OMerge branch 'release/1.0.6'

action/action_compose.yml

@@ -2,7 +2,7 @@ version: '2'
 
 services:
   dcc-action:
-    image: quay.io/ucsc_cgl/action-service:1.0.11
+    image: quay.io/ucsc_cgl/action-service:1.0.12
     container_name: "action-service"
     environment:
       STORAGE_ACCESS_TOKEN: "${storage_access_token}"
@@ -19,7 +19,7 @@ services:
       DOCKSTORE_TOKEN: "${dockstore_token}"
     volumes:
       - ~/dcc-action-service/logs:/home/ubuntu/logs
-      - ~/dcc-action-service/extra:/home/ubuntu/luigi_decider_runs/extra
+      - ~/dcc-action-service/pipeline_deciders:/home/ubuntu/pipeline_deciders
     restart: always
     ports:
       - "8082"

boardwalk/dev.yml

@@ -105,6 +105,8 @@ services:
       L_POSTGRES_PASSWORD: "${login_password}"
       L_POSTGRES_DB: "${login_db}"
       SECRET_KEY: "${secret_key}"
+      LOG_IN_TOKEN: "${login_token}"
+      SERVER_NAME: "${dcc_dashboard_host}"
       DCC_CORE_CLIENT_VERSION: "${core_client_version}"
       ES_SERVICE: "${es_service}"
       BD_POSTGRES_USER: "${login_user}"

boardwalk/prod.yml

@@ -2,7 +2,7 @@ version: '2'
 
 services:
   dcc-metadata-indexer:
-    image: quay.io/ucsc_cgl/metadata-indexer:2.0.9
+    image: quay.io/ucsc_cgl/metadata-indexer:2.0.10
     #build: dcc-metadata-indexer/v2
     environment:
       USER_GROUP: "${user_group}"
@@ -56,7 +56,7 @@ services:
       FLASK_APP: "/app/mapi.py"
       DCC_DASHBOARD_HOST: "${dcc_dashboard_host}"
       SECRET_KEY: "${secret_key}"
-    image: quay.io/ucsc_cgl/dashboard-service:1.0.7
+    image: quay.io/ucsc_cgl/dashboard-service:1.0.8
     volumes:
       - ~/dcc-dashboard-service/logs:/app/log
     #build: dcc-dashboard-service
@@ -77,7 +77,7 @@ services:
       - login-db
     restart: always
   dcc-dashboard:
-    image: quay.io/ucsc_cgl/dashboard:1.0.8
+    image: quay.io/ucsc_cgl/dashboard:1.0.9
     #build: dcc-dashboard
     ports:
       - "80"
@@ -105,6 +105,8 @@ services:
       L_POSTGRES_PASSWORD: "${login_password}"
       L_POSTGRES_DB: "${login_db}"
       SECRET_KEY: "${secret_key}"
+      LOG_IN_TOKEN: "${login_token}"
+      SERVER_NAME: "${dcc_dashboard_host}"
       DCC_CORE_CLIENT_VERSION: "${core_client_version}"
       ES_SERVICE: "${es_service}"
       BD_POSTGRES_USER: "${login_user}"

install_bootstrap

@@ -166,7 +166,12 @@ else
     echo "esnet docker network already exists"
 fi
 
-
+#add the command to
+#start the UCSC Computational Genomics Platform (CGP) container that sets up the
+#Nginx config template with the uuids for each of the containers in the CGP
+#at boot time
+echo "Attempting to add docker start core-config-gen to rc.local"
+sudo ./put_core_start_cmd_in_rc.sh
 
 # RUN THE CONSONANCE INSTALLER
 run_consonance_launcher=''
@@ -901,9 +906,12 @@ while [[ "${run_boardwalk^^}" != 'Y' &&  "${run_boardwalk^^}" != 'N' ]] ; do
       login_password="$(generate_password)"      
       echo "generating SECRET_KEY for login"
       secret_key="$(generate_password)"
+
+      echo "generating LOG_IN_TOKEN for boardwalk check session"
+      login_token="$(generate_password)"
 
       #TODO: The script should snoop the .env file and check if it has a password assigned already and use that. Otherwise, generate a random password.
-      core_client_version='1.1.1'
+      core_client_version='1.1.2'
       # Now write a config for this file.
       [[ -f boardwalk_launcher_config/boardwalk.config ]] || mkdir -p boardwalk_launcher_config
 
@@ -942,6 +950,8 @@ while [[ "${run_boardwalk^^}" != 'Y' &&  "${run_boardwalk^^}" != 'N' ]] ; do
 "LOGIN_POSTGRES_DB":"${login_db}",
 "LOGIN_POSTGRES_PASSWORD":"${login_password}",
 "SECRET_KEY":"${secret_key}",
+"LOG_IN_TOKEN":"${login_token}",
+"SERVER_NAME":"${dcc_dashboard_host}",
 "DCC_CORE_CLIENT_VERSION":"${core_client_version}"
 }
 CONFIG

put_core_start_cmd_in_rc.sh

@@ -0,0 +1,33 @@
+#! /bin/bash
+
+set -o errexit
+set -o pipefail
+set -o nounset
+# set -o xtrace
+
+if [ -e /etc/rc.local ]
+then
+    #add the command to
+    #start the UCSC Computational Genomics Platform (CGP) container that sets up the 
+    #Nginx config template with the uuids for each of the containers in the CGP
+    #at boot time
+    #See dcc-ops/common/base.yml for more details
+    if ! grep -Fxq "sudo docker start core-config-gen" /etc/rc.local
+    then
+        sed -i -e '$i \
+#start the UCSC Computational Genomics Platform (CGP) container that sets up the\
+#Nginx config template with the uuids for each of the containers in the CGP\
+#See dcc-ops/common/base.yml for more details\
+sudo docker start core-config-gen\n'\
+        /etc/rc.local
+
+        echo "Added docker start core-config-gen command to /etc/rc.local"       
+    else
+        echo "Found docker start core-config-gen or similar command in /etc/rc.local \
+so it was not added"
+    fi
+else
+    echo "WARNING: No /etc/rc.local file exists; the command 'sudo docker start \
+core-config-gen' should be manually run after booting up"
+fi
+