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VirtualFlyBrain / VFB_owl

A repository for VFB owl files and the code that generates them
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Probable issue with OWLAPI version is pipeline testing #38

Closed Robbie1977 closed 6 years ago

Robbie1977 commented 6 years ago

https://travis-ci.org/VirtualFlyBrain/pipeline/builds/308434295#L1420

jython /opt/VFB/VFB_owl/src/code/owl2neo/add_anonymous_types.py http://192.168.0.1:7474 neo4j neo4j /opt/VFB/VFB_owl/src/owl/vfb.owl
Traceback (most recent call last):
  File "/opt/VFB/VFB_owl/src/code/owl2neo/add_anonymous_types.py", line 12, in <module>
    vfb = Brain()
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.<init>(OWLOntologyManagerImpl.java:131)
    at org.semanticweb.owlapi.apibinding.OWLManager.createOWLOntologyManager(OWLManager.java:131)
    at org.semanticweb.owlapi.apibinding.OWLManager.createOWLOntologyManager(OWLManager.java:118)
    at uk.ac.ebi.brain.core.Brain.<init>(Brain.java:226)
    at uk.ac.ebi.brain.core.Brain.<init>(Brain.java:153)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
    at org.python.core.PyReflectedConstructor.constructProxy(PyReflectedConstructor.java:211)
java.lang.NoSuchMethodError: java.lang.NoSuchMethodError: org.semanticweb.owlapi.util.CollectionFactory.createSyncList()Ljava/util/List;

Potentially related to: https://stackoverflow.com/questions/26026366/java-lang-nosuchmethoderror-org-semanticweb-hermit-reasoner-initunknown-sour

Robbie1977 commented 6 years ago

Versions built are here: https://travis-ci.org/VirtualFlyBrain/pipeline/builds/308434295#L1292

/opt/VFB/VFB_owl/lib/Brain-1.5.2-SNAPSHOT.jar
/opt/VFB/VFB_owl/lib/OWLTools-Core-0.2.2-SNAPSHOT.jar
/opt/VFB/VFB_owl/lib/README.md
/opt/VFB/VFB_owl/lib/ant-1.8.2.jar
/opt/VFB/VFB_owl/lib/ant-launcher-1.8.2.jar
/opt/VFB/VFB_owl/lib/antlr-3.2.jar
/opt/VFB/VFB_owl/lib/antlr-runtime-3.2.jar
/opt/VFB/VFB_owl/lib/automaton-1.11-8.jar
/opt/VFB/VFB_owl/lib/axiom-api-1.2.14.jar
/opt/VFB/VFB_owl/lib/axiom-c14n-1.2.14.jar
/opt/VFB/VFB_owl/lib/axiom-dom-1.2.14.jar
/opt/VFB/VFB_owl/lib/axiom-impl-1.2.14.jar
/opt/VFB/VFB_owl/lib/commons-io-2.2.jar
/opt/VFB/VFB_owl/lib/commons-logging-1.1.3.jar
/opt/VFB/VFB_owl/lib/commons-math-2.1.jar
/opt/VFB/VFB_owl/lib/elk-owl-implementation-0.4.2.jar
/opt/VFB/VFB_owl/lib/elk-owl-model-0.4.2.jar
/opt/VFB/VFB_owl/lib/elk-owlapi-0.4.2.jar
/opt/VFB/VFB_owl/lib/elk-reasoner-0.4.2.jar
/opt/VFB/VFB_owl/lib/elk-util-collections-0.4.2.jar
/opt/VFB/VFB_owl/lib/elk-util-common-0.4.2.jar
/opt/VFB/VFB_owl/lib/elk-util-concurrent-0.4.2.jar
/opt/VFB/VFB_owl/lib/elk-util-hashing-0.4.2.jar
/opt/VFB/VFB_owl/lib/elk-util-io-0.4.2.jar
/opt/VFB/VFB_owl/lib/elk-util-logging-0.4.2.jar
/opt/VFB/VFB_owl/lib/expression-materializing-reasoner-0.0.5.jar
/opt/VFB/VFB_owl/lib/factplusplus-1.5.2.jar
/opt/VFB/VFB_owl/lib/graphdraw-0.0.1-SNAPSHOT.jar
/opt/VFB/VFB_owl/lib/gson-2.2.4.jar
/opt/VFB/VFB_owl/lib/guava-17.0.jar
/opt/VFB/VFB_owl/lib/jaxen-1.1.4.jar
/opt/VFB/VFB_owl/lib/jcel.core-0.15.0.jar
/opt/VFB/VFB_owl/lib/jcel.ontology-0.15.0.jar
/opt/VFB/VFB_owl/lib/jcel.owlapi-0.15.0.jar
/opt/VFB/VFB_owl/lib/jdom-1.1.1.jar
/opt/VFB/VFB_owl/lib/jfact-1.0.0.jar
/opt/VFB/VFB_owl/lib/jline-0.9.93.jar
/opt/VFB/VFB_owl/lib/jpaul-2.5.1.jar
/opt/VFB/VFB_owl/lib/jython-standalone-2.7.0.jar
/opt/VFB/VFB_owl/lib/log4j-1.2.17.jar
/opt/VFB/VFB_owl/lib/more-reasoner-0.1.5-BBOP-1.jar
/opt/VFB/VFB_owl/lib/mysql-connector-java-5.1.26.jar
/opt/VFB/VFB_owl/lib/oboformat-tools-0.6.0.jar
/opt/VFB/VFB_owl/lib/oppl2-1.5.5.jar
/opt/VFB/VFB_owl/lib/org.osgi.core-1.4.0.jar
/opt/VFB/VFB_owl/lib/org.semanticweb.hermit-1.3.8.2.jar
/opt/VFB/VFB_owl/lib/owlapi-api-3.5.1.jar
/opt/VFB/VFB_owl/lib/owlapi-apibinding-3.5.1.jar
/opt/VFB/VFB_owl/lib/owlapi-distribution-3.4.8.jar
/opt/VFB/VFB_owl/lib/owlapi-impl-3.5.1.jar
/opt/VFB/VFB_owl/lib/owlapi-oboformat-3.5.1.jar
/opt/VFB/VFB_owl/lib/owlapi-parsers-3.5.1.jar
/opt/VFB/VFB_owl/lib/owlapi-tools-3.5.1.jar
/opt/VFB/VFB_owl/lib/parsers-1.5.2.jar
/opt/VFB/VFB_owl/lib/postgresql-9.3-1102-jdbc4.jar
/opt/VFB/VFB_owl/lib/slf4j-api-1.7.2.jar
/opt/VFB/VFB_owl/lib/slf4j-log4j12-1.7.2.jar
/opt/VFB/VFB_owl/lib/sparqldl-api-1.0.0.jar
/opt/VFB/VFB_owl/lib/trove4j-3.0.3.jar
dosumis commented 6 years ago

It feels like we're going round in circles on this (we've definitely had the whole thing working on at least one Edinburgh machine before).

Are you still using all those cached jars? Thought we removed them from the VFB_owl repo ages ago in favour of a maven build.

AFAIK, Heiko's forked version makes brain compatible with OWL-API v4. You should be able to get all the OWL-API libs you need with a maven build that uses the pom on that repo. I don't think these scripts have any dependency on OWLtools anymore. This one certainly doesn't: owl2neo/add_anonymous_types.py

dosumis commented 6 years ago

Scratch that - Still at OWL_API v3.5 from dietze/brain. But that begs the question of where v4 is coming from. Is there an owltools import specified somewhere (I can't see it in pipeline/process.sh). If so, can you try turning it off?

dosumis commented 6 years ago

Perhaps easiest to talk this through?

Robbie1977 commented 6 years ago

Brain generates only:

|-- README.md
|-- gen-key-script
|-- pom.xml
|-- src
|   |-- main
|   |   `-- java
|   |       `-- uk
|   |           `-- ac
|   |               `-- ebi
|   |                   `-- brain
|   |                       |-- core
|   |                       |   `-- Brain.java
|   |                       `-- error
|   |                           |-- BadNameException.java
|   |                           |-- BadPrefixException.java
|   |                           |-- BrainException.java
|   |                           |-- ClassExpressionException.java
|   |                           |-- DataPropertyExpressionException.java
|   |                           |-- DataRangeException.java
|   |                           |-- ExistingAnnotationPropertyException.java
|   |                           |-- ExistingClassException.java
|   |                           |-- ExistingDataPropertyException.java
|   |                           |-- ExistingEntityException.java
|   |                           |-- ExistingNamedIndividualException.java
|   |                           |-- ExistingObjectPropertyException.java
|   |                           |-- NamedIndividualException.java
|   |                           |-- NewOntologyException.java
|   |                           |-- NonExistingAnnotationPropertyException.java
|   |                           |-- NonExistingClassException.java
|   |                           |-- NonExistingDataPropertyException.java
|   |                           |-- NonExistingEntityException.java
|   |                           |-- NonExistingNamedIndividualException.java
|   |                           |-- NonExistingObjectPropertyException.java
|   |                           |-- ObjectPropertyExpressionException.java
|   |                           `-- StorageException.java
|   `-- test
|       |-- java
|       |   `-- uk
|       |       `-- ac
|       |           `-- ebi
|       |               |-- BrainPopulationTest.java
|       |               |-- BrainQueryTest.java
|       |               `-- BrainUtilsTest.java
|       `-- resources
|           |-- cars.jpg
|           |-- cars.owl
|           |-- catalog-v001.xml
|           |-- demo-out.owl
|           |-- demo.owl
|           |-- dev.owl
|           |-- disambiguate.owl
|           |-- go.owl
|           |-- individuals.owl
|           |-- output-prefix.owl
|           |-- output.owl
|           `-- prefix.owl
`-- target
    |-- Brain-1.5.2-SNAPSHOT.jar
    |-- Brain-1.5.2-SNAPSHOT.jar.asc
    |-- Brain-1.5.2-SNAPSHOT.pom
    |-- Brain-1.5.2-SNAPSHOT.pom.asc
    |-- classes
    |   `-- uk
    |       `-- ac
    |           `-- ebi
    |               `-- brain
    |                   |-- core
    |                   |   |-- Brain$ManchesterParser.class
    |                   |   `-- Brain.class
    |                   `-- error
    |                       |-- BadNameException.class
    |                       |-- BadPrefixException.class
    |                       |-- BrainException.class
    |                       |-- ClassExpressionException.class
    |                       |-- DataPropertyExpressionException.class
    |                       |-- DataRangeException.class
    |                       |-- ExistingAnnotationPropertyException.class
    |                       |-- ExistingClassException.class
    |                       |-- ExistingDataPropertyException.class
    |                       |-- ExistingEntityException.class
    |                       |-- ExistingNamedIndividualException.class
    |                       |-- ExistingObjectPropertyException.class
    |                       |-- NamedIndividualException.class
    |                       |-- NewOntologyException.class
    |                       |-- NonExistingAnnotationPropertyException.class
    |                       |-- NonExistingClassException.class
    |                       |-- NonExistingDataPropertyException.class
    |                       |-- NonExistingEntityException.class
    |                       |-- NonExistingNamedIndividualException.class
    |                       |-- NonExistingObjectPropertyException.class
    |                       |-- ObjectPropertyExpressionException.class
    |                       `-- StorageException.class
    |-- generated-sources
    |   `-- annotations
    |-- generated-test-sources
    |   `-- test-annotations
    |-- maven-archiver
    |   `-- pom.properties
    `-- test-classes
        |-- cars.jpg
        |-- cars.owl
        |-- catalog-v001.xml
        |-- demo-out.owl
        |-- demo.owl
        |-- dev.owl
        |-- disambiguate.owl
        |-- go.owl
        |-- individuals.owl
        |-- output-prefix.owl
        |-- output.owl
        |-- prefix.owl
        `-- uk
            `-- ac
                `-- ebi
                    |-- BrainPopulationTest.class
                    |-- BrainQueryTest.class
                    `-- BrainUtilsTest.class
Robbie1977 commented 6 years ago

Should we adjust the version generated here to match brains requirements: https://github.com/VirtualFlyBrain/VFB_owl/blob/master/pom.xml#L11

dosumis commented 6 years ago

Can this be closed?

dosumis commented 6 years ago

No longer relevant as dependence of pipeline on Brain library has been removed now Jython has been ditched.