northwestwitch commented 2 weeks ago

[4.91]

Added

[x] MANE badges on list of variant's Genes/Transcripts/Proteins table, this way also SVs will display MANE annotations
[x] Export variant type and callers-related info fields when exporting variants from variants pages
[x] Cases advanced search on the dashboard page
[x] Possibility to use only signed off panels when building the PanelApp GREEN panel
[x] Variant link to Franklin in database buttons (different depending on rare or cancer track)
Changed
[x] On genes panel page and gene panel PDF export, it's more evident which genes were newly introduced into the panel
[x] WTS outlier position copy button on WTS outliers page
[x] Update IGV.js to v3.0.9
[x] Managed variants VCF export more verbose on SVs
[x] /api/v1/hpo-terms returns pymongo OperationFailure errors when provided query string contains problematic characters
[x] When parsing variants, prioritise caller AF if set in FORMAT.
[x] Expand the submissions information section on the ClinVar submissions page to fully display long text entries
[x] Jarvik for PP1 added to ACMG modification guidelines
[x] Display institute _id + display name on dashboard filters
[x] ClinVar category 8 has changed to "Conflicting classifications of pathogenicity" instead of "interpretations"
[x] Simplify always loading ClinVar CLNSIG P, LP and conflicting annotations slightly
[x] Increased visibility of variant callers's "Pass" or "Filtered" on the following pages: SNV variants (cancer cases), SV variants (both RD and cancer cases)
[x] Names on IGV buttons, including an overview level IGV MT button
[x] Cases query no longer accepts strings for the name_query parameter, only ImmutableMultiDict (form data)
[x] Refactor the loading of PanelApp panels to use the maintained API - Customised PanelApp GREEN panels
[x] Better layout for Consequence cell on cancer SNVs page
[x] Merged Qual and Callers cell on cancer SNVs page
Fixed
[x] Empty custom_images dicts in case load config do not crash
[x] Tracks missing alignment files are skipped on generating IGV views
[x] ClinVar form to accept MedGen phenotypes
[x] Cancer SV variantS page spinner on variant export
[x] STRs variants export
[x] ClinVar submission enquiry status for all submissions after the latest
[x] Typing error when running commands using python 3.9
[x] Refactored and fixed the function creating alignment files (scout.utils.case_append_alignments)
[x] Fix missing "Repeat locus" info on STRs export

Review:

[x] code approved by DN
[x] tests executed by DNIL, CR

codecov[bot] commented 2 weeks ago

Codecov Report

Attention: Patch coverage is 0% with 1 line in your changes missing coverage. Please review.

Project coverage is 84.78%. Comparing base (fb8ae32) to head (8fbcbc9). Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
scout/__version__.py	0.00%	1 Missing :warning:

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dnil commented 2 weeks ago

Great! We should get a hasta release out asap for the cat 8 issue. We may be in a decent position to get #4976 and #4985 in here as well - Ill have a look.

northwestwitch commented 1 week ago

Database update (all tables) - Hasta stage:

Stage updates

Download files for updating

scout --config /home/proj/stage/servers/config/hasta.scilifelab.se/scout-stage.yaml download everything --api-key blablabla

Update HPO terms

scout --config /home/proj/stage/servers/config/hasta.scilifelab.se/scout-stage.yaml update hpo --hpoterms hpo.obo --hpo-to-genes phenotype_to_genes.txt

Updating diseases

scout --config /home/proj/stage/servers/config/hasta.scilifelab.se/scout-stage.yaml update diseases -f .

Updating genes

scout --config /home/proj/stage/servers/config/hasta.scilifelab.se/scout-stage.yaml update genes -f .

Update the OMIM AUTO panel

scout --config /home/proj/stage/servers/config/hasta.scilifelab.se/scout-stage.yaml update omim --institute cust002 --genemap2 genemap2.txt --mim2genes mim2genes.txt

Update the PanelApp green genes panel

scout --config /home/proj/stage/servers/config/hasta.scilifelab.se/scout-stage.yaml update panelapp-green -i cust002 --force

northwestwitch commented 1 week ago

Took me forever to find a variant with conflicting classification, then I reasoned that first I'd find it in the db then I search it in scout:

For instance this query, with limit=1

{"clnsig.value":{"$in":[8]}}

Returns a variant in this case.

In fact if you filter the research variants by conflicting clinsig you get 23 hits

northwestwitch commented 1 week ago

Tested

Empty custom_images dicts in case load config do not crash
Tracks missing alignment files are skipped on generating IGV views

By editing the config file of this case and reuploading it.

In the config file Ive removed the alignment of the first individual and added custom_images: {}, as instructed in the comments of the relative fix PRs.

Case loaded OK:

Unfortunately when I click on this buttom the IGV page crashes:

dnil commented 1 week ago

✅ The issue https://github.com/Clinical-Genomics/scout/issues/4789 is indeed fixed by IGV 3.0.9: Screenshot 2024-11-20 at 10 24 39

dnil commented 1 week ago

✅ Caller AF is now prioritised on a previously problematic balasamic variant, with AD values way off: Screenshot 2024-11-20 at 11 15 55

dnil commented 1 week ago

✅ Same count of ClinVar hits with latest prod version (4.90.1) compared to PR, indicating that the simplified clinvar pathogenic check is ok. Screenshot 2024-11-20 at 12 53 14 Screenshot 2024-11-20 at 11 25 18