Merge branch 'release/1.15.0'

Author: denis-yuen

.github/workflows/codeql.yml

@@ -0,0 +1,42 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "develop", hotfix/*, master, release/*, feature/** ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "develop", hotfix/*, master, release/* ]
+  schedule:
+    - cron: "30 8 * * 3"
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python', 'javascript' ]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v2
+        with:
+          languages: ${{ matrix.language }}
+          queries: +security-and-quality
+
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v2
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v2
+        with:
+          category: "/language:${{ matrix.language }}"

dockstore_launcher_config/compose.config

@@ -6,6 +6,7 @@
 "BITBUCKET_CLIENT_SECRET":"foobared",
 "CHECK_URL_EXISTS_ENDPOINT":"replaceme",
 "CHECK_URL_LAMBDA_VERSION":"n/a",
+"COLAB_IMPORT_URL":"replaceme",
 "COMPOSE_SETUP_VERSION":"foo",
 "CWL_PARSING_LAMBDA_VERSION":"n/a",
 "DATABASE_DOMAIN":"postgres",
@@ -33,13 +34,15 @@
 "GITHUB_APP_PRIVATE_KEY_FILE": "/replaceme",
 "GITHUB_CLIENT2_ID":"foobared",
 "GITHUB_CLIENT2_SECRET":"foobared",
+"GITHUB_CODESPACES_IMPORT_URL":"replaceme",
 "GITLAB_CLIENT_ID":"foobar",
 "GITLAB_CLIENT_SECRET":"foobar",
 "GOOGLE_CLIENT_ID":"potato",
 "GOOGLE_CLIENT_SECRET":"potato",
 "LOGSTASH":false,
 "LOGSTASH_HOST":"replaceme",
 "METRICS_BUCKET_NAME":"replaceme",
+"MYBINDER_IMPORT_URL":"replaceme",
 "NEXTFLOW_PARSING_LAMBDA_VERSION":"n/a",
 "ORCID_CLIENT_ID":"replaceme",
 "ORCID_CLIENT_SECRET":"replaceme",

install_bootstrap

@@ -1,4 +1,4 @@
-#!/usr/bin/env bash
+#!/usr/bin/env sh
 
 # Created by Solomon Shorser
 # Hacked by Denis Yuen

templates/init_migration.sh.template

@@ -12,4 +12,4 @@ java -Ddw.database.user=postgres -Ddw.database.password="{{{ POSTGRES_DBPASSWORD
 # 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 1.8.0,1.9.0,1.10.0,1.11.0,1.12.0,1.13.0,1.14.0
+java -Ddw.database.user=dockstore -Ddw.database.password="{{{ DOCKSTORE_DBPASSWORD }}}" -jar /home/dockstore-webservice-*.jar db migrate web.yml --include 1.8.0,1.9.0,1.10.0,1.11.0,1.12.0,1.13.0,1.14.0,1.15.0

templates/web.yml.template

@@ -112,7 +112,7 @@ database:
   # any properties specific to your JDBC driver:
   properties:
     charSet: UTF-8
-    hibernate.dialect: org.hibernate.dialect.PostgreSQL10Dialect
+    hibernate.dialect: org.hibernate.dialect.PostgreSQLDialect
     # create database as needed, disable in production
     hibernate.hbm2ddl.auto: validate
     hibernate.jdbc.batch_size: 30
@@ -142,8 +142,14 @@ database:
   logAbandonedConnections: true
   removeAbandonedTimeout: 5 minutes
 
-{{#LOGSTASH}}
 server:
+  applicationConnectors:
+    - type: custom-http
+      port: 8080
+  adminConnectors:
+    - type: http
+      port: 8001
+{{#LOGSTASH}}
   requestLog:
     type: classic
     timeZone: UTC
@@ -160,6 +166,9 @@ uiConfig:
   bdCatalystTerraImportUrl: {{ BD_CATALYST_TERRA_IMPORT_URL }}
   bdCatalystSevenBridgesImportUrl: {{ BD_CATALYST_SEVEN_BRIDGES_IMPORT_URL }}
   elwaziImportUrl:  {{ ELWAZI_IMPORT_URL }}
+  colabImportUrl: {{ COLAB_IMPORT_URL }}
+  mybinderImportUrl: {{ MYBINDER_IMPORT_URL }}
+  gitHubCodespacesImportUrl: {{ GITHUB_CODESPACES_IMPORT_URL }}
 
 
   gitHubAuthUrl: https://github.com/login/oauth/authorize
@@ -195,7 +204,6 @@ uiConfig:
   featuredContentUrl: {{ FEATURED_CONTENT_URL }}
   featuredNewsUrl: {{ FEATURED_NEWS_URL }}
 
-  composeSetupVersion: "{{ COMPOSE_SETUP_VERSION }}"
   deployVersion: "{{ DEPLOY_VERSION }}"
   cwlParsingLambdaVersion: {{ CWL_PARSING_LAMBDA_VERSION }}
   wdlParsingLambdaVersion: {{ WDL_PARSING_LAMBDA_VERSION }}