Thanks very much Egon. I imagine I wrote this code but don't have it on my machine at present. Can you give a pointer to the Github repo and I'll have a look - but I'm not very optimistic I can help.
Would love to see some projects that use CMLXom - it has a lot of potential still. P. On Sun, Jul 11, 2021 at 5:16 PM Egon Willighagen <egon.willigha...@gmail.com> wrote: > Hi all, > > On Mon, Jun 28, 2021 at 10:22 PM Egon Willighagen < > egon.willigha...@gmail.com> wrote: > >> Next up is cmlxom :) (And then a PR for the CDK) >> > > I have started working on cmlxom to get it ready for uploading to Maven > Central. > > Today I have done the following things: > > - update JUnit4 > - set up GitHub Actions for compiling and running the tests > > But on GitHub there are currently two tests that fail (with Java 11 and > 8), which do not fail locally (with Java 11 and 8). Second, the fail does > not make sense: > > java.lang.RuntimeException: nu.xom.ParsingException: Atom grandparent must > be not be formula > at org.xmlcml.cml.base.CMLUtil.parseCML(CMLUtil.java:429) > at > org.xmlcml.cml.base.CMLUtilTest.removeNonCMLAttributes(CMLUtilTest.java:531) > > But the CML fragment (a String) in the two failing tests do not have > CMLFormular, and I am puzzled why this exception is thrown... maybe more > later. ideas welcome. > > 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 > -- "I always retain copyright in my papers, and nothing in any contract I sign with any publisher will override that fact. You should do the same". Peter Murray-Rust Reader Emeritus in Molecular Informatics Yusuf Hamied Department of Chemistry University of Cambridge CB2 1EW, UK +44-1223-336432
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