Installation Error: gate.persist.PersistenceException: Some resources cannot be restored

[robkoe...@gmail.com]

I'm trying to install Behemoth, but I am encountering a problem. Not sure what lines of the log to include, but the three snippets below seem to be relevant.
I tried to compile it both on a Mac running OSX 10.7.5 and on a Linux machine (running Ubuntu 14.04). Both gave the same error.

Any help would be appreciated!

Best,

   - Rob




Tests run: 3, Failures: 0, Errors: 3, Skipped: 0, Time elapsed: 7.404 sec <<< FAILURE!

Results :

Tests in error:
  testTokenizationANNIE(com.digitalpebble.behemoth.gate.GATEProcessorTest): gate.persist.PersistenceException: Some resources cannot be restored:
  testTokenizationANNIE2(com.digitalpebble.behemoth.gate.GATEProcessorTest): gate.persist.PersistenceException: Some resources cannot be restored:
  testTokenizationANNIE3(com.digitalpebble.behemoth.gate.GATEProcessorTest): gate.persist.PersistenceException: Some resources cannot be restored:

Tests run: 3, Failures: 0, Errors: 3, Skipped: 0

[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Behemoth Parent ................................... SUCCESS [3.687s]
[INFO] core .............................................. SUCCESS [12.575s]
[INFO] gate .............................................. FAILURE [12.543s]
[INFO] tika .............................................. SKIPPED
[INFO] uima .............................................. SKIPPED
[INFO] io ................................................ SKIPPED
[INFO] mahout ............................................ SKIPPED
[INFO] solr .............................................. SKIPPED
[INFO] language-id ....................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------





15/01/28 15:57:43 ERROR gate.GATEProcessor: Encountered error while initialising GATE
gate.persist.PersistenceException: Some resources cannot be restored:
Error while parsing the grammar (file:/var/folders/0x/jmyjtm1j5q7fmkh2z2wh7mmh0000gq/T/ANNIE/plugins/ANNIE/resources/tokeniser/postprocess.jape):
Error while parsing the grammar (file:/var/folders/0x/jmyjtm1j5q7fmkh2z2wh7mmh0000gq/T/ANNIE/plugins/ANNIE/resources/sentenceSplitter/grammar/main.jape):
Error while parsing the grammar (file:/var/folders/0x/jmyjtm1j5q7fmkh2z2wh7mmh0000gq/T/ANNIE/plugins/ANNIE/resources/NE/main.jape):
    at gate.util.persistence.CollectionPersistence.createObject(CollectionPersistence.java:87)






-------------------------------------------------------
 T E S T S
-------------------------------------------------------
Running com.digitalpebble.behemoth.gate.GATEProcessorTest
/Users/robk/StratifiedMedical/Behemoth/behemoth/gate/target/test-classes/ANNIE.zip
15/01/28 15:57:37 INFO gate.GATEProcessor: Setting GATE_HOME as /var/folders/0x/jmyjtm1j5q7fmkh2z2wh7mmh0000gq/T/ANNIE
15/01/28 15:57:38 INFO creole.CreoleRegisterImpl: CREOLE plugin loaded: file:/var/folders/0x/jmyjtm1j5q7fmkh2z2wh7mmh0000gq/T/ANNIE/plugins/ANNIE/
Compilation error
gate.util.compilers.eclipse.jdt.internal.compiler.classfmt.ClassFormatException
    at gate.util.compilers.eclipse.jdt.internal.compiler.classfmt.ClassFileReader.<init>(ClassFileReader.java:372)

[DigitalPebble]

Hi Rob

Can you see something under /var/folders/0x/jmyjtm1j5q7fmkh2z2wh7mmh0000gq/T/ANNIE ? Do you have read access for that directory?

Julien

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[Rob Koeling]

Hi Julien,

Thanks for the swift reply!

Yes, I can read the contents of that directory. It contains a file ('application.xgapp') and a directory ('plugins').

On the Linux machine these files are under '/tmp/ANNIE' and also there I have read access and the files it is looking for do actually exist.

  - Rob

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[DigitalPebble]

That's not something I've heard of before. Is GATE installed on these machines? I can't think of a reason why it would interfere but you never know.

Is the content of the directory exactly the same as what behemoth/gate/src/test/resources/Annie.zip contains? 

[Rob Koeling]

On Wed, Jan 28, 2015 at 4:56 PM, DigitalPebble <jul...@digitalpebble.com> wrote:

That's not something I've heard of before. Is GATE installed on these machines? I can't think of a reason why it would interfere but you never know.

No,  Gate is not installed on either machine. So, that doesn't seems to introduce the problem

 

Is the content of the directory exactly the same as what behemoth/gate/src/test/resources/Annie.zip contains? 

Yes, it is.

I was just thinking, is it possible that there have been changes recently that introduced unforeseen issues? (I just thought it was odd that I get the same behaviour on two different machines) Would it make sense if you tried to clone the git  project and do a 'mvn install' to see if nothing is broken?

Thanks for your help!

  - Rob

[DigitalPebble]

Hi Rob

I have just re-cloned behemoth and ran the tests : 

Results :

Tests run: 1, Failures: 0, Errors: 0, Skipped: 0

[INFO] ------------------------------------------------------------------------

[INFO] Reactor Summary:

[INFO] 

[INFO] Behemoth Parent ................................... SUCCESS [1.210s]

[INFO] core .............................................. SUCCESS [3.961s]

[INFO] gate .............................................. SUCCESS [17.790s]

[INFO] tika .............................................. SUCCESS [3.686s]

[INFO] uima .............................................. SUCCESS [3.228s]

[INFO] io ................................................ SUCCESS [3.642s]

[INFO] mahout ............................................ SUCCESS [2.167s]

[INFO] solr .............................................. SUCCESS [2.693s]

[INFO] language-id ....................................... SUCCESS [2.501s]

[INFO] ------------------------------------------------------------------------

[INFO] BUILD SUCCESS

[INFO] ------------------------------------------------------------------------

I fixed an issue yesterday but it was related to a recent update of Tika and I doubt it had any impact on the GATE module.

mvn -v

Apache Maven 3.0.4

Maven home: /usr/share/maven

Java version: 1.7.0_51, vendor: Oracle Corporation

Java home: /usr/lib/jvm/java-7-openjdk-amd64/jre

Default locale: en_GB, platform encoding: UTF-8

OS name: "linux", version: "3.8.0-19-generic", arch: "amd64", family: "unix"

what do you get for these?

Thanks

Julien

[Rob Koeling]

Hi Julien,

Thanks for that. The trouble seems to be with my version of Java. I have Java8 installed.

I just tried to compile it with Java7 (on the Linux machine) and all is well:

[INFO] Reactor Summary:
[INFO]
[INFO] Behemoth Parent ................................... SUCCESS [0.993s]
[INFO] core .............................................. SUCCESS [3.362s]
[INFO] gate .............................................. SUCCESS [7.738s]
[INFO] tika .............................................. SUCCESS [1:44.943s]
[INFO] uima .............................................. SUCCESS [15.675s]
[INFO] io ................................................ SUCCESS [58.178s]
[INFO] mahout ............................................ SUCCESS [21.882s]
[INFO] solr .............................................. SUCCESS [8.500s]
[INFO] language-id ....................................... SUCCESS [8.995s]

[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS

I'll get Java7 for the Mac and try to install it there as well. If you don't hear back from me, then all is well.

Thanks again for your help.

Best,

   - Rob

[DigitalPebble]

Hi Rob, 

You are welcome. Glad we got to the bottom of it.

Out of curiosity, what will you be using Behemoth + GATE for?

Julien

[Rob Koeling]

Hi Julien,

Not necessarily using Gate, but the goal is to do large scale document processing within the UIMA framework. I want to store the output in ElasticSearch. So, it looks like Behemoth is just the ticket.

It's all running now, so I'll have a play over the next few days.

Cheers,

   - Rob