Docker Changes

Dockerfile

@@ -0,0 +1,16 @@
+# A simple container for variant-service.
+# Runs service on port 80.
+# Healthchecks service up every 5m.  
+
+FROM python:3.10
+RUN apt update ; apt install -y rsync
+RUN pip install pipenv uvicorn[standard]
+COPY . /app
+WORKDIR /app
+RUN if [ ! -f "Pipfile.lock" ] ; then pipenv lock ; else echo Pipfile.lock exists ; fi
+RUN pipenv sync
+EXPOSE 80
+HEALTHCHECK --interval=5m --timeout=3s \
+    CMD curl -f http://localhost/variation || exit 1
+
+CMD pipenv run uvicorn variation.main:app  --port 80 --host 0.0.0.0

README.md

@@ -198,3 +198,25 @@ From the _root_ directory of the repository:
 ```shell
 pytest tests/
 ```
+
+### Docker Setup
+
+From the root directory , where Docker and docker-compose file are , run the following commands:  
+
+*docker-compose up -d db
+*docker-compose up -d uta
+*docker-compose up -d dynamodb-local
+
+Wait for all containers to start , Db service which is seqrepo container takes time and exits once the sequences download is over. 
+
+Before starting the Variation-normalizer service, check the following:
+
+* Db container(seqrepo) has finished downloading data and has exited.
+* UTA service has dispalyed the message " database system is ready to accept connections" in logs.
+* Dynamodb container is up and running.
+
+Start the Variation Normalizer container with the following commnad: 
+
+docker-compose up -d app
+
+The container will be up and running however , it downloads the gene normalizer data and that takes time. Please wait till the ETL for gene database is done. After that Variation normalizer is ready to use.

docker-compose.yaml

@@ -0,0 +1,58 @@
+version: "3.9"
+
+services:
+  app:
+    build:
+      context: .
+    environment:
+      SEQREPO_ROOT_DIR: /usr/local/share/seqrepo/2024-02-20
+      AWS_ACCESS_KEY_ID: 'DUMMYIDEXAMPLE'
+      AWS_SECRET_ACCESS_KEY: 'DUMMYEXAMPLEKEY'
+      AWS_DEFAULT_REGION: 'us-west-2'
+      GENE_NORM_DB_URL: http://dynamodb-local:8000
+
+    links:
+     - "dynamodb-local"
+
+    ports:
+      - "8001:80"
+
+    volumes:
+      - seqrepo_vol:/usr/local/share/seqrepo
+    command: >
+      sh -c "pipenv run gene_norm_update --update_all --update_merged &&
+             cd src wait_for_db &&
+             pipenv run uvicorn variation.main:app --log-level debug --port 80 --host 0.0.0.0"
+    depends_on:
+      - db
+      - dynamodb-local
+      - uta
+
+  db:
+    image: biocommons/seqrepo:latest
+    volumes:
+      - seqrepo_vol:/usr/local/share/seqrepo
+
+  uta:
+    image: biocommons/uta:uta_20210129b
+    environment:
+      - POSTGRES_PASSWORD=some-password-that-you-make-up
+    volumes:
+      - seqrepo_vol:/var/lib/postgresql/data
+    ports:
+      - 5432:5432
+
+  dynamodb-local:
+    command: "-jar DynamoDBLocal.jar -sharedDb -dbPath ./data"
+    image: "amazon/dynamodb-local:1.18.0"
+    container_name: dynamodb-local
+    ports:
+     - "8000:8000"
+    user: root
+    volumes:
+     - "seqrepo_vol:/home/dynamodblocal/data"
+    working_dir: /home/dynamodblocal
+
+volumes:
+  seqrepo_vol:
+  uta_vol: