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wikipathways / cytoscape-wikipathways-app

WikiPathways app for Cytoscape to open and access pathways from WikiPathways
Apache License 2.0
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Ensembl mapping during import not working completely #108

Closed khanspers closed 4 years ago

khanspers commented 4 years ago

The auto mapping to Ensembl doesn't seem to be working properly. Just tried with AP app version 3.3.7 (released version) and latest CS (and also 3.7.1), and for the human Statin pathway, no mapping happens for Entrez Gene xrefs. Only two Ensembl Xrefs are properly propagated to the new Ensembl column.

As a comparison, BridgeDb maps all 30 Entrez IDs.

AlexanderPico commented 4 years ago

Here's the relevant bit of the stacktrace. Maybe the webservice url changed?? I believe BridgeDb was recently moved to AWS. May be related?

java.io.IOException: HTTP error code : 404
    at org.wikipathways.cytoscapeapp.internal.cmd.mapping.BridgeDbIdMapper.post(BridgeDbIdMapper.java:189)
    at org.wikipathways.cytoscapeapp.internal.cmd.mapping.BridgeDbIdMapper.runQuery(BridgeDbIdMapper.java:220)
    at org.wikipathways.cytoscapeapp.internal.cmd.mapping.BridgeDbIdMapper.map(BridgeDbIdMapper.java:63)
AlexanderPico commented 4 years ago

Indeed same no response from bridgedb webservice via swagger: https://www.bridgedb.org/swagger/#!/Genes/post_organism_xrefsBatch_systemCode

This is a bridgedb bug, not a wikipathways app bug.