Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Updated dependencies to Java 17 #15

Open
wants to merge 4 commits into
base: master
Choose a base branch
from
Open

Updated dependencies to Java 17 #15

wants to merge 4 commits into from

Conversation

nilshoffmann
Copy link
Member

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
Copy link
Member Author

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

bittremieux and others added 3 commits December 15, 2023 17:59
@bittremieux @nilshoffmann
Add DIA workflow to CV table
fdc228b
@bittremieux @nilshoffmann
Add table for deconvoluted data
a78bfff
@mobiusklein @nilshoffmann
Update mzML1.1.1.xsd to use declared namespace
2921e22 
The document declares the `XMLSchema` namespace `xs`, not `xsd`, but the addition for v1.1.1 used `xsd` when creating the new schema elements. This lead to an error when parsing the document strictly. 

This change just fixes the namespace on the added tags.
@nilshoffmann
Copy link
Member Author

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

@edeutsch edeutsch requested a review from ypriverol April 5, 2024 15:48
ypriverol
ypriverol reviewed Apr 5, 2024
View reviewed changes
Copy link
Contributor

@ypriverol ypriverol left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Everything looks OK. The only minor comment is that I saw a version 1.7.11 already in the repo. If we release this version it will not overrite it. You can increase the version or let me know Who has release this version to make sure that is corresponding to this PR.

@nilshoffmann .

@nilshoffmann
Copy link
Member Author

nilshoffmann commented Apr 8, 2024 •
edited
Loading

@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
Copy link
Member Author

nilshoffmann commented Apr 8, 2024 •
edited
Loading

@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
Copy link
Member Author

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
Copy link
Member Author

nilshoffmann commented Apr 8, 2024 •
edited
Loading

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@ypriverol ypriverol ypriverol left review comments

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
4 participants
@nilshoffmann @ypriverol @bittremieux @mobiusklein