Remove HTML escaping to json marshaling

pkg/goutils/goutils.go

@@ -4,6 +4,7 @@ import (
 	"bufio"
 	"bytes"
 	"encoding/gob"
+	"encoding/json"
 	"io"
 	"os"
 	"sync"
@@ -188,3 +189,17 @@ func AtomicCounter(initial ...int) func() int {
 
 	return nextCounter
 }
+
+// Marshal is a UTF-8 friendly marshaler.  Go's json.Marshal is not UTF-8
+// friendly because it replaces the valid UTF-8 and JSON characters "&". "<",
+// ">" with the "slash u" unicode escaped forms (e.g. \u0026).  It preemptively
+// escapes for HTML friendliness.  Where text may include any of these
+// characters, json.Marshal should not be used. Playground of Go breaking a
+// title: https://play.golang.org/p/o2hiX0c62oN
+func JsonMarshal(i interface{}) ([]byte, error) {
+    buffer := &bytes.Buffer{}
+    encoder := json.NewEncoder(buffer)
+    encoder.SetEscapeHTML(false)
+    err := encoder.Encode(i)
+    return bytes.TrimRight(buffer.Bytes(), "\n"), err
+}

pkg/obiformats/fastseq_json_header.go

@@ -6,6 +6,7 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 	"github.com/goccy/go-json"
 )
@@ -70,7 +71,7 @@ func FormatFastSeqJsonHeader(sequence *obiseq.BioSequence) string {
 	annotations := sequence.Annotations()
 
 	if annotations != nil {
-		text, err := json.Marshal(sequence.Annotations())
+		text, err := goutils.JsonMarshal(sequence.Annotations())
 
 		if err != nil {
 			panic(err)

pkg/obiformats/fastseq_obi_header.go

@@ -9,6 +9,7 @@ import (
 	"strconv"
 	"strings"
 
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 	"github.com/goccy/go-json"
 )
@@ -216,10 +217,12 @@ func ParseOBIFeatures(text string, annotations obiseq.Annotation) string {
 						dict := make(map[string]int)
 						err = json.Unmarshal(j, &dict)
 						value = dict
-					case strings.HasSuffix(key, "_status"):
+					case strings.HasSuffix(key, "_status") ||
+						strings.HasSuffix(key, "_mutation"):
 						dict := make(map[string]string)
 						err = json.Unmarshal(j, &dict)
 						value = dict
+
 					default:
 						dict := make(map[string]interface{})
 						err = json.Unmarshal(j, &dict)
@@ -299,9 +302,10 @@ func FormatFastSeqOBIHeader(sequence *obiseq.BioSequence) string {
 			case string:
 				text.WriteString(fmt.Sprintf("%s=%s; ", key, t))
 			case map[string]int,
+				map[string]string,
 				map[string]interface{},
 				obiseq.StatsOnValues:
-				tv, err := json.Marshal(t)
+				tv, err := goutils.JsonMarshal(t)
 				if err != nil {
 					log.Fatalf("Cannot convert %v value", value)
 				}