Merge dev to dev-kube

Dockerfile

@@ -1,24 +1,50 @@
 # Builds an image for CTS calculator celery worker
 
-ARG version=dev
-
-FROM python:3.9-alpine
+FROM mambaorg/micromamba:1.5.8-alpine3.19
 
 ENV APP_USER=www-data
+ENV CONDA_ENV="pyenv"
 
-COPY . /src/
+USER root
 
-WORKDIR /src
+RUN adduser -S $APP_USER -G $APP_USER
 
-RUN pip install -r requirements.txt
+RUN apk add --update --no-cache \
+    build-base \
+    jpeg-dev \
+    zlib-dev \
+    libjpeg \
+    gettext \
+    py3-lxml \
+    py3-pillow \
+    openldap-dev \
+    python3-dev \
+    linux-headers \
+    && rm -rf /var/cache/apk/*
 
-ENV PYTHONPATH /src:$PYTHONPATH
-ENV PATH /src:$PATH
+COPY . /src/
+WORKDIR /src
 
-RUN apk update && \
-	apk upgrade
+RUN micromamba create -n $CONDA_ENV -c conda-forge python=3.10
+RUN micromamba install -n $CONDA_ENV -f /src/environment.yml
+RUN micromamba clean -p -t -l --trash -y
+RUN micromamba run -n $CONDA_ENV pip uninstall -y xhtml2pdf && micromamba run -n $CONDA_ENV pip install xhtml2pdf
+
+# # Removes any trace of pip to resolve an open CVE:
+# RUN rm -rf \
+#     /root/.cache/pip \
+#     /usr/local/bin/pip \
+#     /usr/local/bin/pip3.10 \
+#     /usr/local/bin/pip3 \
+#     /usr/local/lib/python3.10/site-packages/pip \
+#     /usr/local/lib/python3.10/site-packages/pip-23.0.1.dist-info
 
-RUN adduser -S $APP_USER -G $APP_USER
 RUN chown -R $APP_USER:$APP_USER /src
 
+ENV DJANGO_SETTINGS_MODULE "settings"
+EXPOSE 8080
+
+ENV PYTHONPATH /src:$PYTHONPATH
+ENV PATH /src:$PATH
+
 USER $APP_USER

environment.yml

@@ -0,0 +1,13 @@
+name: cts
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - beautifulsoup4=4.12.3
+  - celery=5.3.6
+  - pymongo=4.6.3
+  - python-dotenv=1.0.1
+  - rdkit=2024.3.1
+  - requests=2.31.0
+  - pip:
+    - redis==5.0.3

requirements.txt

@@ -2,5 +2,6 @@ beautifulsoup4==4.10.0
 celery==5.2.3
 pymongo==4.0.2
 python-dotenv==0.19.2
-redis==4.1.4
-requests==2.27.1
+rdkit==2023.3.1
+redis==4.4.4
+requests==2.31.0

start-manager.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+micromamba run -n pyenv celery -A tasks worker -Q manager_queue -l info -n manager_worker -c 1

start-worker.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+micromamba run -n pyenv celery -A tasks worker -Q cts_queue -l info -n cts_worker -c 1