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MICommunity / psimi

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Remove psi25-xml-rdf from psimi and suggest paxtools/psimi-converter #30

Open MaybeJustJames opened 2 years ago

MaybeJustJames commented 2 years ago

As discussed with @IgorRodchenkov here, psi25-xml-rdf should be removed in favour of BioPAX/Paxtools psimi-converter

IgorRodchenkov commented 2 years ago

Sounds good unless someone still actually uses the feature to export PSIMI to those other RDF formats, not just to the default BioPAX RDF/XML, i.e., here https://github.com/MICommunity/psimi/blob/master/psi25-xml-rdf/src/main/java/org/hupo/psi/mi/rdf/PsimiRdfConverter.java#L95

In case you'd keep this module for that or some other reason, you need to upgrade to use the latest Paxtools, SimpleIOHandler, and perhaps, if you still need Jena, use it as a separate dependency, independently rather than using the old paxtools-jena-io and its transitive dependencies (as I recall, the jena version was there too old and required a particular XML api/impl and java 5...)

git4anjali commented 2 years ago

As for intact, we use the psi25-xml-rdf library in psiquic view(psicquic-solr lib) and legacy intact view. legacy-intact-view is going to be extinct in coming months but psicquic view is going to stay for a while. When we think of removing the rdf,turtle etc. export support from psiquic view(have to discuss this with team - who are mostly in holidays) we would be ready to remove this library unless someone else from the community needs it (please message here if that's the case by end of december 2021). If we decide to keep it ... we will incorporate the changes suggested by Igor or discuss here about it. James, we can only accept pull request for develop branch as we have a process for releasing into master which does other stuff as deploying into repo etc. and we do not want our master to be ahead of develop. For all the above reasons here, cannot accept this pull request.