From groscurt at mpiz-koeln.mpg.de Mon Oct 1 07:50:08 2007 From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de) Date: Mon, 1 Oct 2007 13:50:08 +0200 (CEST) Subject: [MOBY-dev] How to get a concrete MobyDataType Message-ID: <57531.195.37.46.22.1191239408.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi all, i have the following question: I have a MobyDataInstance, retrieved from a service call. I know that this service returns a specific datatype (e.g. GO_Term). How to I get the GO_Term object from the MobyDataInstance. I know i can cast the MobyDataInstance to a MobyDataObject (or MobyDataObjectSet respectively) and can get the MobyDataTyp from that - but this is not castable to GO_Term. I could not find any method which returns me anything which is then castable as GO_Term. So - how do I retrieve the actual datatype class from a service result ? Thanks andreas From gordonp at ucalgary.ca Mon Oct 1 09:25:04 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 01 Oct 2007 07:25:04 -0600 Subject: [MOBY-dev] How to get a concrete MobyDataType In-Reply-To: <57531.195.37.46.22.1191239408.squirrel@mpizmail.mpiz-koeln.mpg.de> References: <57531.195.37.46.22.1191239408.squirrel@mpizmail.mpiz-koeln.mpg.de> Message-ID: <4700F530.5000207@ucalgary.ca> Hi Andreas, > I know i can cast the MobyDataInstance to a MobyDataObject (or > MobyDataObjectSet respectively) and can get the MobyDataTyp from that - but > this is not castable to GO_Term. > There is no GO_Term object when you use the General methods you describe with MobyDataInstance, etc.. I think you are trying to mix the general methods with the generated methods. What do you need a GO_Term object for (the MobyDataType should contain all the information you need...unless you're using something else from the generated, i.e. MoSeS, classes)? In general, you need to pick one way or the other in jMOBY, they don't mix well. > I could not find any method which returns me anything which is then castable > as GO_Term. > > So - how do I retrieve the actual datatype class from a service result ? > > Thanks > andreas > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From groscurt at mpiz-koeln.mpg.de Mon Oct 1 09:57:51 2007 From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de) Date: Mon, 1 Oct 2007 15:57:51 +0200 (CEST) Subject: [MOBY-dev] How to get a concrete MobyDataType Message-ID: <48469.195.37.46.22.1191247071.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi Paul, thanks for your answer. Honestly i wanted to have the actual GO_Term object becaus of laziness ;-);-) I know that I can retrieve all information with the general classes, I just hoped that somehow there is written that its a GO_Term and i can cast it and use getxxx somehow :-):-) Thanks for clarification andreas On Monday 01 October 2007 15:25, Paul Gordon wrote: > Hi Andreas, > > > I know i can cast the MobyDataInstance to a MobyDataObject (or > > MobyDataObjectSet respectively) and can get the MobyDataTyp from that - > > but this is not castable to GO_Term. > > There is no GO_Term object when you use the General methods you describe > with MobyDataInstance, etc.. > I think you are trying to mix the general methods with the generated > methods. What do you need a GO_Term > object for (the MobyDataType should contain all the information you > need...unless you're using something else > from the generated, i.e. MoSeS, classes)? In general, you need to pick > one way or the other in jMOBY, they > don't mix well. > > > I could not find any method which returns me anything which is then > > castable as GO_Term. > > > > So - how do I retrieve the actual datatype class from a service result ? > > > > Thanks > > andreas > > > > _______________________________________________ > > 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 groscurt at mpiz-koeln.mpg.de Mon Oct 1 10:07:29 2007 From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de) Date: Mon, 1 Oct 2007 16:07:29 +0200 (CEST) Subject: [MOBY-dev] Logging access of Web Services Message-ID: <38845.195.37.46.22.1191247649.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi all, our group (especially Anika) is developing some Moby services. Out of curiosity we would like to know when which service was called from which ip. Our apache forwards the axis request directly to Jboss where the services are executed, so we dont find any log entries in the apache logs I know one can easily log with the moby api - I was wondering if somehow and somewhere deep in the service implementation (java) I can retrieve the information who called the service (e.g. getting the httprequest). is there a possibility to retrieve these information or is there any common workaround to get such logging ? Thanks andreas From martin.senger at gmail.com Mon Oct 1 15:37:13 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 1 Oct 2007 20:37:13 +0100 Subject: [MOBY-dev] Logging access of Web Services In-Reply-To: <38845.195.37.46.22.1191247649.squirrel@mpizmail.mpiz-koeln.mpg.de> References: <38845.195.37.46.22.1191247649.squirrel@mpizmail.mpiz-koeln.mpg.de> Message-ID: <4d93f07c0710011237t201643c3tdf3e206abb54333f@mail.gmail.com> > Out of > curiosity we would like to know when which service was called from which > ip. If your services are generated by MoSeS, then each of them has a method for that (getCallerAddr()). The details API is here: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/API/org/biomoby/service/BaseService.html . Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Thu Oct 11 14:51:28 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 11 Oct 2007 11:51:28 -0700 Subject: [MOBY-dev] Can someone represent Moby in Rome? Message-ID: Hi all core developers! I've been invited to present Moby at a meeting in Rome on November 28th. Unfortunately, I have a meeting on the 27th here in Vancouver that prevents me from getting to Rome in time. I've asked Martin and Eddie and neither of them are able to do it. It's a presentation to the CASIMIR project (http://www.casimir.org.uk). They are considering things like DAS and MART, and are interested in adding Moby to their overall list of possible data-integration choices. I'd really like to convince them that Moby is a good option! Can anyone else from the core development team attend this meeting and present a good case for Moby? Someone from INB or PlaNet would be **perfect** since you can give first-hand examples of integrating large projects over Moby. Please let me know ASAP. Cheers all! Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From gordonp at ucalgary.ca Thu Oct 11 15:10:49 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 11 Oct 2007 13:10:49 -0600 Subject: [MOBY-dev] Can someone represent Moby in Rome? In-Reply-To: References: Message-ID: <470E7539.4060903@ucalgary.ca> I can go if no Europeans volunteer... > Hi all core developers! > > I've been invited to present Moby at a meeting in Rome on November 28th. > Unfortunately, I have a meeting on the 27th here in Vancouver that > prevents me from getting to Rome in time. I've asked Martin and Eddie and > neither of them are able to do it. > > It's a presentation to the CASIMIR project (http://www.casimir.org.uk). > They are considering things like DAS and MART, and are interested in > adding Moby to their overall list of possible data-integration choices. > I'd really like to convince them that Moby is a good option! > > Can anyone else from the core development team attend this meeting and > present a good case for Moby? Someone from INB or PlaNet would be > **perfect** since you can give first-hand examples of integrating large > projects over Moby. > > Please let me know ASAP. > > Cheers all! > > Mark > > From gordonp at ucalgary.ca Thu Oct 11 15:10:49 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 11 Oct 2007 13:10:49 -0600 Subject: [MOBY-dev] Can someone represent Moby in Rome? In-Reply-To: References: Message-ID: <470E7539.4060903@ucalgary.ca> I can go if no Europeans volunteer... > Hi all core developers! > > I've been invited to present Moby at a meeting in Rome on November 28th. > Unfortunately, I have a meeting on the 27th here in Vancouver that > prevents me from getting to Rome in time. I've asked Martin and Eddie and > neither of them are able to do it. > > It's a presentation to the CASIMIR project (http://www.casimir.org.uk). > They are considering things like DAS and MART, and are interested in > adding Moby to their overall list of possible data-integration choices. > I'd really like to convince them that Moby is a good option! > > Can anyone else from the core development team attend this meeting and > present a good case for Moby? Someone from INB or PlaNet would be > **perfect** since you can give first-hand examples of integrating large > projects over Moby. > > Please let me know ASAP. > > Cheers all! > > Mark > > From Pieter.Neerincx at wur.nl Thu Oct 11 19:04:19 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Fri, 12 Oct 2007 01:04:19 +0200 Subject: [MOBY-dev] Can someone represent Moby in Rome? In-Reply-To: <470E7539.4060903@ucalgary.ca> References: <470E7539.4060903@ucalgary.ca> Message-ID: Hi, I'm in Europe, but have a meeting in Paris the day before and I'll promote Moby there :), but I won't be able to get to Rome in time. Cheers, Pi On 11 Oct 2007, at 21:10, Paul Gordon wrote: > I can go if no Europeans volunteer... >> Hi all core developers! >> >> I've been invited to present Moby at a meeting in Rome on November >> 28th. >> Unfortunately, I have a meeting on the 27th here in Vancouver that >> prevents me from getting to Rome in time. I've asked Martin and >> Eddie and >> neither of them are able to do it. >> >> It's a presentation to the CASIMIR project (http:// >> www.casimir.org.uk). >> They are considering things like DAS and MART, and are interested in >> adding Moby to their overall list of possible data-integration >> choices. >> I'd really like to convince them that Moby is a good option! >> >> Can anyone else from the core development team attend this meeting >> and >> present a good case for Moby? Someone from INB or PlaNet would be >> **perfect** since you can give first-hand examples of integrating >> large >> projects over Moby. >> >> Please let me know ASAP. >> >> Cheers all! >> >> Mark >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- From markw at illuminae.com Fri Oct 12 10:05:13 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 12 Oct 2007 07:05:13 -0700 Subject: [MOBY-dev] Can someone represent Moby in Rome? In-Reply-To: References: <470E7539.4060903@ucalgary.ca> Message-ID: If there are no other offers, I'll tell the CASIMIR people that Paul will attend. Paul, can you confirm 100% that you are available? M On Thu, 11 Oct 2007 16:04:19 -0700, Pieter Neerincx wrote: > Hi, > > I'm in Europe, but have a meeting in Paris the day before and I'll > promote Moby there :), but I won't be able to get to Rome in time. > > Cheers, > > Pi > > On 11 Oct 2007, at 21:10, Paul Gordon wrote: > >> I can go if no Europeans volunteer... >>> Hi all core developers! >>> >>> I've been invited to present Moby at a meeting in Rome on November >>> 28th. >>> Unfortunately, I have a meeting on the 27th here in Vancouver that >>> prevents me from getting to Rome in time. I've asked Martin and >>> Eddie and >>> neither of them are able to do it. >>> >>> It's a presentation to the CASIMIR project (http:// >>> www.casimir.org.uk). >>> They are considering things like DAS and MART, and are interested in >>> adding Moby to their overall list of possible data-integration >>> choices. >>> I'd really like to convince them that Moby is a good option! >>> >>> Can anyone else from the core development team attend this meeting >>> and >>> present a good case for Moby? Someone from INB or PlaNet would be >>> **perfect** since you can give first-hand examples of integrating >>> large >>> projects over Moby. >>> >>> Please let me know ASAP. >>> >>> Cheers all! >>> >>> Mark >>> >>> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 060 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------- > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From schoof at mpiz-koeln.mpg.de Fri Oct 12 11:10:04 2007 From: schoof at mpiz-koeln.mpg.de (Heiko Schoof) Date: Fri, 12 Oct 2007 17:10:04 +0200 Subject: [MOBY-dev] Can someone represent Moby in Rome? In-Reply-To: References: <470E7539.4060903@ucalgary.ca> Message-ID: <4E46C60F-9A5F-4159-B2A2-671ABC8618A8@mpiz-koeln.mpg.de> Hi Mark, we have our scientific advisory board here on that day, so I can't make it, sorry. Best, Heiko On 12. Oct 2007, at 16:05 Uhr, Mark Wilkinson wrote: > If there are no other offers, I'll tell the CASIMIR people that > Paul will > attend. > > Paul, can you confirm 100% that you are available? > > M > > > > > On Thu, 11 Oct 2007 16:04:19 -0700, Pieter Neerincx > wrote: > >> Hi, >> >> I'm in Europe, but have a meeting in Paris the day before and I'll >> promote Moby there :), but I won't be able to get to Rome in time. >> >> Cheers, >> >> Pi >> >> On 11 Oct 2007, at 21:10, Paul Gordon wrote: >> >>> I can go if no Europeans volunteer... >>>> Hi all core developers! >>>> >>>> I've been invited to present Moby at a meeting in Rome on November >>>> 28th. >>>> Unfortunately, I have a meeting on the 27th here in Vancouver that >>>> prevents me from getting to Rome in time. I've asked Martin and >>>> Eddie and >>>> neither of them are able to do it. >>>> >>>> It's a presentation to the CASIMIR project (http:// >>>> www.casimir.org.uk). >>>> They are considering things like DAS and MART, and are >>>> interested in >>>> adding Moby to their overall list of possible data-integration >>>> choices. >>>> I'd really like to convince them that Moby is a good option! >>>> >>>> Can anyone else from the core development team attend this meeting >>>> and >>>> present a good case for Moby? Someone from INB or PlaNet would be >>>> **perfect** since you can give first-hand examples of integrating >>>> large >>>> projects over Moby. >>>> >>>> Please let me know ASAP. >>>> >>>> Cheers all! >>>> >>>> Mark >>>> >>>> >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> >> ------------------------------------------------------------- >> Wageningen University and Research centre (WUR) >> Laboratory of Bioinformatics >> Transitorium (building 312) room 1034 >> >> Dreijenlaan 3 >> 6703 HA Wageningen >> The Netherlands >> >> phone: 0317-483 060 >> fax: 0317-483 584 >> mobile: 06-143 66 783 >> mail: pieter.neerincx at wur.nl >> skype: pieter.online >> ------------------------------------------------------------- >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the > addressee and > may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have > received this > communication in error, please notify the sender immediately by reply > e-mail and delete the original and all copies from your system. > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From ola.spjuth at farmbio.uu.se Mon Oct 15 12:19:39 2007 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Mon, 15 Oct 2007 18:19:39 +0200 Subject: [MOBY-dev] Datatype instantiation in jMoby Message-ID: Hi, In jMoby, I look up a service, and get the first primaryInputs DataType by service.getPrimaryData()[0].getDataType(); This gives me a Datatype with correct name and LSID, but nothing more (no children). If I do the following: String dataTypeName=service.getPrimaryInputs()[i].getDataType ().getName(); primaryData[i] = new MobyDataComposite(dataTypeName); MobyDataType dataType=primaryData[i].getDataType(); Then jMoby reads the ontology and I get a dataType that has relations (children). How can I achieve this without having to instantiate a bogus MobyDataComposite? What is the purpose of this behaviour? Would something like this be an acceptable API-request: service.getPrimaryData()[0].getDataType(); service.getPrimaryData()[0].populateFromOntology(); Next question: I'd like to create MobyDataObjects that I can later populate with values. The line MobyDataObject obj = MobyDataObject.createInstanceFromString (childTypeName,"0"); works fine, but I'd like to do is create an object with no values, like the following: for(MobyRelationship child: dataType.getAllChildren()){ String childName = child.getName(); String childTypeName = child.getDataTypeName(); if(PrimitiveTypes.isPrimitive(childTypeName)){ MobyDataObject obj = new MobyDataObject(childTypeName); primaryComposites[i].put(childName,obj); } } Is it wrong to instantiate the values first and fill them at a later point? Last question: Can a service take only one primitive DataType as primaryInput or does it always require a MobyDataComposite? Is it an error in that case to supply a MobyDataComposite with only one primitive MobyDataObject in it (i.e. is it OK to always send a MobyDataComposite as PrimaryInput to a service)? Thanks, .../Ola From groscurt at mpiz-koeln.mpg.de Tue Oct 16 02:45:51 2007 From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de) Date: Tue, 16 Oct 2007 08:45:51 +0200 (CEST) Subject: [MOBY-dev] Datatype instantiation in jMoby In-Reply-To: References: Message-ID: <64120.89.52.180.204.1192517151.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi Ola, for your first question, MobyDataType.getDataType("DATATYPE"); should retrieve the datataype (check the API for this method). At this morning, I dont have an answer for question two. Question three: of course services can consume a primtive type - like MobyObject or MobyString etc. So I would not always use the composite and just what the service actually require If somethings wrong please correct someone.. andreas > Hi, > > In jMoby, I look up a service, and get the first primaryInputs > DataType by > > service.getPrimaryData()[0].getDataType(); > > This gives me a Datatype with correct name and LSID, but nothing more > (no children). > > If I do the following: > > String dataTypeName=service.getPrimaryInputs()[i].getDataType > ().getName(); > primaryData[i] = new MobyDataComposite(dataTypeName); > MobyDataType dataType=primaryData[i].getDataType(); > > Then jMoby reads the ontology and I get a dataType that has relations > (children). How can I achieve this without having to instantiate a > bogus MobyDataComposite? What is the purpose of this behaviour? Would > something like this be an acceptable API-request: > > service.getPrimaryData()[0].getDataType(); > service.getPrimaryData()[0].populateFromOntology(); > > > Next question: > I'd like to create MobyDataObjects that I can later populate with > values. > > The line > > MobyDataObject obj = MobyDataObject.createInstanceFromString > (childTypeName,"0"); > > works fine, but I'd like to do is create an object with no values, > like the following: > > for(MobyRelationship child: dataType.getAllChildren()){ > String childName = child.getName(); > String childTypeName = child.getDataTypeName(); > if(PrimitiveTypes.isPrimitive(childTypeName)){ > MobyDataObject obj = new MobyDataObject(childTypeName); > primaryComposites[i].put(childName,obj); > } > } > > Is it wrong to instantiate the values first and fill them at a later > point? > > Last question: > Can a service take only one primitive DataType as primaryInput or > does it always require a MobyDataComposite? Is it an error in that > case to supply a MobyDataComposite with only one primitive > MobyDataObject in it (i.e. is it OK to always send a > MobyDataComposite as PrimaryInput to a service)? > > Thanks, > > .../Ola > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From ola.spjuth at farmbio.uu.se Tue Oct 16 04:06:23 2007 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Tue, 16 Oct 2007 10:06:23 +0200 Subject: [MOBY-dev] Datatype instantiation in jMoby In-Reply-To: <64120.89.52.180.204.1192517151.squirrel@mpizmail.mpiz-koeln.mpg.de> References: <64120.89.52.180.204.1192517151.squirrel@mpizmail.mpiz-koeln.mpg.de> Message-ID: <5D00967F-CA9E-4471-A06B-869ECCE8CE0D@farmbio.uu.se> On Oct 16, 2007, at 08:45 , groscurt at mpiz-koeln.mpg.de wrote: > Hi Ola, > > for your first question, > > MobyDataType.getDataType("DATATYPE"); > > should retrieve the datataype (check the API for this method). Great, thanks. Must have missed to check the static methods. > At this morning, I dont have an answer for question two. > > Question three: > of course services can consume a primtive type - like MobyObject or > MobyString etc. So I would not always use the composite and just > what the > service actually require Yes, but would it be acceptable to wrap that MobyObject or MobyString in a MobyComposite and it would still work? Thanks, .../Ola > > > If somethings wrong please correct someone.. > > andreas > > > >> Hi, >> >> In jMoby, I look up a service, and get the first primaryInputs >> DataType by >> >> service.getPrimaryData()[0].getDataType(); >> >> This gives me a Datatype with correct name and LSID, but nothing more >> (no children). >> >> If I do the following: >> >> String dataTypeName=service.getPrimaryInputs()[i].getDataType >> ().getName(); >> primaryData[i] = new MobyDataComposite(dataTypeName); >> MobyDataType dataType=primaryData[i].getDataType(); >> >> Then jMoby reads the ontology and I get a dataType that has relations >> (children). How can I achieve this without having to instantiate a >> bogus MobyDataComposite? What is the purpose of this behaviour? Would >> something like this be an acceptable API-request: >> >> service.getPrimaryData()[0].getDataType(); >> service.getPrimaryData()[0].populateFromOntology(); >> >> >> Next question: >> I'd like to create MobyDataObjects that I can later populate with >> values. >> >> The line >> >> MobyDataObject obj = MobyDataObject.createInstanceFromString >> (childTypeName,"0"); >> >> works fine, but I'd like to do is create an object with no values, >> like the following: >> >> for(MobyRelationship child: dataType.getAllChildren()){ >> String childName = child.getName(); >> String childTypeName = child.getDataTypeName(); >> if(PrimitiveTypes.isPrimitive(childTypeName)){ >> MobyDataObject obj = new MobyDataObject(childTypeName); >> primaryComposites[i].put(childName,obj); >> } >> } >> >> Is it wrong to instantiate the values first and fill them at a later >> point? >> >> Last question: >> Can a service take only one primitive DataType as primaryInput or >> does it always require a MobyDataComposite? Is it an error in that >> case to supply a MobyDataComposite with only one primitive >> MobyDataObject in it (i.e. is it OK to always send a >> MobyDataComposite as PrimaryInput to a service)? >> >> Thanks, >> >> .../Ola >> >> >> _______________________________________________ >> 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 groscurt at mpiz-koeln.mpg.de Wed Oct 17 07:02:05 2007 From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de) Date: Wed, 17 Oct 2007 13:02:05 +0200 (CEST) Subject: [MOBY-dev] Problems with parsing a service result Message-ID: <47508.195.37.46.22.1192618925.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi all, i want to retrieve the results for the service: get_agi_code_by_keyword/mpiz-koeln.mpg.de it returns a collection of Descriptors for a given keyword. Using the dashboard i retrieve a result (e.g. with keyword superman) SUP (SUPERMAN); DNA binding / nucleic acid binding / transcription factor/ zinc ion binding using the simple java client MobyService agiService = new MobyService(); agiService.setCategory( "" ); agiService.setAuthority( "mpiz-koeln.mpg.de" ); agiService.setName( "get_agi_code_by_keyword" ); agiService = central.findService( agiService )[0]; MobyRequest request = new MobyRequest( central ); request.setService( agiService ); request.setInput( new MobyDataObject( "Global_Keyword", "superman" ) ); MobyContentInstance contentInstance = request.invokeService(); MobyDataJob mobyJob = contentInstance.get( contentInstance.keySet().iterator().next() ); MobyDataInstance[] dataInstances = mobyJob.getPrimaryData(); the dataInstance contains nothing :-(:-( (dataInstances.length = 0) the simple java client works for other services, but fails for this one... does anybody know what is wrong ? thanks andreas From edward.kawas at gmail.com Wed Oct 17 09:19:05 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 17 Oct 2007 06:19:05 -0700 Subject: [MOBY-dev] Problems with parsing a service result In-Reply-To: <47508.195.37.46.22.1192618925.squirrel@mpizmail.mpiz-koeln.mpg.de> References: <47508.195.37.46.22.1192618925.squirrel@mpizmail.mpiz-koeln.mpg.de> Message-ID: <001001c810c0$4c197080$6400a8c0@notebook> Hi Andreas, Should new MobyDataObject( "Global_Keyword", "superman" ) ); really be new MobyDataObject( "Global_Keyword", "keyword" ) ); ?? Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > groscurt at mpiz-koeln.mpg.de > Sent: Wednesday, October 17, 2007 4:02 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] Problems with parsing a service result > > Hi all, > > i want to retrieve the results for the service: > > get_agi_code_by_keyword/mpiz-koeln.mpg.de > > it returns a collection of Descriptors for a given keyword. > > Using the dashboard i retrieve a result (e.g. with keyword superman) > > > > > > > > > moby:namespace="AGI_LocusCode"> > moby:articleName="description">SUP (SUPERMAN); DNA binding / > nucleic acid binding / transcription factor/ zinc ion > binding > > > > > > > > using the simple java client > > MobyService agiService = new MobyService(); > agiService.setCategory( "" ); agiService.setAuthority( > "mpiz-koeln.mpg.de" ); agiService.setName( > "get_agi_code_by_keyword" ); agiService = > central.findService( agiService )[0]; MobyRequest request = > new MobyRequest( central ); request.setService( agiService ); > request.setInput( new MobyDataObject( "Global_Keyword", > "superman" ) ); MobyContentInstance contentInstance = > request.invokeService(); MobyDataJob mobyJob = > contentInstance.get( > contentInstance.keySet().iterator().next() ); > MobyDataInstance[] dataInstances = mobyJob.getPrimaryData(); > > the dataInstance contains nothing :-(:-( (dataInstances.length = 0) > > the simple java client works for other services, but fails > for this one... > > does anybody know what is wrong ? > > thanks > andreas > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Wed Oct 17 09:38:41 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 17 Oct 2007 07:38:41 -0600 Subject: [MOBY-dev] [Fwd: Re: Problems with parsing a service result] Message-ID: <47161061.80200@ucalgary.ca> Never mind, I am smoking crack. Didn't check to see that Global_Keyword has no child elements. MobyDataComposite comp = MobyDataComposite("Global_Keyword", "unimportant_article_name", "namespace_if_any", "superman"); -------- Original Message -------- Subject: Re: [MOBY-dev] Problems with parsing a service result Date: Wed, 17 Oct 2007 07:26:21 -0600 From: Paul Gordon To: Core developer announcements References: <47508.195.37.46.22.1192618925.squirrel at mpizmail.mpiz-koeln.mpg.de> <001001c810c0$4c197080$6400a8c0 at notebook> No, the problem is that MobyDataObject is ONLY for base Object (as it says several times in the Java docs :-)) You're using a composite that happens to only have one member. Composites implement the Java Map interface to get/set members: MobyDataComposite comp = MobyDataComposite("Global_Keyword"); comp.put("keyword", new MobyDataString("superman")); > Hi Andreas, > > Should > > new MobyDataObject( "Global_Keyword", "superman" ) ); > > really be > > new MobyDataObject( "Global_Keyword", "keyword" ) ); ?? > > Eddie > > >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of >> groscurt at mpiz-koeln.mpg.de >> Sent: Wednesday, October 17, 2007 4:02 AM >> To: moby-dev at lists.open-bio.org >> Subject: [MOBY-dev] Problems with parsing a service result >> >> Hi all, >> >> i want to retrieve the results for the service: >> >> get_agi_code_by_keyword/mpiz-koeln.mpg.de >> >> it returns a collection of Descriptors for a given keyword. >> >> Using the dashboard i retrieve a result (e.g. with keyword superman) >> >> >> >> >> >> >> >> >> > moby:namespace="AGI_LocusCode"> >> > moby:articleName="description">SUP (SUPERMAN); DNA binding / >> nucleic acid binding / transcription factor/ zinc ion >> binding >> >> >> >> >> >> >> >> using the simple java client >> >> MobyService agiService = new MobyService(); >> agiService.setCategory( "" ); agiService.setAuthority( >> "mpiz-koeln.mpg.de" ); agiService.setName( >> "get_agi_code_by_keyword" ); agiService = >> central.findService( agiService )[0]; MobyRequest request = >> new MobyRequest( central ); request.setService( agiService ); >> request.setInput( new MobyDataObject( "Global_Keyword", >> "superman" ) ); MobyContentInstance contentInstance = >> request.invokeService(); MobyDataJob mobyJob = >> contentInstance.get( >> contentInstance.keySet().iterator().next() ); >> MobyDataInstance[] dataInstances = mobyJob.getPrimaryData(); >> >> the dataInstance contains nothing :-(:-( (dataInstances.length = 0) >> >> the simple java client works for other services, but fails >> for this one... >> >> does anybody know what is wrong ? >> >> thanks >> andreas >> >> _______________________________________________ >> 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 > > !DSPAM:60005,47160a092601617573718! > > > > From gordonp at ucalgary.ca Wed Oct 17 09:26:21 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 17 Oct 2007 07:26:21 -0600 Subject: [MOBY-dev] Problems with parsing a service result In-Reply-To: <001001c810c0$4c197080$6400a8c0@notebook> References: <47508.195.37.46.22.1192618925.squirrel@mpizmail.mpiz-koeln.mpg.de> <001001c810c0$4c197080$6400a8c0@notebook> Message-ID: <47160D7D.2090005@ucalgary.ca> No, the problem is that MobyDataObject is ONLY for base Object (as it says several times in the Java docs :-)) You're using a composite that happens to only have one member. Composites implement the Java Map interface to get/set members: MobyDataComposite comp = MobyDataComposite("Global_Keyword"); comp.put("keyword", new MobyDataString("superman")); > Hi Andreas, > > Should > > new MobyDataObject( "Global_Keyword", "superman" ) ); > > really be > > new MobyDataObject( "Global_Keyword", "keyword" ) ); ?? > > Eddie > > >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of >> groscurt at mpiz-koeln.mpg.de >> Sent: Wednesday, October 17, 2007 4:02 AM >> To: moby-dev at lists.open-bio.org >> Subject: [MOBY-dev] Problems with parsing a service result >> >> Hi all, >> >> i want to retrieve the results for the service: >> >> get_agi_code_by_keyword/mpiz-koeln.mpg.de >> >> it returns a collection of Descriptors for a given keyword. >> >> Using the dashboard i retrieve a result (e.g. with keyword superman) >> >> >> >> >> >> >> >> >> > moby:namespace="AGI_LocusCode"> >> > moby:articleName="description">SUP (SUPERMAN); DNA binding / >> nucleic acid binding / transcription factor/ zinc ion >> binding >> >> >> >> >> >> >> >> using the simple java client >> >> MobyService agiService = new MobyService(); >> agiService.setCategory( "" ); agiService.setAuthority( >> "mpiz-koeln.mpg.de" ); agiService.setName( >> "get_agi_code_by_keyword" ); agiService = >> central.findService( agiService )[0]; MobyRequest request = >> new MobyRequest( central ); request.setService( agiService ); >> request.setInput( new MobyDataObject( "Global_Keyword", >> "superman" ) ); MobyContentInstance contentInstance = >> request.invokeService(); MobyDataJob mobyJob = >> contentInstance.get( >> contentInstance.keySet().iterator().next() ); >> MobyDataInstance[] dataInstances = mobyJob.getPrimaryData(); >> >> the dataInstance contains nothing :-(:-( (dataInstances.length = 0) >> >> the simple java client works for other services, but fails >> for this one... >> >> does anybody know what is wrong ? >> >> thanks >> andreas >> >> _______________________________________________ >> 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 > > !DSPAM:60005,47160a092601617573718! > > > > From groscurt at mpiz-koeln.mpg.de Wed Oct 17 11:44:10 2007 From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de) Date: Wed, 17 Oct 2007 17:44:10 +0200 (CEST) Subject: [MOBY-dev] [Fwd: Re: Problems with parsing a service result] In-Reply-To: <47161061.80200@ucalgary.ca> References: <47161061.80200@ucalgary.ca> Message-ID: <53278.195.37.46.22.1192635850.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi, *doooh* i havent count how often I made the datacomposite mistake :-( stupidity.... thanks again for clearifying andreas > Never mind, I am smoking crack. Didn't check to see that Global_Keyword > has no child elements. > > MobyDataComposite comp = MobyDataComposite("Global_Keyword", > "unimportant_article_name", "namespace_if_any", "superman"); > > -------- Original Message -------- > Subject: Re: [MOBY-dev] Problems with parsing a service result > Date: Wed, 17 Oct 2007 07:26:21 -0600 > From: Paul Gordon > To: Core developer announcements > References: > <47508.195.37.46.22.1192618925.squirrel at mpizmail.mpiz-koeln.mpg.de> > <001001c810c0$4c197080$6400a8c0 at notebook> > > > > No, the problem is that MobyDataObject is ONLY for base Object (as it > says several times in the Java docs :-)) > You're using a composite that happens to only have one member. > Composites implement the Java Map interface to > get/set members: > > MobyDataComposite comp = MobyDataComposite("Global_Keyword"); > comp.put("keyword", new MobyDataString("superman")); >> Hi Andreas, >> >> Should >> >> new MobyDataObject( "Global_Keyword", "superman" ) ); >> >> really be >> >> new MobyDataObject( "Global_Keyword", "keyword" ) ); ?? >> >> Eddie >> >> >>> -----Original Message----- >>> From: moby-dev-bounces at lists.open-bio.org >>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of >>> groscurt at mpiz-koeln.mpg.de >>> Sent: Wednesday, October 17, 2007 4:02 AM >>> To: moby-dev at lists.open-bio.org >>> Subject: [MOBY-dev] Problems with parsing a service result >>> >>> Hi all, >>> >>> i want to retrieve the results for the service: >>> >>> get_agi_code_by_keyword/mpiz-koeln.mpg.de >>> >>> it returns a collection of Descriptors for a given keyword. >>> >>> Using the dashboard i retrieve a result (e.g. with keyword superman) >>> >>> >>> >>> >>> >>> >>> >>> >>> >> moby:namespace="AGI_LocusCode"> >>> >> moby:articleName="description">SUP (SUPERMAN); DNA binding / >>> nucleic acid binding / transcription factor/ zinc ion >>> binding >>> >>> >>> >>> >>> >>> >>> >>> using the simple java client >>> >>> MobyService agiService = new MobyService(); >>> agiService.setCategory( "" ); agiService.setAuthority( >>> "mpiz-koeln.mpg.de" ); agiService.setName( >>> "get_agi_code_by_keyword" ); agiService = >>> central.findService( agiService )[0]; MobyRequest request = >>> new MobyRequest( central ); request.setService( agiService ); >>> request.setInput( new MobyDataObject( "Global_Keyword", >>> "superman" ) ); MobyContentInstance contentInstance = >>> request.invokeService(); MobyDataJob mobyJob = >>> contentInstance.get( >>> contentInstance.keySet().iterator().next() ); >>> MobyDataInstance[] dataInstances = mobyJob.getPrimaryData(); >>> >>> the dataInstance contains nothing :-(:-( (dataInstances.length = 0) >>> >>> the simple java client works for other services, but fails >>> for this one... >>> >>> does anybody know what is wrong ? >>> >>> thanks >>> andreas >>> >>> _______________________________________________ >>> 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 >> >> !DSPAM:60005,47160a092601617573718! >> >> >> >> > > _______________________________________________ > 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 Thu Oct 18 17:21:15 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 18 Oct 2007 14:21:15 -0700 Subject: [MOBY-dev] GET Moby Service WSDL Message-ID: Hi all, Just FYI, I have just set-up a way to retrieve the Moby Service WSDL from a URL. This isn't an official part of the API, but we should probably consider adding it, since almost every SOAP tool expects to be able to retrieve WSDL from a URL. The pattern is: http://biomoby.org/services/wsdl/auth.uri/serviceName e.g. http://biomoby.org/services/wsdl/antirrhinum.net/getDragonAlleleLocus My **intention** is that these URLs are stable. That URL actually proxies through to mobycentral.icapture.ubc.ca so even when we move Moby Central to Calgary next month the URL will not change. Let me know if it doesn't work for you. We're going to use these URLs in an upcoming "Annotation Jamboree" that I hope you will all participate in! We want to improve the search power of Moby Central by adding lots of extra metadata to the service descriptions. My PhD student Ben is currently writing the Jamboree interface, which fits into his thesis on mass-collaborative knowledge capture, so by participating you will not only be improving Moby Central, but you will also be helping Ben Good to graduate ;-) Cheers all! Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From duncan.hull at cs.man.ac.uk Fri Oct 19 05:46:07 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Fri, 19 Oct 2007 10:46:07 +0100 Subject: [MOBY-dev] GET Moby Service WSDL: RESTful BioMOBY In-Reply-To: References: Message-ID: <47187CDF.10107@cs.man.ac.uk> Hi Mark Mark Wilkinson wrote: > Just FYI, I have just set-up a way to retrieve the Moby Service WSDL from > a URL. This isn't an official part of the API, but we should probably > consider adding it, since almost every SOAP tool expects to be able to > retrieve WSDL from a URL. > > The pattern is: > > http://biomoby.org/services/wsdl/auth.uri/serviceName > This is great. If only all services were GETtable, the web would probably be a better place. On a similar subject, you recently said that BioMOBY might be adding a sort-of RESTful API soon. Just curious, can we HTTP POST, PUT and DELETE to these (or any other) BioMOBY URI's in true RESTful style [1]? Avoiding the SOAP-and-WSDL-nightmare completely? Duncan [1] http://www.cs.man.ac.uk/~hulld/q2007-06-30.html -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ +44 (0) 161 306 5139 From duncan.hull at cs.man.ac.uk Fri Oct 19 05:46:07 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Fri, 19 Oct 2007 10:46:07 +0100 Subject: [MOBY-dev] GET Moby Service WSDL: RESTful BioMOBY In-Reply-To: References: Message-ID: <47187CDF.10107@cs.man.ac.uk> Hi Mark Mark Wilkinson wrote: > Just FYI, I have just set-up a way to retrieve the Moby Service WSDL from > a URL. This isn't an official part of the API, but we should probably > consider adding it, since almost every SOAP tool expects to be able to > retrieve WSDL from a URL. > > The pattern is: > > http://biomoby.org/services/wsdl/auth.uri/serviceName > This is great. If only all services were GETtable, the web would probably be a better place. On a similar subject, you recently said that BioMOBY might be adding a sort-of RESTful API soon. Just curious, can we HTTP POST, PUT and DELETE to these (or any other) BioMOBY URI's in true RESTful style [1]? Avoiding the SOAP-and-WSDL-nightmare completely? Duncan [1] http://www.cs.man.ac.uk/~hulld/q2007-06-30.html -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ +44 (0) 161 306 5139 From ddg at ncgr.org Fri Oct 19 11:49:07 2007 From: ddg at ncgr.org (Damian Gessler) Date: Fri, 19 Oct 2007 09:49:07 -0600 Subject: [MOBY-dev] GET Moby Service WSDL: RESTful BioMOBY In-Reply-To: <47187CDF.10107@cs.man.ac.uk> References: <47187CDF.10107@cs.man.ac.uk> Message-ID: > This is great. If only all services were GETtable, the web would > probably be a better place. > FYI, this the model of SSWAP (http://sswap.info)--the new name for what used to be called Semantic MOBY. Service descriptions are available via HTTP GETs, for which a RDF/XML OWL-DL graph is returned. (Search for anything on http://sswap.info and then click on the RDF icon next to a returned service name to see the graph). Service invocation is just as simple: either a HTTP POST to the same URL or a GET w/ the graph in-line as the query substring component of the URL (everything after the '?'). [The latter is fully RESTful and can be bookmarked, but may confuse some old servers or proxies that limit URLs to 1024 chars, etc.]. Damian. From markw at illuminae.com Wed Oct 24 11:49:03 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 24 Oct 2007 08:49:03 -0700 Subject: [MOBY-dev] Is anyone else having problems reaching Moby Central? Message-ID: Hi all, Sebastien is not able to connect to Moby Central from France. I am able to connect from various machines in Canada and the US, so it doesn't seem to be a local problem. Is anyone else having problems? M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From gordonp at ucalgary.ca Wed Oct 24 11:57:37 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 24 Oct 2007 09:57:37 -0600 Subject: [MOBY-dev] Is anyone else having problems reaching Moby Central? In-Reply-To: References: Message-ID: <471F6B71.40102@ucalgary.ca> The connection is okay from Calgary... > Hi all, > > Sebastien is not able to connect to Moby Central from France. I am able > to connect from various machines in Canada and the US, so it doesn't seem > to be a local problem. Is anyone else having problems? > > M > > > From dmitry.repchevski at bsc.es Wed Oct 24 12:19:27 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 24 Oct 2007 18:19:27 +0200 Subject: [MOBY-dev] Is anyone else having problems reaching Moby Central? Message-ID: <471F708F.2060809@bsc.es> http://moby-dev.inab.org/cgi-bin/MOBY-Central.pl work from Spain. From usadel at mpimp-golm.mpg.de Wed Oct 24 12:27:43 2007 From: usadel at mpimp-golm.mpg.de (=?ISO-8859-1?Q?Bj=F6rn_Usadel?=) Date: Wed, 24 Oct 2007 18:27:43 +0200 Subject: [MOBY-dev] Is anyone else having problems reaching Moby Central? In-Reply-To: References: Message-ID: <471F727F.9030006@mpimp-golm.mpg.de> Hi, seems to work from Potsdam, Germany. Anything specific that's broken? bj Mark Wilkinson wrote: > Hi all, > > Sebastien is not able to connect to Moby Central from France. I am able > to connect from various machines in Canada and the US, so it doesn't seem > to be a local problem. Is anyone else having problems? > > M > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the addressee and > may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have received this > communication in error, please notify the sender immediately by reply > e-mail and delete the original and all copies from your system. > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From Pieter.Neerincx at wur.nl Wed Oct 24 12:46:28 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Wed, 24 Oct 2007 18:46:28 +0200 Subject: [MOBY-dev] Is anyone else having problems reaching Moby Central? In-Reply-To: References: Message-ID: <90BDC685-1E0D-4AC7-BCC4-316BBC88F43C@wur.nl> Hi all, Wageningen (NL, Europe) is also fine, so it might be big node that went down, but it's not the entire transatlantic connection. Best wishes, Pi On 24-okt-2007, at 17:49, Mark Wilkinson wrote: > Hi all, > > Sebastien is not able to connect to Moby Central from France. I am > able > to connect from various machines in Canada and the US, so it > doesn't seem > to be a local problem. Is anyone else having problems? > > M > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the > addressee and > may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have > received this > communication in error, please notify the sender immediately by reply > e-mail and delete the original and all copies from your system. > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From Sebastien.Carrere at toulouse.inra.fr Thu Oct 25 03:03:21 2007 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Thu, 25 Oct 2007 09:03:21 +0200 Subject: [MOBY-dev] Is anyone else having problems reaching Moby Central? In-Reply-To: <90BDC685-1E0D-4AC7-BCC4-316BBC88F43C@wur.nl> References: <90BDC685-1E0D-4AC7-BCC4-316BBC88F43C@wur.nl> Message-ID: <47203FB9.9030309@toulouse.inra.fr> Bonjour ? tous, I really don't understand ... I use these parameters: MOBYCENTRAL_URI=http://mobycentral.icapture.ubc.ca/MOBY/Central MOBYCENTRAL_URL=http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl or these ones for the OpenTestRegistry: MOBYCENTRAL_URI=http://bioinfo.icapture.ubc.ca/MOBY/Central MOBYCENTRAL_URL=http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl I did not change my code (using Perl libraries since a while). I can access to the INAB registry without any problem. And I don't think it's a DNS problem because when I paste http://mobycentral.icapture.ubc.ca/ into my web-browser, I can access t this server. So, anyone has an idea ? Merci, Sebastien Pieter Neerincx wrote: > Hi all, > > Wageningen (NL, Europe) is also fine, so it might be big node that > went down, but it's not the entire transatlantic connection. > > Best wishes, > > Pi > > On 24-okt-2007, at 17:49, Mark Wilkinson wrote: > > >> Hi all, >> >> Sebastien is not able to connect to Moby Central from France. I am >> able >> to connect from various machines in Canada and the US, so it >> doesn't seem >> to be a local problem. Is anyone else having problems? >> >> M >> >> >> -- >> -- >> Mark Wilkinson >> Assistant Professor, Dept. Medical Genetics >> University of British Columbia >> PI Bioinformatics >> iCAPTURE Centre, St. Paul's Hospital >> Tel: 604 682 2344 x62129 >> Fax: 604 806 9274 >> >> ***CONFIDENTIALITY NOTICE*** >> This electronic message is intended only for the use of the >> addressee and >> may contain information that is privileged and confidential. Any >> dissemination, distribution or copying of this communication by >> unauthorized individuals is strictly prohibited. If you have >> received this >> communication in error, please notify the sender immediately by reply >> e-mail and delete the original and all copies from your system. >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien.Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/moby-dev/attachments/20071025/1e8f6fe1/attachment-0001.vcf From Sebastien.Carrere at toulouse.inra.fr Thu Oct 25 03:29:34 2007 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Thu, 25 Oct 2007 09:29:34 +0200 Subject: [MOBY-dev] RESOLVED : Is anyone else having problems reaching Moby Central? In-Reply-To: <90BDC685-1E0D-4AC7-BCC4-316BBC88F43C@wur.nl> References: <90BDC685-1E0D-4AC7-BCC4-316BBC88F43C@wur.nl> Message-ID: <472045DE.9070008@toulouse.inra.fr> So, The problem is resolved. It was clearly a DNS problem ... The server I use did not access to a correct DNS server. So, there's no problem between France and the rest of the world !!!! Sorry for inconveniance. Sebastien Pieter Neerincx wrote: > Hi all, > > Wageningen (NL, Europe) is also fine, so it might be big node that > went down, but it's not the entire transatlantic connection. > > Best wishes, > > Pi > > On 24-okt-2007, at 17:49, Mark Wilkinson wrote: > > >> Hi all, >> >> Sebastien is not able to connect to Moby Central from France. I am >> able >> to connect from various machines in Canada and the US, so it >> doesn't seem >> to be a local problem. Is anyone else having problems? >> >> M >> >> >> -- >> -- >> Mark Wilkinson >> Assistant Professor, Dept. Medical Genetics >> University of British Columbia >> PI Bioinformatics >> iCAPTURE Centre, St. Paul's Hospital >> Tel: 604 682 2344 x62129 >> Fax: 604 806 9274 >> >> ***CONFIDENTIALITY NOTICE*** >> This electronic message is intended only for the use of the >> addressee and >> may contain information that is privileged and confidential. Any >> dissemination, distribution or copying of this communication by >> unauthorized individuals is strictly prohibited. If you have >> received this >> communication in error, please notify the sender immediately by reply >> e-mail and delete the original and all copies from your system. >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien.Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/moby-dev/attachments/20071025/5e7de420/attachment.vcf From dmitry.repchevski at bsc.es Fri Oct 26 05:07:16 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Fri, 26 Oct 2007 11:07:16 +0200 Subject: [MOBY-dev] serviceNotes question Message-ID: <4721AE44.7070204@bsc.es> Hello! Could someone explain me it, please. Initially it supposed to be just a additional information that could be returned by service along with the response. Then (somewhere in 2005) it was extended to support exceptions (MobyException). Excuse me if I don't understand the phrase well: *********************************************************************************** BioMOBY has to consider reporting exceptions for every layer of information the service request can contain: whole invocation (mobyContent), individual queries (mobyData), and single objects provided as input to the service (Simples, Collections, or even Simples inside a Collection). *********************************************************************************** Does this mean that the tag may be in any of these structures? (As far as I understand before the exceptions the only tag where it could appear was ). What happen with [value] of the serviceNotes? May it still contain a plain text ([mixed])? Thank you. Dmitry From ola.spjuth at farmbio.uu.se Fri Oct 26 07:57:25 2007 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Fri, 26 Oct 2007 13:57:25 +0200 Subject: [MOBY-dev] Unable to get some cache properties in jMoby Message-ID: <8F535AF1-B2F7-499A-B77A-F380240362BE@farmbio.uu.se> Hi, I have problems getting the cache-size and cache-count values from any of the CACHE_PART_ properties, for example, castWorker.getCacheInfo(CACHE_PART_NAMESPACES) returns the following: Obj: cache-reg-url val: http://mobycentral.icapture.ubc.ca/cgi-bin/ MOBY05/mobycentral.pl Obj: cache-loc val: /tmp/mobycache4/ http58.47.47mobycentral46icapture46ubc46ca47cgi45bin47MOBY0547mobycentra l46pl/namespaces Obj: cache-name val: Cache for Namespaces Obj: cache-size val: null Obj: cache-count val: null ...and the same for the other CACHE_PART_xx. My cache is really filled and I can use it, but the properties are still null. Any ideas how this can be? Cheers, .../Ola From ola.spjuth at farmbio.uu.se Fri Oct 26 08:18:08 2007 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Fri, 26 Oct 2007 14:18:08 +0200 Subject: [MOBY-dev] RegistryCache Message-ID: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> Hi Paul, In jMoby, the CentralDigestCachedImpl deals with caching of namespaces, services, servicetypes, and datatypes. How come this also is required when setting up input for a service: Fetching data type ontology from http://biomoby.org/RESOURCES/MOBY-S/ Objects and Fetching namespace ontology from http://biomoby.org/RESOURCES/MOBY-S/ Namespaces What extra is then downloaded that is not cached in the Central? I would be very happy for some explanation about why this is the case, what the org.biomoby.registry.meta.RegistryCache is and how I can use it to cache these ontologies (as pointed to in earlier mails on moby- dev). Cheers, .../Ola From martin.senger at gmail.com Fri Oct 26 08:51:42 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Oct 2007 13:51:42 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> Message-ID: <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> Hi, In jMoby, the CentralDigestCachedImpl deals with caching of > namespaces, services, servicetypes, and datatypes. That's correct. I wrote this caching - so I can confirm that it does exactly this. (And I will look at the problem with cache properties, you mentioned in a previous email, later.) But I do not know who (what software component) is using this caching, and what else it requires from Moby Central. It may be the RDF files describing services (and their parts) - they are not cached by the client CentralDigestCachedImpl. For long time, I wanted to re-implement this caching mechanism to get data from the central not by calling its API methods but by getting the RDFs (actually I even believe that Eddie wrote some classes for me to help with that). So far, it has not happened - but when/if it does I may consider to keep in the cache (and make it available) also the RDF files (they may have richer contents than the results gotten by the API methods). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Fri Oct 26 08:51:42 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Oct 2007 13:51:42 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> Message-ID: <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> Hi, In jMoby, the CentralDigestCachedImpl deals with caching of > namespaces, services, servicetypes, and datatypes. That's correct. I wrote this caching - so I can confirm that it does exactly this. (And I will look at the problem with cache properties, you mentioned in a previous email, later.) But I do not know who (what software component) is using this caching, and what else it requires from Moby Central. It may be the RDF files describing services (and their parts) - they are not cached by the client CentralDigestCachedImpl. For long time, I wanted to re-implement this caching mechanism to get data from the central not by calling its API methods but by getting the RDFs (actually I even believe that Eddie wrote some classes for me to help with that). So far, it has not happened - but when/if it does I may consider to keep in the cache (and make it available) also the RDF files (they may have richer contents than the results gotten by the API methods). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Fri Oct 26 09:13:49 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 26 Oct 2007 07:13:49 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> Message-ID: <4721E80D.8060503@ucalgary.ca> Hi folks, Yes, the "Fetching ... ontology" does exactly what Martin describes below...builds the definitions for the static MobyDataType.getDataType(), MobyNamespace.getNamespace() etc. methods by downloading the complete RDFs from Moby Central. RegistryCache coordinates when to update the cached copies, etc.. This is the caching mechanism used in Seahawk, which minimizes the number of http connects required to gather all the ontology info the program may need to access. If you use this mechanism, you should not need to access the cache directly, MobyDataType.getDataType(), etc. handle it transparently for you. If you only need to access little bits of the ontologies, CentralDigestCachedImpl may still be your best bet performance-wise. Regards, Paul > But I do not know who (what software component) is using this caching, > and what else it requires from Moby Central. It may be the RDF files > describing services (and their parts) - they are not cached by the > client CentralDigestCachedImpl. For long time, I wanted to > re-implement this caching mechanism to get data from the central not > by calling its API methods but by getting the RDFs (actually I even > believe that Eddie wrote some classes for me to help with that). So > far, it has not happened - but when/if it does I may consider to keep > in the cache (and make it available) also the RDF files (they may have > richer contents than the results gotten by the API methods). > > Cheers, > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger From edward.kawas at gmail.com Fri Oct 26 09:29:26 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 26 Oct 2007 06:29:26 -0700 Subject: [MOBY-dev] serviceNotes question In-Reply-To: <4721AE44.7070204@bsc.es> References: <4721AE44.7070204@bsc.es> Message-ID: <000f01c817d4$3af4b380$6400a8c0@notebook> Hi Dmitry > Does this mean that the tag may be in any of > these structures? No, they can be used to describe errors at these structures. > (As far as I understand before the exceptions the only tag > where it could appear was ). > I believe that you are correct. Eddie From gordonp at ucalgary.ca Fri Oct 26 09:33:56 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 26 Oct 2007 07:33:56 -0600 Subject: [MOBY-dev] serviceNotes question In-Reply-To: <000f01c817d4$3af4b380$6400a8c0@notebook> References: <4721AE44.7070204@bsc.es> <000f01c817d4$3af4b380$6400a8c0@notebook> Message-ID: <4721ECC4.9050703@ucalgary.ca> Edward Kawas wrote: > Hi Dmitry > >> Does this mean that the tag may be in any of >> these structures? >> > No, they can be used to describe errors at these structures. > Correct. To clarify, via the serviceException's query ID and element attributes. From gordonp at ucalgary.ca Fri Oct 26 09:13:49 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 26 Oct 2007 07:13:49 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> Message-ID: <4721E80D.8060503@ucalgary.ca> Hi folks, Yes, the "Fetching ... ontology" does exactly what Martin describes below...builds the definitions for the static MobyDataType.getDataType(), MobyNamespace.getNamespace() etc. methods by downloading the complete RDFs from Moby Central. RegistryCache coordinates when to update the cached copies, etc.. This is the caching mechanism used in Seahawk, which minimizes the number of http connects required to gather all the ontology info the program may need to access. If you use this mechanism, you should not need to access the cache directly, MobyDataType.getDataType(), etc. handle it transparently for you. If you only need to access little bits of the ontologies, CentralDigestCachedImpl may still be your best bet performance-wise. Regards, Paul > But I do not know who (what software component) is using this caching, > and what else it requires from Moby Central. It may be the RDF files > describing services (and their parts) - they are not cached by the > client CentralDigestCachedImpl. For long time, I wanted to > re-implement this caching mechanism to get data from the central not > by calling its API methods but by getting the RDFs (actually I even > believe that Eddie wrote some classes for me to help with that). So > far, it has not happened - but when/if it does I may consider to keep > in the cache (and make it available) also the RDF files (they may have > richer contents than the results gotten by the API methods). > > Cheers, > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger From martin.senger at gmail.com Fri Oct 26 09:45:31 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Oct 2007 14:45:31 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <4721E80D.8060503@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> Message-ID: <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> Hi Paul, This is the caching > mechanism used in Seahawk, which minimizes the number of http connects The old story again, right? You implemented this good thing just for yourself, without putting this good stuff into existing CentralDigestCachedImpl instead. Therefore, we again have two ways of doing things, and we confuse developers. Pity... Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Fri Oct 26 09:45:31 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Oct 2007 14:45:31 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <4721E80D.8060503@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> Message-ID: <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> Hi Paul, This is the caching > mechanism used in Seahawk, which minimizes the number of http connects The old story again, right? You implemented this good thing just for yourself, without putting this good stuff into existing CentralDigestCachedImpl instead. Therefore, we again have two ways of doing things, and we confuse developers. Pity... Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Fri Oct 26 10:14:02 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 26 Oct 2007 08:14:02 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> Message-ID: <4721F62A.5020407@ucalgary.ca> Hi Martin, Actually, I didn't add it to CentralDigestCachedImpl for a several practical reasons: 1. The RDF methodology is very different from the existing methodology, so I did not want to just replace your code. 2. I separated registry calls and ontology definition caching into separate classes (see CentralCachedCallsImpl, which does extend you CentralImpl, and the static methods in MobyDataType etc. respectively), as these are now completely unrelated. 3. The existing CentralDigestCachedImpl methodology is still useful when you just want to get bits of the ontology. I am willing to revamp the CentralDigestCachedImpl code sometime to use the RDF methodology, if you're keen on it. All I would need you to do is build unit tests first, to elucidate the proper behaviour and make sure I don't break any of the current functionality on which Dashboard, etc. depend. Regards, Paul > The old story again, right? You implemented this good thing just for > yourself, without putting this good stuff into existing > CentralDigestCachedImpl instead. Therefore, we again have two ways of doing > things, and we confuse developers. Pity... > From gordonp at ucalgary.ca Fri Oct 26 10:14:02 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 26 Oct 2007 08:14:02 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> Message-ID: <4721F62A.5020407@ucalgary.ca> Hi Martin, Actually, I didn't add it to CentralDigestCachedImpl for a several practical reasons: 1. The RDF methodology is very different from the existing methodology, so I did not want to just replace your code. 2. I separated registry calls and ontology definition caching into separate classes (see CentralCachedCallsImpl, which does extend you CentralImpl, and the static methods in MobyDataType etc. respectively), as these are now completely unrelated. 3. The existing CentralDigestCachedImpl methodology is still useful when you just want to get bits of the ontology. I am willing to revamp the CentralDigestCachedImpl code sometime to use the RDF methodology, if you're keen on it. All I would need you to do is build unit tests first, to elucidate the proper behaviour and make sure I don't break any of the current functionality on which Dashboard, etc. depend. Regards, Paul > The old story again, right? You implemented this good thing just for > yourself, without putting this good stuff into existing > CentralDigestCachedImpl instead. Therefore, we again have two ways of doing > things, and we confuse developers. Pity... > From martin.senger at gmail.com Fri Oct 26 10:23:54 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Oct 2007 15:23:54 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <4721F62A.5020407@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> Message-ID: <4d93f07c0710260723g4d976a1dl8a1180d01548f174@mail.gmail.com> > 3. The existing CentralDigestCachedImpl methodology is still useful when > you just want to get bits of the ontology. Well, if I want just bits I would not use cached one :-) But it is not an important argument I think. I am willing to revamp the CentralDigestCachedImpl code sometime to use > the RDF methodology, if you're keen on it. That would be perfect! All I would need you to do > is build unit tests first Very good point and suggestion. I agree and I consider now holding the ball... I will come back to you when I have the tests ready (you may not believe it but I have never wrote any junit tests - even though I wanted to do it often). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Fri Oct 26 10:23:54 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Oct 2007 15:23:54 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <4721F62A.5020407@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> Message-ID: <4d93f07c0710260723g4d976a1dl8a1180d01548f174@mail.gmail.com> > 3. The existing CentralDigestCachedImpl methodology is still useful when > you just want to get bits of the ontology. Well, if I want just bits I would not use cached one :-) But it is not an important argument I think. I am willing to revamp the CentralDigestCachedImpl code sometime to use > the RDF methodology, if you're keen on it. That would be perfect! All I would need you to do > is build unit tests first Very good point and suggestion. I agree and I consider now holding the ball... I will come back to you when I have the tests ready (you may not believe it but I have never wrote any junit tests - even though I wanted to do it often). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Fri Oct 26 11:19:35 2007 From: markw at illuminae.com (mark wilkinson) Date: Fri, 26 Oct 2007 15:19:35 +0000 GMT Subject: [MOBY-dev] RegistryCache In-Reply-To: <4721F62A.5020407@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca><4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> Message-ID: <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> Can I update the RDF itself to make it more "correct" before you do this? It will only take a day or two... M -- Mark Wilkinson ...on the road! -----Original Message----- From: Paul Gordon Date: Fri, 26 Oct 2007 08:14:02 To:Core developer announcements Cc:mobydev Subject: Re: [MOBY-dev] RegistryCache Hi Martin, Actually, I didn't add it to CentralDigestCachedImpl for a several practical reasons: 1. The RDF methodology is very different from the existing methodology, so I did not want to just replace your code. 2. I separated registry calls and ontology definition caching into separate classes (see CentralCachedCallsImpl, which does extend you CentralImpl, and the static methods in MobyDataType etc. respectively), as these are now completely unrelated. 3. The existing CentralDigestCachedImpl methodology is still useful when you just want to get bits of the ontology. I am willing to revamp the CentralDigestCachedImpl code sometime to use the RDF methodology, if you're keen on it. All I would need you to do is build unit tests first, to elucidate the proper behaviour and make sure I don't break any of the current functionality on which Dashboard, etc. depend. Regards, Paul > The old story again, right? You implemented this good thing just for > yourself, without putting this good stuff into existing > CentralDigestCachedImpl instead. Therefore, we again have two ways of doing > things, and we confuse developers. Pity... > _______________________________________________ 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 Fri Oct 26 11:19:35 2007 From: markw at illuminae.com (mark wilkinson) Date: Fri, 26 Oct 2007 15:19:35 +0000 GMT Subject: [MOBY-dev] RegistryCache In-Reply-To: <4721F62A.5020407@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca><4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> Message-ID: <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> Can I update the RDF itself to make it more "correct" before you do this? It will only take a day or two... M -- Mark Wilkinson ...on the road! -----Original Message----- From: Paul Gordon Date: Fri, 26 Oct 2007 08:14:02 To:Core developer announcements Cc:mobydev Subject: Re: [MOBY-dev] RegistryCache Hi Martin, Actually, I didn't add it to CentralDigestCachedImpl for a several practical reasons: 1. The RDF methodology is very different from the existing methodology, so I did not want to just replace your code. 2. I separated registry calls and ontology definition caching into separate classes (see CentralCachedCallsImpl, which does extend you CentralImpl, and the static methods in MobyDataType etc. respectively), as these are now completely unrelated. 3. The existing CentralDigestCachedImpl methodology is still useful when you just want to get bits of the ontology. I am willing to revamp the CentralDigestCachedImpl code sometime to use the RDF methodology, if you're keen on it. All I would need you to do is build unit tests first, to elucidate the proper behaviour and make sure I don't break any of the current functionality on which Dashboard, etc. depend. Regards, Paul > The old story again, right? You implemented this good thing just for > yourself, without putting this good stuff into existing > CentralDigestCachedImpl instead. Therefore, we again have two ways of doing > things, and we confuse developers. Pity... > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From martin.senger at gmail.com Fri Oct 26 11:41:39 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Oct 2007 16:41:39 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> Message-ID: <4d93f07c0710260841r4f34eaf2y511a626b2e17a91b@mail.gmail.com> > Can I update the RDF itself to make it more "correct" before you do > this? It will only take a day or two... Of course. Don't worry... the junit tests will take for me more time... Thanks for doing it, anyway. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Fri Oct 26 11:41:39 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Oct 2007 16:41:39 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> Message-ID: <4d93f07c0710260841r4f34eaf2y511a626b2e17a91b@mail.gmail.com> > Can I update the RDF itself to make it more "correct" before you do > this? It will only take a day or two... Of course. Don't worry... the junit tests will take for me more time... Thanks for doing it, anyway. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Fri Oct 26 11:32:48 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 26 Oct 2007 09:32:48 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca><4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> Message-ID: <472208A0.1040404@ucalgary.ca> No problem! I won't get a chance to do any updates for a couple weeks anyway... > Can I update the RDF itself to make it more "correct" before you do this? It will only take a day or two... > > M > > > -- > Mark Wilkinson > ...on the road! > > > -----Original Message----- > From: Paul Gordon > Date: Fri, 26 Oct 2007 08:14:02 > To:Core developer announcements > Cc:mobydev > Subject: Re: [MOBY-dev] RegistryCache > > Hi Martin, > > Actually, I didn't add it to CentralDigestCachedImpl for a several > practical reasons: > > 1. The RDF methodology is very different from the existing methodology, > so I did not want to just replace your code. > 2. I separated registry calls and ontology definition caching into > separate classes (see CentralCachedCallsImpl, which does extend you > CentralImpl, and the static methods in MobyDataType etc. respectively), > as these are now completely unrelated. > 3. The existing CentralDigestCachedImpl methodology is still useful when > you just want to get bits of the ontology. > > I am willing to revamp the CentralDigestCachedImpl code sometime to use > the RDF methodology, if you're keen on it. All I would need you to do > is build unit tests first, to elucidate the proper behaviour and make > sure I don't break any of the current functionality on which Dashboard, > etc. depend. > > Regards, > Paul > >> The old story again, right? You implemented this good thing just for >> yourself, without putting this good stuff into existing >> CentralDigestCachedImpl instead. Therefore, we again have two ways of doing >> things, and we confuse developers. Pity... >> >> > > _______________________________________________ > 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 > > !DSPAM:60005,47220606260162728527452! > > > > From gordonp at ucalgary.ca Fri Oct 26 11:32:48 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 26 Oct 2007 09:32:48 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca><4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> Message-ID: <472208A0.1040404@ucalgary.ca> No problem! I won't get a chance to do any updates for a couple weeks anyway... > Can I update the RDF itself to make it more "correct" before you do this? It will only take a day or two... > > M > > > -- > Mark Wilkinson > ...on the road! > > > -----Original Message----- > From: Paul Gordon > Date: Fri, 26 Oct 2007 08:14:02 > To:Core developer announcements > Cc:mobydev > Subject: Re: [MOBY-dev] RegistryCache > > Hi Martin, > > Actually, I didn't add it to CentralDigestCachedImpl for a several > practical reasons: > > 1. The RDF methodology is very different from the existing methodology, > so I did not want to just replace your code. > 2. I separated registry calls and ontology definition caching into > separate classes (see CentralCachedCallsImpl, which does extend you > CentralImpl, and the static methods in MobyDataType etc. respectively), > as these are now completely unrelated. > 3. The existing CentralDigestCachedImpl methodology is still useful when > you just want to get bits of the ontology. > > I am willing to revamp the CentralDigestCachedImpl code sometime to use > the RDF methodology, if you're keen on it. All I would need you to do > is build unit tests first, to elucidate the proper behaviour and make > sure I don't break any of the current functionality on which Dashboard, > etc. depend. > > Regards, > Paul > >> The old story again, right? You implemented this good thing just for >> yourself, without putting this good stuff into existing >> CentralDigestCachedImpl instead. Therefore, we again have two ways of doing >> things, and we confuse developers. Pity... >> >> > > _______________________________________________ > 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 > > !DSPAM:60005,47220606260162728527452! > > > > From edward.kawas at gmail.com Fri Oct 26 12:00:43 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 26 Oct 2007 09:00:43 -0700 Subject: [MOBY-dev] RegistryCache In-Reply-To: <472208A0.1040404@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca><4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca><614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> <472208A0.1040404@ucalgary.ca> Message-ID: <001b01c817e9$5da6cb10$6400a8c0@notebook> Mark, I believe that Paul and Co. use my RDF parsers, so as long as I update those files when I (assuming that it is I that changes the RDF ;-) change the RDF. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon > Sent: Friday, October 26, 2007 8:33 AM > To: markw at illuminae.com; Core developer announcements > Cc: mobydev > Subject: Re: [MOBY-dev] RegistryCache > > No problem! I won't get a chance to do any updates for a > couple weeks anyway... > > Can I update the RDF itself to make it more "correct" > before you do this? It will only take a day or two... > > > > M > > > > > > -- > > Mark Wilkinson > > ...on the road! > > > > > > -----Original Message----- > > From: Paul Gordon > > Date: Fri, 26 Oct 2007 08:14:02 > > To:Core developer announcements > > Cc:mobydev > > Subject: Re: [MOBY-dev] RegistryCache > > > > Hi Martin, > > > > Actually, I didn't add it to CentralDigestCachedImpl for a several > > practical reasons: > > > > 1. The RDF methodology is very different from the existing > > methodology, so I did not want to just replace your code. > > 2. I separated registry calls and ontology definition caching into > > separate classes (see CentralCachedCallsImpl, which does extend you > > CentralImpl, and the static methods in MobyDataType etc. > > respectively), as these are now completely unrelated. > > 3. The existing CentralDigestCachedImpl methodology is still useful > > when you just want to get bits of the ontology. > > > > I am willing to revamp the CentralDigestCachedImpl code sometime to > > use the RDF methodology, if you're keen on it. All I would > need you > > to do is build unit tests first, to elucidate the proper > behaviour and > > make sure I don't break any of the current functionality on which > > Dashboard, etc. depend. > > > > Regards, > > Paul > > > >> The old story again, right? You implemented this good > thing just for > >> yourself, without putting this good stuff into existing > >> CentralDigestCachedImpl instead. Therefore, we again have > two ways of > >> doing things, and we confuse developers. Pity... > >> > >> > > > > _______________________________________________ > > 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 > > > > !DSPAM:60005,47220606260162728527452! > > > > > > > > > > _______________________________________________ > 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 Fri Oct 26 13:56:09 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 26 Oct 2007 10:56:09 -0700 Subject: [MOBY-dev] Fwd: PLoS ONE Decision [07-PONE-RA-01200R1] In-Reply-To: <2311934051859@cl-enclosure2-4> References: <2311934051859@cl-enclosure2-4> Message-ID: Hi All, Well, the manuscript was rejected again, without any additional review (after two months of waiting!). I think that says more about the quality of PLoS ONE than it says about the quality of the manuscript, but... hey... what can you do? So, I guess we need to find another place to send it. Does anyone have any preferences? M ------- Forwarded message ------- From: PLoSONE at plos.org To: markw at illuminae.com Cc: Subject: PLoS ONE Decision [07-PONE-RA-01200R1] Date: Fri, 26 Oct 2007 06:26:25 -0700 Dear Dr. Wilkinson, Thank you for submitting your manuscript "Interoperability with Moby 1.0: It's Better than Sharing your Toothbrush" to PLoS ONE. I am sorry about the delay in the review process. After careful consideration, we have decided that we will not be able to accept this manuscript for publication in the journal in its current form, although we would be willing to review again a much-revised version if you felt able to address the specific concerns detailed below. Should you decide to revise the manuscript for further consideration here, your revisions should address the specific points raised by one of the referees. Please pay close attention to our "Guidelines for Authors" and "Submission Checklist" when revising your manuscript. There are templates available to help authors format papers for publication in PLoS ONE, and include all the relevant information in the appropriate place. You can download them from our instructions for authors at http://www.plosone.org/static/guidelines.action#preparation (under "organization of the manuscript"). The four templates are: Standard Research article, Clinical Trial, Clinical Research article, and Systematic Review/Meta-Analysis - please choose the appropriate one for your particular type of study. When your files are completely ready please resubmit your manuscript by logging on to our journal manuscript system at http://one.plosjms.org/ Thank you for your support of PLoS ONE. Yours sincerely, Dr Jörg Hoheisel Academic Editor, PLoS ONE ------------------------------------------------------------------------ -------------- next part -------------- A non-text attachment was scrubbed... Name: 1_reviewer_attachment_1_1180009995.pdf Type: application/pdf Size: 56743 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/moby-dev/attachments/20071026/461dd7eb/attachment-0001.pdf -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: attachment889.htm Url: http://lists.open-bio.org/pipermail/moby-dev/attachments/20071026/461dd7eb/attachment.ksh From Pieter.Neerincx at wur.nl Sat Oct 27 06:04:02 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Sat, 27 Oct 2007 12:04:02 +0200 Subject: [MOBY-dev] Fwd: PLoS ONE Decision [07-PONE-RA-01200R1] In-Reply-To: References: <2311934051859@cl-enclosure2-4> Message-ID: <3A2D8DD7-EE21-47FC-BA37-72F07E2C1E40@wur.nl> Hi Mark, Bummer, PLoS One looked like a great new magazine, but their review process is a bad joke... not very professional at best :(. I think it would be best for the BioMOBY article if it will be published in an Open Access magazine, but apart from that I don't have preferences. Cheers, Pi On 26 Oct 2007, at 19:56, Mark Wilkinson wrote: > Hi All, > > Well, the manuscript was rejected again, without any additional > review (after two months of waiting!). I think that says more > about the quality of PLoS ONE than it says about the quality of the > manuscript, but... hey... what can you do? > > So, I guess we need to find another place to send it. Does anyone > have any preferences? > > M > > > > > ------- Forwarded message ------- > From: PLoSONE at plos.org > To: markw at illuminae.com > Cc: > Subject: PLoS ONE Decision [07-PONE-RA-01200R1] > Date: Fri, 26 Oct 2007 06:26:25 -0700 > > Dear Dr. Wilkinson, > > Thank you for submitting your manuscript "Interoperability with > Moby 1.0: It's Better than Sharing your Toothbrush" to PLoS ONE. I > am sorry about the delay in the review process. > > After careful consideration, we have decided that we will not be > able to accept this manuscript for publication in the journal in > its current form, although we would be willing to review again a > much-revised version if you felt able to address the specific > concerns detailed below. > > Should you decide to revise the manuscript for further > consideration here, your revisions should address the specific > points raised by one of the referees. > > Please pay close attention to our "Guidelines for Authors" and > "Submission Checklist" when revising your manuscript. > > There are templates available to help authors format papers for > publication in PLoS ONE, and include all the relevant information > in the appropriate place. You can download them from our > instructions for authors at http://www.plosone.org/static/ > guidelines.action#preparation (under "organization of the > manuscript"). The four templates are: Standard Research article, > Clinical Trial, Clinical Research article, and Systematic Review/ > Meta-Analysis - please choose the appropriate one for your > particular type of study. > > When your files are completely ready please resubmit your > manuscript by logging on to our journal manuscript system at http:// > one.plosjms.org/ > > Thank you for your support of PLoS ONE. > > Yours sincerely, > > Dr Jörg Hoheisel > Academic Editor, PLoS ONE > > ---------------------------------------------------------------------- > -- > > <1_reviewer_attachment_1_1180009995.pdf> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- From martin.senger at gmail.com Mon Oct 29 01:56:48 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 29 Oct 2007 06:56:48 +0100 Subject: [MOBY-dev] Announcement: Soaplab2 released Message-ID: <4d93f07c0710282256u22823cfcie7a737835bd77a97@mail.gmail.com> [ I apologize for the cross-posting ] In the early hours of the Monday morning, after last "fixes" that took the whole night :-) I can announce, finally, a release of the completely re-written Soaplab - Soaplab2. Some features are still missing (it is a beta, after all) but the main functionality should be there. Please have a look at http://soaplab.sourceforge.net/soaplab2. As usual: without your feedback and suggestions, it will be hard to improve it. With regards, Martin Senger Mahmut Uludag -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ola.spjuth at farmbio.uu.se Mon Oct 29 12:57:27 2007 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Mon, 29 Oct 2007 17:57:27 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <4721F62A.5020407@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> Message-ID: <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> Hi Paul, So how do I use the CentralCachedCallsImpl? How can I fill/monitor/ update its cache? If I use it, will it completely replace the CentralDigestCachedImpl? I am a bit confused here how to work with BioMoby registries and caches and ontologies... Hope you (or someone else) can help me out. Cheers, .../Ola On Oct 26, 2007, at 16:14 , Paul Gordon wrote: > Hi Martin, > > Actually, I didn't add it to CentralDigestCachedImpl for a several > practical reasons: > > 1. The RDF methodology is very different from the existing > methodology, > so I did not want to just replace your code. > 2. I separated registry calls and ontology definition caching into > separate classes (see CentralCachedCallsImpl, which does extend you > CentralImpl, and the static methods in MobyDataType etc. > respectively), > as these are now completely unrelated. > 3. The existing CentralDigestCachedImpl methodology is still useful > when > you just want to get bits of the ontology. > > I am willing to revamp the CentralDigestCachedImpl code sometime to > use > the RDF methodology, if you're keen on it. All I would need you to do > is build unit tests first, to elucidate the proper behaviour and make > sure I don't break any of the current functionality on which > Dashboard, > etc. depend. > > Regards, > Paul >> The old story again, right? You implemented this good thing just for >> yourself, without putting this good stuff into existing >> CentralDigestCachedImpl instead. Therefore, we again have two ways >> of doing >> things, and we confuse developers. Pity... >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Mon Oct 29 13:06:31 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 29 Oct 2007 11:06:31 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> Message-ID: <47261317.3030406@ucalgary.ca> Hi Ola, If you want to use CentralCachedCallsImpl, simply use it whenever you would use CentralImpl. It takes care of all the caching details for you, you should never have to explicitly check if something is cached or not, just call the methods as the Central interface specifies. I'm not trying to be vague, I just tried to make it easy to use :-) Regards, Paul From gordonp at ucalgary.ca Mon Oct 29 13:06:31 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 29 Oct 2007 11:06:31 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> Message-ID: <47261317.3030406@ucalgary.ca> Hi Ola, If you want to use CentralCachedCallsImpl, simply use it whenever you would use CentralImpl. It takes care of all the caching details for you, you should never have to explicitly check if something is cached or not, just call the methods as the Central interface specifies. I'm not trying to be vague, I just tried to make it easy to use :-) Regards, Paul From ola.spjuth at farmbio.uu.se Mon Oct 29 15:58:05 2007 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Mon, 29 Oct 2007 20:58:05 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <47261317.3030406@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> <47261317.3030406@ucalgary.ca> Message-ID: <77B231CC-2BE8-4121-90A5-A6899C336C7D@farmbio.uu.se> Yes, but how do I fill the cache so that I can use the central offline (I'm building a rich client)? The methods below are not available from the CentralCachedCallsImpl: MobyDataType[] types=castWorker.getDataTypes(); MobyService[] services=castWorker.getServices(); MobyServiceType[] serviceTypes=castWorker.getFullServiceTypes(); and I want to build a full service hierarchy (as in dashboard). Are there other ways of obtaining this information? How can I get the state of the caching (age, size etc) and update it? The CentralCachedCallsImpl seems rather lightweight... Is there a helper class with convenience methods available? Thanks, .../Ola On Oct 29, 2007, at 18:06 , Paul Gordon wrote: > Hi Ola, > > If you want to use CentralCachedCallsImpl, simply use it whenever you > would use CentralImpl. > It takes care of all the caching details for you, you should never > have > to explicitly check if something > is cached or not, just call the methods as the Central interface > specifies. I'm not trying to be vague, > I just tried to make it easy to use :-) > > Regards, > > Paul > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From ola.spjuth at farmbio.uu.se Mon Oct 29 15:58:05 2007 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Mon, 29 Oct 2007 20:58:05 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <47261317.3030406@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> <47261317.3030406@ucalgary.ca> Message-ID: <77B231CC-2BE8-4121-90A5-A6899C336C7D@farmbio.uu.se> Yes, but how do I fill the cache so that I can use the central offline (I'm building a rich client)? The methods below are not available from the CentralCachedCallsImpl: MobyDataType[] types=castWorker.getDataTypes(); MobyService[] services=castWorker.getServices(); MobyServiceType[] serviceTypes=castWorker.getFullServiceTypes(); and I want to build a full service hierarchy (as in dashboard). Are there other ways of obtaining this information? How can I get the state of the caching (age, size etc) and update it? The CentralCachedCallsImpl seems rather lightweight... Is there a helper class with convenience methods available? Thanks, .../Ola On Oct 29, 2007, at 18:06 , Paul Gordon wrote: > Hi Ola, > > If you want to use CentralCachedCallsImpl, simply use it whenever you > would use CentralImpl. > It takes care of all the caching details for you, you should never > have > to explicitly check if something > is cached or not, just call the methods as the Central interface > specifies. I'm not trying to be vague, > I just tried to make it easy to use :-) > > Regards, > > Paul > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Mon Oct 29 20:43:04 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 29 Oct 2007 18:43:04 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: <77B231CC-2BE8-4121-90A5-A6899C336C7D@farmbio.uu.se> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> <47261317.3030406@ucalgary.ca> <77B231CC-2BE8-4121-90A5-A6899C336C7D@farmbio.uu.se> Message-ID: <47267E18.4010509@ucalgary.ca> Hi Ola, If you want to explicitly cache the ontologies, you need to work with the Registry and RegistryCache objects like so: ******** //To delete stale files RegistryCache.deleteExpiredCacheFiles(allowedAgeInMilliseconds); // In what file would the ontology be cached, if it was cached? File namespacesDefFile = RegistryCache.getOntologyFile(preferredRegistry, Central.NAMESPACES_RESOURCE_NAME); URL namespacesDefURL = namespacesDefFile.toURI().toURL(); if(namespacesDefFile.exists()){ // Use the existing cached file rather than actually going to the registry MobyNamespace.loadNamespaces(namespacesDefURL, preferredRegistry); } else{ // Create the cached file from the remote source, then load it into MobyNamespace so MobyNamespace.getNamespace() can retrieve it. RegistryCache.cacheRegistryOntology(preferredRegistry, Central.NAMESPACES_RESOURCE_NAME); MobyNamespace.loadNamespaces(namespacesDefURL, preferredRegistry); } ******** The other relevant fields/methods are Central.DATA_TYPES_RESOURCE_NAME/Central.SERVICE_TYPES_RESOURCE_NAME and MobyDataType.loadDataTypes()/MobyServiceType.loadServiceTypes(). From groscurt at mpiz-koeln.mpg.de Tue Oct 30 04:41:32 2007 From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de) Date: Tue, 30 Oct 2007 09:41:32 +0100 (CET) Subject: [MOBY-dev] RegistryCache In-Reply-To: <77B231CC-2BE8-4121-90A5-A6899C336C7D@farmbio.uu.se> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> <47261317.3030406@ucalgary.ca> <77B231CC-2BE8-4121-90A5-A6899C336C7D@farmbio.uu.se> Message-ID: <46725.195.37.46.22.1193733692.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi, > Yes, but how do I fill the cache so that I can use the central > offline (I'm building a rich client)? if you want to have an 'offline' central you can use the MobySync project which is part of the Moby checkout. Under moby-live/Java/src/support/mobysync/ you can find the README how to establish a local repository and how to run the process to keep it synchronized with the BioMoby central. hope this helps andreas From dmitry.repchevski at bsc.es Tue Oct 30 06:05:26 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 30 Oct 2007 11:05:26 +0100 Subject: [MOBY-dev] findService question Message-ID: <472701E6.8000408@bsc.es> First big thanx to all for your help, I have another question. The only way I found to get a complete description of a service is using "findService" operation. I have a problem with its format. Especially I am interested in Input/Output format. I have ones from xml schema, but the question is - is the format the same as for "mobyContent"? I mean that in mobyContent we can have multiple mobyData with a Simple/Collection. According the scheme there could be List and List, so should I understand it as: Any collection specified will be encapsulated in "mobyData" (one mobyData - one Collection). If I have a List of Simple elements they supposed to be wrapped with Collection inside mobyData. If I have only one Simple in a list - there is a mobyData with a Simple. Sincerely, Dmitry, P.S. or maybe there is better way to find a service description? From dmitry.repchevski at bsc.es Tue Oct 30 07:34:18 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 30 Oct 2007 12:34:18 +0100 Subject: [MOBY-dev] theological question. Message-ID: <472716BA.5020803@bsc.es> Hello! I have a question about the life, universe and web-services. Is there any accordance about the "part name" name in biomoby? Since biomoby use soap web-services it supposed to use wsdl (there is even the operation in the Registry to retrieve it). Within a service there is a parameters' definition part (in moby there are only two - request/result String). Basicly it looks like: Axis is relaxed about the name of parameter unless it can infer it from a call (there is only one method to call). The problem is with another Web-Services stacks like jboss-ws which is trying to be strict to specification. I found that java/perl name the parameters differently ("data" for perl and "arg0" for java). Even more AXIS has a bug putting the namespace into the name of the parameter that goes against the specification (ns1:arg0). Well maybe it just a rhetoric question, but is there a solution? Regards, Dmitry From edward.kawas at gmail.com Tue Oct 30 13:42:44 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 30 Oct 2007 10:42:44 -0700 Subject: [MOBY-dev] findService question In-Reply-To: <472701E6.8000408@bsc.es> References: <472701E6.8000408@bsc.es> Message-ID: <001a01c81b1c$47b6b690$6400a8c0@notebook> Hi Dmitry, I don't really understand your question, but I will take my best shot at addressing it! > Especially I am interested in Input/Output format. I have > ones from xml schema, but the question is - is the format the > same as for "Moby Content"? Not sure what you are asking here ... > I mean that in Moby Content we can have multiple Moby Data with > a Simple/Collection. > According the scheme there could be List and > List, so should I understand it as: > Any collection specified will be encapsulated in "Moby Data" > (one Moby Data - one Collection). Any collection specified in the find Service response will be contained in the Moby Data block of the moby xml message. There would only be one collection in the Moby Data section for each specified collection in the find Service response. The same can be said for simples. Every simple specified in the find Service response will be contained in the Moby Data section of the moby xml. Again, there would only be one simple in the Moby Data section for each specified simple in the find Service response. Moby services can have many inputs/outputs. Each input/output can be either a simple or collection. All of the inputs/outputs are put into the Moby Data section. > If I have a List of Simple elements they supposed to be > wrapped with Collection inside Moby Data. > If I have only one Simple in a list - there is a Moby Data > with a Simple. > > Sincerely, > > Dmitry, > Hope this answers your question ... Eddie > P.S. or maybe there is better way to find a service description? > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Tue Oct 30 14:11:45 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 30 Oct 2007 19:11:45 +0100 Subject: [MOBY-dev] findService question References: 472701E6.8000408@bsc.es Message-ID: <472773E1.3010809@bsc.es> Hello Edward, Acording the schema (findService.xsd) there could be only one input/output per service. Every input/output could have many simple or (and) collections of simple. As far as I understand, in the service every simple/collection is mapped to mobyData. My confusion was in mixing the format of those "Simple" between MobyMessage and this particular service (findService). Now i see that they are different. Thank you very much, Dmitry From edward.kawas at gmail.com Tue Oct 30 17:02:55 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 30 Oct 2007 14:02:55 -0700 Subject: [MOBY-dev] findService question In-Reply-To: <472773E1.3010809@bsc.es> References: 472701E6.8000408@bsc.es <472773E1.3010809@bsc.es> Message-ID: <000001c81b38$3e8066e0$6400a8c0@notebook> Hi Dmitry, > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > Dmitry Repchevsky > Sent: Tuesday, October 30, 2007 11:12 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] findService question > > Hello Edward, > > Acording the schema (findService.xsd) there could be only one > input/output per service. In the findService call, there are sections called Input/Output and you are correct in that there are exactly one of each of these. However, in there can be multiple Simples/Collections declarations in these blocks. That is what I meant when I said services can have >= 1 input/output. > As far as I understand, in the service every > simple/collection is mapped to mobyData. If you mean contained in the mobyData section, then yes. > Thank you very much, Glad to help! Eddie > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From ola.spjuth at farmbio.uu.se Wed Oct 31 06:22:18 2007 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Wed, 31 Oct 2007 11:22:18 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <47267E18.4010509@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> <47261317.3030406@ucalgary.ca> <77B231CC-2BE8-4121-90A5-A6899C336C7D@farmbio.uu.se> <47267E18.4010509@ucalgary.ca> Message-ID: Hi Paul, Thank you for the answers. I think I have found a bug in jMoby, but please correct me if I'm wrong. The following call with reg being my custom Regsitry: MobyDataComposite comp = new MobyDataComposite("DNASequence", reg); calls public MobyDataComposite(String typeName, Registry r){ this(MobyDataType.getDataType(typeName, r)); } calls public MobyDataComposite(MobyDataType type){ this(type, ""); } calls public MobyDataComposite(MobyDataType type, String name){ this(type, name, "", ""); } calls public MobyDataComposite(MobyDataType type, String name, String namespace, String id){ super(namespace, id); setName(name); setDataType(type); members = new ConcurrentHashMap(); } where super calls public MobyDataObject(String namespace, String id){ this(namespace, id, null); } calls public MobyDataObject(String namespace, String id, Registry registry){ super(""); thus having registry=null. This means I will always use the default registry and not my custom registry that I inputted. This prevents me from using my cached registry which you explained below. A second question: When defining my own registry and populating the RegsitryCache like you explained, what Central should I use? CentralDigestCachedImpl? Do I need both caching mechanisms? How do they differ? Thanks for your help, .../Ola On Oct 30, 2007, at 01:43 , Paul Gordon wrote: > Hi Ola, > > If you want to explicitly cache the ontologies, you need to work with > the Registry and RegistryCache objects like so: > > ******** > //To delete stale files > RegistryCache.deleteExpiredCacheFiles(allowedAgeInMilliseconds); > > // In what file would the ontology be cached, if it was cached? > File namespacesDefFile = RegistryCache.getOntologyFile > (preferredRegistry, > > Central.NAMESPACES_RESOURCE_NAME); > URL namespacesDefURL = namespacesDefFile.toURI().toURL(); > if(namespacesDefFile.exists()){ > // Use the existing cached file rather than actually going to > the > registry > MobyNamespace.loadNamespaces(namespacesDefURL, > preferredRegistry); > } > else{ > // Create the cached file from the remote source, then load it > into MobyNamespace so MobyNamespace.getNamespace() can retrieve it. > RegistryCache.cacheRegistryOntology(preferredRegistry, > Central.NAMESPACES_RESOURCE_NAME); > MobyNamespace.loadNamespaces(namespacesDefURL, > preferredRegistry); > } > ******** > > The other relevant fields/methods are > Central.DATA_TYPES_RESOURCE_NAME/Central.SERVICE_TYPES_RESOURCE_NAME > and MobyDataType.loadDataTypes()/MobyServiceType.loadServiceTypes(). > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Wed Oct 31 09:50:55 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 31 Oct 2007 07:50:55 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> <47261317.3030406@ucalgary.ca> <77B231CC-2BE8-4121-90A5-A6899C336C7D@farmbio.uu.se> <47267E18.4010509@ucalgary.ca> Message-ID: <4728883F.8050500@ucalgary.ca> Hi Ola, The registry is associated with datatypes, namespaces, etc., not individual objects, so I don't think the call lineage you give below causes any problem (since the instantiated data type is based through). Feel free to send me a sample program if you run into a case where this association is a problem (i.e. normally to get a registry you'd say object.getDataType().getRegistry(), which actually allows you to do crazy stuff like have data instances from multiple registries concurrently). With regards to your second question, CentralDigestCachedImpl is completely independent of RegistryCache, but we're working to reconcile these. If you use RegistryCache, you only need a CentralImpl for things like findService(), not for datatype, namespace, etc. definitions. You can pick any CentralImpl that suits you, as the service lookup functionality is independent from the definitions (which come from RDF in RegistryCache). __________ I think I have found a bug in jMoby, but please correct me if I'm wrong. The following call with reg being my custom Regsitry: MobyDataComposite comp = new MobyDataComposite("DNASequence", reg); calls public MobyDataComposite(String typeName, Registry r){ this(MobyDataType.getDataType(typeName, r)); } calls public MobyDataComposite(MobyDataType type){ this(type, ""); } calls public MobyDataComposite(MobyDataType type, String name){ this(type, name, "", ""); } calls public MobyDataComposite(MobyDataType type, String name, String namespace, String id){ super(namespace, id); setName(name); setDataType(type); members = new ConcurrentHashMap(); } where super calls public MobyDataObject(String namespace, String id){ this(namespace, id, null); } calls public MobyDataObject(String namespace, String id, Registry registry){ super(""); thus having registry=null. This means I will always use the default registry and not my custom registry that I inputted. This prevents me from using my cached registry which you explained below. From dmitry.repchevski at bsc.es Wed Oct 31 10:36:48 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 31 Oct 2007 15:36:48 +0100 Subject: [MOBY-dev] findService question References: 472773E1.3010809@bsc.es Message-ID: <47289300.4020603@bsc.es> Hello! I have another question about the findService... In the documentation we have: ************************************************************* ************************************************************* The scheme for the operation says: ************************************************************* ... The same for input... ************************************************************* It is not against the err... specification, but in this case there could be only one "Input" per "InputObjects". I just need to clarify it - or the schema is wrong or we have a useless wrapper around "Input" ("inputObjects") in message. Dmitry From edward.kawas at gmail.com Wed Oct 31 10:47:54 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 31 Oct 2007 07:47:54 -0700 Subject: [MOBY-dev] findService question In-Reply-To: <47289300.4020603@bsc.es> References: 472773E1.3010809@bsc.es <47289300.4020603@bsc.es> Message-ID: <000c01c81bcd$060d26f0$6400a8c0@notebook> Hey Dmitry, In the schema I tried to make the schema say that if there exists a section called inputObjects/outputObjects then the sections Input/Output are mandatory. Re-reading the documentation though, it seems that they really both should have max/min of 1. Did I address your question? Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > Dmitry Repchevsky > Sent: Wednesday, October 31, 2007 7:37 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] findService question > > Hello! > > I have another question about the findService... > In the documentation we have: > ************************************************************* > > > > > > > > > > > > > ************************************************************* > > The scheme for the operation says: > > ************************************************************* > > > > > > ... The same for input... > ************************************************************* > > It is not against the err... specification, but in this case > there could be only one "Input" per "InputObjects". > I just need to clarify it - or the schema is wrong or we have > a useless wrapper around "Input" ("inputObjects") in message. > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Wed Oct 31 11:15:53 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 31 Oct 2007 16:15:53 +0100 Subject: [MOBY-dev] findService question References: 47289300.4020603@bsc.es Message-ID: <47289C29.50104@bsc.es> Not exactly... :-( The question was "could it be more than one Input/Output elements inside inputObjects/outputObjects?" If not, my comment was that in this case there is no sense to have inputObjects/outputObjects at all... that was my confusion. Thank you, Dmitry From markw at illuminae.com Wed Oct 31 12:14:58 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 31 Oct 2007 09:14:58 -0700 Subject: [MOBY-dev] [MOBY-guts] biomoby commit In-Reply-To: <200709241853.l8OIrXSm019980@dev.open-bio.org> References: <200709241853.l8OIrXSm019980@dev.open-bio.org> Message-ID: > Modified Files: > WSRF.pm > Log Message: > * Latest WSRF::Lite package has a proper VERSION declaration, > so we can restrict the version of the package to the one > which is known to work. > * WSRF::Lite is not in CPAN, so we have added a warning about > where it can be fetched/found (beware older versions!). While I was in Cambridge two weeks ago I spoke to the WSRF::Lite developers and asked them if they would be kind enough to make a CPAN release for us. Hopefully they will say yes! Mark From markw at illuminae.com Wed Oct 31 12:10:43 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 31 Oct 2007 09:10:43 -0700 Subject: [MOBY-dev] findService question In-Reply-To: <47289C29.50104@bsc.es> References: <47289C29.50104@bsc.es> Message-ID: Yes, it is possible, at multiple levels: 1) a single service invocation might have multiple distinct inputs 2) a single service invocation message might have multiple service invocations Both of these are contained within the single input XML described in the WSDL. Moby is really "document based" not RPC; however, SOAP::Lite doesn't support document based messaging at the moment (working on it!) so we're stuck using RPC messaging for the time being. I hope I have understood your question - I'm only half-paying-attention as I'm sitting in the K-CAP conference listening to presentations :-) Mark On Wed, 31 Oct 2007 08:15:53 -0700, Dmitry Repchevsky wrote: > Not exactly... :-( > > The question was "could it be more than one Input/Output elements inside > inputObjects/outputObjects?" > If not, my comment was that in this case there is no sense to have > inputObjects/outputObjects at all... that was my confusion. > > Thank you, > > Dmitry > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Wed Oct 31 12:47:51 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 31 Oct 2007 17:47:51 +0100 Subject: [MOBY-dev] findService question References: 47289C29.50104@bsc.es Message-ID: <4728B1B7.1000705@bsc.es> Well, Mark, I think you didn't understand our discussion... Here is an excerpt from the the moby doc for findService service (Registry): ************************************************************* The Query object structure is as follows: ************************************************************* So the question is/was could it be more Input inside inputObjects? ex: ************************************************************* ... ************************************************************* My point was if there could be only one why we needed inputObjects tag at all? it could be easy: ************************************************************* ************************************************************* Ok. untill it's clear I'm using the schema from Edward as reference... Cheers, Dmitry From edward.kawas at gmail.com Wed Oct 31 17:35:27 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 31 Oct 2007 14:35:27 -0700 Subject: [MOBY-dev] findService question In-Reply-To: <4728B1B7.1000705@bsc.es> References: 47289C29.50104@bsc.es <4728B1B7.1000705@bsc.es> Message-ID: <000001c81c06$1294c3e0$b466a8c0@notebook> Hi, The answer is no! Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > Dmitry Repchevsky > Sent: Wednesday, October 31, 2007 9:48 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] findService question > > Well, Mark, I think you didn't understand our discussion... > > Here is an excerpt from the the moby doc for findService > service (Registry): > > ************************************************************* > The Query object structure is as follows: > > > > > > > > > > > > ************************************************************* > > So the question is/was could it be more Input inside inputObjects? > > ex: > ************************************************************* > > > > > > > > > > > ... > > > ************************************************************* > > My point was if there could be only one why we needed > inputObjects tag at all? > > it could be easy: > ************************************************************* > > > > > > > ************************************************************* > > Ok. untill it's clear I'm using the schema from Edward as reference... > > > Cheers, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Wed Oct 31 18:40:42 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 31 Oct 2007 23:40:42 +0100 Subject: [MOBY-dev] findService question References: 4728B1B7.1000705@bsc.es Message-ID: <4729046A.3070205@bsc.es> >The answer is no! Could not be more clear :-) Thanx, Dmitry From markw at illuminae.com Wed Oct 31 20:09:23 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 31 Oct 2007 17:09:23 -0700 Subject: [MOBY-dev] findService question In-Reply-To: <4729046A.3070205@bsc.es> References: <4729046A.3070205@bsc.es> Message-ID: Sorry for adding to the confusion :-) LOL! I really should just let Eddie handle these questions, but sometimes I feel inclined to participate :-) I should know better... M On Wed, 31 Oct 2007 15:40:42 -0700, Dmitry Repchevsky wrote: > >The answer is no! > > Could not be more clear :-) > > Thanx, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Mon Oct 1 11:50:08 2007 From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de) Date: Mon, 1 Oct 2007 13:50:08 +0200 (CEST) Subject: [MOBY-dev] How to get a concrete MobyDataType Message-ID: <57531.195.37.46.22.1191239408.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi all, i have the following question: I have a MobyDataInstance, retrieved from a service call. I know that this service returns a specific datatype (e.g. GO_Term). How to I get the GO_Term object from the MobyDataInstance. I know i can cast the MobyDataInstance to a MobyDataObject (or MobyDataObjectSet respectively) and can get the MobyDataTyp from that - but this is not castable to GO_Term. I could not find any method which returns me anything which is then castable as GO_Term. So - how do I retrieve the actual datatype class from a service result ? Thanks andreas From gordonp at ucalgary.ca Mon Oct 1 13:25:04 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 01 Oct 2007 07:25:04 -0600 Subject: [MOBY-dev] How to get a concrete MobyDataType In-Reply-To: <57531.195.37.46.22.1191239408.squirrel@mpizmail.mpiz-koeln.mpg.de> References: <57531.195.37.46.22.1191239408.squirrel@mpizmail.mpiz-koeln.mpg.de> Message-ID: <4700F530.5000207@ucalgary.ca> Hi Andreas, > I know i can cast the MobyDataInstance to a MobyDataObject (or > MobyDataObjectSet respectively) and can get the MobyDataTyp from that - but > this is not castable to GO_Term. > There is no GO_Term object when you use the General methods you describe with MobyDataInstance, etc.. I think you are trying to mix the general methods with the generated methods. What do you need a GO_Term object for (the MobyDataType should contain all the information you need...unless you're using something else from the generated, i.e. MoSeS, classes)? In general, you need to pick one way or the other in jMOBY, they don't mix well. > I could not find any method which returns me anything which is then castable > as GO_Term. > > So - how do I retrieve the actual datatype class from a service result ? > > Thanks > andreas > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From groscurt at mpiz-koeln.mpg.de Mon Oct 1 13:57:51 2007 From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de) Date: Mon, 1 Oct 2007 15:57:51 +0200 (CEST) Subject: [MOBY-dev] How to get a concrete MobyDataType Message-ID: <48469.195.37.46.22.1191247071.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi Paul, thanks for your answer. Honestly i wanted to have the actual GO_Term object becaus of laziness ;-);-) I know that I can retrieve all information with the general classes, I just hoped that somehow there is written that its a GO_Term and i can cast it and use getxxx somehow :-):-) Thanks for clarification andreas On Monday 01 October 2007 15:25, Paul Gordon wrote: > Hi Andreas, > > > I know i can cast the MobyDataInstance to a MobyDataObject (or > > MobyDataObjectSet respectively) and can get the MobyDataTyp from that - > > but this is not castable to GO_Term. > > There is no GO_Term object when you use the General methods you describe > with MobyDataInstance, etc.. > I think you are trying to mix the general methods with the generated > methods. What do you need a GO_Term > object for (the MobyDataType should contain all the information you > need...unless you're using something else > from the generated, i.e. MoSeS, classes)? In general, you need to pick > one way or the other in jMOBY, they > don't mix well. > > > I could not find any method which returns me anything which is then > > castable as GO_Term. > > > > So - how do I retrieve the actual datatype class from a service result ? > > > > Thanks > > andreas > > > > _______________________________________________ > > 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 groscurt at mpiz-koeln.mpg.de Mon Oct 1 14:07:29 2007 From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de) Date: Mon, 1 Oct 2007 16:07:29 +0200 (CEST) Subject: [MOBY-dev] Logging access of Web Services Message-ID: <38845.195.37.46.22.1191247649.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi all, our group (especially Anika) is developing some Moby services. Out of curiosity we would like to know when which service was called from which ip. Our apache forwards the axis request directly to Jboss where the services are executed, so we dont find any log entries in the apache logs I know one can easily log with the moby api - I was wondering if somehow and somewhere deep in the service implementation (java) I can retrieve the information who called the service (e.g. getting the httprequest). is there a possibility to retrieve these information or is there any common workaround to get such logging ? Thanks andreas From martin.senger at gmail.com Mon Oct 1 19:37:13 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 1 Oct 2007 20:37:13 +0100 Subject: [MOBY-dev] Logging access of Web Services In-Reply-To: <38845.195.37.46.22.1191247649.squirrel@mpizmail.mpiz-koeln.mpg.de> References: <38845.195.37.46.22.1191247649.squirrel@mpizmail.mpiz-koeln.mpg.de> Message-ID: <4d93f07c0710011237t201643c3tdf3e206abb54333f@mail.gmail.com> > Out of > curiosity we would like to know when which service was called from which > ip. If your services are generated by MoSeS, then each of them has a method for that (getCallerAddr()). The details API is here: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/API/org/biomoby/service/BaseService.html . Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Thu Oct 11 18:51:28 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 11 Oct 2007 11:51:28 -0700 Subject: [MOBY-dev] Can someone represent Moby in Rome? Message-ID: Hi all core developers! I've been invited to present Moby at a meeting in Rome on November 28th. Unfortunately, I have a meeting on the 27th here in Vancouver that prevents me from getting to Rome in time. I've asked Martin and Eddie and neither of them are able to do it. It's a presentation to the CASIMIR project (http://www.casimir.org.uk). They are considering things like DAS and MART, and are interested in adding Moby to their overall list of possible data-integration choices. I'd really like to convince them that Moby is a good option! Can anyone else from the core development team attend this meeting and present a good case for Moby? Someone from INB or PlaNet would be **perfect** since you can give first-hand examples of integrating large projects over Moby. Please let me know ASAP. Cheers all! Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From gordonp at ucalgary.ca Thu Oct 11 19:10:49 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 11 Oct 2007 13:10:49 -0600 Subject: [MOBY-dev] Can someone represent Moby in Rome? In-Reply-To: References: Message-ID: <470E7539.4060903@ucalgary.ca> I can go if no Europeans volunteer... > Hi all core developers! > > I've been invited to present Moby at a meeting in Rome on November 28th. > Unfortunately, I have a meeting on the 27th here in Vancouver that > prevents me from getting to Rome in time. I've asked Martin and Eddie and > neither of them are able to do it. > > It's a presentation to the CASIMIR project (http://www.casimir.org.uk). > They are considering things like DAS and MART, and are interested in > adding Moby to their overall list of possible data-integration choices. > I'd really like to convince them that Moby is a good option! > > Can anyone else from the core development team attend this meeting and > present a good case for Moby? Someone from INB or PlaNet would be > **perfect** since you can give first-hand examples of integrating large > projects over Moby. > > Please let me know ASAP. > > Cheers all! > > Mark > > From gordonp at ucalgary.ca Thu Oct 11 19:10:49 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 11 Oct 2007 13:10:49 -0600 Subject: [MOBY-dev] Can someone represent Moby in Rome? In-Reply-To: References: Message-ID: <470E7539.4060903@ucalgary.ca> I can go if no Europeans volunteer... > Hi all core developers! > > I've been invited to present Moby at a meeting in Rome on November 28th. > Unfortunately, I have a meeting on the 27th here in Vancouver that > prevents me from getting to Rome in time. I've asked Martin and Eddie and > neither of them are able to do it. > > It's a presentation to the CASIMIR project (http://www.casimir.org.uk). > They are considering things like DAS and MART, and are interested in > adding Moby to their overall list of possible data-integration choices. > I'd really like to convince them that Moby is a good option! > > Can anyone else from the core development team attend this meeting and > present a good case for Moby? Someone from INB or PlaNet would be > **perfect** since you can give first-hand examples of integrating large > projects over Moby. > > Please let me know ASAP. > > Cheers all! > > Mark > > From Pieter.Neerincx at wur.nl Thu Oct 11 23:04:19 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Fri, 12 Oct 2007 01:04:19 +0200 Subject: [MOBY-dev] Can someone represent Moby in Rome? In-Reply-To: <470E7539.4060903@ucalgary.ca> References: <470E7539.4060903@ucalgary.ca> Message-ID: Hi, I'm in Europe, but have a meeting in Paris the day before and I'll promote Moby there :), but I won't be able to get to Rome in time. Cheers, Pi On 11 Oct 2007, at 21:10, Paul Gordon wrote: > I can go if no Europeans volunteer... >> Hi all core developers! >> >> I've been invited to present Moby at a meeting in Rome on November >> 28th. >> Unfortunately, I have a meeting on the 27th here in Vancouver that >> prevents me from getting to Rome in time. I've asked Martin and >> Eddie and >> neither of them are able to do it. >> >> It's a presentation to the CASIMIR project (http:// >> www.casimir.org.uk). >> They are considering things like DAS and MART, and are interested in >> adding Moby to their overall list of possible data-integration >> choices. >> I'd really like to convince them that Moby is a good option! >> >> Can anyone else from the core development team attend this meeting >> and >> present a good case for Moby? Someone from INB or PlaNet would be >> **perfect** since you can give first-hand examples of integrating >> large >> projects over Moby. >> >> Please let me know ASAP. >> >> Cheers all! >> >> Mark >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- From markw at illuminae.com Fri Oct 12 14:05:13 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 12 Oct 2007 07:05:13 -0700 Subject: [MOBY-dev] Can someone represent Moby in Rome? In-Reply-To: References: <470E7539.4060903@ucalgary.ca> Message-ID: If there are no other offers, I'll tell the CASIMIR people that Paul will attend. Paul, can you confirm 100% that you are available? M On Thu, 11 Oct 2007 16:04:19 -0700, Pieter Neerincx wrote: > Hi, > > I'm in Europe, but have a meeting in Paris the day before and I'll > promote Moby there :), but I won't be able to get to Rome in time. > > Cheers, > > Pi > > On 11 Oct 2007, at 21:10, Paul Gordon wrote: > >> I can go if no Europeans volunteer... >>> Hi all core developers! >>> >>> I've been invited to present Moby at a meeting in Rome on November >>> 28th. >>> Unfortunately, I have a meeting on the 27th here in Vancouver that >>> prevents me from getting to Rome in time. I've asked Martin and >>> Eddie and >>> neither of them are able to do it. >>> >>> It's a presentation to the CASIMIR project (http:// >>> www.casimir.org.uk). >>> They are considering things like DAS and MART, and are interested in >>> adding Moby to their overall list of possible data-integration >>> choices. >>> I'd really like to convince them that Moby is a good option! >>> >>> Can anyone else from the core development team attend this meeting >>> and >>> present a good case for Moby? Someone from INB or PlaNet would be >>> **perfect** since you can give first-hand examples of integrating >>> large >>> projects over Moby. >>> >>> Please let me know ASAP. >>> >>> Cheers all! >>> >>> Mark >>> >>> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 060 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------- > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From schoof at mpiz-koeln.mpg.de Fri Oct 12 15:10:04 2007 From: schoof at mpiz-koeln.mpg.de (Heiko Schoof) Date: Fri, 12 Oct 2007 17:10:04 +0200 Subject: [MOBY-dev] Can someone represent Moby in Rome? In-Reply-To: References: <470E7539.4060903@ucalgary.ca> Message-ID: <4E46C60F-9A5F-4159-B2A2-671ABC8618A8@mpiz-koeln.mpg.de> Hi Mark, we have our scientific advisory board here on that day, so I can't make it, sorry. Best, Heiko On 12. Oct 2007, at 16:05 Uhr, Mark Wilkinson wrote: > If there are no other offers, I'll tell the CASIMIR people that > Paul will > attend. > > Paul, can you confirm 100% that you are available? > > M > > > > > On Thu, 11 Oct 2007 16:04:19 -0700, Pieter Neerincx > wrote: > >> Hi, >> >> I'm in Europe, but have a meeting in Paris the day before and I'll >> promote Moby there :), but I won't be able to get to Rome in time. >> >> Cheers, >> >> Pi >> >> On 11 Oct 2007, at 21:10, Paul Gordon wrote: >> >>> I can go if no Europeans volunteer... >>>> Hi all core developers! >>>> >>>> I've been invited to present Moby at a meeting in Rome on November >>>> 28th. >>>> Unfortunately, I have a meeting on the 27th here in Vancouver that >>>> prevents me from getting to Rome in time. I've asked Martin and >>>> Eddie and >>>> neither of them are able to do it. >>>> >>>> It's a presentation to the CASIMIR project (http:// >>>> www.casimir.org.uk). >>>> They are considering things like DAS and MART, and are >>>> interested in >>>> adding Moby to their overall list of possible data-integration >>>> choices. >>>> I'd really like to convince them that Moby is a good option! >>>> >>>> Can anyone else from the core development team attend this meeting >>>> and >>>> present a good case for Moby? Someone from INB or PlaNet would be >>>> **perfect** since you can give first-hand examples of integrating >>>> large >>>> projects over Moby. >>>> >>>> Please let me know ASAP. >>>> >>>> Cheers all! >>>> >>>> Mark >>>> >>>> >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> >> ------------------------------------------------------------- >> Wageningen University and Research centre (WUR) >> Laboratory of Bioinformatics >> Transitorium (building 312) room 1034 >> >> Dreijenlaan 3 >> 6703 HA Wageningen >> The Netherlands >> >> phone: 0317-483 060 >> fax: 0317-483 584 >> mobile: 06-143 66 783 >> mail: pieter.neerincx at wur.nl >> skype: pieter.online >> ------------------------------------------------------------- >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the > addressee and > may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have > received this > communication in error, please notify the sender immediately by reply > e-mail and delete the original and all copies from your system. > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From ola.spjuth at farmbio.uu.se Mon Oct 15 16:19:39 2007 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Mon, 15 Oct 2007 18:19:39 +0200 Subject: [MOBY-dev] Datatype instantiation in jMoby Message-ID: Hi, In jMoby, I look up a service, and get the first primaryInputs DataType by service.getPrimaryData()[0].getDataType(); This gives me a Datatype with correct name and LSID, but nothing more (no children). If I do the following: String dataTypeName=service.getPrimaryInputs()[i].getDataType ().getName(); primaryData[i] = new MobyDataComposite(dataTypeName); MobyDataType dataType=primaryData[i].getDataType(); Then jMoby reads the ontology and I get a dataType that has relations (children). How can I achieve this without having to instantiate a bogus MobyDataComposite? What is the purpose of this behaviour? Would something like this be an acceptable API-request: service.getPrimaryData()[0].getDataType(); service.getPrimaryData()[0].populateFromOntology(); Next question: I'd like to create MobyDataObjects that I can later populate with values. The line MobyDataObject obj = MobyDataObject.createInstanceFromString (childTypeName,"0"); works fine, but I'd like to do is create an object with no values, like the following: for(MobyRelationship child: dataType.getAllChildren()){ String childName = child.getName(); String childTypeName = child.getDataTypeName(); if(PrimitiveTypes.isPrimitive(childTypeName)){ MobyDataObject obj = new MobyDataObject(childTypeName); primaryComposites[i].put(childName,obj); } } Is it wrong to instantiate the values first and fill them at a later point? Last question: Can a service take only one primitive DataType as primaryInput or does it always require a MobyDataComposite? Is it an error in that case to supply a MobyDataComposite with only one primitive MobyDataObject in it (i.e. is it OK to always send a MobyDataComposite as PrimaryInput to a service)? Thanks, .../Ola From groscurt at mpiz-koeln.mpg.de Tue Oct 16 06:45:51 2007 From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de) Date: Tue, 16 Oct 2007 08:45:51 +0200 (CEST) Subject: [MOBY-dev] Datatype instantiation in jMoby In-Reply-To: References: Message-ID: <64120.89.52.180.204.1192517151.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi Ola, for your first question, MobyDataType.getDataType("DATATYPE"); should retrieve the datataype (check the API for this method). At this morning, I dont have an answer for question two. Question three: of course services can consume a primtive type - like MobyObject or MobyString etc. So I would not always use the composite and just what the service actually require If somethings wrong please correct someone.. andreas > Hi, > > In jMoby, I look up a service, and get the first primaryInputs > DataType by > > service.getPrimaryData()[0].getDataType(); > > This gives me a Datatype with correct name and LSID, but nothing more > (no children). > > If I do the following: > > String dataTypeName=service.getPrimaryInputs()[i].getDataType > ().getName(); > primaryData[i] = new MobyDataComposite(dataTypeName); > MobyDataType dataType=primaryData[i].getDataType(); > > Then jMoby reads the ontology and I get a dataType that has relations > (children). How can I achieve this without having to instantiate a > bogus MobyDataComposite? What is the purpose of this behaviour? Would > something like this be an acceptable API-request: > > service.getPrimaryData()[0].getDataType(); > service.getPrimaryData()[0].populateFromOntology(); > > > Next question: > I'd like to create MobyDataObjects that I can later populate with > values. > > The line > > MobyDataObject obj = MobyDataObject.createInstanceFromString > (childTypeName,"0"); > > works fine, but I'd like to do is create an object with no values, > like the following: > > for(MobyRelationship child: dataType.getAllChildren()){ > String childName = child.getName(); > String childTypeName = child.getDataTypeName(); > if(PrimitiveTypes.isPrimitive(childTypeName)){ > MobyDataObject obj = new MobyDataObject(childTypeName); > primaryComposites[i].put(childName,obj); > } > } > > Is it wrong to instantiate the values first and fill them at a later > point? > > Last question: > Can a service take only one primitive DataType as primaryInput or > does it always require a MobyDataComposite? Is it an error in that > case to supply a MobyDataComposite with only one primitive > MobyDataObject in it (i.e. is it OK to always send a > MobyDataComposite as PrimaryInput to a service)? > > Thanks, > > .../Ola > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From ola.spjuth at farmbio.uu.se Tue Oct 16 08:06:23 2007 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Tue, 16 Oct 2007 10:06:23 +0200 Subject: [MOBY-dev] Datatype instantiation in jMoby In-Reply-To: <64120.89.52.180.204.1192517151.squirrel@mpizmail.mpiz-koeln.mpg.de> References: <64120.89.52.180.204.1192517151.squirrel@mpizmail.mpiz-koeln.mpg.de> Message-ID: <5D00967F-CA9E-4471-A06B-869ECCE8CE0D@farmbio.uu.se> On Oct 16, 2007, at 08:45 , groscurt at mpiz-koeln.mpg.de wrote: > Hi Ola, > > for your first question, > > MobyDataType.getDataType("DATATYPE"); > > should retrieve the datataype (check the API for this method). Great, thanks. Must have missed to check the static methods. > At this morning, I dont have an answer for question two. > > Question three: > of course services can consume a primtive type - like MobyObject or > MobyString etc. So I would not always use the composite and just > what the > service actually require Yes, but would it be acceptable to wrap that MobyObject or MobyString in a MobyComposite and it would still work? Thanks, .../Ola > > > If somethings wrong please correct someone.. > > andreas > > > >> Hi, >> >> In jMoby, I look up a service, and get the first primaryInputs >> DataType by >> >> service.getPrimaryData()[0].getDataType(); >> >> This gives me a Datatype with correct name and LSID, but nothing more >> (no children). >> >> If I do the following: >> >> String dataTypeName=service.getPrimaryInputs()[i].getDataType >> ().getName(); >> primaryData[i] = new MobyDataComposite(dataTypeName); >> MobyDataType dataType=primaryData[i].getDataType(); >> >> Then jMoby reads the ontology and I get a dataType that has relations >> (children). How can I achieve this without having to instantiate a >> bogus MobyDataComposite? What is the purpose of this behaviour? Would >> something like this be an acceptable API-request: >> >> service.getPrimaryData()[0].getDataType(); >> service.getPrimaryData()[0].populateFromOntology(); >> >> >> Next question: >> I'd like to create MobyDataObjects that I can later populate with >> values. >> >> The line >> >> MobyDataObject obj = MobyDataObject.createInstanceFromString >> (childTypeName,"0"); >> >> works fine, but I'd like to do is create an object with no values, >> like the following: >> >> for(MobyRelationship child: dataType.getAllChildren()){ >> String childName = child.getName(); >> String childTypeName = child.getDataTypeName(); >> if(PrimitiveTypes.isPrimitive(childTypeName)){ >> MobyDataObject obj = new MobyDataObject(childTypeName); >> primaryComposites[i].put(childName,obj); >> } >> } >> >> Is it wrong to instantiate the values first and fill them at a later >> point? >> >> Last question: >> Can a service take only one primitive DataType as primaryInput or >> does it always require a MobyDataComposite? Is it an error in that >> case to supply a MobyDataComposite with only one primitive >> MobyDataObject in it (i.e. is it OK to always send a >> MobyDataComposite as PrimaryInput to a service)? >> >> Thanks, >> >> .../Ola >> >> >> _______________________________________________ >> 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 groscurt at mpiz-koeln.mpg.de Wed Oct 17 11:02:05 2007 From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de) Date: Wed, 17 Oct 2007 13:02:05 +0200 (CEST) Subject: [MOBY-dev] Problems with parsing a service result Message-ID: <47508.195.37.46.22.1192618925.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi all, i want to retrieve the results for the service: get_agi_code_by_keyword/mpiz-koeln.mpg.de it returns a collection of Descriptors for a given keyword. Using the dashboard i retrieve a result (e.g. with keyword superman) SUP (SUPERMAN); DNA binding / nucleic acid binding / transcription factor/ zinc ion binding using the simple java client MobyService agiService = new MobyService(); agiService.setCategory( "" ); agiService.setAuthority( "mpiz-koeln.mpg.de" ); agiService.setName( "get_agi_code_by_keyword" ); agiService = central.findService( agiService )[0]; MobyRequest request = new MobyRequest( central ); request.setService( agiService ); request.setInput( new MobyDataObject( "Global_Keyword", "superman" ) ); MobyContentInstance contentInstance = request.invokeService(); MobyDataJob mobyJob = contentInstance.get( contentInstance.keySet().iterator().next() ); MobyDataInstance[] dataInstances = mobyJob.getPrimaryData(); the dataInstance contains nothing :-(:-( (dataInstances.length = 0) the simple java client works for other services, but fails for this one... does anybody know what is wrong ? thanks andreas From edward.kawas at gmail.com Wed Oct 17 13:19:05 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 17 Oct 2007 06:19:05 -0700 Subject: [MOBY-dev] Problems with parsing a service result In-Reply-To: <47508.195.37.46.22.1192618925.squirrel@mpizmail.mpiz-koeln.mpg.de> References: <47508.195.37.46.22.1192618925.squirrel@mpizmail.mpiz-koeln.mpg.de> Message-ID: <001001c810c0$4c197080$6400a8c0@notebook> Hi Andreas, Should new MobyDataObject( "Global_Keyword", "superman" ) ); really be new MobyDataObject( "Global_Keyword", "keyword" ) ); ?? Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > groscurt at mpiz-koeln.mpg.de > Sent: Wednesday, October 17, 2007 4:02 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] Problems with parsing a service result > > Hi all, > > i want to retrieve the results for the service: > > get_agi_code_by_keyword/mpiz-koeln.mpg.de > > it returns a collection of Descriptors for a given keyword. > > Using the dashboard i retrieve a result (e.g. with keyword superman) > > > > > > > > > moby:namespace="AGI_LocusCode"> > moby:articleName="description">SUP (SUPERMAN); DNA binding / > nucleic acid binding / transcription factor/ zinc ion > binding > > > > > > > > using the simple java client > > MobyService agiService = new MobyService(); > agiService.setCategory( "" ); agiService.setAuthority( > "mpiz-koeln.mpg.de" ); agiService.setName( > "get_agi_code_by_keyword" ); agiService = > central.findService( agiService )[0]; MobyRequest request = > new MobyRequest( central ); request.setService( agiService ); > request.setInput( new MobyDataObject( "Global_Keyword", > "superman" ) ); MobyContentInstance contentInstance = > request.invokeService(); MobyDataJob mobyJob = > contentInstance.get( > contentInstance.keySet().iterator().next() ); > MobyDataInstance[] dataInstances = mobyJob.getPrimaryData(); > > the dataInstance contains nothing :-(:-( (dataInstances.length = 0) > > the simple java client works for other services, but fails > for this one... > > does anybody know what is wrong ? > > thanks > andreas > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Wed Oct 17 13:38:41 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 17 Oct 2007 07:38:41 -0600 Subject: [MOBY-dev] [Fwd: Re: Problems with parsing a service result] Message-ID: <47161061.80200@ucalgary.ca> Never mind, I am smoking crack. Didn't check to see that Global_Keyword has no child elements. MobyDataComposite comp = MobyDataComposite("Global_Keyword", "unimportant_article_name", "namespace_if_any", "superman"); -------- Original Message -------- Subject: Re: [MOBY-dev] Problems with parsing a service result Date: Wed, 17 Oct 2007 07:26:21 -0600 From: Paul Gordon To: Core developer announcements References: <47508.195.37.46.22.1192618925.squirrel at mpizmail.mpiz-koeln.mpg.de> <001001c810c0$4c197080$6400a8c0 at notebook> No, the problem is that MobyDataObject is ONLY for base Object (as it says several times in the Java docs :-)) You're using a composite that happens to only have one member. Composites implement the Java Map interface to get/set members: MobyDataComposite comp = MobyDataComposite("Global_Keyword"); comp.put("keyword", new MobyDataString("superman")); > Hi Andreas, > > Should > > new MobyDataObject( "Global_Keyword", "superman" ) ); > > really be > > new MobyDataObject( "Global_Keyword", "keyword" ) ); ?? > > Eddie > > >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of >> groscurt at mpiz-koeln.mpg.de >> Sent: Wednesday, October 17, 2007 4:02 AM >> To: moby-dev at lists.open-bio.org >> Subject: [MOBY-dev] Problems with parsing a service result >> >> Hi all, >> >> i want to retrieve the results for the service: >> >> get_agi_code_by_keyword/mpiz-koeln.mpg.de >> >> it returns a collection of Descriptors for a given keyword. >> >> Using the dashboard i retrieve a result (e.g. with keyword superman) >> >> >> >> >> >> >> >> >> > moby:namespace="AGI_LocusCode"> >> > moby:articleName="description">SUP (SUPERMAN); DNA binding / >> nucleic acid binding / transcription factor/ zinc ion >> binding >> >> >> >> >> >> >> >> using the simple java client >> >> MobyService agiService = new MobyService(); >> agiService.setCategory( "" ); agiService.setAuthority( >> "mpiz-koeln.mpg.de" ); agiService.setName( >> "get_agi_code_by_keyword" ); agiService = >> central.findService( agiService )[0]; MobyRequest request = >> new MobyRequest( central ); request.setService( agiService ); >> request.setInput( new MobyDataObject( "Global_Keyword", >> "superman" ) ); MobyContentInstance contentInstance = >> request.invokeService(); MobyDataJob mobyJob = >> contentInstance.get( >> contentInstance.keySet().iterator().next() ); >> MobyDataInstance[] dataInstances = mobyJob.getPrimaryData(); >> >> the dataInstance contains nothing :-(:-( (dataInstances.length = 0) >> >> the simple java client works for other services, but fails >> for this one... >> >> does anybody know what is wrong ? >> >> thanks >> andreas >> >> _______________________________________________ >> 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 > > !DSPAM:60005,47160a092601617573718! > > > > From gordonp at ucalgary.ca Wed Oct 17 13:26:21 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 17 Oct 2007 07:26:21 -0600 Subject: [MOBY-dev] Problems with parsing a service result In-Reply-To: <001001c810c0$4c197080$6400a8c0@notebook> References: <47508.195.37.46.22.1192618925.squirrel@mpizmail.mpiz-koeln.mpg.de> <001001c810c0$4c197080$6400a8c0@notebook> Message-ID: <47160D7D.2090005@ucalgary.ca> No, the problem is that MobyDataObject is ONLY for base Object (as it says several times in the Java docs :-)) You're using a composite that happens to only have one member. Composites implement the Java Map interface to get/set members: MobyDataComposite comp = MobyDataComposite("Global_Keyword"); comp.put("keyword", new MobyDataString("superman")); > Hi Andreas, > > Should > > new MobyDataObject( "Global_Keyword", "superman" ) ); > > really be > > new MobyDataObject( "Global_Keyword", "keyword" ) ); ?? > > Eddie > > >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of >> groscurt at mpiz-koeln.mpg.de >> Sent: Wednesday, October 17, 2007 4:02 AM >> To: moby-dev at lists.open-bio.org >> Subject: [MOBY-dev] Problems with parsing a service result >> >> Hi all, >> >> i want to retrieve the results for the service: >> >> get_agi_code_by_keyword/mpiz-koeln.mpg.de >> >> it returns a collection of Descriptors for a given keyword. >> >> Using the dashboard i retrieve a result (e.g. with keyword superman) >> >> >> >> >> >> >> >> >> > moby:namespace="AGI_LocusCode"> >> > moby:articleName="description">SUP (SUPERMAN); DNA binding / >> nucleic acid binding / transcription factor/ zinc ion >> binding >> >> >> >> >> >> >> >> using the simple java client >> >> MobyService agiService = new MobyService(); >> agiService.setCategory( "" ); agiService.setAuthority( >> "mpiz-koeln.mpg.de" ); agiService.setName( >> "get_agi_code_by_keyword" ); agiService = >> central.findService( agiService )[0]; MobyRequest request = >> new MobyRequest( central ); request.setService( agiService ); >> request.setInput( new MobyDataObject( "Global_Keyword", >> "superman" ) ); MobyContentInstance contentInstance = >> request.invokeService(); MobyDataJob mobyJob = >> contentInstance.get( >> contentInstance.keySet().iterator().next() ); >> MobyDataInstance[] dataInstances = mobyJob.getPrimaryData(); >> >> the dataInstance contains nothing :-(:-( (dataInstances.length = 0) >> >> the simple java client works for other services, but fails >> for this one... >> >> does anybody know what is wrong ? >> >> thanks >> andreas >> >> _______________________________________________ >> 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 > > !DSPAM:60005,47160a092601617573718! > > > > From groscurt at mpiz-koeln.mpg.de Wed Oct 17 15:44:10 2007 From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de) Date: Wed, 17 Oct 2007 17:44:10 +0200 (CEST) Subject: [MOBY-dev] [Fwd: Re: Problems with parsing a service result] In-Reply-To: <47161061.80200@ucalgary.ca> References: <47161061.80200@ucalgary.ca> Message-ID: <53278.195.37.46.22.1192635850.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi, *doooh* i havent count how often I made the datacomposite mistake :-( stupidity.... thanks again for clearifying andreas > Never mind, I am smoking crack. Didn't check to see that Global_Keyword > has no child elements. > > MobyDataComposite comp = MobyDataComposite("Global_Keyword", > "unimportant_article_name", "namespace_if_any", "superman"); > > -------- Original Message -------- > Subject: Re: [MOBY-dev] Problems with parsing a service result > Date: Wed, 17 Oct 2007 07:26:21 -0600 > From: Paul Gordon > To: Core developer announcements > References: > <47508.195.37.46.22.1192618925.squirrel at mpizmail.mpiz-koeln.mpg.de> > <001001c810c0$4c197080$6400a8c0 at notebook> > > > > No, the problem is that MobyDataObject is ONLY for base Object (as it > says several times in the Java docs :-)) > You're using a composite that happens to only have one member. > Composites implement the Java Map interface to > get/set members: > > MobyDataComposite comp = MobyDataComposite("Global_Keyword"); > comp.put("keyword", new MobyDataString("superman")); >> Hi Andreas, >> >> Should >> >> new MobyDataObject( "Global_Keyword", "superman" ) ); >> >> really be >> >> new MobyDataObject( "Global_Keyword", "keyword" ) ); ?? >> >> Eddie >> >> >>> -----Original Message----- >>> From: moby-dev-bounces at lists.open-bio.org >>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of >>> groscurt at mpiz-koeln.mpg.de >>> Sent: Wednesday, October 17, 2007 4:02 AM >>> To: moby-dev at lists.open-bio.org >>> Subject: [MOBY-dev] Problems with parsing a service result >>> >>> Hi all, >>> >>> i want to retrieve the results for the service: >>> >>> get_agi_code_by_keyword/mpiz-koeln.mpg.de >>> >>> it returns a collection of Descriptors for a given keyword. >>> >>> Using the dashboard i retrieve a result (e.g. with keyword superman) >>> >>> >>> >>> >>> >>> >>> >>> >>> >> moby:namespace="AGI_LocusCode"> >>> >> moby:articleName="description">SUP (SUPERMAN); DNA binding / >>> nucleic acid binding / transcription factor/ zinc ion >>> binding >>> >>> >>> >>> >>> >>> >>> >>> using the simple java client >>> >>> MobyService agiService = new MobyService(); >>> agiService.setCategory( "" ); agiService.setAuthority( >>> "mpiz-koeln.mpg.de" ); agiService.setName( >>> "get_agi_code_by_keyword" ); agiService = >>> central.findService( agiService )[0]; MobyRequest request = >>> new MobyRequest( central ); request.setService( agiService ); >>> request.setInput( new MobyDataObject( "Global_Keyword", >>> "superman" ) ); MobyContentInstance contentInstance = >>> request.invokeService(); MobyDataJob mobyJob = >>> contentInstance.get( >>> contentInstance.keySet().iterator().next() ); >>> MobyDataInstance[] dataInstances = mobyJob.getPrimaryData(); >>> >>> the dataInstance contains nothing :-(:-( (dataInstances.length = 0) >>> >>> the simple java client works for other services, but fails >>> for this one... >>> >>> does anybody know what is wrong ? >>> >>> thanks >>> andreas >>> >>> _______________________________________________ >>> 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 >> >> !DSPAM:60005,47160a092601617573718! >> >> >> >> > > _______________________________________________ > 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 Thu Oct 18 21:21:15 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 18 Oct 2007 14:21:15 -0700 Subject: [MOBY-dev] GET Moby Service WSDL Message-ID: Hi all, Just FYI, I have just set-up a way to retrieve the Moby Service WSDL from a URL. This isn't an official part of the API, but we should probably consider adding it, since almost every SOAP tool expects to be able to retrieve WSDL from a URL. The pattern is: http://biomoby.org/services/wsdl/auth.uri/serviceName e.g. http://biomoby.org/services/wsdl/antirrhinum.net/getDragonAlleleLocus My **intention** is that these URLs are stable. That URL actually proxies through to mobycentral.icapture.ubc.ca so even when we move Moby Central to Calgary next month the URL will not change. Let me know if it doesn't work for you. We're going to use these URLs in an upcoming "Annotation Jamboree" that I hope you will all participate in! We want to improve the search power of Moby Central by adding lots of extra metadata to the service descriptions. My PhD student Ben is currently writing the Jamboree interface, which fits into his thesis on mass-collaborative knowledge capture, so by participating you will not only be improving Moby Central, but you will also be helping Ben Good to graduate ;-) Cheers all! Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From duncan.hull at cs.man.ac.uk Fri Oct 19 09:46:07 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Fri, 19 Oct 2007 10:46:07 +0100 Subject: [MOBY-dev] GET Moby Service WSDL: RESTful BioMOBY In-Reply-To: References: Message-ID: <47187CDF.10107@cs.man.ac.uk> Hi Mark Mark Wilkinson wrote: > Just FYI, I have just set-up a way to retrieve the Moby Service WSDL from > a URL. This isn't an official part of the API, but we should probably > consider adding it, since almost every SOAP tool expects to be able to > retrieve WSDL from a URL. > > The pattern is: > > http://biomoby.org/services/wsdl/auth.uri/serviceName > This is great. If only all services were GETtable, the web would probably be a better place. On a similar subject, you recently said that BioMOBY might be adding a sort-of RESTful API soon. Just curious, can we HTTP POST, PUT and DELETE to these (or any other) BioMOBY URI's in true RESTful style [1]? Avoiding the SOAP-and-WSDL-nightmare completely? Duncan [1] http://www.cs.man.ac.uk/~hulld/q2007-06-30.html -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ +44 (0) 161 306 5139 From duncan.hull at cs.man.ac.uk Fri Oct 19 09:46:07 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Fri, 19 Oct 2007 10:46:07 +0100 Subject: [MOBY-dev] GET Moby Service WSDL: RESTful BioMOBY In-Reply-To: References: Message-ID: <47187CDF.10107@cs.man.ac.uk> Hi Mark Mark Wilkinson wrote: > Just FYI, I have just set-up a way to retrieve the Moby Service WSDL from > a URL. This isn't an official part of the API, but we should probably > consider adding it, since almost every SOAP tool expects to be able to > retrieve WSDL from a URL. > > The pattern is: > > http://biomoby.org/services/wsdl/auth.uri/serviceName > This is great. If only all services were GETtable, the web would probably be a better place. On a similar subject, you recently said that BioMOBY might be adding a sort-of RESTful API soon. Just curious, can we HTTP POST, PUT and DELETE to these (or any other) BioMOBY URI's in true RESTful style [1]? Avoiding the SOAP-and-WSDL-nightmare completely? Duncan [1] http://www.cs.man.ac.uk/~hulld/q2007-06-30.html -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ +44 (0) 161 306 5139 From ddg at ncgr.org Fri Oct 19 15:49:07 2007 From: ddg at ncgr.org (Damian Gessler) Date: Fri, 19 Oct 2007 09:49:07 -0600 Subject: [MOBY-dev] GET Moby Service WSDL: RESTful BioMOBY In-Reply-To: <47187CDF.10107@cs.man.ac.uk> References: <47187CDF.10107@cs.man.ac.uk> Message-ID: > This is great. If only all services were GETtable, the web would > probably be a better place. > FYI, this the model of SSWAP (http://sswap.info)--the new name for what used to be called Semantic MOBY. Service descriptions are available via HTTP GETs, for which a RDF/XML OWL-DL graph is returned. (Search for anything on http://sswap.info and then click on the RDF icon next to a returned service name to see the graph). Service invocation is just as simple: either a HTTP POST to the same URL or a GET w/ the graph in-line as the query substring component of the URL (everything after the '?'). [The latter is fully RESTful and can be bookmarked, but may confuse some old servers or proxies that limit URLs to 1024 chars, etc.]. Damian. From markw at illuminae.com Wed Oct 24 15:49:03 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 24 Oct 2007 08:49:03 -0700 Subject: [MOBY-dev] Is anyone else having problems reaching Moby Central? Message-ID: Hi all, Sebastien is not able to connect to Moby Central from France. I am able to connect from various machines in Canada and the US, so it doesn't seem to be a local problem. Is anyone else having problems? M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From gordonp at ucalgary.ca Wed Oct 24 15:57:37 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 24 Oct 2007 09:57:37 -0600 Subject: [MOBY-dev] Is anyone else having problems reaching Moby Central? In-Reply-To: References: Message-ID: <471F6B71.40102@ucalgary.ca> The connection is okay from Calgary... > Hi all, > > Sebastien is not able to connect to Moby Central from France. I am able > to connect from various machines in Canada and the US, so it doesn't seem > to be a local problem. Is anyone else having problems? > > M > > > From dmitry.repchevski at bsc.es Wed Oct 24 16:19:27 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 24 Oct 2007 18:19:27 +0200 Subject: [MOBY-dev] Is anyone else having problems reaching Moby Central? Message-ID: <471F708F.2060809@bsc.es> http://moby-dev.inab.org/cgi-bin/MOBY-Central.pl work from Spain. From usadel at mpimp-golm.mpg.de Wed Oct 24 16:27:43 2007 From: usadel at mpimp-golm.mpg.de (=?ISO-8859-1?Q?Bj=F6rn_Usadel?=) Date: Wed, 24 Oct 2007 18:27:43 +0200 Subject: [MOBY-dev] Is anyone else having problems reaching Moby Central? In-Reply-To: References: Message-ID: <471F727F.9030006@mpimp-golm.mpg.de> Hi, seems to work from Potsdam, Germany. Anything specific that's broken? bj Mark Wilkinson wrote: > Hi all, > > Sebastien is not able to connect to Moby Central from France. I am able > to connect from various machines in Canada and the US, so it doesn't seem > to be a local problem. Is anyone else having problems? > > M > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the addressee and > may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have received this > communication in error, please notify the sender immediately by reply > e-mail and delete the original and all copies from your system. > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From Pieter.Neerincx at wur.nl Wed Oct 24 16:46:28 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Wed, 24 Oct 2007 18:46:28 +0200 Subject: [MOBY-dev] Is anyone else having problems reaching Moby Central? In-Reply-To: References: Message-ID: <90BDC685-1E0D-4AC7-BCC4-316BBC88F43C@wur.nl> Hi all, Wageningen (NL, Europe) is also fine, so it might be big node that went down, but it's not the entire transatlantic connection. Best wishes, Pi On 24-okt-2007, at 17:49, Mark Wilkinson wrote: > Hi all, > > Sebastien is not able to connect to Moby Central from France. I am > able > to connect from various machines in Canada and the US, so it > doesn't seem > to be a local problem. Is anyone else having problems? > > M > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the > addressee and > may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have > received this > communication in error, please notify the sender immediately by reply > e-mail and delete the original and all copies from your system. > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From Sebastien.Carrere at toulouse.inra.fr Thu Oct 25 07:03:21 2007 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Thu, 25 Oct 2007 09:03:21 +0200 Subject: [MOBY-dev] Is anyone else having problems reaching Moby Central? In-Reply-To: <90BDC685-1E0D-4AC7-BCC4-316BBC88F43C@wur.nl> References: <90BDC685-1E0D-4AC7-BCC4-316BBC88F43C@wur.nl> Message-ID: <47203FB9.9030309@toulouse.inra.fr> Bonjour ? tous, I really don't understand ... I use these parameters: MOBYCENTRAL_URI=http://mobycentral.icapture.ubc.ca/MOBY/Central MOBYCENTRAL_URL=http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl or these ones for the OpenTestRegistry: MOBYCENTRAL_URI=http://bioinfo.icapture.ubc.ca/MOBY/Central MOBYCENTRAL_URL=http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl I did not change my code (using Perl libraries since a while). I can access to the INAB registry without any problem. And I don't think it's a DNS problem because when I paste http://mobycentral.icapture.ubc.ca/ into my web-browser, I can access t this server. So, anyone has an idea ? Merci, Sebastien Pieter Neerincx wrote: > Hi all, > > Wageningen (NL, Europe) is also fine, so it might be big node that > went down, but it's not the entire transatlantic connection. > > Best wishes, > > Pi > > On 24-okt-2007, at 17:49, Mark Wilkinson wrote: > > >> Hi all, >> >> Sebastien is not able to connect to Moby Central from France. I am >> able >> to connect from various machines in Canada and the US, so it >> doesn't seem >> to be a local problem. Is anyone else having problems? >> >> M >> >> >> -- >> -- >> Mark Wilkinson >> Assistant Professor, Dept. Medical Genetics >> University of British Columbia >> PI Bioinformatics >> iCAPTURE Centre, St. Paul's Hospital >> Tel: 604 682 2344 x62129 >> Fax: 604 806 9274 >> >> ***CONFIDENTIALITY NOTICE*** >> This electronic message is intended only for the use of the >> addressee and >> may contain information that is privileged and confidential. Any >> dissemination, distribution or copying of this communication by >> unauthorized individuals is strictly prohibited. If you have >> received this >> communication in error, please notify the sender immediately by reply >> e-mail and delete the original and all copies from your system. >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien.Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From Sebastien.Carrere at toulouse.inra.fr Thu Oct 25 07:29:34 2007 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Thu, 25 Oct 2007 09:29:34 +0200 Subject: [MOBY-dev] RESOLVED : Is anyone else having problems reaching Moby Central? In-Reply-To: <90BDC685-1E0D-4AC7-BCC4-316BBC88F43C@wur.nl> References: <90BDC685-1E0D-4AC7-BCC4-316BBC88F43C@wur.nl> Message-ID: <472045DE.9070008@toulouse.inra.fr> So, The problem is resolved. It was clearly a DNS problem ... The server I use did not access to a correct DNS server. So, there's no problem between France and the rest of the world !!!! Sorry for inconveniance. Sebastien Pieter Neerincx wrote: > Hi all, > > Wageningen (NL, Europe) is also fine, so it might be big node that > went down, but it's not the entire transatlantic connection. > > Best wishes, > > Pi > > On 24-okt-2007, at 17:49, Mark Wilkinson wrote: > > >> Hi all, >> >> Sebastien is not able to connect to Moby Central from France. I am >> able >> to connect from various machines in Canada and the US, so it >> doesn't seem >> to be a local problem. Is anyone else having problems? >> >> M >> >> >> -- >> -- >> Mark Wilkinson >> Assistant Professor, Dept. Medical Genetics >> University of British Columbia >> PI Bioinformatics >> iCAPTURE Centre, St. Paul's Hospital >> Tel: 604 682 2344 x62129 >> Fax: 604 806 9274 >> >> ***CONFIDENTIALITY NOTICE*** >> This electronic message is intended only for the use of the >> addressee and >> may contain information that is privileged and confidential. Any >> dissemination, distribution or copying of this communication by >> unauthorized individuals is strictly prohibited. If you have >> received this >> communication in error, please notify the sender immediately by reply >> e-mail and delete the original and all copies from your system. >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien.Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From dmitry.repchevski at bsc.es Fri Oct 26 09:07:16 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Fri, 26 Oct 2007 11:07:16 +0200 Subject: [MOBY-dev] serviceNotes question Message-ID: <4721AE44.7070204@bsc.es> Hello! Could someone explain me it, please. Initially it supposed to be just a additional information that could be returned by service along with the response. Then (somewhere in 2005) it was extended to support exceptions (MobyException). Excuse me if I don't understand the phrase well: *********************************************************************************** BioMOBY has to consider reporting exceptions for every layer of information the service request can contain: whole invocation (mobyContent), individual queries (mobyData), and single objects provided as input to the service (Simples, Collections, or even Simples inside a Collection). *********************************************************************************** Does this mean that the tag may be in any of these structures? (As far as I understand before the exceptions the only tag where it could appear was ). What happen with [value] of the serviceNotes? May it still contain a plain text ([mixed])? Thank you. Dmitry From ola.spjuth at farmbio.uu.se Fri Oct 26 11:57:25 2007 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Fri, 26 Oct 2007 13:57:25 +0200 Subject: [MOBY-dev] Unable to get some cache properties in jMoby Message-ID: <8F535AF1-B2F7-499A-B77A-F380240362BE@farmbio.uu.se> Hi, I have problems getting the cache-size and cache-count values from any of the CACHE_PART_ properties, for example, castWorker.getCacheInfo(CACHE_PART_NAMESPACES) returns the following: Obj: cache-reg-url val: http://mobycentral.icapture.ubc.ca/cgi-bin/ MOBY05/mobycentral.pl Obj: cache-loc val: /tmp/mobycache4/ http58.47.47mobycentral46icapture46ubc46ca47cgi45bin47MOBY0547mobycentra l46pl/namespaces Obj: cache-name val: Cache for Namespaces Obj: cache-size val: null Obj: cache-count val: null ...and the same for the other CACHE_PART_xx. My cache is really filled and I can use it, but the properties are still null. Any ideas how this can be? Cheers, .../Ola From ola.spjuth at farmbio.uu.se Fri Oct 26 12:18:08 2007 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Fri, 26 Oct 2007 14:18:08 +0200 Subject: [MOBY-dev] RegistryCache Message-ID: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> Hi Paul, In jMoby, the CentralDigestCachedImpl deals with caching of namespaces, services, servicetypes, and datatypes. How come this also is required when setting up input for a service: Fetching data type ontology from http://biomoby.org/RESOURCES/MOBY-S/ Objects and Fetching namespace ontology from http://biomoby.org/RESOURCES/MOBY-S/ Namespaces What extra is then downloaded that is not cached in the Central? I would be very happy for some explanation about why this is the case, what the org.biomoby.registry.meta.RegistryCache is and how I can use it to cache these ontologies (as pointed to in earlier mails on moby- dev). Cheers, .../Ola From martin.senger at gmail.com Fri Oct 26 12:51:42 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Oct 2007 13:51:42 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> Message-ID: <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> Hi, In jMoby, the CentralDigestCachedImpl deals with caching of > namespaces, services, servicetypes, and datatypes. That's correct. I wrote this caching - so I can confirm that it does exactly this. (And I will look at the problem with cache properties, you mentioned in a previous email, later.) But I do not know who (what software component) is using this caching, and what else it requires from Moby Central. It may be the RDF files describing services (and their parts) - they are not cached by the client CentralDigestCachedImpl. For long time, I wanted to re-implement this caching mechanism to get data from the central not by calling its API methods but by getting the RDFs (actually I even believe that Eddie wrote some classes for me to help with that). So far, it has not happened - but when/if it does I may consider to keep in the cache (and make it available) also the RDF files (they may have richer contents than the results gotten by the API methods). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Fri Oct 26 12:51:42 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Oct 2007 13:51:42 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> Message-ID: <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> Hi, In jMoby, the CentralDigestCachedImpl deals with caching of > namespaces, services, servicetypes, and datatypes. That's correct. I wrote this caching - so I can confirm that it does exactly this. (And I will look at the problem with cache properties, you mentioned in a previous email, later.) But I do not know who (what software component) is using this caching, and what else it requires from Moby Central. It may be the RDF files describing services (and their parts) - they are not cached by the client CentralDigestCachedImpl. For long time, I wanted to re-implement this caching mechanism to get data from the central not by calling its API methods but by getting the RDFs (actually I even believe that Eddie wrote some classes for me to help with that). So far, it has not happened - but when/if it does I may consider to keep in the cache (and make it available) also the RDF files (they may have richer contents than the results gotten by the API methods). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Fri Oct 26 13:13:49 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 26 Oct 2007 07:13:49 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> Message-ID: <4721E80D.8060503@ucalgary.ca> Hi folks, Yes, the "Fetching ... ontology" does exactly what Martin describes below...builds the definitions for the static MobyDataType.getDataType(), MobyNamespace.getNamespace() etc. methods by downloading the complete RDFs from Moby Central. RegistryCache coordinates when to update the cached copies, etc.. This is the caching mechanism used in Seahawk, which minimizes the number of http connects required to gather all the ontology info the program may need to access. If you use this mechanism, you should not need to access the cache directly, MobyDataType.getDataType(), etc. handle it transparently for you. If you only need to access little bits of the ontologies, CentralDigestCachedImpl may still be your best bet performance-wise. Regards, Paul > But I do not know who (what software component) is using this caching, > and what else it requires from Moby Central. It may be the RDF files > describing services (and their parts) - they are not cached by the > client CentralDigestCachedImpl. For long time, I wanted to > re-implement this caching mechanism to get data from the central not > by calling its API methods but by getting the RDFs (actually I even > believe that Eddie wrote some classes for me to help with that). So > far, it has not happened - but when/if it does I may consider to keep > in the cache (and make it available) also the RDF files (they may have > richer contents than the results gotten by the API methods). > > Cheers, > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger From edward.kawas at gmail.com Fri Oct 26 13:29:26 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 26 Oct 2007 06:29:26 -0700 Subject: [MOBY-dev] serviceNotes question In-Reply-To: <4721AE44.7070204@bsc.es> References: <4721AE44.7070204@bsc.es> Message-ID: <000f01c817d4$3af4b380$6400a8c0@notebook> Hi Dmitry > Does this mean that the tag may be in any of > these structures? No, they can be used to describe errors at these structures. > (As far as I understand before the exceptions the only tag > where it could appear was ). > I believe that you are correct. Eddie From gordonp at ucalgary.ca Fri Oct 26 13:33:56 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 26 Oct 2007 07:33:56 -0600 Subject: [MOBY-dev] serviceNotes question In-Reply-To: <000f01c817d4$3af4b380$6400a8c0@notebook> References: <4721AE44.7070204@bsc.es> <000f01c817d4$3af4b380$6400a8c0@notebook> Message-ID: <4721ECC4.9050703@ucalgary.ca> Edward Kawas wrote: > Hi Dmitry > >> Does this mean that the tag may be in any of >> these structures? >> > No, they can be used to describe errors at these structures. > Correct. To clarify, via the serviceException's query ID and element attributes. From gordonp at ucalgary.ca Fri Oct 26 13:13:49 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 26 Oct 2007 07:13:49 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> Message-ID: <4721E80D.8060503@ucalgary.ca> Hi folks, Yes, the "Fetching ... ontology" does exactly what Martin describes below...builds the definitions for the static MobyDataType.getDataType(), MobyNamespace.getNamespace() etc. methods by downloading the complete RDFs from Moby Central. RegistryCache coordinates when to update the cached copies, etc.. This is the caching mechanism used in Seahawk, which minimizes the number of http connects required to gather all the ontology info the program may need to access. If you use this mechanism, you should not need to access the cache directly, MobyDataType.getDataType(), etc. handle it transparently for you. If you only need to access little bits of the ontologies, CentralDigestCachedImpl may still be your best bet performance-wise. Regards, Paul > But I do not know who (what software component) is using this caching, > and what else it requires from Moby Central. It may be the RDF files > describing services (and their parts) - they are not cached by the > client CentralDigestCachedImpl. For long time, I wanted to > re-implement this caching mechanism to get data from the central not > by calling its API methods but by getting the RDFs (actually I even > believe that Eddie wrote some classes for me to help with that). So > far, it has not happened - but when/if it does I may consider to keep > in the cache (and make it available) also the RDF files (they may have > richer contents than the results gotten by the API methods). > > Cheers, > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger From martin.senger at gmail.com Fri Oct 26 13:45:31 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Oct 2007 14:45:31 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <4721E80D.8060503@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> Message-ID: <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> Hi Paul, This is the caching > mechanism used in Seahawk, which minimizes the number of http connects The old story again, right? You implemented this good thing just for yourself, without putting this good stuff into existing CentralDigestCachedImpl instead. Therefore, we again have two ways of doing things, and we confuse developers. Pity... Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Fri Oct 26 13:45:31 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Oct 2007 14:45:31 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <4721E80D.8060503@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> Message-ID: <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> Hi Paul, This is the caching > mechanism used in Seahawk, which minimizes the number of http connects The old story again, right? You implemented this good thing just for yourself, without putting this good stuff into existing CentralDigestCachedImpl instead. Therefore, we again have two ways of doing things, and we confuse developers. Pity... Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Fri Oct 26 14:14:02 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 26 Oct 2007 08:14:02 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> Message-ID: <4721F62A.5020407@ucalgary.ca> Hi Martin, Actually, I didn't add it to CentralDigestCachedImpl for a several practical reasons: 1. The RDF methodology is very different from the existing methodology, so I did not want to just replace your code. 2. I separated registry calls and ontology definition caching into separate classes (see CentralCachedCallsImpl, which does extend you CentralImpl, and the static methods in MobyDataType etc. respectively), as these are now completely unrelated. 3. The existing CentralDigestCachedImpl methodology is still useful when you just want to get bits of the ontology. I am willing to revamp the CentralDigestCachedImpl code sometime to use the RDF methodology, if you're keen on it. All I would need you to do is build unit tests first, to elucidate the proper behaviour and make sure I don't break any of the current functionality on which Dashboard, etc. depend. Regards, Paul > The old story again, right? You implemented this good thing just for > yourself, without putting this good stuff into existing > CentralDigestCachedImpl instead. Therefore, we again have two ways of doing > things, and we confuse developers. Pity... > From gordonp at ucalgary.ca Fri Oct 26 14:14:02 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 26 Oct 2007 08:14:02 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> Message-ID: <4721F62A.5020407@ucalgary.ca> Hi Martin, Actually, I didn't add it to CentralDigestCachedImpl for a several practical reasons: 1. The RDF methodology is very different from the existing methodology, so I did not want to just replace your code. 2. I separated registry calls and ontology definition caching into separate classes (see CentralCachedCallsImpl, which does extend you CentralImpl, and the static methods in MobyDataType etc. respectively), as these are now completely unrelated. 3. The existing CentralDigestCachedImpl methodology is still useful when you just want to get bits of the ontology. I am willing to revamp the CentralDigestCachedImpl code sometime to use the RDF methodology, if you're keen on it. All I would need you to do is build unit tests first, to elucidate the proper behaviour and make sure I don't break any of the current functionality on which Dashboard, etc. depend. Regards, Paul > The old story again, right? You implemented this good thing just for > yourself, without putting this good stuff into existing > CentralDigestCachedImpl instead. Therefore, we again have two ways of doing > things, and we confuse developers. Pity... > From martin.senger at gmail.com Fri Oct 26 14:23:54 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Oct 2007 15:23:54 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <4721F62A.5020407@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> Message-ID: <4d93f07c0710260723g4d976a1dl8a1180d01548f174@mail.gmail.com> > 3. The existing CentralDigestCachedImpl methodology is still useful when > you just want to get bits of the ontology. Well, if I want just bits I would not use cached one :-) But it is not an important argument I think. I am willing to revamp the CentralDigestCachedImpl code sometime to use > the RDF methodology, if you're keen on it. That would be perfect! All I would need you to do > is build unit tests first Very good point and suggestion. I agree and I consider now holding the ball... I will come back to you when I have the tests ready (you may not believe it but I have never wrote any junit tests - even though I wanted to do it often). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Fri Oct 26 14:23:54 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Oct 2007 15:23:54 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <4721F62A.5020407@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> Message-ID: <4d93f07c0710260723g4d976a1dl8a1180d01548f174@mail.gmail.com> > 3. The existing CentralDigestCachedImpl methodology is still useful when > you just want to get bits of the ontology. Well, if I want just bits I would not use cached one :-) But it is not an important argument I think. I am willing to revamp the CentralDigestCachedImpl code sometime to use > the RDF methodology, if you're keen on it. That would be perfect! All I would need you to do > is build unit tests first Very good point and suggestion. I agree and I consider now holding the ball... I will come back to you when I have the tests ready (you may not believe it but I have never wrote any junit tests - even though I wanted to do it often). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Fri Oct 26 15:19:35 2007 From: markw at illuminae.com (mark wilkinson) Date: Fri, 26 Oct 2007 15:19:35 +0000 GMT Subject: [MOBY-dev] RegistryCache In-Reply-To: <4721F62A.5020407@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca><4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> Message-ID: <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> Can I update the RDF itself to make it more "correct" before you do this? It will only take a day or two... M -- Mark Wilkinson ...on the road! -----Original Message----- From: Paul Gordon Date: Fri, 26 Oct 2007 08:14:02 To:Core developer announcements Cc:mobydev Subject: Re: [MOBY-dev] RegistryCache Hi Martin, Actually, I didn't add it to CentralDigestCachedImpl for a several practical reasons: 1. The RDF methodology is very different from the existing methodology, so I did not want to just replace your code. 2. I separated registry calls and ontology definition caching into separate classes (see CentralCachedCallsImpl, which does extend you CentralImpl, and the static methods in MobyDataType etc. respectively), as these are now completely unrelated. 3. The existing CentralDigestCachedImpl methodology is still useful when you just want to get bits of the ontology. I am willing to revamp the CentralDigestCachedImpl code sometime to use the RDF methodology, if you're keen on it. All I would need you to do is build unit tests first, to elucidate the proper behaviour and make sure I don't break any of the current functionality on which Dashboard, etc. depend. Regards, Paul > The old story again, right? You implemented this good thing just for > yourself, without putting this good stuff into existing > CentralDigestCachedImpl instead. Therefore, we again have two ways of doing > things, and we confuse developers. Pity... > _______________________________________________ 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 Fri Oct 26 15:19:35 2007 From: markw at illuminae.com (mark wilkinson) Date: Fri, 26 Oct 2007 15:19:35 +0000 GMT Subject: [MOBY-dev] RegistryCache In-Reply-To: <4721F62A.5020407@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca><4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> Message-ID: <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> Can I update the RDF itself to make it more "correct" before you do this? It will only take a day or two... M -- Mark Wilkinson ...on the road! -----Original Message----- From: Paul Gordon Date: Fri, 26 Oct 2007 08:14:02 To:Core developer announcements Cc:mobydev Subject: Re: [MOBY-dev] RegistryCache Hi Martin, Actually, I didn't add it to CentralDigestCachedImpl for a several practical reasons: 1. The RDF methodology is very different from the existing methodology, so I did not want to just replace your code. 2. I separated registry calls and ontology definition caching into separate classes (see CentralCachedCallsImpl, which does extend you CentralImpl, and the static methods in MobyDataType etc. respectively), as these are now completely unrelated. 3. The existing CentralDigestCachedImpl methodology is still useful when you just want to get bits of the ontology. I am willing to revamp the CentralDigestCachedImpl code sometime to use the RDF methodology, if you're keen on it. All I would need you to do is build unit tests first, to elucidate the proper behaviour and make sure I don't break any of the current functionality on which Dashboard, etc. depend. Regards, Paul > The old story again, right? You implemented this good thing just for > yourself, without putting this good stuff into existing > CentralDigestCachedImpl instead. Therefore, we again have two ways of doing > things, and we confuse developers. Pity... > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From martin.senger at gmail.com Fri Oct 26 15:41:39 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Oct 2007 16:41:39 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> Message-ID: <4d93f07c0710260841r4f34eaf2y511a626b2e17a91b@mail.gmail.com> > Can I update the RDF itself to make it more "correct" before you do > this? It will only take a day or two... Of course. Don't worry... the junit tests will take for me more time... Thanks for doing it, anyway. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Fri Oct 26 15:41:39 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Oct 2007 16:41:39 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> Message-ID: <4d93f07c0710260841r4f34eaf2y511a626b2e17a91b@mail.gmail.com> > Can I update the RDF itself to make it more "correct" before you do > this? It will only take a day or two... Of course. Don't worry... the junit tests will take for me more time... Thanks for doing it, anyway. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Fri Oct 26 15:32:48 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 26 Oct 2007 09:32:48 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca><4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> Message-ID: <472208A0.1040404@ucalgary.ca> No problem! I won't get a chance to do any updates for a couple weeks anyway... > Can I update the RDF itself to make it more "correct" before you do this? It will only take a day or two... > > M > > > -- > Mark Wilkinson > ...on the road! > > > -----Original Message----- > From: Paul Gordon > Date: Fri, 26 Oct 2007 08:14:02 > To:Core developer announcements > Cc:mobydev > Subject: Re: [MOBY-dev] RegistryCache > > Hi Martin, > > Actually, I didn't add it to CentralDigestCachedImpl for a several > practical reasons: > > 1. The RDF methodology is very different from the existing methodology, > so I did not want to just replace your code. > 2. I separated registry calls and ontology definition caching into > separate classes (see CentralCachedCallsImpl, which does extend you > CentralImpl, and the static methods in MobyDataType etc. respectively), > as these are now completely unrelated. > 3. The existing CentralDigestCachedImpl methodology is still useful when > you just want to get bits of the ontology. > > I am willing to revamp the CentralDigestCachedImpl code sometime to use > the RDF methodology, if you're keen on it. All I would need you to do > is build unit tests first, to elucidate the proper behaviour and make > sure I don't break any of the current functionality on which Dashboard, > etc. depend. > > Regards, > Paul > >> The old story again, right? You implemented this good thing just for >> yourself, without putting this good stuff into existing >> CentralDigestCachedImpl instead. Therefore, we again have two ways of doing >> things, and we confuse developers. Pity... >> >> > > _______________________________________________ > 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 > > !DSPAM:60005,47220606260162728527452! > > > > From gordonp at ucalgary.ca Fri Oct 26 15:32:48 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 26 Oct 2007 09:32:48 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca><4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> Message-ID: <472208A0.1040404@ucalgary.ca> No problem! I won't get a chance to do any updates for a couple weeks anyway... > Can I update the RDF itself to make it more "correct" before you do this? It will only take a day or two... > > M > > > -- > Mark Wilkinson > ...on the road! > > > -----Original Message----- > From: Paul Gordon > Date: Fri, 26 Oct 2007 08:14:02 > To:Core developer announcements > Cc:mobydev > Subject: Re: [MOBY-dev] RegistryCache > > Hi Martin, > > Actually, I didn't add it to CentralDigestCachedImpl for a several > practical reasons: > > 1. The RDF methodology is very different from the existing methodology, > so I did not want to just replace your code. > 2. I separated registry calls and ontology definition caching into > separate classes (see CentralCachedCallsImpl, which does extend you > CentralImpl, and the static methods in MobyDataType etc. respectively), > as these are now completely unrelated. > 3. The existing CentralDigestCachedImpl methodology is still useful when > you just want to get bits of the ontology. > > I am willing to revamp the CentralDigestCachedImpl code sometime to use > the RDF methodology, if you're keen on it. All I would need you to do > is build unit tests first, to elucidate the proper behaviour and make > sure I don't break any of the current functionality on which Dashboard, > etc. depend. > > Regards, > Paul > >> The old story again, right? You implemented this good thing just for >> yourself, without putting this good stuff into existing >> CentralDigestCachedImpl instead. Therefore, we again have two ways of doing >> things, and we confuse developers. Pity... >> >> > > _______________________________________________ > 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 > > !DSPAM:60005,47220606260162728527452! > > > > From edward.kawas at gmail.com Fri Oct 26 16:00:43 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 26 Oct 2007 09:00:43 -0700 Subject: [MOBY-dev] RegistryCache In-Reply-To: <472208A0.1040404@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca><4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca><614437732-1193411982-cardhu_blackberry.rim.net-257-@engine27-cell01> <472208A0.1040404@ucalgary.ca> Message-ID: <001b01c817e9$5da6cb10$6400a8c0@notebook> Mark, I believe that Paul and Co. use my RDF parsers, so as long as I update those files when I (assuming that it is I that changes the RDF ;-) change the RDF. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon > Sent: Friday, October 26, 2007 8:33 AM > To: markw at illuminae.com; Core developer announcements > Cc: mobydev > Subject: Re: [MOBY-dev] RegistryCache > > No problem! I won't get a chance to do any updates for a > couple weeks anyway... > > Can I update the RDF itself to make it more "correct" > before you do this? It will only take a day or two... > > > > M > > > > > > -- > > Mark Wilkinson > > ...on the road! > > > > > > -----Original Message----- > > From: Paul Gordon > > Date: Fri, 26 Oct 2007 08:14:02 > > To:Core developer announcements > > Cc:mobydev > > Subject: Re: [MOBY-dev] RegistryCache > > > > Hi Martin, > > > > Actually, I didn't add it to CentralDigestCachedImpl for a several > > practical reasons: > > > > 1. The RDF methodology is very different from the existing > > methodology, so I did not want to just replace your code. > > 2. I separated registry calls and ontology definition caching into > > separate classes (see CentralCachedCallsImpl, which does extend you > > CentralImpl, and the static methods in MobyDataType etc. > > respectively), as these are now completely unrelated. > > 3. The existing CentralDigestCachedImpl methodology is still useful > > when you just want to get bits of the ontology. > > > > I am willing to revamp the CentralDigestCachedImpl code sometime to > > use the RDF methodology, if you're keen on it. All I would > need you > > to do is build unit tests first, to elucidate the proper > behaviour and > > make sure I don't break any of the current functionality on which > > Dashboard, etc. depend. > > > > Regards, > > Paul > > > >> The old story again, right? You implemented this good > thing just for > >> yourself, without putting this good stuff into existing > >> CentralDigestCachedImpl instead. Therefore, we again have > two ways of > >> doing things, and we confuse developers. Pity... > >> > >> > > > > _______________________________________________ > > 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 > > > > !DSPAM:60005,47220606260162728527452! > > > > > > > > > > _______________________________________________ > 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 Fri Oct 26 17:56:09 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 26 Oct 2007 10:56:09 -0700 Subject: [MOBY-dev] Fwd: PLoS ONE Decision [07-PONE-RA-01200R1] In-Reply-To: <2311934051859@cl-enclosure2-4> References: <2311934051859@cl-enclosure2-4> Message-ID: Hi All, Well, the manuscript was rejected again, without any additional review (after two months of waiting!). I think that says more about the quality of PLoS ONE than it says about the quality of the manuscript, but... hey... what can you do? So, I guess we need to find another place to send it. Does anyone have any preferences? M ------- Forwarded message ------- From: PLoSONE at plos.org To: markw at illuminae.com Cc: Subject: PLoS ONE Decision [07-PONE-RA-01200R1] Date: Fri, 26 Oct 2007 06:26:25 -0700 Dear Dr. Wilkinson, Thank you for submitting your manuscript "Interoperability with Moby 1.0: It's Better than Sharing your Toothbrush" to PLoS ONE. I am sorry about the delay in the review process. After careful consideration, we have decided that we will not be able to accept this manuscript for publication in the journal in its current form, although we would be willing to review again a much-revised version if you felt able to address the specific concerns detailed below. Should you decide to revise the manuscript for further consideration here, your revisions should address the specific points raised by one of the referees. Please pay close attention to our "Guidelines for Authors" and "Submission Checklist" when revising your manuscript. There are templates available to help authors format papers for publication in PLoS ONE, and include all the relevant information in the appropriate place. You can download them from our instructions for authors at http://www.plosone.org/static/guidelines.action#preparation (under "organization of the manuscript"). The four templates are: Standard Research article, Clinical Trial, Clinical Research article, and Systematic Review/Meta-Analysis - please choose the appropriate one for your particular type of study. When your files are completely ready please resubmit your manuscript by logging on to our journal manuscript system at http://one.plosjms.org/ Thank you for your support of PLoS ONE. Yours sincerely, Dr Jörg Hoheisel Academic Editor, PLoS ONE ------------------------------------------------------------------------ -------------- next part -------------- A non-text attachment was scrubbed... Name: 1_reviewer_attachment_1_1180009995.pdf Type: application/pdf Size: 56743 bytes Desc: not available URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: attachment889.htm URL: From Pieter.Neerincx at wur.nl Sat Oct 27 10:04:02 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Sat, 27 Oct 2007 12:04:02 +0200 Subject: [MOBY-dev] Fwd: PLoS ONE Decision [07-PONE-RA-01200R1] In-Reply-To: References: <2311934051859@cl-enclosure2-4> Message-ID: <3A2D8DD7-EE21-47FC-BA37-72F07E2C1E40@wur.nl> Hi Mark, Bummer, PLoS One looked like a great new magazine, but their review process is a bad joke... not very professional at best :(. I think it would be best for the BioMOBY article if it will be published in an Open Access magazine, but apart from that I don't have preferences. Cheers, Pi On 26 Oct 2007, at 19:56, Mark Wilkinson wrote: > Hi All, > > Well, the manuscript was rejected again, without any additional > review (after two months of waiting!). I think that says more > about the quality of PLoS ONE than it says about the quality of the > manuscript, but... hey... what can you do? > > So, I guess we need to find another place to send it. Does anyone > have any preferences? > > M > > > > > ------- Forwarded message ------- > From: PLoSONE at plos.org > To: markw at illuminae.com > Cc: > Subject: PLoS ONE Decision [07-PONE-RA-01200R1] > Date: Fri, 26 Oct 2007 06:26:25 -0700 > > Dear Dr. Wilkinson, > > Thank you for submitting your manuscript "Interoperability with > Moby 1.0: It's Better than Sharing your Toothbrush" to PLoS ONE. I > am sorry about the delay in the review process. > > After careful consideration, we have decided that we will not be > able to accept this manuscript for publication in the journal in > its current form, although we would be willing to review again a > much-revised version if you felt able to address the specific > concerns detailed below. > > Should you decide to revise the manuscript for further > consideration here, your revisions should address the specific > points raised by one of the referees. > > Please pay close attention to our "Guidelines for Authors" and > "Submission Checklist" when revising your manuscript. > > There are templates available to help authors format papers for > publication in PLoS ONE, and include all the relevant information > in the appropriate place. You can download them from our > instructions for authors at http://www.plosone.org/static/ > guidelines.action#preparation (under "organization of the > manuscript"). The four templates are: Standard Research article, > Clinical Trial, Clinical Research article, and Systematic Review/ > Meta-Analysis - please choose the appropriate one for your > particular type of study. > > When your files are completely ready please resubmit your > manuscript by logging on to our journal manuscript system at http:// > one.plosjms.org/ > > Thank you for your support of PLoS ONE. > > Yours sincerely, > > Dr Jörg Hoheisel > Academic Editor, PLoS ONE > > ---------------------------------------------------------------------- > -- > > <1_reviewer_attachment_1_1180009995.pdf> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- From martin.senger at gmail.com Mon Oct 29 05:56:48 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 29 Oct 2007 06:56:48 +0100 Subject: [MOBY-dev] Announcement: Soaplab2 released Message-ID: <4d93f07c0710282256u22823cfcie7a737835bd77a97@mail.gmail.com> [ I apologize for the cross-posting ] In the early hours of the Monday morning, after last "fixes" that took the whole night :-) I can announce, finally, a release of the completely re-written Soaplab - Soaplab2. Some features are still missing (it is a beta, after all) but the main functionality should be there. Please have a look at http://soaplab.sourceforge.net/soaplab2. As usual: without your feedback and suggestions, it will be hard to improve it. With regards, Martin Senger Mahmut Uludag -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ola.spjuth at farmbio.uu.se Mon Oct 29 16:57:27 2007 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Mon, 29 Oct 2007 17:57:27 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <4721F62A.5020407@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> Message-ID: <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> Hi Paul, So how do I use the CentralCachedCallsImpl? How can I fill/monitor/ update its cache? If I use it, will it completely replace the CentralDigestCachedImpl? I am a bit confused here how to work with BioMoby registries and caches and ontologies... Hope you (or someone else) can help me out. Cheers, .../Ola On Oct 26, 2007, at 16:14 , Paul Gordon wrote: > Hi Martin, > > Actually, I didn't add it to CentralDigestCachedImpl for a several > practical reasons: > > 1. The RDF methodology is very different from the existing > methodology, > so I did not want to just replace your code. > 2. I separated registry calls and ontology definition caching into > separate classes (see CentralCachedCallsImpl, which does extend you > CentralImpl, and the static methods in MobyDataType etc. > respectively), > as these are now completely unrelated. > 3. The existing CentralDigestCachedImpl methodology is still useful > when > you just want to get bits of the ontology. > > I am willing to revamp the CentralDigestCachedImpl code sometime to > use > the RDF methodology, if you're keen on it. All I would need you to do > is build unit tests first, to elucidate the proper behaviour and make > sure I don't break any of the current functionality on which > Dashboard, > etc. depend. > > Regards, > Paul >> The old story again, right? You implemented this good thing just for >> yourself, without putting this good stuff into existing >> CentralDigestCachedImpl instead. Therefore, we again have two ways >> of doing >> things, and we confuse developers. Pity... >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Mon Oct 29 17:06:31 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 29 Oct 2007 11:06:31 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> Message-ID: <47261317.3030406@ucalgary.ca> Hi Ola, If you want to use CentralCachedCallsImpl, simply use it whenever you would use CentralImpl. It takes care of all the caching details for you, you should never have to explicitly check if something is cached or not, just call the methods as the Central interface specifies. I'm not trying to be vague, I just tried to make it easy to use :-) Regards, Paul From gordonp at ucalgary.ca Mon Oct 29 17:06:31 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 29 Oct 2007 11:06:31 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> Message-ID: <47261317.3030406@ucalgary.ca> Hi Ola, If you want to use CentralCachedCallsImpl, simply use it whenever you would use CentralImpl. It takes care of all the caching details for you, you should never have to explicitly check if something is cached or not, just call the methods as the Central interface specifies. I'm not trying to be vague, I just tried to make it easy to use :-) Regards, Paul From ola.spjuth at farmbio.uu.se Mon Oct 29 19:58:05 2007 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Mon, 29 Oct 2007 20:58:05 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <47261317.3030406@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> <47261317.3030406@ucalgary.ca> Message-ID: <77B231CC-2BE8-4121-90A5-A6899C336C7D@farmbio.uu.se> Yes, but how do I fill the cache so that I can use the central offline (I'm building a rich client)? The methods below are not available from the CentralCachedCallsImpl: MobyDataType[] types=castWorker.getDataTypes(); MobyService[] services=castWorker.getServices(); MobyServiceType[] serviceTypes=castWorker.getFullServiceTypes(); and I want to build a full service hierarchy (as in dashboard). Are there other ways of obtaining this information? How can I get the state of the caching (age, size etc) and update it? The CentralCachedCallsImpl seems rather lightweight... Is there a helper class with convenience methods available? Thanks, .../Ola On Oct 29, 2007, at 18:06 , Paul Gordon wrote: > Hi Ola, > > If you want to use CentralCachedCallsImpl, simply use it whenever you > would use CentralImpl. > It takes care of all the caching details for you, you should never > have > to explicitly check if something > is cached or not, just call the methods as the Central interface > specifies. I'm not trying to be vague, > I just tried to make it easy to use :-) > > Regards, > > Paul > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From ola.spjuth at farmbio.uu.se Mon Oct 29 19:58:05 2007 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Mon, 29 Oct 2007 20:58:05 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <47261317.3030406@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> <47261317.3030406@ucalgary.ca> Message-ID: <77B231CC-2BE8-4121-90A5-A6899C336C7D@farmbio.uu.se> Yes, but how do I fill the cache so that I can use the central offline (I'm building a rich client)? The methods below are not available from the CentralCachedCallsImpl: MobyDataType[] types=castWorker.getDataTypes(); MobyService[] services=castWorker.getServices(); MobyServiceType[] serviceTypes=castWorker.getFullServiceTypes(); and I want to build a full service hierarchy (as in dashboard). Are there other ways of obtaining this information? How can I get the state of the caching (age, size etc) and update it? The CentralCachedCallsImpl seems rather lightweight... Is there a helper class with convenience methods available? Thanks, .../Ola On Oct 29, 2007, at 18:06 , Paul Gordon wrote: > Hi Ola, > > If you want to use CentralCachedCallsImpl, simply use it whenever you > would use CentralImpl. > It takes care of all the caching details for you, you should never > have > to explicitly check if something > is cached or not, just call the methods as the Central interface > specifies. I'm not trying to be vague, > I just tried to make it easy to use :-) > > Regards, > > Paul > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Tue Oct 30 00:43:04 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 29 Oct 2007 18:43:04 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: <77B231CC-2BE8-4121-90A5-A6899C336C7D@farmbio.uu.se> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> <47261317.3030406@ucalgary.ca> <77B231CC-2BE8-4121-90A5-A6899C336C7D@farmbio.uu.se> Message-ID: <47267E18.4010509@ucalgary.ca> Hi Ola, If you want to explicitly cache the ontologies, you need to work with the Registry and RegistryCache objects like so: ******** //To delete stale files RegistryCache.deleteExpiredCacheFiles(allowedAgeInMilliseconds); // In what file would the ontology be cached, if it was cached? File namespacesDefFile = RegistryCache.getOntologyFile(preferredRegistry, Central.NAMESPACES_RESOURCE_NAME); URL namespacesDefURL = namespacesDefFile.toURI().toURL(); if(namespacesDefFile.exists()){ // Use the existing cached file rather than actually going to the registry MobyNamespace.loadNamespaces(namespacesDefURL, preferredRegistry); } else{ // Create the cached file from the remote source, then load it into MobyNamespace so MobyNamespace.getNamespace() can retrieve it. RegistryCache.cacheRegistryOntology(preferredRegistry, Central.NAMESPACES_RESOURCE_NAME); MobyNamespace.loadNamespaces(namespacesDefURL, preferredRegistry); } ******** The other relevant fields/methods are Central.DATA_TYPES_RESOURCE_NAME/Central.SERVICE_TYPES_RESOURCE_NAME and MobyDataType.loadDataTypes()/MobyServiceType.loadServiceTypes(). From groscurt at mpiz-koeln.mpg.de Tue Oct 30 08:41:32 2007 From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de) Date: Tue, 30 Oct 2007 09:41:32 +0100 (CET) Subject: [MOBY-dev] RegistryCache In-Reply-To: <77B231CC-2BE8-4121-90A5-A6899C336C7D@farmbio.uu.se> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> <47261317.3030406@ucalgary.ca> <77B231CC-2BE8-4121-90A5-A6899C336C7D@farmbio.uu.se> Message-ID: <46725.195.37.46.22.1193733692.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi, > Yes, but how do I fill the cache so that I can use the central > offline (I'm building a rich client)? if you want to have an 'offline' central you can use the MobySync project which is part of the Moby checkout. Under moby-live/Java/src/support/mobysync/ you can find the README how to establish a local repository and how to run the process to keep it synchronized with the BioMoby central. hope this helps andreas From dmitry.repchevski at bsc.es Tue Oct 30 10:05:26 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 30 Oct 2007 11:05:26 +0100 Subject: [MOBY-dev] findService question Message-ID: <472701E6.8000408@bsc.es> First big thanx to all for your help, I have another question. The only way I found to get a complete description of a service is using "findService" operation. I have a problem with its format. Especially I am interested in Input/Output format. I have ones from xml schema, but the question is - is the format the same as for "mobyContent"? I mean that in mobyContent we can have multiple mobyData with a Simple/Collection. According the scheme there could be List and List, so should I understand it as: Any collection specified will be encapsulated in "mobyData" (one mobyData - one Collection). If I have a List of Simple elements they supposed to be wrapped with Collection inside mobyData. If I have only one Simple in a list - there is a mobyData with a Simple. Sincerely, Dmitry, P.S. or maybe there is better way to find a service description? From dmitry.repchevski at bsc.es Tue Oct 30 11:34:18 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 30 Oct 2007 12:34:18 +0100 Subject: [MOBY-dev] theological question. Message-ID: <472716BA.5020803@bsc.es> Hello! I have a question about the life, universe and web-services. Is there any accordance about the "part name" name in biomoby? Since biomoby use soap web-services it supposed to use wsdl (there is even the operation in the Registry to retrieve it). Within a service there is a parameters' definition part (in moby there are only two - request/result String). Basicly it looks like: Axis is relaxed about the name of parameter unless it can infer it from a call (there is only one method to call). The problem is with another Web-Services stacks like jboss-ws which is trying to be strict to specification. I found that java/perl name the parameters differently ("data" for perl and "arg0" for java). Even more AXIS has a bug putting the namespace into the name of the parameter that goes against the specification (ns1:arg0). Well maybe it just a rhetoric question, but is there a solution? Regards, Dmitry From edward.kawas at gmail.com Tue Oct 30 17:42:44 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 30 Oct 2007 10:42:44 -0700 Subject: [MOBY-dev] findService question In-Reply-To: <472701E6.8000408@bsc.es> References: <472701E6.8000408@bsc.es> Message-ID: <001a01c81b1c$47b6b690$6400a8c0@notebook> Hi Dmitry, I don't really understand your question, but I will take my best shot at addressing it! > Especially I am interested in Input/Output format. I have > ones from xml schema, but the question is - is the format the > same as for "Moby Content"? Not sure what you are asking here ... > I mean that in Moby Content we can have multiple Moby Data with > a Simple/Collection. > According the scheme there could be List and > List, so should I understand it as: > Any collection specified will be encapsulated in "Moby Data" > (one Moby Data - one Collection). Any collection specified in the find Service response will be contained in the Moby Data block of the moby xml message. There would only be one collection in the Moby Data section for each specified collection in the find Service response. The same can be said for simples. Every simple specified in the find Service response will be contained in the Moby Data section of the moby xml. Again, there would only be one simple in the Moby Data section for each specified simple in the find Service response. Moby services can have many inputs/outputs. Each input/output can be either a simple or collection. All of the inputs/outputs are put into the Moby Data section. > If I have a List of Simple elements they supposed to be > wrapped with Collection inside Moby Data. > If I have only one Simple in a list - there is a Moby Data > with a Simple. > > Sincerely, > > Dmitry, > Hope this answers your question ... Eddie > P.S. or maybe there is better way to find a service description? > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Tue Oct 30 18:11:45 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 30 Oct 2007 19:11:45 +0100 Subject: [MOBY-dev] findService question References: 472701E6.8000408@bsc.es Message-ID: <472773E1.3010809@bsc.es> Hello Edward, Acording the schema (findService.xsd) there could be only one input/output per service. Every input/output could have many simple or (and) collections of simple. As far as I understand, in the service every simple/collection is mapped to mobyData. My confusion was in mixing the format of those "Simple" between MobyMessage and this particular service (findService). Now i see that they are different. Thank you very much, Dmitry From edward.kawas at gmail.com Tue Oct 30 21:02:55 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 30 Oct 2007 14:02:55 -0700 Subject: [MOBY-dev] findService question In-Reply-To: <472773E1.3010809@bsc.es> References: 472701E6.8000408@bsc.es <472773E1.3010809@bsc.es> Message-ID: <000001c81b38$3e8066e0$6400a8c0@notebook> Hi Dmitry, > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > Dmitry Repchevsky > Sent: Tuesday, October 30, 2007 11:12 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] findService question > > Hello Edward, > > Acording the schema (findService.xsd) there could be only one > input/output per service. In the findService call, there are sections called Input/Output and you are correct in that there are exactly one of each of these. However, in there can be multiple Simples/Collections declarations in these blocks. That is what I meant when I said services can have >= 1 input/output. > As far as I understand, in the service every > simple/collection is mapped to mobyData. If you mean contained in the mobyData section, then yes. > Thank you very much, Glad to help! Eddie > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From ola.spjuth at farmbio.uu.se Wed Oct 31 10:22:18 2007 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Wed, 31 Oct 2007 11:22:18 +0100 Subject: [MOBY-dev] RegistryCache In-Reply-To: <47267E18.4010509@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> <47261317.3030406@ucalgary.ca> <77B231CC-2BE8-4121-90A5-A6899C336C7D@farmbio.uu.se> <47267E18.4010509@ucalgary.ca> Message-ID: Hi Paul, Thank you for the answers. I think I have found a bug in jMoby, but please correct me if I'm wrong. The following call with reg being my custom Regsitry: MobyDataComposite comp = new MobyDataComposite("DNASequence", reg); calls public MobyDataComposite(String typeName, Registry r){ this(MobyDataType.getDataType(typeName, r)); } calls public MobyDataComposite(MobyDataType type){ this(type, ""); } calls public MobyDataComposite(MobyDataType type, String name){ this(type, name, "", ""); } calls public MobyDataComposite(MobyDataType type, String name, String namespace, String id){ super(namespace, id); setName(name); setDataType(type); members = new ConcurrentHashMap(); } where super calls public MobyDataObject(String namespace, String id){ this(namespace, id, null); } calls public MobyDataObject(String namespace, String id, Registry registry){ super(""); thus having registry=null. This means I will always use the default registry and not my custom registry that I inputted. This prevents me from using my cached registry which you explained below. A second question: When defining my own registry and populating the RegsitryCache like you explained, what Central should I use? CentralDigestCachedImpl? Do I need both caching mechanisms? How do they differ? Thanks for your help, .../Ola On Oct 30, 2007, at 01:43 , Paul Gordon wrote: > Hi Ola, > > If you want to explicitly cache the ontologies, you need to work with > the Registry and RegistryCache objects like so: > > ******** > //To delete stale files > RegistryCache.deleteExpiredCacheFiles(allowedAgeInMilliseconds); > > // In what file would the ontology be cached, if it was cached? > File namespacesDefFile = RegistryCache.getOntologyFile > (preferredRegistry, > > Central.NAMESPACES_RESOURCE_NAME); > URL namespacesDefURL = namespacesDefFile.toURI().toURL(); > if(namespacesDefFile.exists()){ > // Use the existing cached file rather than actually going to > the > registry > MobyNamespace.loadNamespaces(namespacesDefURL, > preferredRegistry); > } > else{ > // Create the cached file from the remote source, then load it > into MobyNamespace so MobyNamespace.getNamespace() can retrieve it. > RegistryCache.cacheRegistryOntology(preferredRegistry, > Central.NAMESPACES_RESOURCE_NAME); > MobyNamespace.loadNamespaces(namespacesDefURL, > preferredRegistry); > } > ******** > > The other relevant fields/methods are > Central.DATA_TYPES_RESOURCE_NAME/Central.SERVICE_TYPES_RESOURCE_NAME > and MobyDataType.loadDataTypes()/MobyServiceType.loadServiceTypes(). > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Wed Oct 31 13:50:55 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 31 Oct 2007 07:50:55 -0600 Subject: [MOBY-dev] RegistryCache In-Reply-To: References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <4d93f07c0710260551rf538745mc145626123f8143a@mail.gmail.com> <4721E80D.8060503@ucalgary.ca> <4d93f07c0710260645n3dfb9f32m136c016ceebfbb5a@mail.gmail.com> <4721F62A.5020407@ucalgary.ca> <02EF1B9A-98FF-4C6B-97D0-28F422E671EA@farmbio.uu.se> <47261317.3030406@ucalgary.ca> <77B231CC-2BE8-4121-90A5-A6899C336C7D@farmbio.uu.se> <47267E18.4010509@ucalgary.ca> Message-ID: <4728883F.8050500@ucalgary.ca> Hi Ola, The registry is associated with datatypes, namespaces, etc., not individual objects, so I don't think the call lineage you give below causes any problem (since the instantiated data type is based through). Feel free to send me a sample program if you run into a case where this association is a problem (i.e. normally to get a registry you'd say object.getDataType().getRegistry(), which actually allows you to do crazy stuff like have data instances from multiple registries concurrently). With regards to your second question, CentralDigestCachedImpl is completely independent of RegistryCache, but we're working to reconcile these. If you use RegistryCache, you only need a CentralImpl for things like findService(), not for datatype, namespace, etc. definitions. You can pick any CentralImpl that suits you, as the service lookup functionality is independent from the definitions (which come from RDF in RegistryCache). __________ I think I have found a bug in jMoby, but please correct me if I'm wrong. The following call with reg being my custom Regsitry: MobyDataComposite comp = new MobyDataComposite("DNASequence", reg); calls public MobyDataComposite(String typeName, Registry r){ this(MobyDataType.getDataType(typeName, r)); } calls public MobyDataComposite(MobyDataType type){ this(type, ""); } calls public MobyDataComposite(MobyDataType type, String name){ this(type, name, "", ""); } calls public MobyDataComposite(MobyDataType type, String name, String namespace, String id){ super(namespace, id); setName(name); setDataType(type); members = new ConcurrentHashMap(); } where super calls public MobyDataObject(String namespace, String id){ this(namespace, id, null); } calls public MobyDataObject(String namespace, String id, Registry registry){ super(""); thus having registry=null. This means I will always use the default registry and not my custom registry that I inputted. This prevents me from using my cached registry which you explained below. From dmitry.repchevski at bsc.es Wed Oct 31 14:36:48 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 31 Oct 2007 15:36:48 +0100 Subject: [MOBY-dev] findService question References: 472773E1.3010809@bsc.es Message-ID: <47289300.4020603@bsc.es> Hello! I have another question about the findService... In the documentation we have: ************************************************************* ************************************************************* The scheme for the operation says: ************************************************************* ... The same for input... ************************************************************* It is not against the err... specification, but in this case there could be only one "Input" per "InputObjects". I just need to clarify it - or the schema is wrong or we have a useless wrapper around "Input" ("inputObjects") in message. Dmitry From edward.kawas at gmail.com Wed Oct 31 14:47:54 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 31 Oct 2007 07:47:54 -0700 Subject: [MOBY-dev] findService question In-Reply-To: <47289300.4020603@bsc.es> References: 472773E1.3010809@bsc.es <47289300.4020603@bsc.es> Message-ID: <000c01c81bcd$060d26f0$6400a8c0@notebook> Hey Dmitry, In the schema I tried to make the schema say that if there exists a section called inputObjects/outputObjects then the sections Input/Output are mandatory. Re-reading the documentation though, it seems that they really both should have max/min of 1. Did I address your question? Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > Dmitry Repchevsky > Sent: Wednesday, October 31, 2007 7:37 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] findService question > > Hello! > > I have another question about the findService... > In the documentation we have: > ************************************************************* > > > > > > > > > > > > > ************************************************************* > > The scheme for the operation says: > > ************************************************************* > > > > > > ... The same for input... > ************************************************************* > > It is not against the err... specification, but in this case > there could be only one "Input" per "InputObjects". > I just need to clarify it - or the schema is wrong or we have > a useless wrapper around "Input" ("inputObjects") in message. > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Wed Oct 31 15:15:53 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 31 Oct 2007 16:15:53 +0100 Subject: [MOBY-dev] findService question References: 47289300.4020603@bsc.es Message-ID: <47289C29.50104@bsc.es> Not exactly... :-( The question was "could it be more than one Input/Output elements inside inputObjects/outputObjects?" If not, my comment was that in this case there is no sense to have inputObjects/outputObjects at all... that was my confusion. Thank you, Dmitry From markw at illuminae.com Wed Oct 31 16:14:58 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 31 Oct 2007 09:14:58 -0700 Subject: [MOBY-dev] [MOBY-guts] biomoby commit In-Reply-To: <200709241853.l8OIrXSm019980@dev.open-bio.org> References: <200709241853.l8OIrXSm019980@dev.open-bio.org> Message-ID: > Modified Files: > WSRF.pm > Log Message: > * Latest WSRF::Lite package has a proper VERSION declaration, > so we can restrict the version of the package to the one > which is known to work. > * WSRF::Lite is not in CPAN, so we have added a warning about > where it can be fetched/found (beware older versions!). While I was in Cambridge two weeks ago I spoke to the WSRF::Lite developers and asked them if they would be kind enough to make a CPAN release for us. Hopefully they will say yes! Mark From markw at illuminae.com Wed Oct 31 16:10:43 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 31 Oct 2007 09:10:43 -0700 Subject: [MOBY-dev] findService question In-Reply-To: <47289C29.50104@bsc.es> References: <47289C29.50104@bsc.es> Message-ID: Yes, it is possible, at multiple levels: 1) a single service invocation might have multiple distinct inputs 2) a single service invocation message might have multiple service invocations Both of these are contained within the single input XML described in the WSDL. Moby is really "document based" not RPC; however, SOAP::Lite doesn't support document based messaging at the moment (working on it!) so we're stuck using RPC messaging for the time being. I hope I have understood your question - I'm only half-paying-attention as I'm sitting in the K-CAP conference listening to presentations :-) Mark On Wed, 31 Oct 2007 08:15:53 -0700, Dmitry Repchevsky wrote: > Not exactly... :-( > > The question was "could it be more than one Input/Output elements inside > inputObjects/outputObjects?" > If not, my comment was that in this case there is no sense to have > inputObjects/outputObjects at all... that was my confusion. > > Thank you, > > Dmitry > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Wed Oct 31 16:47:51 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 31 Oct 2007 17:47:51 +0100 Subject: [MOBY-dev] findService question References: 47289C29.50104@bsc.es Message-ID: <4728B1B7.1000705@bsc.es> Well, Mark, I think you didn't understand our discussion... Here is an excerpt from the the moby doc for findService service (Registry): ************************************************************* The Query object structure is as follows: ************************************************************* So the question is/was could it be more Input inside inputObjects? ex: ************************************************************* ... ************************************************************* My point was if there could be only one why we needed inputObjects tag at all? it could be easy: ************************************************************* ************************************************************* Ok. untill it's clear I'm using the schema from Edward as reference... Cheers, Dmitry From edward.kawas at gmail.com Wed Oct 31 21:35:27 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 31 Oct 2007 14:35:27 -0700 Subject: [MOBY-dev] findService question In-Reply-To: <4728B1B7.1000705@bsc.es> References: 47289C29.50104@bsc.es <4728B1B7.1000705@bsc.es> Message-ID: <000001c81c06$1294c3e0$b466a8c0@notebook> Hi, The answer is no! Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > Dmitry Repchevsky > Sent: Wednesday, October 31, 2007 9:48 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] findService question > > Well, Mark, I think you didn't understand our discussion... > > Here is an excerpt from the the moby doc for findService > service (Registry): > > ************************************************************* > The Query object structure is as follows: > > > > > > > > > > > > ************************************************************* > > So the question is/was could it be more Input inside inputObjects? > > ex: > ************************************************************* > > > > > > > > > > > ... > > > ************************************************************* > > My point was if there could be only one why we needed > inputObjects tag at all? > > it could be easy: > ************************************************************* > > > > > > > ************************************************************* > > Ok. untill it's clear I'm using the schema from Edward as reference... > > > Cheers, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Wed Oct 31 22:40:42 2007 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 31 Oct 2007 23:40:42 +0100 Subject: [MOBY-dev] findService question References: 4728B1B7.1000705@bsc.es Message-ID: <4729046A.3070205@bsc.es> >The answer is no! Could not be more clear :-) Thanx, Dmitry