Implement GET / POST with S3 Urls to Loculus

[gordonkoehn]

Determine what exact GET and POSTs Loculus backend requires and write a query for this.

[gordonkoehn]

Chaoron was so kind to already spin up our own WISE Loculus instance.

FYI: they spin up Loculus my simply making a PR with the tag preview.

loculus-project/loculus#3330

Takes about 2 minutes to spin up.

This is the live webpage:

https://wise-seqs.loculus.org/

[gordonkoehn]

By default the the user is:

user:testuser
pw:testuser

but one can also create a new user.

[gordonkoehn]

Steps to upload data:

1. create group in the web UX - get group number

2. Create the files for submission metadata.tsv and sequences.fasta
   2.1) metadata.tsv contains two columns 'submissionId | s3Link' , for each sequence in the other file there is one line
   2.2) 'seqeunces.fasta' contains fasta format like the sequences

      > NNNNNNN```
      just enter NNNN for mock sequences
   

3. Try Drag and Drop to upload these

4. Then try API
   4.1) Get API Keys: get authentication server by logging in and copy URL
   4.2) Add this in the Keycloak URL – see authenticate request in the API - backend-wise-seqs.loculus.org - echoes a json auth token
   4.3) Make submit POST with the echo token we may submit - for the next 15 min or so - so per session

[gordonkoehn]

Example code to submit:

https://github.com/microbio-hackathon-2024/pathinder-client/blob/main/submit.py

[gordonkoehn]

Created a group "sr2silo01" – it has Group ID: 1

[gordonkoehn]

I am running into some errors uploading the metadata in the correct format. Checking with Chaoran. Works now, really need to make sure its a tsv.

[gordonkoehn]

KeycloakURL = authentication-wise-seqs.loculus.org

[gordonkoehn]

Chaoran share this project with me to get the POST working with Authentication:

• https://github.com/microbio-hackathon-2024/pathinder-client/blob/main/submit.py

[gordonkoehn]

backend_url= backend-wise-seqs.loculus.org

[gordonkoehn]

First programmatic submissions where made; check here:
https://wise-seqs.loculus.org/test/submission/1/review