obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

Add managment of the taxonomy alias politic

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

40
pkg/obiseq/taxonomy_methods.go
View File

@ -5,6 +5,7 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
@ -16,7 +17,7 @@ func (s *BioSequence) Taxon(taxonomy *obitax.Taxonomy) *obitax.Taxon {
return nil
}
taxon, _ := taxonomy.Taxon(taxid)
taxon, _, _ := taxonomy.Taxon(taxid)
return taxon
}
@ -28,6 +29,8 @@ func (s *BioSequence) Taxon(taxonomy *obitax.Taxonomy) *obitax.Taxon {
// taxid - the taxid to set.
func (s *BioSequence) SetTaxid(taxid string, rank ...string) {
var err error
var isAlias bool
if taxid == "" {
taxid = "NA"
} else {
@ -35,16 +38,39 @@ func (s *BioSequence) SetTaxid(taxid string, rank ...string) {
taxon := (*obitax.Taxon)(nil)
if taxonomy != nil {
taxon, err = taxonomy.Taxon(taxid)
taxon, isAlias, err = taxonomy.Taxon(taxid)
if err != nil {
log.Warnf("%s: Taxid: %v is unknown from taxonomy (%v)",
s.Id(), taxid, err)
if obidefault.FailOnTaxonomy() {
log.Fatalf("%s: Taxid: %v is unknown from taxonomy (%v)",
s.Id(), taxid, err)
} else {
log.Warnf("%s: Taxid: %v is unknown from taxonomy (%v)",
s.Id(), taxid, err)
}
}
if isAlias {
if obidefault.FailOnTaxonomy() {
log.Fatalf("%s: Taxid: %v is an alias from taxonomy (%v) to %s",
s.Id(), taxid, taxonomy.Name(), taxon.String())
} else {
if obidefault.UpdateTaxid() {
log.Warnf("%s: Taxid: %v is updated to %s",
s.Id(), taxid, taxon.String())
taxid = taxon.String()
} else {
log.Warnf("%s: Taxid %v has to be updated to %s",
s.Id(), taxid, taxon.String())
}
}
} else {
if taxon != nil {
taxid = taxon.String()
}
}
}
if taxon != nil {
taxid = taxon.String()
}
}