diff --git a/CHANGELOG.md b/CHANGELOG.md index 5fa55e81df..513f327504 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,25 +4,29 @@ This project adheres to [Semantic Versioning](http://semver.org/). About changelog [here](https://keepachangelog.com/en/1.0.0/) -## [unreleased] +## [4.82] ### Added -- Tooltip for combined score in tables for compounds and overlapping vars -- Option to filter variants by excluding genes listed in selected gene panels, files or provided as list +- Tooltip for combined score in tables for compounds and overlapping variants +- Checkbox to filter variants by excluding genes listed in selected gene panels, files or provided as list - STR variant information card with database links, replacing empty frequency panel - Display paging and number of HPO terms available in the database on Phenotypes page - On case page, typeahead hints when searching for a disease using substrings containing source ("OMIM:", "ORPHA:") - Button to monitor the status of submissions on ClinVar Submissions page - Option to filter cancer variants by number of observations in somatic and germline archived database - Documentation for integrating chanjo2 +- More up-to-date VEP CSQ dbNSFP frequency keys - Parse PacBio TRGT (Tandem repeat genotyping tool) Short Tandem Repeat VCFs ### Changed - In the case_report #panel-tables has a fixed width - Updated IGV.js to 2.15.11 - Fusion variants in case report now contain same info as on fusion variantS page -- Block submission of somatic variants to ClinVar, until we don't introduce the changes needed to harmonise with their changed API +- Block submission of somatic variants to ClinVar until we harmonise with their changed API - Additional control on the format of conditions provided in ClinVar form - Errors while loading managed variants from file are now displayed on the Managed Variants page - Chanjo2 coverage button visible only when query will contain a list of HGNC gene IDs +- Use Python-Markdown directly instead of the unmaintained Flask-Markdown +- Use Markupsafe instead of long deprecated, now removed Flask Markup +- Prepare to unfreeze Werkzeug, but don't actually activate until chanjo can deal with the change ### Fixed - Submit requests to Chanjo2 using HTML forms instead of JSON data - `Research somatic variants` link name on caseS page @@ -34,7 +38,6 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/) - Diagnoses API search crashing with empty search string - Variant's overlapping panels should show overlapping of variant genes against the latest version of the panel - Case page crashing when case has both variants in a ClinVar submission and pinned not loaded variants -- Prepare to unfreeze Werkzeug, but don't actually activate until chanjo can deal with the change - Installation of git in second build stage of Dockerfile, allowing correct installation of libraries ## [4.81] @@ -110,7 +113,6 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/) - ClinVar submission can now be downloaded as a json file - API endpoint to pin variant - Display common/uncommon/rare on summary of mei variant page -- More up-to-date VEP CSQ dbNSFP frequency keys ### Changed - In the ClinVar form, database and id of assertion criteria citation are now separate inputs - Customise institute settings to be able to display all cases with a certain status on cases page (admin users) diff --git a/scout/__version__.py b/scout/__version__.py index 681189eb9d..0953b6dde5 100644 --- a/scout/__version__.py +++ b/scout/__version__.py @@ -1 +1 @@ -__version__ = "4.81" +__version__ = "4.82" diff --git a/scout/server/app.py b/scout/server/app.py index c592b4edae..1b8db37f06 100644 --- a/scout/server/app.py +++ b/scout/server/app.py @@ -227,7 +227,7 @@ def human_decimal(number, ndigits=4): return round(number, ndigits) @app.template_filter() - def markdown(text: str): + def markdown(text: str) -> Markup: return Markup(python_markdown(text)) @app.template_filter()