reactome-pwp / diagram-exporter Goto Github PK
View Code? Open in Web Editor NEWExporter of the diagram layout to different formats (pptx, svg, png, gif, jpg, sbgn)
Home Page: https://reactome.org
Exporter of the diagram layout to different formats (pptx, svg, png, gif, jpg, sbgn)
Home Page: https://reactome.org
Cris puts new & updated files in /usr/local/reactomes/Reactome/production/Website/static/download/current/ehld
, the Jenkinsfile should be changed:
/usr/local/reactomes/Reactome/production/Website/static/download/$RELEASE_NUMBER/ehld
(create the directory first, if necessary).Jenkinsfile does not create "${env.ABS_DOWNLOAD_PATH}/${releaseVersion}/ehld/" (expands to /usr/local/reactomes/Reactome/production/Website/static/download/76/ehld) and the program fails. The Jenkinsfile needs to check that the directory exists, and raise an error before trying to run the Java application if the directory is missing.
Normally, the "ehld" directory is populated manually by Cris. This step cannot be allowed to run if the directory has not been set up.
Color and identifier support will allow third-party tools (like Newt, newteditor.org) to modify the figures for alternative uses and pairing with analyses.
https://bitbucket.org/vtoure/sbgn-extension/src/master/SBGNextension/examples/glycolysis.sbgn
SBGNML color information is stored as SBML Render content:
http://otto.bioquant.uni-heidelberg.de/sbml/#specifications
<style idList="glyph2 glyph7 glyph13 ">
<g stroke="Color_2" stroke-width="5" fill="yelloComp" />
</style>
SBGNML identifier information is stored as SBML annotations:
https://semanticsbml.org/semanticSBML/static/documentation/annotate.html
<extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#glyph10">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:16761"/>
<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00008"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</extension>
Support for identifiers is provided in the Java libSBGN library (functions by @fbergmann).
Element getAnnotation(SBGNBase sbgnElement, String namespaceURI)
String getAnnotationString(SBGNBase sbgnElement, String namespaceURI)
String wrapRdf(String content) (with all the overloads up to)
String wrapRdf(String content, boolean includeBiol, boolean includeModel, boolean includeDc,
boolean includeVcard)
void addAnnotation(SBGNBase sbgnElement, Reader r) and overloads
that way adding new entries becomes relatively easy:
addAnnotation(glyph,
wrapRdf("<bqbiol:is><rdf:Bag><rdf:li rdf:resource='http://identifiers.org/uniprot/Q96RR4'/></rdf:Bag></bqbiol:is>", true));
and retrieving them is simple enough:
String annotationString = getAnnotationString(map, "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
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