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wikipathways / gpml-sync-action

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Apache License 2.0
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Pathways like WP366 throw errors #1

Open AlexanderPico opened 1 year ago

AlexanderPico commented 1 year ago

https://github.com/wikipathways/wikipathways-database/actions/runs/4776003043/jobs/8490733040

[ 0.028] Info: Recognized format [Namespace: prefix "" is mapped to URI "http://pathvisio.org/GPML/2013a"] Warn: Unknown property: TERM Warn: Unknown property: Ontology [ 0.664] Info: Recognized format [Namespace: prefix "" is mapped to URI "http://pathvisio.org/GPML/2013a"] Warn: Unknown property: TERM Warn: Unknown property: Ontology Warn: Unknown property: TERM Warn: Unknown property: Ontology [ 1.016] Info: Recognized format [Namespace: prefix "" is mapped to URI "http://pathvisio.org/GPML/2013a"] Warn: Unknown property: TERM Warn: Unknown property: Ontology Warn: Unknown property: TERM Warn: Unknown property: Ontology Warn: Unknown property: TERM Warn: Unknown property: Ontology [ 1.253] Info: Recognized format [Namespace: prefix "" is mapped to URI "http://pathvisio.org/GPML/2013a"] Warn: Unknown property: TERM Warn: Unknown property: Ontology Error: Exception in thread "main" java.lang.IllegalArgumentException: Comparison method violates its general contract! at java.util.ComparableTimSort.mergeLo(ComparableTimSort.java:744) at java.util.ComparableTimSort.mergeAt(ComparableTimSort.java:481) at java.util.ComparableTimSort.mergeCollapse(ComparableTimSort.java:406) at java.util.ComparableTimSort.sort(ComparableTimSort.java:213) at java.util.Arrays.sort(Arrays.java:1312) at java.util.Arrays.sort(Arrays.java:1506) at java.util.ArrayList.sort(ArrayList.java:1464) at java.util.Collections.sort(Collections.java:143) at org.pathvisio.core.model.GpmlFormat2013a.createJdom(Unknown Source) at org.pathvisio.core.model.GpmlFormat2013a.writeToXml(Unknown Source) at org.pathvisio.core.model.GpmlFormat2013a.writeToXml(Unknown Source) at org.pathvisio.core.model.GpmlFormat.writeToXml(Unknown Source) at org.pathvisio.core.model.Pathway.writeToXml(Unknown Source) at org.wikipathways.SyncAction.main(Unknown Source) Error: Process completed with exit code 1.

AlexanderPico commented 1 year ago

Please restore "approved" tag on WP366 when pathway or code is fixed.

egonw commented 3 months ago

WP1045 is another one. I also removed the "approved" tag on that one. It's an homology converted pathway, btw.

egonw commented 3 months ago

I can confirm the 2.1 version has the same problem, but it's nice that that one reports the failing pathway.

(Oh, and I think we may have in one of the other repositories another failing pathway somewhere, that may have the same course?)