Status of commands? - Githubissues

wikipathways / cytoscape-wikipathways-app

WikiPathways app for Cytoscape to open and access pathways from WikiPathways

Apache License 2.0

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Status of commands? #45

Closed AlexanderPico closed 6 years ago

AlexanderPico commented 6 years ago

I see 4 commands for the WP app, but they don't seem to do anything...

[x] (Adam) Can we update the argument documentation and confirm that these work?
[x] (All) Then let's make sure we have all the commands we need for typical automation workflows.
[x] (Kristina) Then let's make a tutorial in reveal that runs in CyBrowser and actually uses these commands.

screen shot 2017-08-24 at 3 34 28 pm

AlexanderPico commented 6 years ago

For now, let's keep the two import methods (make them work) and ditch get-species and search. And then add a bit of the new documentation.

AlexanderPico commented 6 years ago

Here is where the Swagger docs show up: http://localhost:1234/v1/swaggerUI/swagger-ui/index.html?url=http%3A%2F%2Flocalhost%3A1234%2Fv1%2Fcommands%2Fswagger.json#!/wikipathways/wikipathways_import_as_network

AlexanderPico commented 6 years ago

This is returning NULL for command line tasks: https://github.com/wikipathways/cytoscape-wikipathways-app/blob/develop/src/main/java/org/wikipathways/cytoscapeapp/impl/WPClientRESTImpl.java#L259

And this is where the GUI leads when searching for WPIDS: https://github.com/wikipathways/cytoscape-wikipathways-app/blob/develop/src/main/java/org/wikipathways/cytoscapeapp/internal/guiclient/GUI.java#L402

AlexanderPico commented 6 years ago

Current error:

java.lang.IllegalArgumentException: No such pathway with ID: WP4 at org.wikipathways.cytoscapeapp.internal.cmd.WPImportCmdTask$1.run(WPImportCmdTask.java:49)

AlexanderPico commented 6 years ago

Ok. It's working now. Yay! Can we still do the following:

[ ] (Adam) Update cld and swagger docs, including descriptions and real example values
[ ] (Kristina) Can you make a short protocol that uses these commands in CyBrowser

The cld syntax is wikipathways import-as-pathway id=WP4

AdamStuart commented 6 years ago

reduced down to one command

AlexanderPico commented 6 years ago

A couple checklist items remain...

AlexanderPico commented 6 years ago

KH: I have a draft tutorial locally that I am adding today. It uses WP App and IDMapper to open pathway, map ids and import/visualize data. Don’t have a clearly defined set of pathway and dataset to use yet, working on it.

khanspers commented 6 years ago

Draft of tutorial that combines WP App and IdMapper is here: https://cytoscape.github.io/cytoscape-tutorials/protocols/WP-DataViz-tutorial.html

AdamStuart commented 6 years ago

Closed: (All) Then let's make sure we have all the commands we need for typical automation workflows. We only support one command in automation workflows: import-as-pathway