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"; } }