Home Fundamentals Research Data Management FAIR Data Principles Metadata Ontologies Data Sharing Data Publications Data Management Plan Version Control & Git Public Data Repositories Persistent Identifiers Electronic Lab Notebooks (ELN) DataPLANT Implementations Annotated Research Context User Journey ARC specification ARC Commander QuickStart QuickStart (Experts) Swate QuickStart Walk-through Best Practices For Data Annotation DataHUB DataPLAN Ontology Service Landscape ARC Commander Manual Setup Git Installation ARC Commander Installation Windows MacOS Linux ARC Commander DataHUB Access Before we start Central Functions Initialize Clone Connect Synchronize Configure Branch ISA Metadata Functions ISA Metadata Investigation Study Assay Update Export ARCitect Manual Installation - Windows Installation - macOS Installation - Linux QuickStart QuickStart - Videos ARCmanager Manual What is the ARCmanager? How to use the ARCmanager Swate Manual QuickStart - Videos Annotation tables Building blocks Building Block Types Adding a Building Block Filling cells with ontology terms Advanced Term Search File Picker Templates Contribute Templates ISA-JSON DataHUB Manual Overview User Settings Generate a Personal Access Token (PAT) Projects Panel ARC Panel Forks Working with files ARC Settings ARC Wiki Groups Panel Create a new user group CQC Pipelines & validation Find and use ARC validation packages Data publications Passing Continuous Quality Control Submitting ARCs with ARChigator Track publication status Use your DOIs Guides ARC User Journey Create your ARC ARC Commander QuickStart ARC Commander QuickStart (Experts) ARCitect QuickStart Annotate Data in your ARC Annotation Principles ISA File Types Best Practices For Data Annotation Swate QuickStart Swate Walk-through Share your ARC Register at the DataHUB DataPLANT account Invite collaborators to your ARC Sharing ARCs via the DataHUB Work with your ARC Using ARCs with Galaxy Computational Workflows CWL Introduction CWL runner installation CWL Examples CWL Metadata Recommended ARC practices Syncing recommendation Keep files from syncing to the DataHUB Working with large data files Adding external data to the ARC ARCs in Enabling Platforms Publication to ARC Troubleshooting Git Troubleshooting Contribute Swate Templates Knowledge Base Teaching Materials Events 2023 Nov: CEPLAS PhD Module Oct: CSCS CEPLAS Start Your ARC Sept: MibiNet CEPLAS Start Your ARC July: RPTU Summer School on RDM July: Data Steward Circle May: CEPLAS Start Your ARC Series Start Your ARC Series - Videos Events 2024 TRR175 Becoming FAIR CEPLAS ARC Trainings – Spring 2024 MibiNet CEPLAS DataPLANT Tool-Workshops TRR175 Tutzing Retreat Frequently Asked Questions

Frequently Asked Questions

last updated at 2023-11-30

πŸ’‘ Please click the β–Ά to the left to see the answers.

Annotated Research Context
Where should the metadata annotation be made. In the same documents containing the data?

No. The metadata describing the data is collected in a separate xlsx-file – called isa.assay.xlsx – that resides in the parent folder of the dataset.

πŸ’‘ For more information, check out our guides on annotating data in your ARC.

Is it necessary to fill in the empty fields in the investigation-file manually?
No. Although it is possible to fill out the workbook manually, we recommend using ARC Commander or ARCitect to add this metadata.
Where in the ARC can I store "external" data?

Research projects rarely start out of the blue. Rather every project builds on previous findings and published datasets. To properly re-use and reference such a dataset, we recommend to add a study to your ARC. Every study by default comes with four parts:

└── <StudyName> β”œβ”€β”€ README.md β”œβ”€β”€ isa.study.xlsx β”œβ”€β”€ protocols └── resources

ARC Commander
Are there any recommendations for titles or identifiers?
Avoid using spaces in the identifier. Use underscores and capital letters instead. There are no specific restrictions regarding the title. Although it is possible to fill in the workbook manually, we recommend using ARC Commander to add this metadata.
How often should I sync my ARC?
We would not want to recommend a fixed time interval (once every hour / day / week) for how often you ideally sync the ARC. In general, the more you work with your ARC, the more you add or update, annotate or analyze data, the more you will want to make sure these changes are saved. Consider the syncing as a way to backup your project's progress as well as an "undo button".

πŸ’‘ For more details, check out the Syncing Recommendations

How to retrieve a valid access token?
Please follow the short instructions below.

Alternatively, please visit #157 in the ARC Commander repository's discussion section for detailed instructions.

Note: This also works for "arc get"


git clone https://oauth2:TOKENSTRING@git.nfdi4plants.org/abc/xyz
In case you created a project access token instead of a personal access token, a GitLab bot will join your project as a member. Please note that this is supportive and not a β€œnegative” bot in case you are not familiar with this. (Thanks to @Zerskk and @j-bauer for providing the background knowledge on this.)
However, for the steps above, you want to create a personal access token.
Why do I get the error `'arc' is not recognized as an internal or external command, operable program or batch file.`?

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.

If this does not do the trick, please follow these steps towards debugging (on Windows):

  1. Open the command prompt (cmd) or powershell in the folder (e.g. C:\Programs\ArcCommander) where you stored the ARC Commander program (e.g. arc.exe). If arc --version shows the version, the executable is intact.
  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)

πŸ’‘ 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.

Why do I get the error `ERROR: GIT: fatal: detected dubious ownership`?

This error occurs when working on a mounted network drive (Fileshare, File Server, NAS). Very simplified: the user on the computer and the owner of the network drive differ and git tries to safe you from working in a folder you do not own.

You can circumvent this error by adding all directories to your list of safe directories via the following command:

git config --global --add safe.directory *

This might however pose a safety risk. Please read the details here: https://www.git-scm.com/docs/git-config#Documentation/git-config.txt-safedirectory

Syncing my ARC to the DataHUB takes forever or gets stuck. What can I do?
This is likely due to handling a big volume of data.

Solution: Increase git's http post buffer

Execute the following command in your command line:

git config --global http.postBuffer 524288000

source: https://stackoverflow.com/questions/6887228/git-hangs-while-writing-objects

I already committed my changes, but they are still displayed in the ARCitect and are not uploaded to the DataHUB.

Sometimes, the ARCitect does not "accept" a commit or when writing a commit message and hitting the "commit" button the changes are still displayed. You can try the following:

  1. Close all windows (e.g. windows explorer) and files (in particular Excel workbooks) related to the ARC
  2. Try to commit again.

πŸ’‘ In general, we recommend to close all isa.investigation.xlsx, isa.study.xlsx and isa.assay.xlsx workbooks when working on your ARC using ARCitect.

Why is the file tree flickering in ARCitect?

So far we only saw this bug on macOS with ARCs stored in a folder that is watched and synced by iCloud (typically the Desktop and Documents folder and sub-folders). Please store your ARCs in folders outside iCloud.

Why do I get the warning "Clone succeeded, but checkout failed."?

This warning is likely due to an issue with your Git or Git LFS installation. If you see this error, when using ARCitect (version β‰₯ 0.0.21) under Windows or Linux, please let us know via e.g. helpdesk.

On macOS ARCitect's git dependency is not yet in place. Please follow this workaround.

What does the "Credential Helper Selector" mean?

During ARCitect login, Windows asks you wether you want to use a "Credential Helper". This can be used to store your DataHUB credentials. You do not need this for ARCitect to work. You can choose "no helper" or "manager" and tick the check box "always use this from now on" to avoid the popup in the future.

Is it possible to use common Excel functionalities?
Yes. In fact, this is one of the reasons why we decided to embed Swate within Excel, as it allows users to continue using the Excel functionality they are accustomed to.
Do I have to fill in all columns when using a template?
No. However, if you want to submit your data to a public data repository, these will require specific metadata. For this purpose we provide the corresponding templates helping you to annotate your data accordingly.
Installation (Windows, manual): How and where to create a shared folder?
Wherever you created your folder-to-be-shared according to these instructions, you need to have the right to share a folder at this particular location.

This might not be possible at 'C:\folder-to-be-shared' but, when you go one level down, into 'Users', 'C:\Users\folder-to-be-shared' might be sharable. You can share a folder when the 'Sharing' tab is shown next to the 'General' tab in the properties dialog window (right click on the folder-to-be-shared, select 'properties').
When you created a folder-to-be-shared, placed the latest manifest(s) from the zip-extracted download into it ('core_manifest.xml', and optional: 'experts_manifest.xml'), finished these steps and continue with these steps in Excel, you should be ready to dive into Swate. - Enjoy πŸš€

Which format must be used to enter a date?
String formatted as ISO8601 date: YYYY-MM-DD

Why do I see banners about "SSH Key", "SAML", "Personal Access Tokens" when logging into the DataHUB?

After login to the DataHUB you see the following banners

If you use DataPLANT tools (ARCitect or ARC commander) to sync your ARC with the DataHUB, you can safely ignore them and click "Don't show again".

Already got an answer to a question or figured out the answer yourself? Please let others benefit from it by adding your suggestion here.

DataPLANT Support

Besides these technical solutions, DataPLANT supports you with community-engaged data stewardship. For further assistance, feel free to reach out via our helpdesk or by contacting us directly .
Contribution Guide πŸ“–
✏️ Edit this page