The version values mismatch

[yy20716]

As suggested, I was trying to follow the instruction but failed due to the version issue, i.e.

[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 13.950 s
[INFO] Finished at: 2018-02-23T17:49:56-08:00
[INFO] Final Memory: 14M/47M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project pdxintegrator: Could not resolve dependencies for project org.jax:pdxintegrator:jar:0.0.4: The following artifacts could not be resolved: com.github.phenomics:ontolib-core:jar:0.1.1, com.github.phenomics:ontolib-io:jar:0.1.1: Could not find artifact com.github.phenomics:ontolib-core:jar:0.1.1 in central (https://repo.maven.apache.org/maven2) -> [Help 1]

So I checked the .m2 directory and realized that the version strings are mismatching, i.e. the current OLPG's version is 0.1.4 while the version string in PDXintegrator's pom.xml is 0.1.1. For this reason, maven cannot retrieve required files, e.g., the core file exists as ontolib-core-0.1.4.jar but maven only looks for ontolib-core-0.1.1.jar (and failed). I guess this may not be an urgent issue but could you please update the version string in pom.xml? Thank you.

[pnrobinson]

I think the latest merge of OLPG is causing some maven enforcer issues -- I am going to try and solve them and will upload a new version of OLPG and then of PDXintegrator

[pnrobinson]

Hmm, the Jackson dependency is difficult to get rid of. I added the following to the top level POM file, where the square brackets tell maven what version you want to have (note the version of org.openrdf.sesame you were using is way out of date, I could not retrieve it).

<!-- the following dependencies are to solve enforcer plugin issues -->
    <!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api -->
    <dependency>
      <groupId>org.slf4j</groupId>
      <artifactId>slf4j-api</artifactId>
      <version>[1.7.24]</version>
    </dependency>

    <!-- the following dependencies are to solve enforcer plugin issues -->
    <dependency>
      <groupId>org.openrdf.sesame</groupId>
      <artifactId>sesame-model</artifactId>
      <version>[4.1.2]</version>
    </dependency>

    <!-- https://mvnrepository.com/artifact/com.github.jsonld-java/jsonld-java -->
    <dependency>
      <groupId>com.github.jsonld-java</groupId>
      <artifactId>jsonld-java</artifactId>
      <version>[0.10.0]</version>
    </dependency>

    <!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.core/jackson-core -->
    <dependency>
      <groupId>com.fasterxml.jackson.core</groupId>
      <artifactId>jackson-core</artifactId>
      <version>[2.9.4]</version>
    </dependency>

This allowed me to go from about 4 pages of dependency errors to just this.

Dependency convergence error for com.fasterxml.jackson.core:jackson-core:2.9.4 paths to dependency are:
+-com.github.phenomics:OLPG:0.1.4
  +-com.github.jsonld-java:jsonld-java:0.10.0
    +-com.fasterxml.jackson.core:jackson-core:2.9.4
and
+-com.github.phenomics:OLPG:0.1.4
  +-com.github.jsonld-java:jsonld-java:0.10.0
    +-com.fasterxml.jackson.core:jackson-databind:2.8.6
      +-com.fasterxml.jackson.core:jackson-core:2.8.6
and
+-com.github.phenomics:OLPG:0.1.4
  +-com.fasterxml.jackson.core:jackson-core:2.9.4

[WARNING] Rule 0: org.apache.maven.plugins.enforcer.DependencyConvergence failed with message:
Failed while enforcing releasability the error(s) are [
Dependency convergence error for com.fasterxml.jackson.core:jackson-core:2.9.4 paths to dependency are:
+-com.github.phenomics:OLPG:0.1.4
  +-com.github.jsonld-java:jsonld-java:0.10.0
    +-com.fasterxml.jackson.core:jackson-core:2.9.4
and
+-com.github.phenomics:OLPG:0.1.4
  +-com.github.jsonld-java:jsonld-java:0.10.0
    +-com.fasterxml.jackson.core:jackson-databind:2.8.6
      +-com.fasterxml.jackson.core:jackson-core:2.8.6
and
+-com.github.phenomics:OLPG:0.1.4
  +-com.fasterxml.jackson.core:jackson-core:2.9.4

I have tried many permutations of the order of the dependencies -- most permutations have more errors. Did OLPG compile without problems on your end? I am not sure why this is only occuring now....

[pnrobinson]

I made a temporary fix of OLPG (see corresponding issue) and revised the code of PDXIntegrator. I am going to add all of the modules and data today so that we can have something concrete to discuss. This is where I am now. The code should run now...

PDXNET:TUMOR-PAT-0  PDXNET:hasSubmitterTumorId
                "TUMOR-PAT-0" ;
        PDXNET:stage                NCIT:C19251 ;
        PDXNET:tissueOfOrigin       UBERON:4423 ;
        PDXNET:tumorCategory        NCIT:C3352 ;
        PDXNET:tumorGrade           NCIT:C28097 ;
        PDXNET:tumorHistology       NCIT:C6332 .

PDXNET:PDX-PAT-0  PDXNET:animalHealthStatusOk
                PDXNET:False ;
        PDXNET:engraftmentPercent     25.71258708808637 ;
        PDXNET:engraftmentTimeInDays  25 ;
        PDXNET:hasStrain              "NOD.Cg-Prkdc<scid> Il2rg<tm1Wj>l/SzJ" ;
        PDXNET:mouseSource            "JAX" ;
        PDXNET:mouseTreatmentForEngraftment
                PDXNET:Estrogen ;
        PDXNET:notEbvNotMouse         PDXNET:False ;
        PDXNET:passageQAperformed     PDXNET:True ;
        PDXNET:pdxTumorCharacterization
                PDXNET:Histology ;
        PDXNET:pdxTumorResponse       PDXNET:Complete_response ;
        PDXNET:strainHumanized        PDXNET:False ;
        PDXNET:tumorPreparation       PDXNET:Suspension .