obo file
Locked
obo file
 
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Dear Intermine developers,
I'm trying to follow the tutorial about malariamine, but I have a problem the "ant clean build-db" step. The problem arise both with version 0.98 and 0.99 Any hits about the possible problem? The obo files seem ok. Best I. create-so-model: [so-model] Starting OboToModel conversion from /home/gmod/intermine_0_98/bio/sources/so/data/so_2_4_4.obo to /home/gmod/intermine_0_98/malariamine/dbmodel/build/model/so_additions.xml. Filtering on 47 obo terms from /home/gmod/intermine_0_98/malariamine/dbmodel/resources/so_term_list.txt BUILD FAILED /home/gmod/intermine_0_98/malariamine/dbmodel/build.xml:12: java.lang.RuntimeException: Parsing obo file failed at org.intermine.bio.ontology.OboToModel.parseOboTerms(OboToModel.java:258) at org.intermine.bio.ontology.OboToModel.createAndWriteModel(OboToModel.java:102) at org.intermine.bio.task.SOToModelTask.execute(SOToModelTask.java:68) at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291) at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) at org.apache.tools.ant.Task.perform(Task.java:348) at org.apache.tools.ant.Target.execute(Target.java:390) at org.apache.tools.ant.Target.performTasks(Target.java:411) at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399) at org.apache.tools.ant.Project.executeTarget(Project.java:1368) at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41) at org.apache.tools.ant.Project.executeTargets(Project.java:1251) at org.apache.tools.ant.Main.runBuild(Main.java:809) at org.apache.tools.ant.Main.startAnt(Main.java:217) at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280) at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109) Caused by: org.bbop.dataadapter.DataAdapterException: Bad configuration at org.obo.dataadapter.SimpleLinkFileAdapter.doOperation(SimpleLinkFileAdapter.java:132) at org.intermine.bio.ontology.OboParser.processRelations(OboParser.java:120) at org.intermine.bio.ontology.OboToModel.parseOboTerms(OboToModel.java:254) ... 18 more _______________________________________________ dev mailing list [hidden email] http://mail.intermine.org/cgi-bin/mailman/listinfo/dev |
Re: obo file
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Hi Ivan,
I just ran than that step on the intermine_0_98 branch and it works fine for me. The code that has gone wrong comes from two jars we use from OBO-Edit we use for parsing ontologies - obo.jar and bbop.jar. Is it possibly you have other versions of these jars on you system and in your classpath? Did you run ant with the -v option to get the error message you sent? If not 'ant -v clean build-db' it should provide a more complete stack trace. Regards, Richard. On 13/03/2012 15:46, Ivan Merelli wrote: > Dear Intermine developers, > I'm trying to follow the tutorial about malariamine, > but I have a problem the "ant clean build-db" step. > > The problem arise both with version 0.98 and 0.99 > Any hits about the possible problem? > The obo files seem ok. > Best > I. > > > > create-so-model: > [so-model] Starting OboToModel conversion from > /home/gmod/intermine_0_98/bio/sources/so/data/so_2_4_4.obo to > /home/gmod/intermine_0_98/malariamine/dbmodel/build/model/so_additions.xml. > Filtering on 47 obo terms from > /home/gmod/intermine_0_98/malariamine/dbmodel/resources/so_term_list.txt > > BUILD FAILED > /home/gmod/intermine_0_98/malariamine/dbmodel/build.xml:12: > java.lang.RuntimeException: Parsing obo file failed > at org.intermine.bio.ontology.OboToModel.parseOboTerms(OboToModel.java:258) > at > org.intermine.bio.ontology.OboToModel.createAndWriteModel(OboToModel.java:102) > > at org.intermine.bio.task.SOToModelTask.execute(SOToModelTask.java:68) > at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291) > at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > > at java.lang.reflect.Method.invoke(Method.java:597) > at > org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) > at org.apache.tools.ant.Task.perform(Task.java:348) > at org.apache.tools.ant.Target.execute(Target.java:390) > at org.apache.tools.ant.Target.performTasks(Target.java:411) > at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399) > at org.apache.tools.ant.Project.executeTarget(Project.java:1368) > at > org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41) > > at org.apache.tools.ant.Project.executeTargets(Project.java:1251) > at org.apache.tools.ant.Main.runBuild(Main.java:809) > at org.apache.tools.ant.Main.startAnt(Main.java:217) > at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280) > at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109) > Caused by: org.bbop.dataadapter.DataAdapterException: Bad configuration > at > org.obo.dataadapter.SimpleLinkFileAdapter.doOperation(SimpleLinkFileAdapter.java:132) > > at > org.intermine.bio.ontology.OboParser.processRelations(OboParser.java:120) > at org.intermine.bio.ontology.OboToModel.parseOboTerms(OboToModel.java:254) > ... 18 more > > > > _______________________________________________ > dev mailing list > [hidden email] > http://mail.intermine.org/cgi-bin/mailman/listinfo/dev > _______________________________________________ dev mailing list [hidden email] http://mail.intermine.org/cgi-bin/mailman/listinfo/dev |
Re: obo file
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Hi Richard,
I tried to compile intermine in another machine and it works. It's very strange because the configuration are almost identical, but there should be some differences in the java environment. It's possible that a java installation in the machine (but not in path or classpath) would interfere with the compilation? However, I fall into another (simpler I think), which seems to be correlated with the high number of requested pubblications. Have you any idea about how to work around this problem? Best, Ivan BUILD FAILED /home/gmod/intermine_0.98/imbuild/integrate.xml:54: The following error occurred while executing this line: /home/gmod/intermine_0.98/bio/sources/update-publications/build.xml:19: java.lang.RuntimeException: failed to get all publications at org.intermine.bio.dataconversion.EntrezPublicationsRetriever.execute(EntrezPublicationsRetriever.java:255) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) at org.apache.tools.ant.TaskAdapter.execute(TaskAdapter.java:154) at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291) at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) at org.apache.tools.ant.Task.perform(Task.java:348) at org.apache.tools.ant.Target.execute(Target.java:390) at org.apache.tools.ant.Target.performTasks(Target.java:411) at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399) at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38) at org.apache.tools.ant.Project.executeTargets(Project.java:1251) at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442) at org.intermine.task.Integrate.performAction(Integrate.java:223) at org.intermine.task.Integrate.performAction(Integrate.java:135) at org.intermine.task.Integrate.execute(Integrate.java:127) at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291) at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) at org.apache.tools.ant.Task.perform(Task.java:348) at org.apache.tools.ant.Target.execute(Target.java:390) at org.apache.tools.ant.Target.performTasks(Target.java:411) at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399) at org.apache.tools.ant.Project.executeTarget(Project.java:1368) at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41) at org.apache.tools.ant.Project.executeTargets(Project.java:1251) at org.apache.tools.ant.Main.runBuild(Main.java:809) at org.apache.tools.ant.Main.startAnt(Main.java:217) at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280) at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109) Caused by: java.io.IOException: Server returned HTTP response code: 413 for URL: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?tool=flymine&db=pubmed&id=1339256,8842143,8982256,16843540,11805111,9230443,9230440,8112347,9449261,8052624,3275622,9724722,2051020,2288911,16956381,7593276,9448314,9724718,8052622,8630491,14730069,8390675,10069007,12368295,8668213,12368292,11805083,9847123,2738582,11562374,11963920,12825828,11805056,10535734,8491711,9829828,12032320,8265339,16439205,11839499,11839498,11839496,9829834,8052647,16034825,12430018,2019586,10438592,8491722,1460533,8203015,1438195,15082709,7990931,10410243,2019595,8203016,11591723,8203019,15153112,10438606,1460542,11910013,8491736,8356049,8462099,12032293,12032297,15153096,11875053,7523953,10675539,1531480,14977918,1647027,11875025,15258264,11591680,7766608,7929272,7990960,3398920,7682712,8877373,7990966,2572197,9724744,10375352,1648106,16407072,9724743,8530482,3419519,14570563,8325512,1339380,15013215,14570569,2357963,1988676,8631297,8325507,9602175,15367656,14570579,12429853,8631325,3092220,11234 020,12429843,10958669,7893120,4071057,8113161,2501756,11910040,16314687,2643922,9151888,12033438,8113189,10037605,2184573,2361956,14699121,8113187,3092189,9725901,14699122,2361961,1491009,8421692,11910018,1709161,1491011,8078761,9370339,1805969,1339315,11805049,1339314,810352,9151968,15047868,16650980,7683665,11513613,11684675,11964120,9448330,9370319,2572081,11684678,9151947,1681580,8325628,10958635,9917067,15755454,8234909,12492443,8631706,10375639,8631704,11839791,8631708,10643909,8631687,11593005,1867713,10506180,7592990,11478874,10817761,15258569,3171483,11592977,2462055,10888672,9846876,6246116,9846873,9846874,9846875,11478849,11264729,12368087,16314571,16314568,70228,2532362,10506132,11784313,9447985,9447981,8390989,10574991,9335523,12368079,10574976,3418353,2184368,10888617,7684040,2358074,9794820,7644482,11593040,3918306,8264558,7644498,9479042,8807285,16469117,12586342,1988958,10852813,11172064,9479038,8703001,9335335,11034354,1988940,8491776,11172090,16983194,9335337,81725 96,9917379,16781736,8738474,8876198,8703012,1646719,9335303,11875103,15288790,14729954,9335308,7613471,1646711,9917402,8703025,15258463,11784326,9917404,3488539,16500040,9478973,8876238,3519213,11478951,10783391,3276522,8052308,12213213,12183381,10783387,11034289,9917369,11804786,8052313,15048107,15048104,15048103,11171974,1744050,10375459,7990141,12213246,2843548,9478926,12457963,7593166,11964380,7990128,12492399,14978743,7593165,2982857,9795152,11928987,9121426,11264467,1709810,10748158,12966076,9548740,11264454,12553912,10606204,3061461,8950276,12553908,10713540,12122015,10471492,12152085,12122003,2890081,12121998,9121443,1620290,12553882,12966028,1491694,2877922,12368867,15471878,12368864,12368870,8806522,12368868,10713515,9572109,11264412,8422392,10852900,9447706,10888872,10713530,8738157,15909982,10068515,12966101,9335269,2149646,10888849,8632014,6060189,10852868,14978306,12966087,10350098,9795118,14769042,12686546,15288868,12368860,10748045,10818442,14729699,16564010,10748030, 7893687,11714714,16227203,11451995,12897056,7954852,14769018,7954845,2219722,12897052,3031010,11452010,11264366,7893643,3031032,11909544,10747978,9152425,1408743,7954826,14729686,7893645,12724372,8631828,3700359,12724373,7954819,12897151,8950484,10783165,10644007,12897137,11095707,10747959,1560845,1560844,10818343,1369099,2602148,7989351,10606266,8017104,8841567,3883995,7893714,2643381,11451956,11451959,17337072,8631890,8113739,10747911,14729625,11805318,1560772,11874691,8114095,8114093,14729328,10889186,15367757,1560779,8841401,9847390,2602367,8841393,1647358,12655644,9847406,10644438,9760239,2253781,8325635,9916798,2392150,10471738,8876648,10713267,11452312,10100640,15186216,12429822,11452311,2184888,7989747,14729263,9847327,16000721,8561899,9121761,7713897,8919789,16500675,9847332,7713895,9847328,9847359,16842832,10644354,3947330,9121551,12121639,9548374,12686643,11714961,12121644,1709933,1647207,947,7836314,7836312,12429613,9121560,7836306,12686638,11373120,15910274,14978252,3542 048,15289326,10536154,12686616,10889041,9830012,6090951,8703509,15506791,11784867,2253617,8491379,10037793,10818110,11276424,10471843,10713131,9882386,2643102,1585456,10993083,2705303,10993081,1585460,9292993,10748213,9829935,9671738,11033765,1682314,7523833,9829924,10037771,12368458,9829949,14729348,12429641,1620116 at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1436) at java.net.URL.openStream(URL.java:1010) at org.intermine.bio.dataconversion.EntrezPublicationsRetriever.getReader(EntrezPublicationsRetriever.java:331) at org.intermine.bio.dataconversion.EntrezPublicationsRetriever.execute(EntrezPublicationsRetriever.java:210) ... 37 more Total time: 17 seconds > Hi Ivan, > I just ran than that step on the intermine_0_98 branch and it works > fine > for me. The code that has gone wrong comes from two jars we use from > OBO-Edit we use for parsing ontologies - obo.jar and bbop.jar. Is it > possibly you have other versions of these jars on you system and in > your classpath? > > Did you run ant with the -v option to get the error message you sent? > If not 'ant -v clean build-db' it should provide a more complete > stack > trace. > > Regards, > Richard. > > > On 13/03/2012 15:46, Ivan Merelli wrote: >> Dear Intermine developers, >> I'm trying to follow the tutorial about malariamine, >> but I have a problem the "ant clean build-db" step. >> >> The problem arise both with version 0.98 and 0.99 >> Any hits about the possible problem? >> The obo files seem ok. >> Best >> I. >> >> >> >> create-so-model: >> [so-model] Starting OboToModel conversion from >> /home/gmod/intermine_0_98/bio/sources/so/data/so_2_4_4.obo to >> >> /home/gmod/intermine_0_98/malariamine/dbmodel/build/model/so_additions.xml. >> Filtering on 47 obo terms from >> >> /home/gmod/intermine_0_98/malariamine/dbmodel/resources/so_term_list.txt >> >> BUILD FAILED >> /home/gmod/intermine_0_98/malariamine/dbmodel/build.xml:12: >> java.lang.RuntimeException: Parsing obo file failed >> at >> org.intermine.bio.ontology.OboToModel.parseOboTerms(OboToModel.java:258) >> at >> >> org.intermine.bio.ontology.OboToModel.createAndWriteModel(OboToModel.java:102) >> >> at >> org.intermine.bio.task.SOToModelTask.execute(SOToModelTask.java:68) >> at >> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291) >> at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source) >> at >> >> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) >> >> at java.lang.reflect.Method.invoke(Method.java:597) >> at >> >> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) >> at org.apache.tools.ant.Task.perform(Task.java:348) >> at org.apache.tools.ant.Target.execute(Target.java:390) >> at org.apache.tools.ant.Target.performTasks(Target.java:411) >> at >> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399) >> at org.apache.tools.ant.Project.executeTarget(Project.java:1368) >> at >> >> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41) >> >> at org.apache.tools.ant.Project.executeTargets(Project.java:1251) >> at org.apache.tools.ant.Main.runBuild(Main.java:809) >> at org.apache.tools.ant.Main.startAnt(Main.java:217) >> at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280) >> at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109) >> Caused by: org.bbop.dataadapter.DataAdapterException: Bad >> configuration >> at >> >> org.obo.dataadapter.SimpleLinkFileAdapter.doOperation(SimpleLinkFileAdapter.java:132) >> >> at >> >> org.intermine.bio.ontology.OboParser.processRelations(OboParser.java:120) >> at >> org.intermine.bio.ontology.OboToModel.parseOboTerms(OboToModel.java:254) >> ... 18 more >> >> >> >> _______________________________________________ >> dev mailing list >> [hidden email] >> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev >> > > > _______________________________________________ > dev mailing list > [hidden email] > http://mail.intermine.org/cgi-bin/mailman/listinfo/dev _______________________________________________ dev mailing list [hidden email] http://mail.intermine.org/cgi-bin/mailman/listinfo/dev |
Re: obo file
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Hi Ivan,
Good to hear the ontology problem is solved. Fetching publication details goes wrong sometimes and the usual solution is to try again. As you can see it batches up pubmed ids and requests details from the NCBI web service. It uses batches of 500 which is the recommended maximum and we haven't had problems with batch size. Can you try a second time and see what happens? I haven't seen a 413 error with this before, it's possibly an NCBI glitch, or could it be a proxy that you're accessing the web through that is actually causing the problem? If the issue persists you could try a smaller number of publications at once by editing the BATCH_SIZE constant in: bio/sources/update-publications/main/src/org/intermine/bio/dataconversion/EntrezPublicationsRetriever.java Regards, Richard. On 14/03/2012 17:07, Ivan Merelli wrote: > Hi Richard, > > I tried to compile intermine in another machine and it works. > It's very strange because the configuration are almost identical, > but there should be some differences in the java environment. > > It's possible that a java installation in the machine (but not > in path or classpath) would interfere with the compilation? > > However, I fall into another (simpler I think), which seems to > be correlated with the high number of requested pubblications. > Have you any idea about how to work around this problem? > > Best, > Ivan > > BUILD FAILED > /home/gmod/intermine_0.98/imbuild/integrate.xml:54: The following error > occurred while executing this line: > /home/gmod/intermine_0.98/bio/sources/update-publications/build.xml:19: > java.lang.RuntimeException: failed to get all publications > at > org.intermine.bio.dataconversion.EntrezPublicationsRetriever.execute(EntrezPublicationsRetriever.java:255) > > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > > at java.lang.reflect.Method.invoke(Method.java:597) > at > org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) > at org.apache.tools.ant.TaskAdapter.execute(TaskAdapter.java:154) > at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291) > at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > > at java.lang.reflect.Method.invoke(Method.java:597) > at > org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) > at org.apache.tools.ant.Task.perform(Task.java:348) > at org.apache.tools.ant.Target.execute(Target.java:390) > at org.apache.tools.ant.Target.performTasks(Target.java:411) > at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399) > at > org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38) > > at org.apache.tools.ant.Project.executeTargets(Project.java:1251) > at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442) > at org.intermine.task.Integrate.performAction(Integrate.java:223) > at org.intermine.task.Integrate.performAction(Integrate.java:135) > at org.intermine.task.Integrate.execute(Integrate.java:127) > at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291) > at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > > at java.lang.reflect.Method.invoke(Method.java:597) > at > org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) > at org.apache.tools.ant.Task.perform(Task.java:348) > at org.apache.tools.ant.Target.execute(Target.java:390) > at org.apache.tools.ant.Target.performTasks(Target.java:411) > at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399) > at org.apache.tools.ant.Project.executeTarget(Project.java:1368) > at > org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41) > > at org.apache.tools.ant.Project.executeTargets(Project.java:1251) > at org.apache.tools.ant.Main.runBuild(Main.java:809) > at org.apache.tools.ant.Main.startAnt(Main.java:217) > at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280) > at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109) > Caused by: java.io.IOException: Server returned HTTP response code: 413 > for URL: > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?tool=flymine&db=pubmed&id=1339256,8842143,8982256,16843540,11805111,9230443,9230440,8112347,9449261,8052624,3275622,9724722,2051020,2288911,16956381,7593276,9448314,9724718,8052622,8630491,14730069,8390675,10069007,12368295,8668213,12368292,11805083,9847123,2738582,11562374,11963920,12825828,11805056,10535734,8491711,9829828,12032320,8265339,16439205,11839499,11839498,11839496,9829834,8052647,16034825,12430018,2019586,10438592,8491722,1460533,8203015,1438195,15082709,7990931,10410243,2019595,8203016,11591723,8203019,15153112,10438606,1460542,11910013,8491736,8356049,8462099,12032293,12032297,15153096,11875053,7523953,10675539,1531480,14977918,1647027,11875025,15258264,11591680,7766608,7929272,7990960,3398920,7682712,8877373,7990966,2572197,9724744,10375352,1648106,16407072,9724743,8530482,3419519,14570563,8325512,1339380,15013215,14570569,2357963,1988676,8631297,8325507,9602175,15367656,14570579,12429853,8631325,3092220,1123 > > 020,12429843,10958669,7893120,4071057,8113161,2501756,11910040,16314687,2643922,9151888,12033438,8113189,10037605,2184573,2361956,14699121,8113187,3092189,9725901,14699122,2361961,1491009,8421692,11910018,1709161,1491011,8078761,9370339,1805969,1339315,11805049,1339314,810352,9151968,15047868,16650980,7683665,11513613,11684675,11964120,9448330,9370319,2572081,11684678,9151947,1681580,8325628,10958635,9917067,15755454,8234909,12492443,8631706,10375639,8631704,11839791,8631708,10643909,8631687,11593005,1867713,10506180,7592990,11478874,10817761,15258569,3171483,11592977,2462055,10888672,9846876,6246116,9846873,9846874,9846875,11478849,11264729,12368087,16314571,16314568,70228,2532362,10506132,11784313,9447985,9447981,8390989,10574991,9335523,12368079,10574976,3418353,2184368,10888617,7684040,2358074,9794820,7644482,11593040,3918306,8264558,7644498,9479042,8807285,16469117,12586342,1988958,10852813,11172064,9479038,8703001,9335335,11034354,1988940,8491776,11172090,16983194,9335337,8172 5 > > 96,9917379,16781736,8738474,8876198,8703012,1646719,9335303,11875103,15288790,14729954,9335308,7613471,1646711,9917402,8703025,15258463,11784326,9917404,3488539,16500040,9478973,8876238,3519213,11478951,10783391,3276522,8052308,12213213,12183381,10783387,11034289,9917369,11804786,8052313,15048107,15048104,15048103,11171974,1744050,10375459,7990141,12213246,2843548,9478926,12457963,7593166,11964380,7990128,12492399,14978743,7593165,2982857,9795152,11928987,9121426,11264467,1709810,10748158,12966076,9548740,11264454,12553912,10606204,3061461,8950276,12553908,10713540,12122015,10471492,12152085,12122003,2890081,12121998,9121443,1620290,12553882,12966028,1491694,2877922,12368867,15471878,12368864,12368870,8806522,12368868,10713515,9572109,11264412,8422392,10852900,9447706,10888872,10713530,8738157,15909982,10068515,12966101,9335269,2149646,10888849,8632014,6060189,10852868,14978306,12966087,10350098,9795118,14769042,12686546,15288868,12368860,10748045,10818442,14729699,16564010,10748030 , > > 7893687,11714714,16227203,11451995,12897056,7954852,14769018,7954845,2219722,12897052,3031010,11452010,11264366,7893643,3031032,11909544,10747978,9152425,1408743,7954826,14729686,7893645,12724372,8631828,3700359,12724373,7954819,12897151,8950484,10783165,10644007,12897137,11095707,10747959,1560845,1560844,10818343,1369099,2602148,7989351,10606266,8017104,8841567,3883995,7893714,2643381,11451956,11451959,17337072,8631890,8113739,10747911,14729625,11805318,1560772,11874691,8114095,8114093,14729328,10889186,15367757,1560779,8841401,9847390,2602367,8841393,1647358,12655644,9847406,10644438,9760239,2253781,8325635,9916798,2392150,10471738,8876648,10713267,11452312,10100640,15186216,12429822,11452311,2184888,7989747,14729263,9847327,16000721,8561899,9121761,7713897,8919789,16500675,9847332,7713895,9847328,9847359,16842832,10644354,3947330,9121551,12121639,9548374,12686643,11714961,12121644,1709933,1647207,947,7836314,7836312,12429613,9121560,7836306,12686638,11373120,15910274,14978252,354 2 > > 048,15289326,10536154,12686616,10889041,9830012,6090951,8703509,15506791,11784867,2253617,8491379,10037793,10818110,11276424,10471843,10713131,9882386,2643102,1585456,10993083,2705303,10993081,1585460,9292993,10748213,9829935,9671738,11033765,1682314,7523833,9829924,10037771,12368458,9829949,14729348,12429641,1620116 > > at > sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1436) > > at java.net.URL.openStream(URL.java:1010) > at > org.intermine.bio.dataconversion.EntrezPublicationsRetriever.getReader(EntrezPublicationsRetriever.java:331) > > at > org.intermine.bio.dataconversion.EntrezPublicationsRetriever.execute(EntrezPublicationsRetriever.java:210) > > ... 37 more > > Total time: 17 seconds > > > > >> Hi Ivan, >> I just ran than that step on the intermine_0_98 branch and it works fine >> for me. The code that has gone wrong comes from two jars we use from >> OBO-Edit we use for parsing ontologies - obo.jar and bbop.jar. Is it >> possibly you have other versions of these jars on you system and in >> your classpath? >> >> Did you run ant with the -v option to get the error message you sent? >> If not 'ant -v clean build-db' it should provide a more complete stack >> trace. >> >> Regards, >> Richard. >> >> >> On 13/03/2012 15:46, Ivan Merelli wrote: >>> Dear Intermine developers, >>> I'm trying to follow the tutorial about malariamine, >>> but I have a problem the "ant clean build-db" step. >>> >>> The problem arise both with version 0.98 and 0.99 >>> Any hits about the possible problem? >>> The obo files seem ok. >>> Best >>> I. >>> >>> >>> >>> create-so-model: >>> [so-model] Starting OboToModel conversion from >>> /home/gmod/intermine_0_98/bio/sources/so/data/so_2_4_4.obo to >>> >>> /home/gmod/intermine_0_98/malariamine/dbmodel/build/model/so_additions.xml. >>> >>> Filtering on 47 obo terms from >>> >>> /home/gmod/intermine_0_98/malariamine/dbmodel/resources/so_term_list.txt >>> >>> BUILD FAILED >>> /home/gmod/intermine_0_98/malariamine/dbmodel/build.xml:12: >>> java.lang.RuntimeException: Parsing obo file failed >>> at >>> org.intermine.bio.ontology.OboToModel.parseOboTerms(OboToModel.java:258) >>> at >>> >>> org.intermine.bio.ontology.OboToModel.createAndWriteModel(OboToModel.java:102) >>> >>> >>> at org.intermine.bio.task.SOToModelTask.execute(SOToModelTask.java:68) >>> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291) >>> at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source) >>> at >>> >>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) >>> >>> >>> at java.lang.reflect.Method.invoke(Method.java:597) >>> at >>> >>> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) >>> >>> at org.apache.tools.ant.Task.perform(Task.java:348) >>> at org.apache.tools.ant.Target.execute(Target.java:390) >>> at org.apache.tools.ant.Target.performTasks(Target.java:411) >>> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399) >>> at org.apache.tools.ant.Project.executeTarget(Project.java:1368) >>> at >>> >>> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41) >>> >>> >>> at org.apache.tools.ant.Project.executeTargets(Project.java:1251) >>> at org.apache.tools.ant.Main.runBuild(Main.java:809) >>> at org.apache.tools.ant.Main.startAnt(Main.java:217) >>> at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280) >>> at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109) >>> Caused by: org.bbop.dataadapter.DataAdapterException: Bad configuration >>> at >>> >>> org.obo.dataadapter.SimpleLinkFileAdapter.doOperation(SimpleLinkFileAdapter.java:132) >>> >>> >>> at >>> >>> org.intermine.bio.ontology.OboParser.processRelations(OboParser.java:120) >>> >>> at >>> org.intermine.bio.ontology.OboToModel.parseOboTerms(OboToModel.java:254) >>> ... 18 more >>> >>> >>> >>> _______________________________________________ >>> dev mailing list >>> [hidden email] >>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev >>> >> >> >> _______________________________________________ >> dev mailing list >> [hidden email] >> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev > > > _______________________________________________ > dev mailing list > [hidden email] > http://mail.intermine.org/cgi-bin/mailman/listinfo/dev > _______________________________________________ dev mailing list [hidden email] http://mail.intermine.org/cgi-bin/mailman/listinfo/dev |
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