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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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Urgent: Edge Table names are missing #107

Closed AlexanderPico closed 2 years ago

AlexanderPico commented 5 years ago

Shared name and name are required fields for cytoscape models. Not sure how we are making networks without them, but it appears that we are. This will cause bugs for any downstream actions that rely on edge names.

Steps to reproduce:

  1. Open any WPID as pathway or network
  2. Look in Edge Table

Obs: Missing name and shared name Exp: Names

AdamStuart commented 5 years ago

Setting name and shared name to src.name + " " + interaction + " " + targ.name

Some names aren't very good: CMA1 mim-catalysis null ATP6AP2 Arrow TFs

AlexanderPico commented 5 years ago

Parens are needed. Open any cytoscape network to see examples. From the manual: http://manual.cytoscape.org/en/stable/Node_and_Edge_Column_Data.html#detailed-file-format-advanced-users

Edge names are all of the form: sourceName (edgeType) targetName Specifically, that is sourceName space openParen edgeType closeParen space targetName

AdamStuart commented 5 years ago

fixed, with Import as Network too

yihangx commented 2 years ago

Reopen because of 3.3.9.

AlexanderPico commented 2 years ago

Fixed in 3.3.10