Docker Image gets stuck and build fails

[Stephan-Linzbach]

Hi,

I tried to install entity fishing with the docker image but it got stuck at loading the model nerfr.
When I try to install entity-fishing directly, some of the tests fail like testGetSequenceMatch_multiTokenAcronym_shouldWork.
Can you help me with that?

[lfoppiano]

@Stephan-Linzbach did you install grobid-ner? See here: https://grobid-ner.readthedocs.io/en/latest/build-and-install/

[Stephan-Linzbach]

Yes i did use this tutorial - https://nerd.readthedocs.io/en/stable/build.html and https://nerd.readthedocs.io/en/stable/docker.html

[lfoppiano]

I don't remember well. Try to build without the tests ./gradlew build -x test should do the trick.

Eventually send the stacktrace of the test failing.

[Stephan-Linzbach]

i tryed building without tests. But it failed at running then. I will send the stacktrace soon.

com.scienceminer.nerd.mention.ProcessTextTest 
> testGetSequenceMatch_multiTokenAcronym_shouldWork FAILED  
java.lang.NullPointerException at ProcessTextTest.java:38                         
com.scienceminer.nerd.service.NerdRestProcessQueryTest
> testMarkUserEnteredEntities_missingOffset_shouldWorkHaveNegativeConfidence STANDARD_OUT   
10:05:58.725 [Test worker] WARN com.scienceminer.nerd.service.NerdRestProcessQuery - The entity { "rawName" : "Austria", 
"confidence_score":0, "wikipediaExternalRef": 123456 } doesn't have valid offset. Ignoring it.                                                                                                                                                                                                                                                                                                                                                                                                                        com.scienceminer.nerd.service.NerdRestProcessQueryTest 
> testMarkUserEnteredEntities_invalidOffset1_shouldWorkHaveNegativeConfidence STANDARD_OUT           
10:05:58.726 [Test worker] WARN com.scienceminer.nerd.service.NerdRestProcessQuery - The entity { "rawName" : "Austria", "offsetStart" : 120, "offsetEnd" : 15, "confidence_score":0 } doesn't have valid offset. Ignoring it.            
com.scienceminer.nerd.service.NerdRestProcessQueryTest 
> testMarkUserEnteredEntities_invalidOffset2_shouldWorkHaveNegativeConfidence STANDARD_OUT        
10:05:58.728 [Test worker] WARN com.scienceminer.nerd.service.NerdRestProcessQuery - The entity { "rawName" : "Austria", "offsetStart" : 12, "offsetEnd" : 15, "confidence_score":0 } doesn't have valid offset. Ignoring it.                             
com.scienceminer.nerd.utilities.mediaWiki.TestMediaWikiParser 
> testWikiMediaToTextWithInternalLinksAndCategoriesOnly_NL STANDARD_OUT                                                                                
10:05:58.744 [Test worker] DEBUG com.scienceminer.nerd.utilities.mediaWiki.MediaWikiParser - Get new instance of MediaWikiParser  
com.scienceminer.nerd.utilities.mediaWiki.TestMediaWikiParser 
> testWikiMediaTextWithDatesFr STANDARD_OUT                                                                                                            *************************                                                                                                     
Emmanuel Macron, né le 21 décembre 1977 à [[Amiens]] ([[France]]), est un [[Haute fonction publique française|haut fonctionnaire]] et [[homme d'État]] [[France|français]]. Il est [[président de la République française]] depuis le 14 mai 2017.      
119 tests completed, 24 failed, 6 skipped                                                                                           
> Task :test FAILED