Merge branch 'master' into update-login-page-logos

.dockerignore

@@ -17,6 +17,6 @@ tests
 scripts
 
 # Docker
-Dockerfile
-docker-compose.yml
+Dockerfile*
+docker-compose.*yml
 volumes

CHANGELOG.md

@@ -18,6 +18,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - API returning case data for a given institute: `/api/v1/institutes/<institute_id>/cases`
 - Added GMS and Lund university hospital to login page
 - Made display of Swedac logo configurable
+- Support for displaying custom images in case view
 
 ### Fixed
 - Updated IGV to v2.8.5 to solve missing gene labels on some zoom levels

Dockerfile

@@ -1,24 +1,61 @@
-FROM python:3.8-alpine3.12
+###########
+# BUILDER #
+###########
+FROM python:3.8.1-slim as builder
 
-LABEL base_image="python:3.8-alpine3.12"
+WORKDIR /usr/src/app
+
+# Set build variables
+ENV PYTHONDONTWRITEBYTECODE=1
+ENV PYTHONUNBUFFERED=1
+
+RUN apt-get update &&                                               \
+    apt-get upgrade -y &&                                           \
+    apt-get install -y --no-install-recommends autoconf automake    \
+	build-essential gcc libbz2-dev libcairo2 libcurl4-gnutls-dev    \
+	libffi-dev libgdk-pixbuf2.0-0 liblzma-dev libpango-1.0-0        \
+	libpangocairo-1.0-0 libssl-dev make python3-cffi python3-dev    \
+	python3-pip python3-wheel shared-mime-info zlib1g-dev           \
+	openssl ca-certificates gcc wget git
+
+# Copy app
+COPY . /usr/src/app
+RUN pip install --upgrade pip &&           \
+    pip wheel --no-cache-dir --no-deps     \
+        --wheel-dir /usr/src/app/wheels    \
+		Cython gunicorn  &&                \
+    pip wheel --no-cache-dir               \
+        --wheel-dir /usr/src/app/wheels    \
+        --editable .[coverage]
+
+
+#########
+# FINAL #
+#########
+
+FROM python:3.8.1-slim
+
+LABEL base_image="python:3.8.1-slim"
 LABEL about.home="https://github.com/Clinical-Genomics/scout"
 LABEL about.documentation="https://clinical-genomics.github.io/scout"
 LABEL about.tags="WGS,WES,Rare diseases,VCF,variants,SNP,Next generation sequencing"
 LABEL about.license="MIT License (MIT)"
 
-# Install required libs
-RUN apk update
-RUN apk --no-cache add make automake gcc g++ linux-headers libffi-dev zlib-dev \
-   jpeg-dev libressl-dev cairo-dev pango-dev gdk-pixbuf ttf-freefont bash
-RUN pip install numpy Cython
-
+# Run app on non-root user
+RUN useradd -m worker && mkdir -p /home/worker/app
 WORKDIR /home/worker/app
-COPY . /home/worker/app
 
-# Install scout app
-RUN pip install -e .
+# Copy pyhon wheels and install scout
+COPY --from=builder /usr/src/app/wheels /wheels
+RUN apt-get update &&                                     \
+    apt-get install -y libgdk-pixbuf2.0-0 libpango-1.0-0  \
+	libcairo2 libpangocairo-1.0-0 ssh sshfs &&            \
+    pip install --no-cache-dir --upgrade pip &&           \
+    pip install --no-cache-dir /wheels/* &&               \
+    rm -rf /var/lib/apt/lists/* /wheels
+
+COPY . /home/worker/app
 
-# Run commands as non-root user
-RUN adduser -D worker
-RUN chown worker:worker -R /home/worker
+# Run app on non-root user
+RUN chown -R worker:worker /home/worker/app
 USER worker

containers/development/docker-compose-chanjo-report.yml

@@ -0,0 +1,97 @@
+# Docker-compose file containing Scout demo and a running chanjo-report instance
+# 1) Move this file under scout/
+# 2) edit scout config file and add these lines:
+# SQLALCHEMY_DATABASE_URI = "mysql+pymysql://chanjoUser:chanjoPassword@mariadb/chanjo4_test" ?
+# REPORT_LANGUAGE = "en"  # or 'sv'
+version: '3'
+# usage:
+# (sudo) docker-compose up -d
+# (sudo) docker-compose down
+services:
+  # mongodb is used by Scout
+  mongodb:
+    image: mvertes/alpine-mongo
+    container_name: mongodb
+    ports:
+      - '27013:27017'
+    expose:
+      - '27017'
+    networks:
+      - custom-net
+
+  # MariaDB is used by Chanjo
+  mariadb:
+    container_name: mariadb
+    image: mariadb:latest
+    restart: 'always'
+    environment:
+      - MYSQL_ROOT_PASSWORD=root
+      - MYSQL_DATABASE=chanjo4_test
+      - MYSQL_USER=chanjoUser
+      - MYSQL_PASSWORD=chanjoPassword
+    healthcheck: # Wait for the service to be ready before accepting incoming connections
+      test: "mysql --user=chanjoUser --password=chanjoPassword --execute \"SHOW DATABASES;\""
+      timeout: 10s
+      retries: 20
+    networks:
+      - custom-net
+
+  # Set up chanjo database and load some demo data
+  chanjo-cli:
+    container_name: chanjo-cli
+    image: clinicalgenomics/chanjo
+    depends_on:
+      mariadb:
+        condition: service_healthy # DB_URI=mysql+pymysql://chanjoUser:chanjoPassword@mariadb/chanjo4_test
+    networks:
+      - custom-net
+    command: bash -c "
+      chanjo -d mysql+pymysql://chanjoUser:chanjoPassword@mariadb/chanjo4_test db setup --reset
+      && chanjo -d mysql+pymysql://chanjoUser:chanjoPassword@mariadb/chanjo4_test init --auto demodata
+      && chanjo --config demodata/chanjo.yaml link demodata/hgnc.grch37p13.exons.bed
+      && chanjo -d mysql+pymysql://chanjoUser:chanjoPassword@mariadb/chanjo4_test load -n sample1 --group-name test_group -g test_group chanjo/init/demo-files/sample1.coverage.bed
+      && chanjo -d mysql+pymysql://chanjoUser:chanjoPassword@mariadb/chanjo4_test load -n sample2 --group-name test_group -g test_group chanjo/init/demo-files/sample2.coverage.bed
+      && chanjo -d mysql+pymysql://chanjoUser:chanjoPassword@mariadb/chanjo4_test load -n sample3 --group-name test_group -g test_group chanjo/init/demo-files/sample3.coverage.bed"
+
+  # Start the chanjo-report app
+  chanjo-report:
+    container_name: chanjo-report
+    expose:
+      - '5000'
+    ports:
+      - '4000:5000'
+    image: clinicalgenomics/chanjo-report
+    depends_on:
+      - mariadb
+      - chanjo-cli
+    networks:
+      - custom-net
+    entrypoint: sh -c "chanjo -d mysql+pymysql://chanjoUser:chanjoPassword@mariadb/chanjo4_test report --render html"
+
+  # Start the scout app containing demo data
+  scout-web:
+    image: clinicalgenomics/scout:latest
+    container_name: scout-web
+    expose:
+      - '5000'
+    ports:
+      - '5000:5000'
+    command: bash -c "
+      scout --host mongodb setup demo
+      && scout --host mongodb --demo serve --host 0.0.0.0"
+    volumes:
+      - ./scout:/home/worker/app/scout
+      - ./volumes/scout/data:/home/worker/data
+    depends_on:
+      - mongodb
+      - chanjo-report
+    networks:
+      - custom-net
+
+networks:
+  custom-net:
+    driver: bridge
+    ipam:
+      driver: default
+      config:
+        - subnet: 172.21.0.0/24

docker-compose.yml

@@ -35,19 +35,71 @@ services:
       - '5000'
     ports:
       - '5000:5000'
-    command: scout --host mongodb --demo serve --host 0.0.0.0
+    environment:
+      - SCOUT_CONFIG=/home/worker/app/scout/server/config.py
+    command: gunicorn --bind 0.0.0.0:5000 scout.server.auto:app
     volumes:
       - ./scout:/home/worker/app/scout
       - ./volumes/scout/data:/home/worker/data
     networks:
       - scout-net
     depends_on:
       - mongodb
+      - mariadb
+
+  mariadb:
+    image: mariadb:latest
+    environment:
+     - MYSQL_ROOT_PASSWORD=root
+     - MYSQL_USER=chanjoUser
+     - MYSQL_PASSWORD=chanjoPassword
+     - MYSQL_DATABASE=chanjo
+    volumes:
+     - ./volumes/mariadb/data:/var/lib/mysql
+    healthcheck: # Wait for the service to be ready before accepting incoming connections
+        test: "mysql --user=chanjoUser --password=chanjoPassword --execute \"SHOW DATABASES;\""
+        timeout: 10s
+        retries: 20
+    networks:
+     - scout-net
+    restart: unless-stopped
+
+  chanjo-cli:
+    build: chanjo
+    environment:
+     - SQLALCHEMY_DATABASE_URI=mysql+pymysql://chanjoUser:chanjoPassword@mariadb/chanjo
+    depends_on:
+      - mariadb
+    volumes:
+     - ./volumes/chanjo:/data
+     - ./chanjo/chanjo:/home/worker/app/chanjo
+    networks:
+     - scout-net
+    restart: unless-stopped
+
+  chanjo-report:
+    build: chanjo-report
+    environment:
+     - SQLALCHEMY_DATABASE_URI=mysql+pymysql://chanjoUser:chanjoPassword@mariadb/chanjo
+    expose:
+      - '5000'
+    ports:
+      - '4000:5000'
+    volumes:
+     - ./volumes/chanjo:/data
+     - ./chanjo-report/chanjo_report:/home/worker/app/chanjo_report
+    depends_on:
+      - mariadb
+      - chanjo-cli
+    networks:
+     - scout-net
+    command: sh -c "chanjo -d mysql+pymysql://chanjoUser:chanjoPassword@mariadb/chanjo report --render html"
+    restart: unless-stopped
 
 networks:
   scout-net:
     driver: bridge
     ipam:
       driver: default
       config:
-        - subnet: 172.21.0.0/24
+        - subnet: 172.30.0.0/24

docs/admin-guide/loading.md

@@ -86,6 +86,32 @@ human_genome_build: 37
 
 ```
 
+#### Adding custom images to a case
+
+Scout can display custom images as new panels on the case view which could be used to display analysis results from a seperate pipeline. The custom images are defined in the case config file and stored in the database. Scout currently supports `gif`, `jpeg`, `png` and `svg` images.
+
+One or more images constitute a group and are rendered together in a accordion-type UI elemment named after the group. The fields `title`, `description` and `path` are mandatory. The image size can be defined with the optional parameters `widht` and `height`. If you dont specify a unit its going to default to use pixels as unit. *Note*: adding images larger than 16mb are not reccomended as it might degrade the performance.
+
+``` yaml
+
+custom_images:
+  group_one:
+    - title: <string> title of image [mandatory]
+      description: <string> replacement description of image [mandatory]
+      width: <string> 500px
+      height: <string> 100px
+      path: <string> scout/demo/images/custom_images/640x480_one.png [mandatory]
+    - title: <string> A jpg image [mandatory]
+      description: <string> A very good description [mandatory]
+      width: <string> 500px
+      path: <string> scout/demo/images/custom_images/640x480_two.jpg [mandatory]
+  group_two:
+    - title: <string> A SVG image [mandatory]
+      description: <string> Another very good description
+      path: <string> scout/demo/images/custom_images/640x480_three.svg [mandatory]
+
+```
+
 ### Load case from CLI without config
 
 Cases can be loaded without config file, in that case the user needs to specify a ped file and optionally one or several VCF files. An example could look like

scout/adapter/mongo/case.py

@@ -753,6 +753,7 @@ def update_case(self, case_obj, keep_date=False):
                     "analysis_date": case_obj["analysis_date"],
                     "chromograph_image_files": case_obj.get("chromograph_image_files"),
                     "chromograph_prefixes": case_obj.get("chromograph_prefixes"),
+                    "custom_images": case_obj.get("custom_images"),
                     "cnv_report": case_obj.get("cnv_report"),
                     "coverage_qc_report": case_obj.get("coverage_qc_report"),
                     "delivery_report": case_obj.get("delivery_report"),

scout/build/case.py

@@ -255,6 +255,8 @@ def build_case(case_data, adapter):
     case_obj["chromograph_image_files"] = case_data.get("chromograph_image_files")
     case_obj["chromograph_prefixes"] = case_data.get("chromograph_prefixes")
 
+    case_obj["custom_images"] = case_data.get("custom_images", {})
+
     for custom_report in CUSTOM_CASE_REPORTS:
         if custom_report in case_data:
             case_obj[custom_report] = case_data.get(custom_report)

scout/demo/643594.config.yaml

@@ -62,6 +62,22 @@ samples:
     mt_bam: scout/demo/reduced_mt.bam
     vcf2cytosure: scout/demo/ADM1059A3.test.cgh
 
+custom_images:
+  section_one:
+    - title: A png image
+      description: A very good description
+      width: 500
+      height: 100
+      path: scout/demo/images/custom_images/640x480_one.png
+    - title: A jpg image
+      description: A very good description
+      width: 500
+      path: scout/demo/images/custom_images/640x480_two.jpg
+  section_two:
+    - title: A SVG image
+      description: Another very good description
+      path: scout/demo/images/custom_images/640x480_three.svg
+
 vcf_snv: scout/demo/643594.clinical.vcf.gz
 vcf_sv: scout/demo/643594.clinical.SV.vcf.gz
 vcf_str: scout/demo/643594.clinical.str.stranger.vcf.gz