[InterMine Dev] obo file

Ivan Merelli ivan.merelli at itb.cnr.it
Wed Mar 14 17:07:54 GMT 2012


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
>> dev at intermine.org
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>
>
> _______________________________________________
> dev mailing list
> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev




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