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EBISPOT / OLS

Ontology Lookup Service from SPOT at EBI
http://www.ebi.ac.uk/ols
Apache License 2.0
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Running ols-neo4j-app fails on all properties files #464

Open jheckman-rt opened 3 years ago

jheckman-rt commented 3 years ago

I have built the apps using the mvn clean package command and the additional files in the build-fix folder. This works fine (as long as I am using the master branch, the most recent release does not build successfully anymore).

However, when I run the jar file with some of the example properties files such as: java -Xmx2g -jar -Dspring.profiles.active=go ols-apps/ols-neo4j-app/target/ols-neo4j-app.jar

I run into the following error: 2021-02-11 15:23:23,863 DEBUG Thread-7 StructuralOWLOntologyLoader.indexOntologyAnnotations - annotationPropertyIri 1 = http://purl.org/dc/elements/1.1/title 2021-02-11 15:23:23,863 DEBUG Thread-7 StructuralOWLOntologyLoader.indexOntologyAnnotations - annotationPropertyIri 1 = http://purl.org/dc/terms/license 2021-02-11 15:23:23,866 ERROR Thread-7 StructuralOWLOntologyLoader.setInitializationException - Failed to initialize StructuralOWLOntologyLoader. Initialization exception updated : null java.lang.NullPointerException: null at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.indexOntologyAnnotations(AbstractOWLOntologyLoader.java:533) at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.loadOntology(AbstractOWLOntologyLoader.java:440) at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.doInitialization(AbstractOWLOntologyLoader.java:355) at uk.ac.ebi.spot.ols.util.Initializable$1.run(Initializable.java:147) at java.lang.Thread.run(Thread.java:748) 2021-02-11 15:23:23,866 ERROR Thread-7 StructuralOWLOntologyLoader.loadOntology - Failed to parse go : null java.lang.NullPointerException: null at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.indexOntologyAnnotations(AbstractOWLOntologyLoader.java:533) at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.loadOntology(AbstractOWLOntologyLoader.java:440) at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.doInitialization(AbstractOWLOntologyLoader.java:355) at uk.ac.ebi.spot.ols.util.Initializable$1.run(Initializable.java:147) at java.lang.Thread.run(Thread.java:748) 2021-02-11 15:23:24,739 DEBUG Thread-7 StructuralOWLOntologyLoader.run - Caught exception whilst initializing, attempting to handle with clean termination java.lang.NullPointerException: null at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.indexOntologyAnnotations(AbstractOWLOntologyLoader.java:533) at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.loadOntology(AbstractOWLOntologyLoader.java:440) at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.doInitialization(AbstractOWLOntologyLoader.java:355) at uk.ac.ebi.spot.ols.util.Initializable$1.run(Initializable.java:147) at java.lang.Thread.run(Thread.java:748) 2021-02-11 15:23:24,739 ERROR main SpringApplication.handleRunFailure - Application startup failed java.lang.IllegalStateException: Failed to execute CommandLineRunner at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:803) at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:784) at org.springframework.boot.SpringApplication.afterRefresh(SpringApplication.java:771) at org.springframework.boot.SpringApplication.run(SpringApplication.java:307) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1185) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1174) at uk.ac.ebi.spot.ols.GraphLoaderApplication.main(GraphLoaderApplication.java:47) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:54) at org.springframework.boot.loader.Launcher.launch(Launcher.java:104) at org.springframework.boot.loader.Launcher.launch(Launcher.java:61) at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:52) Caused by: java.lang.RuntimeException: Failed to lazily instantiate collection for query at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.lazyGet(AbstractOWLOntologyLoader.java:349) at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.getAllClasses(AbstractOWLOntologyLoader.java:1685) at uk.ac.ebi.spot.ols.loader.BatchNeo4JIndexer.indexClasses(BatchNeo4JIndexer.java:308) at uk.ac.ebi.spot.ols.loader.BatchNeo4JIndexer.createIndex(BatchNeo4JIndexer.java:437) at uk.ac.ebi.spot.ols.loader.BatchNeo4JIndexer.createIndex(BatchNeo4JIndexer.java:592) at uk.ac.ebi.spot.ols.GraphLoaderApplication.run(GraphLoaderApplication.java:40) at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:800) ... 14 common frames omitted Caused by: java.lang.IllegalStateException: Initialization of StructuralOWLOntologyLoader failed: null at uk.ac.ebi.spot.ols.util.Initializable.isReady(Initializable.java:75) at uk.ac.ebi.spot.ols.util.Initializable.waitUntilReady(Initializable.java:88) at uk.ac.ebi.spot.ols.util.Initializable.initOrWait(Initializable.java:110) at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.lazyGet(AbstractOWLOntologyLoader.java:342) ... 20 common frames omitted Caused by: java.lang.NullPointerException: null at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.indexOntologyAnnotations(AbstractOWLOntologyLoader.java:533) at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.loadOntology(AbstractOWLOntologyLoader.java:440) at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.doInitialization(AbstractOWLOntologyLoader.java:355) at uk.ac.ebi.spot.ols.util.Initializable$1.run(Initializable.java:147) at java.lang.Thread.run(Thread.java:748) 2021-02-11 15:23:24,739 ERROR Thread-7 StructuralOWLOntologyLoader.setInitializationException - Failed to initialize StructuralOWLOntologyLoader. Initialization exception updated : null java.lang.NullPointerException: null at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.indexOntologyAnnotations(AbstractOWLOntologyLoader.java:533) at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.loadOntology(AbstractOWLOntologyLoader.java:440) at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.doInitialization(AbstractOWLOntologyLoader.java:355) at uk.ac.ebi.spot.ols.util.Initializable$1.run(Initializable.java:147) at java.lang.Thread.run(Thread.java:748) java.lang.RuntimeException: java.lang.reflect.InvocationTargetException at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:62) at org.springframework.boot.loader.Launcher.launch(Launcher.java:104) at org.springframework.boot.loader.Launcher.launch(Launcher.java:61) at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:52) Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:54) ... 3 more Caused by: java.lang.IllegalStateException: Failed to execute CommandLineRunner at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:803) at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:784) at org.springframework.boot.SpringApplication.afterRefresh(SpringApplication.java:771) at org.springframework.boot.SpringApplication.run(SpringApplication.java:307) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1185) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1174) at uk.ac.ebi.spot.ols.GraphLoaderApplication.main(GraphLoaderApplication.java:47) ... 8 more Caused by: java.lang.RuntimeException: Failed to lazily instantiate collection for query at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.lazyGet(AbstractOWLOntologyLoader.java:349) at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.getAllClasses(AbstractOWLOntologyLoader.java:1685) at uk.ac.ebi.spot.ols.loader.BatchNeo4JIndexer.indexClasses(BatchNeo4JIndexer.java:308) at uk.ac.ebi.spot.ols.loader.BatchNeo4JIndexer.createIndex(BatchNeo4JIndexer.java:437) at uk.ac.ebi.spot.ols.loader.BatchNeo4JIndexer.createIndex(BatchNeo4JIndexer.java:592) at uk.ac.ebi.spot.ols.GraphLoaderApplication.run(GraphLoaderApplication.java:40) at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:800) ... 14 more Caused by: java.lang.IllegalStateException: Initialization of StructuralOWLOntologyLoader failed: null at uk.ac.ebi.spot.ols.util.Initializable.isReady(Initializable.java:75) at uk.ac.ebi.spot.ols.util.Initializable.waitUntilReady(Initializable.java:88) at uk.ac.ebi.spot.ols.util.Initializable.initOrWait(Initializable.java:110) at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.lazyGet(AbstractOWLOntologyLoader.java:342) ... 20 more Caused by: java.lang.NullPointerException at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.indexOntologyAnnotations(AbstractOWLOntologyLoader.java:533) at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.loadOntology(AbstractOWLOntologyLoader.java:440) at uk.ac.ebi.spot.ols.loader.AbstractOWLOntologyLoader.doInitialization(AbstractOWLOntologyLoader.java:355) at uk.ac.ebi.spot.ols.util.Initializable$1.run(Initializable.java:147) at java.lang.Thread.run(Thread.java:748)

In fact, I run into this exact same error when I try to run this command for ALL the sample properties files AND for any file I've tried to generate myself.

I've attached the full output of the logs printed to the screen in the output.txt file. output.txt

Please help! Thank you!

henrietteharmse commented 3 years ago

Unfortunately I have to admit that the Neo4J app (and Solr app) is not well maintained nor well tested. In general the indexer (/ols-indexer) is used to index ontologies rather than the apps.

Can you provide a minimal ontology that we can use to try and reproduce the error?

jheckman-rt commented 3 years ago

There's not great documentation on how to set up the properties files (ie what all the parameters mean) so your best bet is to try with the properties files that the app identifies as examples. This is an examples of one: https://github.com/EBISPOT/OLS/blob/master/ols-apps/ols-neo4j-app/src/main/resources/application-go.properties