Fix transcript links to Ensembl and NCBI RefSeq#6041
Fix transcript links to Ensembl and NCBI RefSeq#6041northwestwitch wants to merge 16 commits intomainfrom
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This needs some more fixing and I won't have time on these days. @dnil feel free to continue/modify it if you want! |
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I don't think there is any rush really, but thank you! |
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #6041 +/- ##
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+ Coverage 83.88% 83.93% +0.04%
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Files 336 336
Lines 21022 21019 -3
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+ Hits 17635 17642 +7
+ Misses 3387 3377 -10 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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This now looks good on stage and passes the automatic tests, I'm marking in ready for review |
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| def ensembl_tx(ens_tx_id, build=37): | ||
| link = "http://grch37.ensembl.org/Homo_sapiens/" "Gene/Summary?t={}" | ||
| link = "https://grch37.ensembl.org/Homo_sapiens/Gene/Summary?t={}" |
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| hgnc_transcript = transcripts_dict.get(tx_id) | ||
| # If the tx does not exist in ensembl anymore we skip it | ||
| if not hgnc_transcript: |
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Removing this condition is also a fix
| hgnc_transcript.get("refseq_identifiers", []) if hgnc_transcript else [] | ||
| ) | ||
| transcript["change_str"] = transcript_str(transcript, hgnc_symbol) | ||
| add_tx_links(transcript, genome_build, hgnc_symbol) |
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And of course this is also a fix
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2 participants
This PR adds a functionality or fixes a bug.
Testing on cg-vm1 server (Clinical Genomics Stockholm)
Prepare for testing
scout-stageand the server iscg-vm1.ssh <USER.NAME>@cg-vm1.scilifelab.sesudo -iu hiseq.clinicalssh localhostpodman pssystemctl --user stop scout@<name_of_currently_deployed_branch>systemctl --user start scout@<this_branch>systemctl --user status scout.targetscout-stage) to be used for testing by other users.Testing on hasta server (Clinical Genomics Stockholm)
Prepare for testing
ssh <USER.NAME>@hasta.scilifelab.seus; paxa -u <user> -s hasta -r scout-stage. You can also use the WSGI Pax app available at https://pax.scilifelab.se/.conda activate S_scout; pip freeze | grep scout-browserbash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b <this_branch>us; scout --versionpaxaprocedure, which will release the allocated resource (scout-stage) to be used for testing by other users.How to test:
Expected outcome:
The functionality should be working
Take a screenshot and attach or copy/paste the output.
Review: