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Fix Uniprot decompression and refresh EBI test accessions #56

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Merged
timholy merged 1 commit into from
Jul 20, 2026
Merged

Fix Uniprot decompression and refresh EBI test accessions #56

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11 changes: 7 additions & 4 deletions src/naming_conventions.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -166,9 +166,12 @@ Check the status of a Uniprot ID mapping job. Returns `true` if the results are
ready. Otherwise, returns the status object.
"""
function map_uniprot_status(jobID)
resp = HTTP.get("https://rest.uniprot.org/idmapping/status/$jobID", ["Accept" => "application/json"]; decompress = true)
# `decompress = false` suppresses the `Accept-Encoding: gzip` request header, so the
# body arrives as plain text. Uniprot does not always honor a compression request, and
# unconditionally gunzipping the response fails whenever it returns one uncompressed.
resp = HTTP.get("https://rest.uniprot.org/idmapping/status/$jobID", ["Accept" => "application/json"]; decompress = false)
if resp.status == 200
status = JSON3.read(String(HTTP.decode(resp)))
status = JSON3.read(String(resp.body))
haskey(status, "results") && return true
return status
end
Expand All @@ -181,9 +184,9 @@ end
Retrieve the results of a Uniprot ID mapping job.
"""
function map_uniprot_retrieve(jobID)
resp = HTTP.get("https://rest.uniprot.org/idmapping/stream/$jobID", ["Accept" => "application/json"]; decompress = true)
resp = HTTP.get("https://rest.uniprot.org/idmapping/stream/$jobID", ["Accept" => "application/json"]; decompress = false)
if resp.status == 200
return JSON3.read(String(HTTP.decode(resp)))
return JSON3.read(String(resp.body))
end
return nothing
end
4 changes: 3 additions & 1 deletion test/runtests.jl
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Expand Up @@ -418,7 +418,9 @@ using Test
end
end
@test startswith(query_ebi_proteins("Q7TQA6"; format=:fasta), ">sp|Q7TQA6")
@test count(==('>'), query_ebi_proteins(["C3N734", "H2C869", "Q3V4T1", "P20220"]; format=:fasta)) == 4
# Reviewed (SwissProt) accessions: unreviewed entries get withdrawn when
# the underlying genome annotation changes, silently shrinking the count.
@test count(==('>'), query_ebi_proteins(["P29274", "P29275", "P15409", "Q7TQA6"]; format=:fasta)) == 4
q = query_ncbi(obj)
@test q["total_count"] == 1
end
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