Merge pull request #2227 from broadinstitute/development

Release 1.92.1

Author: jlchang

Dockerfile

@@ -1,8 +1,8 @@
 # use SCP base Rails image, configure only project-specific items here
-FROM gcr.io/broad-singlecellportal-staging/rails-baseimage:2.3.0
+FROM gcr.io/broad-singlecellportal-staging/rails-baseimage:3.0.0
 
 # Set ruby version
-RUN bash -lc 'rvm --default use ruby-3.2.2'
+RUN bash -lc 'rvm --default use ruby-3.4.2'
 RUN bash -lc 'rvm rvmrc warning ignore /home/app/webapp/Gemfile'
 
 # Set up project dir, install gems, set up script to migrate database and precompile static assets on run

Gemfile

@@ -1,7 +1,7 @@
 source 'https://rubygems.org'
 git_source(:github) { |repo| "https://github.com/#{repo}.git" }
 
-ruby '3.2.2'
+ruby '3.4.2'
 
 # Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
 gem 'rails', '6.1.7.9'
@@ -29,7 +29,7 @@ gem 'sdoc', group: :doc
 # gem 'capistrano-rails', group: :development
 
 gem 'bootsnap', require: false
-gem 'minitest', '5.15.0'
+gem 'minitest'
 gem 'minitest-rails'
 gem 'minitest-reporters'
 
@@ -71,7 +71,6 @@ gem 'rack-brotli'
 gem 'time_difference'
 gem 'sys-filesystem', require: 'sys/filesystem'
 gem 'browser'
-gem 'ruby-prof'
 gem 'carrierwave', '~> 2.2'
 gem 'carrierwave-mongoid', :require => 'carrierwave/mongoid'
 gem 'uuid'
@@ -81,6 +80,14 @@ gem 'net-imap'
 gem 'net-pop'
 gem 'exponential-backoff'
 gem 'concurrent-ruby', '1.3.4'
+# gems removed from stdlib in 3.4
+gem 'bigdecimal'
+gem 'mutex_m'
+gem 'observer'
+gem 'ostruct'
+gem 'logger'
+gem 'benchmark'
+gem 'drb'
 
 group :development, :test do
   # Access an IRB console on exception pages or by using <%= console %> in views
@@ -93,6 +100,7 @@ group :development, :test do
   gem 'puma'
   gem 'rubocop', require: false
   gem 'rubocop-rails', require: false
+  gem 'csv'
 
   # Profiling
   gem 'rack-mini-profiler'

Gemfile.lock

@@ -99,6 +99,8 @@ GEM
       execjs
     base64 (0.2.0)
     bcrypt (3.1.16)
+    benchmark (0.4.0)
+    bigdecimal (3.1.9)
     bootsnap (1.13.0)
       msgpack (~> 1.2)
     brakeman (5.0.1)
@@ -129,6 +131,7 @@ GEM
     coffee-script-source (1.12.2)
     concurrent-ruby (1.3.4)
     crass (1.0.6)
+    csv (3.3.2)
     daemons (1.4.0)
     date (3.4.1)
     declarative (0.0.20)
@@ -146,9 +149,10 @@ GEM
       warden (~> 1.2.3)
     digest-crc (0.6.4)
       rake (>= 12.0.0, < 14.0.0)
-    docile (1.3.5)
+    docile (1.4.1)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
+    drb (2.2.1)
     dry-cli (0.7.0)
     easy_diff (1.0.0)
     erubi (1.13.1)
@@ -258,6 +262,7 @@ GEM
     listen (3.5.1)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
+    logger (1.6.6)
     loofah (2.24.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
@@ -277,7 +282,7 @@ GEM
     mime-types-data (3.2021.0225)
     mini_magick (4.12.0)
     mini_mime (1.1.5)
-    minitest (5.15.0)
+    minitest (5.25.5)
     minitest-hooks (1.5.0)
       minitest (> 5.3)
     minitest-rails (6.1.0)
@@ -317,6 +322,7 @@ GEM
     multi_json (1.15.0)
     multi_xml (0.6.0)
     multipart-post (2.3.0)
+    mutex_m (0.3.0)
     naturally (2.2.1)
     net-imap (0.5.6)
       date
@@ -329,18 +335,19 @@ GEM
       net-protocol
     netrc (0.11.0)
     nio4r (2.7.4)
-    nokogiri (1.18.3-arm64-darwin)
+    nokogiri (1.18.4-arm64-darwin)
       racc (~> 1.4)
-    nokogiri (1.18.3-x86_64-darwin)
+    nokogiri (1.18.4-x86_64-darwin)
       racc (~> 1.4)
-    nokogiri (1.18.3-x86_64-linux-gnu)
+    nokogiri (1.18.4-x86_64-linux-gnu)
       racc (~> 1.4)
     oauth2 (1.4.7)
       faraday (>= 0.8, < 2.0)
       jwt (>= 1.0, < 3.0)
       multi_json (~> 1.3)
       multi_xml (~> 0.5)
       rack (>= 1.2, < 3)
+    observer (0.1.2)
     omniauth (2.0.4)
       hashie (>= 3.4.6)
       rack (>= 1.6.2, < 3)
@@ -358,6 +365,7 @@ GEM
       omniauth (~> 2.0)
     orm_adapter (0.5.0)
     os (1.1.4)
+    ostruct (0.6.1)
     parallel (1.22.1)
     parser (3.1.2.1)
       ast (~> 2.4.1)
@@ -446,7 +454,6 @@ GEM
       activesupport (>= 4.2.0)
       rack (>= 1.1)
       rubocop (>= 1.7.0, < 2.0)
-    ruby-prof (1.7.0)
     ruby-progressbar (1.11.0)
     ruby-vips (2.2.1)
       ffi (~> 1.12)
@@ -473,13 +480,13 @@ GEM
       faraday (>= 0.17.5, < 3.a)
       jwt (>= 1.5, < 3.0)
       multi_json (~> 1.10)
-    simplecov (0.21.2)
+    simplecov (0.22.0)
       docile (~> 1.1)
       simplecov-html (~> 0.11)
       simplecov_json_formatter (~> 0.1)
-    simplecov-html (0.12.3)
+    simplecov-html (0.13.1)
     simplecov-lcov (0.8.0)
-    simplecov_json_formatter (0.1.3)
+    simplecov_json_formatter (0.1.4)
     sprockets (4.2.1)
       concurrent-ruby (~> 1.0)
       rack (>= 2.2.4, < 4)
@@ -489,7 +496,7 @@ GEM
       sprockets (>= 3.0.0)
     ssrf_filter (1.1.2)
     stackprof (0.2.17)
-    stringio (3.1.0)
+    stringio (3.1.5)
     swagger-blocks (3.0.0)
     sys-filesystem (1.4.1)
       ffi (~> 1.1)
@@ -541,9 +548,12 @@ PLATFORMS
   x86_64-darwin-20
   x86_64-darwin-21
   x86_64-darwin-23
+  x86_64-darwin-24
   x86_64-linux
 
 DEPENDENCIES
+  benchmark
+  bigdecimal
   bootsnap
   bootstrap-sass!
   brakeman
@@ -554,10 +564,12 @@ DEPENDENCIES
   carrierwave-mongoid
   coffee-rails
   concurrent-ruby (= 1.3.4)
+  csv
   daemons
   delayed_job
   delayed_job_mongoid
   devise
+  drb
   exponential-backoff
   factory_bot_rails
   flamegraph
@@ -573,22 +585,26 @@ DEPENDENCIES
   jquery-fileupload-rails
   jquery-rails
   listen
+  logger
   memory_profiler
-  minitest (= 5.15.0)
+  minitest
   minitest-hooks
   minitest-rails
   minitest-reporters
   mongoid
   mongoid-encrypted-fields
   mongoid-history
   mongoid_rails_migrations
+  mutex_m
   naturally
   nested_form!
   net-imap
   net-pop
   net-smtp
+  observer
   omniauth-google-oauth2
   omniauth-rails_csrf_protection
+  ostruct
   parallel
   puma
   rack-brotli
@@ -597,7 +613,6 @@ DEPENDENCIES
   rest-client
   rubocop
   rubocop-rails
-  ruby-prof
   ruby_native_statistics
   rubyzip
   sass-rails (>= 6)
@@ -619,7 +634,7 @@ DEPENDENCIES
   will_paginate_mongoid
 
 RUBY VERSION
-   ruby 3.2.2p53
+   ruby 3.4.2p28
 
 BUNDLED WITH
-   2.6.1
+   2.6.2

app/javascript/components/upload/upload-utils.js

@@ -111,7 +111,7 @@ export function findBundleChildren(file, files) {
       f.study_file_bundle_id
     ]
     return parentFields.includes(file._id) ||
-      file.study_file_bundle_id && parentFields.includes(file.study_file_bundle_id)
+      file.study_file_bundle_id && parentFields.includes(file.study_file_bundle_id) && f._id !== file._id
   })
 }
 

app/models/batch_api_client.rb

@@ -1,5 +1,3 @@
-# frozen_string_literal: true
-#
 # Wrapper around Google Batch API for submitting for submitting/reporting scp-ingest-service jobs
 class BatchApiClient
   extend ServiceAccountManager

bin/docker-compose-setup.sh

@@ -12,16 +12,18 @@ $0 [OPTION]
 -i  {IMAGE_TAG}  override default GCR image tag of development
 -p  {PORTAL_RAM_GB}  specify as integer the amount of RAM in GB for the single_cell container
 -v  {VITE_RAM_GB}  specify as integer the amount of RAM in GB for the single_cell_vite container
+-l  use a local copy of GCR_IMAGE (for testing build updates)
 -h  print this text
 EOF
 )
 
 DETACHED=""
 VITE_FRONTEND_SERVICE_WORKER_CACHE="false"
 IMAGE_TAG="development"
+LOCAL="false"
 export PORTAL_RAM_GB="6"
 export VITE_RAM_GB="2"
-while getopts "dchi:p:v:" OPTION; do
+while getopts "dchi:p:v:l" OPTION; do
 case $OPTION in
   d)
     echo "### SETTING DETACHED ###"
@@ -48,6 +50,9 @@ case $OPTION in
     echo "### SETTING VITE_RAM_GB TO $OPTARG ###"
     VITE_RAM_GB="$OPTARG"
     ;;
+  l)
+    LOCAL="true"
+    ;;
   *)
     echo "unrecognized option"
     echo "$usage"
@@ -66,9 +71,11 @@ CHANGED=$(git diff "$LOCAL_BRANCH" development --name-only -- Dockerfile)
 if [[ "$CHANGED" = "Dockerfile" ]]; then
   echo "### DOCKERFILE CHANGES DETECTED, BUILDING $GCR_IMAGE LOCALLY ###"
   docker build -t "$GCR_IMAGE" .
-else
+elif [[ "$LOCAL" = "false" ]]; then
   echo "### PULLING UPDATED IMAGE FOR $GCR_IMAGE ###"
   docker pull "$GCR_IMAGE"
+else
+  echo "### USING LOCAL COPY OF $GCR_IMAGE ###"
 fi
 echo "### STARTING SERVICES ###"
 VITE_FRONTEND_SERVICE_WORKER_CACHE="$VITE_FRONTEND_SERVICE_WORKER_CACHE" \

bin/run_tests.sh

@@ -29,29 +29,8 @@ RETURN_CODE=0
 THIS_DIR="$(cd "$(dirname "$BASH_SOURCE")"; pwd)"
 BASE_DIR="$(dirname $THIS_DIR)"
 
-function setup_burp_cert {
-  if [ -n "$BURP_PROXY" ]; then
-    # we will store Burp certificate here
-    local BURP_CERT="/usr/local/share/ca-certificates/burp.crt"
-
-    # fetch Burp certificate from Burp proxy localhost endpoint and store it into $BURP_CERT
-    curl -s --proxy "$BURP_PROXY" burp/cert | openssl x509 -inform DER -out "$BURP_CERT"
-
-    # update system-wide certificate store
-    update-ca-certificates
-
-    # override cacert store for httpclient package (used by Google libraries)
-    ln -sf "$BURP_CERT" /usr/local/rvm/gems/default/gems/httpclient-*/lib/httpclient/cacert.pem
-
-    # override cafile for Yarn (used during package fetching)
-    yarn config set cafile "$BURP_CERT" -g
-
-    # set http_proxy variable, which will make HTTP connections go through the Burp proxy
-    export http_proxy="$BURP_PROXY"
-  fi
-}
-
 export PASSENGER_APP_ENV=test
+export RUBYOPT=--disable-frozen-string-literal
 
 function clean_up {
   echo "Cleaning up..."
@@ -90,7 +69,6 @@ else
   rm -f "$TMP_PIDS_DIR/delayed_job.*.pid"
 fi
 
-setup_burp_cert
 clean_up
 
 echo "*** STARTING DELAYED_JOB for $PASSENGER_APP_ENV env ***"

db/seed/example_studies/human_milk_de_49k_cell/study_info.json

@@ -1,15 +1,15 @@
 {
   "study": {
-    "name": "Human milk - differential expression",
+    "name": "Human milk - differential expression Mar 2025 update",
     "description": "(Based on SCP1671) Human breast milk is a dynamic fluid that contains millions of cells, but their identities and phenotypic properties are poorly understood. We used single-cell RNA-seq (scRNA-seq) to characterize the transcriptomes of cells from human breast milk (hBM) across lactational time from 3 to 632 days postpartum in 15 donors. We find that the majority of cells in human breast milk are lactocytes, a specialized epithelial subset, and cell type frequencies shift over the course of lactation yielding greater epithelial diversity at later points. Analysis of lactocytes reveals a continuum of cell states characterized by transcriptional changes in hormone, growth factor, and milk production related pathways. Generalized additive models suggest that one sub-cluster, LC1 epithelial cells, increase as a function of time postpartum, daycare attendance, and the use of hormonal birth control. We identify several sub-clusters of macrophages in hBM that are enriched for tolerogenic functions, possibly playing a role in protecting the mammary gland during lactation. Our description of the cellular components of breast milk, their association with maternal-infant dyad metadata and quantification of alterations at the gene and pathways levels provides the first detailed longitudinal picture of human breast milk cells across lactational time. This work paves the way for future investigations of how a potential division of cellular labor and differential hormone regulation might be leveraged therapeutically to support healthy lactation and potentially aid in milk production.",
     "data_dir": "test"
   },
   "files": [
     {
       "type": "Metadata",
-      "filename": "MIT_milk_study_metadata.csv.gz",
+      "filename": "MIT_milk_study_metadata_Mar2025update.csv.gz",
       "use_metadata_convention": true,
-      "bucket_url": "gs://broad-singlecellportal-public/test/studies/SCP1671/MIT_milk_study_metadata.csv.gz"
+      "bucket_url": "gs://broad-singlecellportal-public/test/studies/SCP1671/MIT_milk_study_metadata_Mar2025update.csv.gz"
     },
     {
       "type": "Expression Matrix",