Merge branch 'hotfix/1.13.1'

Author: denis-yuen

docker-compose.yml

@@ -5,7 +5,6 @@ services:
   migration: 
     image: quay.io/dockstore/dockstore-webservice@${DOCKSTORE_IMAGE_DIGEST}
     volumes:
-      - log_volume:/dockstore_logs
       - ./config/web.yml:/home/web.yml
       - ./config/init_migration.sh:/home/init_migration.sh
     command: ["bash", "/home/init_migration.sh"]
@@ -21,11 +20,9 @@ services:
     depends_on:
       - migration
     volumes:
-      - log_volume:/dockstore_logs
       - ./config/web.yml:/home/web.yml
       - ./config/init_webservice.sh:/home/init_webservice.sh
       - ${GITHUB_APP_PRIVATE_KEY_FILE}:/dockstore/github-key/dockstore-github-private-key.pem
-      - ../language-plugins/:/root/.dockstore/language-plugins
     command: ["bash", "/home/init_webservice.sh"]
     ports:
       - "8081:8081"
@@ -75,6 +72,5 @@ services:
 #        awslogs-stream: "metricbeat"
 
 volumes:
-  log_volume: 
   esdata1:
     driver: local

install_bootstrap

@@ -66,27 +66,13 @@ function template()
     for f in $(ls templates/rules/); do mustache dockstore_launcher_config/compose.config templates/rules/$f > config/rules/$f; done
 }
 
-# Delete any galaxy plugin versions already in folder and download if a version has been specified.
-function download_galaxy()
-{
-    if [ ! -d "../language-plugins" ] ; then
-        mkdir ../language-plugins
-    fi
-
-    find ../language-plugins -regextype posix-extended -regex '.*dockstore-galaxy-interface.*' -delete
-    wget -nc -P ../language-plugins/ https://artifacts.oicr.on.ca/artifactory/collab-release/com/github/galaxyproject/dockstore-galaxy-interface/dockstore-galaxy-interface/${GALAXY_PLUGIN_VERSION}/dockstore-galaxy-interface-${GALAXY_PLUGIN_VERSION}.jar
-
-}
-
 #Read the config file if it exists
 if [ -f dockstore_launcher_config/compose.config ] ; then
     source <(jq -r 'to_entries|map("\(.key)=\"\(.value|tostring)\"")|.[]' dockstore_launcher_config/compose.config)
 fi
 
 template
 
-download_galaxy "$*"
-
 if [ $IS_FARGATE_DEPLOY == "false" ]; then
     # We need to set the environment variable for the image digest
     source .env

scripts/webservice-image-digest.py

@@ -58,9 +58,10 @@ def get_commit_from_github(tag_or_branch):
 def get_digest_from_s3(directory):
   # downloads the image-digest.txt from a directory in S3
   base_url = "https://gui.dockstore.org"
-  response = requests.get("{}/{}/image-digest.txt".format(base_url, directory))
+  digest_url = "{}/{}/image-digest.txt".format(base_url, directory.replace("/", "_"))
+  response = requests.get(digest_url)
   if (response.status_code != 200):
-    print("Expected a file at {}".format("{}/{}/image-digest.txt".format(base_url, directory)))
+    print("Expected a file at {}".format(digest_url))
     print("The image-digest.txt was not found in S3, did the build succeed?")
     exit(1)
   # There is a newline at the end of the file we rstrip
@@ -70,7 +71,7 @@ def get_digest_from_s3(directory):
   # slashes are replaced with _ in docker image tags
   # check to see if input includes a dash followed by 7 chars
   parsed = args.tag.split('-')
-  if len(parsed) == 2 and len(parsed[1]) == 7 and all(c in string.hexdigits for c in parsed[1]):
+  if len(parsed) >= 2 and len(parsed[-1]) == 7 and all(c in string.hexdigits for c in parsed[-1]):
     directory = args.tag
   else:
     commit = get_commit_from_github(args.tag)

templates/default.nginx_http.security.conf.template

@@ -27,3 +27,7 @@ proxy_hide_header Server;
 add_header X-Content-Type-Options "nosniff" always;
 
 add_header Strict-Transport-Security $hsts_header always;
+
+{{^PRODUCTION}}
+add_header X-Robots-Tag "noindex, nofollow" always;
+{{/PRODUCTION}}

templates/init_migration.sh.template

@@ -4,12 +4,12 @@
 cd "$(dirname "$0")"
 
 {{#DATABASE_GENERATED}}
-java -Ddw.database.user=postgres -Ddw.database.password="{{{ POSTGRES_DBPASSWORD }}}" -jar /home/dockstore-webservice-*.jar db migrate web.yml --include 1.3.0.generated,1.3.1.consistency,1.4.0,1.5.0,1.6.0,1.7.0 | tee --append /dockstore_logs/webservice.out
+java -Ddw.database.user=postgres -Ddw.database.password="{{{ POSTGRES_DBPASSWORD }}}" -jar /home/dockstore-webservice-*.jar db migrate web.yml --include 1.3.0.generated,1.3.1.consistency,1.4.0,1.5.0,1.6.0,1.7.0
 {{/DATABASE_GENERATED}}
 {{^DATABASE_GENERATED}}
-java -Ddw.database.user=postgres -Ddw.database.password="{{{ POSTGRES_DBPASSWORD }}}" -jar /home/dockstore-webservice-*.jar db migrate web.yml --include 1.3.1.consistency,1.4.0,1.5.0,1.6.0,1.7.0 | tee --append /dockstore_logs/webservice.out
+java -Ddw.database.user=postgres -Ddw.database.password="{{{ POSTGRES_DBPASSWORD }}}" -jar /home/dockstore-webservice-*.jar db migrate web.yml --include 1.3.1.consistency,1.4.0,1.5.0,1.6.0,1.7.0
 {{/DATABASE_GENERATED}}
 # this particular migration needs to run as postgres because only postgres can surrender ownership
 java -Ddw.database.user=postgres -Ddw.database.password="{{{ POSTGRES_DBPASSWORD }}}" -jar /home/dockstore-webservice-*.jar db migrate web.yml --include 1.7.0.relinquish
 # future migrations will start here and should be run as dockstore
-java -Ddw.database.user=dockstore -Ddw.database.password="{{{ DOCKSTORE_DBPASSWORD }}}" -jar /home/dockstore-webservice-*.jar db migrate web.yml --include 1.8.0,1.9.0,1.10.0,1.11.0,1.12.0,1.13.0 | tee --append /dockstore_logs/webservice.out
+java -Ddw.database.user=dockstore -Ddw.database.password="{{{ DOCKSTORE_DBPASSWORD }}}" -jar /home/dockstore-webservice-*.jar db migrate web.yml --include 1.8.0,1.9.0,1.10.0,1.11.0,1.12.0,1.13.0

templates/init_webservice.sh.template

@@ -2,6 +2,6 @@
 
 cd "$(dirname "$0")"
 
-java -XX:MaxRAMPercentage=50.0 -XX:+ExitOnOutOfMemoryError -jar /home/dockstore-webservice-*.jar server web.yml | tee --append /dockstore_logs/webservice.out
+java -XX:MaxRAMPercentage=50.0 -XX:+ExitOnOutOfMemoryError -jar /home/dockstore-webservice-*.jar server web.yml