diff --git a/astro.config.mts b/astro.config.mts index ba03f006e..80f01eacf 100644 --- a/astro.config.mts +++ b/astro.config.mts @@ -89,7 +89,6 @@ export default defineConfig({ { label: 'DataHUB', collapsed: true, - // autogenerate: { directory: 'datahub' }, items:[ 'datahub', { @@ -123,7 +122,28 @@ export default defineConfig({ label: 'ARC Commander', // Collapse the group by default. collapsed: true, - autogenerate: { directory: 'arc-commander' }, + items:[ + 'arc-commander', + { + label: 'Setup', + collapsed: false, + autogenerate: { directory: 'arc-commander/setup'}, + }, + 'arc-commander/before-we-start', + 'arc-commander/arc-commander-quick-start', + 'arc-commander/arc-commander-quick-start-expert', + { + label: 'Central Functions', + collapsed: false, + autogenerate: { directory: 'arc-commander/central-functions'}, + }, + { + label: 'ISA metadata', + collapsed: false, + autogenerate: { directory: 'arc-commander/isa'}, + }, + 'arc-commander/lfs', + ] }, { label: 'Swate', diff --git a/package-lock.json b/package-lock.json index 6b16982ce..89406e83f 100755 --- a/package-lock.json +++ b/package-lock.json @@ -3878,9 +3878,9 @@ } }, "node_modules/cross-spawn": { - "version": "7.0.3", - "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.3.tgz", - "integrity": "sha512-iRDPJKUPVEND7dHPO8rkbOnPpyDygcDFtWjpeWNCgy8WP2rXcxXL8TskReQl6OrB2G7+UJrags1q15Fudc7G6w==", + "version": "7.0.6", + "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.6.tgz", + "integrity": "sha512-uV2QOWP2nWzsy2aMp8aRibhi9dlzF5Hgh5SHaB9OiTGEyDTiJJyx0uy51QXdyWbtAHNua4XJzUKca3OzKUd3vA==", "license": "MIT", "dependencies": { "path-key": "^3.1.0", diff --git a/src/content/docs/arc-commander/arc-commander-quick-start-expert.md b/src/content/docs/arc-commander/arc-commander-quick-start-expert.md index d543732e6..de9feb19f 100644 --- a/src/content/docs/arc-commander/arc-commander-quick-start-expert.md +++ b/src/content/docs/arc-commander/arc-commander-quick-start-expert.md @@ -4,6 +4,8 @@ lastUpdated: 2023-01-27 authors: - dominik-brilhaus pagefind: false +sidebar: + order: 4.6 --- ## About this guide diff --git a/src/content/docs/arc-commander/arc-commander-quick-start.mdx b/src/content/docs/arc-commander/arc-commander-quick-start.mdx index c3735a29e..e668140fe 100644 --- a/src/content/docs/arc-commander/arc-commander-quick-start.mdx +++ b/src/content/docs/arc-commander/arc-commander-quick-start.mdx @@ -4,6 +4,8 @@ authors: - martin-kuhl - dominik-brilhaus lastUpdated: 2023-06-09 +sidebar: + order: 4.5 --- import NewARC from '@components/mdx/NewARC.mdx' @@ -14,7 +16,7 @@ In this guide we focus on how to use the [ARC Commander][def] to create your ARC ## Before we can start -☑️ Please [install ARC Commander](/nfdi4plants.knowledgebase/arc-commander/installation) +☑️ Please [install ARC Commander](/nfdi4plants.knowledgebase/arc-commander/setup/installation) ☑️ Find the command line on your system 💡 Consider reading about [ARC](/nfdi4plants.knowledgebase/core-concepts/arc) and the [ARC Commander][def] 💡 After concluding this quickstart, consider exploring the [ARC Commander manual][def] for a more detailed usage instruction. diff --git a/src/content/docs/arc-commander/before-we-start.mdx b/src/content/docs/arc-commander/before-we-start.mdx index eb95a962d..4fda2fdb4 100644 --- a/src/content/docs/arc-commander/before-we-start.mdx +++ b/src/content/docs/arc-commander/before-we-start.mdx @@ -1,10 +1,11 @@ --- -title: "Before we start" +title: Before we start lastUpdated: 2023-06-14 +sidebar: + order: 4 --- - -After the setup steps, you're all set and ready to start using the ARC Commander. 🎉 +After the setup, you're all set and ready to start using the ARC Commander. 🎉 :::tip We recommend trying the [ARC Commander QuickStart](/nfdi4plants.knowledgebase/arc-commander/arc-commander-quick-start) for your first steps with the ARC Commander. diff --git a/src/content/docs/arc-commander/branches.mdx b/src/content/docs/arc-commander/central-functions/branches.mdx similarity index 97% rename from src/content/docs/arc-commander/branches.mdx rename to src/content/docs/arc-commander/central-functions/branches.mdx index e946ff8e4..a26dece21 100644 --- a/src/content/docs/arc-commander/branches.mdx +++ b/src/content/docs/arc-commander/central-functions/branches.mdx @@ -1,8 +1,9 @@ --- title: "Working on an ARC branch" +sidebar: + order: 10 --- - ## Challenge - No direct access rights to the main branch (which can be handled via the [DataHUB](/nfdi4plants.knowledgebase/datahub)) or diff --git a/src/content/docs/arc-commander/config.mdx b/src/content/docs/arc-commander/central-functions/config.mdx similarity index 97% rename from src/content/docs/arc-commander/config.mdx rename to src/content/docs/arc-commander/central-functions/config.mdx index 550c00514..2aa726f4d 100644 --- a/src/content/docs/arc-commander/config.mdx +++ b/src/content/docs/arc-commander/central-functions/config.mdx @@ -1,6 +1,8 @@ --- title: Config User lastUpdated: 2022-12-13 +sidebar: + order: 9 --- diff --git a/src/content/docs/arc-commander/connect.mdx b/src/content/docs/arc-commander/central-functions/connect.mdx similarity index 96% rename from src/content/docs/arc-commander/connect.mdx rename to src/content/docs/arc-commander/central-functions/connect.mdx index d5d1004aa..ccf9ccdd2 100644 --- a/src/content/docs/arc-commander/connect.mdx +++ b/src/content/docs/arc-commander/central-functions/connect.mdx @@ -1,6 +1,8 @@ --- title: "Connect an ARC to the DataHUB" lastUpdated: 2022-12-13 +sidebar: + order: 7 --- In case you have not yet connected your local repository to a remote one, you can specify the remote repository with the flag `--repositoryaddress` or `-r` in combination with a URL + ".git", e.g., diff --git a/src/content/docs/arc-commander/get.mdx b/src/content/docs/arc-commander/central-functions/get.mdx similarity index 85% rename from src/content/docs/arc-commander/get.mdx rename to src/content/docs/arc-commander/central-functions/get.mdx index b0ca6c274..3c8dec731 100644 --- a/src/content/docs/arc-commander/get.mdx +++ b/src/content/docs/arc-commander/central-functions/get.mdx @@ -1,15 +1,17 @@ --- -title: "Clone an ARC from the DataHUB" +title: Clone an ARC from the DataHUB lastUpdated: 2022-12-20 authors: - martin-kuhl +sidebar: + order: 6 --- Using `arc get -r` followed by a URL + ".git" enables you to clone an already existing ARC as a local repository, e.g., ```bash -arc get -r https://github.com/nfdi4plants/ARC.git +arc get -r https://git.nfdi4plants.org/muehlhaus/ArcPrototype ``` :::tip diff --git a/src/content/docs/arc-commander/initialization.mdx b/src/content/docs/arc-commander/central-functions/initialization.mdx similarity index 91% rename from src/content/docs/arc-commander/initialization.mdx rename to src/content/docs/arc-commander/central-functions/initialization.mdx index 4a34fdb04..f08ac9f1d 100644 --- a/src/content/docs/arc-commander/initialization.mdx +++ b/src/content/docs/arc-commander/central-functions/initialization.mdx @@ -1,6 +1,8 @@ --- -title: "Initialize an ARC" +title: Initialize an ARC lastUpdated: 2022-12-13 +sidebar: + order: 5 --- - The basic ARC folder structure can be created using `arc init` diff --git a/src/content/docs/arc-commander/synchronization.mdx b/src/content/docs/arc-commander/central-functions/synchronization.mdx similarity index 96% rename from src/content/docs/arc-commander/synchronization.mdx rename to src/content/docs/arc-commander/central-functions/synchronization.mdx index 5e5f64b1d..bc161e5b7 100644 --- a/src/content/docs/arc-commander/synchronization.mdx +++ b/src/content/docs/arc-commander/central-functions/synchronization.mdx @@ -1,6 +1,8 @@ --- title: "Sychronize an ARC" lastUpdated: 2022-12-13 +sidebar: + order: 8 --- The command `arc sync` handles multiple operations for your ARC in one step. It will diff --git a/src/content/docs/arc-commander/isa.mdx b/src/content/docs/arc-commander/isa.mdx deleted file mode 100644 index 7d9148423..000000000 --- a/src/content/docs/arc-commander/isa.mdx +++ /dev/null @@ -1,12 +0,0 @@ ---- -title: "ISA Metadata" -lastUpdated: 2022-12-13 -sidebar: - badge: - text: wip - variant: note ---- - -TODO: Maybe use Starlight cards? - -The following pages shows how the ARC commander helps in metadata handling. diff --git a/src/content/docs/arc-commander/export.mdx b/src/content/docs/arc-commander/isa/export.mdx similarity index 98% rename from src/content/docs/arc-commander/export.mdx rename to src/content/docs/arc-commander/isa/export.mdx index ecc738843..8447e4202 100644 --- a/src/content/docs/arc-commander/export.mdx +++ b/src/content/docs/arc-commander/isa/export.mdx @@ -3,6 +3,8 @@ title: "Export ARC metadata" lastUpdated: 2022-12-20 authors: - martin-kuhl +sidebar: + order: 15 --- diff --git a/src/content/docs/arc-commander/isa-assay.mdx b/src/content/docs/arc-commander/isa/isa-assay.mdx similarity index 99% rename from src/content/docs/arc-commander/isa-assay.mdx rename to src/content/docs/arc-commander/isa/isa-assay.mdx index 381657850..56aa29c94 100644 --- a/src/content/docs/arc-commander/isa-assay.mdx +++ b/src/content/docs/arc-commander/isa/isa-assay.mdx @@ -1,6 +1,8 @@ --- title: "Assay" lastUpdated: 2022-12-13 +sidebar: + order: 13 --- ## Addition of assays diff --git a/src/content/docs/arc-commander/isa-investigation.mdx b/src/content/docs/arc-commander/isa/isa-investigation.mdx similarity index 99% rename from src/content/docs/arc-commander/isa-investigation.mdx rename to src/content/docs/arc-commander/isa/isa-investigation.mdx index 4713d600a..6ee3a7dcd 100644 --- a/src/content/docs/arc-commander/isa-investigation.mdx +++ b/src/content/docs/arc-commander/isa/isa-investigation.mdx @@ -1,6 +1,8 @@ --- title: "Investigation" lastUpdated: 2022-12-13 +sidebar: + order: 11 --- :::caution diff --git a/src/content/docs/arc-commander/isa-study.mdx b/src/content/docs/arc-commander/isa/isa-study.mdx similarity index 99% rename from src/content/docs/arc-commander/isa-study.mdx rename to src/content/docs/arc-commander/isa/isa-study.mdx index 9d911682c..2d9001c0d 100644 --- a/src/content/docs/arc-commander/isa-study.mdx +++ b/src/content/docs/arc-commander/isa/isa-study.mdx @@ -1,8 +1,8 @@ --- title: "Study" lastUpdated: 2022-12-13 -tableOfContents: - maxHeadingLevel: 4 +sidebar: + order: 12 --- :::caution diff --git a/src/content/docs/arc-commander/update.mdx b/src/content/docs/arc-commander/isa/isa-update.mdx similarity index 92% rename from src/content/docs/arc-commander/update.mdx rename to src/content/docs/arc-commander/isa/isa-update.mdx index 4f5b0090a..377598946 100644 --- a/src/content/docs/arc-commander/update.mdx +++ b/src/content/docs/arc-commander/isa/isa-update.mdx @@ -1,8 +1,9 @@ --- title: "Update ISA metadata" lastUpdated: 2022-12-21 +sidebar: + order: 14 --- - Users have the possibility to update the metadata in the isa.investigation.xlsx by filling it with metadata from the study and assay files in the respective subdirectories via the command ```bash diff --git a/src/content/docs/arc-commander/lfs.mdx b/src/content/docs/arc-commander/lfs.mdx index 2f6c24b2f..c758175bd 100644 --- a/src/content/docs/arc-commander/lfs.mdx +++ b/src/content/docs/arc-commander/lfs.mdx @@ -3,6 +3,8 @@ title: Large File Storage (LFS) lastUpdated: 2024-10-31 author: - dominik-brilhaus +sidebar: + order: 16 --- diff --git a/src/content/docs/arc-commander/access.mdx b/src/content/docs/arc-commander/setup/access.mdx similarity index 99% rename from src/content/docs/arc-commander/access.mdx rename to src/content/docs/arc-commander/setup/access.mdx index c6c4553b8..b77472b61 100644 --- a/src/content/docs/arc-commander/access.mdx +++ b/src/content/docs/arc-commander/setup/access.mdx @@ -5,6 +5,8 @@ author: - martin-kuhl - dominik-brilhaus - david-zimmer +sidebar: + order: 3 --- diff --git a/src/content/docs/arc-commander/installation-git.mdx b/src/content/docs/arc-commander/setup/installation-git.mdx similarity index 97% rename from src/content/docs/arc-commander/installation-git.mdx rename to src/content/docs/arc-commander/setup/installation-git.mdx index d9be27285..5a31938a0 100644 --- a/src/content/docs/arc-commander/installation-git.mdx +++ b/src/content/docs/arc-commander/setup/installation-git.mdx @@ -1,9 +1,12 @@ --- title: Installation of Git and Git LFS lastUpdated: 2023-11-24 +author: + - dominik-brilhaus +sidebar: + order: 1 --- - In order to use the ARC Commander, Git (version ≥ 2.32.0) and Git LFS must be installed on your computer. :::tip diff --git a/src/content/docs/arc-commander/installation.mdx b/src/content/docs/arc-commander/setup/installation.mdx similarity index 99% rename from src/content/docs/arc-commander/installation.mdx rename to src/content/docs/arc-commander/setup/installation.mdx index d39115f31..387bfe249 100644 --- a/src/content/docs/arc-commander/installation.mdx +++ b/src/content/docs/arc-commander/setup/installation.mdx @@ -1,6 +1,8 @@ --- title: "Installing the ARC Commander" lastUpdated: 2022-12-20 +sidebar: + order: 2 --- import { Steps } from '@astrojs/starlight/components'; import { Tabs, TabItem } from '@astrojs/starlight/components'; diff --git a/src/content/docs/git/git-syncing-recommendation.mdx b/src/content/docs/git/git-syncing-recommendation.mdx index c7197c1b6..895cd95b0 100644 --- a/src/content/docs/git/git-syncing-recommendation.mdx +++ b/src/content/docs/git/git-syncing-recommendation.mdx @@ -21,7 +21,7 @@ In DataPLANT tools and services, the individual sync steps are called "commit". ## Add a message to communicate your ARC's evolution We recommend adding a message that shortly summarizes, what you did since you last synced your ARC. -Commit messages can be added via [ARCitect's](/nfdi4plants.knowledgebase/arcitect) commit menu or via [ARC commander](/nfdi4plants.knowledgebase/arc-commander/synchronization). +Commit messages can be added via [ARCitect's](/nfdi4plants.knowledgebase/arcitect) commit menu or via [ARC commander](/nfdi4plants.knowledgebase/arc-commander/central-functions/synchronization). The following exemplifies Viola's commit messages along with the progress of her ARC: diff --git a/src/content/docs/git/git-troubleshooting.md b/src/content/docs/git/git-troubleshooting.md index 506643c95..3d70d52c5 100644 --- a/src/content/docs/git/git-troubleshooting.md +++ b/src/content/docs/git/git-troubleshooting.md @@ -15,8 +15,8 @@ authors: Some reasons, why we now sometimes run into git issues - Over the past years we asked users (e.g. during trainings) to install git with minium required guidance -- Even though more advanced tools (ARCitect) now bring their own git installation, there might still occur interferences with older installations -- There might also be issues of tools (e.g. ARCitect and ARC commander) or different versions of those tools handling git-related tasks a bit differently or more / less strict (e.g. things like `main` as the default branch) +- Even though more advanced tools ([ARCitect](/nfdi4plants.knowledgebase/arcitect/)) now bring their own git installation, there might still occur interferences with older installations +- There might also be issues of tools (e.g. [ARCitect](/nfdi4plants.knowledgebase/arcitect/) and [ARC commander](/nfdi4plants.knowledgebase/arc-commander/)) or different versions of those tools handling git-related tasks a bit differently or more / less strict (e.g. things like `main` as the default branch) - The current (versions of) tools were not really built for collaboration with many people on one ARC (at least not with default settings from DataHUB side). So common errors are related to merge conflicts (multiple users changing files) and divergent branches (e.g. between local and remote clones of the ARC). - Some behaviors are simply very use-case or setup specific and will in any case and even with the best tooling require some stewardship @@ -34,6 +34,7 @@ Some reasons, why we now sometimes run into git issues - On macOS: right-click ARC folder-->"Services"--> "New Terminal at Folder" - On windows: open folder via Explorer; type "cmd" or "powershell" into the address field on top of Explorer - On linux / macOS terminal: `cd path/to/ARC` +- From inside ARCitect: Tools -> Command Window 3. try some of the git commands and debugging below @@ -266,7 +267,7 @@ It usually helps to just retrieve new ones. If not, you might have to remove exi #### Authenticate the computer -Option 1: [via ARC Commander](/nfdi4plants.knowledgebase/arc-commander/access) +Option 1: [via ARC Commander](/nfdi4plants.knowledgebase/arc-commander/setup/access) Option 2: "by hand" 1. Login to the [DataHUB](https://git.nfdi4plants.org/) diff --git a/src/content/docs/git/git-working-with-branches.mdx b/src/content/docs/git/git-working-with-branches.mdx index d8cfebdea..402535186 100644 --- a/src/content/docs/git/git-working-with-branches.mdx +++ b/src/content/docs/git/git-working-with-branches.mdx @@ -25,6 +25,6 @@ import ARCitectBranches from '../arcitect/arcitect-branches.mdx' ## ARC Commander -import ARCCommanderBranches from '../arc-commander/branches.mdx' +import ARCCommanderBranches from '../arc-commander/central-functions/branches.mdx' diff --git a/src/content/docs/vault/faqs.md b/src/content/docs/vault/faqs.md index 4271e999a..beb5ab5fb 100644 --- a/src/content/docs/vault/faqs.md +++ b/src/content/docs/vault/faqs.md @@ -98,7 +98,7 @@ Why do I get the error `'arc' is not recognized as an internal or external comma Your machine cannot find your ARC commander executable. Possible reasons are that you have not yet installed the ARC commander or that the `arc` executable was not added to your path. -Please carefully retry the [ARC Commander setup](/nfdi4plants.knowledgebase/arc-commander/installation). +Please carefully retry the [ARC Commander setup](/nfdi4plants.knowledgebase/arc-commander/setup/installation). If this does not do the trick, please follow these steps towards debugging (on Windows): @@ -106,7 +106,7 @@ If this does not do the trick, please follow these steps towards debugging (on W 2. Next, execute `path` to check wether the folder (e.g. `C:\Programs\ArcCommander`) appears in your path. 3. Adapt the user's path (not admin) -:bulb: If you do not have admin rights on the computer, please open the settings "Edit environment variables for your account" and follow steps described in the [ARC Commander setup](/nfdi4plants.knowledgebase/arc-commander/installation). +:bulb: If you do not have admin rights on the computer, please open the settings "Edit environment variables for your account" and follow steps described in the [ARC Commander setup](/nfdi4plants.knowledgebase/arc-commander/setup/installation).