model build with model merger error

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

model build with model merger error

Pengcheng Yang
Hi miners,

I am encounter an error during build-db. the following listed are the
error message from build-db [1] and the message from pbuild.log [2].

The error message told me that the data model file has an error, but
didn't give specific information about where the error was from the
model file.

Could anyone please give some suggestions?

Best,

Pengcheng Yang


##################

1. error message from build-db


Fri Aug  3 18:27:46 CST 2018


running: psql -U postgres -h localhost -d postgres -l

not creating locustmine as it already exists

Fri Aug  3 18:27:46 CST 2018


building db: ant -v build-db

Fri Aug  3 18:27:46 CST 2018

starting command: ant -v clean

Fri Aug  3 18:27:47 CST 2018

finished


Fri Aug  3 18:27:47 CST 2018

starting command: ant -v build-db


BUILD FAILED
/home/pengchy/soft/intermine/imbuild/objectstore.xml:161: exception
while invoking execute on org.intermine.task.ModelMergerTask
         at
org.intermine.task.MergeSourceModelsTask.execute(MergeSourceModelsTask.java:162)
         at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
         at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
         at java.lang.reflect.Method.invoke(Method.java:498)
         at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
         at org.apache.tools.ant.Task.perform(Task.java:352)
         at org.apache.tools.ant.Target.execute(Target.java:437)
         at org.apache.tools.ant.Target.performTasks(Target.java:458)
         at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1405)
         at org.apache.tools.ant.Project.executeTarget(Project.java:1376)
         at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
         at org.apache.tools.ant.Project.executeTargets(Project.java:1260)
         at org.apache.tools.ant.Main.runBuild(Main.java:857)
         at org.apache.tools.ant.Main.startAnt(Main.java:236)
         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:286)
         at org.apache.tools.ant.launch.Launcher.main(Launcher.java:112)
Caused by: java.lang.reflect.InvocationTargetException
         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
         at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
         at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
         at java.lang.reflect.Method.invoke(Method.java:498)
         at
org.intermine.task.MergeSourceModelsTask.execute(MergeSourceModelsTask.java:160)
         ... 16 more
Caused by: Failed to parse model from input files
         at
org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:85)
         ... 21 more
Caused by: org.intermine.metadata.MetaDataException: Exception while
merging
/home/pengchy/Project/LocustMine/testdata/merged_model/merged_model_split_manual.xml
into
/home/pengchy/soft/intermine/locustmine/dbmodel/build/model/genomic_model.xml
         at
org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:66)
         at
org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:80)
         ... 21 more
Caused by: org.intermine.metadata.ModelParserException:
java.lang.NullPointerException
         at
org.intermine.metadata.InterMineModelParser.generateClassDescriptors(InterMineModelParser.java:72)
         at
org.intermine.modelproduction.ModelFileMerger.processFile(ModelFileMerger.java:86)
         at
org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:64)
         ... 22 more
Caused by: java.lang.NullPointerException
         at
org.intermine.metadata.InterMineModelParser$SkeletonClass.<init>(InterMineModelParser.java:220)
         at
org.intermine.metadata.InterMineModelParser$ModelHandler.startElement(InterMineModelParser.java:114)
         at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:509)
         at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(XMLDocumentFragmentScannerImpl.java:1359)
         at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2784)
         at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
         at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)
         at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:842)
         at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:771)
         at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
         at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213)
         at
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:643)
         at
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java:327)
         at org.intermine.metadata.SAXParser.parse(SAXParser.java:59)
         at org.intermine.metadata.SAXParser.parse(SAXParser.java:42)
         at
org.intermine.metadata.InterMineModelParser.generateClassDescriptors(InterMineModelParser.java:69)
         ... 24 more

Total time: 5 seconds
Fri Aug  3 18:27:53 CST 2018

finished


ERROR: 256
failed with exit code 0: ant -v build-db

check log: pbuild.log

############################

2. error message from pbuild.log

===============

   [ant] -load-web-tasks:
   [ant] Skipped because property 'antlib-web-available' not set.
   [ant]
   [ant] -load-task-taskdefs:
   [ant]
   [ant] -init-macrodef-build-db:
   [ant]  [macrodef] creating macro
http://www.intermine.org/ns/im-task-proj/1:build-db
   [ant]
   [ant] -init-task-xml:
   [ant]
   [ant] -init-build-db:
   [ant]
   [ant] -define-macrodef-merge-additions:
   [ant]  [macrodef] creating macro  merge-additions
   [ant]
   [ant] create-so-model:
   [ant]  [so-model] Total terms: 1935
   [ant]  [so-model] Total terms, post-pruning: 85
   [ant]  [so-model] Total terms, post-flattening: 47
   [ant]  [so-model] Wrote
/home/pengchy/soft/intermine/locustmine/dbmodel/build/model/so_additions.xml
   [ant]
   [ant] -pre-init-merge:
   [ant]
   [ant] -init-merge:
   [ant]      [copy] Copying 1 file to
/home/pengchy/soft/intermine/locustmine/dbmodel/build/model
   [ant]      [copy] Copying
/home/pengchy/soft/intermine/bio/core/core.xml to
/home/pengchy/soft/intermine/locustmine/dbmodel/build/model/genomic_model.xml
   [ant]
   [ant] -init-extra-models-start:
   [ant] Skipped because property 'extra.model.paths.start' set.
   [ant]
   [ant] -init-extra-models-end:
   [ant]
   [ant] -merge-models:
   [ant] [merge-source-models] merging model additions from:
/home/pengchy/soft/intermine/locustmine/dbmodel/build/model/so_additions.xml
   [ant] [merge-source-models] merging model additions from:
/home/pengchy/soft/intermine/bio/core/genomic_additions.xml
Fri Aug  3 18:27:53 CST 2018

finished


failed with exit code 0: ant -v build-db

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: model build with model merger error

Pengcheng Yang
Hi miners,

In case the future similar problem, I listed the reason caused this problem:

1. redundant "/" at the end of the name of the class:
WRONG: <class name="SOTerm" extends="OntologyTerm"
is-interface="true"/></class>
WRIGHT: <class name="SOTerm" extends="OntologyTerm"
is-interface="true"></class>

2. absence of "/" at the end tag </class>
WRONG: <class name="SOTerm" extends="OntologyTerm"
is-interface="true"><class>
WRIGHT: <class name="SOTerm" extends="OntologyTerm"
is-interface="true"></class>

Best,
Pengcheng

On 2018-8-3 18:38, Pengcheng Yang wrote:

> Hi miners,
>
> I am encounter an error during build-db. the following listed are the
> error message from build-db [1] and the message from pbuild.log [2].
>
> The error message told me that the data model file has an error, but
> didn't give specific information about where the error was from the
> model file.
>
> Could anyone please give some suggestions?
>
> Best,
>
> Pengcheng Yang
>
>
> ##################
>
> 1. error message from build-db
>
>
> Fri Aug  3 18:27:46 CST 2018
>
>
> running: psql -U postgres -h localhost -d postgres -l
>
> not creating locustmine as it already exists
>
> Fri Aug  3 18:27:46 CST 2018
>
>
> building db: ant -v build-db
>
> Fri Aug  3 18:27:46 CST 2018
>
> starting command: ant -v clean
>
> Fri Aug  3 18:27:47 CST 2018
>
> finished
>
>
> Fri Aug  3 18:27:47 CST 2018
>
> starting command: ant -v build-db
>
>
> BUILD FAILED
> /home/pengchy/soft/intermine/imbuild/objectstore.xml:161: exception
> while invoking execute on org.intermine.task.ModelMergerTask
>         at
> org.intermine.task.MergeSourceModelsTask.execute(MergeSourceModelsTask.java:162)
>         at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>         at java.lang.reflect.Method.invoke(Method.java:498)
>         at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>         at org.apache.tools.ant.Task.perform(Task.java:352)
>         at org.apache.tools.ant.Target.execute(Target.java:437)
>         at org.apache.tools.ant.Target.performTasks(Target.java:458)
>         at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1405)
>         at org.apache.tools.ant.Project.executeTarget(Project.java:1376)
>         at
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>         at org.apache.tools.ant.Project.executeTargets(Project.java:1260)
>         at org.apache.tools.ant.Main.runBuild(Main.java:857)
>         at org.apache.tools.ant.Main.startAnt(Main.java:236)
>         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:286)
>         at org.apache.tools.ant.launch.Launcher.main(Launcher.java:112)
> Caused by: java.lang.reflect.InvocationTargetException
>         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>         at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>         at java.lang.reflect.Method.invoke(Method.java:498)
>         at
> org.intermine.task.MergeSourceModelsTask.execute(MergeSourceModelsTask.java:160)
>         ... 16 more
> Caused by: Failed to parse model from input files
>         at
> org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:85)
>         ... 21 more
> Caused by: org.intermine.metadata.MetaDataException: Exception while
> merging
> /home/pengchy/Project/LocustMine/testdata/merged_model/merged_model_split_manual.xml
> into
> /home/pengchy/soft/intermine/locustmine/dbmodel/build/model/genomic_model.xml
>         at
> org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:66)
>         at
> org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:80)
>         ... 21 more
> Caused by: org.intermine.metadata.ModelParserException:
> java.lang.NullPointerException
>         at
> org.intermine.metadata.InterMineModelParser.generateClassDescriptors(InterMineModelParser.java:72)
>         at
> org.intermine.modelproduction.ModelFileMerger.processFile(ModelFileMerger.java:86)
>         at
> org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:64)
>         ... 22 more
> Caused by: java.lang.NullPointerException
>         at
> org.intermine.metadata.InterMineModelParser$SkeletonClass.<init>(InterMineModelParser.java:220)
>         at
> org.intermine.metadata.InterMineModelParser$ModelHandler.startElement(InterMineModelParser.java:114)
>         at
> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:509)
>         at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(XMLDocumentFragmentScannerImpl.java:1359)
>         at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2784)
>         at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
>         at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)
>         at
> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:842)
>         at
> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:771)
>         at
> com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
>         at
> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213)
>         at
> com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:643)
>         at
> com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java:327)
>         at org.intermine.metadata.SAXParser.parse(SAXParser.java:59)
>         at org.intermine.metadata.SAXParser.parse(SAXParser.java:42)
>         at
> org.intermine.metadata.InterMineModelParser.generateClassDescriptors(InterMineModelParser.java:69)
>         ... 24 more
>
> Total time: 5 seconds
> Fri Aug  3 18:27:53 CST 2018
>
> finished
>
>
> ERROR: 256
> failed with exit code 0: ant -v build-db
>
> check log: pbuild.log
>
> ############################
>
> 2. error message from pbuild.log
>
> ===============
>
>   [ant] -load-web-tasks:
>   [ant] Skipped because property 'antlib-web-available' not set.
>   [ant]
>   [ant] -load-task-taskdefs:
>   [ant]
>   [ant] -init-macrodef-build-db:
>   [ant]  [macrodef] creating macro
> http://www.intermine.org/ns/im-task-proj/1:build-db
>   [ant]
>   [ant] -init-task-xml:
>   [ant]
>   [ant] -init-build-db:
>   [ant]
>   [ant] -define-macrodef-merge-additions:
>   [ant]  [macrodef] creating macro  merge-additions
>   [ant]
>   [ant] create-so-model:
>   [ant]  [so-model] Total terms: 1935
>   [ant]  [so-model] Total terms, post-pruning: 85
>   [ant]  [so-model] Total terms, post-flattening: 47
>   [ant]  [so-model] Wrote
> /home/pengchy/soft/intermine/locustmine/dbmodel/build/model/so_additions.xml
>   [ant]
>   [ant] -pre-init-merge:
>   [ant]
>   [ant] -init-merge:
>   [ant]      [copy] Copying 1 file to
> /home/pengchy/soft/intermine/locustmine/dbmodel/build/model
>   [ant]      [copy] Copying
> /home/pengchy/soft/intermine/bio/core/core.xml to
> /home/pengchy/soft/intermine/locustmine/dbmodel/build/model/genomic_model.xml
>   [ant]
>   [ant] -init-extra-models-start:
>   [ant] Skipped because property 'extra.model.paths.start' set.
>   [ant]
>   [ant] -init-extra-models-end:
>   [ant]
>   [ant] -merge-models:
>   [ant] [merge-source-models] merging model additions from:
> /home/pengchy/soft/intermine/locustmine/dbmodel/build/model/so_additions.xml
>   [ant] [merge-source-models] merging model additions from:
> /home/pengchy/soft/intermine/bio/core/genomic_additions.xml
> Fri Aug  3 18:27:53 CST 2018
>
> finished
>
>
> failed with exit code 0: ant -v build-db
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev