Merge pull request #2194 from broadinstitute/development

Release 1.89.0

Author: jlchang

Gemfile

@@ -4,7 +4,7 @@ git_source(:github) { |repo| "https://github.com/#{repo}.git" }
 ruby '3.2.2'
 
 # Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
-gem 'rails', '6.1.7.8'
+gem 'rails', '6.1.7.9'
 # Use SCSS for stylesheets
 gem 'sass-rails', '>= 6'
 # Use CoffeeScript for .coffee assets and views
@@ -40,6 +40,7 @@ gem 'googleauth'
 gem 'google-cloud-storage', require: 'google/cloud/storage'
 gem 'google-cloud-bigquery', require: 'google/cloud/bigquery'
 gem 'google-apis-lifesciences_v2beta', require: 'google/apis/lifesciences_v2beta'
+gem 'google-apis-batch_v1', require: 'google/apis/batch_v1'
 gem 'bootstrap-sass', :git => 'https://github.com/twbs/bootstrap-sass'
 gem 'font-awesome-sass', git: 'https://github.com/FortAwesome/font-awesome-sass'
 gem 'mongoid'
@@ -79,6 +80,7 @@ gem 'net-smtp'
 gem 'net-imap'
 gem 'net-pop'
 gem 'exponential-backoff'
+gem 'concurrent-ruby', '1.3.4'
 
 group :development, :test do
   # Access an IRB console on exception pages or by using <%= console %> in views

Gemfile.lock

@@ -32,60 +32,60 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    actioncable (6.1.7.8)
-      actionpack (= 6.1.7.8)
-      activesupport (= 6.1.7.8)
+    actioncable (6.1.7.9)
+      actionpack (= 6.1.7.9)
+      activesupport (= 6.1.7.9)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
-    actionmailbox (6.1.7.8)
-      actionpack (= 6.1.7.8)
-      activejob (= 6.1.7.8)
-      activerecord (= 6.1.7.8)
-      activestorage (= 6.1.7.8)
-      activesupport (= 6.1.7.8)
+    actionmailbox (6.1.7.9)
+      actionpack (= 6.1.7.9)
+      activejob (= 6.1.7.9)
+      activerecord (= 6.1.7.9)
+      activestorage (= 6.1.7.9)
+      activesupport (= 6.1.7.9)
       mail (>= 2.7.1)
-    actionmailer (6.1.7.8)
-      actionpack (= 6.1.7.8)
-      actionview (= 6.1.7.8)
-      activejob (= 6.1.7.8)
-      activesupport (= 6.1.7.8)
+    actionmailer (6.1.7.9)
+      actionpack (= 6.1.7.9)
+      actionview (= 6.1.7.9)
+      activejob (= 6.1.7.9)
+      activesupport (= 6.1.7.9)
       mail (~> 2.5, >= 2.5.4)
       rails-dom-testing (~> 2.0)
-    actionpack (6.1.7.8)
-      actionview (= 6.1.7.8)
-      activesupport (= 6.1.7.8)
+    actionpack (6.1.7.9)
+      actionview (= 6.1.7.9)
+      activesupport (= 6.1.7.9)
       rack (~> 2.0, >= 2.0.9)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.2.0)
-    actiontext (6.1.7.8)
-      actionpack (= 6.1.7.8)
-      activerecord (= 6.1.7.8)
-      activestorage (= 6.1.7.8)
-      activesupport (= 6.1.7.8)
+    actiontext (6.1.7.9)
+      actionpack (= 6.1.7.9)
+      activerecord (= 6.1.7.9)
+      activestorage (= 6.1.7.9)
+      activesupport (= 6.1.7.9)
       nokogiri (>= 1.8.5)
-    actionview (6.1.7.8)
-      activesupport (= 6.1.7.8)
+    actionview (6.1.7.9)
+      activesupport (= 6.1.7.9)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.1, >= 1.2.0)
-    activejob (6.1.7.8)
-      activesupport (= 6.1.7.8)
+    activejob (6.1.7.9)
+      activesupport (= 6.1.7.9)
       globalid (>= 0.3.6)
-    activemodel (6.1.7.8)
-      activesupport (= 6.1.7.8)
-    activerecord (6.1.7.8)
-      activemodel (= 6.1.7.8)
-      activesupport (= 6.1.7.8)
-    activestorage (6.1.7.8)
-      actionpack (= 6.1.7.8)
-      activejob (= 6.1.7.8)
-      activerecord (= 6.1.7.8)
-      activesupport (= 6.1.7.8)
+    activemodel (6.1.7.9)
+      activesupport (= 6.1.7.9)
+    activerecord (6.1.7.9)
+      activemodel (= 6.1.7.9)
+      activesupport (= 6.1.7.9)
+    activestorage (6.1.7.9)
+      actionpack (= 6.1.7.9)
+      activejob (= 6.1.7.9)
+      activerecord (= 6.1.7.9)
+      activesupport (= 6.1.7.9)
       marcel (~> 1.0)
       mini_mime (>= 1.1.0)
-    activesupport (6.1.7.8)
+    activesupport (6.1.7.9)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -97,6 +97,7 @@ GEM
     ast (2.4.2)
     autoprefixer-rails (10.2.4.0)
       execjs
+    base64 (0.2.0)
     bcrypt (3.1.16)
     bootsnap (1.13.0)
       msgpack (~> 1.2)
@@ -126,10 +127,10 @@ GEM
       coffee-script-source
       execjs
     coffee-script-source (1.12.2)
-    concurrent-ruby (1.3.3)
+    concurrent-ruby (1.3.4)
     crass (1.0.6)
     daemons (1.4.0)
-    date (3.3.4)
+    date (3.4.1)
     declarative (0.0.20)
     delayed_job (4.1.10)
       activesupport (>= 3.0, < 8.0)
@@ -150,7 +151,7 @@ GEM
       unf (>= 0.0.5, < 1.0.0)
     dry-cli (0.7.0)
     easy_diff (1.0.0)
-    erubi (1.13.0)
+    erubi (1.13.1)
     execjs (2.7.0)
     exponential-backoff (0.0.4)
     factory_bot (6.1.0)
@@ -186,6 +187,8 @@ GEM
     gibberish (2.1.1)
     globalid (1.2.1)
       activesupport (>= 6.1)
+    google-apis-batch_v1 (0.27.0)
+      google-apis-core (>= 0.11.0, < 2.a)
     google-apis-bigquery_v2 (0.54.0)
       google-apis-core (>= 0.11.0, < 2.a)
     google-apis-core (0.11.0)
@@ -235,7 +238,7 @@ GEM
     http-cookie (1.0.3)
       domain_name (~> 0.5)
     httpclient (2.8.3)
-    i18n (1.14.5)
+    i18n (1.14.7)
       concurrent-ruby (~> 1.0)
     image_processing (1.12.2)
       mini_magick (>= 4.9.5, < 5)
@@ -255,7 +258,7 @@ GEM
     listen (3.5.1)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
-    loofah (2.23.1)
+    loofah (2.24.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
     macaddr (1.7.2)
@@ -315,7 +318,7 @@ GEM
     multi_xml (0.6.0)
     multipart-post (2.3.0)
     naturally (2.2.1)
-    net-imap (0.4.13)
+    net-imap (0.5.5)
       date
       net-protocol
     net-pop (0.1.2)
@@ -325,12 +328,12 @@ GEM
     net-smtp (0.5.0)
       net-protocol
     netrc (0.11.0)
-    nio4r (2.7.3)
-    nokogiri (1.16.8-arm64-darwin)
+    nio4r (2.7.4)
+    nokogiri (1.18.2-arm64-darwin)
       racc (~> 1.4)
-    nokogiri (1.16.8-x86_64-darwin)
+    nokogiri (1.18.2-x86_64-darwin)
       racc (~> 1.4)
-    nokogiri (1.16.8-x86_64-linux)
+    nokogiri (1.18.2-x86_64-linux-gnu)
       racc (~> 1.4)
     oauth2 (1.4.7)
       faraday (>= 0.8, < 2.0)
@@ -365,7 +368,7 @@ GEM
     puma (5.6.9)
       nio4r (~> 2.0)
     racc (1.8.1)
-    rack (2.2.9)
+    rack (2.2.10)
     rack-brotli (1.1.0)
       brotli (>= 0.1.7)
       rack (>= 1.4)
@@ -375,33 +378,33 @@ GEM
       rack
     rack-proxy (0.6.5)
       rack
-    rack-test (2.1.0)
+    rack-test (2.2.0)
       rack (>= 1.3)
-    rails (6.1.7.8)
-      actioncable (= 6.1.7.8)
-      actionmailbox (= 6.1.7.8)
-      actionmailer (= 6.1.7.8)
-      actionpack (= 6.1.7.8)
-      actiontext (= 6.1.7.8)
-      actionview (= 6.1.7.8)
-      activejob (= 6.1.7.8)
-      activemodel (= 6.1.7.8)
-      activerecord (= 6.1.7.8)
-      activestorage (= 6.1.7.8)
-      activesupport (= 6.1.7.8)
+    rails (6.1.7.9)
+      actioncable (= 6.1.7.9)
+      actionmailbox (= 6.1.7.9)
+      actionmailer (= 6.1.7.9)
+      actionpack (= 6.1.7.9)
+      actiontext (= 6.1.7.9)
+      actionview (= 6.1.7.9)
+      activejob (= 6.1.7.9)
+      activemodel (= 6.1.7.9)
+      activerecord (= 6.1.7.9)
+      activestorage (= 6.1.7.9)
+      activesupport (= 6.1.7.9)
       bundler (>= 1.15.0)
-      railties (= 6.1.7.8)
+      railties (= 6.1.7.9)
       sprockets-rails (>= 2.0.0)
     rails-dom-testing (2.2.0)
       activesupport (>= 5.0.0)
       minitest
       nokogiri (>= 1.6)
-    rails-html-sanitizer (1.6.1)
+    rails-html-sanitizer (1.6.2)
       loofah (~> 2.21)
       nokogiri (>= 1.15.7, != 1.16.7, != 1.16.6, != 1.16.5, != 1.16.4, != 1.16.3, != 1.16.2, != 1.16.1, != 1.16.0.rc1, != 1.16.0)
-    railties (6.1.7.8)
-      actionpack (= 6.1.7.8)
-      activesupport (= 6.1.7.8)
+    railties (6.1.7.9)
+      actionpack (= 6.1.7.9)
+      activesupport (= 6.1.7.9)
       method_source
       rake (>= 12.2)
       thor (~> 1.0)
@@ -480,7 +483,7 @@ GEM
     sprockets (4.2.1)
       concurrent-ruby (~> 1.0)
       rack (>= 2.2.4, < 4)
-    sprockets-rails (3.5.1)
+    sprockets-rails (3.5.2)
       actionpack (>= 6.1)
       activesupport (>= 6.1)
       sprockets (>= 3.0.0)
@@ -493,11 +496,11 @@ GEM
     systemu (2.6.5)
     test-unit (3.4.1)
       power_assert
-    thor (1.3.1)
+    thor (1.3.2)
     tilt (2.0.10)
     time_difference (0.5.0)
       activesupport
-    timeout (0.4.1)
+    timeout (0.4.3)
     trailblazer-option (0.1.2)
     truncate_html (0.9.3)
     tzinfo (2.0.6)
@@ -519,7 +522,8 @@ GEM
     warden (1.2.9)
       rack (>= 2.0.9)
     webrick (1.8.2)
-    websocket-driver (0.7.6)
+    websocket-driver (0.7.7)
+      base64
       websocket-extensions (>= 0.1.0)
     websocket-extensions (0.1.5)
     will_paginate (3.3.0)
@@ -528,7 +532,7 @@ GEM
     will_paginate_mongoid (2.0.1)
       mongoid
       will_paginate (~> 3.0)
-    zeitwerk (2.6.16)
+    zeitwerk (2.7.1)
 
 PLATFORMS
   arm64-darwin-21
@@ -549,6 +553,7 @@ DEPENDENCIES
   carrierwave (~> 2.2)
   carrierwave-mongoid
   coffee-rails
+  concurrent-ruby (= 1.3.4)
   daemons
   delayed_job
   delayed_job_mongoid
@@ -558,6 +563,7 @@ DEPENDENCIES
   flamegraph
   font-awesome-sass!
   gibberish
+  google-apis-batch_v1
   google-apis-lifesciences_v2beta
   google-cloud-bigquery
   google-cloud-storage
@@ -587,7 +593,7 @@ DEPENDENCIES
   puma
   rack-brotli
   rack-mini-profiler
-  rails (= 6.1.7.8)
+  rails (= 6.1.7.9)
   rest-client
   rubocop
   rubocop-rails

README.md

@@ -122,7 +122,7 @@ about service accounts.  To export the credentials:
 	  * Editor (project level)
 	  * Cloud Datastore Owner
 	  * Storage Object Viewer
-	  * Genomics Service Agent
+	  * Batch Administrator
 	*  Select 'JSON' and export and save the key locally
 	*  Additionally, a 'read-only' service account is now used for streaming GCS assets to the client in some instances,
 	so create a second service account and set the role to 'Storage Object Viewer' (see READ-ONLY SERVICE ACCOUNT at the
@@ -134,7 +134,7 @@ about service accounts.  To export the credentials:
 	* Google Cloud APIs
 	* Google Cloud Billing API
 	* Google Cloud Storage JSON API
-	* Google Cloud Genomics API
+	* Google Cloud Batch API
 
 * **Registering your Service Account as a Terra user**: Once you have configured and booted your instance of the portal,
 you will need to register your service account as a Terra user in order to create a billing project and create studies.
@@ -279,8 +279,8 @@ OAUTH_CLIENT_SECRET variables are necessary for allowing Google user authenticat
 
 ### INGEST PIPELINE AND NETWORK ENVIRONMENT VARIABLES
 The Single Cell Portal handles ingesting data into MongoDB via an [ingest pipeline](https://github.com/broadinstitute/scp-ingest-pipeline)
-that runs via the Google Genomics API (also known as the Pipelines API, or PAPI).  This API should have been enabled as
-a previous step to this (see [DEPLOYING A PRIVATE INSTANCE](#local-development-or-deploying-a-private-instance)).
+that runs via the Google Batch API.  This API should have been enabled as a previous step to this (see 
+[DEPLOYING A PRIVATE INSTANCE](#local-development-or-deploying-a-private-instance)).
 
 In order for the ingest pipeline to connect to MongoDB, and in addition to the variables relating to MongoDB as described
 in [DOCKER RUN COMMAND ENVIRONMENT VARIABLES](#docker-run-command-environment-variables), there are two further environment

app/controllers/application_controller.rb

@@ -27,8 +27,8 @@ class ApplicationController < ActionController::Base
 
   rescue_from ActionController::InvalidAuthenticityToken, with: :invalid_csrf
 
-  def self.life_sciences_api_client
-    @@life_sciences_api_client ||= LifeSciencesApiClient.new
+  def self.batch_api_client
+    @@batch_api_client ||= BatchApiClient.new
   end
 
   def self.big_query_client