Merge pull request #635 from RNAcentral/export-app

Add microservice to export data

.gitlab-ci.yml

@@ -1,6 +1,5 @@
 stages:
 #  - test
-#  - build
   - deploy
 
 #test_image:
@@ -25,17 +24,6 @@ stages:
 #      python rnacentral/manage.py test portal
 #      python rnacentral/manage.py test sequence_search
 
-#build_image:
-#  stage: build
-#  variables:
-#    DOCKER_USER: $DOCKER_USER
-#    DOCKER_PASSWORD: $DOCKER_PASSWORD
-#  before_script:
-#    - docker login -u $DOCKER_USER -p $DOCKER_PASSWORD
-#  script:
-#    - docker build -f Dockerfile -t rnacentral/rnacentral-webcode:${CI_COMMIT_BRANCH} .
-#    - docker push rnacentral/rnacentral-webcode:${CI_COMMIT_BRANCH}
-
 deploy_image:
   stage: deploy
   image:
@@ -61,3 +49,4 @@ deploy_image:
 #        - rnacentral/*
     - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
       when: manual
+

Dockerfile

@@ -12,34 +12,21 @@ RUN apt-get update && apt-get install -y \
     curl \
     tar \
     git \
-    vim \
-    supervisor && \
+    vim && \
     rm -rf /var/lib/apt/lists/*
 
 ENV RNACENTRAL_LOCAL=/srv/rnacentral/local
-ENV SUPERVISOR_CONF_DIR=/srv/rnacentral/supervisor
 ARG LOCAL_DEVELOPMENT
 
 # Create folders
 RUN \
     mkdir -p $RNACENTRAL_LOCAL && \
-    mkdir -p $SUPERVISOR_CONF_DIR && \
     mkdir /srv/rnacentral/log && \
     mkdir /srv/rnacentral/static
 
-# Install Infernal and node.js
+# Install node.js
 RUN \
     cd $RNACENTRAL_LOCAL && \
-    curl -OL http://eddylab.org/infernal/infernal-1.1.1.tar.gz && \
-    tar -xvzf infernal-1.1.1.tar.gz && \
-    cd infernal-1.1.1 && \
-    ./configure --prefix=$RNACENTRAL_LOCAL/infernal-1.1.1 && \
-    make && \
-    make install && \
-    cd easel && \
-    make install && \
-    cd $RNACENTRAL_LOCAL && \
-    rm infernal-1.1.1.tar.gz && \
     curl -sL https://deb.nodesource.com/setup_lts.x | bash - && \
     apt-get install -y nodejs
 
@@ -83,5 +70,4 @@ USER rnacentral
 COPY ./entrypoint.sh $RNACENTRAL_HOME
 ENTRYPOINT ["/srv/rnacentral/rnacentral-webcode/entrypoint.sh"]
 
-# Supervisor
-CMD [ "/bin/sh", "-c", "/usr/bin/supervisord -c ${SUPERVISOR_CONF_DIR}/supervisord.conf" ]
+CMD ["gunicorn", "--chdir", "/srv/rnacentral/rnacentral-webcode/rnacentral", "--bind", "0.0.0.0:8000", "rnacentral.wsgi:application", "--workers", "4", "--timeout", "120", "--log-level=debug", "--access-logfile", "/dev/stdout", "--error-logfile", "/dev/stderr"]

README.md

@@ -22,20 +22,10 @@ The [public postgres database](https://rnacentral.org/help/public-database) is c
 If you want to use another database, add the following environment variables: `DB_HOST`, `DB_NAME`, `DB_USER`,
 `DB_PASSWORD`, and `DB_PORT`.
 
-3. For Mac OS users, install [mutagen](https://mutagen.io/) (Docker on Mac has some performance issues)
+3. Run the app using [Docker](https://www.docker.com):
 
   ```
-  brew install mutagen-io/mutagen/mutagen-beta
-  ```
-
-4. Run the app using [Docker](https://www.docker.com):
-
-  ```
-  For Linux users:
-  docker-compose -f docker-compose.local.yml up --build
-
-  For Mac OS users:
-  mutagen compose -f docker-compose.local.mac.yml up --build
+  docker-compose up --build
   ```
 
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