[InterMine Dev] obo file

Richard Smith richard at flymine.org
Thu Mar 15 12:12:44 GMT 2012


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
4
>
> 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
>>> dev at intermine.org
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>
>>
>>
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>> dev mailing list
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>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
>
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