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mwittepmwittep
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Merge pull request #55 from Integrative-Transcriptomics:redis-config-improve
Renames config file for correct running
2 parents 28c6a9f + e212b1b commit f306a57

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‎.github/workflows/docker.yml

Lines changed: 63 additions & 61 deletions
Original file line numberDiff line numberDiff line change
@@ -2,72 +2,74 @@ name: Build and Push Docker Image
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# when to run the workflow
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on:
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push:
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branches: [main]
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push:
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branches: [main]
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# the jobs to run
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jobs:
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build:
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# the os to run the job on
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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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build:
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# the os to run the job on
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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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# build the image now
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- name: Build Docker image
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run: docker compose --env-file variables_tsspredator.env build
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# build the image now
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- name: Build Docker image
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run: docker compose --env-file variables_tsspredator.env build
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- name: save images
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run: |
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docker save tsspredator_web:latest | gzip > image_tsspredator_web.tar.gz
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docker save tsspredator_celery_app:latest | gzip > image_tsspredator_celery_app.tar.gz
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- name: save images
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run: |
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docker save tsspredator_web:latest | gzip > image_tsspredator_web.tar.gz
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docker save tsspredator_celery_app:latest | gzip > image_tsspredator_celery_app.tar.gz
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- name: Install SSH client
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run: sudo apt-get install -qq -y openssh-client
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- name: Install SSH client
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run: sudo apt-get install -qq -y openssh-client
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- name: Transfer Docker images to server
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env:
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SSH_PRIVATE_KEY: ${{secrets.SSH_PRIVATE_KEY}}
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SSH_CONFIG: ${{secrets.SSH_CONFIG}}
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SERVER_IP: ${{secrets.SERVER_IP}}
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KNOWN_HOSTS: ${{secrets.KNOWN_HOSTS}}
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TARGET: ${{secrets.TARGET}}
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DEPLOY_FILE: ${{secrets.DEPLOY_FILE}}
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DEPLOY_FILE_NAME: ${{secrets.DEPLOY_FILE_NAME}}
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ENV_FILE: ${{secrets.ENV_FILE}}
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ENV_FILE_NAME: ${{secrets.ENV_FILE_NAME}}
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run: |
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mkdir -p ~/.ssh && chmod 700 ~/.ssh
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echo "$SSH_CONFIG" > ~/.ssh/config
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echo "$SSH_PRIVATE_KEY" > ~/.ssh/github-actions
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echo "$KNOWN_HOSTS" > ~/.ssh/known_hosts
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chmod 600 ~/.ssh/config
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chmod 600 ~/.ssh/github-actions
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chmod 600 ~/.ssh/known_hosts
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echo "$DEPLOY_FILE" > $DEPLOY_FILE_NAME
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echo "$ENV_FILE" > variables_tsspredator.env
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scp -o UserKnownHostsFile=~/.ssh/known_hosts image_tsspredator_web.tar.gz $SERVER_IP:$TARGET
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scp -o UserKnownHostsFile=~/.ssh/known_hosts image_tsspredator_celery_app.tar.gz $SERVER_IP:$TARGET
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scp -o UserKnownHostsFile=~/.ssh/known_hosts docker-compose.yml $SERVER_IP:$TARGET
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scp -o UserKnownHostsFile=~/.ssh/known_hosts $ENV_FILE_NAME $SERVER_IP:$TARGET
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scp -o UserKnownHostsFile=~/.ssh/known_hosts $DEPLOY_FILE_NAME $SERVER_IP:$TARGET
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- name: Restart service
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env:
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SSH_PRIVATE_KEY: ${{secrets.SSH_PRIVATE_KEY}}
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SSH_CONFIG: ${{secrets.SSH_CONFIG}}
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SERVER_IP: ${{secrets.SERVER_IP}}
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KNOWN_HOSTS: ${{secrets.KNOWN_HOSTS}}
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TARGET: ${{secrets.TARGET}}
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UPDATE_CMDS: ${{secrets.UPDATE_CMDS}}
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run: |
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mkdir -p ~/.ssh && chmod 700 ~/.ssh
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echo "$SSH_CONFIG" > ~/.ssh/config
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echo "$SSH_PRIVATE_KEY" > ~/.ssh/github-actions
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echo "$KNOWN_HOSTS" > ~/.ssh/known_hosts
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chmod 600 ~/.ssh/config
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chmod 600 ~/.ssh/github-actions
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chmod 600 ~/.ssh/known_hosts
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ssh -t -o UserKnownHostsFile=~/.ssh/known_hosts $SERVER_IP "cd $TARGET; chmod +x $UPDATE_CMDS; $UPDATE_CMDS"
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- name: Transfer Docker images to server
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env:
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SSH_PRIVATE_KEY: ${{secrets.SSH_PRIVATE_KEY}}
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SSH_CONFIG: ${{secrets.SSH_CONFIG}}
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SERVER_IP: ${{secrets.SERVER_IP}}
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KNOWN_HOSTS: ${{secrets.KNOWN_HOSTS}}
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TARGET: ${{secrets.TARGET}}
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DEPLOY_FILE: ${{secrets.DEPLOY_FILE}}
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DEPLOY_FILE_NAME: ${{secrets.DEPLOY_FILE_NAME}}
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ENV_FILE: ${{secrets.ENV_FILE}}
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ENV_FILE_NAME: ${{secrets.ENV_FILE_NAME}}
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REDIS_CONFIG_FILE: ${{secrets.REDIS_CONFIG_FILE}}
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73-
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run: |
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mkdir -p ~/.ssh && chmod 700 ~/.ssh
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echo "$SSH_CONFIG" > ~/.ssh/config
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echo "$SSH_PRIVATE_KEY" > ~/.ssh/github-actions
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echo "$KNOWN_HOSTS" > ~/.ssh/known_hosts
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chmod 600 ~/.ssh/config
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chmod 600 ~/.ssh/github-actions
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chmod 600 ~/.ssh/known_hosts
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echo "$DEPLOY_FILE" > $DEPLOY_FILE_NAME
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echo "$ENV_FILE" > variables_tsspredator.env
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echo "$REDIS_CONFIG_FILE" > redis.config
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scp -o UserKnownHostsFile=~/.ssh/known_hosts image_tsspredator_web.tar.gz $SERVER_IP:$TARGET
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scp -o UserKnownHostsFile=~/.ssh/known_hosts image_tsspredator_celery_app.tar.gz $SERVER_IP:$TARGET
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scp -o UserKnownHostsFile=~/.ssh/known_hosts docker-compose.yml $SERVER_IP:$TARGET
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scp -o UserKnownHostsFile=~/.ssh/known_hosts $ENV_FILE_NAME $SERVER_IP:$TARGET
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scp -o UserKnownHostsFile=~/.ssh/known_hosts redis.config $SERVER_IP:$TARGET
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scp -o UserKnownHostsFile=~/.ssh/known_hosts $DEPLOY_FILE_NAME $SERVER_IP:$TARGET
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- name: Restart service
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env:
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SSH_PRIVATE_KEY: ${{secrets.SSH_PRIVATE_KEY}}
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SSH_CONFIG: ${{secrets.SSH_CONFIG}}
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SERVER_IP: ${{secrets.SERVER_IP}}
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KNOWN_HOSTS: ${{secrets.KNOWN_HOSTS}}
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TARGET: ${{secrets.TARGET}}
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UPDATE_CMDS: ${{secrets.UPDATE_CMDS}}
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run: |
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mkdir -p ~/.ssh && chmod 700 ~/.ssh
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echo "$SSH_CONFIG" > ~/.ssh/config
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echo "$SSH_PRIVATE_KEY" > ~/.ssh/github-actions
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echo "$KNOWN_HOSTS" > ~/.ssh/known_hosts
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chmod 600 ~/.ssh/config
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chmod 600 ~/.ssh/github-actions
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chmod 600 ~/.ssh/known_hosts
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ssh -t -o UserKnownHostsFile=~/.ssh/known_hosts $SERVER_IP "cd $TARGET; chmod +x $UPDATE_CMDS; $UPDATE_CMDS"

‎.gitignore

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -32,3 +32,5 @@ server_tsspredator.egg-info/PKG-INFO
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celerybeat-schedule.db
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server_tsspredator/exampleData/campylobacter/files.zip
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server_tsspredator/exampleData/pseudomonas/files.zip
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celery/redis.config
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server_tsspredator/redisdb/redis.config

‎docker-compose.yml

Lines changed: 10 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -24,9 +24,13 @@ services:
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redis:
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image: "redis:alpine"
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ports:
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- "${TSSPREDATOR_REDIS_PORT}:6379"
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command: redis-server
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restart: always
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volumes:
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- type: bind
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source: ${REDIS_DATA_PATH}
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target: /data
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command: redis-server /data/redis.config
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celery:
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image: tsspredator_celery_app:latest
@@ -38,7 +42,10 @@ services:
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- tmpDataPredator:/tmpData
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depends_on:
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- redis
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volumes:
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tmpDataPredator:
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‎variables_tsspredator.env

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,4 @@
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DATA_PREDATOR_PATH="/Users/pacha/Documents/github_projects/tsspredator_web/TSSpredator-GUI/data"
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PORT_OUTPUT=5001
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TSSPREDATOR_REDIS_PORT=6379
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REDIS_DATA_PATH="/Users/pacha/Documents/github_projects/tsspredator_web/TSSpredator-GUI/server_tsspredator/redisdb"

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