Updates Dockerfiles to use local package install instead of pypi.

Author: Robert Chu

.github/workflows/publish.yml

@@ -71,7 +71,6 @@ jobs:
           password: ${{ secrets.PYPI_API_TOKEN }}
 
   publish-docker:
-    needs: publish-pypi
     if: startsWith(github.ref, 'refs/tags')
     name: Publish script-runner to dockerhub
     runs-on: ubuntu-latest
@@ -119,7 +118,7 @@ jobs:
       - name: Push to Docker Hub
         uses: docker/build-push-action@v2
         with:
-          context: ./docker
+          context: ./
           file: ./docker/Dockerfile
           builder: ${{ steps.buildx.outputs.name }}
           push: ${{ github.event_name != 'pull_request' }}
@@ -135,7 +134,6 @@ jobs:
             PYTHON_IMAGE_TAG=${{ steps.prep.outputs.pyversion }}
 
   publish-docker-example:
-    needs: publish-pypi
     if: startsWith(github.ref, 'refs/tags')
     name: Publish script-runner-example to dockerhub
     runs-on: ubuntu-latest
@@ -181,7 +179,7 @@ jobs:
       - name: Push to Docker Hub
         uses: docker/build-push-action@v2
         with:
-          context: ./docker
+          context: ./
           file: ./docker/Dockerfile.example
           builder: ${{ steps.buildx.outputs.name }}
           push: ${{ github.event_name != 'pull_request' }}

example-config.json config.jsonexample-config.json renamed to config.json

@@ -3,8 +3,8 @@ services:
   server:
     image: labflow/script-runner-example:latest
     build:
-      dockerfile: ./Dockerfile.example
-      context: ./docker
+      dockerfile: ./docker/Dockerfile.example
+      context: ./
       args:
         SERVER_VERSION: local+devcontainer
     command: "python3 -m flask run --host=0.0.0.0 --port=5000"
@@ -23,8 +23,8 @@ services:
   worker:
     image: labflow/script-runner-example:latest
     build:
-      dockerfile: ./Dockerfile.example
-      context: ./docker
+      dockerfile: ./docker/Dockerfile.example
+      context: ./
       args:
         SERVER_VERSION: local+devcontainer
     command: "python3 -m celery -A script_runner.analysis worker"

docker-compose.yaml

@@ -2,18 +2,12 @@ ARG PYTHON_IMAGE_TAG=alpine
 
 FROM python:${PYTHON_IMAGE_TAG}
 
-ARG SCRIPT_RUNNER_VERSION=local+container
-
 WORKDIR /app
 
-RUN pip install \
-    script-runner-api==${SCRIPT_RUNNER_VERSION}
-
-COPY ./entrypoint.sh /entrypoint.sh
-RUN dos2unix /entrypoint.sh
-RUN chmod +x /entrypoint.sh
+COPY . /script-runner
+RUN pip install /script-runner
+RUN rm -rf /script-runner
 
 ENV FLASK_APP=script_runner.main:app
-ENV SERVER_VERSION=$SERVER_VERSION
 
-ENTRYPOINT [ "/entrypoint.sh" ]
+CMD "python3 -m gunicorn.app.wsgiapp --timeout 240 --bind 0.0.0.0:${PORT} --access-logfile - --error-logfile - --workers 4 ${FLASK_APP}"

docker/Dockerfile

@@ -1,7 +1,6 @@
 FROM rocker/verse:3.6.3
 
 ARG SERVER_VERSION=local+container
-ARG SCRIPT_RUNNER_VERSION=local+container
 
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # Install extra *nix utils
@@ -63,13 +62,13 @@ RUN git clone git://github.com/lab-grid/swabseq-analysis /app
 # Python Env
 WORKDIR /app
 
-RUN pip3 install \
-    pandas \
-    script-runner-api==${SCRIPT_RUNNER_VERSION}
+RUN pip3 install pandas
 
-COPY ./entrypoint.sh /entrypoint.sh
-RUN dos2unix /entrypoint.sh
-RUN chmod +x /entrypoint.sh
+COPY . /script-runner
+RUN pip3 install /script-runner
+RUN rm -rf /script-runner
+
+COPY ./config.json /app/config.json
 
 RUN mkdir /base-rundir
 RUN wget -qO- https://swabseq-analysis-examples.s3-us-west-1.amazonaws.com/bcls/H3FY3K.tar.gz \
@@ -79,4 +78,4 @@ ENV PYTHONPATH="${RBASE}:${PYTHONPATH}"
 ENV FLASK_APP=script_runner.main:app
 ENV SERVER_VERSION=$SERVER_VERSION
 
-ENTRYPOINT [ "/entrypoint.sh" ]
+CMD "python3 -m gunicorn.app.wsgiapp --timeout 240 --bind 0.0.0.0:${PORT} --access-logfile - --error-logfile - --workers 4 ${FLASK_APP}"

docker/Dockerfile.example

@@ -0,0 +1,14 @@
+SERVER_NAME=localhost:5000
+
+REDIS_PASSWORD=my-redis-password
+
+AUTH_PROVIDER=none
+AUTH0_DOMAIN=
+AUTH0_CLIENT_ID=
+
+AUTH0_API_AUTHORITY=
+AUTH0_API_AUDIENCE=
+
+AUTH0_AUTHORIZATION_URL=
+AUTH0_TOKEN_URL=
+

docker/entrypoint.sh

@@ -14,7 +14,7 @@ terraform {
 # IAM -------------------------------------------------------------------------
 
 resource "aws_iam_role" "labflow_role" {
-  name = "${input.stack_name}-role"
+  name = "${var.stack_name}-role"
 
   # May be necessary: https://registry.terraform.io/providers/hashicorp/aws/latest/docs/resources/iam_role
   # force_detach_policies = true
@@ -47,7 +47,7 @@ EOF
 module "vpc" {
   source = "terraform-aws-modules/vpc/aws"
 
-  name = "${input.stack_name}-vpc"
+  name = "${var.stack_name}-vpc"
 
   enable_nat_gateway   = true
   enable_dns_hostnames = true
@@ -61,7 +61,7 @@ module "vpc" {
 module "ecs" {
   source = "terraform-aws-modules/ecs/aws"
 
-  name = "${input.stack_name}-ecs"
+  name = "${var.stack_name}-ecs"
 
   container_insights = true