public static function merge_concepts($args)
{
$taxon_concept_id_1 = @$args['id1'];
$taxon_concept_id_2 = @$args['id2'];
$confirmation = @$args['confirmed'];
if (!$taxon_concept_id_1 || !is_numeric($taxon_concept_id_1) || !$taxon_concept_id_2 || !is_numeric($taxon_concept_id_2)) {
throw new \Exception("supercede_concepts.php [id1] [id2] [confirmed]");
}
if ($confirmation == 'confirmed') {
\CodeBridge::print_message("Merging TC# {$taxon_concept_id_1} to {$taxon_concept_id_2}");
TaxonConcept::supercede_by_ids($taxon_concept_id_1, $taxon_concept_id_2, true);
// Only applicable if run via resque, but safe *enough* otherwise:
TaxonConcept::unlock_classifications_by_id($taxon_concept_id_1);
TaxonConcept::unlock_classifications_by_id($taxon_concept_id_2);
\CodeBridge::print_message("Done. Pages {$taxon_concept_id_1} and {$taxon_concept_id_2} have been merged to: " . min($taxon_concept_id_1, $taxon_concept_id_2));
} else {
$descendant_objects = TaxonConcept::count_descendants_objects($taxon_concept_id_1);
$descendants = TaxonConcept::count_descendants($taxon_concept_id_1);
echo "\n\nTaxonConcept1: " . $taxon_concept_id_1 . "\n";
echo "Descendant Objects: {$descendant_objects}\n";
echo "Descendant Concepts: {$descendants}\n";
$descendant_objects = TaxonConcept::count_descendants_objects($taxon_concept_id_2);
$descendants = TaxonConcept::count_descendants($taxon_concept_id_2);
echo "\n\nTaxonConcept2: " . $taxon_concept_id_2 . "\n";
echo "Descendant Objects: {$descendant_objects}\n";
echo "Descendant Concepts: {$descendants}\n";
}
}
public static function split_entry($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: {$descendant_objects}\n\n";
}
}
public static function reindex_concept($args)
{
$taxon_concept_id = $args['taxon_concept_id'];
if (!$taxon_concept_id || !is_numeric($taxon_concept_id)) {
throw new \Exception("The TaxonConceptID was missing or was not a number");
return;
}
Tasks::update_taxon_concept_names(array($taxon_concept_id));
$he = new FlattenHierarchies();
$he->flatten_hierarchies_from_concept_id($taxon_concept_id);
TaxonConcept::reindex_descendants_objects($taxon_concept_id);
TaxonConcept::reindex_for_search($taxon_concept_id);
TaxonConcept::unlock_classifications_by_id($taxon_concept_id);
}
public static function update_concept($taxon_concept_id)
{
if (!$taxon_concept_id || !is_numeric($taxon_concept_id)) {
echo "\n\n\t#update_concept([taxon_concept_id])\n\n";
return false;
}
$taxon_concept = TaxonConcept::find($taxon_concept_id);
Tasks::update_taxon_concept_names($taxon_concept_id);
$he = new FlattenHierarchies();
$he->flatten_hierarchies_from_concept_id($taxon_concept_id);
// make sure hierarchy info is up-to-date
TaxonConcept::reindex_descendants_objects($taxon_concept_id);
// make sure objects are indexed for display
TaxonConcept::reindex_for_search($taxon_concept_id);
// make sure objects are indexed for search
}
public static function assign_concepts_across_hierarchies($hierarchy1, $hierarchy2, $confirmed_exclusions = array(), $use_synonyms_for_merging = false)
{
$mysqli =& $GLOBALS['mysqli_connection'];
debug("Assigning concepts from {$hierarchy2->label} ({$hierarchy2->id}) to {$hierarchy1->label} ({$hierarchy1->id})");
// hierarchy is the same and its 'complete' meaning its been curated and
// all nodes should be different taxa so there no need to compare it to
// itself. Other hierarchies are not 'complete' such as Flickr which can
// have several entries for the same taxon
if ($hierarchy1->id == $hierarchy2->id && $hierarchy1->complete) {
debug("Skipping:: Hierarchies are equivilant and Complete");
return;
}
// store all changes made this session
$superceded = array();
$entries_matched = array();
$concepts_seen = array();
$visible_id = Visibility::visible()->id;
$preview_id = Visibility::preview()->id;
$solr = new SolrAPI(SOLR_SERVER, 'hierarchy_entry_relationship');
$main_query = "hierarchy_id_1:{$hierarchy1->id} AND (visibility_id_1:{$visible_id} OR visibility_id_1:{$preview_id}) AND hierarchy_id_2:{$hierarchy2->id} AND (visibility_id_2:{$visible_id} OR visibility_id_2:{$preview_id}) AND same_concept:false&sort=relationship asc, visibility_id_1 asc, visibility_id_2 asc, confidence desc, hierarchy_entry_id_1 asc, hierarchy_entry_id_2 asc";
$response = $solr->query($main_query . "&rows=1");
$total_results = $response->numFound;
unset($response);
debug("querying solr(hierarchy_entry_relationship), got {$total_results} relations..");
$mysqli->begin_transaction();
for ($i = 0; $i < $total_results; $i += self::$solr_iteration_size) {
// the global variable which will hold all mathces for this iteration
$GLOBALS['hierarchy_entry_matches'] = array();
$this_query = $main_query . "&rows=" . self::$solr_iteration_size . "&start={$i}";
$entries = $solr->get_results($this_query);
foreach ($entries as $entry) {
if ($entry->relationship == 'syn') {
if (!$use_synonyms_for_merging) {
continue;
}
if ($entry->confidence < 0.25) {
continue;
}
}
$id1 = $entry->hierarchy_entry_id_1;
$visibility_id1 = $entry->visibility_id_1;
$tc_id1 = $entry->taxon_concept_id_1;
$id2 = $entry->hierarchy_entry_id_2;
$visibility_id2 = $entry->visibility_id_2;
$tc_id2 = $entry->taxon_concept_id_2;
$score = $entry->confidence;
// this node in hierarchy 1 has already been matched
if ($hierarchy1->complete && isset($entries_matched[$id2])) {
continue;
}
if ($hierarchy2->complete && isset($entries_matched[$id1])) {
continue;
}
$entries_matched[$id1] = 1;
$entries_matched[$id2] = 1;
// this comparison happens here instead of the query to ensure
// the sorting is always the same if this happened in the query
// and the entry was related to more than one taxa, and this
// function is run more than once then we'll start to get huge
// groups of concepts - all transitively related to one another
if ($tc_id1 == $tc_id2) {
continue;
}
// get all the recent supercedures withouth looking in the DB
while (isset($superceded[$tc_id1])) {
$tc_id1 = $superceded[$tc_id1];
}
while (isset($superceded[$tc_id2])) {
$tc_id2 = $superceded[$tc_id2];
}
if ($tc_id1 == $tc_id2) {
continue;
}
$tc_id1 = TaxonConcept::get_superceded_by($tc_id1);
$tc_id2 = TaxonConcept::get_superceded_by($tc_id2);
if ($tc_id1 == $tc_id2) {
continue;
}
// if even after all recent changes we still have different
// concepts, merge them
if ($tc_id1 != $tc_id2) {
debug("Comparing hierarchy_entry({$id1}) :: hierarchy_entry({$id2})");
// compare visible entries to other published entries
if ($hierarchy1->complete && $visibility_id1 == $visible_id && self::concept_published_in_hierarchy($tc_id2, $hierarchy1->id)) {
debug("NO: concept 2 published in hierarchy 1");
continue;
}
if ($hierarchy2->complete && $visibility_id2 == $visible_id && self::concept_published_in_hierarchy($tc_id1, $hierarchy2->id)) {
debug("NO: concept 1 published in hierarchy 2");
continue;
}
// compare preview entries to entries in the latest harvest events
if ($hierarchy1->complete && $visibility_id1 == $preview_id && self::concept_preview_in_hierarchy($tc_id2, $hierarchy1->id)) {
debug("NO: concept 2 preview in hierarchy 1");
continue;
}
if ($hierarchy2->complete && $visibility_id2 == $preview_id && self::concept_preview_in_hierarchy($tc_id1, $hierarchy2->id)) {
debug("NO: concept 1 preview in hierarchy 2");
continue;
}
if (self::curators_denied_relationship($id1, $tc_id1, $id2, $tc_id2, $superceded, $confirmed_exclusions)) {
debug("The merger of {$id1} and {$id2} (concepts {$tc_id1} and {$tc_id2}) has been rejected by a curator");
continue;
}
if ($hierarchy_id = self::concept_merger_effects_other_hierarchies($tc_id1, $tc_id2)) {
debug("The merger of {$id1} and {$id2} (concepts {$tc_id1} and {$tc_id2}) is not allowed by a curated hierarchy ({$hierarchy_id})");
continue;
}
debug("TaxonMatch::({$tc_id1}) = ({$tc_id2})");
debug("TaxonConcept::supercede_by_ids({$tc_id1}, {$tc_id2})");
TaxonConcept::supercede_by_ids($tc_id1, $tc_id2);
$superceded[max($tc_id1, $tc_id2)] = min($tc_id1, $tc_id2);
static $count = 0;
$count++;
if ($count % 50 == 0) {
$mysqli->commit();
}
}
}
}
$mysqli->end_transaction();
}
private function get_stats_for_family($taxon_concept_id)
{
$query = "SELECT COUNT(DISTINCT he_children.taxon_concept_id) as count\n FROM hierarchy_entries he\n JOIN hierarchy_entries_flattened hef on (he.id=hef.ancestor_id)\n JOIN hierarchy_entries he_children on (hef.hierarchy_entry_id=he_children.id)\n JOIN taxon_concepts tc on (he_children.taxon_concept_id=tc.id)\n JOIN hierarchies h on (he_children.hierarchy_id=h.id)\n LEFT JOIN taxon_concept_metrics tcm ON (he_children.taxon_concept_id=tcm.taxon_concept_id)\n WHERE he.taxon_concept_id={$taxon_concept_id}\n AND he.published=1\n AND tc.published=1\n AND tc.supercedure_id=0\n AND he.visibility_id=" . Visibility::visible()->id . "\n AND he_children.rank_id IN (" . Rank::find_by_translated('label', 'sp.')->id . ", " . Rank::find_by_translated('label', 'species')->id . ")\n AND tcm.richness_score >= .4";
$count_of_rich_species = $this->mysqli->select_value($query);
$media_counts = TaxonConcept::media_counts($taxon_concept_id);
$all_media_count = @$media_counts['image'] + @$media_counts['video'] + @$media_counts['sound'];
return array('NumberRichSpeciesPagesInEOL' => $count_of_rich_species, 'NumberImagesInEOL' => @$media_counts['image'], 'NumberArticlesInEOL' => @$media_counts['text'], 'NumberMediaInEOL' => $all_media_count, 'RichPageOnEOL' => $count_of_rich_species >= 0 ? 'http://eol.org/schema/terms/yes' : 'http://eol.org/schema/terms/no');
}
public static function move_entry($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";
}
}