes dependencies to find that a class whose source > code has not been changed should be recompiled because a source code of a > class used by that class was changed. I am not aware of such feature in Ant > - but if it exists I would be glad to add it there. Please tell us. > > Cheers, > Martin > > From gordonp at ucalgary.ca Mon May 28 14:54:45 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 28 May 2007 08:54:45 -0600 Subject: [MOBY-dev] Dashboard and date types In-Reply-To: <4d93f07c0705210101q11e43c79g36abdc2986346e8c@mail.gmail.com> References: <4614FCE8.70904@mmb.pcb.ub.es> <4d93f07c0705201757y656fd6danfe60fb26bd81193d@mail.gmail.com> <465144D1.7070706@cnio.es> <4d93f07c0705210101q11e43c79g36abdc2986346e8c@mail.gmail.com> Message-ID: <465AED35.6010600@ucalgary.ca> The ISO8601 parsing code is pretty much ripped directly from a W3C library (and attributed in the comments), so I left the thinking to someone else too. :-) I'll have a look at this timezone issue in the next couple of days though. > HI, > > have you taken into account that daylight saving is currently in effect? > > > No, but I thought about it. Then I let the thinking to Paul (after all, I am > using his method to convert a calendar to a string :-)). > > GMT > From martin.senger at gmail.com Mon May 28 15:35:45 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 28 May 2007 16:35:45 +0100 Subject: [MOBY-dev] Dashboard and date types In-Reply-To: <465AED35.6010600@ucalgary.ca> References: <4614FCE8.70904@mmb.pcb.ub.es> <4d93f07c0705201757y656fd6danfe60fb26bd81193d@mail.gmail.com> <465144D1.7070706@cnio.es> <4d93f07c0705210101q11e43c79g36abdc2986346e8c@mail.gmail.com> <465AED35.6010600@ucalgary.ca> Message-ID: <4d93f07c0705280835l4e03bb4et1ab19b012ab20e3a@mail.gmail.com> > The ISO8601 parsing code is pretty much ripped directly from a W3C > library (and attributed in the comments), so I left the thinking to > someone else too. :-) > > I'll have a look at this timezone issue in the next couple of days though. Okay, glad to hear it. For me (us), it does not matter much that the method was ripped from someone else's code, the important is whether it is correct or not. Thanks for looking into it. This is just a reminder of my observations regarding this method: Last, and actually the main question, is that I suspect a bug in the method > MobyDataDateTime.getString(calendar). When I feed it with the calendar > created from the string "2007-05-21T00:40:35+01:00" I will get a string > "2007-05-21T02:40:35Z". The method removed timezone (and replaced it with a > single Z letter, which is correct) but the time - that should be now in GMT > - is now bigger by two hours when I expected decrease by one hour (moving > from my BST time which is +01 to the GMT). Is this a bug or my > misinterpretation of the times? > Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Mon May 28 21:22:56 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 28 May 2007 22:22:56 +0100 Subject: [MOBY-dev] looking for a functioning asynchronous service... Message-ID: <4d93f07c0705281422g5c195438tddb885de14d9fa2@mail.gmail.com> ...preferable one that does not take too long to finish. Any help here? If yes please let me know also some good input data for it. Many thanks. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Tue May 29 03:56:11 2007 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 29 May 2007 04:56:11 +0100 Subject: [MOBY-dev] few fixes in jMoby Message-ID: <4d93f07c0705282056lb746cc8t9de9d3a24d9bfd52@mail.gmail.com> Few fixes dealing with the fact that we do not have anymore just services with 'moby' category but also with 'moby-async' category. Until now (before this fix), the latter ones were not included in search results - not even in the Dashboard browser. Cheers, Martin ChangeLog -------------- 2007-05-29 Martin Senger * Fixed: on various place where a service was looking for, the used service pattern has now category empty (so not only services with the default 'moby' category are found). * Changed: the output list with names of found services (created by MobyCmdLineClient) contains now also service authority. * Added: MobyCmdLineClient has a new option -fc for finding services by category. -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Tue May 29 21:45:16 2007 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 29 May 2007 22:45:16 +0100 Subject: [MOBY-dev] is anything wrong with asynchrounous services? Message-ID: <4d93f07c0705291445l31af2064y60fd60981d3027ea@mail.gmail.com> I have just spent a day trying to implement the asynchronous services spec in jMoby. Thanks to an immediate help from Natalia, Johan, Romina, Ivan a probably others, I was able to call an asynchronous service and make some progress. The progress stopped, however, soon, and I am now wondering where is the problem. It can be in the asynchronous specification itself, or in the implementation of a service I was trying to call, or in my lack of knowledge of web services protocols. Please help me clarify the situation. The problem starts immediately at the beginning, with the first response, so we do not need to go and dive into the SOAP headers. Just as the spec says, the first step is that a client sends a request (submit) to an asynchronous service: "This message is identical to the BioMOBY XML to request synchronous service > execution. The only difference is that > the client sends the request to the servicename_submit SOAP method." > This went fine, in my case. The second step is that the service responds with a body that contains a WS-Addressing-based EndpointReference. The service I was using, indeed, did so. The problem is not with the contents of such response, but with its format (well, now I am already expressing my opinions, which I should not do...). It looks like this: http://inb.bsc.es/cgi-bin/mobyServices/asyncDispatcher.cgi 5627142941072148070044 The above is exactly what the biomoby spec for async. services says it should be. That's why I do not think that the problem is in the implementation. I believe that it is either in the spec or in my understanding (or better the lack of understanding). What I see is that this is not an RPC/Encoded response. This looks more like a document/literal response. And, indeed, the Axis toolkit I am using, refuses to parse such message complaining that there are some unexpected children elements. And it is true: in the RPC/Encoded style, the contents of the tag (or its child, I am not sure) should be a string without any (visible, not-encoded) XML. Like in any normal Biomoby response. Shortly, this response should look, XML-encoding-wise, like any other Biomoby response. Which it does not I think. So where is the problem? It is just me who do not fully understand the difference between RPC/Encoded and document/literal style? Even if so, I wonder if anybody can "convince" Axis to send a request as RPC/encoded (as the spec requires) and receive a response as document/literal. You may ask why this does not matter in the Eddie's AsyncClient? As I see it it is because Eddie creates there everything manually, so he is allowed to send a request one style and parse the response in another style. Which I feel is not a right way to do. Of course, I said already several times that I will be glad if someone explains that I see it in a wrong way. I really appreciate any answers, especially please soon answers - because the next weekend there is a small meeting of Java biomoby developers in Vancouver and we may discuss this issue there if we have some background explanations and opinions from you. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Tue May 29 23:59:06 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 29 May 2007 17:59:06 -0600 Subject: [MOBY-dev] Dashboard and date types In-Reply-To: <4d93f07c0705280835l4e03bb4et1ab19b012ab20e3a@mail.gmail.com> References: <4614FCE8.70904@mmb.pcb.ub.es> <4d93f07c0705201757y656fd6danfe60fb26bd81193d@mail.gmail.com> <465144D1.7070706@cnio.es> <4d93f07c0705210101q11e43c79g36abdc2986346e8c@mail.gmail.com> <465AED35.6010600@ucalgary.ca> <4d93f07c0705280835l4e03bb4et1ab19b012ab20e3a@mail.gmail.com> Message-ID: <465CBE4A.5020308@ucalgary.ca> After going crazy for hours trying to get SimpleDateFormat to work properly, I rolled my own formatter. I also now keep the timezone offset data, rather than converting to Zulu time (a.k.a. GMT). I have added some test cases too, so it definitely works for samples from Central European times (daylight and standard), Halifax (Canada) standard, and Newfoundland (which uses a half-hour zone). One minor point: "2007-05-21T00:40:35+01:00" is the time in London (i.e. ISO8601 does not store daylight data, so time zones flip offsets in autumn and spring relative to GMT) This should now be Case Closed! >> The ISO8601 parsing code is pretty much ripped directly from a W3C >> library (and attributed in the comments), so I left the thinking to >> someone else too. :-) >> >> I'll have a look at this timezone issue in the next couple of days though. >> > > > Okay, glad to hear it. For me (us), it does not matter much that the method > was ripped from someone else's code, the important is whether it is correct > or not. Thanks for looking into it. This is just a reminder of my > observations regarding this method: > > Last, and actually the main question, is that I suspect a bug in the method > >> MobyDataDateTime.getString(calendar). When I feed it with the calendar >> created from the string "2007-05-21T00:40:35+01:00" I will get a string >> "2007-05-21T02:40:35Z". The method removed timezone (and replaced it with a >> single Z letter, which is correct) but the time - that should be now in GMT >> - is now bigger by two hours when I expected decrease by one hour (moving >> from my BST time which is +01 to the GMT). Is this a bug or my >> misinterpretation of the times? >> >> > > Cheers, > Martin > > > From L.Barboza at cgiar.org Thu May 31 03:12:32 2007 From: L.Barboza at cgiar.org (Barboza, Lord Hendrix (IRRI)) Date: Thu, 31 May 2007 11:12:32 +0800 Subject: [MOBY-dev] help: local registry installation Message-ID: I have already got and installed the biomoby code in the server. Then running the "make test" give me this result: PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Central.....................ok t/Client-Central..............ok 22/0:7: parser error : Sequence ']]>' not allowed in content ]]>]]> ^ :7: parser error : internal error ]]>]]> ^ :7: parser error : Extra content at the end of the document ]]>]]> ^ at /usr/local/moby-live/Perl/blib/lib/MOBY/Client/Central.pm line 2107 t/Client-Central..............ok 23/0# Looks like your test died just after 23. t/Client-Central..............dubious Test returned status 255 (wstat 65280, 0xff00) after all the subtests completed successfully t/Client-CollectionArticle....ok t/Client-OntologyServer.......ok t/Client-Registration.........ok t/Client-SecondaryArticle.....ok t/Client-Service..............ok 2/0:7: parser error : Sequence ']]>' not allowed in content ]]>]]> ^ :7: parser error : internal error ]]>]]> ^ :7: parser error : Extra content at the end of the document ]]>]]> ^ at /usr/local/moby-live/Perl/blib/lib/MOBY/Client/Central.pm line 2107 # Looks like your test died just after 2. t/Client-Service..............dubious Test returned status 255 (wstat 65280, 0xff00) after all the subtests completed successfully t/Client-ServiceInstance......ok t/Client-SimpleArticle........ok t/CommonSubs..................ok t/Config......................skipped all skipped: Required only when you have your own local MOBY Central t/CrossReference..............ok t/Template....................ok Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------ ------- t/Client-Central.t 255 65280 23 0 0.00% ?? t/Client-Service.t 255 65280 2 0 0.00% ?? 1 test skipped. Failed 2/13 test scripts, 84.62% okay. 0/235 subtests failed, 100.00% okay. make: *** [test_dynamic] Error 255 lbarboza at cropwiki:/usr/local/moby-live/Perl$ -bash: syntax error near unexpected token `newline' I am using perl v5.8.4. pls help thanks Lord Hendrix A. Barbozax` Programmer - Web Services Crop Research Informatics Laboratory (CRIL) From maliha.aziz at asu.edu Thu May 31 07:15:28 2007 From: maliha.aziz at asu.edu (Maliha Aziz) Date: Thu, 31 May 2007 00:15:28 -0700 Subject: [MOBY-dev] dashboard error ! Message-ID: hi does anyone know why dashboard is giving me the following error as soon as it builds and the main screen comes up and it tires to populate its lists of services , datatypes etc the following is the text displayed on the screen ( window) An error happened when accessing a list of available services Check please values in text fields( in Registry Browser) specifying registry endpoint and namespace , and in the one specifying directory used as local cache. Then right-click in the data types area and select 'Reload'. the actual error is http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.plnull From martin.senger at gmail.com Thu May 31 16:15:18 2007 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 31 May 2007 17:15:18 +0100 Subject: [MOBY-dev] dashboard error ! In-Reply-To: References: Message-ID: <4d93f07c0705310915t44a66786yde17f3ceb61eb236@mail.gmail.com> > An error happened when accessing a list of available services > Check please values in text fields( in Registry Browser) specifying > registry > endpoint and namespace , and in the one specifying directory used as local > cache. So what are those values in your case? I am attaching (as an image) what I see in my dashboard. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger -------------- next part -------------- A non-text attachment was scrubbed... Name: browser-screen.png Type: image/png Size: 9221 bytes Desc: not available URL: From markw at illuminae.com Thu May 31 16:06:16 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 31 May 2007 09:06:16 -0700 Subject: [MOBY-dev] help: local registry installation In-Reply-To: References: Message-ID: Never seen that error before... perhaps check that your LibXML C libraries are up-to-date? They are used by the XML::LibXML module that Moby uses for XML parsing. M On Wed, 30 May 2007 20:12:32 -0700, Barboza, Lord Hendrix (IRRI) wrote: > I have already got and installed the biomoby code in the server. Then > running the "make test" give me this result: > > > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > > t/Central.....................ok > > > t/Client-Central..............ok 22/0:7: parser error : Sequence ']]>' > not allowed in content > > ]]>]]> > > ^ > > :7: parser error : internal error > > ]]>]]> > > ^ > > :7: parser error : Extra content at the end of the document > > ]]>]]> > > ^ > > at /usr/local/moby-live/Perl/blib/lib/MOBY/Client/Central.pm line 2107 > > t/Client-Central..............ok 23/0# Looks like your test died just > after 23. > > t/Client-Central..............dubious > > > Test returned status 255 (wstat 65280, 0xff00) > > after all the subtests completed successfully > > t/Client-CollectionArticle....ok > > > t/Client-OntologyServer.......ok > > > t/Client-Registration.........ok > > > t/Client-SecondaryArticle.....ok > > > t/Client-Service..............ok 2/0:7: parser error : Sequence ']]>' > not allowed in content > > ]]>]]> > > ^ > > :7: parser error : internal error > > ]]>]]> > > ^ > > :7: parser error : Extra content at the end of the document > > ]]>]]> > > ^ > > at /usr/local/moby-live/Perl/blib/lib/MOBY/Client/Central.pm line 2107 > > # Looks like your test died just after 2. > > t/Client-Service..............dubious > > > Test returned status 255 (wstat 65280, 0xff00) > > after all the subtests completed successfully > > t/Client-ServiceInstance......ok > > > t/Client-SimpleArticle........ok > > > t/CommonSubs..................ok > > > t/Config......................skipped > > all skipped: Required only when you have your own local MOBY > Central > > t/CrossReference..............ok > > > t/Template....................ok > > > Failed Test Stat Wstat Total Fail Failed List of Failed > > ------------------------------------------------------------------------ > ------- > > t/Client-Central.t 255 65280 23 0 0.00% ?? > > t/Client-Service.t 255 65280 2 0 0.00% ?? > > 1 test skipped. > > Failed 2/13 test scripts, 84.62% okay. 0/235 subtests failed, 100.00% > okay. > > make: *** [test_dynamic] Error 255 > > lbarboza at cropwiki:/usr/local/moby-live/Perl$ > > -bash: syntax error near unexpected token `newline' > > > > I am using perl v5.8.4. pls help > > > thanks > > > Lord Hendrix A. Barbozax` > > Programmer - Web Services > > Crop Research Informatics Laboratory (CRIL) > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From Pieter.Neerincx at wur.nl Thu May 31 19:01:29 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 31 May 2007 21:01:29 +0200 Subject: [MOBY-dev] help: local registry installation In-Reply-To: References: Message-ID: Hi, I also didn't see this specific case before, but it looks like a double encoded CDATA section. We've had problems with double encoded stuff before due to the way some versions of SOAP::Lite were handling encoding/decoding. If you are running SOAP::Lite < 0.69 please upgrade to 0.69. If you are running something more recent please let us know. Might be a new S::L peculiarity in that case... Cheers, Pi On 31 May 2007, at 18:06, Mark Wilkinson wrote: > Never seen that error before... > > perhaps check that your LibXML C libraries are up-to-date? They > are used > by the XML::LibXML module that Moby uses for XML parsing. > > M > > > > On Wed, 30 May 2007 20:12:32 -0700, Barboza, Lord Hendrix (IRRI) > wrote: > >> I have already got and installed the biomoby code in the server. Then >> running the "make test" give me this result: >> >> >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >> >> t/Central.....................ok >> >> >> t/Client-Central..............ok 22/0:7: parser error : Sequence >> ']]>' >> not allowed in content >> >> ]]>]]> >> >> ^ >> >> :7: parser error : internal error >> >> ]]>]]> >> >> ^ >> >> :7: parser error : Extra content at the end of the document >> >> ]]>]]> >> >> ^ >> >> at /usr/local/moby-live/Perl/blib/lib/MOBY/Client/Central.pm line >> 2107 >> >> t/Client-Central..............ok 23/0# Looks like your test died just >> after 23. >> >> t/Client-Central..............dubious >> >> >> Test returned status 255 (wstat 65280, 0xff00) >> >> after all the subtests completed successfully >> >> t/Client-CollectionArticle....ok >> >> >> t/Client-OntologyServer.......ok >> >> >> t/Client-Registration.........ok >> >> >> t/Client-SecondaryArticle.....ok >> >> >> t/Client-Service..............ok 2/0:7: parser error : Sequence ']]>' >> not allowed in content >> >> ]]>]]> >> >> ^ >> >> :7: parser error : internal error >> >> ]]>]]> >> >> ^ >> >> :7: parser error : Extra content at the end of the document >> >> ]]>]]> >> >> ^ >> >> at /usr/local/moby-live/Perl/blib/lib/MOBY/Client/Central.pm line >> 2107 >> >> # Looks like your test died just after 2. >> >> t/Client-Service..............dubious >> >> >> Test returned status 255 (wstat 65280, 0xff00) >> >> after all the subtests completed successfully >> >> t/Client-ServiceInstance......ok >> >> >> t/Client-SimpleArticle........ok >> >> >> t/CommonSubs..................ok >> >> >> t/Config......................skipped >> >> all skipped: Required only when you have your own local MOBY >> Central >> >> t/CrossReference..............ok >> >> >> t/Template....................ok >> >> >> Failed Test Stat Wstat Total Fail Failed List of Failed >> >> --------------------------------------------------------------------- >> --- >> ------- >> >> t/Client-Central.t 255 65280 23 0 0.00% ?? >> >> t/Client-Service.t 255 65280 2 0 0.00% ?? >> >> 1 test skipped. >> >> Failed 2/13 test scripts, 84.62% okay. 0/235 subtests failed, 100.00% >> okay. >> >> make: *** [test_dynamic] Error 255 >> >> lbarboza at cropwiki:/usr/local/moby-live/Perl$ >> >> -bash: syntax error near unexpected token `newline' >> >> >> >> I am using perl v5.8.4. pls help >> >> >> thanks >> >> >> Lord Hendrix A. Barbozax` >> >> Programmer - Web Services >> >> Crop Research Informatics Laboratory (CRIL) >> >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the > addressee and > may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have > received this > communication in error, please notify the sender immediately by reply > e-mail and delete the original and all copies from your system. > > > _______________________________________________ > 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: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online -------------------------------------------------------------