public static function split_entry($args)
{
$hierarchy_entry_id = @$args['hierarchy_entry_id'];
$bad_match_hierarchy_entry_id = @$args['bad_match_hierarchy_entry_id'];
$confirmation = @$args['confirmed'];
if (!$hierarchy_entry_id || !is_numeric($hierarchy_entry_id) || !$bad_match_hierarchy_entry_id || !is_numeric($bad_match_hierarchy_entry_id)) {
throw new \Exception("split_entry.php [hierarchy_entry_id] [bad_match_hierarchy_entry_id] [confirmed]");
}
\CodeBridge::print_message("Splitting HE# {$hierarchy_entry_id} from {$bad_match_hierarchy_entry_id}");
$he = HierarchyEntry::find($hierarchy_entry_id);
$bad_he = HierarchyEntry::find($hierarchy_entry_id);
if (!$he->id || !$bad_he->id) {
throw new \Exception("Invalid ID");
}
if ($he->taxon_concept_id != $bad_he->taxon_concept_id) {
throw new \Exception("The bad match ID isn't from the same concept");
}
if ($confirmation == 'confirmed') {
$user_id = 13;
# 13 is Patrick's user ID - TODO - this should be an argument. :|
$new_taxon_concept_id = HierarchyEntry::split_from_concept_static($hierarchy_entry_id);
$GLOBALS['db_connection']->query("INSERT IGNORE INTO curated_hierarchy_entry_relationships (hierarchy_entry_id_1, hierarchy_entry_id_2, user_id, equivalent)\n VALUES ({$hierarchy_entry_id}, {$bad_match_hierarchy_entry_id}, {$user_id}, 0)");
\CodeBridge::print_message("Done. HE# {$hierarchy_entry_id} was split into a new concept # {$new_taxon_concept_id}");
} else {
echo "\n\nRemoving:\n";
print_r($he);
echo "Name: " . $he->name->string . "\n\nFrom:\n";
print_r($he->taxon_concept);
$descendant_objects = TaxonConcept::count_descendants_objects($he->taxon_concept_id);
echo "\n\nDescendant Objects: {$descendant_objects}\n\n";
}
}
function details_tcs($id)
{
$entry = HierarchyEntry::find($id);
if (@(!$entry->id)) {
return false;
}
$nomenclaturalCode = "Zoological";
$rankCode = "";
switch (strtolower($entry->rank->translation->label)) {
case "kingdom":
$rankCode = "reg";
break;
case "phylum":
$rankCode = "phyl_div";
break;
case "class":
$rankCode = "cl";
break;
case "order":
$rankCode = "ord";
break;
case "family":
$rankCode = "fam";
break;
case "genus":
$rankCode = "gen";
break;
case "species":
$rankCode = "sp";
break;
}
$return = "";
$return .= " <TaxonNames>\n";
$return .= " <TaxonName id='n" . $entry->name->id . "' nomenclaturalCode='{$nomenclaturalCode}'>\n";
$return .= " <Simple>" . htmlspecialchars($entry->name->string) . "</Simple>\n";
if ($rankCode) {
$return .= " <Rank code='{$rankCode}'>" . ucfirst(strtolower($entry->rank->translation->label)) . "</Rank>\n";
}
$return .= " <CanonicalName>\n";
$return .= " <Simple>" . htmlspecialchars($entry->name->canonical_form->string) . "</Simple>\n";
$return .= " </CanonicalName>\n";
if ($ahe = $entry->agents_hierarchy_entries) {
$return .= " <ProviderSpecificData>\n";
$return .= " <NameSources>\n";
foreach ($ahe as $k => $v) {
$return .= " <NameSource>\n";
$return .= " <Simple>" . htmlspecialchars($v->agent->full_name) . "</Simple>\n";
if ($v->agent_role) {
$return .= " <Role>" . htmlspecialchars($v->agent_role->translation->label) . "</Role>\n";
}
$return .= " </NameSource>\n";
}
$return .= " </NameSources>\n";
$return .= " </ProviderSpecificData>\n";
}
$return .= " </TaxonName>\n";
$return .= " </TaxonNames>\n";
$return .= " <TaxonConcepts>\n";
$return .= " <TaxonConcept id='c" . $entry->id . "'>\n";
$return .= " <Name scientific='true' ref='n" . $entry->name->id . "'>" . htmlspecialchars($entry->name->string) . "</Name>\n";
if ($rankCode) {
$return .= " <Rank code='{$rankCode}'>" . ucfirst(strtolower($entry->rank->translation->label)) . "</Rank>\n";
}
$return .= " <TaxonRelationships>\n";
if ($parent = $entry->parent()) {
$return .= " <TaxonRelationship type='is child taxon of'>\n";
$return .= " <ToTaxonConcept ref='{$this->api_url}?function=details_tcs&id=" . $parent->id . "' linkType='external'/>\n";
$return .= " </TaxonRelationship>\n";
}
if ($children = $entry->children()) {
foreach ($children as $k => $v) {
$return .= " <TaxonRelationship type='is parent taxon of'>\n";
$return .= " <ToTaxonConcept ref='{$this->api_url}?function=details_tcs&id=" . $v->id . "' linkType='external'/>\n";
$return .= " </TaxonRelationship>\n";
}
}
if ($synonyms = $entry->synonyms()) {
foreach ($synonyms as $k => $v) {
$relationship = "has synonym";
if (strtolower($v->synonym_relation->translation->label) == "common name") {
$relationship = "has vernacular";
}
$return .= " <TaxonRelationship type='{$relationship}'>\n";
$return .= " <ToTaxonConcept ref='{$this->api_url}?function=details_tcs&sid=" . $v->id . "' linkType='external'/>\n";
$return .= " </TaxonRelationship>\n";
}
}
$return .= " </TaxonRelationships>\n";
$return .= " </TaxonConcept>\n";
$return .= " </TaxonConcepts>\n";
return $return;
}
public static function move_entry($args)
{
$taxon_concept_id_from = @$args['taxon_concept_id_from'];
$hierarchy_entry_id = @$args['hierarchy_entry_id'];
$taxon_concept_id_to = @$args['taxon_concept_id_to'];
$bad_match_hierarchy_entry_id = @$args['bad_match_hierarchy_entry_id'];
$confirmation = @$args['confirmed'];
if (!$taxon_concept_id_from || !is_numeric($taxon_concept_id_from) || !$hierarchy_entry_id || !is_numeric($hierarchy_entry_id) || !$taxon_concept_id_to || !is_numeric($taxon_concept_id_to) || !$bad_match_hierarchy_entry_id || !is_numeric($bad_match_hierarchy_entry_id)) {
throw new \Exception("split_concept.php [taxon_concept_id_from] [hierarchy_entry_id] [taxon_concept_id_to] [bad_match_hierarchy_entry_id] [confirmed] [reindex?]");
}
\CodeBridge::print_message("Moving HE# {$hierarchy_entry_id} from TC# {$taxon_concept_id_from} to TC# " . "{$taxon_concept_id_to} avoiding HE# {$bad_match_hierarchy_entry_id}");
$tc_from = TaxonConcept::find($taxon_concept_id_from);
$tc_to = TaxonConcept::find($taxon_concept_id_to);
$he = HierarchyEntry::find($hierarchy_entry_id);
$bad_he = HierarchyEntry::find($bad_match_hierarchy_entry_id);
if (!$he->id || !$tc_from->id || !$tc_to->id || !$bad_he->id) {
throw new \Exception("Invalid ID");
}
if ($he->taxon_concept_id != $tc_from->id) {
throw new \Exception("This entry is not in the source concept");
}
if ($he->taxon_concept_id != $bad_he->taxon_concept_id) {
throw new \Exception("The bad match ID isn't from the same concept");
}
if ($confirmation == 'confirmed' || $confirmation == 'force') {
if ($confirmation == 'force') {
$force_move_if_disallowed = true;
} else {
$force_move_if_disallowed = false;
}
$user_id = 13;
# 13 is Patrick's user ID
// TODO Need to look through all the HEs in the TC we're moving *to* and cycle through them to make sure none of
// them are blocking the move:
foreach ($tc_to->hierarchy_entries as $tc_he) {
$GLOBALS['db_connection']->query("DELETE FROM curated_hierarchy_entry_relationships\n WHERE hierarchy_entry_id_1={$hierarchy_entry_id} AND hierarchy_entry_id_2=" . $tc_he->id . " AND equivalent=0");
}
$moved = HierarchyEntry::move_to_concept_static($hierarchy_entry_id, $taxon_concept_id_to, $force_move_if_disallowed, true);
if (!$moved) {
\CodeBridge::print_message("NOT ALLOWED: throwing exception");
throw new \Exception("This move is not allowed; it would affect other hierarchies");
}
$GLOBALS['db_connection']->query("INSERT IGNORE INTO curated_hierarchy_entry_relationships VALUES ({$hierarchy_entry_id}, {$bad_match_hierarchy_entry_id}, {$user_id}, 0)");
\CodeBridge::print_message("Done. Moved {$hierarchy_entry_id} to {$taxon_concept_id_to}");
} else {
echo "\n\nRemoving:\n";
print_r($he);
echo "Name: " . $he->name->string . "\n\nFrom:\n";
print_r($tc_from);
echo "To:\n";
print_r($tc_to);
$descendant_objects = TaxonConcept::count_descendants_objects($tc_from->id);
$descendants = TaxonConcept::count_descendants($tc_from->id);
echo "\n\nTaxonConcept1: {$tc_from->id}\n";
echo "Descendant Objects: {$descendant_objects}\n";
echo "Descendant Concepts: {$descendants}\n";
$descendant_objects = TaxonConcept::count_descendants_objects($tc_to->id);
$descendants = TaxonConcept::count_descendants($tc_to->id);
echo "\n\nTaxonConcept1: {$tc_to->id}\n";
echo "Descendant Objects: {$descendant_objects}\n";
echo "Descendant Concepts: {$descendants}\n";
echo "\n\nDon't forget to solr_update_concept.php\n\n";
}
}
