Release 2.2

.dockerignore

@@ -0,0 +1,7 @@
+data
+test
+Automappa.egg-info
+build
+dist
+.vscode
+.pytest_cache

.env

@@ -0,0 +1,31 @@
+# Required for docker-compose.yml
+SERVER_ROOT_UPLOAD_FOLDER="/usr/src/app/uploads"
+SERVER_HOST="0.0.0.0"
+SERVER_PORT=8050
+# By default remove debugging tools --> For development switch this to `True`
+SERVER_DEBUG=False
+POSTGRES_USER="admin"
+POSTGRES_PASSWORD="mypass"
+POSTGRES_DB="automappa"
+POSTGRES_URL="postgresql+psycopg2://${POSTGRES_USER}:${POSTGRES_PASSWORD}@postgres:5432/${POSTGRES_DB}"
+POSTGRES_POOL_SIZE=1
+POSTGRES_POOL_PRE_PING=False
+RABBITMQ_DEFAULT_USER="user"
+RABBITMQ_DEFAULT_PASS="pass"
+RABBITMQ_URL="amqp://${RABBITMQ_DEFAULT_USER}:${RABBITMQ_DEFAULT_PASS}@rabbitmq:5672/"
+REDIS_BACKEND_HOST='redis'
+REDIS_BACKEND_PORT='6379'
+REDIS_BACKEND_DB='0'
+REDIS_BACKEND_PASSWORD='RedisPassword'
+CELERY_BACKEND_URL='redis://redis:6379/0'
+CELERY_BROKER_URL="amqp://${RABBITMQ_DEFAULT_USER}:${RABBITMQ_DEFAULT_PASS}@rabbitmq:5672//"
+FLOWER_BROKER_API_URL="http://${RABBITMQ_DEFAULT_USER}:${RABBITMQ_DEFAULT_PASS}@rabbitmq:15672/api"
+# https://github.com/mher/flower/issues/1036
+
+# Grafana configuration
+# Allow anonymous authentication or not
+GF_AUTH_DISABLE_LOGIN_FORM="false"
+# Role of anonymous user
+GF_AUTH_ANONYMOUS_ENABLED="false"
+# Install plugins here our in your own config file
+GF_AUTH_ANONYMOUS_ORG_ROLE="Admin"

.gitignore

@@ -8,4 +8,11 @@ app/__pycache__
 .DS_Store
 dist
 build
-Automappa.egg-info
+Automappa.egg-info
+.env
+data
+!automappa/data
+db-data
+file_system_backend
+*.db
+uploads

Dockerfile

@@ -1,15 +1,17 @@
-FROM condaforge/miniforge3:latest
+FROM condaforge/mambaforge:latest
 
-COPY environment.yml ./environment.yml
+COPY environment.yml /tmp/environment.yml
+RUN mamba env update -n base -f /tmp/environment.yml && \
+    mamba clean --all --force-pkgs-dirs --yes
 
-RUN conda env update -n base -f=environment.yml \
-    && conda clean --all --force-pkgs-dirs --yes
+COPY . /usr/src/app
+WORKDIR /usr/src/app
 
-# Test command is functional
-COPY . /Automappa/
-WORKDIR /Automappa/
 RUN python -m pip install . --ignore-installed --no-deps -vvv
-RUN automappa -h
 
-CMD [ "-h" ]
-ENTRYPOINT [ "automappa" ]
+# Create an unprivileged user for automappa celery worker
+RUN adduser --disabled-password --gecos '' automappa
+RUN mkdir -p /usr/src/app/uploads && \
+    chown -R automappa:automappa /usr/src/app
+
+# CMD ["automappa", "-h"]

Makefile

@@ -45,10 +45,32 @@ endif
 image: Dockerfile
 	docker build . -f $< -t evanrees/automappa:`git branch --show-current`
 
+## Remove automappa-{web,flower,queue} docker images
+rm-images: Dockerfile
+	docker rmi -f `docker images -q automappa-web`
+	docker rmi -f `docker images -q automappa-queue`
+	docker rmi -f `docker images -q automappa-flower`
+
 ## Install automappa entrypoint into current environment
 install: 
 	$(PYTHON_INTERPRETER) -m pip install . --ignore-installed --no-deps -vvv
 
+## docker compose build from docker-compose.yml
+build: docker-compose.yml
+	docker compose build
+
+## alias for docker-compose up --always-recreate-deps --remove-orphans --force-recreate
+up: docker-compose.yml
+	docker compose up --always-recreate-deps --remove-orphans --force-recreate
+
+## alias for docker-compose down --remove-orphans
+down: docker-compose.yml
+	docker compose down --remove-orphans
+
+## alias for docker-compose down --remove-orphans --volumes
+down-v: docker-compose.yml
+	docker compose down --remove-orphans -v
+
 # Run Automappa on test data
 # test: test_data
 # 	$(PYTHON_INTERPRETER) index.py -i test/bins.tsv
@@ -64,13 +86,13 @@ test_environment: scripts/test_environment.py
 	$(PYTHON_INTERPRETER) $<
 
 ## Set up python interpreter environment
-create_environment: requirements.txt
+create_environment: environment.yml
 ifeq (True,$(HAS_CONDA))
 	@echo ">>> Detected conda, creating conda environment."
 ifeq (3,$(findstring 3,$(PYTHON_INTERPRETER)))
-	conda create -c conda-forge --name $(PROJECT_NAME) python=3.7 --file=$<
+	mamba env create --name $(PROJECT_NAME) --file=$<
 else
-	conda create -c conda-forge --name $(PROJECT_NAME) python=3.7 --file=$<
+	mamba env create --name $(PROJECT_NAME) --file=$<
 endif
 	@echo ">>> New conda env created. Activate with:\nsource activate $(PROJECT_NAME)"
 else