Merge branch 'main' into devices-text-changes

ComPlat · Aug 20, 2024 · ecc1265 · ecc1265
2 parents 9f78314 + dba38d7
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diff --git a/.devcontainer.json b/.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.
@@ -17,31 +14,52 @@
           "*.mdx": "markdown"
         },
         "editor.rulers": [100],
+        "editor.defaultFormatter": "esbenp.prettier-vscode",
         "editor.codeActionsOnSave": {
-          "source.fixAll.eslint": true,
-          "source.fixAll.markdownlint": true
+          "source.fixAll.eslint": "always",
+          "source.fixAll.markdownlint": "always"
         },
-        "cSpell.enableFiletypes": ["md", "mdx", "!js", "!json", "!jsonc"],
-        "cSpell.words": ["Chemotion", "helpdesk"],
-        "markdownlint.config": {
-          "MD033": { "allowed_elements": ["kbd"] }
+        "eslint.options": {
+          "extensions": [".js", ".jsx", ".md", ".mdx", ".ts", ".tsx"]
         },
-        "markdownlint.run": "onSave"
+        "eslint.validate": [
+          "markdown",
+          "mdx",
+          "javascript",
+          "javascriptreact",
+          "typescript",
+          "typescriptreact"
+        ],
+        "Workspace_Formatter.includePattern": ["*.mdx", "*.md"],
+        "cSpell.enableFiletypes": ["md", "mdx", "!js", "!json", "!jsonc"],
+        "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",
+        "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.

diff --git a/.eslintrc.json b/.eslintrc.json
@@ -1,15 +1,7 @@
 {
-  "env": {
-    "browser": true,
-    "es2021": true,
-    "node": true
-  },
-  "extends": ["plugin:react/recommended", "airbnb"],
-  "overrides": [],
+  "extends": ["plugin:@docusaurus/recommended"],
   "parserOptions": {
-    "ecmaVersion": "latest",
-    "sourceType": "module"
+    "ecmaVersion": "latest"
   },
-  "plugins": ["react"],
-  "rules": {}
+  "plugins": ["react", "frontmatter"]
 }
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -13,13 +13,23 @@ jobs:
 
       - uses: actions/setup-node@v4
         with:
+          node-version: 20
           cache: "npm"
 
+      - name: Download YT Thumbnails
+        run: |
+          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: Build
         id: build
         run: |
+          npm install -g npm
           npm install
-          npm run build --if-present
+          npm run build
 
       - name: Deploy
         if: steps.build.outcome == 'success' && github.ref == 'refs/heads/main' && !contains(github.event.head_commit.message, 'skip deploy')

diff --git a/docs/_old_pages/2020-01-31.md b/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.
diff --git a/docs/_old_pages/2020-02-25.md b/docs/_old_pages/2020-02-25.md
@@ -4,7 +4,7 @@ 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-nocookie.com/embed/EpJmuMFtvag" frameborder="0" allow="accelerometer; 
 autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowFullScreen></iframe>

diff --git a/docs/_old_pages/Newsroom.mdx b/docs/_old_pages/Newsroom.mdx
@@ -4,5 +4,3 @@ title: "Newsroom"
 ---
 
 This is the blog of the Chemotion Repository.
-
-
diff --git a/docs/_old_pages/native_installation.mdx b/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)

diff --git a/docs/_old_pages/review_glossary.mdx b/docs/_old_pages/review_glossary.mdx
@@ -7,7 +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).

diff --git a/docs/development/ci.mdx b/docs/development/ci.mdx
@@ -15,11 +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
 

diff --git a/docs/development/debugging.mdx b/docs/development/debugging.mdx
@@ -4,27 +4,22 @@ 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)
diff --git a/docs/development/environment.mdx b/docs/development/environment.mdx
@@ -3,7 +3,9 @@ title: Development Environment
 ---
 
 :::info
+
 [Contact us](/helpdesk) us if you're having trouble setting up your development environment.
+
 :::
 
 ## Prerequisites
@@ -20,15 +22,16 @@ This keeps your machine free of clutter, and more importantly,
 it can ensure consistent development environments across contributors (i.e., avoiding "works on my machine" scenarios).
 
 In the following you find guides for setting up a dockerized development environment for the Chemotion ELN on
-[Windows](#windows-heading-id), [Linux](#linux-heading-id), and [macOS](#macos-heading-id).
+[Windows](environment#windows), [Linux](environment#linux), and [macOS](environment#macos).
+
+## Windows
 
-## Windows {#windows-heading-id}
+:::important[Call to action]
 
-:::important Call to action
 The following instructions are tested on Windows 10 only.
 If you're on Windows 11, please consider contributing your experiences.
-You can propose additions / changes to this documentation by opening a pull request on
-<https://github.com/ComPlat/chemotion_saurus>. Thank you!
+You can propose additions / changes to this documentation by opening a pull request in its [repository](https://github.com/ComPlat/chemotion_saurus). Thank you!
+
 :::
 
 This guide will help you getting started developing with containers on Windows using `Docker Desktop` along with the [Windows Subsystem for Linux](https://learn.microsoft.com/en-us/windows/wsl/about) (referred to as `WSL` in the following).
@@ -75,9 +78,9 @@ You won't be able to run bash scripts from PowerShell.
 
 On your Windows machine, [open the `Ubuntu` terminal](https://devblogs.microsoft.com/commandline/a-guide-to-invoking-wsl/#comments).
 Next, start `Docker Desktop`. You can confirm that `Docker Desktop` is running by typing `docker --version` in the `Ubuntu` terminal.
-If you get a response you're now ready to run the ELN in a [Docker container](#eln-in-docker) (any IDE) or in a [Visual Studio Code devcontainer](#eln-in-devcontainer) (recommended!).
+If you get a response you're now ready to run the ELN in a [Docker container](#eln-in-docker-container) (any IDE) or in a [Visual Studio Code devcontainer](#eln-in-devcontainer) (recommended!).
 
-## Linux {#linux-heading-id}
+## Linux
 
 We assume that you're on a fresh installation of a Linux operating system, either on a physical or virtual machine.
 The instructions have been tested on 64-bit Ubuntu Focal 20.04 (LTS) and 22.04 (LTS).
@@ -86,34 +89,36 @@ The instructions have been tested on 64-bit Ubuntu Focal 20.04 (LTS) and 22.04 (
 
 #### Docker Engine
 
-Install Docker Engine according to <https://docs.docker.com/engine/install/ubuntu/#install-using-the-repository>,
-and make sure that non-root users can issue Docker commands: <https://docs.docker.com/engine/install/linux-postinstall/#manage-docker-as-a-non-root-user>.
+Install Docker Engine according to the [official instructions](https://docs.docker.com/engine/install/ubuntu/#install-using-the-repository),
+and make sure that non-root users can issue Docker commands by following the post-installation [instructions](https://docs.docker.com/engine/install/linux-postinstall/#manage-docker-as-a-non-root-user).
+
+You're now ready to run the ELN in a [Docker container](#eln-in-docker-container) (any IDE) or in a [Visual Studio Code devcontainer](#eln-in-devcontainer) (recommended!).
 
-You're now ready to run the ELN in a [Docker container](#eln-in-docker) (any IDE) or in a [Visual Studio Code devcontainer](#eln-in-devcontainer) (recommended!).
+## macOS
 
-## macOS {#macos-heading-id}
+:::important[Call to action]
 
-:::important Call to action
 We haven't extensively tested our containerized development environment on macOS.
 If you're on macOS, please consider contributing your experiences.
-You can propose additions / changes to this documentation by opening a pull request on
-<https://github.com/ComPlat/chemotion_saurus>. Thank you!
+You can propose additions / changes to this documentation by opening a pull request in its [repository](https://github.com/ComPlat/chemotion_saurus). Thank you!
+
 :::
 
-Install Docker (<https://docs.docker.com/desktop/install/mac-install/>)
-and run the ELN in a [Docker container](#eln-in-docker) (any IDE)
+[Install Docker](https://docs.docker.com/desktop/install/mac-install/)
+and run the ELN in a [Docker container](#eln-in-docker-container) (any IDE)
 or in a [Visual Studio Code devcontainer](#eln-in-devcontainer) (recommended!).
 
-Alternatively, we recommend setting up a Ubuntu virtual machine and following the [Linux installation](#linux-heading-id).
+Alternatively, we recommend setting up a Ubuntu virtual machine and following the [Linux installation](environment#linux).
 
-## ELN in a Docker container {#eln-in-docker}
+## ELN in Docker container
+
+:::info[Operating system requirements]
+
+Make sure you've followed the instructions for your operating system ([Windows](environment#windows), [Linux](environment#linux), [macOS](environment#macos)).
 
-:::caution operating system requirements
-Make sure you've followed the instructions for your operating system ([Windows](#windows-heading-id), [Linux](#linux-heading-id), [macOS](#macos-heading-id)).
 :::
 
-Start by cloning <https://github.com/ComPlat/chemotion_ELN>.
-The repository contains the ELN's source code and Docker configuration (`docker-compose.dev.yml`).
+Start by cloning the [repository](https://github.com/ComPlat/chemotion_ELN). It contains the ELN's source code and Docker configuration (`docker-compose.dev.yml`).
 
 From the root of the repository (i.e., `pwd` is `chemotion_ELN`),
 you can instantiate the development environment with
@@ -158,34 +163,36 @@ To stop the development environment (i.e., shut down all three containers) run
 docker compose -f docker-compose.dev.yml down
 ```
 
-## ELN in a Visual Studio Code devcontainer {#eln-in-devcontainer}
+## ELN in devcontainer
+
+:::info[Operating system requirements]
+
+Make sure you've followed the instructions for your operating system ([Windows](#windows), [Linux](#linux), [macOS](#macos)).
 
-:::caution operating system requirements
-Make sure you've followed the instructions for your operating system ([Windows](#windows-heading-id), [Linux](#linux-heading-id), [macOS](#macos-heading-id)).
 :::
 
-:::caution Windows Docker Desktop
+:::info[Windows Docker Desktop]
+
 If you're using Docker Desktop (opposed to the Docker Engine on Linux)
 make sure that Docker Desktop is running before starting the devcontainer.
+
 :::
 
 Visual Studio Code devcontainers allow you to run your entire development environment inside a Docker container.
-For more context visit <https://code.visualstudio.com/docs/devcontainers/containers>.
+For more context visit its [documentation](https://code.visualstudio.com/docs/devcontainers/container).
 
 ### Dependencies
 
 #### Visual Studio Code
 
-Install Visual Studio Code (referred to as `VSCode` in the following) on you operating system: <https://code.visualstudio.com>.
+Install [Visual Studio Code](https://code.visualstudio.com) (referred to as `VSCode` in the following) on you operating system.
 Note that if you're on Windows, please install VSCode on Windows, not on the Ubuntu system that's running under WSL.
 
-Once you've got VSCode running, install the `Dev Containers` extension (ms-vscode-remote.remote-containers):
-<https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers>.
+Once you've got VSCode running, install the `Dev Containers` extension [`ms-vscode-remote.remote-containers`](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers).
 
 ### Setup
 
-Start by cloning <https://github.com/ComPlat/chemotion_ELN>.
-The repository contains the ELN's source code as well as the configuration for the devcontainer (`.devcontainer/`).
+Start by cloning [the repository](https://github.com/ComPlat/chemotion_ELN). It contains the ELN's source code as well as the configuration for the devcontainer (`.devcontainer/`).
 
 Start VSCode from the root of the repository (i.e., `pwd` is `chemotion_ELN`), by running
 
@@ -208,7 +215,7 @@ development environment.
 
 ### Clean Docker
 
-Make sure that you're working with a clean Docker system: <https://docs.docker.com/config/pruning/>.
+Make sure that you're working with a clean Docker system by [pruning](https://docs.docker.com/config/pruning/) it.
 
 ### Remove `node_modules` directory