fix: log4j booboo by bundling cordra-2.3.0 in docker image

.dockerignore

@@ -3,4 +3,8 @@
 docker-compose.yml
 .dockerignore
 docker-build.sh
-deployment
+deployment
+.eggs
+.pytest_cache
+build
+dist

docker-compose.yml

@@ -68,14 +68,10 @@ services:
       - "8000:8000"
     env_file:
       - .env
-    command: ["/start-reload.sh"]
-    environment:
-      MODULE_NAME: "nmdc_runtime.api.main"
-      PORT: 8000
     depends_on:
       - mongo
     volumes:
-      - .:/app
+      - .:/code
 
   mongo:
     image: mongo:4.4-bionic

nmdc_runtime/fastapi.Dockerfile

@@ -1,33 +1,14 @@
 # Best practice: Choose a stable base image and tag.
-FROM tiangolo/uvicorn-gunicorn:python3.8-slim
+FROM python:3.9
 
-# Install security updates, and some useful packages.
-#
-# Best practices:
-# * Make sure apt-get doesn't run in interactive mode.
-# * Update system packages.
-# * Pre-install some useful tools.
-# * Minimize system package installation.
-RUN export DEBIAN_FRONTEND=noninteractive && \
-  apt-get update && \
-  apt-get -y upgrade && \
-  apt-get install -y --no-install-recommends tini procps net-tools \
-  build-essential git make zip && \
-  apt-get -y clean && \
-  rm -rf /var/lib/apt/lists/*
+WORKDIR /code
 
+COPY ./requirements/main.txt /code/requirements.txt
 
-# Install requirements
-# WORKDIR is /app/ FROM tiangolo/uvicorn-gunicorn:python3.8-slim
-COPY requirements/main.txt requirements.txt
-RUN pip install --no-cache-dir -r requirements.txt
+RUN pip install --no-cache-dir --upgrade -r /code/requirements.txt
 
 # Add repository code
-COPY . .
+COPY . /code
 RUN pip install --no-cache-dir --editable .
 
-# Best practices: Prepare for C crashes.
-ENV PYTHONFAULTHANDLER=1
-
-# For development: CMD ["/start-reload.sh"]
-CMD ["/start.sh"]
+CMD ["uvicorn", "nmdc_runtime.api.main:app", "--proxy-headers", "--host", "0.0.0.0", "--port", "8000"]

requirements/dev.txt

@@ -8,11 +8,11 @@ attrs==21.4.0
     # via
     #   -c requirements/main.txt
     #   pytest
-black==22.1.0
+black==22.3.0
     # via
     #   -c requirements/main.txt
     #   -r requirements/dev.in
-bleach==4.1.0
+bleach==5.0.0
     # via
     #   -c requirements/main.txt
     #   readme-renderer
@@ -24,12 +24,12 @@ charset-normalizer==2.0.12
     # via
     #   -c requirements/main.txt
     #   requests
-click==8.0.4
+click==8.1.2
     # via
     #   -c requirements/main.txt
     #   black
-colorama==0.4.4
-    # via twine
+commonmark==0.9.1
+    # via rich
 docutils==0.17.1
     # via
     #   -c requirements/main.txt
@@ -60,7 +60,6 @@ mypy-extensions==0.4.3
 packaging==21.3
     # via
     #   -c requirements/main.txt
-    #   bleach
     #   pytest
     #   setuptools-scm
 pathspec==0.9.0
@@ -87,6 +86,7 @@ pygments==2.11.2
     # via
     #   -c requirements/main.txt
     #   readme-renderer
+    #   rich
 pyparsing==3.0.7
     # via
     #   -c requirements/main.txt
@@ -104,6 +104,8 @@ requests-toolbelt==0.9.1
     # via twine
 rfc3986==2.0.0
     # via twine
+rich==12.2.0
+    # via twine
 setuptools-scm==6.4.2
     # via -r requirements/dev.in
 six==1.16.0
@@ -116,16 +118,13 @@ tomli==2.0.1
     #   black
     #   pytest
     #   setuptools-scm
-tqdm==4.63.0
-    # via
-    #   -c requirements/main.txt
-    #   twine
-twine==3.8.0
+twine==4.0.0
     # via -r requirements/dev.in
 typing-extensions==4.1.1
     # via
     #   -c requirements/main.txt
     #   black
+    #   rich
 urllib3==1.26.9
     # via
     #   -c requirements/main.txt
@@ -135,7 +134,7 @@ webencodings==0.5.1
     # via
     #   -c requirements/main.txt
     #   bleach
-zipp==3.7.0
+zipp==3.8.0
     # via
     #   -c requirements/main.txt
     #   importlib-metadata