Updated dependencies to Java 17

nilshoffmann commented 11 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 11 months ago

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

nilshoffmann commented 11 months ago

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

nilshoffmann commented 7 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 7 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 7 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 7 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