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ProteoRE tool 'reactome' #593

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ProteoRE tool 'reactome' #593

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combesf
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@combesf combesf commented May 11, 2021

Another ProteoRE tool : "reactome" or "proteore_pathway_enrichement_analysis_reactome"

Thank you for the review,
Florence.

@yvandenb yvandenb assigned yvandenb, vloux and combesf and unassigned yvandenb May 11, 2021
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Dear Galaxy-P maintainers,
all checks being passed, and as newcomers who want to do things properly, we'd like to know whether it's our role to launch the "merge PR" action or yours ? in other words are we supposed to continue this process until its closure or should we wait for a green light from you ? - thx for your help

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@combesf @yvandenb if this PR is ready to go please remove the WIP label and then someone will review the PR.

PRs can only be merged if they get at least one review. I will do a few reviews over the weekend, promised. Please indicate if you thing you are ready by removing the WIP.

@yvandenb yvandenb changed the title [WIP] Adding ProteoRE tool 'reactome' Version 2021.04.20 Adding ProteoRE tool 'reactome' Version 2021.04.20 May 21, 2021
@yvandenb yvandenb changed the title Adding ProteoRE tool 'reactome' Version 2021.04.20 ProteoRE tool 'reactome' Version 2021.04.20 Jun 2, 2021
@yvandenb yvandenb changed the title ProteoRE tool 'reactome' Version 2021.04.20 [WIP] ProteoRE tool 'reactome' Version 2021.04.20 Jun 2, 2021
@combesf combesf changed the title [WIP] ProteoRE tool 'reactome' Version 2021.04.20 ProteoRE tool 'reactome' Jun 3, 2021
bgruening
bgruening reviewed Jun 5, 2021
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tools/proteore_reactome/reactome_analysis.py
trash = id_valid(idens)[1]
# print(json_string)
j = json.loads(json_string)
print("Identifiers not found: " + str(j["identifiersNotFound"]))
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you could use f-strings, they are super cool: https://tirkarthi.github.io/programming/2019/05/08/f-string-debugging.html

@yvandenb yvandenb added the wip label Jun 8, 2021
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combesf commented Jun 15, 2021 •
edited by yvandenb
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@bgruening
This tool makes an error during the automatic tests on 'tools-galaxyp' Github,
but all tests are OK on our server.
We suspect the error occurs on the call of the line 71 in the python file.
So it seems to us that it is a "network" problem.
Does this ring a bell to you ??
Thanks,
Florence.

@bgruening => ping

@combesf combesf mentioned this pull request Sep 16, 2021
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@reid-wagner reid-wagner mentioned this pull request Jan 31, 2024
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