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Add NDEx Pathways Integration #4069

Merged
merged 17 commits into from
May 12, 2022
Merged

Add NDEx Pathways Integration #4069

merged 17 commits into from
May 12, 2022

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inodb
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@inodb inodb commented Dec 1, 2021

Adds NDEx pathways on pathways tab in the results view page. Related to cBioPortal/icebox#343.

Test URL: https://bit.ly/3vddazA

Screen Shot 2022-04-26 at 8 54 06 AM

TODO:

  • add iframe with iquery page that searches for queried genes rather than just an iframe of the homepage
  • Do we want to combine pathwaymapper and NDEx as single tab, but using pills to navigate between them? So you would have one pill for pathwaymapper and one for NDEx inside of a pathways tab.
  • Explain difference between NDEx and PathwayMapper in UI

We decieded not to include other alteration frequencies yet as part of this release:

  • current alteration frequency does not reflect queries study and subset alteration frequency. We prolly need to pass that over. Sample IDs, plus study ids. Or we pass over a session id. Addressing later in: Endpoint to retrieve alteration frequencies icebox#383
    • decide interface (JSON format).
      "geneAnnotationServices": { "mutation": "https://iquery-cbio.dev.ucsd.edu/integratedsearch/v1/mutationfrequency", "alteration": "http://localhost/" }

Follow up with tests: cBioPortal/icebox#331

Let's use squash on merge button

@inodb inodb changed the title add ndex iframe Add NDEx Pathways Integration May 6, 2022
@@ -47,6 +47,7 @@ const ServerConfigDefaults: Partial<IServerConfig> = {
show_mutation_mapper_tool_grch38: true,
show_transcript_dropdown: false,
show_signal: true,
show_ndex: true,
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@inodb should this really default to true?

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thanks for checking - yeah i think it makes sense to have this be the default for all installations

}

if (
urlResponse &&
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FYI, you can now do urlResponse?.body?.webUrl?.startWith('...') and it will evaluate false if anything is undefined

@inodb inodb merged commit bacad97 into master May 12, 2022
@dippindots dippindots deleted the ndex branch July 20, 2023 18:42
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2 participants