Fix Uniprot decompression and refresh EBI test accessions - #56
Merged
Conversation
Uniprot serves ID-mapping responses uncompressed unless the client negotiates gzip, and does not always honor the request when it does. Requesting compression and then unconditionally gunzipping the response therefore fails intermittently with a ZlibError. Suppress the Accept-Encoding header via `decompress = false` and read the body directly. The EBI batch-query test used accession C3N734, which has since been withdrawn from Uniprot, so the query returned three records instead of four. Reviewed (SwissProt) accessions are not withdrawn the way unreviewed entries are; use four GPCR entries already exercised elsewhere in the suite. Assisted-by: Claude Opus 4.8 <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Uniprot serves ID-mapping responses uncompressed unless the client negotiates gzip, and does not always honor the request when it does. Requesting compression and then unconditionally gunzipping the response therefore fails intermittently with a ZlibError. Suppress the Accept-Encoding header via
decompress = falseand read the body directly.The EBI batch-query test used accession C3N734, which has since been withdrawn from Uniprot, so the query returned three records instead of four. Reviewed (SwissProt) accessions are not withdrawn the way unreviewed entries are; use four GPCR entries already exercised elsewhere in the suite.
Assisted-by: Claude Opus 4.8 noreply@anthropic.com