search

clulab / reach

Reach Biomedical Information Extraction
Other
96 stars 39 forks source link

Modernize, i.e., update to processors using Stanford CoreNLP 4.4.0 #772

Open kwalcock opened 2 years ago

kwalcock commented 2 years ago

This implies an update to Lucene 7.5.0. This is a draft used to explore the repercussions.

kwalcock commented 2 years ago

Failing tests include TestFastBioNLPProcessor in processors/test

[info] - should parse dependencies correctly *** FAILED *** (18 milliseconds)
[info]   false was not true (TestFastBioNLPProcessor.scala:147)
kwalcock commented 2 years ago

It's much worse for main/test. Note that I did not recalculate any indexes or whatever they are. I have to look up what that was about.

[info] *** 559 TESTS FAILED ***
[error] Failed tests:
[error]     org.clulab.reach.DemoTests2
[error]     org.clulab.reach.TestMentionSerialization
[error]     org.clulab.reach.TestBindingEvents
[error]     org.clulab.reach.TestNERLabeling
[error]     org.clulab.reach.TestGrounding
[error]     org.clulab.reach.DemoTests3
[error]     org.clulab.reach.PolaritySuite
[error]     org.clulab.reach.TestDeModifications
[error]     org.clulab.reach.TestTranscriptionEvents
[error]     org.clulab.reach.TestTemplaticSimpleDeEvents
[error]     org.clulab.reach.TestTemplaticAutoEvents
[error]     org.clulab.reach.TestPolarity
[error]     org.clulab.reach.TestHyphenedEvents
[error]     org.clulab.reach.NegationTests
[error]     org.clulab.reach.TestActivationEvents
[error]     org.clulab.reach.TestCoreference
[error]     org.clulab.reach.TestTranslocationEvents
[error]     org.clulab.reach.TestReachGrounder
[error]     org.clulab.reach.DemoTests1
[error]     org.clulab.reach.TestModifications
[error]     org.clulab.reach.ExperimentalRegulationTests
[error]     org.clulab.reach.TestRegulationEvents
[error]     org.clulab.reach.TestTemplaticSimpleEvents
[error]     org.clulab.reach.TestDependencyUtils
[error]     org.clulab.reach.TestConversionEvents
kwalcock commented 2 years ago

For causalAssembly/test:

[info] *** 21 TESTS FAILED ***
[error] Failed tests:
[error]     org.clulab.reach.assembly.TestAssemblySieves
[error]     org.clulab.reach.assembly.TestAssemblyManager
kwalcock commented 2 years ago

For export/test

[info] *** 27 TESTS FAILED ***
[error] Failed tests:
[error]     org.clulab.reach.export.TestFeedback2
[error]     org.clulab.reach.export.TestApi
[error]     org.clulab.reach.export.TestFriesOutput
[error]     org.clulab.reach.export.TestOutputDegrader
enoriega commented 1 year ago

Hi @kwalcock . Will this change be backwards compatible with serialized files that have already been annotated with an older version of processors? (i.e. the serialized papers from PubMed).

I think it will, because the Document class won't change. But we should make sure we don't loose the ability of de-serializing files

kwalcock commented 1 year ago

@enoriega, was this comment for a different PR? This one is a year old. I should probably track down a unit test that checks on the serialization to be sure.

enoriega commented 1 year ago

Ah! I saw a notification on an email and ended up here by mistake. Sorry!