TPA-mix (#1873)

.devcontainer/devcontainer.json

@@ -53,11 +53,11 @@
   ],
   "postCreateCommand": [
     "/bin/bash",
-    ".devcontainer/post_create.sh"
+    "prepare-ruby-dev.sh"
   ],
   "remoteUser": "chemotion-dev", // see https: //aka.ms/vscode-remote/containers/non-root
   "shutdownAction": "stopCompose", // stop compose when quitting
-  "overrideCommand": true, // override the commands in the compose file
+  "overrideCommand": true, // The 'app' container (which vscode is using as the devontainer) dies, as soon as we are killing the rails server that is started in the 'app' container command. To prevent this we override the 'app' container command from the the compose file.
   "containerEnv": {
     "RAILS_ENV": "development"
   },

.dockerignore

@@ -2,6 +2,7 @@
 backup
 uploads
 public
+!/public/ontologies_default/
 .gitignore
 node_modules
 tmp

.eslintrc

@@ -20,6 +20,13 @@
     "no-relative-import-paths/no-relative-import-paths": [
       "error",
       { "allowSameFolder": false, "rootDir": "app/packs" }
+    ],
+    "max-len": [
+      "error",
+      {
+        "code": 120,
+        "ignoreComments": true
+      }
     ]
   },
   "settings": {

.github/workflows/ci.yml

@@ -21,11 +21,10 @@ jobs:
 
       - uses: ruby/setup-ruby@v1
         with:
-          ruby-version: '2.7.7'
+          ruby-version: '3.3.0'
 
       - name: install linting dependencies
-        # IMPORTANT: install rubocop first for pinning to take effect (`gem` doesn't resolve dependencies but simply installs gems in order)
-        run: gem install rubocop:1.37.1 pronto pronto-rubocop rubocop-rspec rubocop-rails rubocop-performance    # TODO: unpin rubocop once it's not breaking pronto anymore (as does rubocop:1.38.0)
+        run: gem install rubocop pronto pronto-rubocop rubocop-rspec rubocop-rails rubocop-performance
 
       - name: run Pronto
         run: pronto run -f github_status github_pr_review -c origin/${{ github.base_ref }}
@@ -49,7 +48,7 @@ jobs:
       run:
         shell: bash
 
-    container: complat/chemotion_eln_runner:v1.6.0-1
+    container: complat/chemotion_eln_runner:main
 
     services:
       postgres:

.gitignore

@@ -48,6 +48,8 @@
 /config/scifinder_n.yml
 /config/radar.yml
 
+/doc/*
+
 /node_modules
 
 /public/images/molecules/*
@@ -93,6 +95,8 @@
 !/public/ontologies/rxno.default.json
 !/public/ontologies/rxno.default.edited.json
 
+/public/data_type.json
+
 /uploads/*
 !/public/attachments/.keep
 
@@ -145,6 +149,7 @@
 aliasifyConfig.js
 /app/assets/javascripts/components/extra/*
 /app/packs/src/components/extra/*
+/app/packs/klasses.json
 
 # Backups folder
 backup/deploy_backup
@@ -189,3 +194,8 @@ public/sprite.png
 
 #svgeditor
 /public/svgedit
+
+!spec/fixtures/import/sample_import_template.xlsx
+
+# generic elements
+data/klasses.json

.nvmrc

@@ -1 +1 @@
-v14.21.3
+v18.19.1

.service-dependencies

@@ -1,4 +1,5 @@
 #syntax=v1
-CONVERTER=ComPlat/chemotion-converter-app@v0.9.0
+CONVERTER=ComPlat/chemotion-converter-app@v1.2.0
 KETCHER=ptrxyz/chemotion-ketchersvc@main
-SPECTRA=ComPlat/chem-spectra-app@0.12.0
+SPECTRA=ComPlat/chem-spectra-app@1.1.1
+NMRIUMWRAPPER=NFDI4Chem/nmrium-react-wrapper@v0.4.0

.tool-versions

@@ -1,2 +1,2 @@
-nodejs 14.21.3
-ruby 2.7.7
+nodejs 18.19.1
+ruby 2.7.8

.vscode/settings.json

@@ -0,0 +1,24 @@
+{
+    "sqltools.connections": [
+        {
+          "previewLimit": 50,
+          "server": "postgres",
+          "port": 5432,
+          "driver": "PostgreSQL",
+          "name": "development",
+          "database": "chemotion_dev",
+          "username": "postgres",
+          "password": ""
+        },
+        {
+          "previewLimit": 50,
+          "server": "postgres",
+          "port": 5432,
+          "driver": "PostgreSQL",
+          "name": "test",
+          "database": "chemotion_test",
+          "username": "postgres",
+          "password": ""
+        }
+      ],
+}

.vscode/tasks.json

@@ -14,6 +14,11 @@
       "type": "shell",
       "command": "RAILS_ENV=test $(which bundle) exec rails server -b 0.0.0.0 -p 3000"
     },
+    {
+      "label": "Rails - delayed job worker",
+      "type": "shell",
+      "command": "RAILS_ENV=development $(which bundle) exec rake jobs:work"
+    },
     {
       "label": "RSpec - all",
       "type": "shell",
@@ -40,4 +45,4 @@
       "command": "$(which bundle) exec rubocop -c .rubocop.yml -a ${file}",
     },
   ]
-}
+}

Dockerfile.chemotion-dev

@@ -6,15 +6,11 @@
 FROM --platform=linux/amd64 ubuntu:jammy
 
 ARG DEBIAN_FRONTEND=noninteractive
-ARG VRUBY=2.7.7
-ARG VNODE=14.21.3
-ARG VNODENEXT=16.16.0
-ARG ASDF_BRANCH=v0.11.3
 
 RUN set -xe  && apt-get update -yqqq --fix-missing && apt-get upgrade -y
 RUN apt update && apt-get install -yqq --fix-missing bash ca-certificates wget apt-transport-https git gpg\
       imagemagick libmagic-dev libmagickcore-dev libmagickwand-dev curl gnupg2 \
-      build-essential nodejs sudo postgresql-client libappindicator1 swig \
+      build-essential sudo postgresql-client libappindicator1 swig \
       gconf-service libasound2 libgconf-2-4 cmake \
       libnspr4 libnss3 libpango1.0-0 libxss1 xdg-utils tzdata libpq-dev \
       gtk2-engines-pixbuf \
@@ -25,7 +21,8 @@ RUN apt update && apt-get install -yqq --fix-missing bash ca-certificates wget a
       fonts-crosextra-caladea fonts-crosextra-carlito \
       fonts-dejavu fonts-dejavu-core fonts-dejavu-extra fonts-liberation2 fonts-liberation \
       fonts-linuxlibertine fonts-noto-core fonts-noto-extra fonts-noto-ui-core \
-      fonts-opensymbol fonts-sil-gentium fonts-sil-gentium-basic inkscape
+      fonts-opensymbol fonts-sil-gentium fonts-sil-gentium-basic inkscape \
+      libgtk2.0-0 libgtk-3-0 libgbm-dev libnotify-dev libxtst6 xauth xvfb
 RUN  wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add - \
     && echo "deb http://dl.google.com/linux/chrome/deb/ stable main" > /etc/apt/sources.list.d/google.list \
     && apt-get update -yqqq && apt-get -y install google-chrome-stable \
@@ -49,20 +46,10 @@ RUN mkdir /home/chemotion-dev/node_modules
 
 SHELL ["/bin/bash", "-c"]
 
-RUN git clone https://github.com/asdf-vm/asdf.git ~/.asdf --branch $ASDF_BRANCH
-
+# Even if asdf and the related tools are only installed by running run-ruby-dev.sh, we set the PATH variables here, so when we enter the container via docker exec, we have the path set correctly
 ENV ASDF_DIR=/home/chemotion-dev/.asdf
 ENV PATH=/home/chemotion-dev/.asdf/shims:/home/chemotion-dev/.asdf/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
 
-RUN asdf plugin add nodejs https://github.com/asdf-vm/asdf-nodejs.git
-RUN asdf install nodejs $VNODE
-RUN asdf install nodejs $VNODENEXT
-RUN asdf global nodejs $VNODE
-
-RUN asdf plugin add ruby https://github.com/asdf-vm/asdf-ruby.git
-RUN asdf install ruby $VRUBY
-RUN asdf global ruby $VRUBY
-
 RUN echo 'network-timeout 600000' > /home/chemotion-dev/.yarnrc
 # use node modules from outside the application directory
 RUN echo '--modules-folder /home/chemotion-dev/node_modules/' >> /home/chemotion-dev/.yarnrc

Dockerfile.github-ci

@@ -1,8 +1,9 @@
-FROM ptrxyz/chemotion:eln-1.5.0
+FROM ptrxyz/internal:eln-1.8.0-rc4
 ARG BRANCH=main
 RUN apt-get install -y --no-install-recommends --autoremove --fix-missing \
   build-essential\
-  openssh-server
+  openssh-server\
+  libgtk2.0-0 libgtk-3-0 libgbm-dev libnotify-dev libgconf-2-4 libnss3 libxss1 libasound2 libxtst6 xauth xvfb
 
 WORKDIR "/chemotion/app"
 

Gemfile

@@ -30,6 +30,7 @@ gem 'dotenv-rails', require: 'dotenv/rails-now'
 
 gem 'ed25519'
 
+gem 'faker', require: false
 gem 'faraday'
 gem 'faraday-follow_redirects'
 gem 'faraday-multipart'
@@ -60,7 +61,10 @@ gem 'kaminari'
 gem 'kaminari-grape'
 gem 'ketcherails', git: 'https://github.com/complat/ketcher-rails.git', branch: 'upgrade-to-rails-6'
 
+gem 'labimotion', '1.1.4'
+
 gem 'mimemagic', '0.3.10'
+gem 'mime-types'
 
 # locked to enforce latest version of net-scp. without lock net-ssh would be updated first which locks
 # out newer net-scp versions
@@ -88,9 +92,9 @@ gem 'pundit'
 
 gem 'rack'
 gem 'rack-cors', require: 'rack/cors'
-gem 'rails', '~> 6.1.7.3'
+gem 'rails', '~> 6.1.7.7'
 gem 'rdkit_chem', git: 'https://github.com/ptrxyz/rdkit_chem.git', branch: 'pk01'
-gem 'rinchi-gem', '1.0.1', git: 'https://git.scc.kit.edu/ComPlat/rinchi-gem.git'
+gem 'rinchi-gem', '1.0.1', git: 'https://github.com/ComPlat/rinchi-gem.git'
 gem 'rmagick'
 gem 'roo'
 gem 'rqrcode' # required for Barby to work but not listed as its dependency -_-
@@ -104,6 +108,8 @@ gem 'sassc-rails'
 gem 'scenic'
 gem 'schmooze'
 gem 'semacode', git: 'https://github.com/toretore/semacode.git', branch: 'master' # required for Barby but not listed...
+
+gem 'sentry-delayed_job'
 gem 'sentry-rails'
 gem 'sentry-ruby'
 gem 'shrine', '~> 3.0'
@@ -186,12 +192,13 @@ group :test do
   gem 'database_cleaner-active_record'
 
   gem 'factory_bot_rails'
-  gem 'faker'
 
   gem 'launchy'
 
   gem 'rspec-repeat'
 
+  gem 'shoulda-matchers'
+
   gem 'simplecov', require: false
   gem 'simplecov-lcov', require: false