From edward.kawas at gmail.com Wed Aug 4 13:29:35 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 4 Aug 2010 10:29:35 -0700 Subject: [MOBY-dev] Error message on fresh install of Taverna 2.2.0 on Linux Message-ID: <006201cb33fa$9c5248f0$d4f6dad0$@gmail.com> Hi All, I am not sure why the BioMoby plugin works fine in versions prior to Taverna 2.2, yet in 2.2 encounters an error in 'GetOntologyThread' that points to too many open files. I have found if you increase the file descriptor limit (for example, http://hausheer.osola.com/docs/11). This error disappears and the plugin functions normally. This should allow you to use the plugin until the root cause of the problem is fixed. Thanks, Eddie From guilhem.sempere at cirad.fr Tue Aug 31 05:06:40 2010 From: guilhem.sempere at cirad.fr (Guilhem Sempere) Date: Tue, 31 Aug 2010 11:06:40 +0200 Subject: [MOBY-dev] GCP_GenomicFeatureVariant in biomoby-datatypes-1.3.0.jar + CVS problem Message-ID: <4C7CC620.8090109@cirad.fr> Hi I am basically taking over an application which contains Moby clients, and am expected to add new clients to it. I am using Maven so the datatype jars available to me are those found here : http://cropwiki.irri.org/m2repo/org/generationcp/moby/biomoby-datatypes/ The client I am currently adding requires the following datatype : GCP_SimpleIdentifierWithTypeOperatorAndCount, which can only be found in version 1.3.0 However, when I switch to version 1.3.0, a previously existing client starts to fail, warning that it is "Ignoring unknown element : GCP_GenomicFeatureVariant", although this class does exist in the jar. After investigations I decompiled class org.biomoby.shared.datatypes.MapDataTypes in versions 1.2.0 and 1.3.0, and found out that the following line, that was present in 1.2.0, is missing in 1.3.0 : type2class.put("GCP_GenomicFeatureVariant", "org.biomoby.shared.datatypes.GCP_GenomicFeatureVariant"); I guess this is the reason to my problem, but can anyone tell me why this line has disappeared? Second issue : I also tried to get the latest versions from CVS (assuming this is the correct location :pserver:cvs at cvs.open-bio.org:/home/repository/moby) but when I try to connect I always get a message saying "can't create temporary directory" : does that mean the CVS server is out of diskpace? Help much appreciated, thanks in advance. G.S. From martin.senger at gmail.com Tue Aug 31 05:59:30 2010 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 31 Aug 2010 12:59:30 +0300 Subject: [MOBY-dev] GCP_GenomicFeatureVariant in biomoby-datatypes-1.3.0.jar + CVS problem In-Reply-To: <4C7CC620.8090109@cirad.fr> References: <4C7CC620.8090109@cirad.fr> Message-ID: Hi, I am using Maven so the datatype jars available to me are those found here : > http://cropwiki.irri.org/m2repo/org/generationcp/moby/biomoby-datatypes/ > The biomoby-datatypes library was put into maven repository in order to have an easier way to resolve Java dependencies (for some applications). But generally this library should be re-generated from the current state of the Moby repository you are just using. It will then guarantee that you do not have any existing data type missing. The jMoby docs describes how to use an Ant task to generate this library. If you cannot find how, let me know and I will resurrect it for you. Second issue : I also tried to get the latest versions from CVS (assuming > this is the correct location :pserver:cvs at cvs.open-bio.org:/home/repository/moby) > but when I try to connect I always get a message saying "can't create > temporary directory" : does that mean the CVS server is out of diskpace? > It may be the case (it happened in the past). Perhaps someone else can reply to this issue? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,martin.senger at kaust.edu.sa skype: martinsenger From guilhem.sempere at cirad.fr Tue Aug 31 07:40:25 2010 From: guilhem.sempere at cirad.fr (Guilhem Sempere) Date: Tue, 31 Aug 2010 13:40:25 +0200 Subject: [MOBY-dev] GCP_GenomicFeatureVariant in biomoby-datatypes-1.3.0.jar + CVS problem In-Reply-To: References: <4C7CC620.8090109@cirad.fr> Message-ID: <4C7CEA29.6040403@cirad.fr> Thanks Martin for your answer. Is this the correct place to look at? http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Moses-generators.html I may be wrong but I feel like I'm stuck as long as the CVS server is down or? Unless there is some other place where I can get the project from... Martin Senger a ?crit : > Hi, > > I am using Maven so the datatype jars available to me are those found here : > >> http://cropwiki.irri.org/m2repo/org/generationcp/moby/biomoby-datatypes/ >> >> > > The biomoby-datatypes library was put into maven repository in order to have > an easier way to resolve Java dependencies (for some applications). But > generally this library should be re-generated from the current state of the > Moby repository you are just using. It will then guarantee that you do not > have any existing data type missing. The jMoby docs describes how to use an > Ant task to generate this library. If you cannot find how, let me know and I > will resurrect it for you. > > Second issue : I also tried to get the latest versions from CVS (assuming > >> this is the correct location :pserver:cvs at cvs.open-bio.org:/home/repository/moby) >> but when I try to connect I always get a message saying "can't create >> temporary directory" : does that mean the CVS server is out of diskpace? >> >> > > It may be the case (it happened in the past). Perhaps someone else can reply > to this issue? > > Cheers, > Martin > > From martin.senger at gmail.com Tue Aug 31 08:05:06 2010 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 31 Aug 2010 15:05:06 +0300 Subject: [MOBY-dev] GCP_GenomicFeatureVariant in biomoby-datatypes-1.3.0.jar + CVS problem In-Reply-To: <4C7CEA29.6040403@cirad.fr> References: <4C7CC620.8090109@cirad.fr> <4C7CEA29.6040403@cirad.fr> Message-ID: > Is this the correct place to look at? > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Moses-generators.html > Yes, it is. > I may be wrong but I feel like I'm stuck as long as the CVS server is down > or? Unless there is some other place where I can get the project from... > No, sorry, I know only about the CVS. Martin -- Martin Senger email: martin.senger at gmail.com,martin.senger at kaust.edu.sa skype: martinsenger From guilhem.sempere at cirad.fr Tue Aug 31 10:14:23 2010 From: guilhem.sempere at cirad.fr (Guilhem Sempere) Date: Tue, 31 Aug 2010 16:14:23 +0200 Subject: [MOBY-dev] GCP_GenomicFeatureVariant in biomoby-datatypes-1.3.0.jar + CVS problem In-Reply-To: References: <4C7CC620.8090109@cirad.fr> <4C7CEA29.6040403@cirad.fr> Message-ID: <4C7D0E3F.4010308@cirad.fr> I managed to get a version of the Moby project from a colleague here and could indeed generate a jar file named biomoby-datatypes.jar However it doesn't contain class GCP_SimpleIdentifierWithTypeOperatorAndCount which is the one required for using Milko's service... Martin Senger a ?crit : >> Is this the correct place to look at? >> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Moses-generators.html >> >> > > Yes, it is. > > > >> I may be wrong but I feel like I'm stuck as long as the CVS server is down >> or? Unless there is some other place where I can get the project from... >> >> > > No, sorry, I know only about the CVS. > > Martin > > From edward.kawas at gmail.com Tue Aug 31 12:36:22 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 31 Aug 2010 09:36:22 -0700 Subject: [MOBY-dev] GCP_GenomicFeatureVariant in biomoby-datatypes-1.3.0.jar + CVS problem In-Reply-To: <4C7CC620.8090109@cirad.fr> References: <4C7CC620.8090109@cirad.fr> Message-ID: <002801cb492a$a6c3e060$f44ba120$@gmail.com> Hello, > > Second issue : I also tried to get the latest versions from CVS (assuming this is > the correct location > :pserver:cvs at cvs.open-bio.org:/home/repository/moby) but when I try to > connect I always get a message saying "can't create temporary directory" > : does that mean the CVS server is out of diskpace? > > Help much appreciated, thanks in advance. > > G.S. > I don't know too much about the inner workings of CVS, but I would assume that if all you are doing is an anonymous checkout, I don't see why the CVS would need disk space (or create a tmp directory). I was able to successfully do a checkout (both anonymously and as a developer). For anon access, I did the following: ~/foo>cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby login [entered the password 'cvs'] ~/foo> cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co -P moby-live Maybe your machine ran out of disk space? If that is the case, maybe do a : ~/foo> cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co -P moby-live/Java This will only checkout the java source code from the CVS. Eddie _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Wed Aug 4 17:29:35 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 4 Aug 2010 10:29:35 -0700 Subject: [MOBY-dev] Error message on fresh install of Taverna 2.2.0 on Linux Message-ID: <006201cb33fa$9c5248f0$d4f6dad0$@gmail.com> Hi All, I am not sure why the BioMoby plugin works fine in versions prior to Taverna 2.2, yet in 2.2 encounters an error in 'GetOntologyThread' that points to too many open files. I have found if you increase the file descriptor limit (for example, http://hausheer.osola.com/docs/11). This error disappears and the plugin functions normally. This should allow you to use the plugin until the root cause of the problem is fixed. Thanks, Eddie From guilhem.sempere at cirad.fr Tue Aug 31 09:06:40 2010 From: guilhem.sempere at cirad.fr (Guilhem Sempere) Date: Tue, 31 Aug 2010 11:06:40 +0200 Subject: [MOBY-dev] GCP_GenomicFeatureVariant in biomoby-datatypes-1.3.0.jar + CVS problem Message-ID: <4C7CC620.8090109@cirad.fr> Hi I am basically taking over an application which contains Moby clients, and am expected to add new clients to it. I am using Maven so the datatype jars available to me are those found here : http://cropwiki.irri.org/m2repo/org/generationcp/moby/biomoby-datatypes/ The client I am currently adding requires the following datatype : GCP_SimpleIdentifierWithTypeOperatorAndCount, which can only be found in version 1.3.0 However, when I switch to version 1.3.0, a previously existing client starts to fail, warning that it is "Ignoring unknown element : GCP_GenomicFeatureVariant", although this class does exist in the jar. After investigations I decompiled class org.biomoby.shared.datatypes.MapDataTypes in versions 1.2.0 and 1.3.0, and found out that the following line, that was present in 1.2.0, is missing in 1.3.0 : type2class.put("GCP_GenomicFeatureVariant", "org.biomoby.shared.datatypes.GCP_GenomicFeatureVariant"); I guess this is the reason to my problem, but can anyone tell me why this line has disappeared? Second issue : I also tried to get the latest versions from CVS (assuming this is the correct location :pserver:cvs at cvs.open-bio.org:/home/repository/moby) but when I try to connect I always get a message saying "can't create temporary directory" : does that mean the CVS server is out of diskpace? Help much appreciated, thanks in advance. G.S. From martin.senger at gmail.com Tue Aug 31 09:59:30 2010 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 31 Aug 2010 12:59:30 +0300 Subject: [MOBY-dev] GCP_GenomicFeatureVariant in biomoby-datatypes-1.3.0.jar + CVS problem In-Reply-To: <4C7CC620.8090109@cirad.fr> References: <4C7CC620.8090109@cirad.fr> Message-ID: Hi, I am using Maven so the datatype jars available to me are those found here : > http://cropwiki.irri.org/m2repo/org/generationcp/moby/biomoby-datatypes/ > The biomoby-datatypes library was put into maven repository in order to have an easier way to resolve Java dependencies (for some applications). But generally this library should be re-generated from the current state of the Moby repository you are just using. It will then guarantee that you do not have any existing data type missing. The jMoby docs describes how to use an Ant task to generate this library. If you cannot find how, let me know and I will resurrect it for you. Second issue : I also tried to get the latest versions from CVS (assuming > this is the correct location :pserver:cvs at cvs.open-bio.org:/home/repository/moby) > but when I try to connect I always get a message saying "can't create > temporary directory" : does that mean the CVS server is out of diskpace? > It may be the case (it happened in the past). Perhaps someone else can reply to this issue? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,martin.senger at kaust.edu.sa skype: martinsenger From guilhem.sempere at cirad.fr Tue Aug 31 11:40:25 2010 From: guilhem.sempere at cirad.fr (Guilhem Sempere) Date: Tue, 31 Aug 2010 13:40:25 +0200 Subject: [MOBY-dev] GCP_GenomicFeatureVariant in biomoby-datatypes-1.3.0.jar + CVS problem In-Reply-To: References: <4C7CC620.8090109@cirad.fr> Message-ID: <4C7CEA29.6040403@cirad.fr> Thanks Martin for your answer. Is this the correct place to look at? http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Moses-generators.html I may be wrong but I feel like I'm stuck as long as the CVS server is down or? Unless there is some other place where I can get the project from... Martin Senger a ?crit : > Hi, > > I am using Maven so the datatype jars available to me are those found here : > >> http://cropwiki.irri.org/m2repo/org/generationcp/moby/biomoby-datatypes/ >> >> > > The biomoby-datatypes library was put into maven repository in order to have > an easier way to resolve Java dependencies (for some applications). But > generally this library should be re-generated from the current state of the > Moby repository you are just using. It will then guarantee that you do not > have any existing data type missing. The jMoby docs describes how to use an > Ant task to generate this library. If you cannot find how, let me know and I > will resurrect it for you. > > Second issue : I also tried to get the latest versions from CVS (assuming > >> this is the correct location :pserver:cvs at cvs.open-bio.org:/home/repository/moby) >> but when I try to connect I always get a message saying "can't create >> temporary directory" : does that mean the CVS server is out of diskpace? >> >> > > It may be the case (it happened in the past). Perhaps someone else can reply > to this issue? > > Cheers, > Martin > > From martin.senger at gmail.com Tue Aug 31 12:05:06 2010 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 31 Aug 2010 15:05:06 +0300 Subject: [MOBY-dev] GCP_GenomicFeatureVariant in biomoby-datatypes-1.3.0.jar + CVS problem In-Reply-To: <4C7CEA29.6040403@cirad.fr> References: <4C7CC620.8090109@cirad.fr> <4C7CEA29.6040403@cirad.fr> Message-ID: > Is this the correct place to look at? > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Moses-generators.html > Yes, it is. > I may be wrong but I feel like I'm stuck as long as the CVS server is down > or? Unless there is some other place where I can get the project from... > No, sorry, I know only about the CVS. Martin -- Martin Senger email: martin.senger at gmail.com,martin.senger at kaust.edu.sa skype: martinsenger From guilhem.sempere at cirad.fr Tue Aug 31 14:14:23 2010 From: guilhem.sempere at cirad.fr (Guilhem Sempere) Date: Tue, 31 Aug 2010 16:14:23 +0200 Subject: [MOBY-dev] GCP_GenomicFeatureVariant in biomoby-datatypes-1.3.0.jar + CVS problem In-Reply-To: References: <4C7CC620.8090109@cirad.fr> <4C7CEA29.6040403@cirad.fr> Message-ID: <4C7D0E3F.4010308@cirad.fr> I managed to get a version of the Moby project from a colleague here and could indeed generate a jar file named biomoby-datatypes.jar However it doesn't contain class GCP_SimpleIdentifierWithTypeOperatorAndCount which is the one required for using Milko's service... Martin Senger a ?crit : >> Is this the correct place to look at? >> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Moses-generators.html >> >> > > Yes, it is. > > > >> I may be wrong but I feel like I'm stuck as long as the CVS server is down >> or? Unless there is some other place where I can get the project from... >> >> > > No, sorry, I know only about the CVS. > > Martin > > From edward.kawas at gmail.com Tue Aug 31 16:36:22 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 31 Aug 2010 09:36:22 -0700 Subject: [MOBY-dev] GCP_GenomicFeatureVariant in biomoby-datatypes-1.3.0.jar + CVS problem In-Reply-To: <4C7CC620.8090109@cirad.fr> References: <4C7CC620.8090109@cirad.fr> Message-ID: <002801cb492a$a6c3e060$f44ba120$@gmail.com> Hello, > > Second issue : I also tried to get the latest versions from CVS (assuming this is > the correct location > :pserver:cvs at cvs.open-bio.org:/home/repository/moby) but when I try to > connect I always get a message saying "can't create temporary directory" > : does that mean the CVS server is out of diskpace? > > Help much appreciated, thanks in advance. > > G.S. > I don't know too much about the inner workings of CVS, but I would assume that if all you are doing is an anonymous checkout, I don't see why the CVS would need disk space (or create a tmp directory). I was able to successfully do a checkout (both anonymously and as a developer). For anon access, I did the following: ~/foo>cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby login [entered the password 'cvs'] ~/foo> cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co -P moby-live Maybe your machine ran out of disk space? If that is the case, maybe do a : ~/foo> cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co -P moby-live/Java This will only checkout the java source code from the CVS. Eddie _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev