#442 - Upgrade to UIMAv3 #443
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- Pull UIMA and uimaFIT versions up to 3.3.0
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I'm no longer active in ClearTK development, but I think upgrading ClearTK to UIMAv3 would be excellent. Feel free to go ahead and make any changes necessary. Do you have the permissions to make a new ClearTK release when complete? If not, let's get them for you. I think dependabot is yelling at us to make an updated release too, so it would be good to merge those changes as well. |
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I have full permissions on this repo/org. I do not have sufficient permissions for releases on Sonatype OSS (which I think ClearTK uses as well). That said, I also have very little resources at hand. I've posted to the cTAKES list hoping to motivate somebody to join the effort. |
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It will be an excellent migration to support UIMAV3. |
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Contributions are welcome. |
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I have added a small todo list at the top - in particular currently tests are not successful - not even on the main branch against v2. |
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@reckart JCas Class "de.tudarmstadt.ukp.dkpro.core.api.metadata.type.DocumentMetaData", loaded from "jar:file:/home/vagrant/.m2/repository/de/tudarmstadt/ukp/dkpro/core/de.tudarmstadt.ukp.dkpro.core.api.metadata-asl/1.10.0/de.tudarmstadt.ukp.dkpro.core.api.metadata-asl-1.10.0.jar!/de/tudarmstadt/ukp/dkpro/core/api/metadata/type/DocumentMetaData.class", is missing required constructor; likely cause is wrong version (UIMA version 3 or later JCas required). |
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I dkpro needs and an upgrade to 3.x of uima first. |
i ran the tests on master and it was failing because of svm_learn executables so i dsabled that test and it started passing all other tests. i am not sure how to make svm tests pass. But having said that skipping same tests on your branch did not help it was failing some tests that i have explained in earlier comment |
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DKPro Core 2.2.0 is based on UIMAv3. |
- Bump DKPro Core dependency to 2.2.0
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I have bumped the DKPro Core dependency to 2.2.0 in this branch. |
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@azazali30 could you open a PR with your changes against the branch |
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@reckart sure |
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@reckart i am getting failure with below exception in clearTK TimeML module Any clue |
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Not really - another user reported this issue with as well when upgrading a scenario from UIMAv2 to UIMAv3 but so far has not been able to provide a reproducible sharable scenario. If we can reproduce this consistently using open source ClearTK, I can have investigate it. It may take some days before I am able to get to this though. |
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If you have any changes so far, it would be great if you could provide in a PR them so I start off on the latest status. Meanwhile, feel free check the other modules. |
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sure lemme create a pr |
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added a pr to your branch |
@reckart if i skip these two modules all the tests are passing with my changes merged in your branch I am able to run tests successfully if i skip these two modules which has tests failing
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…Av3-fork Refactoring/442 upgrade to UImav3 fork
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The error is a pretty pathological one - I'm trying to implement a workaround in UIMA: apache/uima-uimaj#243 |
3 tasks
- Workaround apache/uima-uimaj#234 by explicitly creating a dummy CAS before the test - Add Apache SNAPSHOT repo - Add slf4j-simple dependency for basic logging in timeml test
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@azazali30 I have pushed a workaround for the apache/uima-uimaj#234 issue to this branch. However, the timeml tests still do not complete successfully on my machine because the order of annotations in the TimeML output changes compared to v2 (the content is the same, but the order is different) - and the test case is not robust against this change. Could you look into that maybe? |
- Use stable jcasgen plugin - we do not need the SNAPSHOT version - Remove Apache SNAPSHOT repo for plugins
- Back to stable UIMAv3 release - Remove all SNAPSHOT repos
- Back to stable UIMAv3 release - Remove all SNAPSHOT repos
- Switch another test to assertj to get a better failure message
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@azazali30 I have switched to tests in cleartk-ml to use assertj to get better failure messages. Looks like for some reason the manifest that ClearTK generates there is in the GitHub build different from what ClearTK expects. Locally, it works for me... it seems to be a question of which Java version is used to build. With Java 8 it seems to work as ClearTK expects, with Java 11 the test also fails locally for me. |
* master: Update maven.yml Create maven.yml
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Switched to build to using Java 8... now we have this: @azazali30 could you look into that maybe? |
Not sure how it was working before the error seems to be - |
* master: No issue. Bump version to 3.0.0-SNAPSHOT No issue. Bump version to 2.1.0-SNAPSHOT Issue #446 - Remove Eclipse metadata from repository Issue #446 - Remove Eclipse metadata from repository % Conflicts: % cleartk-berkeleyparser/.classpath % cleartk-berkeleyparser/.settings/org.eclipse.jdt.core.prefs % cleartk-clearnlp/.classpath % cleartk-clearnlp/.settings/org.eclipse.jdt.core.prefs % cleartk-corpus/.classpath % cleartk-corpus/.settings/org.eclipse.jdt.core.prefs % cleartk-eval/.classpath % cleartk-eval/.settings/org.eclipse.jdt.core.prefs % cleartk-examples/.classpath % cleartk-examples/.settings/org.eclipse.jdt.core.prefs % cleartk-feature/.classpath % cleartk-feature/.settings/org.eclipse.jdt.core.prefs % cleartk-maltparser/.classpath % cleartk-maltparser/.settings/org.eclipse.jdt.core.prefs % cleartk-ml-crfsuite/.classpath % cleartk-ml-crfsuite/.settings/org.eclipse.jdt.core.prefs % cleartk-ml-liblinear/.classpath % cleartk-ml-liblinear/.settings/org.eclipse.jdt.core.prefs % cleartk-ml-libsvm-tk/.classpath % cleartk-ml-libsvm-tk/.settings/org.eclipse.jdt.core.prefs % cleartk-ml-libsvm/.classpath % cleartk-ml-libsvm/.settings/org.eclipse.jdt.core.prefs % cleartk-ml-mallet/.classpath % cleartk-ml-mallet/.settings/org.eclipse.jdt.core.prefs % cleartk-ml-opennlp-maxent/.classpath % cleartk-ml-opennlp-maxent/.settings/org.eclipse.jdt.core.prefs % cleartk-ml-script/.classpath % cleartk-ml-script/.settings/org.eclipse.jdt.core.prefs % cleartk-ml-svmlight/.classpath % cleartk-ml-svmlight/.settings/org.eclipse.jdt.core.prefs % cleartk-ml-tksvmlight/.classpath % cleartk-ml-tksvmlight/.settings/org.eclipse.jdt.core.prefs % cleartk-ml-weka/.classpath % cleartk-ml-weka/.settings/org.eclipse.jdt.core.prefs % cleartk-ml/.classpath % cleartk-ml/.settings/org.eclipse.jdt.core.prefs % cleartk-opennlp-tools/.classpath % cleartk-opennlp-tools/.settings/org.eclipse.jdt.core.prefs % cleartk-snowball/.classpath % cleartk-snowball/.settings/org.eclipse.jdt.core.prefs % cleartk-stanford-corenlp/.classpath % cleartk-stanford-corenlp/.settings/org.eclipse.jdt.core.prefs % cleartk-summarization/.classpath % cleartk-summarization/.settings/org.eclipse.jdt.core.prefs % cleartk-test-util/.classpath % cleartk-test-util/.settings/org.eclipse.jdt.core.prefs % cleartk-timeml/.classpath % cleartk-timeml/.settings/org.eclipse.jdt.core.prefs % cleartk-token/.classpath % cleartk-token/.settings/org.eclipse.jdt.core.prefs % cleartk-type-system/.classpath % cleartk-type-system/.settings/org.eclipse.jdt.core.prefs % cleartk-util/.classpath % cleartk-util/.settings/org.eclipse.jdt.core.prefs
* main: Issue 448 - Update dependencies Issue 448 - Update dependencies Issue 448 - Update dependencies Issue 448 - Update dependencies Issue 448 - Update dependencies No issue. Update branchs in GitHub actions No issue. Update branchs in GitHub actions % Conflicts: % cleartk-ml/pom.xml % cleartk-ml/src/test/java/org/cleartk/ml/jar/JarDataWriterTest.java % cleartk-ml/src/test/java/org/cleartk/ml/viterbi/ViterbiDataWriterTest.java % cleartk-timeml/pom.xml % cleartk-timeml/src/test/java/org/cleartk/timeml/TimeMlAnnotateTest.java % pom.xml
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uima.tcas.Annotationnot being in the type system (slot 21 = null) in TimeML module