Gens v3.0.0

.dockerignore

@@ -32,6 +32,7 @@ docker-compose.yml
 
 # volumes
 volumes/
+dump/
 
 # other
 *.aed

.eslintrc.yml

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

.github/workflows/docker_push.yml

@@ -0,0 +1,36 @@
+name: Publish to Docker
+
+on:
+  release:
+    types:
+      - created
+
+jobs:
+  docker-push:
+    name: Create 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: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: ./
+          file: ./Dockerfile
+          push: true
+          tags: "clinicalgenomics/gens:${{ github.event.release.tag_name }}, clinicalgenomics/gens:latest"

.github/workflows/keep_a_changelog.yml

@@ -8,8 +8,8 @@ jobs:
   changelog:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: dangoslen/changelog-enforcer@v1.4.0
+    - uses: actions/checkout@v4
+    - uses: dangoslen/changelog-enforcer@v3
       with:
         changeLogPath: 'CHANGELOG.md'
-        skipLabel: 'Skip-Changelog'
+        skipLabels: 'Skip-Changelog'

.github/workflows/preproc_docker_push.yml

@@ -0,0 +1,36 @@
+name: Publish preproc to Docker
+
+on:
+  release:
+    types:
+      - created
+
+jobs:
+  docker-preproc-push:
+    name: Create preproc 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: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: ./utils/
+          file: ./utils/Dockerfile
+          push: true
+          tags: "clinicalgenomics/gens-preproc:${{ 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/stage_docker_push.yml

@@ -0,0 +1,39 @@
+name: Publish to Docker stage
+
+on:
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - master
+
+jobs:
+  docker-stage-push:
+    name: Create staging 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: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: ./
+          file: ./Dockerfile
+          push: true
+          tags: "clinicalgenomics/gens-stage:${{steps.branch-name.outputs.current_branch}}, clinicalgenomics/gens-stage:latest"

.github/workflows/stale.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/stale@v3
+    - uses: actions/stale@v9
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         stale-issue-message: 'Stale issue message'

.github/workflows/tests.yml

@@ -9,17 +9,17 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7]
-        mongodb-version: ["3.6"]
+        python-version: [3.8]
+        mongodb-version: ["7"]
 
     steps:
 
     # Check out Scout code
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     # Set up python
     - name: Set up Python ${{ matrix.python-version}}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version}}
 
@@ -49,9 +49,9 @@ jobs:
         # See supported Node.js release schedule at https://nodejs.org/en/about/releases/
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Use Node.js ${{ matrix.node-version }}
-      uses: actions/setup-node@v1
+      uses: actions/setup-node@v4
       with:
         node-version: ${{ matrix.node-version }}
     - run: npm ci

.gitignore

@@ -4,6 +4,9 @@
 tags
 coverage
 *.aed
+dump/
+frontend/
+docker-compose.override.yml
 
 # python
 *.pyc
@@ -16,6 +19,7 @@ utils/hg38_annotations/
 venv/
 *.egg-info
 .eggs
+.idea
 
 # node
 node_modules

CHANGELOG.md

@@ -4,14 +4,69 @@ This project adheres to [Semantic Versioning](http://semver.org/)
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
-## [x.x.x]
+## 3.0.0 - Merging Solnas and Lunds changes
+### Added
+ - `--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 (Solna)]
 ### 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
+ - Archive prod docker image with release tag name. Update action versions.
 ### Fixed
- - Fixed bug that prevented updating annotation tracks
+ - Error image background static path
+ - GitHub action DockerHub push on release
+
+## [2.2 (Solna)]
+### 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
+
+## [2.1.1b (Solna)]
+### 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
+
+## [2.1.1 (Solna)]
+### Added
+### Changed
+ - Updated flask and pinned connexion to v2
+ - Updated node version of github action to 17.x
+### Fixed
+ - Fixed annotation tracks being hidden behind other elements
+ - Use sample id as individual id to link out from Gens home sample list
+ - Some fixes from MHKC CG-Lund, e.g. status codes and a JSON error
+ - Removes some leading `/` that were breaking links
+ - Increased contrast of region selector
+ - Chromosome bands are displayed properly
 
-## [2.1.2]
+## [2.1.2 (Lund)]
 ### Added
 ### Changed
  - Changed cached method from simple to file system as it would be thread safe
@@ -20,7 +75,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
  - Fixed cache issue that could result in chromosome information not being updated
  - Fixed max arg error when searching for some genes
 
-## [2.1.1]
+## [2.1.1 (Lund)]
 ### Added
 ### Changed
  - Updated flask and pinned connexion to v2
@@ -75,6 +130,7 @@ 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

@@ -2,7 +2,7 @@
 # BUILDER PYTHON #
 ##################
 
-FROM python:3.8.1-slim as python-builder
+FROM python:3.8.1-slim AS python-builder
 
 # Set build variables
 ENV PYTHONDONTWRITEBYTECODE=1
@@ -24,7 +24,7 @@ RUN apt-get update &&                                                     \
 # BUILDER NODE #
 ################
 
-FROM node:20.8.1-alpine as node-builder
+FROM node:20.8.1-alpine AS node-builder
 WORKDIR /usr/src/app
 COPY package.json package-lock.json webpack.config.js gulpfile.js ./
 COPY assets assets
@@ -58,10 +58,29 @@ COPY utils utils
 
 # copy compiled web assetes
 COPY --from=node-builder /usr/src/app/build/css/error.min.css gens/static/css/
-COPY --from=node-builder /usr/src/app/build/css/home.min.css /usr/src/app/build/css/about.min.css gens/blueprints/home/static/
+COPY --from=node-builder /usr/src/app/build/css/home.min.css /usr/src/app/build/css/landing.min.css /usr/src/app/build/css/about.min.css gens/blueprints/home/static/
 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 /fs1/results_dev && chown -R app:app /home/app/app /access /fs1 /fs1/results_dev
 # Change the user to app
 USER app
+
+ENV GUNICORN_WORKERS=1
+ENV GUNICORN_THREADS=1
+ENV GUNICORN_BIND="0.0.0.0:5000"
+ENV GUNICORN_TIMEOUT=400
+
+CMD gunicorn \
+    --workers=$GUNICORN_WORKERS \
+    --bind=$GUNICORN_BIND  \
+    --threads=$GUNICORN_THREADS \
+    --timeout=$GUNICORN_TIMEOUT \
+    --chdir /home/app/app/ \
+    --proxy-protocol \
+    --forwarded-allow-ips="10.0.2.100,127.0.0.1" \
+    --log-syslog \
+    --access-logfile - \
+    --error-logfile - \
+    --log-level="debug" \
+    gens.wsgi:app