GPML Labels should be CyAnnotations

wikipathways / cytoscape-wikipathways-app

WikiPathways app for Cytoscape to open and access pathways from WikiPathways

Apache License 2.0

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GPML Labels should be CyAnnotations #100

Closed ariutta closed 5 years ago

ariutta commented 5 years ago

GPML Label elements should be converted to CyAnnotations.

When I import a pathway from WikiPathways and try exporting to NDEx or to CX, I get this error:

Error parsing element in CX stream: Error status received in CX document. Error message: Failed to create complete network from cyNDEx: java.lang.Double cannot be cast to java.lang.Integer

@AlexanderPico and I tested this, and it appears we only get this error for pathways that have Labels.

(Related to #30?)

AlexanderPico commented 5 years ago

Let's punt on this one since it seems to be fixed on the Cytoscape side of things and and handling connections between nodes and annotations will be tricky.