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cytoscape / cytoscape-automation

Collection of scripts that include programmatic io and control of Cytoscape
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Problem with rWikiPathways and RCy3 protocol in Binder #50

Closed khanspers closed 4 years ago

khanspers commented 4 years ago

Can’t get past this command:

commandsRun(paste0('wikipathways import-as-pathway id=',human.gbm.wpids[1]))

which produces this error:

Error in commandsGET(cmd.string, base.url)

Running the same Rmd in standalone RStudio works fine.

https://github.com/cytoscape/cytoscape-automation/blob/master/for-scripters/R/notebooks/rWikiPathways-and-RCy3.Rmd

AlexanderPico commented 4 years ago

Here also, it would help to distinguish between memory limit vs buggy command. @khanspers Can you run this command alone at the very beginning of a Binder session, e.g., with a specific WPID?

khanspers commented 4 years ago

OK, tried opening Sandbox before running anything else. It fails:

commandsRun(paste0('wikipathways import-as-pathway id=WP4')) RCy3::commandsGET, HTTP Error Code: 404 url=http://localhost:1234/v1/commands/wikipathways/import-as-pathway?id=WP4 Error in commandsGET(cmd.string, base.url) :

AlexanderPico commented 4 years ago

Ah! Is the WikiPathways app installed? Would need to first run install.app("WikiPathways") and maybe check a few functions.

khanspers commented 4 years ago

That was it! Duh. But its weird because I originally ran all previous commands which include installing WP app...... Closing.

AlexanderPico commented 4 years ago

Right. So this confirms the test that the function runs fine, but this is still an open bug that might be due to memory capacity or something other than this function. The overall noteboook still fails, right?

khanspers commented 4 years ago

Actually, I just fixed a typo in the Rmd that made the code to install the WP app look commented out. I think that was the problem. That line was fine in Kozo's other WP Rmd, so I was thinking I had installed in this Rmd too. Once its installed everything runs as expected, until openSession(), which is a known bug. So I can't test the rest as-is.