Fisrt functional version

pkg/obiseq/taxonomy_predicate.go

@@ -0,0 +1,98 @@
+package obiseq
+
+import (
+	log "github.com/sirupsen/logrus"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
+)
+
+func IsAValidTaxon(taxonomy *obitax.Taxonomy, withAutoCorrection ...bool) SequencePredicate {
+	// deprecatedTaxidsWarning := make(map[string]bool)
+
+	autocorrection := false
+	if len(withAutoCorrection) > 0 {
+		autocorrection = withAutoCorrection[0]
+	}
+
+	f := func(sequence *BioSequence) bool {
+		taxon := sequence.Taxon(taxonomy)
+
+		if taxon != nil {
+			taxid := sequence.Taxid()
+			ttaxid := taxon.String()
+			if taxid != ttaxid {
+				if autocorrection {
+					sequence.SetTaxid(ttaxid)
+					log.Printf(
+						"Sequence %s : Taxid %d updated with %d",
+						sequence.Id(),
+						taxid,
+						ttaxid,
+					)
+				} //  else {
+				// 	if _, ok := deprecatedTaxidsWarning[taxid]; !ok {
+				// 		deprecatedTaxidsWarning[taxid] = true
+				// 		log.Printf("Taxid %d is deprecated and must be replaced by %d", taxid, taxon.taxid)
+				// 	}
+				// }
+			}
+		}
+
+		return taxon != nil
+	}
+
+	return f
+}
+
+// A function that takes a taxonomy and a taxid as arguments and returns a function that takes a
+// pointer to a BioSequence as an argument and returns a boolean.
+func IsSubCladeOf(taxonomy *obitax.Taxonomy, taxid string) SequencePredicate {
+	parent := taxonomy.Taxon(taxid)
+
+	if parent == nil {
+		log.Fatalf("Cannot find taxon : %s in taxonomy %s",
+			taxid,
+			taxonomy.Name())
+	}
+
+	f := func(sequence *BioSequence) bool {
+		taxon := sequence.Taxon(taxonomy)
+		return taxon != nil && taxon.IsSubCladeOf(parent)
+	}
+
+	return f
+}
+
+func IsSubCladeOfSlot(taxonomy *obitax.Taxonomy, key string) SequencePredicate {
+
+	f := func(sequence *BioSequence) bool {
+		val, ok := sequence.GetStringAttribute(key)
+
+		if ok {
+			parent := taxonomy.Taxon(val)
+			taxon := sequence.Taxon(taxonomy)
+			return parent != nil && taxon != nil && taxon.IsSubCladeOf(parent)
+		}
+
+		return false
+	}
+
+	return f
+}
+
+func HasRequiredRank(taxonomy *obitax.Taxonomy, rank string) SequencePredicate {
+
+	if !obiutils.Contains(taxonomy.RankList(), rank) {
+		log.Fatalf("%s is not a valid rank (allowed ranks are %v)",
+			rank,
+			taxonomy.RankList())
+	}
+
+	f := func(sequence *BioSequence) bool {
+		taxon := sequence.Taxon(taxonomy)
+		return taxon != nil && taxon.HasRankDefined(rank)
+	}
+
+	return f
+}