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feat: add JSON input support for biological sequences

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Introduce a streaming JSON parser that decodes biological sequences using `goccy/go-json` with configurable batching to minimize memory overhead. Extend the CLI, file suffix filters, and MIME type detection to automatically recognize and route JSON inputs. Refactor header parsing into a centralized switch-case handler for improved maintainability.
This commit is contained in:
Eric Coissac
2026-07-03 10:16:55 +02:00
parent 9de463ef1e
commit d735ac6188
6 changed files with 273 additions and 97 deletions
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pkg/obiutils/mimetypes.go
+6
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@@ -102,6 +102,11 @@ func RegisterOBIMimeType() {
return ok
}
jsonDetector := func(raw []byte, limit uint32) bool {
raw = bytes.TrimLeft(raw, " \t\r\n")
return len(raw) > 0 && (raw[0] == '[' || raw[0] == '{')
}
mimetype.Lookup("text/plain").Extend(fastaDetector, "text/fasta", ".fasta")
mimetype.Lookup("text/plain").Extend(fastqDetector, "text/fastq", ".fastq")
mimetype.Lookup("text/plain").Extend(ecoPCR2Detector, "text/ecopcr2", ".ecopcr")
@@ -115,6 +120,7 @@ func RegisterOBIMimeType() {
mimetype.Lookup("application/octet-stream").Extend(genbankDetector, "text/genbank", ".seq")
mimetype.Lookup("application/octet-stream").Extend(emblDetector, "text/embl", ".dat")
mimetype.Lookup("application/octet-stream").Extend(csv, "text/csv", ".csv")
mimetype.Lookup("application/octet-stream").Extend(jsonDetector, "application/json", ".json")
}
__obimimetype_registred__ = true
}