Updated dependencies to Java 17

nilshoffmann commented 8 months ago

This PR updates the mzML validator application to use updated dependencies, new Maven repository locations and EBI and some minor implementation changes reflecting the differing dependencies.

nilshoffmann commented 8 months ago

Potentially, ontologies.xml needs to be updated on my side. Not sure if it is still current.

nilshoffmann commented 8 months ago

I have rebased my fork against master, so it should now also contain the upstream changes.

nilshoffmann commented 5 months ago

@ypriverol This updates the jmzml dependency to 1.7.11. The released version of the semantic validator would be 1.2 (currently 1.2-SNAPSHOT). I do not know who can actually perform and push the release.

nilshoffmann commented 5 months ago

@ypriverol Just checked, there seems to be a remaining (or new?) issue with resolving OBOs (PATO mainly) via the psidev.psi.tools validator library (v2.1.0 and v2.1.1) and OLS (code: https://github.com/HUPO-PSI/psi-tools). This comes from here:

Extracting /ms-mapping.xml to directory: /tmp/ms-mapping.xml
Extracting /ObjectRules.xml to directory: /tmp/ObjectRules.xml
Error: Expected :.
on line: 1 of http://purl.obolibrary.org/obo/pato.obo
charnum: 0
line: <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
    at org.obo.dataadapter.OBOParseEngine.translateException(OBOParseEngine.java:1444)
    at org.obo.dataadapter.OBOParseEngine.translateAndThrow(OBOParseEngine.java:1436)
    at org.obo.dataadapter.OBOParseEngine.doParse(OBOParseEngine.java:325)
    at org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:48)
    at org.obo.dataadapter.DefaultOBOParser.readImport(DefaultOBOParser.java:513)
    at org.obo.dataadapter.OBOParseEngine.parseTagValue(OBOParseEngine.java:431)
    at org.obo.dataadapter.OBOParseEngine.parseTag(OBOParseEngine.java:988)
    at org.obo.dataadapter.OBOParseEngine.doParse(OBOParseEngine.java:398)
    at org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:48)
    at org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:72)
    at org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:273)
    at uk.ac.ebi.ols.loader.parser.OBO2FormatParser.<init>(OBO2FormatParser.java:33)
    at psidev.psi.tools.ontology_manager.impl.local.OboLoader.configure(OboLoader.java:50)
    at psidev.psi.tools.ontology_manager.impl.local.AbstractOboLoader.parseOboFile(AbstractOboLoader.java:116)
    at psidev.psi.tools.ontology_manager.impl.local.AbstractOboLoader.parseOboFile(AbstractOboLoader.java:358)
    at psidev.psi.tools.ontology_manager.impl.local.AbstractLocalOntology.loadOntology(AbstractLocalOntology.java:113)
    at psidev.psi.tools.ontology_manager.OntologyManagerTemplate.loadOntologies(OntologyManagerTemplate.java:182)
    at psidev.psi.tools.ontology_manager.OntologyManagerTemplate.<init>(OntologyManagerTemplate.java:63)
    at psidev.psi.tools.ontology_manager.OntologyManager.<init>(OntologyManager.java:56)
    at psidev.psi.tools.validator.Validator.setOntologyManager(Validator.java:187)
    at psidev.psi.tools.validator.Validator.<init>(Validator.java:164)
    at psidev.psi.ms.MzMLValidator.<init>(MzMLValidator.java:117)
    at psidev.psi.ms.MzMLValidatorGUI$4.construct(MzMLValidatorGUI.java:507)
    at psidev.psi.ms.swingworker.SwingWorker$2.run(SwingWorker.java:122)
    at java.base/java.lang.Thread.run(Thread.java:1623)
Error: Expected :.
on line: 1 of http://purl.obolibrary.org/obo/pato.obo
charnum: 7
line: <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">

nilshoffmann commented 5 months ago

The issue seems to be line 6 of the PSI-MS OBO file, which imports PATO:

https://github.com/HUPO-PSI/psi-ms-CV/blob/6dd9f6b2303a4b4da18059d097cc5294fafd0faf/psi-ms.obo#L6

import: http://purl.obolibrary.org/obo/pato.obo

This is a redirect to https://raw.githubusercontent.com/pato-ontology/pato/master/pato.obo which the OLS OBO2FormatParser then chokes on.

nilshoffmann commented 5 months ago

The breaking code is in https://www.ebi.ac.uk/Tools/maven/repos/service/rest/repository/browse/ebi-repo/uk/ac/ebi/ols/ols-core/1.19/ This should come from this (archived) repository: https://github.com/EBISPOT/OLS/tree/dev/ols-core

Update: the actual code comes from obo:obo 2.0 jar, but I am currently not able to locate its source code.

HUPO-PSI / mzML

Updated dependencies to Java 17 #15