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Xprize update

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Former-commit-id: d38919a897961e4d40da3b844057c3fb94fdb6d7
This commit is contained in:
Eric Coissac
2024-07-25 18:09:03 -04:00
parent 4e4fac491f
commit 67665a6b40
18 changed files with 895 additions and 29 deletions
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24
pkg/obitax/sequence_methods.go
View File

@ -66,3 +66,27 @@ func (taxonomy *Taxonomy) SetPath(sequence *obiseq.BioSequence) string {
return tpath
}
func (taxonomy *Taxonomy) SetScientificName(sequence *obiseq.BioSequence) string {
taxid, err := taxonomy.Taxon(sequence.Taxid())
if err != nil {
log.Fatalf("Taxid %d not defined in the current taxonomy", sequence.Taxid())
}
sequence.SetAttribute("scienctific_name", taxid.ScientificName())
return taxid.ScientificName()
}
func (taxonomy *Taxonomy) SetTaxonomicRank(sequence *obiseq.BioSequence) string {
taxid, err := taxonomy.Taxon(sequence.Taxid())
if err != nil {
log.Fatalf("Taxid %d not defined in the current taxonomy", sequence.Taxid())
}
sequence.SetAttribute("taxonomic_rank", taxid.Rank())
return taxid.Rank()
}

17
pkg/obitax/sequence_predicate.go
View File

@ -57,6 +57,23 @@ func (taxonomy *Taxonomy) IsSubCladeOf(taxid int) obiseq.SequencePredicate {
return f
}
func (taxonomy *Taxonomy) IsSubCladeOfSlot(key string) obiseq.SequencePredicate {
f := func(sequence *obiseq.BioSequence) bool {
val, ok := sequence.GetStringAttribute(key)
if ok {
parent, err1 := taxonomy.Taxon(val)
taxon, err2 := taxonomy.Taxon(sequence.Taxid())
return err1 == nil && err2 == nil && taxon.IsSubCladeOf(parent)
}
return false
}
return f
}
func (taxonomy *Taxonomy) HasRequiredRank(rank string) obiseq.SequencePredicate {
if !obiutils.Contains(taxonomy.RankList(), rank) {

41
pkg/obitax/taxonomy.go
View File

@ -2,6 +2,8 @@ package obitax
import (
"fmt"
"regexp"
"strconv"
)
type TaxName struct {
@ -54,11 +56,43 @@ func (taxonomy *Taxonomy) AddNewTaxa(taxid, parent int, rank string, replace boo
return n, nil
}
func (taxonomy *Taxonomy) Taxon(taxid int) (*TaxNode, error) {
t, ok := (*taxonomy.nodes)[taxid]
// func (taxonomy *Taxonomy) Taxon(taxid int) (*TaxNode, error) {
// t, ok := (*taxonomy.nodes)[taxid]
// if !ok {
// a, aok := taxonomy.alias[taxid]
// if !aok {
// return nil, fmt.Errorf("Taxid %d is not part of the taxonomy", taxid)
// }
// t = a
// }
// return t, nil
// }
func (taxonomy *Taxonomy) Taxon(taxid interface{}) (*TaxNode, error) {
var itaxid int
var err error
switch v := taxid.(type) {
case int:
itaxid = v
case string:
itaxid, err = strconv.Atoi(v)
if err != nil {
re := regexp.MustCompile(`TX:(\d+)`)
parts := re.FindStringSubmatch(v)
if len(parts) != 2 {
return nil, fmt.Errorf("I cannot parse taxid from %s", v)
}
itaxid, _ = strconv.Atoi(parts[1])
}
}
t, ok := (*taxonomy.nodes)[itaxid]
if !ok {
a, aok := taxonomy.alias[taxid]
a, aok := taxonomy.alias[itaxid]
if !aok {
return nil, fmt.Errorf("Taxid %d is not part of the taxonomy", taxid)
}
@ -66,7 +100,6 @@ func (taxonomy *Taxonomy) Taxon(taxid int) (*TaxNode, error) {
}
return t, nil
}
func (taxonomy *Taxonomy) AddNewName(taxid int, name, nameclass *string) error {
node, node_err := taxonomy.Taxon(taxid)
if node_err != nil {