public function __construct()
{
$this->mysqli =& $GLOBALS['mysqli_connection'];
if ($GLOBALS['ENV_NAME'] == 'production' && environment_defined('slave')) {
$this->mysqli_slave = load_mysql_environment('slave');
} else {
$this->mysqli_slave =& $this->mysqli;
}
$this->sparql_client = SparqlClient::connection();
$this->published_id = TranslatedResourceStatus::find_or_create_by_label('Published')->id;
$this->trusted_id = Vetted::trusted()->id;
$this->unknown_id = Vetted::unknown()->id;
$this->untrusted_id = Vetted::untrusted()->id;
$this->visible_id = Visibility::visible()->id;
$this->invisible_id = Visibility::invisible()->id;
$this->master_curator_id = CuratorLevel::master_curator()->id;
$this->full_curator_id = CuratorLevel::full_curator()->id;
$this->assistant_curator_id = CuratorLevel::assistant_curator()->id;
$this->curator_ids = CuratorLevel::curator_ids();
$this->data_object_scope = ChangeableObjectType::data_object_scope();
$this->worms_content_partner_id = ContentPartner::find_or_create_by_full_name('World Register of Marine Species')->id;
$this->col_hierarchy_id = Hierarchy::find_or_create_by_label('Species 2000 & ITIS Catalogue of Life: Annual Checklist 2011')->id;
$this->latest_harvest_event_ids();
$this->worms_latest_harvest_event_id();
}
public function __construct()
{
$this->mysqli =& $GLOBALS['db_connection'];
if ($GLOBALS['ENV_NAME'] == 'production' && environment_defined('slave')) {
$this->mysqli_slave = load_mysql_environment('slave');
} else {
$this->mysqli_slave =& $this->mysqli;
}
$this->vetted_sort_orders = array();
$this->vetted_sort_orders[Vetted::trusted()->id] = 1;
$this->vetted_sort_orders[Vetted::unknown()->id] = 2;
$this->vetted_sort_orders[Vetted::untrusted()->id] = 3;
}
function get_word_count($taxon_concept_id, $chapter)
{
$concept_data_object_counts = array();
$text_id = DataType::find_or_create_by_schema_value('http://purl.org/dc/dcmitype/Text')->id;
$trusted_id = Vetted::trusted()->id;
$untrusted_id = Vetted::untrusted()->id;
$unreviewed_id = Vetted::unknown()->id;
if ($chapter == "brief summary") {
$toc_id = TranslatedTableOfContent::find_or_create_by_label('Brief Summary')->table_of_contents_id;
} elseif ($chapter == "comprehensive description") {
$toc_id = TranslatedTableOfContent::find_or_create_by_label('Comprehensive Description')->table_of_contents_id;
}
$query = "SELECT dotoc.toc_id,do.description, dohe.vetted_id FROM data_objects_taxon_concepts dotc \n JOIN data_objects do ON dotc.data_object_id = do.id LEFT JOIN data_objects_table_of_contents dotoc ON do.id = dotoc.data_object_id \n JOIN data_objects_hierarchy_entries dohe on do.id = dohe.data_object_id\n WHERE do.published = 1 AND dohe.visibility_id =" . Visibility::visible()->id . " AND do.data_type_id = {$text_id} AND dotc.taxon_concept_id = {$taxon_concept_id} AND dotoc.toc_id = {$toc_id}\n UNION\n SELECT dotoc.toc_id,do.description, udo.vetted_id FROM data_objects_taxon_concepts dotc \n JOIN data_objects do ON dotc.data_object_id = do.id LEFT JOIN data_objects_table_of_contents dotoc ON do.id = dotoc.data_object_id \n JOIN users_data_objects udo on do.id = udo.data_object_id\n WHERE do.published = 1 AND udo.visibility_id =" . Visibility::visible()->id . " AND do.data_type_id = {$text_id} AND dotc.taxon_concept_id = {$taxon_concept_id} AND dotoc.toc_id = {$toc_id}";
$result = $this->mysqli_slave->query($query);
while ($result && ($row = $result->fetch_assoc())) {
$description = $row['description'];
$vetted_id = $row['vetted_id'];
$words_count = str_word_count(strip_tags($description), 0);
@($concept_data_object_counts['total_w'] += $words_count);
if ($vetted_id == $trusted_id) {
@($concept_data_object_counts['t_w'] += $words_count);
} elseif ($vetted_id == $untrusted_id) {
@($concept_data_object_counts['ut_w'] += $words_count);
} elseif ($vetted_id == $unreviewed_id) {
@($concept_data_object_counts['ur_w'] += $words_count);
}
}
return @$concept_data_object_counts['total_w'];
}
function get_data_objects_count($batch_size = 100000)
{
$image_id = DataType::image()->id;
$text_id = DataType::text()->id;
$video_id = DataType::video()->id;
$sound_id = DataType::sound()->id;
$flash_id = DataType::flash()->id;
$youtube_id = DataType::youtube()->id;
$iucn_id = DataType::iucn()->id;
$data_type_label[$text_id] = 'text';
$data_type_label[$video_id] = 'video';
$data_type_label[$sound_id] = 'sound';
$data_type_label[$flash_id] = 'flash';
$data_type_label[$youtube_id] = 'youtube';
$data_type_label[$iucn_id] = 'iucn';
$data_type_order_in_file = array("text", "video", "sound", "flash", "youtube", "iucn");
$trusted_id = Vetted::trusted()->id;
$untrusted_id = Vetted::untrusted()->id;
$unreviewed_id = Vetted::unknown()->id;
$raw_stats = array();
$concept_info_items = array();
$concept_references = array();
for ($i = $this->min_taxon_concept_id; $i <= $this->max_taxon_concept_id; $i += $batch_size) {
$this->print_status($i, $batch_size);
$sql = "SELECT do.guid,\n dotc.taxon_concept_id,\n do.data_type_id,\n doii.info_item_id,\n dor.ref_id,\n REPLACE(REPLACE(do.description, '\\\\n', ' '), '\\\\r', ' '),\n dohe.vetted_id,\n do.id\n FROM data_objects_taxon_concepts dotc\n STRAIGHT_JOIN data_objects do ON (dotc.data_object_id = do.id)\n JOIN data_objects_hierarchy_entries dohe ON (do.id=dohe.data_object_id)\n LEFT JOIN data_objects_info_items doii ON (do.id = doii.data_object_id)\n LEFT JOIN data_objects_refs dor ON (do.id = dor.data_object_id)\n WHERE do.published = 1 AND dohe.visibility_id = " . Visibility::visible()->id . " AND do.data_type_id != {$image_id}";
if ($this->test_taxon_concept_ids) {
$sql .= " AND dotc.taxon_concept_id IN (" . $this->test_taxon_concept_ids . ")";
} else {
$sql .= " AND dotc.taxon_concept_id BETWEEN {$i} AND " . ($i + $batch_size);
}
$counted_data_objects = array();
foreach ($this->mysqli_slave->iterate_file($sql) as $row_number => $row) {
$taxon_concept_id = trim($row[0]);
$data_type_id = trim($row[1]);
$info_item_id = trim($row[2]);
$ref_id = trim($row[3]);
$description = trim($row[4]);
$vetted_id = trim($row[5]);
$data_object_id = trim($row[6]);
if (isset($counted_data_objects[$taxon_concept_id][$data_object_id])) {
continue;
}
$counted_data_objects[$taxon_concept_id][$data_object_id] = 1;
$label = @$data_type_label[$data_type_id];
$words_count = str_word_count(strip_tags($description), 0);
@$raw_stats[$taxon_concept_id][$label]['total']++;
@($raw_stats[$taxon_concept_id][$label]['total_w'] += $words_count);
if ($vetted_id == $trusted_id) {
@$raw_stats[$taxon_concept_id][$label]['t']++;
@($raw_stats[$taxon_concept_id][$label]['t_w'] += $words_count);
} elseif ($vetted_id == $untrusted_id) {
@$raw_stats[$taxon_concept_id][$label]['ut']++;
@($raw_stats[$taxon_concept_id][$label]['ut_w'] += $words_count);
} elseif ($vetted_id == $unreviewed_id) {
@$raw_stats[$taxon_concept_id][$label]['ur']++;
@($raw_stats[$taxon_concept_id][$label]['ur_w'] += $words_count);
}
$concept_info_items[$taxon_concept_id][$info_item_id] = '';
$concept_references[$taxon_concept_id][$ref_id] = '';
}
foreach ($raw_stats as $taxon_concept_id => $stats) {
$new_value = "";
# the stats need to go into the file in a certain order to be imported into the MySQL table
foreach ($data_type_order_in_file as $data_type) {
$new_value = @$stats[$data_type]['total'];
$new_value .= "\t" . @$stats[$data_type]['t'];
$new_value .= "\t" . @$stats[$data_type]['ut'];
$new_value .= "\t" . @$stats[$data_type]['ur'];
$new_value .= "\t" . @$stats[$data_type]['total_w'];
$new_value .= "\t" . @$stats[$data_type]['t_w'];
$new_value .= "\t" . @$stats[$data_type]['ut_w'];
$new_value .= "\t" . @$stats[$data_type]['ur_w'];
}
$raw_stats[$taxon_concept_id] = $new_value;
}
$this->save_category_stats($raw_stats, "get_data_objects_count");
$raw_stats = array();
if ($this->test_taxon_concept_ids) {
break;
}
}
// $this->save_to_json_file($concept_info_items, "concept_info_items");
// unset($concept_info_items);
//
// $this->save_to_json_file($concept_references, "concept_references");
// unset($concept_references);
}
function get_data_objects_count($batch_size = 100000)
{
$time_start = time_elapsed();
$concept_data_object_counts = array();
$concept_data_object_maps = array();
$concept_info_items = array();
$concept_references = array();
$image_id = DataType::image()->id;
$map_id = DataType::map()->id;
$text_id = DataType::text()->id;
$video_id = DataType::video()->id;
$sound_id = DataType::sound()->id;
$flash_id = DataType::flash()->id;
$youtube_id = DataType::youtube()->id;
$iucn_id = DataType::iucn()->id;
$data_type_label[$image_id] = 'image';
$data_type_label[$sound_id] = 'sound';
$data_type_label[$text_id] = 'text';
$data_type_label[$video_id] = 'video';
$data_type_label[$iucn_id] = 'iucn';
$data_type_label[$flash_id] = 'flash';
$data_type_label[$youtube_id] = 'youtube';
$trusted_id = Vetted::trusted()->id;
$untrusted_id = Vetted::untrusted()->id;
$unreviewed_id = Vetted::unknown()->id;
for ($i = $this->min_taxon_concept_id; $i <= $this->max_taxon_concept_id; $i += $batch_size) {
print "\n dataObjects, its infoItems, its references [2 of 14] {$i} \n";
$sql = "SELECT dotc.taxon_concept_id tc_id, do.data_type_id, doii.info_item_id, dor.ref_id, do.description, dohe.vetted_id, do.data_subtype_id\r\n FROM data_objects_taxon_concepts dotc \r\n JOIN data_objects do ON dotc.data_object_id = do.id \r\n LEFT JOIN data_objects_info_items doii ON do.id = doii.data_object_id \r\n LEFT JOIN data_objects_refs dor ON do.id = dor.data_object_id \r\n JOIN data_objects_hierarchy_entries dohe on do.id = dohe.data_object_id\r\n WHERE do.published=1 AND dohe.visibility_id=" . Visibility::visible()->id . " AND dohe.vetted_id != {$untrusted_id} ";
//." AND do.data_type_id <> $image_id "; this has to be removed to count maps
if (isset($GLOBALS['test_taxon_concept_ids'])) {
$sql .= " and dotc.taxon_concept_id IN (" . implode(",", $GLOBALS['test_taxon_concept_ids']) . ")";
} else {
$sql .= " AND dotc.taxon_concept_id BETWEEN {$i} AND " . ($i + $batch_size);
}
$sql .= "\r\n UNION\r\n SELECT dotc.taxon_concept_id tc_id, do.data_type_id, doii.info_item_id, dor.ref_id, do.description, udo.vetted_id, do.data_subtype_id\r\n FROM data_objects_taxon_concepts dotc \r\n JOIN data_objects do ON dotc.data_object_id = do.id \r\n LEFT JOIN data_objects_info_items doii ON do.id = doii.data_object_id \r\n LEFT JOIN data_objects_refs dor ON do.id = dor.data_object_id \r\n JOIN users_data_objects udo on do.id = udo.data_object_id\r\n WHERE do.published=1 AND udo.visibility_id=" . Visibility::visible()->id . "\r\n ";
if (isset($GLOBALS['test_taxon_concept_ids'])) {
$sql .= " and dotc.taxon_concept_id IN (" . implode(",", $GLOBALS['test_taxon_concept_ids']) . ")";
} else {
$sql .= " AND dotc.taxon_concept_id BETWEEN {$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]);
$data_type_id = trim($fields[1]);
$info_item_id = trim($fields[2]);
$ref_id = trim($fields[3]);
$description = trim($fields[4]);
$vetted_id = trim($fields[5]);
$data_subtype_id = trim($fields[6]);
$label = @$data_type_label[$data_type_id];
if ($data_subtype_id != $map_id) {
$words_count = str_word_count(strip_tags($description), 0);
@$concept_data_object_counts[$tc_id][$label]['total']++;
@($concept_data_object_counts[$tc_id][$label]['total_w'] += $words_count);
if ($vetted_id == $trusted_id) {
@$concept_data_object_counts[$tc_id][$label]['t']++;
@($concept_data_object_counts[$tc_id][$label]['t_w'] += $words_count);
} elseif ($vetted_id == $untrusted_id) {
@$concept_data_object_counts[$tc_id][$label]['ut']++;
@($concept_data_object_counts[$tc_id][$label]['ut_w'] += $words_count);
} elseif ($vetted_id == $unreviewed_id) {
@$concept_data_object_counts[$tc_id][$label]['ur']++;
@($concept_data_object_counts[$tc_id][$label]['ur_w'] += $words_count);
}
$concept_info_items[$tc_id][$info_item_id] = '';
$concept_references[$tc_id][$ref_id] = '';
} else {
@$concept_data_object_maps[$tc_id][$label]['total']++;
if ($vetted_id == $trusted_id) {
@$concept_data_object_maps[$tc_id][$label]['t']++;
} elseif ($vetted_id == $untrusted_id) {
@$concept_data_object_maps[$tc_id][$label]['ut']++;
} elseif ($vetted_id == $unreviewed_id) {
@$concept_data_object_maps[$tc_id][$label]['ur']++;
}
}
}
}
fclose($FILE);
unlink($outfile);
print "\n num_rows: {$num_rows}";
}
self::save_to_json_file($concept_info_items, "concept_info_items");
unset($concept_info_items);
self::save_to_json_file($concept_references, "concept_references");
unset($concept_references);
//save map data to be accessed later
self::save_to_json_file($concept_data_object_maps, "map_counts");
unset($concept_data_object_maps);
//convert associative array to a regular array
$data_type_order_in_file = array("text", "video", "sound", "flash", "youtube", "iucn");
foreach ($concept_data_object_counts as $taxon_concept_id => $taxon_object_counts) {
$new_value = "";
foreach ($data_type_order_in_file as $data_type) {
$new_value .= "\t" . @$taxon_object_counts[$data_type]['total'];
$new_value .= "\t" . @$taxon_object_counts[$data_type]['t'];
$new_value .= "\t" . @$taxon_object_counts[$data_type]['ut'];
$new_value .= "\t" . @$taxon_object_counts[$data_type]['ur'];
$new_value .= "\t" . @$taxon_object_counts[$data_type]['total_w'];
$new_value .= "\t" . @$taxon_object_counts[$data_type]['t_w'];
$new_value .= "\t" . @$taxon_object_counts[$data_type]['ut_w'];
$new_value .= "\t" . @$taxon_object_counts[$data_type]['ur_w'];
}
$concept_data_object_counts[$taxon_concept_id] = $new_value;
}
print "\n get_data_objects_count():" . (time_elapsed() - $time_start) / 60 . " minutes";
self::save_totals_to_cumulative_txt($concept_data_object_counts, "tpm_data_objects");
unset($concept_data_object_counts);
}
