Merge pull request #34 from bento-platform/user-dropdown

chore: service user drop down in dockerfile

Dockerfile

@@ -1,13 +1,14 @@
-FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.02.09 AS base-deps
+FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.02.27 AS base-deps
+
+SHELL ["/bin/bash", "-c"]
 
 # Install system packages for HTSLib + SAMtools + curl and jq for workflows
 # OpenJDK is for running WOMtool/Cromwell
+# Then, boostrap dependencies for setting up and running the Python application
 RUN apt-get update -y && \
     apt-get install -y samtools tabix bcftools curl jq openjdk-17-jre && \
-    rm -rf /var/lib/apt/lists/*
-
-# Boostrap dependencies for setting up and running the Python application
-RUN pip install --no-cache-dir poetry==1.3.2 gunicorn==20.1.0 "pysam>=0.20.0,<0.21.0"
+    rm -rf /var/lib/apt/lists/* && \
+    pip install --no-cache-dir poetry==1.3.2 gunicorn==20.1.0 "pysam>=0.20.0,<0.21.0"
 
 WORKDIR /
 ENV CROMWELL_VERSION=84
@@ -33,11 +34,13 @@ RUN poetry install --without dev --no-root
 # Manually copy only what's relevant
 # (Don't use .dockerignore, which allows us to have development containers too)
 COPY bento_wes bento_wes
-COPY entrypoint.bash entrypoint.bash
-COPY LICENSE LICENSE
-COPY README.md README.md
+COPY entrypoint.bash .
+COPY run.bash .
+COPY LICENSE .
+COPY README.md .
 
 # Install the module itself, locally (similar to `pip install -e .`)
 RUN poetry install --without dev
 
-CMD [ "bash", "./entrypoint.bash" ]
+ENTRYPOINT [ "bash", "./entrypoint.bash" ]
+CMD [ "bash", "./run.bash" ]

dev.Dockerfile

@@ -1,13 +1,15 @@
-FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.02.09 AS base-deps
+FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.02.27 AS base-deps
+
+SHELL ["/bin/bash", "-c"]
 
 # Install system packages for HTSLib + SAMtools + curl and jq for workflows
 # OpenJDK is for running WOMtool/Cromwell
+# Then, bootstrap dependencies for setting up and running the Python application
 RUN apt-get update -y && \
     apt-get install -y samtools tabix bcftools curl jq openjdk-17-jre && \
-    rm -rf /var/lib/apt/lists/*
-
-# Boostrap dependencies for setting up and running the Python application
-RUN pip install --no-cache-dir poetry==1.3.2 gunicorn==20.1.0 "pysam>=0.20.0,<0.21.0"
+    rm -rf /var/lib/apt/lists/* && \
+    source /env/bin/activate && \
+    pip install --no-cache-dir gunicorn==20.1.0 "pysam>=0.20.0,<0.21.0"
 
 WORKDIR /
 ENV CROMWELL_VERSION=84
@@ -28,9 +30,11 @@ COPY poetry.lock .
 # Install production + development dependencies
 # Without --no-root, we get errors related to the code not being copied in yet.
 # But we don't want the code here, otherwise Docker cache doesn't work well.
-RUN poetry install --no-root
+RUN source /env/bin/activate && poetry install --no-root
 
-# Copy in the entrypoint so we have somewhere to start
-COPY entrypoint.dev.bash .
+# Copy in the entrypoint & run script so we have somewhere to start
+COPY entrypoint.bash .
+COPY run.dev.bash .
 
-CMD [ "bash", "./entrypoint.dev.bash" ]
+ENTRYPOINT [ "bash", "./entrypoint.bash" ]
+CMD [ "bash", "./run.dev.bash" ]

entrypoint.bash

@@ -1,38 +1,16 @@
 #!/bin/bash
 
-export FLASK_DEBUG=false
-if [ -z "${INTERNAL_PORT}" ]; then
-  # Set default internal port to 5000
-  export INTERNAL_PORT=5000
-fi
+cd /wes || exit
 
-# Clean up after any crashed previous container runs
-job_store_path="${SERVICE_TEMP:-tmp}/toil_job_store"
-if [ -d "${job_store_path}" ]; then
-  echo "[bento_wes] [entrypoint] Cleaning Toil job store"
-  toil clean "file:${SERVICE_TEMP:-tmp}/toil_job_store"
-fi
+# Create bento_user + home
+source /create_service_user.bash
 
-# Start Celery worker with log level dependent on BENTO_DEBUG
-echo "[bento_wes] [entrypoint] Starting celery worker"
-celery_log_level="INFO"
-if [[
-  "${BENTO_DEBUG}" == "true" ||
-  "${BENTO_DEBUG}" == "True" ||
-  "${BENTO_DEBUG}" == "1" ||
-  "${CHORD_DEBUG}" == "true" ||
-  "${CHORD_DEBUG}" == "True" ||
-  "${CHORD_DEBUG}" == "1"
-]]; then
-  celery_log_level="DEBUG"
+# Fix permissions on /wes
+chown -R bento_user:bento_user /wes
+chmod -R o-rwx /wes/tmp  # Remove all access from others for /wes/tmp
+if [[ -d /env ]]; then
+  chown -R bento_user:bento_user /env
 fi
-celery --app bento_wes.app worker --loglevel="${celery_log_level}" &
 
-# Start API server
-echo "[bento_wes] [entrypoint] Starting gunicorn"
-# using 1 worker, multiple threads
-# see https://stackoverflow.com/questions/38425620/gunicorn-workers-and-threads
-gunicorn bento_wes.app:application \
-  --workers 1 \
-  --threads "$(( 2 * $(nproc --all) + 1))" \
-  --bind "0.0.0.0:${INTERNAL_PORT}"
+# Drop into bento_user from root and execute the CMD specified for the image
+exec gosu bento_user "$@"

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "bento_wes"
-version = "0.8.3"
+version = "0.8.4"
 description = "Workflow execution service for the Bento platform."
 authors = [
     "David Lougheed <[email protected]>",

run.bash

@@ -0,0 +1,38 @@
+#!/bin/bash
+
+export FLASK_DEBUG=false
+if [ -z "${INTERNAL_PORT}" ]; then
+  # Set default internal port to 5000
+  export INTERNAL_PORT=5000
+fi
+
+# Clean up after any crashed previous container runs
+job_store_path="${SERVICE_TEMP:-tmp}/toil_job_store"
+if [ -d "${job_store_path}" ]; then
+  echo "[bento_wes] [entrypoint] Cleaning Toil job store"
+  toil clean "file:${SERVICE_TEMP:-tmp}/toil_job_store"
+fi
+
+# Start Celery worker with log level dependent on BENTO_DEBUG
+echo "[bento_wes] [entrypoint] Starting celery worker"
+celery_log_level="INFO"
+if [[
+  "${BENTO_DEBUG}" == "true" ||
+  "${BENTO_DEBUG}" == "True" ||
+  "${BENTO_DEBUG}" == "1" ||
+  "${CHORD_DEBUG}" == "true" ||
+  "${CHORD_DEBUG}" == "True" ||
+  "${CHORD_DEBUG}" == "1"
+]]; then
+  celery_log_level="DEBUG"
+fi
+celery --app bento_wes.app worker --loglevel="${celery_log_level}" &
+
+# Start API server
+echo "[bento_wes] [entrypoint] Starting gunicorn"
+# using 1 worker, multiple threads
+# see https://stackoverflow.com/questions/38425620/gunicorn-workers-and-threads
+gunicorn bento_wes.app:application \
+  --workers 1 \
+  --threads "$(( 2 * $(nproc --all) + 1))" \
+  --bind "0.0.0.0:${INTERNAL_PORT}"

entrypoint.dev.bash → run.dev.bash

@@ -3,15 +3,21 @@
 # Set .gitconfig for development
 /set_gitconfig.bash
 
+# Source the development virtual environment
+source /env/bin/activate
+
+# Update dependencies and install module locally (similar to pip install -e: "editable mode")
+poetry install
+
 export FLASK_APP="bento_wes.app:application"
 
 if [ -z "${INTERNAL_PORT}" ]; then
   # Set default internal port to 5000
   export INTERNAL_PORT=5000
 fi
 
-# Install any dependency changes if needed
-python -m poetry install
+# Create temporary directory if needed
+mkdir -p /wes/tmp
 
 # Clean up after any crashed previous container runs
 job_store_path="${SERVICE_TEMP:-tmp}/toil_job_store"