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($concept_references);
}
public static function read_taxon_xml($t, $resource)
{
$t_dc = $t->children("http://purl.org/dc/elements/1.1/");
$t_dcterms = $t->children("http://purl.org/dc/terms/");
$t_dwc = $t->children("http://rs.tdwg.org/dwc/dwcore/");
$taxon_parameters = array();
$taxon_parameters["identifier"] = Functions::import_decode($t_dc->identifier);
$taxon_parameters["source_url"] = Functions::import_decode($t_dc->source);
$taxon_parameters["kingdom"] = Functions::import_decode($t_dwc->Kingdom);
$taxon_parameters["phylum"] = Functions::import_decode($t_dwc->Phylum);
$taxon_parameters["class"] = Functions::import_decode($t_dwc->Class);
$taxon_parameters["order"] = Functions::import_decode($t_dwc->Order);
$taxon_parameters["family"] = Functions::import_decode($t_dwc->Family);
$taxon_parameters["genus"] = Functions::import_decode($t_dwc->Genus);
$taxon_parameters["scientific_name"] = Functions::import_decode($t_dwc->ScientificName);
$taxon_parameters["rank"] = Rank::find_or_create_by_translated_label(Functions::import_decode($t->rank));
$taxon_parameters["taxon_created_at"] = trim($t_dcterms->created);
$taxon_parameters["taxon_modified_at"] = trim($t_dcterms->modified);
if ($taxon_parameters["scientific_name"]) {
$taxon_parameters["name"] = Name::find_or_create_by_string($taxon_parameters["scientific_name"]);
} else {
if ($name = $taxon_parameters["genus"]) {
$taxon_parameters["scientific_name"] = $name;
$taxon_parameters["name"] = Name::find_or_create_by_string($name);
$taxon_parameters["genus"] = "";
} elseif ($name = $taxon_parameters["family"]) {
$taxon_parameters["scientific_name"] = $name;
$taxon_parameters["name"] = Name::find_or_create_by_string($name);
$taxon_parameters["family"] = "";
} elseif ($name = $taxon_parameters["order"]) {
$taxon_parameters["scientific_name"] = $name;
$taxon_parameters["name"] = Name::find_or_create_by_string($name);
$taxon_parameters["order"] = "";
} elseif ($name = $taxon_parameters["class"]) {
$taxon_parameters["scientific_name"] = $name;
$taxon_parameters["name"] = Name::find_or_create_by_string($name);
$taxon_parameters["class"] = "";
} elseif ($name = $taxon_parameters["phylum"]) {
$taxon_parameters["scientific_name"] = $name;
$taxon_parameters["name"] = Name::find_or_create_by_string($name);
$taxon_parameters["phylum"] = "";
} elseif ($name = $taxon_parameters["kingdom"]) {
$taxon_parameters["scientific_name"] = $name;
$taxon_parameters["name"] = Name::find_or_create_by_string($name);
$taxon_parameters["kingdom"] = "";
} else {
return;
}
}
$taxon_parameters["common_names"] = array();
foreach ($t->commonName as $c) {
$common_name = Functions::import_decode((string) $c);
if (!$common_name) {
continue;
}
$xml_attr = $c->attributes("http://www.w3.org/XML/1998/namespace");
$params = array("name" => $common_name, "language" => Language::find_or_create_for_parser(@Functions::import_decode($xml_attr["lang"])));
$taxon_parameters["common_names"][] = $params;
}
$taxon_parameters["synonyms"] = array();
foreach ($t->synonym as $s) {
$synonym = Functions::import_decode((string) $s);
if (!$synonym) {
continue;
}
$attr = $s->attributes();
if (!@$attr["relationship"]) {
$attr["relationship"] = 'synonym';
}
$params = array("name" => Name::find_or_create_by_string($synonym), "synonym_relation" => SynonymRelation::find_or_create_by_translated_label(trim($attr["relationship"])));
$taxon_parameters["synonyms"][] = $params;
}
$taxon_parameters["agents"] = array();
foreach ($t->agent as $a) {
$agent_name = Functions::import_decode((string) $a);
if (!$agent_name) {
continue;
}
$attr = $a->attributes();
$params = array("full_name" => Functions::import_decode((string) $a, 0, 0), "homepage" => @Functions::import_decode($attr["homepage"]), "logo_url" => @Functions::import_decode($attr["logoURL"]), "agent_role" => AgentRole::find_or_create_by_translated_label(@trim($attr["role"])));
$taxon_parameters["agents"][] = $params;
unset($params);
}
$taxon_parameters["refs"] = array();
foreach ($t->reference as $r) {
$reference = Functions::import_decode((string) $r, 0, 0);
if (!$reference) {
continue;
}
$ref = Reference::find_or_create_by_full_reference($reference);
$taxon_parameters["refs"][] = $ref;
$id_labels = array("bici", "coden", "doi", "eissn", "handle", "issn", "isbn", "lsid", "oclc", "sici", "url", "urn");
$attr = $r->attributes();
foreach ($id_labels as $label) {
if ($id = @Functions::import_decode($attr[$label], 0, 0)) {
$type = RefIdentifierType::find_or_create_by_label($label);
$ref->add_ref_identifier(@$type->id ?: 0, $id);
}
}
}
$taxon_parameters["data_objects"] = array();
foreach ($t->dataObject as $d) {
$d_dc = $d->children("http://purl.org/dc/elements/1.1/");
$d_dcterms = $d->children("http://purl.org/dc/terms/");
$d_geo = $d->children("http://www.w3.org/2003/01/geo/wgs84_pos#");
$data_object = new DataObject();
$data_object->identifier = Functions::import_decode($d_dc->identifier);
$data_object->data_type = DataType::find_or_create_by_schema_value(Functions::import_decode($d->dataType));
$data_object->mime_type = MimeType::find_or_create_by_translated_label(Functions::import_decode($d->mimeType));
$data_object->object_created_at = Functions::import_decode($d_dcterms->created);
$data_object->object_modified_at = Functions::import_decode($d_dcterms->modified);
$data_object->object_title = Functions::import_decode($d_dc->title, 0, 0);
$data_object->language = Language::find_or_create_for_parser(Functions::import_decode($d_dc->language));
$data_object->license = License::find_or_create_for_parser(Functions::import_decode($d->license));
$data_object->rights_statement = Functions::import_decode($d_dc->rights, 0, 0);
$data_object->rights_holder = Functions::import_decode($d_dcterms->rightsHolder, 0, 0);
$data_object->bibliographic_citation = Functions::import_decode($d_dcterms->bibliographicCitation, 0, 0);
$data_object->source_url = Functions::import_decode($d_dc->source);
$data_object->description = Functions::import_decode($d_dc->description, 0, 0);
$data_object->object_url = Functions::import_decode($d->mediaURL);
$data_object->thumbnail_url = Functions::import_decode($d->thumbnailURL);
$data_object->location = Functions::import_decode($d->location, 0, 0);
if (@$d->additionalInformation) {
$data_object->additional_information = (array) $d->additionalInformation;
}
if ($r = (string) @$d->additionalInformation->rating) {
if (is_numeric($r) && $r > 0 && $r <= 5) {
$data_object->data_rating = $r;
}
}
if ($subtype = @$d->additionalInformation->subtype) {
if ($dt = DataType::find_or_create_by_schema_value(Functions::import_decode($subtype))) {
$data_object->data_subtype_id = $dt->id;
}
}
$data_object_parameters = array();
if (!$data_object->language) {
$xml_attr = $d_dc->description->attributes("http://www.w3.org/XML/1998/namespace");
$data_object->language = Language::find_or_create_for_parser(@Functions::import_decode($xml_attr["lang"]));
}
if (!$data_object->language && $resource->language) {
$data_object->language = $resource->language;
}
//TODO - update this
if ($data_object->mime_type && $data_object->mime_type->equals(MimeType::flash()) && $data_object->is_video()) {
$data_object->data_type = DataType::youtube();
$data_object->data_type_id = DataType::youtube()->id;
}
//take the taxon's source_url if none present
if (!@$data_object->source_url && @$taxon_parameters["source_url"]) {
$data_object->source_url = $taxon_parameters["source_url"];
}
// Turn newlines into paragraphs
$data_object->description = str_replace("\n", "</p><p>", $data_object->description);
/* Checking requirements*/
//if text: must have description
if ($data_object->data_type->equals(DataType::text()) && !$data_object->description) {
continue;
}
//if image, movie or sound: must have object_url
if (($data_object->data_type->equals(DataType::video()) || $data_object->data_type->equals(DataType::sound()) || $data_object->data_type->equals(DataType::image())) && !$data_object->object_url) {
continue;
}
$data_object->latitude = 0;
$data_object->longitude = 0;
$data_object->altitude = 0;
foreach ($d_geo->Point as $p) {
$p_geo = $p->children("http://www.w3.org/2003/01/geo/wgs84_pos#");
$data_object->latitude = Functions::import_decode($p_geo->lat);
$data_object->longitude = Functions::import_decode($p_geo->long);
$data_object->altitude = Functions::import_decode($p_geo->alt);
}
$data_object_parameters["agents"] = array();
foreach ($d->agent as $a) {
$agent_name = Functions::import_decode((string) $a);
if (!$agent_name) {
continue;
}
$attr = $a->attributes();
$params = array("full_name" => Functions::import_decode((string) $a, 0, 0), "homepage" => @Functions::import_decode($attr["homepage"]), "logo_url" => @Functions::import_decode($attr["logoURL"]), "agent_role" => AgentRole::find_or_create_by_translated_label(@trim($attr["role"])));
$data_object_parameters["agents"][] = $params;
unset($params);
}
$data_object_parameters["audiences"] = array();
foreach ($d->audience as $a) {
$data_object_parameters["audiences"][] = Audience::find_or_create_by_translated_label(trim((string) $a));
}
$data_object_parameters["info_items"] = array();
foreach ($d->subject as $s) {
$data_object_parameters["info_items"][] = InfoItem::find_or_create_by_schema_value(trim((string) $s));
}
if ($subject = @$d->additionalInformation->subject) {
if ($ii = InfoItem::find_or_create_by_schema_value(trim((string) $subject))) {
$data_object_parameters["info_items"] = array($ii);
}
}
// EXCEPTIONS
if ($data_object->is_text()) {
if ($resource->title == "BOLD Systems Resource") {
// EXCEPTION - overriding the subject for BOLD
$data_object_parameters["info_items"] = array(InfoItem::find_or_create_by_schema_value('http://www.eol.org/voc/table_of_contents#Barcode'));
} elseif ($resource->title == "Wikipedia") {
// EXCEPTION - overriding the subject for Wikipedia
$data_object_parameters["info_items"] = array(InfoItem::find_or_create_by_schema_value('http://www.eol.org/voc/table_of_contents#Wikipedia'));
} elseif ($resource->title == "IUCN Red List") {
if ($data_object->object_title == "IUCNConservationStatus") {
// EXCEPTION - overriding the data type for IUCN text
$data_object->data_type_id = DataType::iucn()->id;
$data_object->data_type = DataType::iucn();
}
}
}
$data_object_parameters["refs"] = array();
foreach ($d->reference as $r) {
$reference = Functions::import_decode((string) $r, 0, 0);
if (!$reference) {
continue;
}
$ref = Reference::find_or_create_by_full_reference($reference);
$data_object_parameters["refs"][] = $ref;
$id_labels = array("bici", "coden", "doi", "eissn", "handle", "issn", "isbn", "lsid", "oclc", "sici", "url", "urn");
$attr = $r->attributes();
foreach ($id_labels as $label) {
if ($id = @Functions::import_decode($attr[$label], 0, 0)) {
$type = RefIdentifierType::find_or_create_by_label($label);
$ref->add_ref_identifier(@$type->id ?: 0, $id);
}
}
}
$taxon_parameters["data_objects"][] = array($data_object, $data_object_parameters);
unset($data_object);
}
return $taxon_parameters;
}
function get_data_objects_count($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);
}
