// Validate validates that a taxon is valid in the database, and set some
// canonical values. It returns an error if the taxon is not valid.
func (t *taxonomy) validate(tax *jdh.Taxon) error {
tax.Id = strings.TrimSpace(tax.Id)
tax.Name = strings.Join(strings.Fields(tax.Name), " ")
if (len(tax.Id) == 0) || (len(tax.Name) == 0) {
return errors.New("taxon without identification")
}
if _, ok := t.ids[tax.Id]; ok {
return fmt.Errorf("taxon id %s already in use", tax.Id)
}
p := t.root
if tax.Rank > jdh.Species {
tax.Rank = jdh.Unranked
}
if len(tax.Parent) > 0 {
var ok bool
if p, ok = t.ids[tax.Parent]; !ok {
return fmt.Errorf("taxon %s parent [%s] not in database", tax.Name, tax.Parent)
}
}
if p == t.root {
if !tax.IsValid {
return fmt.Errorf("taxon %s is a synonym without a parent", tax.Name)
}
} else if !p.data.IsValid {
return fmt.Errorf("taxon %s parent [%s] is a synonym", tax.Name, p.data.Name)
}
if !p.isDescValid(tax.Rank, tax.IsValid) {
return fmt.Errorf("taxon %s rank incompatible with database hierarchy", tax.Name)
}
ext := tax.Extern
tax.Extern = nil
for _, e := range ext {
serv, id, err := jdh.ParseExtern(e)
if err != nil {
continue
}
if len(id) == 0 {
continue
}
add := true
for _, ex := range tax.Extern {
if strings.HasPrefix(ex, serv) {
add = false
break
}
}
if !add {
continue
}
if _, ok := t.ids[e]; !ok {
tax.Extern = append(tax.Extern, e)
}
}
return nil
}
// Add adds a new taxon to the database.
func (t *taxonomy) add(tax *jdh.Taxon) (string, error) {
id := strconv.FormatInt(t.next, 10)
tax.Id = id
if err := t.validate(tax); err != nil {
return "", err
}
t.addTaxon(tax)
t.next++
t.changed = true
return id, nil
}
// TxSyncUpdate implements the update option of tx.sync.
func txSyncUpdate(c *cmdapp.Command, tax *jdh.Taxon) {
// first process the descendants (as it is possible that a taxon
// will be set as synonym, and then thier descendant set will change)
l := getTaxDesc(c, localDB, tax.Id, true)
txSyncUpdateNav(c, l)
l = getTaxDesc(c, localDB, tax.Id, false)
txSyncUpdateNav(c, l)
if len(tax.Id) == 0 {
return
}
eid := searchExtern(extDBFlag, tax.Extern)
if len(eid) == 0 {
return
}
ext := taxon(c, extDB, eid)
if len(ext.Id) == 0 {
fmt.Fprintf(os.Stderr, "unable to retrieve %s:%s\n", tax.Extern, eid)
return
}
if validFlag {
if tax.IsValid != ext.IsValid {
args := new(jdh.Values)
args.Add(jdh.KeyId, tax.Id)
if ext.IsValid {
args.Add(jdh.TaxValid, "")
localDB.Exec(jdh.Set, jdh.Taxonomy, args)
} else {
p := taxon(c, localDB, extDBFlag+":"+ext.Parent)
if len(p.Id) == 0 {
exPar := taxon(c, extDB, ext.Parent)
p = txSyncAddToTaxonomy(c, exPar)
}
args.Add(jdh.TaxSynonym, p.Id)
localDB.Exec(jdh.Set, jdh.Taxonomy, args)
}
}
}
if !updateFlag {
return
}
if len(ext.Authority) > 0 {
args := new(jdh.Values)
args.Add(jdh.KeyId, tax.Id)
args.Add(jdh.TaxAuthority, ext.Authority)
localDB.Exec(jdh.Set, jdh.Taxonomy, args)
}
if ext.Rank != jdh.Unranked {
args := new(jdh.Values)
args.Add(jdh.KeyId, tax.Id)
args.Add(jdh.TaxRank, ext.Rank.String())
localDB.Exec(jdh.Set, jdh.Taxonomy, args)
}
if len(ext.Comment) > 0 {
if len(tax.Comment) > 0 {
tax.Comment += "\n"
}
tax.Comment += ext.Comment
args := new(jdh.Values)
args.Add(jdh.KeyId, tax.Id)
args.Add(jdh.KeyComment, tax.Comment)
localDB.Exec(jdh.Set, jdh.Taxonomy, args)
}
}