From johan at ac.uma.es Mon Oct 2 08:51:00 2006 From: johan at ac.uma.es (Johan Karlsson) Date: Mon, 02 Oct 2006 14:51:00 +0200 Subject: [MOBY-dev] Reminder: Vote async proposal In-Reply-To: <1158947474.5704.30.camel@bioinfo.icapture.ubc.ca> References: <45125B5A.1070402@ac.uma.es> <4d93f07c0609220945l2fadb6f5tc2bca1820f0f44ad@mail.gmail.com> <1158947474.5704.30.camel@bioinfo.icapture.ubc.ca> Message-ID: <45210B34.7020705@ac.uma.es> Mark Wilkinson wrote: >> There is really no such thing as an RFC committee... >> > > Well... there is a group of us who have agreed to be "the deciders" (to > quote George Bush... I'll never do that again, I promise!) > > > >> But yes, I agree to >> have a vote - if the political issue (regardinr using a SOAP-specific >> technology) is considered to be solved. How is it, Mark? >> > > > There was no significant discussion of this issue beyond the brief > conversation that we had on the mailing list. My own opinion is that we > have (possibly regrettably) already bought-in to the SOAP > infrastructure, so using a SOAP-specific technology is a reasonable > thing to do at this point. It does make it more difficult to change our > minds later on, but I suspect that any mind-changing in the future is > going to be on an much larger scale than just the transport protocol, so > this small detail is not particularly relevant in that context. In my > opinion, that discussion is resolved. Does anyone disagree? > > v.v. the Asynch proposal - let's call for the vote right now. All > voting members please read the proposal carefully and submit your vote > by October 1. > > M > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -- 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 martin.senger at gmail.com Mon Oct 2 09:14:03 2006 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 2 Oct 2006 14:14:03 +0100 Subject: [MOBY-dev] Reminder: Vote async proposal In-Reply-To: <45210B34.7020705@ac.uma.es> References: <45125B5A.1070402@ac.uma.es> <4d93f07c0609220945l2fadb6f5tc2bca1820f0f44ad@mail.gmail.com> <1158947474.5704.30.camel@bioinfo.icapture.ubc.ca> <45210B34.7020705@ac.uma.es> Message-ID: <4d93f07c0610020614h508d2ffch61ef0e941de07e42@mail.gmail.com> Well, I am still not sure that I understand the proposal fully (not because it is a bad proposal but because I have not spent enough time on it). But I believe fully in the wisdom of our Spanish colleagues, the wisdom I hope to learn when I will be implementing the async behaviour in Moses) - and therefore I vote YES. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From dgpisano at cnb.uam.es Mon Oct 2 09:30:45 2006 From: dgpisano at cnb.uam.es (David G. Pisano) Date: Mon, 2 Oct 2006 15:30:45 +0200 Subject: [MOBY-dev] Reminder: Vote async proposal In-Reply-To: <4d93f07c0610020614h508d2ffch61ef0e941de07e42@mail.gmail.com> References: <45125B5A.1070402@ac.uma.es><4d93f07c0609220945l2fadb6f5tc2bca18 20f0f44ad@mail.gmail.com><1158947474.5704.30.camel@bioinfo.icapture.ubc.ca> <45210B34.7020705@ac.uma.es> <4d93f07c0610020614h508d2ffch61ef0e941de07e42@mail.gmail.com> Message-ID: Voting YES here too (no surprises) ;-) David On 02/10/2006, at 15:14, Martin Senger wrote: > Well, I am still not sure that I understand the proposal fully (not > because > it is a bad proposal but because I have not spent enough time on > it). But I > believe fully in the wisdom of our Spanish colleagues, the wisdom I > hope to > learn when I will be implementing the async behaviour in Moses) - and > therefore I vote YES. > > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From Pieter.Neerincx at wur.nl Mon Oct 2 10:39:56 2006 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Mon, 2 Oct 2006 16:39:56 +0200 Subject: [MOBY-dev] Reminder: Vote async proposal In-Reply-To: <4d93f07c0610020614h508d2ffch61ef0e941de07e42@mail.gmail.com> References: <45125B5A.1070402@ac.uma.es> <4d93f07c0609220945l2fadb6f5tc2bca1820f0f44ad@mail.gmail.com> <1158947474.5704.30.camel@bioinfo.icapture.ubc.ca> <45210B34.7020705@ac.uma.es> <4d93f07c0610020614h508d2ffch61ef0e941de07e42@mail.gmail.com> Message-ID: <9AB24052-73B0-451C-9971-01C146E9F0D2@wur.nl> Hi, Well, I read the proposal and the involved standards. I think it's very important to have a standard for asynchronous services and the process of getting there already took a lot of time. I also think that such a standard should be very robust and ready for the future. Adding things shouldn't be too much of a hassle, but once we implement this it will be a pain if we have to modify it in such a way that all asynchronous services "break". So I think this standard should be damned good from the start :). As mentioned before I feel the way the queryIDs are passed around in the XMl is sub-optimal, making asynchronous service behaviour unnecessarily complicated. More explicitly with what I understand from the WSRF standard I'm not comfortable with "dynamic" resource properties (individual resource properties for status / fetching results for each individual queryID). Therefore - although I like the big picture - I vote NO on the current proposal. I will support any proposal that gets accepted for the sake of interoperability as this is paramount for BioMOBY, but I would prefer a more elegant solution. Cheers, Pi On 2-Oct-2006, at 3:14 PM, Martin Senger wrote: > Well, I am still not sure that I understand the proposal fully (not > because > it is a bad proposal but because I have not spent enough time on > it). But I > believe fully in the wisdom of our Spanish colleagues, the wisdom I > hope to > learn when I will be implementing the async behaviour in Moses) - and > therefore I vote YES. > > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl From edward.kawas at gmail.com Mon Oct 2 10:27:03 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 2 Oct 2006 07:27:03 -0700 Subject: [MOBY-dev] Reminder: Vote async proposal In-Reply-To: <4d93f07c0610020614h508d2ffch61ef0e941de07e42@mail.gmail.com> Message-ID: <004501c6e62e$d5baefc0$6400a8c0@notebook> I vote yes as well. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > Martin Senger > Sent: Monday, October 02, 2006 6:14 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Reminder: Vote async proposal > > Well, I am still not sure that I understand the proposal > fully (not because it is a bad proposal but because I have > not spent enough time on it). But I believe fully in the > wisdom of our Spanish colleagues, the wisdom I hope to learn > when I will be implementing the async behaviour in Moses) - > and therefore I vote YES. > > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From johan at ac.uma.es Mon Oct 2 15:36:16 2006 From: johan at ac.uma.es (Johan Karlsson) Date: Mon, 02 Oct 2006 21:36:16 +0200 Subject: [MOBY-dev] Reminder: Vote async proposal In-Reply-To: <9AB24052-73B0-451C-9971-01C146E9F0D2@wur.nl> References: <45125B5A.1070402@ac.uma.es> <4d93f07c0609220945l2fadb6f5tc2bca1820f0f44ad@mail.gmail.com> <1158947474.5704.30.camel@bioinfo.icapture.ubc.ca> <45210B34.7020705@ac.uma.es> <4d93f07c0610020614h508d2ffch61ef0e941de07e42@mail.gmail.com> <9AB24052-73B0-451C-9971-01C146E9F0D2@wur.nl> Message-ID: <45216A30.6080803@ac.uma.es> Hi Pieter, Sorry to hear that you have a negative opinion of the proposal. From our point of view, the details you are mentioning are minor (in the sense that they are simply choices where to place the information). The same information is sent, the number of SOAP calls are the same. It is not more (or less) optimal to send the queryIDs in the SOAP header than it is to send it in the SOAP body, so we do not understand what you mean with "sub-optimal". As we wrote before, it is possible (you agreed with this also earlier) to implement a getResourcePropertyDocument operation in the future with the approach in the proposal. With only two properties named "status" and "result", the structure would be more "fixed", but the values must still be put there by the service, so the document is not "static" but must be dynamically generated. With dynamic property-names the client must construct these names by appending the queryID to status or result but this is really, as you put it, far from "rocket-science". All these details are hidden by API functions (that we are providing), so it is not critical to change in the future if necessary. Kind regards, Johan Pieter Neerincx wrote: > Hi, > > Well, I read the proposal and the involved standards. I think it's > very important to have a standard for asynchronous services and the > process of getting there already took a lot of time. I also think > that such a standard should be very robust and ready for the future. > Adding things shouldn't be too much of a hassle, but once we > implement this it will be a pain if we have to modify it in such a > way that all asynchronous services "break". So I think this standard > should be damned good from the start :). > > As mentioned before I feel the way the queryIDs are passed around in > the XMl is sub-optimal, making asynchronous service behaviour > unnecessarily complicated. More explicitly with what I understand > from the WSRF standard I'm not comfortable with "dynamic" resource > properties (individual resource properties for status / fetching > results for each individual queryID). Therefore - although I like the > big picture - I vote NO on the current proposal. > > I will support any proposal that gets accepted for the sake of > interoperability as this is paramount for BioMOBY, but I would prefer > a more elegant solution. > > Cheers, > > Pi > > On 2-Oct-2006, at 3:14 PM, Martin Senger wrote: > > >> Well, I am still not sure that I understand the proposal fully (not >> because >> it is a bad proposal but because I have not spent enough time on >> it). But I >> believe fully in the wisdom of our Spanish colleagues, the wisdom I >> hope to >> learn when I will be implementing the async behaviour in Moses) - and >> therefore I vote YES. >> >> Martin >> >> -- >> Martin Senger >> email: martin.senger at gmail.com >> skype: martinsenger >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > phone: 0317-483 060 > fax: 0317-483 584 > mobile: 06-143 66 783 > pieter.neerincx at wur.nl > > > > _______________________________________________ > 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 Oct 2 17:30:44 2006 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 2 Oct 2006 22:30:44 +0100 Subject: [MOBY-dev] small updates to Dashboard Message-ID: <4d93f07c0610021430x56f003a1l34d233fb43eb0e09@mail.gmail.com> I have added a list of well-known registries to the registry browser panel (so changing registry should be easier now, one does not need to remember their URLs). It i also possible to add your own registry - that you wish to keep just for your site (see Dashboard documentation how to do it). Dirk gave me an idea to add a new button "Call RDF Agent". The button is now in the service registration panel. Further testing of its usefulness is needed - please let me know how to improve it. Therefore, please, cvs update... Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Mon Oct 2 18:54:24 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 02 Oct 2006 15:54:24 -0700 Subject: [MOBY-dev] Asynch proposal Message-ID: <1159829664.30244.28.camel@bioinfo.icapture.ubc.ca> I just re-read it and it looks great! YES from here! We are waiting on three more votes, four positive votes so far, one negative. Democratically we can't call it without one more positive vote. I have c.c.'d the three absentees on this message. M -- Mark Wilkinson Asst. Professor, Dept. of Medical Genetics University of British Columbia PI in Bioinformatics, iCAPTURE Centre St. Paul's Hospital, Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 "Since the point of a definition is to explain the meaning of a term to someone who is unfamiliar with its proper application, the use of language that doesn't help such a person learn how to apply the term is pointless. Thus, "happiness is a warm puppy" may be a lovely thought, but it is a lousy definition." K?hler et al, 2006 From markw at illuminae.com Mon Oct 2 18:33:41 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 02 Oct 2006 15:33:41 -0700 Subject: [MOBY-dev] Asynchronous service Message-ID: <1159828421.30244.5.camel@bioinfo.icapture.ubc.ca> I've just re-read it and it looks great to me. YES! 4 votes for YES 1 vote for NO 3 votes still missing We're missing Paul Gordon, Frank Gibbons, and Simon Twigger (c.c.'d on this message in case they aren't reading the MOBY mailing list) Democratically, we have only half the YES votes necessary for success so far, so we need them to vote. M -- Mark Wilkinson Asst. Professor, Dept. of Medical Genetics University of British Columbia PI in Bioinformatics, iCAPTURE Centre St. Paul's Hospital, Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 "Since the point of a definition is to explain the meaning of a term to someone who is unfamiliar with its proper application, the use of language that doesn't help such a person learn how to apply the term is pointless. Thus, "happiness is a warm puppy" may be a lovely thought, but it is a lousy definition." K?hler et al, 2006 From Pieter.Neerincx at wur.nl Mon Oct 2 19:14:15 2006 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Tue, 3 Oct 2006 01:14:15 +0200 Subject: [MOBY-dev] Reminder: Vote async proposal In-Reply-To: <45216A30.6080803@ac.uma.es> References: <45125B5A.1070402@ac.uma.es> <4d93f07c0609220945l2fadb6f5tc2bca1820f0f44ad@mail.gmail.com> <1158947474.5704.30.camel@bioinfo.icapture.ubc.ca> <45210B34.7020705@ac.uma.es> <4d93f07c0610020614h508d2ffch61ef0e941de07e42@mail.gmail.com> <9AB24052-73B0-451C-9971-01C146E9F0D2@wur.nl> <45216A30.6080803@ac.uma.es> Message-ID: <4C022C4C-F667-4E0E-9555-C6AFFA6305CD@wur.nl> Hi Johan, On 02 Oct 2006, at 21:36, Johan Karlsson wrote: > Hi Pieter, > > Sorry to hear that you have a negative opinion of the proposal. It's not that dramatic. Like I said I'm very happy the people at the INB took the effort to write a proposal (twice!) for asynchronous service behaviour. I also think using WS Adressing and the WSRF standards is a good idea and the big picture of how to implement this for BioMOBY looks good! But you have called a vote on the current version of the proposal and I can not vote yes for 97%. It's either a yes or a no. > From our point of view, the details you are mentioning are minor (in > the sense that they are simply choices where to place the > information). Correct. > The same information is sent, the number of SOAP calls are the same. Indeed. > It is not more (or less) optimal to send the queryIDs in the SOAP > header > than it is to send it in the SOAP body, so we do not understand > what you > mean with "sub-optimal". Ok, let my try to explain with another example then. One of the strengths of BioMOBY is the Object ontology which greatly improves interoperability. The objects in this ontology are described using "self-describing" XML. It is possible though to send for example "lagacy" tab delimited data inside a String object. We do have such objects for backwards copatibility, but it's not an elegant way to send data around. Using tab delimited data defeats the purpose of the object ontology as a client can not figure out the relationships between the data within the tab delimited text block. A client has no way to figure what is in column 1,2,3, etc. and the data from column 2 can not easily be parsed using an XML parser to send it as input to another service. Surely you can write a rather simple piece of code that uses a regular expression to fetch the values from column 2 wrap it in new XML tags and send it to the next service and although this is not rocket science it's not elegant and it hampers interoperability. In the current proposal the queryIDs jump around the XMl as part of an element name, as an attribute and as part of raw text. Especially the resource properties are problematic in my point of view. You are doing something similar to wrapping tab delimited data when you combine: * the kind of resource property you want to request (status or result) * with the ID of an individual job of a batch (queryID) and send these merged as a text string like in: status_queryID01, status_queryID02, status_queryID03, etc. and result_queryID01, result_queryID02, result_queryID03, etc. Surely you can write code to fetch the raw text from a node and use a regular expression to split on "_" and hence seperate the kind of resource property requested from the job ID, but just like with tab delimited data it's an ugly approach to put different types of data inside raw text. You lose the semantics and it's not necessary! Some time ago I send some XML examples to show that with some minor tweaks to the XML passed around we can still use WS addressing and WSRF and make sure the queryIDs remain attributes like with the current synchronous services. It makes the XML more consequent and less confusing. > As we wrote before, it is possible (you agreed with this also earlier) > to implement a getResourcePropertyDocument operation in the future > with > the approach in the proposal. True, but with the current proposal you would have to generate a ResourcePropertyDocument dynamically for each service invocation, whereas with a few minor tweaks you can have a static ResourcePropertyDocument for a service which is the same for each invocation. It's not rocket science to create a ResourcePropertyDocument for each service request, but it is simply unnecessary overhead. > With only two properties named "status" > and "result", the structure would be more "fixed", but the values must > still be put there by the service, so the document is not "static" but > must be dynamically generated. No, the ResourcePropertyDocument would be static if the queryIDs move to the EPR. Making the actual request to get resource properties would be a dynamic thing as the queryIDs have to be there somewhere in the data structure, but if they are part of the EPR a client can simply take them from the successful service invocation and echo them back. This would simply require less logic. Finally I feel the current proposal is sub-optimal because, the result XML from an asynchronous service is slightly different from the XML produced by a synchronous service. For an asynchronous service result there are extra and redundant tags. Having a few more tags makes life not impossible - the prototype surely works - but again I think it's ugly and most of all not necessary. With a few minor tweaks the results of asynchronous and synchronous services can be exactly the same which is more transparent in my point of view. Since it requires only minor tweaks to the XML that is send around to make the asynchronous service behavior more transparent, I assume it won't be a big deal to change the proposal and the prototype, but please correct me if I overlooked something here... Hope it's more clear now and with kind regards, Pi > With dynamic property-names the client > must construct these names by appending the queryID to status or > result > but this is really, as you put it, far from "rocket-science". > > All these details are hidden by API functions (that we are providing), > so it is not critical to change in the future if necessary. > Kind regards, > Johan > > > Pieter Neerincx wrote: >> Hi, >> >> Well, I read the proposal and the involved standards. I think it's >> very important to have a standard for asynchronous services and the >> process of getting there already took a lot of time. I also think >> that such a standard should be very robust and ready for the future. >> Adding things shouldn't be too much of a hassle, but once we >> implement this it will be a pain if we have to modify it in such a >> way that all asynchronous services "break". So I think this standard >> should be damned good from the start :). >> >> As mentioned before I feel the way the queryIDs are passed around in >> the XMl is sub-optimal, making asynchronous service behaviour >> unnecessarily complicated. More explicitly with what I understand >> from the WSRF standard I'm not comfortable with "dynamic" resource >> properties (individual resource properties for status / fetching >> results for each individual queryID). Therefore - although I like the >> big picture - I vote NO on the current proposal. >> >> I will support any proposal that gets accepted for the sake of >> interoperability as this is paramount for BioMOBY, but I would prefer >> a more elegant solution. >> >> Cheers, >> >> Pi >> >> On 2-Oct-2006, at 3:14 PM, Martin Senger wrote: >> >> >>> Well, I am still not sure that I understand the proposal fully (not >>> because >>> it is a bad proposal but because I have not spent enough time on >>> it). But I >>> believe fully in the wisdom of our Spanish colleagues, the wisdom I >>> hope to >>> learn when I will be implementing the async behaviour in Moses) - >>> and >>> therefore I vote YES. >>> >>> Martin >>> >>> -- >>> Martin Senger >>> email: martin.senger at gmail.com >>> skype: martinsenger >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> >> >> Wageningen University and Research centre (WUR) >> Laboratory of Bioinformatics >> Transitorium (building 312) room 1034 >> Dreijenlaan 3 >> 6703 HA Wageningen >> The Netherlands >> phone: 0317-483 060 >> fax: 0317-483 584 >> mobile: 06-143 66 783 >> pieter.neerincx at wur.nl >> >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1038 Dreijenlaan 3 6703 HA Wageningen phone: 0317-484 706 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl From simont at hmgc.mcw.edu Tue Oct 3 10:13:34 2006 From: simont at hmgc.mcw.edu (Twigger Simon) Date: Tue, 3 Oct 2006 09:13:34 -0500 Subject: [MOBY-dev] Asynch proposal In-Reply-To: <1159829664.30244.28.camel@bioinfo.icapture.ubc.ca> References: <1159829664.30244.28.camel@bioinfo.icapture.ubc.ca> Message-ID: Looks good to me. Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw On Oct 2, 2006, at 5:54 PM, Mark Wilkinson wrote: > I just re-read it and it looks great! YES from here! > > We are waiting on three more votes, four positive votes so far, one > negative. Democratically we can't call it without one more positive > vote. > > I have c.c.'d the three absentees on this message. > > M > > > -- > Mark Wilkinson > Asst. Professor, Dept. of Medical Genetics > University of British Columbia > PI in Bioinformatics, iCAPTURE Centre > St. Paul's Hospital, Rm. 166, 1081 Burrard St. > Vancouver, BC, V6Z 1Y6 > tel: 604 682 2344 x62129 > fax: 604 806 9274 > > "Since the point of a definition is to explain the meaning of a > term to > someone who is unfamiliar with its proper application, the use of > language that doesn't help such a person learn how to apply the > term is > pointless. Thus, "happiness is a warm puppy" may be a lovely thought, > but it is a lousy definition." > > K?hler et al, 2006 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Tue Oct 3 12:37:32 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 03 Oct 2006 09:37:32 -0700 Subject: [MOBY-dev] Asynch proposal - accepted In-Reply-To: References: <1159829664.30244.28.camel@bioinfo.icapture.ubc.ca> Message-ID: <1159893452.7243.29.camel@bioinfo.icapture.ubc.ca> And with that vote, the Asynch RFC is passed. Thanks INB team! Mark On Tue, 2006-10-03 at 09:13 -0500, Twigger Simon wrote: > Looks good to me. > > Simon. > > -- > > Simon N. Twigger, Ph.D. > Assistant Professor, Department of Physiology > Medical College of Wisconsin > 8701 Watertown Plank Road, > Milwaukee, WI, USA > tel: 414-456-8802 > fax: 414-456-6595 > AIM/iChat: simontatmcw > > > On Oct 2, 2006, at 5:54 PM, Mark Wilkinson wrote: > > > I just re-read it and it looks great! YES from here! > > > > We are waiting on three more votes, four positive votes so far, one > > negative. Democratically we can't call it without one more positive > > vote. > > > > I have c.c.'d the three absentees on this message. > > > > M > > > > > > -- > > Mark Wilkinson > > Asst. Professor, Dept. of Medical Genetics > > University of British Columbia > > PI in Bioinformatics, iCAPTURE Centre > > St. Paul's Hospital, Rm. 166, 1081 Burrard St. > > Vancouver, BC, V6Z 1Y6 > > tel: 604 682 2344 x62129 > > fax: 604 806 9274 > > > > "Since the point of a definition is to explain the meaning of a > > term to > > someone who is unfamiliar with its proper application, the use of > > language that doesn't help such a person learn how to apply the > > term is > > pointless. Thus, "happiness is a warm puppy" may be a lovely thought, > > but it is a lousy definition." > > > > K?hler et al, 2006 > > > > _______________________________________________ > > MOBY-dev mailing list > > MOBY-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Mark Wilkinson Asst. Professor, Dept. of Medical Genetics University of British Columbia PI in Bioinformatics, iCAPTURE Centre St. Paul's Hospital, Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 "Since the point of a definition is to explain the meaning of a term to someone who is unfamiliar with its proper application, the use of language that doesn't help such a person learn how to apply the term is pointless. Thus, "happiness is a warm puppy" may be a lovely thought, but it is a lousy definition." K?hler et al, 2006 From johan at ac.uma.es Wed Oct 4 06:15:28 2006 From: johan at ac.uma.es (Johan Karlsson) Date: Wed, 04 Oct 2006 12:15:28 +0200 Subject: [MOBY-dev] Asynch proposal - accepted In-Reply-To: <1159893452.7243.29.camel@bioinfo.icapture.ubc.ca> References: <1159829664.30244.28.camel@bioinfo.icapture.ubc.ca> <1159893452.7243.29.camel@bioinfo.icapture.ubc.ca> Message-ID: <452389C0.4030704@ac.uma.es> The RFC that was accepted is specified in this document: http://twiki.inab.org/twiki/pub/INB/INBDocsRoot/BioMOBY_Asynchronous_Service_Call_Proposal_WSRF_v2.3.pdf Of course, the information there must be added to the official BioMOBY documentation but until that happens the RFC document is important. As you already know, INB has provided a Perl library to help develop asynchronous services (compatible with the RFC, of course): http://bioinfo.pcm.uam.es/prototype/ Support for asynchronous BioMOBY services in Java is being implemented in Moses by Martin Senger (not sure when this will be available but keep an eye on the moby-dev list). Kind regards, Johan -- 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 Mark Wilkinson wrote: > And with that vote, the Asynch RFC is passed. > > Thanks INB team! > > Mark From d.haase at gsf.de Wed Oct 4 09:14:08 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 4 Oct 2006 15:14:08 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <1159375710.27141.55.camel@bioinfo.icapture.ubc.ca> References: <002401c6e242$996cc880$6400a8c0@notebook> <4d93f07c0609270944kb959b6ep41f2d159a76eef7a@mail.gmail.com> <1159375710.27141.55.camel@bioinfo.icapture.ubc.ca> Message-ID: <200610041514.12997.d.haase@gsf.de> On Wednesday 27 September 2006 18:48, Mark Wilkinson wrote: > Call it being overly cautious :-) If there were a bug in the agent > that we hadn't noticed during testing, we didn't want to wipe-out the > registry (though it is backed-up daily, so we could recover anyway). > > It looks like there are no obvious bugs... Nevertheless de-registration by agent is still not activated it seems... Still objections? Best, dirk From edward.kawas at gmail.com Wed Oct 4 09:19:17 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 4 Oct 2006 06:19:17 -0700 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <200610041514.12997.d.haase@gsf.de> Message-ID: <002c01c6e7b7$b3aeda10$6400a8c0@notebook> Hi Dirk, What makes you say that? De-registration is enabled ... Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Wednesday, October 04, 2006 6:14 AM > To: markw at illuminae.com; Core developer announcements > Subject: Re: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration > > On Wednesday 27 September 2006 18:48, Mark Wilkinson wrote: > > Call it being overly cautious :-) If there were a bug in > the agent > > that we hadn't noticed during testing, we didn't want to > wipe-out the > > registry (though it is backed-up daily, so we could recover anyway). > > > > It looks like there are no obvious bugs... > > Nevertheless de-registration by agent is still not activated > it seems... Still objections? > > Best, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From d.haase at gsf.de Wed Oct 4 10:06:05 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 4 Oct 2006 16:06:05 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <002c01c6e7b7$b3aeda10$6400a8c0@notebook> References: <002c01c6e7b7$b3aeda10$6400a8c0@notebook> Message-ID: <200610041606.05821.d.haase@gsf.de> On Wednesday 04 October 2006 15:19, Edward Kawas wrote: > Hi Dirk, > > What makes you say that? De-registration is enabled ... Strange things are happening... For example, the mips.gsf.de service 'getClonesByName' formerly was included in the multi-service rdf at http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf but then I created a separate document for it: http://mips.gsf.de/proj/planet/moby/RDF/getClonesByName.rdf Last week I got an error message from the agent that the service was registered with a double signature URL. So I tried to de-register it by deleting it from the multi-service file and called the agent. But the service is still in the registry with the old signature URL (where it is not mentioned anymore). If de-registration was working correctly, it should not be listed at all... The real funny thing is that I have seen that service this morning with its new (and correct) signature URL. Any clue? Thanks From ivanp at mmb.pcb.ub.es Wed Oct 4 10:10:12 2006 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Wed, 04 Oct 2006 16:10:12 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <002c01c6e7b7$b3aeda10$6400a8c0@notebook> References: <002c01c6e7b7$b3aeda10$6400a8c0@notebook> Message-ID: <4523C0C4.4030600@mmb.pcb.ub.es> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, It's enabled and it's working well because I'm playing with it right now. Martin, it would be very useful, I think, that the "unregister service" button on Dashboard performed a call to unregister the service according with the new API (an "empty query" with just the signatureURL tag) and not the old unregister call that is not longer working, don't you think? Iv?n Edward Kawas escribi?: > Hi Dirk, > > What makes you say that? De-registration is enabled ... > > Thanks, > > Eddie > >> -----Original Message----- From: >> moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk >> Haase Sent: Wednesday, October 04, 2006 6:14 AM To: >> markw at illuminae.com; Core developer announcements Subject: Re: >> [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration >> >> On Wednesday 27 September 2006 18:48, Mark Wilkinson wrote: >>> Call it being overly cautious :-) If there were a bug in >> the agent >>> that we hadn't noticed during testing, we didn't want to >> wipe-out the >>> registry (though it is backed-up daily, so we could recover >>> anyway). >>> >>> It looks like there are no obvious bugs... >> Nevertheless de-registration by agent is still not activated it >> seems... Still objections? >> >> Best, dirk _______________________________________________ >> MOBY-dev mailing list MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ MOBY-dev mailing > list MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev - -- - ------------------------------------------------ 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 - ------------------------------------------------ -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFFI8DCLWwmlDjmrRYRArkNAJoCQ0E0FdllYpc9KK1H3FHGPmpBlgCfYhi2 dupW9IIP2Dgn0kqCAUj4kjQ= =l9J1 -----END PGP SIGNATURE----- From markw at illuminae.com Wed Oct 4 10:28:16 2006 From: markw at illuminae.com (mark wilkinson) Date: Wed, 4 Oct 2006 14:28:16 +0000 GMT Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <002c01c6e7b7$b3aeda10$6400a8c0@notebook> References: <200610041514.12997.d.haase@gsf.de> <002c01c6e7b7$b3aeda10$6400a8c0@notebook> Message-ID: <1821246256-1159972172-cardhu_blackberry.rim.net-15136-@engine26-cell01> I can confirm that I got a deregistration email overnight when the agent ran, so it appears to be working properly for my service RDF's ...?? M -- Mark Wilkinson ...on the road! -----Original Message----- From: "Edward Kawas" Date: Wed, 4 Oct 2006 06:19:17 To:"'Core developer announcements'" , Subject: Re: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration Hi Dirk, What makes you say that? De-registration is enabled ... Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Wednesday, October 04, 2006 6:14 AM > To: markw at illuminae.com; Core developer announcements > Subject: Re: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration > > On Wednesday 27 September 2006 18:48, Mark Wilkinson wrote: > > Call it being overly cautious :-) If there were a bug in > the agent > > that we hadn't noticed during testing, we didn't want to > wipe-out the > > registry (though it is backed-up daily, so we could recover anyway). > > > > It looks like there are no obvious bugs... > > Nevertheless de-registration by agent is still not activated > it seems... Still objections? > > Best, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Wed Oct 4 10:59:56 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 04 Oct 2006 07:59:56 -0700 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <4d93f07c0610040748sf9a701ei68a592a0a6aa9392@mail.gmail.com> References: <200610041514.12997.d.haase@gsf.de> <002c01c6e7b7$b3aeda10$6400a8c0@notebook> <1821246256-1159972172-cardhu_blackberry.rim.net-15136-@engine26-cell01> <4d93f07c0610040748sf9a701ei68a592a0a6aa9392@mail.gmail.com> Message-ID: I think those are slightly different scenario's. I didn't ask the agent to come, I simply moved my RDF file to see if it would notice (and it did). I believe that if I ask the agent to come, it does come immediately... though I agree that it would be a more useful behaviour if an explicit agent call waited until the agent had finished its task and returned an informative message, versus the "you have successfully launched the agent" message you get currently. M On Wed, 04 Oct 2006 07:48:38 -0700, Martin Senger wrote: >> I can confirm that I got a deregistration email > > > This is one of the agent problems - I have discussed it yesterday with > Eddie. If I call an agent to come, it should come at once and my call > should > wait until the agent finishes his journey and my call should get back a > message about it. The email is something that can be used also, but > primarily I would expect synchronous behaviour first. Eddie seems to > agree > with that - and the only reason why it does not work yet like this is > that > he is investigating some behaviour of the perl 'sytem()' call... (AFAIK). > > Martin > > -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital From martin.senger at gmail.com Wed Oct 4 11:07:17 2006 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 4 Oct 2006 16:07:17 +0100 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: References: <200610041514.12997.d.haase@gsf.de> <002c01c6e7b7$b3aeda10$6400a8c0@notebook> <1821246256-1159972172-cardhu_blackberry.rim.net-15136-@engine26-cell01> <4d93f07c0610040748sf9a701ei68a592a0a6aa9392@mail.gmail.com> Message-ID: <4d93f07c0610040807p76a8ddc0ma34d2821fcf1d1d9@mail.gmail.com> > I think those are slightly different scenario's. I didn't ask the agent > to come, I simply moved my RDF file Yes, correct, these are two ways. And - as you said - I was referring to the one used from the Dashboard. That one should be synchronous. Eddie, do you need any help to fix the problem with the 'system()' call? Please let me know, I am at your service. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From d.haase at gsf.de Wed Oct 4 11:08:37 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 4 Oct 2006 17:08:37 +0200 Subject: [MOBY-dev] gbrowse_moby at mobycentral Message-ID: <200610041708.37507.d.haase@gsf.de> Mark and/or Eddie, when I use your gbrowse_moby, I'm missing a certain service by 'seedgenes.org' called 'SeedGenesEmbryoImageByAgiCode'. It should be displayed when 'AGI_LocusCode' was selected as namespace. My first guess was that you recently switched to exclude services without signature URLs but eg. 'EvocName2ID' is listed in spite of not having one. So I'm wondering why the seedgenes.org service can not be accessed. Thanks, dirk From martin.senger at gmail.com Wed Oct 4 10:41:44 2006 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 4 Oct 2006 15:41:44 +0100 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <4523C0C4.4030600@mmb.pcb.ub.es> References: <002c01c6e7b7$b3aeda10$6400a8c0@notebook> <4523C0C4.4030600@mmb.pcb.ub.es> Message-ID: <4d93f07c0610040741p50de8720h5559262520939233@mail.gmail.com> > Martin, it would be very useful, I think, that the "unregister > service" button on Dashboard performed a call to unregister the > service according with the new API (an "empty query" with just the > signatureURL tag) Perhaps you missed my email yesterday (or the day before yesterday) announcing that the dashboard has now a new button "call rdf agent" which does exactly that. (Well, I hope it does, but it is hard to be sure - everybody knows my deep doubts about how this agent behaviour is documented and implemented - sorry, Eddie, I should shut up.) > and not the old unregister call that is not longer working The old way should still work. We agreed that agent will deal with services that have registered their signature url, and old-fashioned unregistration api call will deal with so-called 'services in testing stage' that do not have a signature url. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Wed Oct 4 10:48:38 2006 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 4 Oct 2006 15:48:38 +0100 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <1821246256-1159972172-cardhu_blackberry.rim.net-15136-@engine26-cell01> References: <200610041514.12997.d.haase@gsf.de> <002c01c6e7b7$b3aeda10$6400a8c0@notebook> <1821246256-1159972172-cardhu_blackberry.rim.net-15136-@engine26-cell01> Message-ID: <4d93f07c0610040748sf9a701ei68a592a0a6aa9392@mail.gmail.com> > I can confirm that I got a deregistration email This is one of the agent problems - I have discussed it yesterday with Eddie. If I call an agent to come, it should come at once and my call should wait until the agent finishes his journey and my call should get back a message about it. The email is something that can be used also, but primarily I would expect synchronous behaviour first. Eddie seems to agree with that - and the only reason why it does not work yet like this is that he is investigating some behaviour of the perl 'sytem()' call... (AFAIK). Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From edward.kawas at gmail.com Wed Oct 4 10:19:31 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 4 Oct 2006 07:19:31 -0700 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <200610041606.05821.d.haase@gsf.de> Message-ID: <003a01c6e7c0$1db5f940$6400a8c0@notebook> Hi Dirk, I have looked into the logs and I have noticed that the agent was able to find the service description for getClonesByName in the RDF at the url 'all_mips_services.rdf'. When I resolve the url, it isnt there. Did you recently remove the service from that document? Also, do you mind if I call the agent on your URL? Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Wednesday, October 04, 2006 7:06 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration > > On Wednesday 04 October 2006 15:19, Edward Kawas wrote: > > Hi Dirk, > > > > What makes you say that? De-registration is enabled ... > > Strange things are happening... > > For example, the mips.gsf.de service 'getClonesByName' > formerly was included in the multi-service rdf at > http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf > but then I created a separate document for it: > http://mips.gsf.de/proj/planet/moby/RDF/getClonesByName.rdf > > Last week I got an error message from the agent that the > service was registered with a double signature URL. So I > tried to de-register it by deleting it from the multi-service > file and called the agent. But the service is still in the > registry with the old signature URL (where it is not > mentioned anymore). If de-registration was working correctly, > it should not be listed at all... > > The real funny thing is that I have seen that service this > morning with its new (and correct) signature URL. > > Any clue? > > Thanks > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Wed Oct 4 11:13:35 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 4 Oct 2006 08:13:35 -0700 Subject: [MOBY-dev] gbrowse_moby at mobycentral In-Reply-To: <200610041708.37507.d.haase@gsf.de> Message-ID: <004201c6e7c7$ab8c88e0$6400a8c0@notebook> Hey Dirk, Try again. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Wednesday, October 04, 2006 8:09 AM > To: Core developer announcements > Subject: [MOBY-dev] gbrowse_moby at mobycentral > > Mark and/or Eddie, > > when I use your gbrowse_moby, I'm missing a certain service > by 'seedgenes.org' > called 'SeedGenesEmbryoImageByAgiCode'. It should be > displayed when 'AGI_LocusCode' was selected as namespace. > > My first guess was that you recently switched to exclude > services without signature URLs but eg. 'EvocName2ID' is > listed in spite of not having one. So I'm wondering why the > seedgenes.org service can not be accessed. > > Thanks, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From ivanp at mmb.pcb.ub.es Wed Oct 4 11:21:56 2006 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Wed, 04 Oct 2006 17:21:56 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <4d93f07c0610040741p50de8720h5559262520939233@mail.gmail.com> References: <002c01c6e7b7$b3aeda10$6400a8c0@notebook> <4523C0C4.4030600@mmb.pcb.ub.es> <4d93f07c0610040741p50de8720h5559262520939233@mail.gmail.com> Message-ID: <4523D194.8020602@mmb.pcb.ub.es> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, Yes, you're right, sorry. In fact I read about it and I updated from CVS but I forgot to recompile. Thanks, Iv?n Martin Senger escribi?: >> Martin, it would be very useful, I think, that the "unregister >> service" button on Dashboard performed a call to unregister the >> service according with the new API (an "empty query" with just >> the signatureURL tag) > > > Perhaps you missed my email yesterday (or the day before yesterday) > announcing that the dashboard has now a new button "call rdf > agent" which does exactly that. (Well, I hope it does, but it is > hard to be sure - everybody knows my deep doubts about how this > agent behaviour is documented and implemented - sorry, Eddie, I > should shut up.) > > >> and not the old unregister call that is not longer working > > > The old way should still work. We agreed that agent will deal with > services that have registered their signature url, and > old-fashioned unregistration api call will deal with so-called > 'services in testing stage' that do not have a signature url. > > Martin > > - -- - ------------------------------------------------ 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 - ------------------------------------------------ -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFFI9GULWwmlDjmrRYRArv9AKC3lQ0pa/zgMus034/Oj6IGaS3XjwCgyguz hTUa7p182ZsZOd4UMhZhsZY= =spVW -----END PGP SIGNATURE----- From d.haase at gsf.de Wed Oct 4 11:29:37 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 4 Oct 2006 17:29:37 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <003a01c6e7c0$1db5f940$6400a8c0@notebook> References: <003a01c6e7c0$1db5f940$6400a8c0@notebook> Message-ID: <200610041729.37393.d.haase@gsf.de> On Wednesday 04 October 2006 16:19, Edward Kawas wrote: > Hi Dirk, > > I have looked into the logs and I have noticed that the agent was able to > find the service description for getClonesByName in the RDF at the url > 'all_mips_services.rdf'. When I resolve the url, it isnt there. Did you > recently remove the service from that document? It depends on the definition of 'recently': Yes, if 'recently' = 'today'. No, if 'recently' = 'after the last agent call on that rdf' That was why I was asking... > Also, do you mind if I call the agent on your URL? No, go ahead. I'm curious if your agent call has a different effect than mine ;-) Best, dirk From edward.kawas at gmail.com Wed Oct 4 11:34:07 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 4 Oct 2006 08:34:07 -0700 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <200610041729.37393.d.haase@gsf.de> Message-ID: <004701c6e7ca$892bd8c0$6400a8c0@notebook> Hey Dirk, I ran the agent, and the following was in the log: Service getClonesByName, mips.gsf.de has been removed. The agent wanted to remove the service because Service was not found in the RDF document located at: http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf It did what we expected ... I used the following perl code: use SOAP::Lite + trace; use MOBY::Client::Central; my $m = MOBY::Client::Central->new( Registries => { mobycentral => { URL => 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl', URI => 'http://mobycentral.icapture.ubc.ca/MOBY/Central'} } ); my $REG = $m->registerService( serviceName => "", serviceType => "", authURI => "", contactEmail => '', description => "", category => "", URL => "", signatureURL => "http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf", ); Also, Martin, the system code DOES indeed wait. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Wednesday, October 04, 2006 8:30 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration > > On Wednesday 04 October 2006 16:19, Edward Kawas wrote: > > Hi Dirk, > > > > I have looked into the logs and I have noticed that the > agent was able > > to find the service description for getClonesByName in the > RDF at the > > url 'all_mips_services.rdf'. When I resolve the url, it isnt there. > > Did you recently remove the service from that document? > > It depends on the definition of 'recently': > Yes, if 'recently' = 'today'. > No, if 'recently' = 'after the last agent call on that rdf' > > That was why I was asking... > > > Also, do you mind if I call the agent on your URL? > > No, go ahead. I'm curious if your agent call has a different > effect than mine ;-) > > Best, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From d.haase at gsf.de Wed Oct 4 11:34:45 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 4 Oct 2006 17:34:45 +0200 Subject: [MOBY-dev] gbrowse_moby at mobycentral In-Reply-To: <004201c6e7c7$ab8c88e0$6400a8c0@notebook> References: <004201c6e7c7$ab8c88e0$6400a8c0@notebook> Message-ID: <200610041734.46002.d.haase@gsf.de> On Wednesday 04 October 2006 17:13, Edward Kawas wrote: > Hey Dirk, > > Try again. Many thanks! dirk From martin.senger at gmail.com Wed Oct 4 11:36:00 2006 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 4 Oct 2006 16:36:00 +0100 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <200610041729.37393.d.haase@gsf.de> References: <003a01c6e7c0$1db5f940$6400a8c0@notebook> <200610041729.37393.d.haase@gsf.de> Message-ID: <4d93f07c0610040836r1c728504t4f7baea6042d559f@mail.gmail.com> > No, go ahead. I'm curious if your agent call has a different effect than > mine ;-) It is still possible that an undesired effect is created by a wrong implementation of the "call rdf agent" button in dashboard. That's why I am so keen that you two are tetsing it now. Are you both calling the agent from dashboard? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Wed Oct 4 11:45:08 2006 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 4 Oct 2006 16:45:08 +0100 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <004701c6e7ca$892bd8c0$6400a8c0@notebook> References: <200610041729.37393.d.haase@gsf.de> <004701c6e7ca$892bd8c0$6400a8c0@notebook> Message-ID: <4d93f07c0610040845r5d594274n383c8ea85d06f8@mail.gmail.com> > Also, Martin, the system code DOES indeed wait. Fine, so you can report it back now to the waiting call, right? Make a table where you assign various exit codes to various text messages (we can later improve it to get a real message from the run-script - e.g. your run-agent script can print the error message on stderr where the perl code (registry) can read it from - but wait with this - it is an optimalozation). Let me know when I can try to call agent from dashboard - and to see that I am getting an error message (because I will send a non-existing URL). Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Wed Oct 4 12:59:50 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 04 Oct 2006 09:59:50 -0700 Subject: [MOBY-dev] [moby] gbrowse_moby at mobycentral In-Reply-To: <200610041708.37507.d.haase@gsf.de> References: <200610041708.37507.d.haase@gsf.de> Message-ID: <1159981190.20597.54.camel@bioinfo.icapture.ubc.ca> The current gbrowse_moby filters services based on the "isAlive" tag that is added to the MOBY Central copy of the RDF Signature. Eddie will confirm, since I haven't tested this, but I believe that you can get this RDF metadata as one of the two ports that is provided to you by the LSID Authority server when you attempt to resolve a service instance LSID (one port is the address of the RDF document owned by the service provider,and the other is the RDF document as generated by MOBY Central containing various other metadata) isAlive is generated every hour by a cron that sends a "ping" to the service (as defined in earlier threads - an empty tag) - it it gets the expected response (an empty block) then it "isAlive=true", anything else sets "isAlive=false". So... does your service respond correctly to the ping? This is getting further and further from my own knowledge, since it is largely Eddie now that looks after all MOBY code... M On Wed, 2006-10-04 at 17:08 +0200, Dirk Haase wrote: > Mark and/or Eddie, > > when I use your gbrowse_moby, I'm missing a certain service by 'seedgenes.org' > called 'SeedGenesEmbryoImageByAgiCode'. It should be displayed > when 'AGI_LocusCode' was selected as namespace. > > My first guess was that you recently switched to exclude services without > signature URLs but eg. 'EvocName2ID' is listed in spite of not having one. So > I'm wondering why the seedgenes.org service can not be accessed. > > Thanks, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Mark Wilkinson Asst. Professor, Dept. of Medical Genetics University of British Columbia PI in Bioinformatics, iCAPTURE Centre St. Paul's Hospital, Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 "Since the point of a definition is to explain the meaning of a term to someone who is unfamiliar with its proper application, the use of language that doesn't help such a person learn how to apply the term is pointless. Thus, "happiness is a warm puppy" may be a lovely thought, but it is a lousy definition." K?hler et al, 2006 From edward.kawas at gmail.com Wed Oct 4 13:03:59 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 4 Oct 2006 10:03:59 -0700 Subject: [MOBY-dev] [moby] gbrowse_moby at mobycentral In-Reply-To: <1159981190.20597.54.camel@bioinfo.icapture.ubc.ca> Message-ID: <005a01c6e7d7$179f0440$6400a8c0@notebook> The problem was because isAlive in the cached lsid RDF was false. What happens is that you register a service. In the time between service testing for 'isAlive', any question of the isAlive status of a service returns false. Since gbrowse uses this information, your service initially is invisible to gbrowse. Make sense? Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > Mark Wilkinson > Sent: Wednesday, October 04, 2006 10:00 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [moby] gbrowse_moby at mobycentral > > The current gbrowse_moby filters services based on the > "isAlive" tag that is added to the MOBY Central copy of the > RDF Signature. Eddie will confirm, since I haven't tested > this, but I believe that you can get this RDF metadata as one > of the two ports that is provided to you by the LSID > Authority server when you attempt to resolve a service > instance LSID (one port is the address of the RDF document > owned by the service provider,and the other is the RDF > document as generated by MOBY Central containing various > other metadata) > > isAlive is generated every hour by a cron that sends a "ping" > to the service (as defined in earlier threads - an empty > tag) - it it gets the expected response (an > empty block) then it "isAlive=true", anything > else sets "isAlive=false". > > So... does your service respond correctly to the ping? > > This is getting further and further from my own knowledge, > since it is largely Eddie now that looks after all MOBY code... > > M > > > > On Wed, 2006-10-04 at 17:08 +0200, Dirk Haase wrote: > > Mark and/or Eddie, > > > > when I use your gbrowse_moby, I'm missing a certain service > by 'seedgenes.org' > > called 'SeedGenesEmbryoImageByAgiCode'. It should be displayed when > > 'AGI_LocusCode' was selected as namespace. > > > > My first guess was that you recently switched to exclude services > > without signature URLs but eg. 'EvocName2ID' is listed in > spite of not > > having one. So I'm wondering why the seedgenes.org service > can not be accessed. > > > > Thanks, > > dirk > > _______________________________________________ > > MOBY-dev mailing list > > MOBY-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- > Mark Wilkinson > Asst. Professor, Dept. of Medical Genetics University of > British Columbia PI in Bioinformatics, iCAPTURE Centre St. > Paul's Hospital, Rm. 166, 1081 Burrard St. > Vancouver, BC, V6Z 1Y6 > tel: 604 682 2344 x62129 > fax: 604 806 9274 > > "Since the point of a definition is to explain the meaning of > a term to > someone who is unfamiliar with its proper application, the > use of language that doesn't help such a person learn how to > apply the term is pointless. Thus, "happiness is a warm > puppy" may be a lovely thought, > but it is a lousy definition." > > K?hler et al, 2006 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From d.haase at gsf.de Wed Oct 4 13:38:29 2006 From: d.haase at gsf.de (Haase, Dirk) Date: Wed, 4 Oct 2006 19:38:29 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration References: <003a01c6e7c0$1db5f940$6400a8c0@notebook><200610041729.37393.d.haase@gsf.de> <4d93f07c0610040836r1c728504t4f7baea6042d559f@mail.gmail.com> Message-ID: <1D78CE9FD586024AB0E0102F6F9A7CF86A089A@sw-rz010.gsf.de> I think Eddie does not use dashboard but I do. I'll try to figure out what is going on with some more testing. But tomorrow, not today - my working day is already done :-) Best, dirk -----Original Message----- From: moby-dev-bounces at lists.open-bio.org on behalf of Martin Senger Sent: Wed 10/4/2006 5:36 PM To: Core developer announcements Subject: Re: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration > No, go ahead. I'm curious if your agent call has a different effect than > mine ;-) It is still possible that an undesired effect is created by a wrong implementation of the "call rdf agent" button in dashboard. That's why I am so keen that you two are tetsing it now. Are you both calling the agent from dashboard? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 3244 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/moby-dev/attachments/20061004/f00b87a4/attachment.bin From martin.senger at gmail.com Wed Oct 4 14:03:42 2006 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 4 Oct 2006 19:03:42 +0100 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <1D78CE9FD586024AB0E0102F6F9A7CF86A089A@sw-rz010.gsf.de> References: <003a01c6e7c0$1db5f940$6400a8c0@notebook> <200610041729.37393.d.haase@gsf.de> <4d93f07c0610040836r1c728504t4f7baea6042d559f@mail.gmail.com> <1D78CE9FD586024AB0E0102F6F9A7CF86A089A@sw-rz010.gsf.de> Message-ID: <4d93f07c0610041103h577d4584p2e2deb6504288690@mail.gmail.com> Hi, > I think Eddie does not use dashboard but I do. I'll try to figure out > what is going on with some more testing. If you (or Eddie) want to see what Dasboard produces after pressing the new button "Call RDF Agent" you can use the Java TCP Monitor (I can explain more if somebody does not know how to use tcpmon). For example, this is a full soap message coming from Dashboard: --- begin --- POST /cgi-bin/MOBY05/mobycentral.pl HTTP/1.0 Content-Type: text/xml; charset=utf-8 Accept: application/soap+xml, application/dime, multipart/related, text/* User-Agent: Axis/1.2.1 Host: mobycentral.icapture.ubc.ca:9999 Cache-Control: no-cache Pragma: no-cache SOAPAction: "http://mobycentral.icapture.ubc.ca/MOBY/Central#registerService" Content-Length: 1113 <registerService><Category>moby</Category><serviceName></serviceName><serviceType></serviceType><serviceLSID></serviceLSID><authURI></authURI><signatureURL>http://yes.no</signatureURL><URL></URL><contactEmail></contactEmail><authoritativeService>1</authoritativeService><Description><![CDATA[]]></Description><Input></Input><secondaryArticles></secondaryArticles><Output></Output></registerService> ---end --- Eddie, is the request correct? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From d.haase at gsf.de Thu Oct 5 08:39:22 2006 From: d.haase at gsf.de (Dirk Haase) Date: Thu, 5 Oct 2006 14:39:22 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <004701c6e7ca$892bd8c0$6400a8c0@notebook> References: <004701c6e7ca$892bd8c0$6400a8c0@notebook> Message-ID: <200610051439.23013.d.haase@gsf.de> On Wednesday 04 October 2006 17:34, Edward Kawas wrote: > Hey Dirk, > > I ran the agent, and the following was in the log: > > Service getClonesByName, mips.gsf.de has been removed. > The agent wanted to remove the service because Service was not found in the > RDF document located at: > http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf > > > It did what we expected ... Either I am constantly making a very stupid error or in fact there is a difference between my agent calls and yours... Today I removed 'getSplicedSequence' from the rdf mentioned above and called the agent 1) by dashboard button 'Call RDF Agent' 2) by dashboard button 'Register from XML' with the following XML file: http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf 3) by a perl script with this core my $REG = $C->registerService( signatureURL=> 'http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf' ); Each time I got a 'success' message but still the service is not unregistered. For the perl script, I used 'SOAP + trace' mode, the outgoing message you can see below. BTW: registration works perfectly with the new dashboard button. Best, dirk And here is the SOAP trace of my registerService call: SOAP::Transport::HTTP::Client::send_receive: POST http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl HTTP/1.1 Accept: text/xml Accept: multipart/* Content-Length: 951 Content-Type: text/xml; charset=utf-8 SOAPAction: "http://mobycentral.icapture.ubc.ca/MOBY/Central#registerService" <registerService> <Category></Category> <serviceName></serviceName> <serviceType></serviceType> <Description></Description> <signatureURL>http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf</signatureURL> <URL></URL> <authURI></authURI> <contactEmail></contactEmail> </registerService> From edward.kawas at gmail.com Thu Oct 5 09:42:57 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 5 Oct 2006 06:42:57 -0700 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <200610051439.23013.d.haase@gsf.de> Message-ID: <002101c6e884$2c2f1cd0$6400a8c0@notebook> Hi Dirk, The agent is finding the service in the RDF: Oct 5, 2006 5:04:40 AM org.biomoby.registry.rdfagent.util.Log info INFO: Found a service (getSplicedSequence/mips.gsf.de) in the registry that matches the one in the RDF ... Comparing them ... I tried resolving your URL right now, and I didn't see the service. What happens if you try again? Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Thursday, October 05, 2006 5:39 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration > > On Wednesday 04 October 2006 17:34, Edward Kawas wrote: > > Hey Dirk, > > > > I ran the agent, and the following was in the log: > > > > Service getClonesByName, mips.gsf.de has been removed. > > The agent wanted to remove the service because Service was > not found > > in the RDF document located at: > > http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf > > > > > > It did what we expected ... > > Either I am constantly making a very stupid error or in fact > there is a difference between my agent calls and yours... > Today I removed 'getSplicedSequence' from the rdf mentioned > above and called the agent > 1) by dashboard button 'Call RDF Agent' > 2) by dashboard button 'Register from XML' with the following > XML file: > > http://mips.gsf.de/proj/planet/moby/RDF/all_mips _services.rdf > > 3) by a perl script with this core > my $REG = $C->registerService( > signatureURL=> > 'http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf' > ); > > Each time I got a 'success' message but still the service is > not unregistered. > > For the perl script, I used 'SOAP + trace' mode, the outgoing > message you can see below. > > BTW: registration works perfectly with the new dashboard button. > > Best, > dirk > > And here is the SOAP trace of my registerService call: > > SOAP::Transport::HTTP::Client::send_receive: POST > http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral. pl HTTP/1.1 > Accept: text/xml > Accept: multipart/* > Content-Length: 951 > Content-Type: text/xml; charset=utf-8 > SOAPAction: > "http://mobycentral.icapture.ubc.ca/MOBY/Central#registerService" > > xmlns:xsi="http://www.w3.org/1999/XMLSchema-instance" > xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/" > xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/" > xmlns:xsd="http://www.w3.org/1999/XMLSchema" > SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encodi > ng/"> xmlns:namesp1="http://mobycentral.icapture.ubc.ca/MOBY/Central "> xsi:type="xsd:string"> > <registerService> > <Category></Category> > <serviceName></serviceName> > <serviceType></serviceType> > <Description></Description> > > <signatureURL>http://mips.gsf.de/proj/planet/moby/RDF/all_m ips_services.rdf</signatureURL> > <URL></URL> > <authURI></authURI> > <contactEmail></contactEmail> > > </registerService> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From d.haase at gsf.de Thu Oct 5 10:24:44 2006 From: d.haase at gsf.de (Dirk Haase) Date: Thu, 5 Oct 2006 16:24:44 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <002101c6e884$2c2f1cd0$6400a8c0@notebook> References: <002101c6e884$2c2f1cd0$6400a8c0@notebook> Message-ID: <200610051624.44502.d.haase@gsf.de> On Thursday 05 October 2006 15:42, Edward Kawas wrote: > Hi Dirk, > > The agent is finding the service in the RDF: > Oct 5, 2006 5:04:40 AM org.biomoby.registry.rdfagent.util.Log info > INFO: > Found a service (getSplicedSequence/mips.gsf.de) in the registry that > matches the one in the RDF ... > Comparing them ... The timestamp in my SOAP trace is "05 Oct 2006 12:08:30 GMT" which translates to 7:08 pacific standard time (your log timestamps are PST?), so this is not the log entry for my call I guess. > I tried resolving your URL right now, and I didn't see the service. What > happens if you try again? It is gone now... Could it be that there is simply a delay between the unregistration in the database and the time this is displayed to the outside (encyclopedia/dashboard) ? That would explain some things... Best, dirk From d.haase at gsf.de Fri Oct 6 12:00:03 2006 From: d.haase at gsf.de (Dirk Haase) Date: Fri, 6 Oct 2006 18:00:03 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <200610051624.44502.d.haase@gsf.de> References: <002101c6e884$2c2f1cd0$6400a8c0@notebook> <200610051624.44502.d.haase@gsf.de> Message-ID: <200610061800.03418.d.haase@gsf.de> On Thursday 05 October 2006 16:24, Dirk Haase wrote: > It is gone now... Could it be that there is simply a delay between the > unregistration in the database and the time this is displayed to the > outside (encyclopedia/dashboard) ? That would explain some things... Eddie, I have the strong feeling that the agent accesses some sort of cache/web proxy - at least when I call it. I turned to play around with single service RDF files and now I get the message "No services in the registry match the given URL and the signatureURL didn't contain any services. The RDF agent was called, but found nothing useful." for a file which does contain a service description now (but did not ~ 15 minutes ago). Best, dirk From edward.kawas at gmail.com Fri Oct 6 12:52:19 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 6 Oct 2006 09:52:19 -0700 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <200610061800.03418.d.haase@gsf.de> Message-ID: <003701c6e967$ca1f4cb0$6700a8c0@notebook> Hi Dirk, I think that I have fixed this issue. Can you confirm? Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Friday, October 06, 2006 9:00 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration > > On Thursday 05 October 2006 16:24, Dirk Haase wrote: > > It is gone now... Could it be that there is simply a delay > between the > > unregistration in the database and the time this is > displayed to the > > outside (encyclopedia/dashboard) ? That would explain some things... > > Eddie, I have the strong feeling that the agent accesses some > sort of cache/web proxy - at least when I call it. I turned > to play around with single service RDF files and now I get > the message "No services in the registry match the given URL > and the signatureURL didn't contain any services. The RDF > agent was called, but found nothing useful." > for a file which does contain a service description now (but > did not ~ 15 minutes ago). > > Best, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Fri Oct 6 12:02:06 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 6 Oct 2006 09:02:06 -0700 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <200610061800.03418.d.haase@gsf.de> Message-ID: <003001c6e960$c698e940$6700a8c0@notebook> I had a feeling that the agent may be caching. I will look into the possible reasons/solutions. Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Friday, October 06, 2006 9:00 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration > > On Thursday 05 October 2006 16:24, Dirk Haase wrote: > > It is gone now... Could it be that there is simply a delay > between the > > unregistration in the database and the time this is > displayed to the > > outside (encyclopedia/dashboard) ? That would explain some things... > > Eddie, I have the strong feeling that the agent accesses some > sort of cache/web proxy - at least when I call it. I turned > to play around with single service RDF files and now I get > the message "No services in the registry match the given URL > and the signatureURL didn't contain any services. The RDF > agent was called, but found nothing useful." > for a file which does contain a service description now (but > did not ~ 15 minutes ago). > > Best, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From d.haase at gsf.de Mon Oct 9 02:53:29 2006 From: d.haase at gsf.de (Dirk Haase) Date: Mon, 9 Oct 2006 08:53:29 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <003701c6e967$ca1f4cb0$6700a8c0@notebook> References: <003701c6e967$ca1f4cb0$6700a8c0@notebook> Message-ID: <200610090853.30087.d.haase@gsf.de> On Friday 06 October 2006 18:52, Edward Kawas wrote: > Hi Dirk, > > I think that I have fixed this issue. Can you confirm? Yes! This morning all my tests were successful. Thank you and all the best, dirk From d.haase at gsf.de Mon Oct 9 03:34:16 2006 From: d.haase at gsf.de (Dirk Haase) Date: Mon, 9 Oct 2006 09:34:16 +0200 Subject: [MOBY-dev] small updates to Dashboard In-Reply-To: <4d93f07c0610021430x56f003a1l34d233fb43eb0e09@mail.gmail.com> References: <4d93f07c0610021430x56f003a1l34d233fb43eb0e09@mail.gmail.com> Message-ID: <200610090934.17267.d.haase@gsf.de> Hi Martin, On Monday 02 October 2006 23:30, Martin Senger wrote: > Dirk gave me an idea to add a new button "Call RDF Agent". The button is > now in the service registration panel. Further testing of its usefulness is > needed - please let me know how to improve it. After all my issues with the unregistration via agent are solved I can now confirm that the new button works as expected. It might be confusing however that the 'signature URL' field and all the other inputs can be totally unrelated and that in fact all other fields are ignored when the 'Call RDF Agent' button is used. Users could think their changes eg. in input/output data were directly transferred to the RDF document and read by the agent (and then they are happy when it says "RDF Agent call was successful"...). Maybe another check-box 'Agent Mode' within the "Service RDF Signature" section could make things clearer. When checked, the 'Call RDF Agent' button would become active, all other input fields - except the signature URL field - and buttons inactive. Best, dirk From martin.senger at gmail.com Fri Oct 13 18:18:13 2006 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 13 Oct 2006 23:18:13 +0100 Subject: [MOBY-dev] Perl MoSeS update Message-ID: <4d93f07c0610131518u3da9bdccu7859cd3129134341@mail.gmail.com> First of all, I would like to thank Dirk for his feedback on Perl Moses. I am going now through his suggestions and implementing them. I have started with this one - which is quite important: For me it was quite complicated to make sure that the old Perl libraries and > the moses packages can be used simultaneously (by different services of > course). It would be much easier if you had chosen a directory name > different > than 'MOBY'... There is also a nameclash with regard to the MOBY::Config > package (which also exists in the old libraries). It is always annoying to make such dramatic change - but better now than later (when more people will be using it). I apologize for any inconvenience I caused. But Dirk is right, it's better to use a different package names. So I changed all module names from MOBY::* to MOSES::MOBY::*. I hope I did it on all places, including the documentation. If not and you will see some not-so-far- known bugs or behaviour please let me know asap. What you need to do now is: cvs update -dP and - if you already using generate data types - regenerate them, and to check what you do in your service implementation - perhaps to change the module names there as well. With regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Sat Oct 14 16:52:54 2006 From: martin.senger at gmail.com (Martin Senger) Date: Sat, 14 Oct 2006 21:52:54 +0100 Subject: [MOBY-dev] Perl MoSeS update 2 Message-ID: <4d93f07c0610141352w1764103cu96fffd63dd3f248c@mail.gmail.com> I am continuing to address feedback issues sent by Dirk (again, thanks for them): One thing I missed was how to set namespace and id in the output object. > Maybe a small section explaining the general object methods would be > valuable. I have updated documentation to show how to do various things in your implementation (including the mentioned id and namespace settings). You can find it in the section "How to write a service implementation". [The full perldoc documentation is still missing... sorry; time problems...] Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From Yogaraj.Khanal at usd.edu Sat Oct 14 17:09:32 2006 From: Yogaraj.Khanal at usd.edu (Yogaraj.Khanal at usd.edu) Date: Sat, 14 Oct 2006 14:09:32 -0700 Subject: [MOBY-dev] Perl MoSeS update 2 Message-ID: <205681206fff.206fff205681@usd.edu> hi Martin, Can you please send me some materials on how to handle secondary input parameteres in Taverna. Regards, Yogaraj RA,USD ----- Original Message ----- From: Martin Senger Date: Saturday, October 14, 2006 1:52 pm Subject: [MOBY-dev] Perl MoSeS update 2 > I am continuing to address feedback issues sent by Dirk (again, > thanks for > them): > > One thing I missed was how to set namespace and id in the output > object.> Maybe a small section explaining the general object > methods would be > > valuable. > > > I have updated documentation to show how to do various things in your > implementation (including the mentioned id and namespace > settings). You can > find it in the section "How to write a service implementation". > [The full > perldoc documentation is still missing... sorry; time problems...] > > Cheers, > Martin > > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From martin.senger at gmail.com Sat Oct 14 20:28:25 2006 From: martin.senger at gmail.com (Martin Senger) Date: Sun, 15 Oct 2006 01:28:25 +0100 Subject: [MOBY-dev] Perl MoSeS update 2 In-Reply-To: <205681206fff.206fff205681@usd.edu> References: <205681206fff.206fff205681@usd.edu> Message-ID: <4d93f07c0610141728j45d81883o4e4fc9b62361abbe@mail.gmail.com> Hi, Can you please send me some materials on how to handle secondary input > parameteres in Taverna. I am sorry, I cannot do that (it is a long time I worked with Taverna, and things have changed there). But Eddie wrote a pretty good guide about moby and taverna - why don't you look there? It is at http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/guide/index.html . I remember that you also asked me and Eddie about how to get a list of primary and secondary parameters for all services. I would recommend you to try to start BioMoby Dashboard (I can help you with that if you need) - there are panels that can do it for you (I hope). Regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From groscurt at mpiz-koeln.mpg.de Thu Oct 19 05:19:15 2006 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 19 Oct 2006 11:19:15 +0200 Subject: [MOBY-dev] Retrieving the latest changes in the Moby Registry Message-ID: <200610191119.15253.groscurt@mpiz-koeln.mpg.de> Hi everybody, I"m looking for a simple way to retrieve the latest changes in the Moby registry. So if for example a new services has been registered or modified anyhow I would like to retrieve those services from the registry. Is this doable with the current implementation structure and if so how ? Thanks and greetings Andreas -- Andreas Groscurth Diplom Bioinformatik - PhD Student International Max Planck Research School (IMPRS) Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From markw at illuminae.com Thu Oct 19 11:15:16 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 19 Oct 2006 08:15:16 -0700 Subject: [MOBY-dev] [moby] Retrieving the latest changes in the Moby Registry In-Reply-To: <200610191119.15253.groscurt@mpiz-koeln.mpg.de> References: <200610191119.15253.groscurt@mpiz-koeln.mpg.de> Message-ID: <1161270916.19851.33.camel@bioinfo.icapture.ubc.ca> There's no *formal* way to do this with the API, but you could do it in an ad hoc (but hopefully reliable) way by retrieving the LSID's for all of the services (a variety of API calls provide this for you), and then checking the timestamp at the end of each one. I'm running to a meeting, but if this isn't clear I'll write a more comprehensive answer later today, Mark On Thu, 2006-10-19 at 11:19 +0200, Andreas Groscurth wrote: > Hi everybody, > > I"m looking for a simple way to retrieve the latest changes in the Moby > registry. So if for example a new services has been registered or modified > anyhow I would like to retrieve those services from the registry. > > Is this doable with the current implementation structure and if so how ? > > Thanks and greetings > Andreas > -- Mark Wilkinson Asst. Professor, Dept. of Medical Genetics University of British Columbia PI in Bioinformatics, iCAPTURE Centre St. Paul's Hospital, Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 "Since the point of a definition is to explain the meaning of a term to someone who is unfamiliar with its proper application, the use of language that doesn't help such a person learn how to apply the term is pointless. Thus, "happiness is a warm puppy" may be a lovely thought, but it is a lousy definition." K?hler et al, 2006 From martin.senger at gmail.com Thu Oct 19 17:12:13 2006 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 20 Oct 2006 06:12:13 +0900 Subject: [MOBY-dev] Retrieving the latest changes in the Moby Registry In-Reply-To: <200610191119.15253.groscurt@mpiz-koeln.mpg.de> References: <200610191119.15253.groscurt@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0610191412w449dfe57rdf1def9576a45b17@mail.gmail.com> > Is this doable with the current implementation structure and if so how ? As Mark suggested, the LSIDs are the way to do this. I would even say that "it is part of the API" - so you can rely on it. You can looked into jMoby code in CentralDigestCachedImpl.,java - this code does it. Regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Tue Oct 24 17:00:51 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 24 Oct 2006 14:00:51 -0700 Subject: [MOBY-dev] publications page updated Message-ID: Hi all, on the BioMoby website publication list (http://biomoby.open-bio.org/index.php/what-is-moby/publications), I've added several publications that have come out of the community in the past year or two. Please let me know if I have missed yours, or if I have included you but you do not wish to be included. Cheers! Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital From gss at ncgr.org Tue Oct 24 17:49:30 2006 From: gss at ncgr.org (Gary Schiltz) Date: Tue, 24 Oct 2006 15:49:30 -0600 Subject: [MOBY-dev] publications page updated In-Reply-To: References: Message-ID: <453E8A6A.5080801@ncgr.org> If you would be so kind, please add the the following citation (under either "Peer reviewed and books" - it was reviewed by the workshop organizers - or under "Other press and manuscripts"): Schiltz G, Gessler D, Stein L (2004). Semantic MOBY. Position paper for the 2004 W3C Workshop on Semantic Web for Life Sciences. I would suggest linking "Semantic MOBY" in the citation to the URL http://lists.w3.org/Archives/Public/public-swls-ws/2004Sep/att-0036/smoby-w3c-sw-ls.pdf. The link to the workshop report is http://www.w3.org/2004/10/swls-workshop-report.html, and I would suggest linking that URL to the text "W3C Workshop on Semantic Web for Life Sciences" in the citation. // Gary Mark Wilkinson wrote: > Hi all, > > on the BioMoby website publication list > (http://biomoby.open-bio.org/index.php/what-is-moby/publications), I've > added several publications that have come out of the community in the past > year or two. Please let me know if I have missed yours, or if I have > included you but you do not wish to be included. > > Cheers! > > Mark > > > > From duncan.hull at cs.man.ac.uk Wed Oct 25 05:40:49 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Wed, 25 Oct 2006 10:40:49 +0100 Subject: [MOBY-dev] publications page updated In-Reply-To: References: Message-ID: <453F3121.1080106@cs.man.ac.uk> Hi Mark Mark Wilkinson wrote: > on the BioMoby website publication list > (http://biomoby.open-bio.org/index.php/what-is-moby/publications), Maybe you could add a link to http://www.connotea.org/tag/biomoby ? Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From d.haase at gsf.de Wed Oct 25 10:14:36 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 25 Oct 2006 16:14:36 +0200 Subject: [MOBY-dev] publications page updated In-Reply-To: <453F3121.1080106@cs.man.ac.uk> References: <453F3121.1080106@cs.man.ac.uk> Message-ID: <200610251614.36696.d.haase@gsf.de> On Wednesday 25 October 2006 11:40, Duncan Hull wrote: > Hi Mark > > Mark Wilkinson wrote: > > on the BioMoby website publication list > > (http://biomoby.open-bio.org/index.php/what-is-moby/publications), > > Maybe you could add a link to http://www.connotea.org/tag/biomoby ? Nice idea, but it is weeks ago that I last received more than a header from the connotea web server... Does it still work for you? dirk From duncan.hull at cs.man.ac.uk Wed Oct 25 11:02:19 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Wed, 25 Oct 2006 16:02:19 +0100 Subject: [MOBY-dev] publications page updated; MobyConnotea In-Reply-To: <200610251614.36696.d.haase@gsf.de> References: <453F3121.1080106@cs.man.ac.uk> <200610251614.36696.d.haase@gsf.de> Message-ID: <453F7C7B.7070307@cs.man.ac.uk> Hi Dirk Dirk Haase wrote: >> Maybe you could add a link to http://www.connotea.org/tag/biomoby ? >> > > Nice idea, but it is weeks ago that I last received more than a header from > the connotea web server... Does it still work for you? > The connotea server has been fairly responsive for me, not had any performance issues here (yet)... Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From johan at ac.uma.es Mon Oct 2 12:51:00 2006 From: johan at ac.uma.es (Johan Karlsson) Date: Mon, 02 Oct 2006 14:51:00 +0200 Subject: [MOBY-dev] Reminder: Vote async proposal In-Reply-To: <1158947474.5704.30.camel@bioinfo.icapture.ubc.ca> References: <45125B5A.1070402@ac.uma.es> <4d93f07c0609220945l2fadb6f5tc2bca1820f0f44ad@mail.gmail.com> <1158947474.5704.30.camel@bioinfo.icapture.ubc.ca> Message-ID: <45210B34.7020705@ac.uma.es> Mark Wilkinson wrote: >> There is really no such thing as an RFC committee... >> > > Well... there is a group of us who have agreed to be "the deciders" (to > quote George Bush... I'll never do that again, I promise!) > > > >> But yes, I agree to >> have a vote - if the political issue (regardinr using a SOAP-specific >> technology) is considered to be solved. How is it, Mark? >> > > > There was no significant discussion of this issue beyond the brief > conversation that we had on the mailing list. My own opinion is that we > have (possibly regrettably) already bought-in to the SOAP > infrastructure, so using a SOAP-specific technology is a reasonable > thing to do at this point. It does make it more difficult to change our > minds later on, but I suspect that any mind-changing in the future is > going to be on an much larger scale than just the transport protocol, so > this small detail is not particularly relevant in that context. In my > opinion, that discussion is resolved. Does anyone disagree? > > v.v. the Asynch proposal - let's call for the vote right now. All > voting members please read the proposal carefully and submit your vote > by October 1. > > M > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -- 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 martin.senger at gmail.com Mon Oct 2 13:14:03 2006 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 2 Oct 2006 14:14:03 +0100 Subject: [MOBY-dev] Reminder: Vote async proposal In-Reply-To: <45210B34.7020705@ac.uma.es> References: <45125B5A.1070402@ac.uma.es> <4d93f07c0609220945l2fadb6f5tc2bca1820f0f44ad@mail.gmail.com> <1158947474.5704.30.camel@bioinfo.icapture.ubc.ca> <45210B34.7020705@ac.uma.es> Message-ID: <4d93f07c0610020614h508d2ffch61ef0e941de07e42@mail.gmail.com> Well, I am still not sure that I understand the proposal fully (not because it is a bad proposal but because I have not spent enough time on it). But I believe fully in the wisdom of our Spanish colleagues, the wisdom I hope to learn when I will be implementing the async behaviour in Moses) - and therefore I vote YES. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From dgpisano at cnb.uam.es Mon Oct 2 13:30:45 2006 From: dgpisano at cnb.uam.es (David G. Pisano) Date: Mon, 2 Oct 2006 15:30:45 +0200 Subject: [MOBY-dev] Reminder: Vote async proposal In-Reply-To: <4d93f07c0610020614h508d2ffch61ef0e941de07e42@mail.gmail.com> References: <45125B5A.1070402@ac.uma.es><4d93f07c0609220945l2fadb6f5tc2bca18 20f0f44ad@mail.gmail.com><1158947474.5704.30.camel@bioinfo.icapture.ubc.ca> <45210B34.7020705@ac.uma.es> <4d93f07c0610020614h508d2ffch61ef0e941de07e42@mail.gmail.com> Message-ID: Voting YES here too (no surprises) ;-) David On 02/10/2006, at 15:14, Martin Senger wrote: > Well, I am still not sure that I understand the proposal fully (not > because > it is a bad proposal but because I have not spent enough time on > it). But I > believe fully in the wisdom of our Spanish colleagues, the wisdom I > hope to > learn when I will be implementing the async behaviour in Moses) - and > therefore I vote YES. > > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From Pieter.Neerincx at wur.nl Mon Oct 2 14:39:56 2006 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Mon, 2 Oct 2006 16:39:56 +0200 Subject: [MOBY-dev] Reminder: Vote async proposal In-Reply-To: <4d93f07c0610020614h508d2ffch61ef0e941de07e42@mail.gmail.com> References: <45125B5A.1070402@ac.uma.es> <4d93f07c0609220945l2fadb6f5tc2bca1820f0f44ad@mail.gmail.com> <1158947474.5704.30.camel@bioinfo.icapture.ubc.ca> <45210B34.7020705@ac.uma.es> <4d93f07c0610020614h508d2ffch61ef0e941de07e42@mail.gmail.com> Message-ID: <9AB24052-73B0-451C-9971-01C146E9F0D2@wur.nl> Hi, Well, I read the proposal and the involved standards. I think it's very important to have a standard for asynchronous services and the process of getting there already took a lot of time. I also think that such a standard should be very robust and ready for the future. Adding things shouldn't be too much of a hassle, but once we implement this it will be a pain if we have to modify it in such a way that all asynchronous services "break". So I think this standard should be damned good from the start :). As mentioned before I feel the way the queryIDs are passed around in the XMl is sub-optimal, making asynchronous service behaviour unnecessarily complicated. More explicitly with what I understand from the WSRF standard I'm not comfortable with "dynamic" resource properties (individual resource properties for status / fetching results for each individual queryID). Therefore - although I like the big picture - I vote NO on the current proposal. I will support any proposal that gets accepted for the sake of interoperability as this is paramount for BioMOBY, but I would prefer a more elegant solution. Cheers, Pi On 2-Oct-2006, at 3:14 PM, Martin Senger wrote: > Well, I am still not sure that I understand the proposal fully (not > because > it is a bad proposal but because I have not spent enough time on > it). But I > believe fully in the wisdom of our Spanish colleagues, the wisdom I > hope to > learn when I will be implementing the async behaviour in Moses) - and > therefore I vote YES. > > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl From edward.kawas at gmail.com Mon Oct 2 14:27:03 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 2 Oct 2006 07:27:03 -0700 Subject: [MOBY-dev] Reminder: Vote async proposal In-Reply-To: <4d93f07c0610020614h508d2ffch61ef0e941de07e42@mail.gmail.com> Message-ID: <004501c6e62e$d5baefc0$6400a8c0@notebook> I vote yes as well. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > Martin Senger > Sent: Monday, October 02, 2006 6:14 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Reminder: Vote async proposal > > Well, I am still not sure that I understand the proposal > fully (not because it is a bad proposal but because I have > not spent enough time on it). But I believe fully in the > wisdom of our Spanish colleagues, the wisdom I hope to learn > when I will be implementing the async behaviour in Moses) - > and therefore I vote YES. > > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From johan at ac.uma.es Mon Oct 2 19:36:16 2006 From: johan at ac.uma.es (Johan Karlsson) Date: Mon, 02 Oct 2006 21:36:16 +0200 Subject: [MOBY-dev] Reminder: Vote async proposal In-Reply-To: <9AB24052-73B0-451C-9971-01C146E9F0D2@wur.nl> References: <45125B5A.1070402@ac.uma.es> <4d93f07c0609220945l2fadb6f5tc2bca1820f0f44ad@mail.gmail.com> <1158947474.5704.30.camel@bioinfo.icapture.ubc.ca> <45210B34.7020705@ac.uma.es> <4d93f07c0610020614h508d2ffch61ef0e941de07e42@mail.gmail.com> <9AB24052-73B0-451C-9971-01C146E9F0D2@wur.nl> Message-ID: <45216A30.6080803@ac.uma.es> Hi Pieter, Sorry to hear that you have a negative opinion of the proposal. From our point of view, the details you are mentioning are minor (in the sense that they are simply choices where to place the information). The same information is sent, the number of SOAP calls are the same. It is not more (or less) optimal to send the queryIDs in the SOAP header than it is to send it in the SOAP body, so we do not understand what you mean with "sub-optimal". As we wrote before, it is possible (you agreed with this also earlier) to implement a getResourcePropertyDocument operation in the future with the approach in the proposal. With only two properties named "status" and "result", the structure would be more "fixed", but the values must still be put there by the service, so the document is not "static" but must be dynamically generated. With dynamic property-names the client must construct these names by appending the queryID to status or result but this is really, as you put it, far from "rocket-science". All these details are hidden by API functions (that we are providing), so it is not critical to change in the future if necessary. Kind regards, Johan Pieter Neerincx wrote: > Hi, > > Well, I read the proposal and the involved standards. I think it's > very important to have a standard for asynchronous services and the > process of getting there already took a lot of time. I also think > that such a standard should be very robust and ready for the future. > Adding things shouldn't be too much of a hassle, but once we > implement this it will be a pain if we have to modify it in such a > way that all asynchronous services "break". So I think this standard > should be damned good from the start :). > > As mentioned before I feel the way the queryIDs are passed around in > the XMl is sub-optimal, making asynchronous service behaviour > unnecessarily complicated. More explicitly with what I understand > from the WSRF standard I'm not comfortable with "dynamic" resource > properties (individual resource properties for status / fetching > results for each individual queryID). Therefore - although I like the > big picture - I vote NO on the current proposal. > > I will support any proposal that gets accepted for the sake of > interoperability as this is paramount for BioMOBY, but I would prefer > a more elegant solution. > > Cheers, > > Pi > > On 2-Oct-2006, at 3:14 PM, Martin Senger wrote: > > >> Well, I am still not sure that I understand the proposal fully (not >> because >> it is a bad proposal but because I have not spent enough time on >> it). But I >> believe fully in the wisdom of our Spanish colleagues, the wisdom I >> hope to >> learn when I will be implementing the async behaviour in Moses) - and >> therefore I vote YES. >> >> Martin >> >> -- >> Martin Senger >> email: martin.senger at gmail.com >> skype: martinsenger >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > phone: 0317-483 060 > fax: 0317-483 584 > mobile: 06-143 66 783 > pieter.neerincx at wur.nl > > > > _______________________________________________ > 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 Oct 2 21:30:44 2006 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 2 Oct 2006 22:30:44 +0100 Subject: [MOBY-dev] small updates to Dashboard Message-ID: <4d93f07c0610021430x56f003a1l34d233fb43eb0e09@mail.gmail.com> I have added a list of well-known registries to the registry browser panel (so changing registry should be easier now, one does not need to remember their URLs). It i also possible to add your own registry - that you wish to keep just for your site (see Dashboard documentation how to do it). Dirk gave me an idea to add a new button "Call RDF Agent". The button is now in the service registration panel. Further testing of its usefulness is needed - please let me know how to improve it. Therefore, please, cvs update... Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Mon Oct 2 22:54:24 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 02 Oct 2006 15:54:24 -0700 Subject: [MOBY-dev] Asynch proposal Message-ID: <1159829664.30244.28.camel@bioinfo.icapture.ubc.ca> I just re-read it and it looks great! YES from here! We are waiting on three more votes, four positive votes so far, one negative. Democratically we can't call it without one more positive vote. I have c.c.'d the three absentees on this message. M -- Mark Wilkinson Asst. Professor, Dept. of Medical Genetics University of British Columbia PI in Bioinformatics, iCAPTURE Centre St. Paul's Hospital, Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 "Since the point of a definition is to explain the meaning of a term to someone who is unfamiliar with its proper application, the use of language that doesn't help such a person learn how to apply the term is pointless. Thus, "happiness is a warm puppy" may be a lovely thought, but it is a lousy definition." K?hler et al, 2006 From markw at illuminae.com Mon Oct 2 22:33:41 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 02 Oct 2006 15:33:41 -0700 Subject: [MOBY-dev] Asynchronous service Message-ID: <1159828421.30244.5.camel@bioinfo.icapture.ubc.ca> I've just re-read it and it looks great to me. YES! 4 votes for YES 1 vote for NO 3 votes still missing We're missing Paul Gordon, Frank Gibbons, and Simon Twigger (c.c.'d on this message in case they aren't reading the MOBY mailing list) Democratically, we have only half the YES votes necessary for success so far, so we need them to vote. M -- Mark Wilkinson Asst. Professor, Dept. of Medical Genetics University of British Columbia PI in Bioinformatics, iCAPTURE Centre St. Paul's Hospital, Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 "Since the point of a definition is to explain the meaning of a term to someone who is unfamiliar with its proper application, the use of language that doesn't help such a person learn how to apply the term is pointless. Thus, "happiness is a warm puppy" may be a lovely thought, but it is a lousy definition." K?hler et al, 2006 From Pieter.Neerincx at wur.nl Mon Oct 2 23:14:15 2006 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Tue, 3 Oct 2006 01:14:15 +0200 Subject: [MOBY-dev] Reminder: Vote async proposal In-Reply-To: <45216A30.6080803@ac.uma.es> References: <45125B5A.1070402@ac.uma.es> <4d93f07c0609220945l2fadb6f5tc2bca1820f0f44ad@mail.gmail.com> <1158947474.5704.30.camel@bioinfo.icapture.ubc.ca> <45210B34.7020705@ac.uma.es> <4d93f07c0610020614h508d2ffch61ef0e941de07e42@mail.gmail.com> <9AB24052-73B0-451C-9971-01C146E9F0D2@wur.nl> <45216A30.6080803@ac.uma.es> Message-ID: <4C022C4C-F667-4E0E-9555-C6AFFA6305CD@wur.nl> Hi Johan, On 02 Oct 2006, at 21:36, Johan Karlsson wrote: > Hi Pieter, > > Sorry to hear that you have a negative opinion of the proposal. It's not that dramatic. Like I said I'm very happy the people at the INB took the effort to write a proposal (twice!) for asynchronous service behaviour. I also think using WS Adressing and the WSRF standards is a good idea and the big picture of how to implement this for BioMOBY looks good! But you have called a vote on the current version of the proposal and I can not vote yes for 97%. It's either a yes or a no. > From our point of view, the details you are mentioning are minor (in > the sense that they are simply choices where to place the > information). Correct. > The same information is sent, the number of SOAP calls are the same. Indeed. > It is not more (or less) optimal to send the queryIDs in the SOAP > header > than it is to send it in the SOAP body, so we do not understand > what you > mean with "sub-optimal". Ok, let my try to explain with another example then. One of the strengths of BioMOBY is the Object ontology which greatly improves interoperability. The objects in this ontology are described using "self-describing" XML. It is possible though to send for example "lagacy" tab delimited data inside a String object. We do have such objects for backwards copatibility, but it's not an elegant way to send data around. Using tab delimited data defeats the purpose of the object ontology as a client can not figure out the relationships between the data within the tab delimited text block. A client has no way to figure what is in column 1,2,3, etc. and the data from column 2 can not easily be parsed using an XML parser to send it as input to another service. Surely you can write a rather simple piece of code that uses a regular expression to fetch the values from column 2 wrap it in new XML tags and send it to the next service and although this is not rocket science it's not elegant and it hampers interoperability. In the current proposal the queryIDs jump around the XMl as part of an element name, as an attribute and as part of raw text. Especially the resource properties are problematic in my point of view. You are doing something similar to wrapping tab delimited data when you combine: * the kind of resource property you want to request (status or result) * with the ID of an individual job of a batch (queryID) and send these merged as a text string like in: status_queryID01, status_queryID02, status_queryID03, etc. and result_queryID01, result_queryID02, result_queryID03, etc. Surely you can write code to fetch the raw text from a node and use a regular expression to split on "_" and hence seperate the kind of resource property requested from the job ID, but just like with tab delimited data it's an ugly approach to put different types of data inside raw text. You lose the semantics and it's not necessary! Some time ago I send some XML examples to show that with some minor tweaks to the XML passed around we can still use WS addressing and WSRF and make sure the queryIDs remain attributes like with the current synchronous services. It makes the XML more consequent and less confusing. > As we wrote before, it is possible (you agreed with this also earlier) > to implement a getResourcePropertyDocument operation in the future > with > the approach in the proposal. True, but with the current proposal you would have to generate a ResourcePropertyDocument dynamically for each service invocation, whereas with a few minor tweaks you can have a static ResourcePropertyDocument for a service which is the same for each invocation. It's not rocket science to create a ResourcePropertyDocument for each service request, but it is simply unnecessary overhead. > With only two properties named "status" > and "result", the structure would be more "fixed", but the values must > still be put there by the service, so the document is not "static" but > must be dynamically generated. No, the ResourcePropertyDocument would be static if the queryIDs move to the EPR. Making the actual request to get resource properties would be a dynamic thing as the queryIDs have to be there somewhere in the data structure, but if they are part of the EPR a client can simply take them from the successful service invocation and echo them back. This would simply require less logic. Finally I feel the current proposal is sub-optimal because, the result XML from an asynchronous service is slightly different from the XML produced by a synchronous service. For an asynchronous service result there are extra and redundant tags. Having a few more tags makes life not impossible - the prototype surely works - but again I think it's ugly and most of all not necessary. With a few minor tweaks the results of asynchronous and synchronous services can be exactly the same which is more transparent in my point of view. Since it requires only minor tweaks to the XML that is send around to make the asynchronous service behavior more transparent, I assume it won't be a big deal to change the proposal and the prototype, but please correct me if I overlooked something here... Hope it's more clear now and with kind regards, Pi > With dynamic property-names the client > must construct these names by appending the queryID to status or > result > but this is really, as you put it, far from "rocket-science". > > All these details are hidden by API functions (that we are providing), > so it is not critical to change in the future if necessary. > Kind regards, > Johan > > > Pieter Neerincx wrote: >> Hi, >> >> Well, I read the proposal and the involved standards. I think it's >> very important to have a standard for asynchronous services and the >> process of getting there already took a lot of time. I also think >> that such a standard should be very robust and ready for the future. >> Adding things shouldn't be too much of a hassle, but once we >> implement this it will be a pain if we have to modify it in such a >> way that all asynchronous services "break". So I think this standard >> should be damned good from the start :). >> >> As mentioned before I feel the way the queryIDs are passed around in >> the XMl is sub-optimal, making asynchronous service behaviour >> unnecessarily complicated. More explicitly with what I understand >> from the WSRF standard I'm not comfortable with "dynamic" resource >> properties (individual resource properties for status / fetching >> results for each individual queryID). Therefore - although I like the >> big picture - I vote NO on the current proposal. >> >> I will support any proposal that gets accepted for the sake of >> interoperability as this is paramount for BioMOBY, but I would prefer >> a more elegant solution. >> >> Cheers, >> >> Pi >> >> On 2-Oct-2006, at 3:14 PM, Martin Senger wrote: >> >> >>> Well, I am still not sure that I understand the proposal fully (not >>> because >>> it is a bad proposal but because I have not spent enough time on >>> it). But I >>> believe fully in the wisdom of our Spanish colleagues, the wisdom I >>> hope to >>> learn when I will be implementing the async behaviour in Moses) - >>> and >>> therefore I vote YES. >>> >>> Martin >>> >>> -- >>> Martin Senger >>> email: martin.senger at gmail.com >>> skype: martinsenger >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> >> >> Wageningen University and Research centre (WUR) >> Laboratory of Bioinformatics >> Transitorium (building 312) room 1034 >> Dreijenlaan 3 >> 6703 HA Wageningen >> The Netherlands >> phone: 0317-483 060 >> fax: 0317-483 584 >> mobile: 06-143 66 783 >> pieter.neerincx at wur.nl >> >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1038 Dreijenlaan 3 6703 HA Wageningen phone: 0317-484 706 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl From simont at hmgc.mcw.edu Tue Oct 3 14:13:34 2006 From: simont at hmgc.mcw.edu (Twigger Simon) Date: Tue, 3 Oct 2006 09:13:34 -0500 Subject: [MOBY-dev] Asynch proposal In-Reply-To: <1159829664.30244.28.camel@bioinfo.icapture.ubc.ca> References: <1159829664.30244.28.camel@bioinfo.icapture.ubc.ca> Message-ID: Looks good to me. Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw On Oct 2, 2006, at 5:54 PM, Mark Wilkinson wrote: > I just re-read it and it looks great! YES from here! > > We are waiting on three more votes, four positive votes so far, one > negative. Democratically we can't call it without one more positive > vote. > > I have c.c.'d the three absentees on this message. > > M > > > -- > Mark Wilkinson > Asst. Professor, Dept. of Medical Genetics > University of British Columbia > PI in Bioinformatics, iCAPTURE Centre > St. Paul's Hospital, Rm. 166, 1081 Burrard St. > Vancouver, BC, V6Z 1Y6 > tel: 604 682 2344 x62129 > fax: 604 806 9274 > > "Since the point of a definition is to explain the meaning of a > term to > someone who is unfamiliar with its proper application, the use of > language that doesn't help such a person learn how to apply the > term is > pointless. Thus, "happiness is a warm puppy" may be a lovely thought, > but it is a lousy definition." > > K?hler et al, 2006 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Tue Oct 3 16:37:32 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 03 Oct 2006 09:37:32 -0700 Subject: [MOBY-dev] Asynch proposal - accepted In-Reply-To: References: <1159829664.30244.28.camel@bioinfo.icapture.ubc.ca> Message-ID: <1159893452.7243.29.camel@bioinfo.icapture.ubc.ca> And with that vote, the Asynch RFC is passed. Thanks INB team! Mark On Tue, 2006-10-03 at 09:13 -0500, Twigger Simon wrote: > Looks good to me. > > Simon. > > -- > > Simon N. Twigger, Ph.D. > Assistant Professor, Department of Physiology > Medical College of Wisconsin > 8701 Watertown Plank Road, > Milwaukee, WI, USA > tel: 414-456-8802 > fax: 414-456-6595 > AIM/iChat: simontatmcw > > > On Oct 2, 2006, at 5:54 PM, Mark Wilkinson wrote: > > > I just re-read it and it looks great! YES from here! > > > > We are waiting on three more votes, four positive votes so far, one > > negative. Democratically we can't call it without one more positive > > vote. > > > > I have c.c.'d the three absentees on this message. > > > > M > > > > > > -- > > Mark Wilkinson > > Asst. Professor, Dept. of Medical Genetics > > University of British Columbia > > PI in Bioinformatics, iCAPTURE Centre > > St. Paul's Hospital, Rm. 166, 1081 Burrard St. > > Vancouver, BC, V6Z 1Y6 > > tel: 604 682 2344 x62129 > > fax: 604 806 9274 > > > > "Since the point of a definition is to explain the meaning of a > > term to > > someone who is unfamiliar with its proper application, the use of > > language that doesn't help such a person learn how to apply the > > term is > > pointless. Thus, "happiness is a warm puppy" may be a lovely thought, > > but it is a lousy definition." > > > > K?hler et al, 2006 > > > > _______________________________________________ > > MOBY-dev mailing list > > MOBY-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Mark Wilkinson Asst. Professor, Dept. of Medical Genetics University of British Columbia PI in Bioinformatics, iCAPTURE Centre St. Paul's Hospital, Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 "Since the point of a definition is to explain the meaning of a term to someone who is unfamiliar with its proper application, the use of language that doesn't help such a person learn how to apply the term is pointless. Thus, "happiness is a warm puppy" may be a lovely thought, but it is a lousy definition." K?hler et al, 2006 From johan at ac.uma.es Wed Oct 4 10:15:28 2006 From: johan at ac.uma.es (Johan Karlsson) Date: Wed, 04 Oct 2006 12:15:28 +0200 Subject: [MOBY-dev] Asynch proposal - accepted In-Reply-To: <1159893452.7243.29.camel@bioinfo.icapture.ubc.ca> References: <1159829664.30244.28.camel@bioinfo.icapture.ubc.ca> <1159893452.7243.29.camel@bioinfo.icapture.ubc.ca> Message-ID: <452389C0.4030704@ac.uma.es> The RFC that was accepted is specified in this document: http://twiki.inab.org/twiki/pub/INB/INBDocsRoot/BioMOBY_Asynchronous_Service_Call_Proposal_WSRF_v2.3.pdf Of course, the information there must be added to the official BioMOBY documentation but until that happens the RFC document is important. As you already know, INB has provided a Perl library to help develop asynchronous services (compatible with the RFC, of course): http://bioinfo.pcm.uam.es/prototype/ Support for asynchronous BioMOBY services in Java is being implemented in Moses by Martin Senger (not sure when this will be available but keep an eye on the moby-dev list). Kind regards, Johan -- 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 Mark Wilkinson wrote: > And with that vote, the Asynch RFC is passed. > > Thanks INB team! > > Mark From d.haase at gsf.de Wed Oct 4 13:14:08 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 4 Oct 2006 15:14:08 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <1159375710.27141.55.camel@bioinfo.icapture.ubc.ca> References: <002401c6e242$996cc880$6400a8c0@notebook> <4d93f07c0609270944kb959b6ep41f2d159a76eef7a@mail.gmail.com> <1159375710.27141.55.camel@bioinfo.icapture.ubc.ca> Message-ID: <200610041514.12997.d.haase@gsf.de> On Wednesday 27 September 2006 18:48, Mark Wilkinson wrote: > Call it being overly cautious :-) If there were a bug in the agent > that we hadn't noticed during testing, we didn't want to wipe-out the > registry (though it is backed-up daily, so we could recover anyway). > > It looks like there are no obvious bugs... Nevertheless de-registration by agent is still not activated it seems... Still objections? Best, dirk From edward.kawas at gmail.com Wed Oct 4 13:19:17 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 4 Oct 2006 06:19:17 -0700 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <200610041514.12997.d.haase@gsf.de> Message-ID: <002c01c6e7b7$b3aeda10$6400a8c0@notebook> Hi Dirk, What makes you say that? De-registration is enabled ... Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Wednesday, October 04, 2006 6:14 AM > To: markw at illuminae.com; Core developer announcements > Subject: Re: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration > > On Wednesday 27 September 2006 18:48, Mark Wilkinson wrote: > > Call it being overly cautious :-) If there were a bug in > the agent > > that we hadn't noticed during testing, we didn't want to > wipe-out the > > registry (though it is backed-up daily, so we could recover anyway). > > > > It looks like there are no obvious bugs... > > Nevertheless de-registration by agent is still not activated > it seems... Still objections? > > Best, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From d.haase at gsf.de Wed Oct 4 14:06:05 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 4 Oct 2006 16:06:05 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <002c01c6e7b7$b3aeda10$6400a8c0@notebook> References: <002c01c6e7b7$b3aeda10$6400a8c0@notebook> Message-ID: <200610041606.05821.d.haase@gsf.de> On Wednesday 04 October 2006 15:19, Edward Kawas wrote: > Hi Dirk, > > What makes you say that? De-registration is enabled ... Strange things are happening... For example, the mips.gsf.de service 'getClonesByName' formerly was included in the multi-service rdf at http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf but then I created a separate document for it: http://mips.gsf.de/proj/planet/moby/RDF/getClonesByName.rdf Last week I got an error message from the agent that the service was registered with a double signature URL. So I tried to de-register it by deleting it from the multi-service file and called the agent. But the service is still in the registry with the old signature URL (where it is not mentioned anymore). If de-registration was working correctly, it should not be listed at all... The real funny thing is that I have seen that service this morning with its new (and correct) signature URL. Any clue? Thanks From ivanp at mmb.pcb.ub.es Wed Oct 4 14:10:12 2006 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Wed, 04 Oct 2006 16:10:12 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <002c01c6e7b7$b3aeda10$6400a8c0@notebook> References: <002c01c6e7b7$b3aeda10$6400a8c0@notebook> Message-ID: <4523C0C4.4030600@mmb.pcb.ub.es> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, It's enabled and it's working well because I'm playing with it right now. Martin, it would be very useful, I think, that the "unregister service" button on Dashboard performed a call to unregister the service according with the new API (an "empty query" with just the signatureURL tag) and not the old unregister call that is not longer working, don't you think? Iv?n Edward Kawas escribi?: > Hi Dirk, > > What makes you say that? De-registration is enabled ... > > Thanks, > > Eddie > >> -----Original Message----- From: >> moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk >> Haase Sent: Wednesday, October 04, 2006 6:14 AM To: >> markw at illuminae.com; Core developer announcements Subject: Re: >> [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration >> >> On Wednesday 27 September 2006 18:48, Mark Wilkinson wrote: >>> Call it being overly cautious :-) If there were a bug in >> the agent >>> that we hadn't noticed during testing, we didn't want to >> wipe-out the >>> registry (though it is backed-up daily, so we could recover >>> anyway). >>> >>> It looks like there are no obvious bugs... >> Nevertheless de-registration by agent is still not activated it >> seems... Still objections? >> >> Best, dirk _______________________________________________ >> MOBY-dev mailing list MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ MOBY-dev mailing > list MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev - -- - ------------------------------------------------ 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 - ------------------------------------------------ -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFFI8DCLWwmlDjmrRYRArkNAJoCQ0E0FdllYpc9KK1H3FHGPmpBlgCfYhi2 dupW9IIP2Dgn0kqCAUj4kjQ= =l9J1 -----END PGP SIGNATURE----- From markw at illuminae.com Wed Oct 4 14:28:16 2006 From: markw at illuminae.com (mark wilkinson) Date: Wed, 4 Oct 2006 14:28:16 +0000 GMT Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <002c01c6e7b7$b3aeda10$6400a8c0@notebook> References: <200610041514.12997.d.haase@gsf.de> <002c01c6e7b7$b3aeda10$6400a8c0@notebook> Message-ID: <1821246256-1159972172-cardhu_blackberry.rim.net-15136-@engine26-cell01> I can confirm that I got a deregistration email overnight when the agent ran, so it appears to be working properly for my service RDF's ...?? M -- Mark Wilkinson ...on the road! -----Original Message----- From: "Edward Kawas" Date: Wed, 4 Oct 2006 06:19:17 To:"'Core developer announcements'" , Subject: Re: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration Hi Dirk, What makes you say that? De-registration is enabled ... Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Wednesday, October 04, 2006 6:14 AM > To: markw at illuminae.com; Core developer announcements > Subject: Re: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration > > On Wednesday 27 September 2006 18:48, Mark Wilkinson wrote: > > Call it being overly cautious :-) If there were a bug in > the agent > > that we hadn't noticed during testing, we didn't want to > wipe-out the > > registry (though it is backed-up daily, so we could recover anyway). > > > > It looks like there are no obvious bugs... > > Nevertheless de-registration by agent is still not activated > it seems... Still objections? > > Best, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Wed Oct 4 14:59:56 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 04 Oct 2006 07:59:56 -0700 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <4d93f07c0610040748sf9a701ei68a592a0a6aa9392@mail.gmail.com> References: <200610041514.12997.d.haase@gsf.de> <002c01c6e7b7$b3aeda10$6400a8c0@notebook> <1821246256-1159972172-cardhu_blackberry.rim.net-15136-@engine26-cell01> <4d93f07c0610040748sf9a701ei68a592a0a6aa9392@mail.gmail.com> Message-ID: I think those are slightly different scenario's. I didn't ask the agent to come, I simply moved my RDF file to see if it would notice (and it did). I believe that if I ask the agent to come, it does come immediately... though I agree that it would be a more useful behaviour if an explicit agent call waited until the agent had finished its task and returned an informative message, versus the "you have successfully launched the agent" message you get currently. M On Wed, 04 Oct 2006 07:48:38 -0700, Martin Senger wrote: >> I can confirm that I got a deregistration email > > > This is one of the agent problems - I have discussed it yesterday with > Eddie. If I call an agent to come, it should come at once and my call > should > wait until the agent finishes his journey and my call should get back a > message about it. The email is something that can be used also, but > primarily I would expect synchronous behaviour first. Eddie seems to > agree > with that - and the only reason why it does not work yet like this is > that > he is investigating some behaviour of the perl 'sytem()' call... (AFAIK). > > Martin > > -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital From martin.senger at gmail.com Wed Oct 4 15:07:17 2006 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 4 Oct 2006 16:07:17 +0100 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: References: <200610041514.12997.d.haase@gsf.de> <002c01c6e7b7$b3aeda10$6400a8c0@notebook> <1821246256-1159972172-cardhu_blackberry.rim.net-15136-@engine26-cell01> <4d93f07c0610040748sf9a701ei68a592a0a6aa9392@mail.gmail.com> Message-ID: <4d93f07c0610040807p76a8ddc0ma34d2821fcf1d1d9@mail.gmail.com> > I think those are slightly different scenario's. I didn't ask the agent > to come, I simply moved my RDF file Yes, correct, these are two ways. And - as you said - I was referring to the one used from the Dashboard. That one should be synchronous. Eddie, do you need any help to fix the problem with the 'system()' call? Please let me know, I am at your service. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From d.haase at gsf.de Wed Oct 4 15:08:37 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 4 Oct 2006 17:08:37 +0200 Subject: [MOBY-dev] gbrowse_moby at mobycentral Message-ID: <200610041708.37507.d.haase@gsf.de> Mark and/or Eddie, when I use your gbrowse_moby, I'm missing a certain service by 'seedgenes.org' called 'SeedGenesEmbryoImageByAgiCode'. It should be displayed when 'AGI_LocusCode' was selected as namespace. My first guess was that you recently switched to exclude services without signature URLs but eg. 'EvocName2ID' is listed in spite of not having one. So I'm wondering why the seedgenes.org service can not be accessed. Thanks, dirk From martin.senger at gmail.com Wed Oct 4 14:41:44 2006 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 4 Oct 2006 15:41:44 +0100 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <4523C0C4.4030600@mmb.pcb.ub.es> References: <002c01c6e7b7$b3aeda10$6400a8c0@notebook> <4523C0C4.4030600@mmb.pcb.ub.es> Message-ID: <4d93f07c0610040741p50de8720h5559262520939233@mail.gmail.com> > Martin, it would be very useful, I think, that the "unregister > service" button on Dashboard performed a call to unregister the > service according with the new API (an "empty query" with just the > signatureURL tag) Perhaps you missed my email yesterday (or the day before yesterday) announcing that the dashboard has now a new button "call rdf agent" which does exactly that. (Well, I hope it does, but it is hard to be sure - everybody knows my deep doubts about how this agent behaviour is documented and implemented - sorry, Eddie, I should shut up.) > and not the old unregister call that is not longer working The old way should still work. We agreed that agent will deal with services that have registered their signature url, and old-fashioned unregistration api call will deal with so-called 'services in testing stage' that do not have a signature url. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Wed Oct 4 14:48:38 2006 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 4 Oct 2006 15:48:38 +0100 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <1821246256-1159972172-cardhu_blackberry.rim.net-15136-@engine26-cell01> References: <200610041514.12997.d.haase@gsf.de> <002c01c6e7b7$b3aeda10$6400a8c0@notebook> <1821246256-1159972172-cardhu_blackberry.rim.net-15136-@engine26-cell01> Message-ID: <4d93f07c0610040748sf9a701ei68a592a0a6aa9392@mail.gmail.com> > I can confirm that I got a deregistration email This is one of the agent problems - I have discussed it yesterday with Eddie. If I call an agent to come, it should come at once and my call should wait until the agent finishes his journey and my call should get back a message about it. The email is something that can be used also, but primarily I would expect synchronous behaviour first. Eddie seems to agree with that - and the only reason why it does not work yet like this is that he is investigating some behaviour of the perl 'sytem()' call... (AFAIK). Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From edward.kawas at gmail.com Wed Oct 4 14:19:31 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 4 Oct 2006 07:19:31 -0700 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <200610041606.05821.d.haase@gsf.de> Message-ID: <003a01c6e7c0$1db5f940$6400a8c0@notebook> Hi Dirk, I have looked into the logs and I have noticed that the agent was able to find the service description for getClonesByName in the RDF at the url 'all_mips_services.rdf'. When I resolve the url, it isnt there. Did you recently remove the service from that document? Also, do you mind if I call the agent on your URL? Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Wednesday, October 04, 2006 7:06 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration > > On Wednesday 04 October 2006 15:19, Edward Kawas wrote: > > Hi Dirk, > > > > What makes you say that? De-registration is enabled ... > > Strange things are happening... > > For example, the mips.gsf.de service 'getClonesByName' > formerly was included in the multi-service rdf at > http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf > but then I created a separate document for it: > http://mips.gsf.de/proj/planet/moby/RDF/getClonesByName.rdf > > Last week I got an error message from the agent that the > service was registered with a double signature URL. So I > tried to de-register it by deleting it from the multi-service > file and called the agent. But the service is still in the > registry with the old signature URL (where it is not > mentioned anymore). If de-registration was working correctly, > it should not be listed at all... > > The real funny thing is that I have seen that service this > morning with its new (and correct) signature URL. > > Any clue? > > Thanks > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Wed Oct 4 15:13:35 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 4 Oct 2006 08:13:35 -0700 Subject: [MOBY-dev] gbrowse_moby at mobycentral In-Reply-To: <200610041708.37507.d.haase@gsf.de> Message-ID: <004201c6e7c7$ab8c88e0$6400a8c0@notebook> Hey Dirk, Try again. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Wednesday, October 04, 2006 8:09 AM > To: Core developer announcements > Subject: [MOBY-dev] gbrowse_moby at mobycentral > > Mark and/or Eddie, > > when I use your gbrowse_moby, I'm missing a certain service > by 'seedgenes.org' > called 'SeedGenesEmbryoImageByAgiCode'. It should be > displayed when 'AGI_LocusCode' was selected as namespace. > > My first guess was that you recently switched to exclude > services without signature URLs but eg. 'EvocName2ID' is > listed in spite of not having one. So I'm wondering why the > seedgenes.org service can not be accessed. > > Thanks, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From ivanp at mmb.pcb.ub.es Wed Oct 4 15:21:56 2006 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Wed, 04 Oct 2006 17:21:56 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <4d93f07c0610040741p50de8720h5559262520939233@mail.gmail.com> References: <002c01c6e7b7$b3aeda10$6400a8c0@notebook> <4523C0C4.4030600@mmb.pcb.ub.es> <4d93f07c0610040741p50de8720h5559262520939233@mail.gmail.com> Message-ID: <4523D194.8020602@mmb.pcb.ub.es> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, Yes, you're right, sorry. In fact I read about it and I updated from CVS but I forgot to recompile. Thanks, Iv?n Martin Senger escribi?: >> Martin, it would be very useful, I think, that the "unregister >> service" button on Dashboard performed a call to unregister the >> service according with the new API (an "empty query" with just >> the signatureURL tag) > > > Perhaps you missed my email yesterday (or the day before yesterday) > announcing that the dashboard has now a new button "call rdf > agent" which does exactly that. (Well, I hope it does, but it is > hard to be sure - everybody knows my deep doubts about how this > agent behaviour is documented and implemented - sorry, Eddie, I > should shut up.) > > >> and not the old unregister call that is not longer working > > > The old way should still work. We agreed that agent will deal with > services that have registered their signature url, and > old-fashioned unregistration api call will deal with so-called > 'services in testing stage' that do not have a signature url. > > Martin > > - -- - ------------------------------------------------ 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 - ------------------------------------------------ -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFFI9GULWwmlDjmrRYRArv9AKC3lQ0pa/zgMus034/Oj6IGaS3XjwCgyguz hTUa7p182ZsZOd4UMhZhsZY= =spVW -----END PGP SIGNATURE----- From d.haase at gsf.de Wed Oct 4 15:29:37 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 4 Oct 2006 17:29:37 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <003a01c6e7c0$1db5f940$6400a8c0@notebook> References: <003a01c6e7c0$1db5f940$6400a8c0@notebook> Message-ID: <200610041729.37393.d.haase@gsf.de> On Wednesday 04 October 2006 16:19, Edward Kawas wrote: > Hi Dirk, > > I have looked into the logs and I have noticed that the agent was able to > find the service description for getClonesByName in the RDF at the url > 'all_mips_services.rdf'. When I resolve the url, it isnt there. Did you > recently remove the service from that document? It depends on the definition of 'recently': Yes, if 'recently' = 'today'. No, if 'recently' = 'after the last agent call on that rdf' That was why I was asking... > Also, do you mind if I call the agent on your URL? No, go ahead. I'm curious if your agent call has a different effect than mine ;-) Best, dirk From edward.kawas at gmail.com Wed Oct 4 15:34:07 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 4 Oct 2006 08:34:07 -0700 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <200610041729.37393.d.haase@gsf.de> Message-ID: <004701c6e7ca$892bd8c0$6400a8c0@notebook> Hey Dirk, I ran the agent, and the following was in the log: Service getClonesByName, mips.gsf.de has been removed. The agent wanted to remove the service because Service was not found in the RDF document located at: http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf It did what we expected ... I used the following perl code: use SOAP::Lite + trace; use MOBY::Client::Central; my $m = MOBY::Client::Central->new( Registries => { mobycentral => { URL => 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl', URI => 'http://mobycentral.icapture.ubc.ca/MOBY/Central'} } ); my $REG = $m->registerService( serviceName => "", serviceType => "", authURI => "", contactEmail => '', description => "", category => "", URL => "", signatureURL => "http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf", ); Also, Martin, the system code DOES indeed wait. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Wednesday, October 04, 2006 8:30 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration > > On Wednesday 04 October 2006 16:19, Edward Kawas wrote: > > Hi Dirk, > > > > I have looked into the logs and I have noticed that the > agent was able > > to find the service description for getClonesByName in the > RDF at the > > url 'all_mips_services.rdf'. When I resolve the url, it isnt there. > > Did you recently remove the service from that document? > > It depends on the definition of 'recently': > Yes, if 'recently' = 'today'. > No, if 'recently' = 'after the last agent call on that rdf' > > That was why I was asking... > > > Also, do you mind if I call the agent on your URL? > > No, go ahead. I'm curious if your agent call has a different > effect than mine ;-) > > Best, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From d.haase at gsf.de Wed Oct 4 15:34:45 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 4 Oct 2006 17:34:45 +0200 Subject: [MOBY-dev] gbrowse_moby at mobycentral In-Reply-To: <004201c6e7c7$ab8c88e0$6400a8c0@notebook> References: <004201c6e7c7$ab8c88e0$6400a8c0@notebook> Message-ID: <200610041734.46002.d.haase@gsf.de> On Wednesday 04 October 2006 17:13, Edward Kawas wrote: > Hey Dirk, > > Try again. Many thanks! dirk From martin.senger at gmail.com Wed Oct 4 15:36:00 2006 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 4 Oct 2006 16:36:00 +0100 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <200610041729.37393.d.haase@gsf.de> References: <003a01c6e7c0$1db5f940$6400a8c0@notebook> <200610041729.37393.d.haase@gsf.de> Message-ID: <4d93f07c0610040836r1c728504t4f7baea6042d559f@mail.gmail.com> > No, go ahead. I'm curious if your agent call has a different effect than > mine ;-) It is still possible that an undesired effect is created by a wrong implementation of the "call rdf agent" button in dashboard. That's why I am so keen that you two are tetsing it now. Are you both calling the agent from dashboard? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Wed Oct 4 15:45:08 2006 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 4 Oct 2006 16:45:08 +0100 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <004701c6e7ca$892bd8c0$6400a8c0@notebook> References: <200610041729.37393.d.haase@gsf.de> <004701c6e7ca$892bd8c0$6400a8c0@notebook> Message-ID: <4d93f07c0610040845r5d594274n383c8ea85d06f8@mail.gmail.com> > Also, Martin, the system code DOES indeed wait. Fine, so you can report it back now to the waiting call, right? Make a table where you assign various exit codes to various text messages (we can later improve it to get a real message from the run-script - e.g. your run-agent script can print the error message on stderr where the perl code (registry) can read it from - but wait with this - it is an optimalozation). Let me know when I can try to call agent from dashboard - and to see that I am getting an error message (because I will send a non-existing URL). Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Wed Oct 4 16:59:50 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 04 Oct 2006 09:59:50 -0700 Subject: [MOBY-dev] [moby] gbrowse_moby at mobycentral In-Reply-To: <200610041708.37507.d.haase@gsf.de> References: <200610041708.37507.d.haase@gsf.de> Message-ID: <1159981190.20597.54.camel@bioinfo.icapture.ubc.ca> The current gbrowse_moby filters services based on the "isAlive" tag that is added to the MOBY Central copy of the RDF Signature. Eddie will confirm, since I haven't tested this, but I believe that you can get this RDF metadata as one of the two ports that is provided to you by the LSID Authority server when you attempt to resolve a service instance LSID (one port is the address of the RDF document owned by the service provider,and the other is the RDF document as generated by MOBY Central containing various other metadata) isAlive is generated every hour by a cron that sends a "ping" to the service (as defined in earlier threads - an empty tag) - it it gets the expected response (an empty block) then it "isAlive=true", anything else sets "isAlive=false". So... does your service respond correctly to the ping? This is getting further and further from my own knowledge, since it is largely Eddie now that looks after all MOBY code... M On Wed, 2006-10-04 at 17:08 +0200, Dirk Haase wrote: > Mark and/or Eddie, > > when I use your gbrowse_moby, I'm missing a certain service by 'seedgenes.org' > called 'SeedGenesEmbryoImageByAgiCode'. It should be displayed > when 'AGI_LocusCode' was selected as namespace. > > My first guess was that you recently switched to exclude services without > signature URLs but eg. 'EvocName2ID' is listed in spite of not having one. So > I'm wondering why the seedgenes.org service can not be accessed. > > Thanks, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Mark Wilkinson Asst. Professor, Dept. of Medical Genetics University of British Columbia PI in Bioinformatics, iCAPTURE Centre St. Paul's Hospital, Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 "Since the point of a definition is to explain the meaning of a term to someone who is unfamiliar with its proper application, the use of language that doesn't help such a person learn how to apply the term is pointless. Thus, "happiness is a warm puppy" may be a lovely thought, but it is a lousy definition." K?hler et al, 2006 From edward.kawas at gmail.com Wed Oct 4 17:03:59 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 4 Oct 2006 10:03:59 -0700 Subject: [MOBY-dev] [moby] gbrowse_moby at mobycentral In-Reply-To: <1159981190.20597.54.camel@bioinfo.icapture.ubc.ca> Message-ID: <005a01c6e7d7$179f0440$6400a8c0@notebook> The problem was because isAlive in the cached lsid RDF was false. What happens is that you register a service. In the time between service testing for 'isAlive', any question of the isAlive status of a service returns false. Since gbrowse uses this information, your service initially is invisible to gbrowse. Make sense? Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > Mark Wilkinson > Sent: Wednesday, October 04, 2006 10:00 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [moby] gbrowse_moby at mobycentral > > The current gbrowse_moby filters services based on the > "isAlive" tag that is added to the MOBY Central copy of the > RDF Signature. Eddie will confirm, since I haven't tested > this, but I believe that you can get this RDF metadata as one > of the two ports that is provided to you by the LSID > Authority server when you attempt to resolve a service > instance LSID (one port is the address of the RDF document > owned by the service provider,and the other is the RDF > document as generated by MOBY Central containing various > other metadata) > > isAlive is generated every hour by a cron that sends a "ping" > to the service (as defined in earlier threads - an empty > tag) - it it gets the expected response (an > empty block) then it "isAlive=true", anything > else sets "isAlive=false". > > So... does your service respond correctly to the ping? > > This is getting further and further from my own knowledge, > since it is largely Eddie now that looks after all MOBY code... > > M > > > > On Wed, 2006-10-04 at 17:08 +0200, Dirk Haase wrote: > > Mark and/or Eddie, > > > > when I use your gbrowse_moby, I'm missing a certain service > by 'seedgenes.org' > > called 'SeedGenesEmbryoImageByAgiCode'. It should be displayed when > > 'AGI_LocusCode' was selected as namespace. > > > > My first guess was that you recently switched to exclude services > > without signature URLs but eg. 'EvocName2ID' is listed in > spite of not > > having one. So I'm wondering why the seedgenes.org service > can not be accessed. > > > > Thanks, > > dirk > > _______________________________________________ > > MOBY-dev mailing list > > MOBY-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- > Mark Wilkinson > Asst. Professor, Dept. of Medical Genetics University of > British Columbia PI in Bioinformatics, iCAPTURE Centre St. > Paul's Hospital, Rm. 166, 1081 Burrard St. > Vancouver, BC, V6Z 1Y6 > tel: 604 682 2344 x62129 > fax: 604 806 9274 > > "Since the point of a definition is to explain the meaning of > a term to > someone who is unfamiliar with its proper application, the > use of language that doesn't help such a person learn how to > apply the term is pointless. Thus, "happiness is a warm > puppy" may be a lovely thought, > but it is a lousy definition." > > K?hler et al, 2006 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From d.haase at gsf.de Wed Oct 4 17:38:29 2006 From: d.haase at gsf.de (Haase, Dirk) Date: Wed, 4 Oct 2006 19:38:29 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration References: <003a01c6e7c0$1db5f940$6400a8c0@notebook><200610041729.37393.d.haase@gsf.de> <4d93f07c0610040836r1c728504t4f7baea6042d559f@mail.gmail.com> Message-ID: <1D78CE9FD586024AB0E0102F6F9A7CF86A089A@sw-rz010.gsf.de> I think Eddie does not use dashboard but I do. I'll try to figure out what is going on with some more testing. But tomorrow, not today - my working day is already done :-) Best, dirk -----Original Message----- From: moby-dev-bounces at lists.open-bio.org on behalf of Martin Senger Sent: Wed 10/4/2006 5:36 PM To: Core developer announcements Subject: Re: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration > No, go ahead. I'm curious if your agent call has a different effect than > mine ;-) It is still possible that an undesired effect is created by a wrong implementation of the "call rdf agent" button in dashboard. That's why I am so keen that you two are tetsing it now. Are you both calling the agent from dashboard? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 3244 bytes Desc: not available URL: From martin.senger at gmail.com Wed Oct 4 18:03:42 2006 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 4 Oct 2006 19:03:42 +0100 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <1D78CE9FD586024AB0E0102F6F9A7CF86A089A@sw-rz010.gsf.de> References: <003a01c6e7c0$1db5f940$6400a8c0@notebook> <200610041729.37393.d.haase@gsf.de> <4d93f07c0610040836r1c728504t4f7baea6042d559f@mail.gmail.com> <1D78CE9FD586024AB0E0102F6F9A7CF86A089A@sw-rz010.gsf.de> Message-ID: <4d93f07c0610041103h577d4584p2e2deb6504288690@mail.gmail.com> Hi, > I think Eddie does not use dashboard but I do. I'll try to figure out > what is going on with some more testing. If you (or Eddie) want to see what Dasboard produces after pressing the new button "Call RDF Agent" you can use the Java TCP Monitor (I can explain more if somebody does not know how to use tcpmon). For example, this is a full soap message coming from Dashboard: --- begin --- POST /cgi-bin/MOBY05/mobycentral.pl HTTP/1.0 Content-Type: text/xml; charset=utf-8 Accept: application/soap+xml, application/dime, multipart/related, text/* User-Agent: Axis/1.2.1 Host: mobycentral.icapture.ubc.ca:9999 Cache-Control: no-cache Pragma: no-cache SOAPAction: "http://mobycentral.icapture.ubc.ca/MOBY/Central#registerService" Content-Length: 1113 <registerService><Category>moby</Category><serviceName></serviceName><serviceType></serviceType><serviceLSID></serviceLSID><authURI></authURI><signatureURL>http://yes.no</signatureURL><URL></URL><contactEmail></contactEmail><authoritativeService>1</authoritativeService><Description><![CDATA[]]></Description><Input></Input><secondaryArticles></secondaryArticles><Output></Output></registerService> ---end --- Eddie, is the request correct? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From d.haase at gsf.de Thu Oct 5 12:39:22 2006 From: d.haase at gsf.de (Dirk Haase) Date: Thu, 5 Oct 2006 14:39:22 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <004701c6e7ca$892bd8c0$6400a8c0@notebook> References: <004701c6e7ca$892bd8c0$6400a8c0@notebook> Message-ID: <200610051439.23013.d.haase@gsf.de> On Wednesday 04 October 2006 17:34, Edward Kawas wrote: > Hey Dirk, > > I ran the agent, and the following was in the log: > > Service getClonesByName, mips.gsf.de has been removed. > The agent wanted to remove the service because Service was not found in the > RDF document located at: > http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf > > > It did what we expected ... Either I am constantly making a very stupid error or in fact there is a difference between my agent calls and yours... Today I removed 'getSplicedSequence' from the rdf mentioned above and called the agent 1) by dashboard button 'Call RDF Agent' 2) by dashboard button 'Register from XML' with the following XML file: http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf 3) by a perl script with this core my $REG = $C->registerService( signatureURL=> 'http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf' ); Each time I got a 'success' message but still the service is not unregistered. For the perl script, I used 'SOAP + trace' mode, the outgoing message you can see below. BTW: registration works perfectly with the new dashboard button. Best, dirk And here is the SOAP trace of my registerService call: SOAP::Transport::HTTP::Client::send_receive: POST http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl HTTP/1.1 Accept: text/xml Accept: multipart/* Content-Length: 951 Content-Type: text/xml; charset=utf-8 SOAPAction: "http://mobycentral.icapture.ubc.ca/MOBY/Central#registerService" <registerService> <Category></Category> <serviceName></serviceName> <serviceType></serviceType> <Description></Description> <signatureURL>http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf</signatureURL> <URL></URL> <authURI></authURI> <contactEmail></contactEmail> </registerService> From edward.kawas at gmail.com Thu Oct 5 13:42:57 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 5 Oct 2006 06:42:57 -0700 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <200610051439.23013.d.haase@gsf.de> Message-ID: <002101c6e884$2c2f1cd0$6400a8c0@notebook> Hi Dirk, The agent is finding the service in the RDF: Oct 5, 2006 5:04:40 AM org.biomoby.registry.rdfagent.util.Log info INFO: Found a service (getSplicedSequence/mips.gsf.de) in the registry that matches the one in the RDF ... Comparing them ... I tried resolving your URL right now, and I didn't see the service. What happens if you try again? Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Thursday, October 05, 2006 5:39 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration > > On Wednesday 04 October 2006 17:34, Edward Kawas wrote: > > Hey Dirk, > > > > I ran the agent, and the following was in the log: > > > > Service getClonesByName, mips.gsf.de has been removed. > > The agent wanted to remove the service because Service was > not found > > in the RDF document located at: > > http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf > > > > > > It did what we expected ... > > Either I am constantly making a very stupid error or in fact > there is a difference between my agent calls and yours... > Today I removed 'getSplicedSequence' from the rdf mentioned > above and called the agent > 1) by dashboard button 'Call RDF Agent' > 2) by dashboard button 'Register from XML' with the following > XML file: > > http://mips.gsf.de/proj/planet/moby/RDF/all_mips _services.rdf > > 3) by a perl script with this core > my $REG = $C->registerService( > signatureURL=> > 'http://mips.gsf.de/proj/planet/moby/RDF/all_mips_services.rdf' > ); > > Each time I got a 'success' message but still the service is > not unregistered. > > For the perl script, I used 'SOAP + trace' mode, the outgoing > message you can see below. > > BTW: registration works perfectly with the new dashboard button. > > Best, > dirk > > And here is the SOAP trace of my registerService call: > > SOAP::Transport::HTTP::Client::send_receive: POST > http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral. pl HTTP/1.1 > Accept: text/xml > Accept: multipart/* > Content-Length: 951 > Content-Type: text/xml; charset=utf-8 > SOAPAction: > "http://mobycentral.icapture.ubc.ca/MOBY/Central#registerService" > > xmlns:xsi="http://www.w3.org/1999/XMLSchema-instance" > xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/" > xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/" > xmlns:xsd="http://www.w3.org/1999/XMLSchema" > SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encodi > ng/"> xmlns:namesp1="http://mobycentral.icapture.ubc.ca/MOBY/Central "> xsi:type="xsd:string"> > <registerService> > <Category></Category> > <serviceName></serviceName> > <serviceType></serviceType> > <Description></Description> > > <signatureURL>http://mips.gsf.de/proj/planet/moby/RDF/all_m ips_services.rdf</signatureURL> > <URL></URL> > <authURI></authURI> > <contactEmail></contactEmail> > > </registerService> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From d.haase at gsf.de Thu Oct 5 14:24:44 2006 From: d.haase at gsf.de (Dirk Haase) Date: Thu, 5 Oct 2006 16:24:44 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <002101c6e884$2c2f1cd0$6400a8c0@notebook> References: <002101c6e884$2c2f1cd0$6400a8c0@notebook> Message-ID: <200610051624.44502.d.haase@gsf.de> On Thursday 05 October 2006 15:42, Edward Kawas wrote: > Hi Dirk, > > The agent is finding the service in the RDF: > Oct 5, 2006 5:04:40 AM org.biomoby.registry.rdfagent.util.Log info > INFO: > Found a service (getSplicedSequence/mips.gsf.de) in the registry that > matches the one in the RDF ... > Comparing them ... The timestamp in my SOAP trace is "05 Oct 2006 12:08:30 GMT" which translates to 7:08 pacific standard time (your log timestamps are PST?), so this is not the log entry for my call I guess. > I tried resolving your URL right now, and I didn't see the service. What > happens if you try again? It is gone now... Could it be that there is simply a delay between the unregistration in the database and the time this is displayed to the outside (encyclopedia/dashboard) ? That would explain some things... Best, dirk From d.haase at gsf.de Fri Oct 6 16:00:03 2006 From: d.haase at gsf.de (Dirk Haase) Date: Fri, 6 Oct 2006 18:00:03 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <200610051624.44502.d.haase@gsf.de> References: <002101c6e884$2c2f1cd0$6400a8c0@notebook> <200610051624.44502.d.haase@gsf.de> Message-ID: <200610061800.03418.d.haase@gsf.de> On Thursday 05 October 2006 16:24, Dirk Haase wrote: > It is gone now... Could it be that there is simply a delay between the > unregistration in the database and the time this is displayed to the > outside (encyclopedia/dashboard) ? That would explain some things... Eddie, I have the strong feeling that the agent accesses some sort of cache/web proxy - at least when I call it. I turned to play around with single service RDF files and now I get the message "No services in the registry match the given URL and the signatureURL didn't contain any services. The RDF agent was called, but found nothing useful." for a file which does contain a service description now (but did not ~ 15 minutes ago). Best, dirk From edward.kawas at gmail.com Fri Oct 6 16:52:19 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 6 Oct 2006 09:52:19 -0700 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <200610061800.03418.d.haase@gsf.de> Message-ID: <003701c6e967$ca1f4cb0$6700a8c0@notebook> Hi Dirk, I think that I have fixed this issue. Can you confirm? Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Friday, October 06, 2006 9:00 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration > > On Thursday 05 October 2006 16:24, Dirk Haase wrote: > > It is gone now... Could it be that there is simply a delay > between the > > unregistration in the database and the time this is > displayed to the > > outside (encyclopedia/dashboard) ? That would explain some things... > > Eddie, I have the strong feeling that the agent accesses some > sort of cache/web proxy - at least when I call it. I turned > to play around with single service RDF files and now I get > the message "No services in the registry match the given URL > and the signatureURL didn't contain any services. The RDF > agent was called, but found nothing useful." > for a file which does contain a service description now (but > did not ~ 15 minutes ago). > > Best, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Fri Oct 6 16:02:06 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 6 Oct 2006 09:02:06 -0700 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <200610061800.03418.d.haase@gsf.de> Message-ID: <003001c6e960$c698e940$6700a8c0@notebook> I had a feeling that the agent may be caching. I will look into the possible reasons/solutions. Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Friday, October 06, 2006 9:00 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration > > On Thursday 05 October 2006 16:24, Dirk Haase wrote: > > It is gone now... Could it be that there is simply a delay > between the > > unregistration in the database and the time this is > displayed to the > > outside (encyclopedia/dashboard) ? That would explain some things... > > Eddie, I have the strong feeling that the agent accesses some > sort of cache/web proxy - at least when I call it. I turned > to play around with single service RDF files and now I get > the message "No services in the registry match the given URL > and the signatureURL didn't contain any services. The RDF > agent was called, but found nothing useful." > for a file which does contain a service description now (but > did not ~ 15 minutes ago). > > Best, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From d.haase at gsf.de Mon Oct 9 06:53:29 2006 From: d.haase at gsf.de (Dirk Haase) Date: Mon, 9 Oct 2006 08:53:29 +0200 Subject: [MOBY-dev] [personal] Re: [moby] Re: RDF deregistration In-Reply-To: <003701c6e967$ca1f4cb0$6700a8c0@notebook> References: <003701c6e967$ca1f4cb0$6700a8c0@notebook> Message-ID: <200610090853.30087.d.haase@gsf.de> On Friday 06 October 2006 18:52, Edward Kawas wrote: > Hi Dirk, > > I think that I have fixed this issue. Can you confirm? Yes! This morning all my tests were successful. Thank you and all the best, dirk From d.haase at gsf.de Mon Oct 9 07:34:16 2006 From: d.haase at gsf.de (Dirk Haase) Date: Mon, 9 Oct 2006 09:34:16 +0200 Subject: [MOBY-dev] small updates to Dashboard In-Reply-To: <4d93f07c0610021430x56f003a1l34d233fb43eb0e09@mail.gmail.com> References: <4d93f07c0610021430x56f003a1l34d233fb43eb0e09@mail.gmail.com> Message-ID: <200610090934.17267.d.haase@gsf.de> Hi Martin, On Monday 02 October 2006 23:30, Martin Senger wrote: > Dirk gave me an idea to add a new button "Call RDF Agent". The button is > now in the service registration panel. Further testing of its usefulness is > needed - please let me know how to improve it. After all my issues with the unregistration via agent are solved I can now confirm that the new button works as expected. It might be confusing however that the 'signature URL' field and all the other inputs can be totally unrelated and that in fact all other fields are ignored when the 'Call RDF Agent' button is used. Users could think their changes eg. in input/output data were directly transferred to the RDF document and read by the agent (and then they are happy when it says "RDF Agent call was successful"...). Maybe another check-box 'Agent Mode' within the "Service RDF Signature" section could make things clearer. When checked, the 'Call RDF Agent' button would become active, all other input fields - except the signature URL field - and buttons inactive. Best, dirk From martin.senger at gmail.com Fri Oct 13 22:18:13 2006 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 13 Oct 2006 23:18:13 +0100 Subject: [MOBY-dev] Perl MoSeS update Message-ID: <4d93f07c0610131518u3da9bdccu7859cd3129134341@mail.gmail.com> First of all, I would like to thank Dirk for his feedback on Perl Moses. I am going now through his suggestions and implementing them. I have started with this one - which is quite important: For me it was quite complicated to make sure that the old Perl libraries and > the moses packages can be used simultaneously (by different services of > course). It would be much easier if you had chosen a directory name > different > than 'MOBY'... There is also a nameclash with regard to the MOBY::Config > package (which also exists in the old libraries). It is always annoying to make such dramatic change - but better now than later (when more people will be using it). I apologize for any inconvenience I caused. But Dirk is right, it's better to use a different package names. So I changed all module names from MOBY::* to MOSES::MOBY::*. I hope I did it on all places, including the documentation. If not and you will see some not-so-far- known bugs or behaviour please let me know asap. What you need to do now is: cvs update -dP and - if you already using generate data types - regenerate them, and to check what you do in your service implementation - perhaps to change the module names there as well. With regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Sat Oct 14 20:52:54 2006 From: martin.senger at gmail.com (Martin Senger) Date: Sat, 14 Oct 2006 21:52:54 +0100 Subject: [MOBY-dev] Perl MoSeS update 2 Message-ID: <4d93f07c0610141352w1764103cu96fffd63dd3f248c@mail.gmail.com> I am continuing to address feedback issues sent by Dirk (again, thanks for them): One thing I missed was how to set namespace and id in the output object. > Maybe a small section explaining the general object methods would be > valuable. I have updated documentation to show how to do various things in your implementation (including the mentioned id and namespace settings). You can find it in the section "How to write a service implementation". [The full perldoc documentation is still missing... sorry; time problems...] Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From Yogaraj.Khanal at usd.edu Sat Oct 14 21:09:32 2006 From: Yogaraj.Khanal at usd.edu (Yogaraj.Khanal at usd.edu) Date: Sat, 14 Oct 2006 14:09:32 -0700 Subject: [MOBY-dev] Perl MoSeS update 2 Message-ID: <205681206fff.206fff205681@usd.edu> hi Martin, Can you please send me some materials on how to handle secondary input parameteres in Taverna. Regards, Yogaraj RA,USD ----- Original Message ----- From: Martin Senger Date: Saturday, October 14, 2006 1:52 pm Subject: [MOBY-dev] Perl MoSeS update 2 > I am continuing to address feedback issues sent by Dirk (again, > thanks for > them): > > One thing I missed was how to set namespace and id in the output > object.> Maybe a small section explaining the general object > methods would be > > valuable. > > > I have updated documentation to show how to do various things in your > implementation (including the mentioned id and namespace > settings). You can > find it in the section "How to write a service implementation". > [The full > perldoc documentation is still missing... sorry; time problems...] > > Cheers, > Martin > > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From martin.senger at gmail.com Sun Oct 15 00:28:25 2006 From: martin.senger at gmail.com (Martin Senger) Date: Sun, 15 Oct 2006 01:28:25 +0100 Subject: [MOBY-dev] Perl MoSeS update 2 In-Reply-To: <205681206fff.206fff205681@usd.edu> References: <205681206fff.206fff205681@usd.edu> Message-ID: <4d93f07c0610141728j45d81883o4e4fc9b62361abbe@mail.gmail.com> Hi, Can you please send me some materials on how to handle secondary input > parameteres in Taverna. I am sorry, I cannot do that (it is a long time I worked with Taverna, and things have changed there). But Eddie wrote a pretty good guide about moby and taverna - why don't you look there? It is at http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/guide/index.html . I remember that you also asked me and Eddie about how to get a list of primary and secondary parameters for all services. I would recommend you to try to start BioMoby Dashboard (I can help you with that if you need) - there are panels that can do it for you (I hope). Regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From groscurt at mpiz-koeln.mpg.de Thu Oct 19 09:19:15 2006 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 19 Oct 2006 11:19:15 +0200 Subject: [MOBY-dev] Retrieving the latest changes in the Moby Registry Message-ID: <200610191119.15253.groscurt@mpiz-koeln.mpg.de> Hi everybody, I"m looking for a simple way to retrieve the latest changes in the Moby registry. So if for example a new services has been registered or modified anyhow I would like to retrieve those services from the registry. Is this doable with the current implementation structure and if so how ? Thanks and greetings Andreas -- Andreas Groscurth Diplom Bioinformatik - PhD Student International Max Planck Research School (IMPRS) Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From markw at illuminae.com Thu Oct 19 15:15:16 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 19 Oct 2006 08:15:16 -0700 Subject: [MOBY-dev] [moby] Retrieving the latest changes in the Moby Registry In-Reply-To: <200610191119.15253.groscurt@mpiz-koeln.mpg.de> References: <200610191119.15253.groscurt@mpiz-koeln.mpg.de> Message-ID: <1161270916.19851.33.camel@bioinfo.icapture.ubc.ca> There's no *formal* way to do this with the API, but you could do it in an ad hoc (but hopefully reliable) way by retrieving the LSID's for all of the services (a variety of API calls provide this for you), and then checking the timestamp at the end of each one. I'm running to a meeting, but if this isn't clear I'll write a more comprehensive answer later today, Mark On Thu, 2006-10-19 at 11:19 +0200, Andreas Groscurth wrote: > Hi everybody, > > I"m looking for a simple way to retrieve the latest changes in the Moby > registry. So if for example a new services has been registered or modified > anyhow I would like to retrieve those services from the registry. > > Is this doable with the current implementation structure and if so how ? > > Thanks and greetings > Andreas > -- Mark Wilkinson Asst. Professor, Dept. of Medical Genetics University of British Columbia PI in Bioinformatics, iCAPTURE Centre St. Paul's Hospital, Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 "Since the point of a definition is to explain the meaning of a term to someone who is unfamiliar with its proper application, the use of language that doesn't help such a person learn how to apply the term is pointless. Thus, "happiness is a warm puppy" may be a lovely thought, but it is a lousy definition." K?hler et al, 2006 From martin.senger at gmail.com Thu Oct 19 21:12:13 2006 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 20 Oct 2006 06:12:13 +0900 Subject: [MOBY-dev] Retrieving the latest changes in the Moby Registry In-Reply-To: <200610191119.15253.groscurt@mpiz-koeln.mpg.de> References: <200610191119.15253.groscurt@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0610191412w449dfe57rdf1def9576a45b17@mail.gmail.com> > Is this doable with the current implementation structure and if so how ? As Mark suggested, the LSIDs are the way to do this. I would even say that "it is part of the API" - so you can rely on it. You can looked into jMoby code in CentralDigestCachedImpl.,java - this code does it. Regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Tue Oct 24 21:00:51 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 24 Oct 2006 14:00:51 -0700 Subject: [MOBY-dev] publications page updated Message-ID: Hi all, on the BioMoby website publication list (http://biomoby.open-bio.org/index.php/what-is-moby/publications), I've added several publications that have come out of the community in the past year or two. Please let me know if I have missed yours, or if I have included you but you do not wish to be included. Cheers! Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital From gss at ncgr.org Tue Oct 24 21:49:30 2006 From: gss at ncgr.org (Gary Schiltz) Date: Tue, 24 Oct 2006 15:49:30 -0600 Subject: [MOBY-dev] publications page updated In-Reply-To: References: Message-ID: <453E8A6A.5080801@ncgr.org> If you would be so kind, please add the the following citation (under either "Peer reviewed and books" - it was reviewed by the workshop organizers - or under "Other press and manuscripts"): Schiltz G, Gessler D, Stein L (2004). Semantic MOBY. Position paper for the 2004 W3C Workshop on Semantic Web for Life Sciences. I would suggest linking "Semantic MOBY" in the citation to the URL http://lists.w3.org/Archives/Public/public-swls-ws/2004Sep/att-0036/smoby-w3c-sw-ls.pdf. The link to the workshop report is http://www.w3.org/2004/10/swls-workshop-report.html, and I would suggest linking that URL to the text "W3C Workshop on Semantic Web for Life Sciences" in the citation. // Gary Mark Wilkinson wrote: > Hi all, > > on the BioMoby website publication list > (http://biomoby.open-bio.org/index.php/what-is-moby/publications), I've > added several publications that have come out of the community in the past > year or two. Please let me know if I have missed yours, or if I have > included you but you do not wish to be included. > > Cheers! > > Mark > > > > From duncan.hull at cs.man.ac.uk Wed Oct 25 09:40:49 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Wed, 25 Oct 2006 10:40:49 +0100 Subject: [MOBY-dev] publications page updated In-Reply-To: References: Message-ID: <453F3121.1080106@cs.man.ac.uk> Hi Mark Mark Wilkinson wrote: > on the BioMoby website publication list > (http://biomoby.open-bio.org/index.php/what-is-moby/publications), Maybe you could add a link to http://www.connotea.org/tag/biomoby ? Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From d.haase at gsf.de Wed Oct 25 14:14:36 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 25 Oct 2006 16:14:36 +0200 Subject: [MOBY-dev] publications page updated In-Reply-To: <453F3121.1080106@cs.man.ac.uk> References: <453F3121.1080106@cs.man.ac.uk> Message-ID: <200610251614.36696.d.haase@gsf.de> On Wednesday 25 October 2006 11:40, Duncan Hull wrote: > Hi Mark > > Mark Wilkinson wrote: > > on the BioMoby website publication list > > (http://biomoby.open-bio.org/index.php/what-is-moby/publications), > > Maybe you could add a link to http://www.connotea.org/tag/biomoby ? Nice idea, but it is weeks ago that I last received more than a header from the connotea web server... Does it still work for you? dirk From duncan.hull at cs.man.ac.uk Wed Oct 25 15:02:19 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Wed, 25 Oct 2006 16:02:19 +0100 Subject: [MOBY-dev] publications page updated; MobyConnotea In-Reply-To: <200610251614.36696.d.haase@gsf.de> References: <453F3121.1080106@cs.man.ac.uk> <200610251614.36696.d.haase@gsf.de> Message-ID: <453F7C7B.7070307@cs.man.ac.uk> Hi Dirk Dirk Haase wrote: >> Maybe you could add a link to http://www.connotea.org/tag/biomoby ? >> > > Nice idea, but it is weeks ago that I last received more than a header from > the connotea web server... Does it still work for you? > The connotea server has been fairly responsive for me, not had any performance issues here (yet)... Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677