Open nilshoffmann opened 8 months ago
Potentially, ontologies.xml needs to be updated on my side. Not sure if it is still current.
I have rebased my fork against master, so it should now also contain the upstream changes.
@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.
@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">
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.
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.
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.