Make sequence files recognized as a taxonomy

pkg/obiutils/mimetypes.go

@@ -0,0 +1,95 @@
+package obiutils
+
+import (
+	"bytes"
+	"encoding/csv"
+	"errors"
+	"io"
+	"regexp"
+
+	"github.com/gabriel-vasile/mimetype"
+)
+
+func DropLastLine(b []byte, readLimit uint32) []byte {
+	if readLimit == 0 || uint32(len(b)) < readLimit {
+		return b
+	}
+	for i := len(b) - 1; i > 0; i-- {
+		if b[i] == '\n' {
+			return b[:i]
+		}
+	}
+	return b
+}
+
+var __obimimetype_registred__ = false
+
+func RegisterOBIMimeType() {
+	if !__obimimetype_registred__ {
+		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
+		}
+
+		fastqDetector := func(raw []byte, limit uint32) bool {
+			ok, err := regexp.Match("^@[^ ].*\n[A-Za-z.-]+", raw)
+			return ok && err == nil
+		}
+
+		ecoPCR2Detector := func(raw []byte, limit uint32) bool {
+			ok := bytes.HasPrefix(raw, []byte("#@ecopcr-v2"))
+			return ok
+		}
+
+		genbankDetector := func(raw []byte, limit uint32) bool {
+			ok2 := bytes.HasPrefix(raw, []byte("LOCUS       "))
+			ok1, err := regexp.Match("^[^ ]* +Genetic Sequence Data Bank *\n", raw)
+			return ok2 || (ok1 && err == nil)
+		}
+
+		emblDetector := func(raw []byte, limit uint32) bool {
+			ok := bytes.HasPrefix(raw, []byte("ID   "))
+			return ok
+		}
+
+		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")
+		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")
+	}
+	__obimimetype_registred__ = true
+}