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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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9
cmd/obitools/obitaxonomy/main.go
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@ -3,6 +3,7 @@ package main
import (
"os"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
@ -52,13 +53,19 @@ func main() {
case obitaxonomy.CLIRequestsPathForTaxid() != "NA":
taxon, err := obitax.DefaultTaxonomy().Taxon(obitaxonomy.CLIRequestsPathForTaxid())
taxon, isAlias, err := obitax.DefaultTaxonomy().Taxon(obitaxonomy.CLIRequestsPathForTaxid())
if err != nil {
log.Fatalf("Cannot identify the requested taxon: %s (%v)",
obitaxonomy.CLIRequestsPathForTaxid(), err)
}
if isAlias {
if obidefault.FailOnTaxonomy() {
log.Fatalf("Taxon %s is an alias for %s", taxon.String(), taxon.Parent().String())
}
}
s := taxon.Path()
if s == nil {