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make it possible to return sequences as JSON or NDJSON #971

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fengelniederhammer opened this issue Oct 2, 2024 · 2 comments · Fixed by #983 or #989
Closed

make it possible to return sequences as JSON or NDJSON #971

fengelniederhammer opened this issue Oct 2, 2024 · 2 comments · Fixed by #983 or #989
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enhancement New feature or request LAPIS Tasks/PR related to LAPIS

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@fengelniederhammer
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Currently, the sequences endpoints only return FASTA, which is nice for downloading files. But when working with LAPIS programmatically, a structured response would be better.

Implement getting the sequences as JSON or NDJSON (or both, if easily possible). The default should still be FASTA.

Make sure that the result can still be streamed properly.

  • This should be straight forward for NDJSON.
  • Think about how to stream JSON. (Maybe just write [, then NDJSON lines separated by , and then ]?)
@corneliusroemer
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It seems the default is now no longer FASTA? See loculus-project/loculus#3077 (comment)

corneliusroemer added a commit to loculus-project/loculus that referenced this issue Oct 25, 2024
anna-parker pushed a commit to loculus-project/loculus that referenced this issue Oct 25, 2024
@fengelniederhammer
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It seems the default is now no longer FASTA? See loculus-project/loculus#3077 (comment)

AFAICS the issue has been resolved in Loculus?

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Labels
enhancement New feature or request LAPIS Tasks/PR related to LAPIS
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