Merge branch 'main' into fix-data_types

.devcontainer.json

@@ -2,9 +2,6 @@
 // https://github.com/microsoft/vscode-dev-containers/tree/v0.195.0/containers/javascript-node
 {
   "name": "Docusaurus",
-  // Update 'VARIANT' to pick a Node version: 16, 14, 12.
-  // Append -bullseye or -buster to pin to an OS version.
-  // Use -bullseye variants on local arm64/Apple Silicon.
   "image": "mcr.microsoft.com/devcontainers/javascript-node",
 
   // Configure tool-specific properties.
@@ -17,34 +14,52 @@
           "*.mdx": "markdown"
         },
         "editor.rulers": [100],
-        "[markdown]": {
-          "editor.defaultFormatter": "esbenp.prettier-vscode"
+        "editor.defaultFormatter": "esbenp.prettier-vscode",
+        "editor.codeActionsOnSave": {
+          "source.fixAll.eslint": "always",
+          "source.fixAll.markdownlint": "always"
         },
-        "[javascript]": {
-          "editor.defaultFormatter": "esbenp.prettier-vscode"
+        "eslint.options": {
+          "extensions": [".js", ".jsx", ".md", ".mdx", ".ts", ".tsx"]
         },
+        "eslint.validate": [
+          "markdown",
+          "mdx",
+          "javascript",
+          "javascriptreact",
+          "typescript",
+          "typescriptreact"
+        ],
+        "Workspace_Formatter.includePattern": ["*.mdx", "*.md"],
         "cSpell.enableFiletypes": ["md", "mdx", "!js", "!json", "!jsonc"],
-        "cSpell.words": ["Chemotion", "helpdesk"],
-        "markdownlint.config": {
-          "MD033": { "allowed_elements": ["kbd"] }
-        },
-        "markdownlint.run": "onSave"
+        "cSpell.words": [
+          "Chemotion",
+          "helpdesk",
+          "Labimotion",
+          "fortawesome",
+          "fontawesome",
+          "subcomponent",
+          "wellplate"
+        ],
+        "cSpell.suggestionMenuType": "quickFix"
       },
 
       // Add the IDs of extensions you want installed when the container is created.
       "extensions": [
         "dbaeumer.vscode-eslint",
         "streetsidesoftware.code-spell-checker",
-        "DavidAnson.vscode-markdownlint",
-        "esbenp.prettier-vscode"
+        "esbenp.prettier-vscode",
+        "franneck94.workspace-formatter"
       ]
     }
   },
-
   // Use 'forwardPorts' to make a list of ports inside the container available locally.
   "forwardPorts": [3000],
 
-  // Use 'postCreateCommand' to run commands after the container is created.
+  // Use 'updateContentCommand' to run commands after the container is created and before the project is cloned.
+  "updateContentCommand": "npm install -g npm",
+
+  // Use 'postCreateCommand' to run commands after the project has been cloned into the container.
   "postCreateCommand": "npm install",
 
   // Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.

.eslintrc.json

@@ -0,0 +1,7 @@
+{
+  "extends": ["plugin:@docusaurus/recommended"],
+  "parserOptions": {
+    "ecmaVersion": "latest"
+  },
+  "plugins": ["react", "frontmatter"]
+}

.github/workflows/build.yml

@@ -1,53 +1,38 @@
 name: chemotion_saurus GitHub Actions
 
 on:
-  workflow_dispatch:
   push:
-    branches: [main]
 
 jobs:
-  build:
-    if: ${{ true }}
+  build_deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
-      - uses: actions/cache@v2
+      - uses: actions/setup-node@v4
         with:
-          path: build
-          key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-gems-
+          node-version: 20
+          cache: "npm"
 
-      - name: Build
-        env:
-          ALGOLIA_SEARCH_API_KEY: ${{ secrets.ALGOLIA_SEARCH_API_KEY }}
-          ALGOLIA_APP_ID: ${{ secrets.ALGOLIA_APP_ID }}
-          INDEX_NAME: ${{ secrets.INDEX_NAME }}
+      - name: Download YT Thumbnails
         run: |
-          npm i
-          npm run build --if-present
+          for file in $(grep -roP 'youtube-nocookie.com/embed/.{11}' docs | rev | cut -d / -f 1 | rev); do
+            if [ ! -f "static/img/yt_thumbnails/$file.jpg" ]; then
+              wget -O "static/img/yt_thumbnails/$file.jpg" "https://img.youtube.com/vi/$file/hqdefault.jpg" || wget -O "static/img/yt_thumbnails/$file.jpg" "https://img.youtube.com/vi/$file/0.jpg"
+            fi
+          done
 
-      - name: Upload build artifacts
-        uses: actions/upload-artifact@v2
-        with:
-          name: public
-          path: build
-
-  deploy:
-    if: "!contains(github.event.commits[0].message, 'skip deploy')"
-    runs-on: ubuntu-latest
-    needs: build
-    steps:
-      - name: Download build artifacts
-        uses: actions/download-artifact@v2
-        with:
-          name: public
-          path: public
+      - name: Build
+        id: build
+        run: |
+          npm install -g npm
+          npm install
+          npm run build
 
-      - name: Setup ssh and deploy2
+      - name: Deploy
+        if: steps.build.outcome == 'success' && github.ref == 'refs/heads/main' && !contains(github.event.head_commit.message, 'skip deploy')
         env:
           SSH_PRIVATE_KEY: ${{ secrets.SSH_PRIVATE_KEY }}
         run: |
@@ -62,4 +47,4 @@ jobs:
           touch ~/.ssh/known_hosts
           ssh-keyscan github.com >> ~/.ssh/known_hosts
           chmod 600 ~/.ssh/known_hosts
-          rsync -e "ssh -o StrictHostKeyChecking=no" -az --delete ./public/ docusaurus@eln.chemotion.net:chemotion_saurus/.
+          rsync -e "ssh -o StrictHostKeyChecking=no" -az --delete ./build/ saurus@chemotion.net:docs/chemotion_saurus/.

README.md

@@ -51,3 +51,16 @@ npm run serve
 ![code status](https://github.com/ComPlat/chemotion_saurus/actions/workflows/build.yml/badge.svg)
 
 The website is deployed with GitHub Actions [here](https://github.com/ComPlat/chemotion_saurus/blob/aa6fe5cc1ade8517f855a7df1ef4f6d648c67f26/.github/workflows/build.yml#L40).
+
+
+## Acknowledgments
+
+This project has been funded by the **[DFG]**.
+
+[![DFG Logo]][DFG]
+
+
+Funded by the [Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)](https://www.dfg.de/) under the [National Research Data Infrastructure – NFDI4Chem](https://nfdi4chem.de/) – Projektnummer **441958208** since 2020.
+
+[DFG]: https://www.dfg.de/en/
+[DFG Logo]: https://chemotion.net/img/logos/DFG_logo.png

docs/_old_pages/2020-01-31.md

@@ -5,13 +5,13 @@ author: Nicole Jung
 ---
 
 <img
-  src={require('/img/310120.png').default}
-  alt="select authors"
+src={require('/img/310120.png').default}
+alt="select authors"
 />
 
 For new submissions: please ensure that you add yourself as author and not only as contributor which is set as default.
 The change of the procedure applies to the tab to initialize the publication and review process.
 
 We introduced this procedure to ensure that one is able to add data on behalf of others. A requirement for a listing as
-author is the registration in the chemotion repository. If you use this function, please take care that all authors
+author is the registration in the Chemotion repository. If you use this function, please take care that all authors
 agreed to be mentioned.

docs/_old_pages/2020-02-16.md

@@ -7,5 +7,5 @@ author: Nicole Jung
 See the new You-Tube video to learn how to add collaborators to your profile. Collaborators should be created to enable
 the addition of additional authors to data publications in the publishing process:
 
-<iframe width="640" height="360" src="https://www.youtube.com/embed/mNL0REP76Gc" frameborder="0" allow="accelerometer; 
+<iframe width="640" height="360" src="https://www.youtube-nocookie.com/embed/mNL0REP76Gc" frameborder="0" allow="accelerometer; 
 autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowFullScreen></iframe>

docs/_old_pages/2020-02-25.md

@@ -4,9 +4,9 @@ title: "Data Assignment in Chemotion Repository"
 author: Nicole Jung
 ---
 
-This video shows the basics to add data to the right place in the repository chemotion.
+This video shows the basics to add data to the right place in the Chemotion repository.
 
-<iframe width="640" height="360" src="https://www.youtube.com/embed/EpJmuMFtvag" frameborder="0" allow="accelerometer; 
+<iframe width="640" height="360" src="https://www.youtube-nocookie.com/embed/EpJmuMFtvag" frameborder="0" allow="accelerometer; 
 autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowFullScreen></iframe>
 
 Another video, part B, will be provided soon. Part B will then give some examples included to a demo of the repository.

docs/_old_pages/Newsroom.mdx

@@ -4,5 +4,3 @@ title: "Newsroom"
 ---
 
 This is the blog of the Chemotion Repository.
-
-

docs/_old_pages/native_installation.mdx

@@ -6,7 +6,9 @@ slug: native_installation
 ---
 
 :::info
+
 Documentation and processes are being reworked and improved at the moment. It may happen that you miss information. If you face problems, please let us know, we are there to support you. You may contact the [helpdesk](https://helpdesk.nfdi4chem.de) if you plan to install or test Chemotion.
+
 :::
 
 This documentation detailed an installation solution example of the the chemotion_ELN system and associated services on Ubuntu servers with NGINX as web server and Phusion-passenger as app server.
@@ -24,7 +26,9 @@ The code for the web-application (server- and client- sides) and the workers is
 For a few users, all this components can be installed on a single machine (2 cpu s, 4GB memory) using the [installation script](https://github.com/ComPlat/chemotion_ELN/blob/development-5/scripts/install_production.sh) that will set up all these components and basic configurations.
 
 :::info
+
 Use a sudo user, not root, to run the script!
+
 :::
 
 ![architecture_ELN](/img/architecture_ELN_base.svg)

docs/_old_pages/review_glossary.mdx

@@ -1,5 +1,4 @@
 ---
-id: review_glossary
 title: Review Glossary
 author: Nicole Jung
 ---
@@ -8,7 +7,7 @@ author: Nicole Jung
 
 All review reports and comments are given with the initials of the referee (e.g. "NJ:"). Hints for a better understanding of the referees' comments are given in brackets "[hint]". Please refer to the following descriptions if _short comments_ are given in your review reports:
 
-<!--truncate-->
+{/* truncate */}
 
 - **"amount"**: Please check the given amount of your starting materials/reagents in table and text for inaccuracies [text-table]. Brackets may give an indication where the inconsistency was detected.
 - **"analytics-format"**: Please check the formatting of your analytic contents. Please have a look at the How-To page ["Details for analytics"](details_analytics).

docs/development/architecture.mdx

@@ -1,5 +1,4 @@
 ---
-id: architecture
 title: Application Architecture
 ---
 

docs/development/ci.mdx

@@ -1,5 +1,4 @@
 ---
-id: ci
 title: Continuous Integration
 ---
 
@@ -16,11 +15,10 @@ Our CI is configured in this following workflow [file](https://github.com/ComPla
 
 Because of large Ruby and npm dependencies, the CI is running inside a Docker container with prebuilt libraries
 in order to speed up CI runs.
-Our Docker image for CI is hosted at <https://hub.docker.com/r/complat/complat-ubuntu-runner>.
+Our Docker image for CI is hosted at [here](https://hub.docker.com/r/complat/complat-ubuntu-runner).
 The CI image is built from the following [Dockerfile](https://github.com/ComPlat/chemotion_ELN/blob/main/Dockerfile.github-ci).
 
-We're using a PostgreSQL container to run the database alongside the ELN application:
-<https://hub.docker.com/_/postgres>.
+We're using a [PostgreSQL container](https://hub.docker.com/_/postgres) to run the database alongside the ELN application.
 
 ## Troubleshooting
 

docs/development/debugging.mdx

@@ -1,31 +1,25 @@
 ---
-id: debugging
 title: Debugging
 ---
 
 ## JavaScript
 
-You can use your browser's developer tools:
-
-<https://developer.mozilla.org/en-US/docs/Learn/Common_questions/What_are_browser_developer_tools>
+You can use your browser's [developer tools](https://developer.mozilla.org/en-US/docs/Learn/Common_questions/What_are_browser_developer_tools).
 
 ## Ruby (Rails application)
 
 Below are two options for "live"-debugging Ruby code (i.e., while the application is running).
 
 ### Pry
 
-Install [`pry`](https://github.com/pry/pry) and set `binding.pry` breakpoints in your Ruby code:
-<https://docs.gitlab.com/ee/development/pry_debugging.html>. Pry should work independently of your IDE.
+Install [`pry`](https://github.com/pry/pry) and set `binding.pry` breakpoints to [debug](https://docs.gitlab.com/ee/development/pry_debugging.html) your Ruby code. Pry should work independently of your IDE.
 
 ### Visual Studio Code
 
 If you're using the Visual Studio Code IDE, you can use it's visual / GUI debugger.
-The configuration depends on your local setup, however, following these instructions should get you started fine:
-
-<https://andyv.me/til/debug-a-ruby-on-rails-server-using-vs-code/>.
+The configuration depends on your local setup, however, [these instructions](https://andyv.me/til/debug-a-ruby-on-rails-server-using-vs-code/) could help you get started.
 
 In case debugging doesn't work yet, have a look at the following resources to fine-tune your configuration:
 
-<https://github.com/rubyide/vscode-ruby/blob/main/docs/debugger.md>
-<https://github.com/Microsoft/vscode-recipes/blob/2174a750102a76142378ea08dbbb4a576dc6d1d5/debugging-Ruby-on-Rails/README.md>
+0. [Rubyide Debugger](https://github.com/rubyide/vscode-ruby/blob/main/docs/debugger.md)
+1. [VSCode recipe for Ruby on Rails](https://github.com/Microsoft/vscode-recipes/blob/2174a750102a76142378ea08dbbb4a576dc6d1d5/debugging-Ruby-on-Rails/README.md)