ebi-ait / ebi-ait/checklist

generate excel/tsv submission template for ENA samples

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#47 33 comments 0 reactions 3 assignees Claimed by @amnonkhen View on GitHub
checklist FAIRification Submissions
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Description

## Description
There is code on the Webin portal on ENA that generates excel templates for submitters from XML checklists. XML checklists are being deprecated, and JSON checklists will replace them. We need to retain this functionality for submitters to generate excel templates from JSON checklists.

## Specific Requirements
- revise the excel template generation code or rewrite it to use JSON checklists
- example json checklist: _add here_
- example template:
- ena sample [Checklist_GSC-MIxS air_1722522471257 tsv file](https://api.zenhub.com/attachedFiles/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBN1ltQmc9PSIsImV4cCI6bnVsbCwicHVyIjoiYmxvYl9pZCJ9fQ==--0a3359e094c1aba4337545544db3b2b062182087/Checklist_GSC-MIxS%20air_1722522471257.tsv.txt)
```tsv
Checklist ERC000012 GSC MIxS air
tax_id scientific_name altitude
#units m
```

- excel template generation [on webin portal](https://www.ebi.ac.uk/ena/submit/webin/app-checklist/sample/true)
- have control on what additional metadata is added to template:
- field description
- mandatory requirement
- human readable name

## Definition of Done
- [ ] Users logging into webin can generate excel templates from the migrated JSON templates
- [ ] reuse (possibly extend) the HCA template generation code
- [ ] add api call
- [ ] change in webin portal to use the BioSamples api - should be done by Submissions team
- [ ] use for MorPhiC as well

## Deadline and reasoning for deadline
November, as this is when we expect the back-end of the checklist editor to be running smoothly by then, and this is a required component

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