Merge pull request #6 from CorreiaEduardo/feature/dockerfile

Feature/dockerfile
G2BC · Dec 17, 2024 · e8442c4 · e8442c4
2 parents 400683e + 3c5de24
commit e8442c4
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diff --git a/.dockerignore b/.dockerignore
@@ -2,4 +2,6 @@ blastdb/
 temp_genomes/
 results/
 .vscode/
-tests/
+tests/
+__init__.py
+docs/
diff --git a/Dockerfile b/Dockerfile
@@ -1,29 +1,58 @@
-FROM ubuntu:20.04
-
+FROM docker:24.0.2-dind as builder
+USER root
+ENV DEBIAN_FRONTEND=noninteractive
 COPY . /app
-
 WORKDIR /app
 
-RUN apt-get update && apt-get install -y \
-    # apt-transport-https \
-    # ca-certificates \
-    # build-essential \
-    curl \
-    # gnupg-agent \
-    # software-properties-common && \
-    curl -fsSL https://download.docker.com/linux/ubuntu/gpg | apt-key add - && \
-    add-apt-repository \
-    "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
-    $(lsb_release -cs) stable" && \
-    apt-get install -y docker-ce docker-ce-cli containerd.io && \
-    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
-    sudo apt install python3.11
-
-
-RUN curl -sSL https://install.python-poetry.org | python3 - &&\
-    poetry install --no-root
-
+RUN apk update && apk add --no-cache \
+  ca-certificates \
+  curl \
+  bash \
+  tzdata \
+  build-base \
+  python3 \
+  python3-dev \
+  libffi-dev \
+  openssl-dev \
+  musl-dev \
+  gcc \
+  make \
+  docker-cli \
+  zlib \
+  bzip2 \
+  libgcc \
+  libstdc++ \
+  libgomp \
+  gcompat 
+
+# RUN apk add --no-cache bash curl binutils \
+#     && curl -Lo /etc/apk/keys/sgerrand.rsa.pub https://alpine-pkgs.sgerrand.com/sgerrand.rsa.pub \
+#     && curl -Lo /glibc.apk https://github.com/sgerrand/alpine-pkg-glibc/releases/download/2.35-r0/glibc-2.35-r0.apk \
+#     && curl -Lo /glibc-bin.apk https://github.com/sgerrand/alpine-pkg-glibc/releases/download/2.35-r0/glibc-bin-2.35-r0.apk \
+#     && apk add --no-cache --force-overwrite /glibc.apk /glibc-bin.apk \
+#     && rm /glibc.apk /glibc-bin.apk
+
+# RUN curl -o ncbi-blast.tar.gz https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.16.0+-x64-linux.tar.gz && \
+#   tar -xzvf ncbi-blast.tar.gz && \
+#   rm ncbi-blast.tar.gz
+# ENV BLAST_PATH="/app/ncbi-blast-2.16.0+/bin"
+# ENV PATH="${BLAST_PATH}:${PATH}"
+
+RUN curl -o fam-substrate-mapping-08012023.tsv https://bcb.unl.edu/dbCAN2/download/Databases/fam-substrate-mapping-08012023.tsv && \
+  mv fam-substrate-mapping-08012023.tsv fam-substrate-mapping.tsv
+
+ENV POETRY_NO_INTERACTION=1 \
+  POETRY_VIRTUALENVS_CREATE=false \
+  POETRY_CACHE_DIR='/var/cache/pypoetry' \
+  POETRY_HOME='/usr/local' \
+  POETRY_VERSION=1.5.1
+
+RUN curl -sSL https://install.python-poetry.org | python3 -
+RUN poetry install --no-root
 RUN chmod +x /app/start.sh
-
+RUN dos2unix /app/start.sh
+RUN chmod +x /app/run_flask.sh
+RUN dos2unix /app/run_flask.sh
+ENV FLASK_APP=plasticome.routes.app.py
+FROM builder as runner
 CMD [ "/bin/bash", "/app/start.sh" ]
-
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -0,0 +1,121 @@
+services:
+  metadata:
+    container_name: plasticome_metadata
+    # build:
+    #   context: ./plasticome-metadata
+    #   dockerfile: Dockerfile
+    image: correiaeduardo/plasticome-metadata:final-1
+    environment:
+      - C_FORCE_ROOT=true
+      - FLASK_RUN_HOST=metadata
+      - JWT_SECRET_KEY=${JWT_SECRET_KEY}
+      - DATABASE_NAME=${DATABASE_NAME}
+      - DATABASE_USER=${DATABASE_USER}
+      - DATABASE_PASSWORD=${DATABASE_PASSWORD}
+      - DATABASE_PORT=${DATABASE_PORT}
+      - DATABASE_HOST=${DATABASE_HOST}
+    restart: always
+    ports:
+      - "5001:5000"
+    volumes:
+      - data:/metadata
+      - ./plasticome-metadata:/app
+    depends_on:
+      - postgres
+    networks:
+      - plasticome
+      # - internal
+
+  backend:
+    container_name: plasticome_backend
+    build:
+      context: ./plasticome-backend
+      dockerfile: Dockerfile
+    privileged: true
+    environment:
+      - DOCKER_HOST=tcp://localhost:2375
+      - [email protected]
+      - RABBIT_MQ_URL=amqp://guest:guest@plasticome_rabbitmq:5672//
+      - CELERY_BROKER_URL=amqp://guest:guest@plasticome_rabbitmq:5672//
+      - RESULT_BACKEND=redis://plasticome_redis:6379/0
+      - PLASTICOME_METADATA_URL=http://metadata:5000/
+      - C_FORCE_ROOT=true
+      - FLASK_RUN_HOST=backend
+      - PLASTICOME_USER=${PLASTICOME_USER}
+      - PLASTICOME_PASSWORD=${PLASTICOME_PASSWORD}
+      - MAIL_USER=${MAIL_USER}
+      - MAIL_SERVER=${MAIL_SERVER}
+      - MAIL_SECRET=${MAIL_SECRET}
+      - MAIL_ACCESS_PORT=${MAIL_ACCESS_PORT}
+    restart: always
+    ports:
+      - "5002:5000"
+    depends_on:
+      - rabbitmq
+      - metadata
+    volumes:
+      - data:/backend
+      - ./plasticome-backend/plasticome:/app/plasticome
+      - ./temp_genomes:/app/temp_genomes
+    networks:
+      - plasticome
+      # - internal
+
+  rabbitmq:
+    container_name: plasticome_rabbitmq
+    image: rabbitmq:management
+    ports:
+      - "5672:5672"
+      - "15672:15672"
+    environment:
+      - RABBITMQ_DEFAULT_VHOST=
+      - RABBITMQ_DEFAULT_USER=guest
+      - RABBITMQ_DEFAULT_PASS=guest
+    depends_on:
+      - redis
+    networks:
+      - plasticome
+      # - internal
+    volumes:
+      - rabbitmq_data:/data
+
+  redis:
+    container_name: plasticome_redis
+    image: redis
+    ports:
+      - "6379:6379"
+    networks:
+      - plasticome
+      # - internal
+    volumes:
+      - redis_data:/data
+
+  postgres:
+    container_name: plasticome_postgres
+    image: postgres
+    volumes:
+      - ./pg_data:/var/lib/postgresql/data
+      - ./plasticome-metadata/scripts:/scripts
+      - ./plasticome-metadata/dump/plasticome-psql-v1.sql.lzo:/dump/plasticome-psql-v1.sql.lzo
+    environment:
+      POSTGRES_DB: ${DATABASE_NAME}
+      POSTGRES_USER: ${DATABASE_USER}
+      POSTGRES_PASSWORD: ${DATABASE_PASSWORD}
+    ports:
+      - "33805:5432"
+    networks:
+      - plasticome
+      # - internal
+
+networks:
+  plasticome:
+    driver: bridge
+    # internal:
+    # external: true
+volumes:
+  data:
+  rabbitmq_data:
+  pg_data:
+  redis_data:
+
+
diff --git a/plasticome-compose.yml b/plasticome-compose.yml
@@ -0,0 +1,136 @@
+services:
+  metadata:
+    container_name: plasticome_metadata
+    # build:
+    #   context: ./plasticome-metadata
+    #   dockerfile: Dockerfile
+    image: correiaeduardo/plasticome-metadata:final-1
+    environment:
+      - C_FORCE_ROOT=true
+      - FLASK_RUN_HOST=metadata
+      - JWT_SECRET_KEY=${JWT_SECRET_KEY}
+      - DATABASE_NAME=${DATABASE_NAME}
+      - DATABASE_USER=${DATABASE_USER}
+      - DATABASE_PASSWORD=${DATABASE_PASSWORD}
+      - DATABASE_PORT=${DATABASE_PORT}
+      - DATABASE_HOST=${DATABASE_HOST}
+    restart: always
+    ports:
+      - "5001:5000"
+    volumes:
+      - data:/metadata
+      - ./plasticome-metadata:/app
+    depends_on:
+      - postgres
+    networks:
+      - plasticome
+      # - internal
+
+  backend:
+    container_name: plasticome_backend
+    build:
+      context: ./plasticome-backend
+      dockerfile: Dockerfile
+    privileged: true
+    environment:
+      - DOCKER_HOST=tcp://localhost:2375
+      - [email protected]
+      - RABBIT_MQ_URL=amqp://guest:guest@plasticome_rabbitmq:5672//
+      - CELERY_BROKER_URL=amqp://guest:guest@plasticome_rabbitmq:5672//
+      - RESULT_BACKEND=redis://plasticome_redis:6379/0
+      - PLASTICOME_METADATA_URL=http://metadata:5000/
+      - C_FORCE_ROOT=true
+      - FLASK_RUN_HOST=backend
+      - PLASTICOME_USER=${PLASTICOME_USER}
+      - PLASTICOME_PASSWORD=${PLASTICOME_PASSWORD}
+      - MAIL_USER=${MAIL_USER}
+      - MAIL_SERVER=${MAIL_SERVER}
+      - MAIL_SECRET=${MAIL_SECRET}
+      - MAIL_ACCESS_PORT=${MAIL_ACCESS_PORT}
+    restart: always
+    ports:
+      - "5002:5000"
+    depends_on:
+      - rabbitmq
+      - metadata
+    volumes:
+      - data:/backend
+      - ./plasticome-backend/plasticome:/app/plasticome
+      - ./temp_genomes:/app/temp_genomes
+    networks:
+      - plasticome
+      # - internal
+
+  frontend:
+    container_name: plasticome_frontend
+    build:
+      context: ./plasticome-frontend
+      dockerfile: Dockerfile
+    volumes:
+      - ./plasticome-frontend:/usr/share/nginx/html
+    depends_on:
+      - backend
+    ports:
+      - "3000:80"
+    networks:
+      - plasticome
+      # - internal
+
+  rabbitmq:
+    container_name: plasticome_rabbitmq
+    image: rabbitmq:management
+    ports:
+      - "5672:5672"
+      - "15672:15672"
+    environment:
+      - RABBITMQ_DEFAULT_VHOST=
+      - RABBITMQ_DEFAULT_USER=guest
+      - RABBITMQ_DEFAULT_PASS=guest
+    depends_on:
+      - redis
+    networks:
+      - plasticome
+      # - internal
+    volumes:
+      - rabbitmq_data:/data
+
+  redis:
+    container_name: plasticome_redis
+    image: redis
+    ports:
+      - "6379:6379"
+    networks:
+      - plasticome
+      # - internal
+    volumes:
+      - redis_data:/data
+
+  postgres:
+    container_name: plasticome_postgres
+    image: postgres
+    volumes:
+      - ./pg_data:/var/lib/postgresql/data
+      - ./plasticome-metadata/scripts:/scripts
+      - ./plasticome-metadata/dump/plasticome-psql-v1.sql.lzo:/dump/plasticome-psql-v1.sql.lzo
+    environment:
+      POSTGRES_DB: ${DATABASE_NAME}
+      POSTGRES_USER: ${DATABASE_USER}
+      POSTGRES_PASSWORD: ${DATABASE_PASSWORD}
+    ports:
+      - "33805:5432"
+    networks:
+      - plasticome
+      # - internal
+
+networks:
+  plasticome:
+    driver: bridge
+    # internal:
+    # external: true
+volumes:
+  data:
+  rabbitmq_data:
+  pg_data:
+  redis_data:
+
+
diff --git a/plasticome/config/__init__.py b/plasticome/config/__init__.py
@@ -0,0 +1,3 @@
+from .celery import celery_app
+
+__all__ = ("celery_app",)
diff --git a/plasticome/config/celery_config.py → plasticome/config/celery.py b/plasticome/config/celery_config.py → plasticome/config/celery.py
@@ -7,7 +7,7 @@
 
 celery_app = Celery(
     'celery_config',
-    broker=os.getenv('RABBIT_MQ_URL'),
+    broker='amqp://guest:guest@rabbitmq:5672//',
     include=[
         'plasticome.services.dbcan_service',
         'plasticome.services.ecpred_service',

diff --git a/plasticome/controllers/fungi_controller.py b/plasticome/controllers/fungi_controller.py
@@ -1,4 +1,4 @@
-from plasticome.services.genbank_service import search_fungi_id_by_name
+from ..services.genbank_service import search_fungi_id_by_name
 
 
 def search_fungi_by_name(fungi_name: str):

diff --git a/plasticome/routes/app.py b/plasticome/routes/app.py
@@ -1,9 +1,9 @@
 from flask import Flask, request
-from flask_cors import CORS
+from flask_cors import CORS, cross_origin
 from flask_pydantic_spec import FlaskPydanticSpec
 
-from plasticome.controllers.fungi_controller import search_fungi_by_name
-from plasticome.controllers.pipeline_controller import execute_main_pipeline
+from ..controllers.fungi_controller import search_fungi_by_name
+from ..controllers.pipeline_controller import execute_main_pipeline
 
 server = Flask(__name__)
 CORS(server)
@@ -24,6 +24,7 @@ def get_fungi_id_by_name(fungi_name):
 
 
 @server.post('/analyze')
+@cross_origin()
 def execute_pipeline():
     return execute_main_pipeline(request.json)
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		from .celery import celery_app

		__all__ = ("celery_app",)