Truncate long HGVS descriptions on cancer SNVS and SNV pages #5183
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## main #5183 +/- ##
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Tested with this case, check the second page of the SNVs Main branch
This branch
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| @@ -235,10 +235,10 @@ <h6 class="card-header">Variant callers</h6> | |||
| <span class="text-muted">exon </span><strong>{{ primary_gene.exon }}</strong> | |||
| {% endif %} | |||
| {% if primary_transcript and primary_transcript.coding_sequence_name %} | |||
| {{ primary_transcript.coding_sequence_name | url_decode }} | |||
| {{ primary_transcript.coding_sequence_name | url_decode | truncate(50, True) }} | |||
| <a target="_blank" href="{{ url_for('variant.cancer_variant', institute_id=institute._id, case_name=case.display_name, | ||
| variant_id=variant._id, cancer='yes') }}"> | ||
| {% if variant.first_rep_gene.hgvs_identifier %} | ||
| <div>{{ variant.first_rep_gene.hgvs_identifier }}</div> | ||
| <div>{{ (variant.first_rep_gene.hgvsp_identifier or '') |url_decode }}</div> | ||
| <div>{{ variant.first_rep_gene.hgvs_identifier|truncate(30, True) }}</div> |
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This is better than current main on layout, but we should ideally have like a pretty print for these as well, e.g. giving coord and ins and/or del and the number of bp instead of the exact sequence of each if it goes over an annoying number of chars in total.
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Ideally it would be nice to have a common way for cancer and non-cancer variants (the HGVS of these are handled in an easier way). Here it is complicated by the first and second representative gene which can be missing also. Felt safer to keep the code basically the same and just truncate strings if they are long. Let's merge and revisit if we touch this code in the future
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.targetsystemctl --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: