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Update github actions and JDK 11 #164

Merged
merged 13 commits into from
Jan 6, 2025
Merged

Update github actions and JDK 11 #164

merged 13 commits into from
Jan 6, 2025

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lfoppiano
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I managed to have the build work and it seems that there are issues with the tests. I haven't tried to run it, yet.

Here the broken test classes:

KBUtilitiesTest
CustomisationTest
ProcessTextTest

All the failing test are due to the same error, and I think it's due to the fact that I lmdbjni does not exists for arm 64.

Could not load library. Reasons: [no lmdbjni64-0.4.6 in java.library.path: [/Users/lfoppiano/Library/Java/Extensions, /Library/Java/Extensions, /Network/Library/Java/Extensions, /System/Library/Java/Extensions, /usr/lib/java, .], no lmdbjni-0.4.6 in java.library.path: [/Users/lfoppiano/Library/Java/Extensions, /Library/Java/Extensions, /Network/Library/Java/Extensions, /System/Library/Java/Extensions, /usr/lib/java, .], no lmdbjni in java.library.path: [/Users/lfoppiano/Library/Java/Extensions, /Library/Java/Extensions, /Network/Library/Java/Extensions, /System/Library/Java/Extensions, /usr/lib/java, .], Can't load library: /var/folders/mk/scd8428n18jfgh3jdthbvpz00000gn/T/liblmdbjni-64-0-7539440420833364823.4]
java.lang.UnsatisfiedLinkError: Could not load library. Reasons: [no lmdbjni64-0.4.6 in java.library.path: [/Users/lfoppiano/Library/Java/Extensions, /Library/Java/Extensions, /Network/Library/Java/Extensions, /System/Library/Java/Extensions, /usr/lib/java, .], no lmdbjni-0.4.6 in java.library.path: [/Users/lfoppiano/Library/Java/Extensions, /Library/Java/Extensions, /Network/Library/Java/Extensions, /System/Library/Java/Extensions, /usr/lib/java, .], no lmdbjni in java.library.path: [/Users/lfoppiano/Library/Java/Extensions, /Library/Java/Extensions, /Network/Library/Java/Extensions, /System/Library/Java/Extensions, /usr/lib/java, .], Can't load library: /var/folders/mk/scd8428n18jfgh3jdthbvpz00000gn/T/liblmdbjni-64-0-7539440420833364823.4]
	at org.fusesource.hawtjni.runtime.Library.doLoad(Library.java:187)
	at org.fusesource.hawtjni.runtime.Library.load(Library.java:143)
	at org.fusesource.lmdbjni.JNI.<clinit>(JNI.java:41)
	at org.fusesource.lmdbjni.Env.create(Env.java:57)
	at org.fusesource.lmdbjni.Env.<init>(Env.java:51)
	at com.scienceminer.nerd.kb.db.KBDatabase.<init>(KBDatabase.java:39)
	at com.scienceminer.nerd.kb.db.StringRecordDatabase.<init>(StringRecordDatabase.java:20)
	at com.scienceminer.nerd.kb.db.ConceptDatabase.<init>(ConceptDatabase.java:18)
	at com.scienceminer.nerd.kb.db.KBUpperEnvironment.buildConceptDatabase(KBUpperEnvironment.java:220)
	at com.scienceminer.nerd.kb.db.KBUpperEnvironment.initDatabases(KBUpperEnvironment.java:117)
	at com.scienceminer.nerd.kb.db.KBUpperEnvironment.<init>(KBUpperEnvironment.java:59)
	at com.scienceminer.nerd.kb.UpperKnowledgeBase.<init>(UpperKnowledgeBase.java:76)
	at com.scienceminer.nerd.kb.UpperKnowledgeBase.getNewInstance(UpperKnowledgeBase.java:58)
	at com.scienceminer.nerd.kb.UpperKnowledgeBase.getInstance(UpperKnowledgeBase.java:48)
	at com.scienceminer.nerd.kb.KBUtilitiesTest.setUp(KBUtilitiesTest.java:15)

[...]

@lfoppiano
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@kermitt2 I've created a Github action that should be able to build it. I tried to run the tests but they fail because there is no data in the database. It should work with the latest grobid version compiled with JDK 11.

@kermitt2
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kermitt2 commented Jul 4, 2024

Hi @lfoppiano ! Thank you.

Indeed simply removing the --add-opens jdk.incubator.foreign makes it working with jdk 11, which is funny because I added all these modules, including this specific one, to have it running on jdk >8.

About the tests, they can be run only after downloading the data files and installing them, I think it has always been like that. But I can confirm that the tests are fine with the data.

I will merge the PR when grobid version 0.8.1 is published - I updated the master so that it works with version 0.8.0 and jdk 11.

@lfoppiano
Merge branch 'master' into grobid-0.8.1
ee4ff92 
# Conflicts:
#	build.gradle
@lfoppiano lfoppiano marked this pull request as ready for review January 4, 2025 16:55
@lfoppiano lfoppiano changed the title update to jdk 11, and grobid 0.8.1 Update github actions and JDK 11 Jan 4, 2025
@lfoppiano lfoppiano merged commit ac8bd03 into master Jan 6, 2025
2 checks passed
@lfoppiano lfoppiano deleted the grobid-0.8.1 branch January 6, 2025 08:18
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@lfoppiano @kermitt2