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Configure quick links (vc_links.js) via settings #758

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davmlaw opened this issue Feb 20, 2023 · 2 comments
Open

Configure quick links (vc_links.js) via settings #758

davmlaw opened this issue Feb 20, 2023 · 2 comments

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@davmlaw
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davmlaw commented Feb 20, 2023

Quick links is used on variant page, and classification, driven by vc_links.js

I've had 2 requests to modify quick links (IGV from Shariant, Varsome in SAP)

Would be nice to have this driven by config. Perhaps a dict of true/false like the menu config

Need to modify SAP settings to disable varsome (should be ok adding new setting not used in old version)

@davmlaw davmlaw changed the title Configure quick links via settings Configure quick links (vc_links.js) via settings Feb 20, 2023
@davmlaw
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davmlaw commented May 13, 2024

Now added settings:

# Can only use block or allow list. Use "text" value of link (see vc_links.js)
VARIANT_DETAILS_QUICK_LINKS_ALLOW_LIST = []
VARIANT_DETAILS_QUICK_LINKS_BLOCK_LIST = []

this leaves allele/classification alone (only affects variant page)

TODO:

  • I added geneLink boolean which you can use to determine whether it's variant or gene based
  • Use this to add quick links to gene page, and gene_symbol_info_tab.html page
        let geneLinks = links.filter(link => link.geneLink);
        let geneAnchors = geneLinks.map(link => link.asAnchor("bootstrap"));
        $('#gene-quick-links').html($("<ul>", {class:"list-group", html:geneAnchors}));


    <div>
        <a id='show-gene-quick-links' class="toggle-link" data-toggle="collapse" href=".full-gene-quick-links">Show gene quick links</a>
        <div class="full-gene-quick-links collapse">
            {% labelled id="gene-quick-links" label="Quick Links" %}Loading...{% endlabelled %}
        </div>
    </div>

davmlaw added a commit that referenced this issue May 14, 2024
davmlaw added a commit that referenced this issue May 14, 2024
TheMadBug pushed a commit that referenced this issue May 22, 2024
TheMadBug added a commit that referenced this issue Jun 18, 2024
* Panal App VUS/GUS relationship download

* Panal App VUS/GUS relationship download

* Providing methods to find more useful relationships between term and gene symbol for report

* issue #2647 - liftover refactor

* issue #2647 - start of bcftools liftover

* Issue #2647 - BCFTools liftover

* Issue #2647 - Remove vestigial NCBI remap traces

* Issue #2647 - enable in vg test

* Stop warning that doesn't apply here

* Issue #2647 - be able to create variant for long ones...

* This occasionally failed - execution continued after asking to change window

* issue #1054 - make bcftools liftover part of standard ANNOTATION settings

* issue #1054 - misc liftover issues

* Issue #1052 - analysis template version

* Make VEP have version in path

* Shariant test config - enable BCFTools liftover

* Upload initially shows error wrongly in pipeline race condition

* issue #818 - don't uniq on preprocess anymore

* issue #1056 - vcf_clean_and_filter convert contig headers

* issue #1057 - VEP deployment change to explicit version

* vg test config

* issue #980 - karyomapping use symbol instead of gene

* Renamed counts to Counts(germline only) on overlaps page (#1046)

* Fix issue where alleleOriginToggle was being called with undefined

* WIP fixing conda dependencies

* Update of conda environment (works again in conda)

* Add new evidence key for somatic testing

* Show better quick clinical significance values (for somatic and germline)

* Fix recently introduced bug in suggested terms for an allele

* Allow link for condition matching to appear on a classification even when not in edit mode

* issue #1059 - all variants node

* issue #1059 - all variants node

* Adjust node counts a little

* issue #1043 - export VCF

* Tidy up server status page removing redundant data (now go to Overall Status)

* Fix the evidence key values

* Get c.HGVS showing properly on variant details page again

* issue #758 - configure quick links via settings

* More comments in conda file

* Move condition text match from classification.html to JSON to keep things in sync
More requirements on when you will be linked to condition resolution

* Style fixes for new liftover

* Put liftover date on form

* Move overall data to the splash server status page

* Add Clinical Trails gov to quick links

* Add liftover to settings menu if variants menu disabled

* Update shariant prod settings to use VEP v108

* Make liftover page side menu change based on settings

* Better wording for changing clinical contexts within a discordance

* Tighten up the handling of embedded card or modal (used for triage but affected other modals by mistake)

* Better safety around condition text relationships

* For view metrics use heading of "Users" not "User"

* Add overall stats to liftover pages

* Slight formatting on liftover note

* Rework the internals of the view user activity reports

* More styling on liftover runs page

* More styling on liftover pages

* Tiny column alignment issue on liftover

* linting

* Fix exclusion of blank searches in metrics

* Subtle change of header wording for activity report

* Improve the formatting of missing IDs when making a batch for ClinVar

* Proper int to string handling for missing IDs

* issue #758 - quick links via settings

* Reworking of Lab Differences using new zippable functionality for ExportRow

* Put the allele URL into the lab compare (I think it was there before)

* Enable SEARCH_HGVS_GENE_SYMBOL_USE_MANE for shariant test

* Also try enabling SEARCH_HGVS_GENE_SYMBOL

* Fix bug where condition URL was calculated before seeing if we had condition text

* Enable extra variant annotations for testing

* Attempt at parsing OncogenicityClassification for pulling in ClinVar records

* issue #1193 - analysis audit log

* issue #1193 - analysis audit log

* issue #1193 - analysis audit log

* issue #1193 - analysis audit log

* issue #1193 - analysis audit log

* variantgrid_private#1193 - Audit log for analysis

* Get audit log name right in requirements

* issue #1060  - variant details page, create allele for all variants not just shorty clingen ones

* Sometimes can't reload analysis #1061

* issue #1193 - disable audit log for template copies etc

* issue #1193 - Audit log for analysis - click to expand and see JSON

* issue #1193 - Don't audit node cloning (was causing tests to fail)

* temp fix for #1053 - will work out data fix later

* Better categorising of ClinVar's Somatic/Germline records

* issue #1053 - cohort genotype versions - make common cohort version match cohort.version

* linting - format whitespace

* linting - remove unused imports

* Unused file

* linting - f string w/o interpolation

* linting - use generator

* Increase the ClinVar parser version to purge old cache

* Add django-audit-log to conda environment

* ClinVar REcords More work on parsing condition

* issue #1053 - missing import, make sure we retrieve only 1 cgc per cohort

* issue #877 - Export column - c_hgvs_compat

* Add MeSH as a non-local ontology set

* Ability to render multiple conditions against a single ClinVar record

* Don't abbreviate ref/alt in VCF

* Fix bug with filtering out non-human clinvar records

* Count homo sapiens, homo-sapiens, homosapiens the same as human for ClinVar records

* A script to close manually raised flags

* Raise classification change flag for both Classification and Somatic Clinical Significance

* Filter based on creator of flag

* Added prefixed clinvar batch export CB_ and clinvar export CE_ search functionality (#1066)

* issue #3604 - COSMIC search

* Update changelog

* Tidy up code for close flags, allow it to re-open flags

* Bug fixes for the condition checking code

* panalapp work

* PanelApp Compare: Fixes to stop infinite recurssion, correct method signatures.

* #3591 panel app export

---------

Co-authored-by: TheMadBug <[email protected]>
Co-authored-by: Dave Lawrence <[email protected]>
@davmlaw davmlaw closed this as completed Aug 18, 2024
@EmmaTudini
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RE-opening as need to test in Shariant

@EmmaTudini EmmaTudini reopened this Aug 23, 2024
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