public function insert_data_object($row, $parameters) { self::debug_iterations("Inserting DataObject"); $this->commit_iterations("DataObject", 20); if ($this->archive_validator->has_error_by_line('http://eol.org/schema/media/document', $parameters['archive_table_definition']->location, $parameters['archive_line_number'])) { write_to_resource_harvesting_log("ERROR: insert_data_object: has_error_by_line" . ",file_location:" . $parameters['archive_table_definition']->location . ",line_number:" . $parameters['archive_line_number']); return false; } $object_taxon_ids = self::get_foreign_keys_from_row($row, 'http://rs.tdwg.org/dwc/terms/taxonID'); $object_taxon_info = array(); if ($object_taxon_ids) { foreach ($object_taxon_ids as $taxon_id) { if ($taxon_info = @$this->taxon_ids_inserted[$taxon_id]) { self::uncompress_array($taxon_info); $object_taxon_info[] = $taxon_info; } } } if (!$object_taxon_info) { return false; } if ($this->harvest_event->resource->is_eol_flickr_group() && self::is_this_flickr_image_in_inaturalist($row)) { return false; } $data_object = new DataObject(); $data_object->identifier = @self::field_decode($row['http://purl.org/dc/terms/identifier']); if (isset($this->media_ids_inserted[$data_object->identifier])) { return false; } $data_object->data_type = DataType::find_or_create_by_schema_value(@self::field_decode($row['http://purl.org/dc/terms/type'])); if ($dt = DataType::find_or_create_by_schema_value(@self::field_decode($row['http://rs.tdwg.org/audubon_core/subtype']))) { $data_object->data_subtype_id = $dt->id; } $data_object->mime_type = MimeType::find_or_create_by_translated_label(@self::field_decode($row['http://purl.org/dc/terms/format'])); $data_object->object_created_at = @self::field_decode($row['http://ns.adobe.com/xap/1.0/CreateDate']); $data_object->object_modified_at = @self::field_decode($row['http://purl.org/dc/terms/modified']); $data_object->available_at = @self::field_decode($row['http://purl.org/dc/terms/available']); $data_object->object_title = @self::field_decode($row['http://purl.org/dc/terms/title']); $data_object->language = Language::find_or_create_for_parser(@self::field_decode($row['http://purl.org/dc/terms/language'])); // check multiple fields for a value of license if (isset($row['http://purl.org/dc/terms/license'])) { $license_string = @self::field_decode($row['http://purl.org/dc/terms/license']); } else { $license_string = @self::field_decode($row['http://ns.adobe.com/xap/1.0/rights/UsageTerms']); } // convert British licences to American licenses $license_string = str_replace("creativecommons.org/licences/", "creativecommons.org/licenses/", $license_string); if (!$license_string && $this->harvest_event->resource->license && $this->harvest_event->resource->license->source_url) { $license_string = $this->harvest_event->resource->license->source_url; } if (!$license_string || !\eol_schema\MediaResource::valid_license($license_string)) { return false; } $data_object->license = License::find_or_create_for_parser($license_string); $data_object->rights_statement = @self::field_decode($row['http://purl.org/dc/terms/rights']); $data_object->rights_holder = @self::field_decode($row['http://ns.adobe.com/xap/1.0/rights/Owner']); $data_object->bibliographic_citation = @self::field_decode($row['http://purl.org/dc/terms/bibliographicCitation']); $data_object->source_url = @self::field_decode($row['http://rs.tdwg.org/ac/terms/furtherInformationURL']); $data_object->derived_from = @self::field_decode($row['http://rs.tdwg.org/ac/terms/derivedFrom']); $data_object->description = @self::field_decode($row['http://purl.org/dc/terms/description']); // Turn newlines into paragraphs $data_object->description = str_replace("\n", "</p><p>", $data_object->description); $data_object->object_url = @self::field_decode($row['http://rs.tdwg.org/ac/terms/accessURI']); $data_object->thumbnail_url = @self::field_decode($row['http://eol.org/schema/media/thumbnailURL']); $data_object->location = @self::field_decode($row['http://iptc.org/std/Iptc4xmpExt/1.0/xmlns/LocationCreated']); $data_object->spatial_location = @self::field_decode($row['http://purl.org/dc/terms/spatial']); $data_object->latitude = @self::field_decode($row['http://www.w3.org/2003/01/geo/wgs84_pos#lat']); $data_object->longitude = @self::field_decode($row['http://www.w3.org/2003/01/geo/wgs84_pos#long']); $data_object->altitude = @self::field_decode($row['http://www.w3.org/2003/01/geo/wgs84_pos#alt']); $rating = @self::field_decode($row['http://ns.adobe.com/xap/1.0/Rating']); // ratings may be 0 to 5 // TODO: technically 0 means untrusted, and then anywhere from 1-5 is OK. // 0.5 for example isn't really valid acording to the schema if (is_numeric($rating) && $rating > 0 && $rating <= 5) { $data_object->data_rating = $rating; } //TODO - update this if ($data_object->mime_type && $data_object->mime_type->equals(MimeType::flash()) && $data_object->is_video()) { $data_object->data_type = DataType::youtube(); $data_object->data_type_id = DataType::youtube()->id; } // //take the first available source_url of one of this object's taxa if (!@$data_object->source_url && @$taxon_parameters["source_url"]) { foreach ($object_taxon_info as $taxon_info) { if ($source_url = $taxon_info['source_url']) { $data_object->source_url = $source_url; break; } } } /* Checking requirements */ // if text: must have description if ($data_object->data_type->equals(DataType::text()) && !$data_object->description) { return false; } // if image, movie or sound: must have object_url if (($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) { return false; } /* ADDING THE DATA OBJECT */ list($data_object, $status) = DataObject::find_and_compare($this->harvest_event->resource, $data_object, $this->content_manager); if (@(!$data_object->id)) { return false; } $this->media_ids_inserted[$data_object->identifier] = $data_object->id; $this->harvest_event->add_data_object($data_object, $status); $data_object->delete_hierarchy_entries(); $vetted_id = Vetted::unknown()->id; $visibility_id = Visibility::preview()->id; foreach ($object_taxon_info as $taxon_info) { $he_id = $taxon_info['hierarchy_entry_id']; $tc_id = $taxon_info['taxon_concept_id']; $this->mysqli->insert("INSERT IGNORE INTO data_objects_hierarchy_entries (hierarchy_entry_id, data_object_id, vetted_id, visibility_id) VALUES ({$he_id}, {$data_object->id}, {$vetted_id}, {$visibility_id})"); $this->mysqli->insert("INSERT IGNORE INTO data_objects_taxon_concepts (taxon_concept_id, data_object_id) VALUES ({$tc_id}, {$data_object->id})"); } // a few things to add after the DataObject is inserted // keep track of reference foreign keys self::append_foreign_keys_from_row($row, 'http://eol.org/schema/reference/referenceID', $this->media_reference_ids, $data_object->id, $data_object->guid); // keep track of agent foreign keys self::append_foreign_keys_from_row($row, 'http://eol.org/schema/agent/agentID', $this->media_agent_ids, $data_object->id); $data_object->delete_info_items(); $data_object->delete_table_of_contents(); if ($s = @self::field_decode($row['http://iptc.org/std/Iptc4xmpExt/1.0/xmlns/CVterm'])) { $ii = InfoItem::find_or_create_by_schema_value($s); $data_object->add_info_item($ii->id); unset($ii); } if ($a = @self::field_decode($row['http://purl.org/dc/terms/audience'])) { $a = Audience::find_or_create_by_translated_label(trim((string) $a)); $data_object->add_audience($a->id); unset($a); } $data_object_parameters["agents"] = array(); self::append_agents($row, $data_object_parameters, 'http://purl.org/dc/terms/creator', 'Creator'); self::append_agents($row, $data_object_parameters, 'http://purl.org/dc/terms/publisher', 'Publisher'); self::append_agents($row, $data_object_parameters, 'http://purl.org/dc/terms/contributor', 'Contributor'); $data_object->delete_agents(); $i = 0; foreach ($data_object_parameters['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(); } } $data_object->add_agent($agent->id, @$a['agent_role']->id ?: 0, $i); unset($a); $i++; } if (!isset($this->object_references_deleted[$data_object->id])) { $data_object->delete_refs(); $this->object_references_deleted[$data_object->id] = true; } // add data object info to resource contribution if ($status != "Unchanged") { $result = $this->mysqli->query("SELECT id, source_url, taxon_concept_id, hierarchy_id, identifier FROM hierarchy_entries inner join data_objects_hierarchy_entries on hierarchy_entries.id = data_objects_hierarchy_entries.hierarchy_entry_id where data_object_id =" . $data_object->id); if ($result && ($row = $result->fetch_assoc())) { $hierarchy_entry_id = $row["id"]; $source = "'" . $this->get_hierarchy_entry_outlink($row["hierarchy_id"], $row["identifier"], preg_replace('/\'/', "\\'", $row["source_url"])) . "'"; $identifier = "'" . $row["identifier"] . "'"; $taxon_concept_id = $row["taxon_concept_id"]; } $resource_id = $this->harvest_event->resource_id; $this->mysqli->insert("INSERT IGNORE INTO resource_contributions (resource_id, data_object_id, data_point_uri_id, hierarchy_entry_id, taxon_concept_id, source, object_type, identifier, data_object_type) VALUES ({$resource_id}, {$data_object->id}, NULL, {$hierarchy_entry_id}, {$taxon_concept_id}, {$source}, 'data_object', {$identifier}, {$data_object->data_type_id})"); } }
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; }