function add_taxon($t) { $hierarchy_entry = HierarchyEntry::create_entries_for_taxon($t, $this->resource->hierarchy_id); if (@(!$hierarchy_entry->id)) { return false; } $this->resource->harvest_event->add_hierarchy_entry($hierarchy_entry, 'inserted'); $hierarchy_entry->delete_common_names(); if (@$t['common_names']) { foreach ($t['common_names'] as &$c) { $name = Name::find_or_create_by_string($c['name']); $hierarchy_entry->add_synonym($name->id, SynonymRelation::find_or_create_by_translated_label('common name')->id, @$c['language']->id ?: 0, 0); } } $hierarchy_entry->delete_synonyms(); if (@$t['synonyms']) { foreach ($t['synonyms'] as &$s) { $hierarchy_entry->add_synonym($s['name']->id, @$s['synonym_relation']->id ?: 0, 0, 0); } } $hierarchy_entry->delete_agents(); if (@$t['agents']) { $i = 0; foreach ($t['agents'] as &$a) { $agent = Agent::find_or_create($a); if ($agent->logo_url && !$agent->logo_cache_url) { if ($logo_cache_url = $this->content_manager->grab_file($agent->logo_url, "partner")) { $agent->logo_cache_url = $logo_cache_url; $agent->save(); } } $hierarchy_entry->add_agent($agent->id, @$a['agent_role']->id ?: 0, $i); unset($a); $i++; } } $hierarchy_entry->delete_refs(); if (@$t['refs']) { foreach ($t['refs'] as &$r) { if (@$r->id) { $hierarchy_entry->add_reference($r->id); $r->publish(); } unset($r); } } foreach ($t['data_objects'] as &$d) { $this->add_data_object($hierarchy_entry, $d); unset($d); } return $hierarchy_entry; }
public function insert_vernacular_names($row, $parameters) { self::debug_iterations("Inserting VernacularName"); $this->commit_iterations("VernacularName", 500); if ($this->archive_validator->has_error_by_line('http://rs.gbif.org/terms/1.0/vernacularname', $parameters['archive_table_definition']->location, $parameters['archive_line_number'])) { write_to_resource_harvesting_log("ERROR: insert_vernacular_names: has_error_by_line" . ",file_location:" . $parameters['archive_table_definition']->location . ",line_number:" . $parameters['archive_line_number']); return false; } $taxon_ids = self::get_foreign_keys_from_row($row, 'http://rs.tdwg.org/dwc/terms/taxonID'); $taxon_info = array(); if ($taxon_ids) { foreach ($taxon_ids as $taxon_id) { if ($taxon_info = @$this->taxon_ids_inserted[$taxon_id]) { self::uncompress_array($taxon_info); $taxon_info[] = $taxon_info; } } } if (!$taxon_info) { return false; } $vernacularName = @self::field_decode($row['http://rs.tdwg.org/dwc/terms/vernacularName']); $source = @self::field_decode($row['http://purl.org/dc/terms/source']); $languageString = @self::field_decode($row['http://purl.org/dc/terms/language']); $locality = @self::field_decode($row['http://rs.tdwg.org/dwc/terms/locality']); $countryCode = @self::field_decode($row['http://rs.tdwg.org/dwc/terms/countryCode']); $isPreferredName = @self::field_decode($row['http://rs.gbif.org/terms/1.0/isPreferredName']); $taxonRemarks = @self::field_decode($row['http://rs.tdwg.org/dwc/terms/taxonRemarks']); $name = Name::find_or_create_by_string($vernacularName); $language = Language::find_or_create_for_parser($languageString); if (!$name) { return false; } foreach ($taxon_info as $info) { $he_id = $taxon_info['hierarchy_entry_id']; $tc_id = $taxon_info['taxon_concept_id']; $common_name_relation = SynonymRelation::find_or_create_by_translated_label('common name'); $result = $this->mysqli->query("SELECT SQL_NO_CACHE id FROM synonyms" . " WHERE name_id = " . $name->id . " AND synonym_relation_id = " . $common_name_relation->id . " AND hierarchy_entry_id = " . $he_id . " AND hierarchy_id = " . $this->harvest_event->resource->hierarchy_id . " AND identifier = " . $taxon_ids[0]); if ($result && $result->fetch_assoc()) { $l_id = @$language->id ?: 0; $GLOBALS['db_connection']->update("UPDATE synonyms SET" . " language_id = " . $l_id . ", published = 0" . ", taxon_remarks = '" . $taxonRemarks . "' WHERE name_id = " . $name->id . " AND synonym_relation_id = " . $common_name_relation->id . " AND hierarchy_entry_id = " . $he_id . " AND hierarchy_id = " . $this->harvest_event->resource->hierarchy_id . "AND identifier = " . $taxon_ids[0]); break; } else { Synonym::find_or_create(array('name_id' => $name->id, 'synonym_relation_id' => $common_name_relation->id, 'language_id' => @$language->id ?: 0, 'hierarchy_entry_id' => $he_id, 'preferred' => $isPreferredName != '', 'hierarchy_id' => $this->harvest_event->resource->hierarchy_id, 'vetted_id' => 0, 'published' => 0, 'taxonRemarks' => $taxonRemarks, 'identifier' => $taxon_ids[0])); break; } } }
public static function read_taxon_xml($t) { $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); $taxon_parameters["taxon_created_at"] = trim($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); } $taxon_parameters["data_objects"] = array(); foreach ($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); $data_object->object_created_at = Functions::import_decode($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)); $data_object->rights_statement = Functions::import_decode($d_dc->rights, 0, 0); $data_object->rights_holder = Functions::import_decode($d_dcterms->rightsHolder, 0, 0); $data_object->description = Functions::import_decode($d_dc->description, 0, 0); $data_object->location = Functions::import_decode($d->location, 0, 0); $data_object_parameters = array(); if (!$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"])); } //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"]; } $data_object_parameters["agents"] = array(); foreach ($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); } if ($translation_information = @$d->additionalInformation->translation) { $data_object->EOLDataObjectID = (string) $translation_information->EOLDataObjectID; if ($translator = (string) $translation_information->translator) { $data_object_parameters["agents"][] = self::translation_agent($translator, 'Translator'); } if ($scientificReviewer = (string) $translation_information->scientificReviewer) { $data_object_parameters["agents"][] = self::translation_agent($scientificReviewer, 'Scientific Reviewer'); } if ($linguisticReviewer = (string) $translation_information->linguisticReviewer) { $data_object_parameters["agents"][] = self::translation_agent($linguisticReviewer, 'Linguistic Reviewer'); } } $taxon_parameters["data_objects"][] = array($data_object, $data_object_parameters); unset($data_object); } return $taxon_parameters; }
public static function read_taxon_xml($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; }