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Add managment of the taxonomy alias politic

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This commit is contained in:
Eric Coissac
2025-02-10 14:05:47 +01:00
parent e2563cd8df
commit 6a8061cc4f
16 changed files with 114 additions and 48 deletions
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22
pkg/obiformats/fastseq_json_header.go
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@ -9,7 +9,6 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
"github.com/buger/jsonparser"
)
@ -201,8 +200,6 @@ func _parse_json_array_interface(str []byte, sequence *obiseq.BioSequence) ([]in
}
func _parse_json_header_(header string, sequence *obiseq.BioSequence) string {
taxonomy := obitax.DefaultTaxonomy()
annotations := sequence.Annotations()
start := -1
stop := -1
@ -291,13 +288,8 @@ func _parse_json_header_(header string, sequence *obiseq.BioSequence) string {
case skey == "taxid":
if dataType == jsonparser.Number || dataType == jsonparser.String {
taxid := obiutils.UnsafeString(value)
taxon, err := taxonomy.Taxon(taxid)
if err == nil {
sequence.SetTaxon(taxon)
} else {
sequence.SetTaxid(string(value))
}
taxid := string(value)
sequence.SetTaxid(taxid)
} else {
log.Fatalf("%s: Cannot parse taxid %s", sequence.Id(), string(value))
}
@ -306,15 +298,7 @@ func _parse_json_header_(header string, sequence *obiseq.BioSequence) string {
if dataType == jsonparser.Number || dataType == jsonparser.String {
rank, _ := obiutils.SplitInTwo(skey, '_')
taxid := obiutils.UnsafeString(value)
taxon, err := taxonomy.Taxon(taxid)
if err == nil {
taxid = taxon.String()
} else {
taxid = string(value)
}
taxid := string(value)
sequence.SetTaxid(taxid, rank)
} else {
log.Fatalf("%s: Cannot parse taxid %s", sequence.Id(), string(value))