trial and error for circleci app

KarrLab · Apr 29, 2019 · 58fc61c · 58fc61c
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Showing 7 changed files with 43 additions and 64 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -3,45 +3,22 @@ jobs:
   build:
     working_directory: /root/project
     docker:
-      - image: circleci/node:7.10
       - image: karrlab/wc_env_dependencies:latest
       - image: circleci/postgres:11.2-alpine-ram
         name: postgres_service
         environment:
           POSTGRES_USER: postgres
           POSTGRES_DB: CommonSchema
-      - image: mongo
-        name: mongo
       - image: circleci/node:7.10
 
     steps:
       # Clone repository
       - checkout
-      - setup_remote_docker
-
       # Load packages from cache
       - restore_cache:
           keys:
             - v4-{{ arch }}-{{ .Branch }}-{{ checksum "/etc/docker-image-tag" }}-{{ checksum "requirements.txt" }}
 
-      - run:
-          name: Install Docker Compose
-          command: |
-            sudo chown -R $(whoami) /usr/local/bin
-            set -x
-            curl -L https://github.com/docker/compose/releases/download/1.24.0/docker-compose-`uname -s`-`uname -m` -o /root/docker-compose
-            chmod +x /root/docker-compose
-            sudo mv /root/docker-compose /usr/local/bin/docker-compose
-
-      - run:
-          name: Start container and verify it's working
-          command: |
-            set -x
-            docker-compose -f .circleci/docker-compose.yml up -d
-            docker-compose -f .circleci/docker-compose.yml logs
-
-      - run: npm install
-
       # Python 3 installation tasks
       - run:
           name: Install pkg_utils (Python 3)
@@ -129,9 +106,22 @@ jobs:
           path: /root/project/docs/_build/html
           destination: docs
 
-# workflows:
-#   version: 2
-#   build:
-#     jobs:
-#       - build:
-#           context: karr_lab
+      - setup_remote_docker
+
+      - run:
+          name: Install Docker Compose
+          command: |
+            sudo chown -R $(whoami) /usr/local/bin
+            set -x
+            curl -L https://github.com/docker/compose/releases/download/1.24.0/docker-compose-`uname -s`-`uname -m` -o /root/docker-compose
+            chmod +x /root/docker-compose
+            sudo mv /root/docker-compose /usr/local/bin/docker-compose
+
+      - run:
+          name: Start container and verify it's working
+          command: |
+            set -x
+            docker-compose -f .circleci/docker-compose.yml up -d
+            docker-compose -f .circleci/docker-compose.yml logs
+
+      - run: npm install
diff --git a/.circleci/docker-compose.yml b/.circleci/docker-compose.yml
@@ -24,37 +24,41 @@ services:
   mongo-datanator-1:
     image: 'mongo-start'
     build: ./mongo-datanator-1
-    volumes:
-    - ../datanator/data_source/cache/db_volumes/mongo-datanator-1:/data/db
-    - ../../:/root/host/karr_lab
     ports:
-    - "27017:27017" 
+      - "27017:27017" 
+    volumes:
+      - ./mongo-datanator-1/data:/data/db
     depends_on:
       - 'mongo-datanator-2'
       - 'mongo-datanator-3'
 
   mongo-datanator-2:
     image: 'mongo'
     restart: always
-    volumes:
-    - ../datanator/data_source/cache/db_volumes/mongo-datanator-2:/data/db
-    - ./mongo-datanator-2/conf:/conf
-    - ../../:/root/host/karr_lab
+    command: --replSet datanator
+    command: --config ./conf/mongo.conf
     ports:
-    - "27018:27018"
+      - "27018:27018"
+    volumes:
+      - ./mongo-datanator-2/data:/data/db
+      - ./mongo-datanator-2/conf:/conf
+
 
   mongo-datanator-3:
     image: 'mongo'
+    command: --replSet datanator
+    command: --config ./conf/mongo.conf
     ports:
       - '27019:27019'
     volumes:
-    - ../datanator/data_source/cache/db_volumes/mongo-datanator-3:/data/db
-    - ./mongo-datanator-3/conf:/conf
-    - ../../:/root/host/karr_lab
-    restart: always      
+      - ./mongo-datanator-3/data:/data/db
+      - ./mongo-datanator-3/conf:/conf
+    restart: always    
+    depends_on:
+      - mongo-datanator-2  
 
   setup-rs:
-    image: 'setup-datanator'
+    image: 'setup-rs'
     build: ./setup
     depends_on:
       - 'mongo-datanator-1'
@@ -68,9 +72,7 @@ services:
       environment:
           - WEB_USER='user'
           - WEB_PASS='pass'
+      depends_on:
+        - 'mongo-datanator-1'
+        - 'setup-rs'
       command: sh -c 'sleep 10 && tini -- node app'
-
-volumes:
-  mongo-datanator-1:
-  mongo-datanator-2:
-  mongo-datanator-3:
diff --git a/.circleci/mongo-datanator-1/mongo.conf b/.circleci/mongo-datanator-1/mongo.conf
@@ -1,6 +1,5 @@
-
 replication:
     oplogSizeMB: 1024
     replSetName: datanator
 net:
-	port: 27017
+	port: 27017
diff --git a/.circleci/mongo-datanator-2/conf/mongo.conf b/.circleci/mongo-datanator-2/conf/mongo.conf
@@ -1,6 +1,5 @@
-
 replication:
     oplogSizeMB: 1024
     replSetName: datanator
 net:
-	port: 27018
+	port: 27018
diff --git a/.circleci/mongo-datanator-2/mongo.conf b/.circleci/mongo-datanator-2/mongo.conf
diff --git a/.circleci/mongo-datanator-3/conf/mongo.conf b/.circleci/mongo-datanator-3/conf/mongo.conf
@@ -1,6 +1,5 @@
-
 replication:
     oplogSizeMB: 1024
     replSetName: datanator
 net:
-	port: 27019
+	port: 27019
diff --git a/.circleci/mongo-datanator-3/mongo.conf b/.circleci/mongo-datanator-3/mongo.conf