function get_all_taxa()
{
require_library('connectors/INBioAPI');
$func = new INBioAPI();
$paths = $func->extract_archive_file($this->dwca_file, "meta.xml");
$archive_path = $paths['archive_path'];
$temp_dir = $paths['temp_dir'];
$harvester = new ContentArchiveReader(NULL, $archive_path);
$tables = $harvester->tables;
if (!($this->fields["taxa"] = $tables["http://rs.tdwg.org/dwc/terms/taxon"][0]->fields)) {
debug("Invalid archive file. Program will terminate.");
return false;
}
self::build_taxa_rank_array($harvester->process_row_type('http://rs.tdwg.org/dwc/terms/Taxon'));
self::create_instances_from_taxon_object($harvester->process_row_type('http://rs.tdwg.org/dwc/terms/Taxon'));
self::get_objects($harvester->process_row_type('http://eol.org/schema/media/Document'));
self::get_references($harvester->process_row_type('http://rs.gbif.org/terms/1.0/Reference'));
self::get_agents($harvester->process_row_type('http://eol.org/schema/agent/Agent'));
self::get_vernaculars($harvester->process_row_type('http://rs.gbif.org/terms/1.0/VernacularName'));
$this->archive_builder->finalize(TRUE);
// remove temp dir
recursive_rmdir($temp_dir);
echo "\n temporary directory removed: " . $temp_dir;
print_r($this->debug);
}
function export_gbif_to_eol($params)
{
require_library('connectors/INBioAPI');
$func = new INBioAPI();
$paths = $func->extract_archive_file($params["dwca_file"], "meta.xml");
$archive_path = $paths['archive_path'];
$temp_dir = $paths['temp_dir'];
$harvester = new ContentArchiveReader(NULL, $archive_path);
$tables = $harvester->tables;
if (!($this->fields["occurrence"] = $tables["http://rs.tdwg.org/dwc/terms/occurrence"][0]->fields)) {
debug("Invalid archive file. Program will terminate.");
return false;
}
/*
$harvester->process_row_type() - this will convert rows into array.
*/
// $r = $harvester->process_row_type('http://rs.tdwg.org/dwc/terms/occurrence');
// $r = $harvester->process_row_type('http://rs.gbif.org/terms/1.0/Multimedia');
// print_r($r); exit;
self::create_instances_from_taxon_object($harvester->process_row_type('http://rs.tdwg.org/dwc/terms/occurrence'));
self::get_media_objects($harvester->process_row_type('http://rs.gbif.org/terms/1.0/Multimedia'));
// self::get_objects($harvester->process_row_type('http://eol.org/schema/media/Document'));
// self::get_references($harvester->process_row_type('http://rs.gbif.org/terms/1.0/Reference'));
// self::get_agents($harvester->process_row_type('http://eol.org/schema/agent/Agent'));
// self::get_vernaculars($harvester->process_row_type('http://rs.gbif.org/terms/1.0/VernacularName'));
$this->archive_builder->finalize(TRUE);
// remove temp dir
recursive_rmdir($temp_dir);
echo "\n temporary directory removed: " . $temp_dir;
}
function check_unique_ids($resource_id, $file_extension = ".tab")
{
$harvester = new ContentArchiveReader(NULL, CONTENT_RESOURCE_LOCAL_PATH . $resource_id . "/");
$tables = $harvester->tables;
$tables = array_keys($tables);
// $tables = array_diff($tables, array("http://rs.tdwg.org/dwc/terms/measurementorfact")); //exclude measurementorfact
$tables = array_diff($tables, array("http://rs.gbif.org/terms/1.0/vernacularname"));
//exclude vernacular name
print_r($tables);
foreach ($tables as $table) {
self::process_fields($harvester->process_row_type($table), pathinfo($table, PATHINFO_BASENAME));
}
}
function get_all_taxa()
{
require_library('connectors/INBioAPI');
$func = new INBioAPI();
$paths = $func->extract_archive_file($this->dwca_file, "meta.xml");
$archive_path = $paths['archive_path'];
$harvester = new ContentArchiveReader(NULL, $archive_path);
$tables = $harvester->tables;
if (!($this->fields["taxa"] = $tables["http://rs.tdwg.org/dwc/terms/taxon"][0]->fields)) {
debug("Invalid archive file. Program will terminate.");
return false;
}
$row_types = self::get_XML_fields($paths["temp_dir"] . "meta.xml", "rowType");
/* manual assignment, use this if some referenceID in Measurements don't exist in References.tab
$row_types = array("http://eol.org/schema/reference/Reference", "http://rs.tdwg.org/dwc/terms/Taxon", "http://rs.tdwg.org/dwc/terms/MeasurementOrFact", "http://rs.tdwg.org/dwc/terms/Occurrence");
*/
print_r($row_types);
foreach ($row_types as $row_type) {
$basename = pathinfo($row_type, PATHINFO_BASENAME);
if ($basename == "Taxon") {
$allowed_fields = array("taxonID", "scientificName", "parentNameUsageID", "kingdom", "phylum", "class", "order", "family", "genus", "taxonRank", "furtherInformationURL", "taxonomicStatus", "taxonRemarks", "namePublishedIn", "referenceID");
} else {
$allowed_fields = self::get_XML_fields($this->extensions[$basename], "property name");
}
//manual adjustment
if ($row_type == "VernacularName") {
$allowed_fields[] = "taxonID";
}
self::process_fields($harvester->process_row_type($row_type), $basename, $allowed_fields);
// e.g. self::process_fields($harvester->process_row_type('http://rs.tdwg.org/dwc/terms/Taxon'), "Taxon");
}
$this->archive_builder->finalize(TRUE);
recursive_rmdir($paths['temp_dir']);
// remove temp dir
echo "\n temporary directory removed: " . $paths['temp_dir'];
print_r($this->debug);
}
function get_all_taxa()
{
require_library('connectors/INBioAPI');
$func = new INBioAPI();
$paths = $func->extract_archive_file($this->dwca_file, "meta.xml");
$archive_path = $paths['archive_path'];
$harvester = new ContentArchiveReader(NULL, $archive_path);
$tables = $harvester->tables;
if (!($this->fields["taxa"] = $tables["http://rs.tdwg.org/dwc/terms/taxon"][0]->fields)) {
debug("Invalid archive file. Program will terminate.");
return false;
}
if ($records = $harvester->process_row_type('http://rs.gbif.org/terms/1.0/Reference')) {
self::get_references($records);
}
if ($records = $harvester->process_row_type('http://rs.tdwg.org/dwc/terms/Taxon')) {
$taxa_id_list = self::get_taxa_id_list($records);
self::create_instances_from_taxon_object($records, $taxa_id_list);
}
if ($this->params["process occurrence"]) {
echo "\nProcessed OCCURRENCE\n";
if ($records = $harvester->process_row_type('http://rs.tdwg.org/dwc/terms/Occurrence')) {
$this->uris = self::get_uris();
self::get_occurrences($records);
}
}
if ($records = $harvester->process_row_type('http://rs.gbif.org/terms/1.0/Distribution')) {
self::get_distributions($records);
}
if ($records = $harvester->process_row_type('http://rs.gbif.org/terms/1.0/Image')) {
self::get_images($records);
}
//http://eol.org/content_partners/159/resources/345
if ($records = $harvester->process_row_type('http://rs.gbif.org/terms/1.0/Description')) {
self::get_descriptions($records);
}
//http://eol.org/content_partners/159/resources/332
if ($records = $harvester->process_row_type('http://rs.gbif.org/terms/1.0/VernacularName')) {
self::get_vernaculars($records);
}
$this->archive_builder->finalize(TRUE);
// remove temp dir
recursive_rmdir($paths['temp_dir']);
echo "\n temporary directory removed: " . $paths['temp_dir'];
print_r($this->debug);
}
private function combine_all_temp_archives($batches, $resource_id)
{
$this->path_to_archive_directory = CONTENT_RESOURCE_LOCAL_PATH . '/' . $resource_id . '_working/';
$this->archive_builder = new \eol_schema\ContentArchiveBuilder(array('directory_path' => $this->path_to_archive_directory));
for ($i = 1; $i <= $batches; $i++) {
$dir = CONTENT_RESOURCE_LOCAL_PATH . $resource_id . "_" . $i . "_working/";
$harvester = new ContentArchiveReader(NULL, $dir);
$tables = $harvester->tables;
if (!($this->fields["taxa"] = $tables["http://rs.tdwg.org/dwc/terms/taxon"][0]->fields)) {
return false;
}
// take note the index key is all lower case
foreach (array_keys($tables) as $table) {
self::process_fields($harvester->process_row_type($table), pathinfo($table, PATHINFO_BASENAME));
}
/* debug - uncomment in normal operation
//delete temp dir and file.tar.gz
if(is_dir($dir)) recursive_rmdir($dir);
$file = CONTENT_RESOURCE_LOCAL_PATH . $resource_id . "_" . $i . "_working.tar.gz";
if(is_file($file)) unlink($file);
*/
}
$this->archive_builder->finalize(TRUE);
}
public function read_data()
{
$this->column_labels = array();
$this->column_indices = array();
foreach (new FileIterator($this->text_path["obis"]["ranges_OBIS"]) as $line_number => $line) {
if ($line_number % 1000 == 0) {
echo "{$line_number} :: " . time_elapsed() . " :: " . memory_get_usage() . "\n";
}
$line_data = ContentArchiveReader::line_to_array($line, ",", "\"");
if ($line_number == 0) {
$this->column_labels = $line_data;
foreach ($this->column_labels as $k => $v) {
$this->column_indices[$v] = $k;
}
continue;
}
$this->process_line_data($line_data);
}
}
public static function get_all_taxa()
{
self::$MAPPINGS = self::assign_mappings();
$all_taxa = array();
$final_taxa = array();
$used_collection_ids = array();
$harvester = new ContentArchiveReader(NULL, DOC_ROOT . "temp/dwca_iabin");
$tables = $harvester->tables;
if (!($GLOBALS['fields'] = $tables["http://www.pliniancore.org/plic/pcfcore/pliniancore2.3"][0]->fields)) {
debug("Invalid archive file. Program will terminate.");
return false;
}
$images = self::get_images($harvester->process_row_type('http://rs.gbif.org/terms/1.0/image'));
$references = self::get_references($harvester->process_row_type('http://rs.gbif.org/terms/1.0/reference'));
$vernacular_names = self::get_vernacular_names($harvester->process_row_type('http://rs.gbif.org/terms/1.0/vernacularname'));
$taxon_media = array();
$media = $harvester->process_row_type('http://www.pliniancore.org/plic/pcfcore/PlinianCore2.3');
foreach ($media as $m) {
$taxon_id = $m['http://rs.tdwg.org/dwc/terms/taxonID'];
@($taxon_media[$taxon_id][] = $m);
}
$taxa = $harvester->process_row_type('http://rs.tdwg.org/dwc/terms/Taxon');
$i = 0;
$total = sizeof($taxa);
foreach ($taxa as $taxon) {
$i++;
debug(" {$i} of {$total}");
$taxon_id = @$taxon['http://rs.tdwg.org/dwc/terms/taxonID'];
$taxon["id"] = $taxon_id;
$taxon["image"] = @$images[$taxon_id];
$taxon["reference"] = @$references[$taxon_id];
$taxon["vernacular_name"] = @$vernacular_names[$taxon_id];
$taxon["media"] = $taxon_media[$taxon_id];
$arr = self::get_iabin_taxa($taxon, $used_collection_ids);
$page_taxa = $arr[0];
$used_collection_ids = $arr[1];
//do in batches to speed it up.
if ($page_taxa) {
$all_taxa = array_merge($all_taxa, $page_taxa);
}
if (count($all_taxa) == 1000) {
$final_taxa = array_merge($final_taxa, $all_taxa);
$all_taxa = array();
}
}
//last writes
$final_taxa = array_merge($final_taxa, $all_taxa);
return $final_taxa;
}
public function build_archive()
{
$this->path_to_archive_directory = CONTENT_RESOURCE_LOCAL_PATH . "/{$this->resource_id}/";
$this->archive_builder = new \eol_schema\ContentArchiveBuilder(array('directory_path' => $this->path_to_archive_directory));
$this->column_labels = array();
$this->column_indices = array();
$this->taxon_occurrences = array();
foreach (new FileIterator(self::TAXA_URL) as $line_number => $line) {
if ($line_number % 1000 == 0) {
echo "{$line_number} :: " . time_elapsed() . " :: " . memory_get_usage() . "\n";
}
$line_data = ContentArchiveReader::line_to_array($line, ",", "\"");
if ($line_number == 0) {
$this->column_labels = $line_data;
foreach ($this->column_labels as $k => $v) {
$this->column_indices[$v] = $k;
}
continue;
}
$taxon = $this->add_taxon($line_data);
$this->taxon_occurrences[$taxon->taxonID] = $this->add_occurrence($line_data, $taxon);
}
$this->column_labels = array();
$this->column_indices = array();
foreach (new FileIterator(self::DUMP_URL) as $line_number => $line) {
if ($line_number % 1000 == 0) {
echo "{$line_number} :: " . time_elapsed() . " :: " . memory_get_usage() . "\n";
}
$line_data = ContentArchiveReader::line_to_array($line, ",", "\"");
if ($line_number == 0) {
$this->column_labels = $line_data;
foreach ($this->column_labels as $k => $v) {
$this->column_indices[$v] = $k;
}
continue;
}
$this->process_line_data($line_data);
}
$this->archive_builder->finalize(true);
}
function get_all_taxa($dwca_file)
{
self::$MAPPINGS = self::assign_mappings();
$all_taxa = array();
$used_collection_ids = array();
$paths = self::extract_archive_file($dwca_file, "meta.xml");
$archive_path = $paths['archive_path'];
$temp_dir = $paths['temp_dir'];
$harvester = new ContentArchiveReader(NULL, $archive_path);
$tables = $harvester->tables;
if (!($GLOBALS['fields'] = $tables["http://www.pliniancore.org/plic/pcfcore/pliniancore2.3"][0]->fields)) {
debug("Invalid archive file. Program will terminate.");
return false;
}
$images = self::get_images($harvester->process_row_type('http://rs.gbif.org/terms/1.0/image'));
$references = self::get_references($harvester->process_row_type('http://rs.gbif.org/terms/1.0/reference'));
$vernacular_names = self::get_vernacular_names($harvester->process_row_type('http://rs.gbif.org/terms/1.0/vernacularname'));
$taxon_media = array();
$media = $harvester->process_row_type('http://www.pliniancore.org/plic/pcfcore/PlinianCore2.3');
foreach ($media as $m) {
@($taxon_media[$m['http://rs.tdwg.org/dwc/terms/taxonID']] = $m);
}
$taxa = $harvester->process_row_type('http://rs.tdwg.org/dwc/terms/Taxon');
$i = 0;
$total = sizeof($taxa);
foreach ($taxa as $taxon) {
$i++;
debug("{$i} of {$total}");
$taxon_id = @$taxon['http://rs.tdwg.org/dwc/terms/taxonID'];
$taxon["id"] = $taxon_id;
$taxon["image"] = @$images[$taxon_id];
$taxon["reference"] = @$references[$taxon_id];
$taxon["vernacular_name"] = @$vernacular_names[$taxon_id];
$taxon["media"] = $taxon_media[$taxon_id];
$arr = self::get_inbio_taxa($taxon, $used_collection_ids);
$page_taxa = $arr[0];
$used_collection_ids = $arr[1];
if ($page_taxa) {
$all_taxa = array_merge($all_taxa, $page_taxa);
}
}
// remove tmp dir
if ($temp_dir) {
shell_exec("rm -fr {$temp_dir}");
}
return $all_taxa;
}
