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Cris puts new & updated files in /usr/local/reactomes/Reactome/production/Website/static/download/current/ehld, the Jenkinsfile should be changed:

• remove the simple check for the existence of the ehld directory
• prompt the user with a question: "Has Cris updated the files in /usr/local/reactomes/Reactome/production/Website/static/download/current/ehld ?"
• If they choose "yes", copy the files to /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.

Example file with color and identifiers

https://bitbucket.org/vtoure/sbgn-extension/src/master/SBGNextension/examples/glycolysis.sbgn

Colors

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>

Identifiers

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>

libSBGN Support

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#");