Stockholm transfer

.eslintrc.yml

@@ -3,6 +3,8 @@ env:
   es2021: true
 extends:
   - standard
+  - "eslint:recommended"
+  - "prettier"
 parserOptions:
   ecmaVersion: 12
   sourceType: module

.github/workflows/docker_push.yml

@@ -1,12 +1,12 @@
 name: Publish to Docker
 
 on:
-  push:
-    branches:
-      - master
+  release:
+    types:
+      - created
 
 jobs:
-  docker-stage-push:
+  docker-push:
     name: Create docker image
     runs-on: ubuntu-latest
     steps:
@@ -33,4 +33,4 @@ jobs:
           context: ./
           file: ./Dockerfile
           push: true
-          tags: "clinicalgenomics/gens:${{steps.branch-name.outputs.current_branch}}, clinicalgenomics/gens:latest"
+          tags: "clinicalgenomics/gens:${{ github.event.release.tag_name }}, clinicalgenomics/gens:latest"

.github/workflows/keep_a_changelog.yml

@@ -12,4 +12,4 @@ jobs:
     - uses: dangoslen/changelog-enforcer@v3
       with:
         changeLogPath: 'CHANGELOG.md'
-        skipLabel: 'Skip-Changelog'
+        skipLabels: 'Skip-Changelog'

.github/workflows/preproc_docker_push.yml

@@ -1,13 +1,13 @@
-name: Publish preproc to Docker stage
+name: Publish preproc to Docker
 
 on:
-  pull_request:
-    branches:
-      - master
+  release:
+    types:
+      - created
 
 jobs:
   docker-preproc-push:
-    name: Create preproc docker image
+    name: Create preproc Docker image
     runs-on: ubuntu-latest
     steps:
       - name: Check out git repository
@@ -28,10 +28,9 @@ jobs:
         uses: docker/setup-buildx-action@v3
 
       - name: Build and push
-        if: steps.branch-name.outputs.is_default == 'false'
         uses: docker/build-push-action@v5
         with:
           context: ./utils/
           file: ./utils/Dockerfile
           push: true
-          tags: "clinicalgenomics/gens-preproc:${{steps.branch-name.outputs.current_branch}}, clinicalgenomics/gens-preproc:latest, clinicalgenomics/gens-preproc:1.0.0"
+          tags: "clinicalgenomics/gens-preproc:${{ github.event.release.tag_name }}, clinicalgenomics/gens-preproc:latest"

.github/workflows/preproc_stage_docker_push.yml

@@ -0,0 +1,37 @@
+name: Publish preproc to Docker stage
+
+on:
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  docker-preproc-stage-push:
+    name: Create preproc stage Docker image
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out git repository
+        uses: actions/checkout@v4
+
+      - name: Get branch name
+        id: branch-name
+        uses: tj-actions/branch-names@v7
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build and push
+        if: steps.branch-name.outputs.is_default == 'false'
+        uses: docker/build-push-action@v5
+        with:
+          context: ./utils/
+          file: ./utils/Dockerfile
+          push: true
+          tags: "clinicalgenomics/gens-preproc-stage:${{steps.branch-name.outputs.current_branch}}, clinicalgenomics/gens-preproc-stage:latest"

.github/workflows/stale.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/stale@v8
+    - uses: actions/stale@v9
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         stale-issue-message: 'Stale issue message'

.github/workflows/tests.yml

@@ -19,7 +19,7 @@ jobs:
 
     # Set up python
     - name: Set up Python ${{ matrix.python-version}}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version}}
 
@@ -49,7 +49,7 @@ jobs:
         # See supported Node.js release schedule at https://nodejs.org/en/about/releases/
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Use Node.js ${{ matrix.node-version }}
       uses: actions/setup-node@v4
       with:

.gitignore

@@ -4,6 +4,9 @@
 tags
 coverage
 *.aed
+dump/
+frontend/
+docker-compose.override.yml
 
 # python
 *.pyc

CHANGELOG.md

@@ -4,23 +4,62 @@ This project adheres to [Semantic Versioning](http://semver.org/)
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
-## [x.x.x]
+## [Unreleased]
 ### Added
-- Document track processing and loading
-- OAuth authentication
+ - `--force` flag to `gens loads sample` for overwriting any existing sample in case of key conflict.
+ - `--force` flag prints a warning to stderr when overwriting an existing sample.
+ - `gens delete sample` command
+ - Height ordering for variants track.
+### Fixed
+ - Pan able to exit chrosome when using genome build 17 
+ - `--force` flag `update_one` call not being called properly
+ - Incorrect total sample count on home page.
+ - Some typos and documentation.
+ - Labels often not being visible on larger variants.
+### Merged for Solna from Lund 2.1.2
+#### Changed
+ - Changed cached method from simple to file system as it would be thread safe
+#### Fixed
+ - Fixed cache issue that could result in chromosome information not being updated
+ - Fixed max arg error when searching for some genes
+ - Fixed bug that prevented updating annotation tracks
+
+## [2.3]
+### Added
+ - Link out to Scout: introduce config variable for base URL
+ - Link out to Scout: case links on home sample list
+ - Link out to Scout: click variant to open Scout page
 ### Changed
-- Use sample id instead of display name for variant retrieval
-- Hide balanced variants
-- Keyboard pan speed increased
+ - Archive prod docker image with release tag name. Update action versions.
+### Fixed
+ - Error image background static path
+ - GitHub action DockerHub push on release
 
+## [2.2]
+### Added
+ - Document track processing and loading
+ - OAuth authentication
+### Changed
+ - Use sample id instead of display name for variant retrieval
+ - Hide balanced variants
+ - Keyboard pan speed increased
+ - Don't shrink pan window when attemting to pan over start
 
-## [2.1.1]
+## [2.1.1b]
 ### Added
 ### Changed
  - Changes the main view's page title to be `sample_name` and adds `sample_name` and `case_id` to the header title
  - Updated external images used in GitHub actions, including tj-actions/branch-names to v7 (fixes a security issue)
  - Updated Python and MongoDB version used in tests workflow to 3.8 and 7 respectively
+
+## [2.1.2 Lund only - Solna version in Unreleased/2.4]
+### Added
+### Changed
+ - Changed cached method from simple to file system as it would be thread safe
 ### Fixed
+ - Fixed cache issue that could result in chromosome information not being updated
+ - Fixed max arg error when searching for some genes 
+ - Fixed bug that prevented updating annotation tracks
 
 ## [2.1.1]
 ### Added
@@ -34,6 +73,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
  - Removes some leading `/` that were breaking links
  - Increased contrast of region selector
  - Chromosome bands are displayed properly
+ - Use sample id as individual id to link out from Gens home sample list
 
 ## [2.1.0]
 ### Added
@@ -80,6 +120,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
  - Reinstated tooltips to display additional information on genetic elements
 ### Changed
  - Use popper for positioning tooltips
+ - Prettier for code formatting
 ### Fixed
 
 ## [1.2.0]

Dockerfile

@@ -62,7 +62,7 @@ COPY --from=node-builder /usr/src/app/build/css/home.min.css /usr/src/app/build/
 COPY --from=node-builder /usr/src/app/build/*/gens.min.* gens/blueprints/gens/static/
 
 # make mountpoints and change ownership of app
-RUN mkdir -p /access /fs1/results && chown -R app:app /home/app/app /access /fs1
+RUN mkdir -p /access /fs1/results /fs1/results_dev && chown -R app:app /home/app/app /access /fs1 /fs1/results_dev
 # Change the user to app
 USER app
 

assets/__mocks__/fileMock.js

@@ -1,3 +1,3 @@
 // __mocks__/fileMock.js
 
-module.exports = 'test-file-stub';
+module.exports = "test-file-stub";

assets/__mocks__/styleMock.js

@@ -1,3 +1,3 @@
 // __mocks__/styleMock.js
 
-module.exports = {};
+module.exports = {};