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Sabrina Zander committed Dec 9, 2024
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14 changes: 6 additions & 8 deletions src/content/docs/resources/elab2ARC.mdx
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Expand Up @@ -32,10 +32,6 @@ These features streamline workflows, ensuring efficient and standardized data ma

## Setting up elab2ARC

:::note
At the moment you can only use the tool on the eLabFTW Demo or eLabFTW HHU Instance.
:::


### Create an Project Access Token in DataHUB

Expand Down Expand Up @@ -72,7 +68,7 @@ import DataHubPat from '../datahub/navigation-settings/datahub-generate-project-
## How to use elab2ARC

<Steps>
1. Select your elabFTW Instance [1]
1. Select your elabFTW Instance or add your instance [1]
2. Paste eLabFTW API key [2]
3. Paste DataHUB Project Access Token [3]
![](@images/elab2ARC/elab2ARC-tool-usage.png)
Expand All @@ -85,10 +81,12 @@ import DataHubPat from '../datahub/navigation-settings/datahub-generate-project-

## Conversion

![](@images/elab2ARC/elab2ARC-conversion.png)

The elab2ARC tool will automatically convert your elabFTW experiments into ARC format
- create a new assay folder with eLabFTW experiment name as assay name
- create a new assay folder with eLabFTW experiment name as assay name (green)
- create the assay folder structure (dataset/protocols/isa.assay)
- convert experiment main text into a .md file and store it in the protocol folder
- add all attachments of the eLabFTW experiment into the dataset folder
- convert experiment main text into a .md file and store it in the protocol folder (purple)
- add all attachments of the eLabFTW experiment into the dataset folder (yellow)
- enter name/email/affiliation of the eLabFTW experiment metadata into the isa.assay sheet

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