On Sun, Jul 11, 2021 at 8:51 PM Peter Murray-Rust <pm...@cam.ac.uk> wrote:
> As you've probably found the message comes from CMLAtom, and is one of the > hardcoded validation rules for CML (these would be better done with an > XPath-type tool like Schematron, but that's irrelevant). > That's okay. > The error makes no sense! > Agreed :) It took me a while to figure out that the error was actually not because of the test, but triggered but something that (did not) happened in some other test. > My guess would be that it's picked up the wrong version of some library. > I haven't used Java recently - my suggestion would be to see if it is true > with other Java versions. If I understand it right, the error occurs in the > repository tests when building the system. > Actually, my current understanding is that it is not a dependency, nor a Java version, but likely a concurrency problem. The factory orchestrating the generation of the internal data model uses static/global variables and somewhere it forgot to clean the stack of parents, so that when the cml:atom is creating, it falsely believes it has an atomArray parent with an cml:formula grandparent... In the end, I could work around the problem to have the test (about removing non-CML attributes) not use cml:atom but cml:cml. I also filed a bug report to rework the code to not use global variables (which may be tricky...). Egon -- This year I am stepping down as co-Editor-in-Chief of the Journal of Cheminformatics, because of a conflict of interest with Springer Nature. See https://twitter.com/egonwillighagen/status/1403299501947899907 ----- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Twitter/Mastodon: @egonwillighagen <https://twitter.com/egonwillighagen> / @egonw <https://scholar.social/@egonw> Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: https://www.zotero.org/egonw ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286> ImpactStory: https://impactstory.org/u/egonwillighagen
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