Commit 27cc7a9d authored by Alexander Kirbis's avatar Alexander Kirbis
Browse files

update for user guide

parent 20af219e
......@@ -2,6 +2,7 @@
Contents:
- [Introduction]()
- [Quick start guide](#quick-start-guide)
- [Windows/Linux installation](#windowslinux-installation)
- [MacOS installation](#macos-installation)
......@@ -38,7 +39,7 @@ The quick start guide describes how to set up the necessary tools to access Data
## Windows/Linux installation
- open the Windows PowerShell with administrator rights and install the Windows subsystem for Linux (WSL) and the Linux distribution Ubuntu with the following command:
- open the Windows PowerShell with administrator rights and install the Windows subsystem for Linux (WSL) and the Linux distribution Ubuntu with the following command (a system restart is required to finalize the installation):
```
wsl --install -d Ubuntu
......@@ -60,7 +61,7 @@ sudo apt-get upgrade
sudo apt-get install git-lfs
```
- then, download the latest release of arcCommander and add the executable to a directory in your PATH with this series of commands:
- execute the following series of commands to (a) check if a directory exists where executable files will be stored, (b) download the latest release of arcCommander, (c) make the downloaded file executable, and (d) refresh the current shell environment to make the arc executable available independent of your current working directory:
```
mkdir -p ~/bin
......@@ -130,11 +131,12 @@ You should see the following or similar message:
- go to the [DataHUB webpage](https://gitlab.nfdi4plants.de/)
- klick on the "Sign In" button in the top right corner. You will be asked to chose an identity provider and enter your login credentials
- when logged in, you can create new projects, manage your existing projects, and share your projects with colleagues
- generate an access token (User settings > Access Tokens) with write permissions, which will be used as a password when pushing your local ARC to the DataHUB
- generate an access token (User preferences > Access Tokens) with write permissions (check the box 'write_repository'), which will be used as a password when pushing your local ARC to the DataHUB. The token will be displayed only once, so make sure to save it somewhere.
## Creating and managing ARCs
- The ARC file structure is generated on your local computer by using the arcCommander through the Linux shell. All neccessary commands to create and manage ARCs are detailed [here](arc_cheatsheet.md/#reference-sheet-for-arccommander).
- The arcCommander will create and edit the ARC in your current working directory. Make sure to make a fresh directory and change to it before creating files with the arcCommander.
- To push your local ARCs to the DataHUB, first create an empty project on the [DataHUB webpage](https://gitlab.nfdi4plants.de/). Then, use the commands to synchronize your ARC with DataHUB, as detailed in the [arcCommander reference sheet](arc_cheatsheet.md/#synchronize-arcs-with-datahub).
## Metadata recording with SWATE
......@@ -312,7 +314,7 @@ On the next page, choose a name for your ARC, set the visibility level to "priva
### Create an access token
For authorization when uploading files to the DataHUB you need to create an access token. To do so, klick on your avatar in the top right corner, go to "User settings", and klick on "Access Tokens" in the list on the left side. Enter a name of your access token and check the box next to "write repository"
For authorization when uploading files to the DataHUB you need to create an access token. To do so, klick on your avatar in the top right corner, go to "User preferences", and klick on "Access Tokens" in the list on the left side. Enter a name of your access token and check the box next to "write repository"
![first_arc_04](images/first_arc_04.png)
......@@ -384,7 +386,7 @@ git commit -m "initial commit"
and push the local ARC to the DataHUB
```
git push -u origin master
git push -u origin main
```
When pushing, you will be asked for your username and your password. You can find out your user name by clicking on your avatar in the top-right corner of the DataHUB homepage (the name behind the @ is your username). As a password you can use the access token that you created [earlier](#create-an-access-token).
......@@ -427,7 +429,7 @@ The workflow of uploading changes of your local ARC to the DataHUB will always b
1. Add the changes you made to the staging index using `git add`
2. Commit the changes to the local copy of your ARC with a message that describes what was done using `git commit -m "your message here"`
3. Push the changes to the remote copy of your ARC on DataHUB using `git push -u origin master`
3. Push the changes to the remote copy of your ARC on DataHUB using `git push -u origin main`
More infos about how to synchronize your local ARC with the DataHUB can be found in the [arcCommander reference sheet](arc_cheatsheet.md).
......
......@@ -103,7 +103,7 @@ To add changes of your local ARC to the remote copy on DataHUB, the following co
| ---------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `git add .` | Adds changes you made locally to the staging index. The `.` at the end adds all files within the ARC, but files and directories can also be specified by their path. |
| `git commit -m "<commit message>"` | Adds the staged changes to the local copy of the repository. The commit message will be displayed publicly. |
| `git push -u origin master` | Uploads your local changes to the remote ARC. You will be asked for your DataHUB user name and a password. The password can be generated on the DataHUB web page under edit profile > access tokens. Read and write access is needed for uploading changes. |
| `git push -u origin main` | Uploads your local changes to the remote ARC. You will be asked for your DataHUB user name and a password. The password can be generated on the DataHUB web page under edit profile > access tokens. Read and write access is needed for uploading changes. |
DataHUB is able to handle files with a total size of up to 1 Gb with the above commands. Files that exceed this limit and persistent files in general, like raw data or large images, can be uploaded using the large file storage (LFS) system. To use LFS, git-lfs needs to be installed on the client side. Ubuntu users can install it with `sudo apt-get install git-lfs`, for other operating systems check https://git-lfs.github.com/.
......
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