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correction of several small bugs

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This commit is contained in:
Eric Coissac
2024-09-03 06:08:07 -03:00
parent 373464cb06
commit 65ae82622e
22 changed files with 770 additions and 79 deletions
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30
pkg/obiformats/universal_read.go
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@ -3,6 +3,8 @@ package obiformats
import (
"bufio"
"bytes"
"encoding/csv"
"errors"
"io"
"path"
"regexp"
@ -39,6 +41,31 @@ type SequenceReader func(reader io.Reader, options ...WithOption) (obiiter.IBioS
// - io.Reader: A modified reader with the read data.
// - error: Any error encountered during the process.
func OBIMimeTypeGuesser(stream io.Reader) (*mimetype.MIME, io.Reader, error) {
csv := func(in []byte, limit uint32) bool {
in = dropLastLine(in, limit)
br := bytes.NewReader(in)
r := csv.NewReader(br)
r.Comma = ','
r.ReuseRecord = true
r.LazyQuotes = true
r.Comment = '#'
lines := 0
for {
_, err := r.Read()
if errors.Is(err, io.EOF) {
break
}
if err != nil {
return false
}
lines++
}
return r.FieldsPerRecord > 1 && lines > 1
}
fastaDetector := func(raw []byte, limit uint32) bool {
ok, err := regexp.Match("^>[^ ]", raw)
return ok && err == nil
@ -70,12 +97,14 @@ func OBIMimeTypeGuesser(stream io.Reader) (*mimetype.MIME, io.Reader, error) {
mimetype.Lookup("text/plain").Extend(ecoPCR2Detector, "text/ecopcr2", ".ecopcr")
mimetype.Lookup("text/plain").Extend(genbankDetector, "text/genbank", ".seq")
mimetype.Lookup("text/plain").Extend(emblDetector, "text/embl", ".dat")
mimetype.Lookup("text/plain").Extend(csv, "text/csv", ".csv")
mimetype.Lookup("application/octet-stream").Extend(fastaDetector, "text/fasta", ".fasta")
mimetype.Lookup("application/octet-stream").Extend(fastqDetector, "text/fastq", ".fastq")
mimetype.Lookup("application/octet-stream").Extend(ecoPCR2Detector, "text/ecopcr2", ".ecopcr")
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")
// Create a buffer to store the read data
buf := make([]byte, 1024*128)
@ -87,6 +116,7 @@ func OBIMimeTypeGuesser(stream io.Reader) (*mimetype.MIME, io.Reader, error) {
// Detect the MIME type using the mimetype library
mimeType := mimetype.Detect(buf)
if mimeType == nil {
return nil, nil, err
}