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Add ability to upload a file and use it as a non-editable sequence for an assembly #406

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garrettjstevens opened this issue Jul 2, 2024 · 0 comments
Open

Add ability to upload a file and use it as a non-editable sequence for an assembly #406

garrettjstevens opened this issue Jul 2, 2024 · 0 comments
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@dariober

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@garrettjstevens
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Currently we have the options to

  • upload a file (GFF3 or FASTA) and use it to load an assembly with sequence in the database
  • use an external URL to create an assembly that doesn't store the sequence in the database

I think we need a third option:

  • upload a file (FASTA) and use it to create an assembly that doesn't store the sequence in the database

The steps I see are:

  • Allow user to upload either a FASTA/FAI or FASTA.GZ/FAI/GZI set of files.
  • Store the file IDs in the assembly (modify assembly.schema.ts) similar to the externalLocation in the assembly (perhaps called fileLocation).
  • In sequence.service.ts, check to see if the assembly has a fileLocation and if it does, fetch the sequence from the file similar to how the externalLocation fetches from a URL.
dariober added a commit that referenced this issue Jul 22, 2024
@dariober
Handling of gzip input and bgzip'd & indexed fasta
587f67b 
* CLI can upload and add assembly from gzip files (#405 and #407)

* CLI can add assembly in non-editable mode with `--no-db` flag, i.e. without loading
  sequence to mongodb (#406). Only bgzip'd & indexed fasta file are
  supported, not plain fa/fai files.

See tests in test.py: `testFeatureChecksIndexed`, `testFileUploadGzip`,
`testAddAssemblyWithoutLoadingInMongo`
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@dariober @garrettjstevens