Fix #4958 - IGV button names and IGV MT overview link #4976
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## main #4976 +/- ##
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Nice! Simpler for the users, which will be pleased.
A couple of minor things:
- For consistency, would be nice to deactivate the MT button when the mt_bam are missing (see my comment on the case sidebar)
- Add a tooltip on variant page, explaining the the DNA button us deactivated because the bam files are missing:
scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html
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Let me know when you are ready for another review on this one @dnil. I was thinking that perhaps we can merge this and create a new release with what we have today? |
Good points! Both should now be addressed; happy for a new review when you have time! |
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I've been testing only with demo samples for now and noticed that with the demo RD case, which has mito bams for the individuals, if you go on a mt variant, then alignments are not available: 
It's not the expected behavior I guess? I'll continue testing! |
| @@ -29,6 +30,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/) | |||
| - STRs variants export | |||
| - ClinVar submission enquiry status for all submissions after the latest | |||
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| @@ -355,11 +355,17 @@ <h6>Phenotype terms (HPO):</h6> | |||
| {% endif %} | |||
| </div> | |||
| <div class="col-3"> | |||
| {% if variant.is_mitochondrial and case.mt_bams or case.bam_files %} | |||
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Perhaps to keep it simple one could keep the original if and else (which were working) and in the case of else put the code for a button which is deactivated and has the tooltip. Because honestly it would be easier to maintain..
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Sure, though that will be a bit redundant. I would prefer not to keep this statement, as it is very hard to read. Jinja dont really make there operator priority super clear, and it lacks parenthesis to disambiguate
(variant.is_mitochondrial and case.mt_bams) or case.bam_files from variant.is_mitochondrial and (case.mt_bams or case.bam_files)
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Sure, though that will be a bit redundant. I would prefer not to keep this statement, as it is very hard to read. Jinja dont really make there operator priority super clear, and it lacks parenthesis to disambiguate
(variant.is_mitochondrial and case.mt_bams) or case.bam_filesfromvariant.is_mitochondrial and (case.mt_bams or case.bam_files)
You can also keep it as it was:
else: "No alignments available"
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Ok, here goes - a bit more redundant html, but the logic is easier and actually works for all the views and missing/not missing combos instead. You win some and loose some. 😉 |
| <div class="panel-default"> | ||
| {{ comments_panel(institute, case, current_user, comments) }} | ||
| </div> | ||
| <div class="col-xs-12 col-md-12">{{ smn_individuals_table(case, institute, tissue_types) }}</div> |
| </span> | ||
| {% endif %} | ||
| {% if case.vcf_files.vcf_sv %} | ||
| <span class="d-flex"> |
| <span class="me-3"> | ||
| <form action="{{url_for('variants.sv_variants', institute_id=institute._id, case_name=case.display_name) }}"> | ||
| <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="SMN1, SMN2"></input> | ||
| <input type="hidden" id="gene_panels" name="gene_panels" value="['']"></input> | ||
| <button type="submit" class="btn btn-secondary btn-sm" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="Structural variants view filtered for the genes SMN1 and SMN2">SVs</button></span> | ||
| <button type="submit" class="btn btn-secondary btn-sm" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="Structural variants view filtered for the genes SMN1 and SMN2">SVs</button> |
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formatting error fix en passant
| <div class="col-sm-12">{{activity_panel(events)}}</div> | ||
| </div> | ||
| <span class="me-3" | ||
| {% if not case.bam_files %}title="Alignment file(s) missing" data-bs-toggle="tooltip"{% endif %}> |
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We could loop these, but there will only ever be two.
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| {{ modal_synopsis() }} | ||
| <div class="row"> |
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same actual order as before
| {% else %} | ||
| - BAM file(s) missing | ||
| {% endif %} | ||
| {% if variant.is_mitochondrial and not case.mt_bams %} |
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a little repetitive, but an easier read
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I like it, redability is important
| <div href="#" class="bg-dark list-group-item d-inline-block text-white"> | ||
| {% if case.bam_files %} | ||
| <div href="#" class="bg-dark list-group-item d-inline-block text-white" | ||
| {% if not case.bam_files %} data-bs-toggle="tooltip" title="Alignment file(s) missing" {% endif %}> |
| {% else %} | ||
| - BAM file(s) missing | ||
| {% endif %} | ||
| {% if variant.is_mitochondrial and not case.mt_bams %} |
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I like it, redability is important
| <form action="{{url_for('alignviewers.sashimi_igv', institute_id=case['owner'], case_name=case['display_name']) }}" target="_blank" rel="noopener"> | ||
| <button role="submit" data-bs-toggle="tooltip" data-bs-placement="top" title="Available in build GRCh{{ case.rna_genome_build or '38' }}" class="btn btn-xs form-control btn-secondary">R<span class="menu-collapsed">NA splicing</span></button> | ||
| </div> | ||
| <div href="#" class="bg-dark list-group-item d-inline-block text-white" |
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Nice, this way it's much clearer what can be viewed in IGV!
| @@ -76,7 +76,7 @@ | |||
| disabled" title="Alignment file(s) missing" data-bs-toggle="tooltip" aria-disabled="true"><span class="fa fa-times-circle fa-fw me-1"></span>IGV mtDNA | |||
| </a> | |||
| </span> | |||
| {% elif not case.bam_files %} | |||
| {% elif not case.bam_files and not variant.is_mitochondrial %} | |||
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Ok, let's go. Demo case with mtDNA alignments and RNA tracksOn RD mt SNV
On RD gDNA SNV
On STR view
On MEI view
On SMA view
On overview
Test case with gDNA alignment
Somatic demo, mtDNA only
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This PR changes the names on IGV buttons (to IGV DNA, IGV RNA, IGV MT), avoiding the "viewer" tautology and the use of "splicing" when we also have full RNA alignments. Also adds an IGV MT overview button from the collapsible toolbar. Also added a magnifying glass icon for existing data, and use the ring-X icon consistently for missing data.
Partly by following the style on one page, I reverted to disable and tooltip to indicate missing alignments. The tooltips are not really available without viewing source on disabled buttons in the current bootstrap. It would be possible to get them displayed by moving them to regular html title tooltips, or a separate js tooltip class, setting
pointer-events: none;to avoid the bootstrap pointer block, if we feel this is important.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: