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Change CTS to use REST API #257

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Aariq opened this issue May 19, 2020 · 6 comments
Open

Change CTS to use REST API #257

Aariq opened this issue May 19, 2020 · 6 comments
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enhancement New feature or enhancement low priority

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@Aariq
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Aariq commented May 19, 2020

While puzzling through some problems with cts_*() functions (see #255, #243 ) I noticed that CTS has a REST API that is not currently implemented in the cts_*() functions.
https://cts.fiehnlab.ucdavis.edu/services

@Aariq Aariq added the enhancement New feature or enhancement label May 19, 2020
@Aariq Aariq self-assigned this Jun 2, 2020
@Aariq
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Aariq commented Jun 2, 2020

The REST API currently seems broken, but I'm watching an issue and will take a crack at this when the API is working again. https://bitbucket.org/fiehnlab/ctsproxy/issues/24/ssl-certificate-has-expired-for-rest-api

@stitam
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stitam commented Jul 3, 2020

Could httr::RETRY() mitigate our difficulties with the cts functions? If yes, then this may be a simple fix, I am happy to submit it.

@Aariq
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Aariq commented Jul 9, 2020

If it's an easy change, then it might be a good stopgap measure until CTS gets fixed.

@stitam
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stitam commented Jul 9, 2020

Ok, then I'll jump in on this one.

@stitam
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stitam commented Sep 17, 2020

I am closing this issue as REST API would still be nice, but CTS seems to be working fine so I'll just mark it as low priority.

@Aariq
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Aariq commented Jul 31, 2023

REST API seems to be working now! Features available by REST that are not currently in webchem::cts_* functions:

  • Convert from chemical name to InChiKey with either a "popularity" or "biological" (?) score—could be integrated with the match = argument for cts_convert().
  • Convert InChiKey to MOL/SDF
  • Count biological IDs. I think this means 'how many hits are there for this InChiKey in various biological molecule databases?' Only works with InChiKey as input.

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