function get_synonyms_count($batch_size = 500000)
{
$raw_stats = array();
for ($i = $this->min_taxon_concept_id; $i <= $this->max_taxon_concept_id; $i += $batch_size) {
$this->print_status($i, $batch_size);
$sql = "SELECT he.taxon_concept_id, s.name_id, s.hierarchy_id\n FROM hierarchy_entries he FORCE INDEX (concept_published_visible)\n JOIN synonyms s ON he.id = s.hierarchy_entry_id JOIN hierarchies h ON s.hierarchy_id = h.id\n WHERE s.synonym_relation_id NOT IN (" . SynonymRelation::find_by_translated('label', "common name")->id . "," . SynonymRelation::find_by_translated('label', "genbank common name")->id . ")\n AND h.browsable=1 AND he.published=1 AND he.visibility_id=" . Visibility::visible()->id;
if ($this->test_taxon_concept_ids) {
$sql .= " AND he.taxon_concept_id IN (" . $this->test_taxon_concept_ids . ")";
} else {
$sql .= " AND he.taxon_concept_id BETWEEN {$i} AND " . ($i + $batch_size);
}
foreach ($this->mysqli_slave->iterate_file($sql) as $row_number => $row) {
$taxon_concept_id = trim($row[0]);
$name_id = trim($row[1]);
$hierarchy_id = trim($row[2]);
$raw_stats[$taxon_concept_id]['synonyms'][$name_id] = 1;
$raw_stats[$taxon_concept_id]['synonym_providers'][$hierarchy_id] = 1;
}
//convert associative array to a regular array
foreach ($raw_stats as $taxon_concept_id => $stats) {
$new_value = isset($stats['synonyms']) ? count($stats['synonyms']) : '';
$new_value .= "\t" . (isset($stats['synonym_providers']) ? count($stats['synonym_providers']) : '');
$raw_stats[$taxon_concept_id] = $new_value;
}
$this->save_category_stats($raw_stats, "get_synonyms_count");
$raw_stats = array();
if ($this->test_taxon_concept_ids) {
break;
}
}
}
function get_synonyms_count($batch_size = 500000)
{
$time_start = time_elapsed();
$arr_taxa = array();
$enable = 1;
if (!$enable) {
self::save_totals_to_cumulative_txt($arr_taxa, "tpm_synonyms");
unset($arr_taxa);
return;
}
$tc_name_id = array();
$tc_hierarchy_id = array();
for ($i = $this->min_taxon_concept_id; $i <= $this->max_taxon_concept_id; $i += $batch_size) {
print "\n synonyms and its providers [11 of 14] {$i} \n";
$sql = "SELECT he.taxon_concept_id tc_id, s.name_id, s.hierarchy_id h_id FROM hierarchy_entries he JOIN synonyms s ON he.id = s.hierarchy_entry_id JOIN hierarchies h ON s.hierarchy_id = h.id WHERE s.synonym_relation_id NOT IN (" . SynonymRelation::find_by_translated('label', "common name")->id . "," . SynonymRelation::find_by_translated('label', "genbank common name")->id . ") AND h.browsable=1 AND he.published=1 AND he.visibility_id=" . Visibility::visible()->id;
if (isset($GLOBALS['test_taxon_concept_ids'])) {
$sql .= " and he.taxon_concept_id IN (" . implode(",", $GLOBALS['test_taxon_concept_ids']) . ")";
} else {
$sql .= " AND he.taxon_concept_id BETWEEN {$i} AND " . ($i + $batch_size);
}
$outfile = $this->mysqli_slave->select_into_outfile($sql);
$FILE = fopen($outfile, "r");
if (!$FILE) {
print "!! ERROR: Could not read {$outfile}";
debug("!! ERROR: Could not read {$outfile}");
return;
}
$num_rows = 0;
while (!feof($FILE)) {
if ($line = fgets($FILE)) {
$num_rows++;
$line = trim($line);
$fields = explode("\t", $line);
$tc_id = trim($fields[0]);
$name_id = trim($fields[1]);
$h_id = trim($fields[2]);
$tc_name_id[$tc_id][$name_id] = '';
$tc_hierarchy_id[$tc_id][$h_id] = '';
}
}
fclose($FILE);
unlink($outfile);
print "\n num_rows: {$num_rows}";
}
foreach ($tc_name_id as $id => $rec) {
@($arr_taxa[$id]['count'] = sizeof($rec));
}
unset($tc_name_id);
foreach ($tc_hierarchy_id as $id => $rec) {
@($arr_taxa[$id]['providers'] = sizeof($rec));
}
unset($tc_hierarchy_id);
//convert associative array to a regular array
foreach ($arr_taxa as $tc_id => $taxon_synonym_counts) {
$new_value = "";
$new_value .= "\t" . @$taxon_synonym_counts['count'];
$new_value .= "\t" . @$taxon_synonym_counts['providers'];
$arr_taxa[$tc_id] = $new_value;
}
print "\n get_synonyms_count():" . (time_elapsed() - $time_start) / 60 . " minutes";
self::save_totals_to_cumulative_txt($arr_taxa, "tpm_synonyms");
unset($arr_taxa);
}
