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Remove HTML escaping to json marshaling

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This commit is contained in:
Eric Coissac
2022-09-20 22:01:52 +02:00
parent 3cd8aabd83
commit 49b4d97803
3 changed files with 24 additions and 4 deletions
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15
pkg/goutils/goutils.go
View File

@ -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
}

3
pkg/obiformats/fastseq_json_header.go
View File

@ -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)

10
pkg/obiformats/fastseq_obi_header.go
View File

@ -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"
)
@ -216,16 +217,18 @@ 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)
value = dict
}
if err != nil {
value = string(bvalue)
}
@ -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)
}