Merge pull request #7979 from scinote-eln/develop

October 2024 Release

.gitignore

@@ -95,3 +95,7 @@ public/marvin4js-license.cxl
 
 /app/assets/builds/*
 !/app/assets/builds/.keep
+
+# Ignore automatically generated js-routes files.
+/app/javascript/routes.js
+/app/javascript/routes.d.ts

.travis.yml

@@ -13,6 +13,7 @@ before_install:
   - curl -L https://github.com/docker/compose/releases/download/${DOCKER_COMPOSE_VERSION}/docker-compose-linux-x86_64 > docker-compose
   - chmod +x docker-compose
   - sudo mv docker-compose /usr/local/bin
+  - sudo chown --recursive 1000 .
   - make docker-ci
 script:
   - make tests-ci

Dockerfile

@@ -1,4 +1,4 @@
-FROM ruby:3.2.2-bookworm
+FROM ruby:3.2-bookworm
 MAINTAINER SciNote <info@scinote.net>
 
 # additional dependecies
@@ -20,21 +20,26 @@ RUN apt-get update -qq && \
   fonts-wqy-microhei \
   fonts-wqy-zenhei \
   libfile-mimeinfo-perl \
-  chromium-driver \
+  chromium \
+  chromium-sandbox \
   yarnpkg && \
   ln -s /usr/lib/x86_64-linux-gnu/libvips.so.42 /usr/lib/x86_64-linux-gnu/libvips.so && \
   rm -rf /var/lib/apt/lists/*
 
 ENV PATH=/usr/share/nodejs/yarn/bin:$PATH
 
-RUN yarn add puppeteer@npm:puppeteer-core 
+RUN yarn add puppeteer@npm:puppeteer-core@^22.15.0
 
 ENV BUNDLE_PATH /usr/local/bundle/
 
 # create app directory
 ENV APP_HOME /usr/src/app
 ENV PATH $APP_HOME/bin:$PATH
 RUN mkdir $APP_HOME
+RUN adduser --uid 1000 scinote
+RUN chown scinote:scinote $APP_HOME
+USER scinote
+ENV CHROMIUM_PATH=$APP_HOME/bin/chromium
 WORKDIR $APP_HOME
 
 CMD rails s -b 0.0.0.0

Dockerfile.production

@@ -1,5 +1,5 @@
 # Building stage
-FROM ruby:3.2.2-bookworm AS builder
+FROM ruby:3.2-bookworm AS builder
 
 RUN rm -f /etc/apt/apt.conf.d/docker-clean; echo 'Binary::apt::APT::Keep-Downloaded-Packages "true";' > /etc/apt/apt.conf.d/keep-cache
 RUN \
@@ -23,7 +23,7 @@ COPY . $APP_HOME
 RUN rm -f $APP_HOME/config/application.yml $APP_HOME/production.env
 WORKDIR $APP_HOME
 RUN \
-  --mount=target=$APP_HOME/tmp/bundle,type=cache \
+  --mount=target=/usr/src/app/tmp/bundle,type=cache \
   bundle config set without 'development test' && \
   bundle config set path '/usr/src/app/tmp/bundle' && \
   bundle install --jobs `nproc` && \
@@ -34,14 +34,14 @@ RUN \
 
 RUN \
   --mount=type=cache,target=/usr/local/share/.cache/yarn/v6,sharing=locked \
-  --mount=type=cache,target=$APP_HOME/node_modules,sharing=locked \
+  --mount=type=cache,target=/usr/src/app/node_modules,sharing=locked \
   DATABASE_URL=postgresql://postgres@db/scinote_production \
   SECRET_KEY_BASE=dummy \
   DEFACE_ENABLED=true \
-  bash -c "rake assets:precompile && rake deface:precompile"
+  bash -c "rake assets:precompile && rake deface:precompile && rm -rf ./tmp/cache"
 
 # Final stage
-FROM ruby:3.2.2-bookworm AS runner
+FROM ruby:3.2-bookworm AS runner
 MAINTAINER SciNote <info@scinote.net>
 
 RUN rm -f /etc/apt/apt.conf.d/docker-clean; echo 'Binary::apt::APT::Keep-Downloaded-Packages "true";' > /etc/apt/apt.conf.d/keep-cache
@@ -76,6 +76,7 @@ RUN \
   libvips42 \
   graphviz \
   chromium \
+  chromium-sandbox \
   libfile-mimeinfo-perl \
   yarnpkg && \
   /usr/share/nodejs/yarn/bin/yarn add puppeteer@npm:puppeteer-core@^22.15.0 && \
@@ -88,6 +89,8 @@ RUN \
   --mount=type=cache,target=/var/lib/apt,sharing=locked \
   touch /etc/build-${BUILD_TIMESTAMP} && \
   DEBIAN_FRONTEND=noninteractive \
+  apt-get remove -y *-dev && \
+  apt-get autoremove -y && \
   apt-get update -qq && \
   apt-get upgrade -y && \
   rm -rf /var/lib/apt/lists/*
@@ -98,7 +101,10 @@ ENV GEM_HOME=$APP_HOME/vendor/bundle/ruby/3.2.0
 ENV PATH=$GEM_HOME/bin:$PATH
 ENV BUNDLE_APP_CONFIG=.bundle
 
-COPY --from=builder $APP_HOME $APP_HOME
+RUN adduser --uid 1000 scinote
+USER scinote
+
+COPY --from=builder --chown=scinote:scinote $APP_HOME $APP_HOME
 
 WORKDIR $APP_HOME
 

Gemfile

@@ -2,7 +2,7 @@
 
 source 'http://rubygems.org'
 
-ruby '3.2.2'
+ruby '~> 3.2.2'
 
 gem 'activerecord-session_store'
 gem 'bootsnap', require: false
@@ -62,6 +62,7 @@ gem 'logging', '~> 2.0.0'
 gem 'nested_form_fields'
 gem 'nokogiri', '~> 1.16.5' # HTML/XML parser
 gem 'noticed'
+gem 'oj'
 gem 'rails_autolink', '~> 1.1', '>= 1.1.6'
 gem 'rgl' # Graph framework for project diagram calculations
 gem 'roo', '~> 2.10.0' # Spreadsheet parser
@@ -81,9 +82,6 @@ gem 'aws-sdk-lambda'
 gem 'aws-sdk-rails'
 gem 'aws-sdk-s3'
 gem 'delayed_job_active_record'
-gem 'devise-async',
-    git: 'https://github.com/mhfs/devise-async.git',
-    branch: 'devise-4.x'
 gem 'image_processing'
 gem 'img2zpl', git: 'https://github.com/scinote-eln/img2zpl'
 gem 'rufus-scheduler'
@@ -94,6 +92,7 @@ gem 'graphviz'
 
 gem 'cssbundling-rails'
 gem 'jsbundling-rails'
+gem 'js-routes'
 
 gem 'tailwindcss-rails', '~> 2.4'
 

Gemfile.lock

@@ -5,14 +5,6 @@ GIT
     sneaky-save (0.1.3)
       activerecord (>= 3.2.0)
 
-GIT
-  remote: https://github.com/mhfs/devise-async.git
-  revision: 177f6363a002f7ff28f1d289c8cab7ad8d9cb8c5
-  branch: devise-4.x
-  specs:
-    devise-async (0.10.2)
-      devise (>= 4.0)
-
 GIT
   remote: https://github.com/scinote-eln/canaid
   revision: bba1b817d1c9b0c7e0440a83d0f62848aabc0a1b
@@ -105,9 +97,9 @@ GEM
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.1, >= 1.2.0)
-    active_model_serializers (0.10.13)
-      actionpack (>= 4.1, < 7.1)
-      activemodel (>= 4.1, < 7.1)
+    active_model_serializers (0.10.14)
+      actionpack (>= 4.1)
+      activemodel (>= 4.1)
       case_transform (>= 0.2)
       jsonapi-renderer (>= 0.1.1.beta1, < 0.3)
     activejob (7.0.8.4)
@@ -203,14 +195,15 @@ GEM
       erubi (>= 1.0.0)
       rack (>= 0.9.0)
       rouge (>= 1.0.0)
+    bigdecimal (3.1.8)
     bindata (2.5.0)
     binding_of_caller (1.0.0)
       debug_inspector (>= 0.0.1)
     bootsnap (1.16.0)
       msgpack (~> 1.2)
     brakeman (6.1.2)
       racc
-    builder (3.2.4)
+    builder (3.3.0)
     bullet (7.0.7)
       activesupport (>= 3.0.0)
       uniform_notifier (~> 1.11)
@@ -324,7 +317,7 @@ GEM
       railties (>= 5)
     down (5.4.1)
       addressable (~> 2.8)
-    erubi (1.12.0)
+    erubi (1.13.0)
     et-orbi (1.2.11)
       tzinfo
     execjs (2.8.1)
@@ -372,22 +365,24 @@ GEM
     httparty (0.21.0)
       mini_mime (>= 1.0.0)
       multi_xml (>= 0.5.2)
-    i18n (1.14.5)
+    i18n (1.14.6)
       concurrent-ruby (~> 1.0)
     i18n-js (3.9.2)
       i18n (>= 0.6.6)
     image_processing (1.12.2)
       mini_magick (>= 4.9.5, < 5)
       ruby-vips (>= 2.0.17, < 3)
     iniparse (1.5.0)
-    jbuilder (2.11.5)
+    jbuilder (2.13.0)
       actionview (>= 5.0.0)
       activesupport (>= 5.0.0)
     jmespath (1.6.2)
     jquery-rails (4.5.1)
       rails-dom-testing (>= 1, < 3)
       railties (>= 4.2.0)
       thor (>= 0.14, < 2.0)
+    js-routes (2.2.8)
+      railties (>= 4)
     jsbundling-rails (1.1.1)
       railties (>= 6.0.0)
     json (2.6.3)
@@ -441,8 +436,7 @@ GEM
     mime-types-data (3.2023.0218.1)
     mini_magick (4.12.0)
     mini_mime (1.1.5)
-    mini_portile2 (2.8.7)
-    minitest (5.23.1)
+    minitest (5.25.1)
     msgpack (1.7.1)
     multi_json (1.15.0)
     multi_test (1.1.0)
@@ -463,13 +457,13 @@ GEM
     net-smtp (0.4.0.1)
       net-protocol
     newrelic_rpm (9.2.2)
-    nio4r (2.7.0)
-    nokogiri (1.16.5)
+    nio4r (2.7.3)
+    nokogiri (1.16.7)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
-    nokogiri (1.16.5-arm64-darwin)
+    nokogiri (1.16.7-arm64-darwin)
       racc (~> 1.4)
-    nokogiri (1.16.5-x86_64-linux)
+    nokogiri (1.16.7-x86_64-linux)
       racc (~> 1.4)
     noticed (1.6.3)
       http (>= 4.0.0)
@@ -481,7 +475,10 @@ GEM
       rack (>= 1.2, < 4)
       snaky_hash (~> 2.0)
       version_gem (~> 1.1)
-    omniauth (2.1.1)
+    oj (3.16.6)
+      bigdecimal (>= 3.0)
+      ostruct (>= 0.2)
+    omniauth (2.1.2)
       hashie (>= 3.4.6)
       rack (>= 2.2.3)
       rack-protection
@@ -495,9 +492,9 @@ GEM
     omniauth-rails_csrf_protection (1.0.1)
       actionpack (>= 4.2)
       omniauth (~> 2.0)
-    omniauth-saml (2.1.0)
-      omniauth (~> 2.0)
-      ruby-saml (~> 1.12)
+    omniauth-saml (2.2.1)
+      omniauth (~> 2.1)
+      ruby-saml (~> 1.17)
     omniauth_openid_connect (0.7.1)
       omniauth (>= 1.9, < 3)
       openid_connect (~> 2.2)
@@ -515,6 +512,7 @@ GEM
       validate_url
       webfinger (~> 2.0)
     orm_adapter (0.5.0)
+    ostruct (0.6.0)
     overcommit (0.60.0)
       childprocess (>= 0.6.3, < 5)
       iniparse (~> 1.4)
@@ -545,7 +543,7 @@ GEM
       pry (>= 0.10.4)
     psych (3.3.4)
     public_suffix (5.0.1)
-    puma (6.4.2)
+    puma (6.4.3)
       nio4r (~> 2.0)
     raabro (1.4.0)
     racc (1.8.1)
@@ -561,8 +559,9 @@ GEM
       faraday-follow_redirects
       json-jwt (>= 1.11.0)
       rack (>= 2.1.0)
-    rack-protection (3.0.6)
-      rack
+    rack-protection (3.2.0)
+      base64 (>= 0.1.0)
+      rack (~> 2.2, >= 2.2.4)
     rack-test (2.1.0)
       rack (>= 1.3)
     rails (7.0.8.4)
@@ -827,6 +826,7 @@ DEPENDENCIES
   image_processing
   img2zpl!
   jbuilder
+  js-routes
   jsbundling-rails
   json-jwt
   json_matchers
@@ -839,6 +839,7 @@ DEPENDENCIES
   newrelic_rpm
   nokogiri (~> 1.16.5)
   noticed
+  oj
   omniauth (~> 2.1)
   omniauth-azure-activedirectory-v2
   omniauth-linkedin-oauth2
@@ -897,4 +898,4 @@ RUBY VERSION
    ruby 3.2.2p53
 
 BUNDLED WITH
-   2.4.10
+   2.5.11

Makefile

@@ -22,13 +22,13 @@ heroku:
 	@echo "Set environment variables, DATABASE_URL, RAILS_SERVE_STATIC_FILES, RAKE_ENV, RAILS_ENV, SECRET_KEY_BASE"
 
 docker:
-	@docker-compose build
+	@docker-compose --progress plain build
 
 docker-ci:
 	@docker-compose --progress plain build web
 
 docker-production:
-	@docker-compose -f docker-compose.production.yml build --build-arg BUILD_TIMESTAMP=$(BUILD_TIMESTAMP)
+	@docker-compose --progress plain -f docker-compose.production.yml build --build-arg BUILD_TIMESTAMP=$(BUILD_TIMESTAMP)
 
 config-production:
 ifeq (production.env,$(wildcard production.env))

Rakefile

@@ -5,3 +5,5 @@ require File.expand_path('../config/application', __FILE__)
 
 Rails.application.load_tasks
 Doorkeeper::Rake.load_tasks
+# Update js-routes file before javascript build
+task 'javascript:build' => 'js:routes:typescript'

VERSION

@@ -1 +1 @@
-1.36.2.2
+1.37.0

app/assets/javascripts/repositories/repository_datatable.js

@@ -317,9 +317,7 @@ var RepositoryDatatable = (function(global) {
 
       checkAvailableColumns();
 
-      RepositoryDatatableRowEditor.switchRowToEditMode(row);
-
-      changeToEditMode();
+      RepositoryDatatableRowEditor.switchRowToEditMode(row, changeToEditMode);
     });
   }
 
@@ -692,6 +690,7 @@ var RepositoryDatatable = (function(global) {
       },
       rowCallback: function(row, data) {
         $(row).attr('data-editable', data.recordEditable);
+        $(row).attr('data-info-url', data.recordInfoUrl);
         $(row).attr('data-manage-stock-url', data.manageStockUrl);
         // Get row ID
         let rowId = data.DT_RowId;
@@ -1003,10 +1002,8 @@ var RepositoryDatatable = (function(global) {
       $(TABLE_ID).find('.repository-row-edit-icon').remove();
 
       rowsSelected.forEach(function(rowNumber) {
-        RepositoryDatatableRowEditor.switchRowToEditMode(TABLE.row('#' + rowNumber));
+        RepositoryDatatableRowEditor.switchRowToEditMode(TABLE.row('#' + rowNumber), changeToEditMode);
       });
-
-      changeToEditMode();
     })
     .on('click', '#assignRepositoryRecords', function(e) {
       e.preventDefault();