PC xml:base is there hard-coded

[IgorRodchenkov]

Thing is that not only the PC endpoint URL can be different (for e.g., the beta, textmining, yeast, human PC web services) ut also BioPAX xml:base (i.e., URI prefix for the entities, etc.).
Currently, only URL is configurable via system variable, bit xml base is hard-coded somewhere...

[IgorRodchenkov]

E.g., PC9 and PC10 (beta) have xml:base=http://pathwaycommons.org/pc2/, whereas yeast.pathwaycommons.org/pc2/ uses xml:base=http://pathwaycommons.org/yeast1/...

PS:
Perhaps, thats why this app instance runing at yeast.pathwaycommons.org fails to provide any node detailes in the view (I've just locally edited the src/server/graph-generation/generic-physical-entities/index.js file, re-built and restarted the app with PC_URL="http://yeast.pathwaycommons.org/pc2/"; it did not help...)

[IgorRodchenkov]

This problem is actually caused by BioPAX/Paxtools/issues/39 !

[IgorRodchenkov]

Fixed (but we can do even better in the future - java Paxtools/sbgn-converter could generate and insert biopax URIs, type, various metadata right into SBGN-ML using the Notes and Extensions XML elements!)