예제 #1
0
 public function insert_references($row, $parameters)
 {
     self::debug_iterations("Inserting reference");
     $this->commit_iterations("Reference", 500);
     if ($this->archive_validator->has_error_by_line('http://eol.org/schema/reference/reference', $parameters['archive_table_definition']->location, $parameters['archive_line_number'])) {
         write_to_resource_harvesting_log("ERROR: insert_references: has_error_by_line" . ",file_location:" . $parameters['archive_table_definition']->location . ",line_number:" . $parameters['archive_line_number']);
         return false;
     }
     $reference_id = @self::field_decode($row['http://purl.org/dc/terms/identifier']);
     $reference_taxon_ids = self::get_foreign_keys_from_row($row, 'http://rs.tdwg.org/dwc/terms/taxonID');
     $reference_taxon_info = array();
     if ($reference_taxon_ids) {
         foreach ($reference_taxon_ids as $taxon_id) {
             if ($taxon_info = @$this->taxon_ids_inserted[$taxon_id]) {
                 self::uncompress_array($taxon_info);
                 $reference_taxon_info[] = $taxon_info;
             }
         }
     }
     $full_reference = @self::field_decode($row['http://eol.org/schema/reference/full_reference']);
     $title = @self::field_decode($row['http://purl.org/dc/terms/title']);
     $pages = @self::field_decode($row['http://purl.org/ontology/bibo/pages']);
     $pageStart = @self::field_decode($row['http://purl.org/ontology/bibo/pageStart']);
     $pageEnd = @self::field_decode($row['http://purl.org/ontology/bibo/pageEnd']);
     $volume = @self::field_decode($row['http://purl.org/ontology/bibo/volume']);
     $edition = @self::field_decode($row['http://purl.org/ontology/bibo/edition']);
     $publisher = @self::field_decode($row['http://purl.org/dc/terms/publisher']);
     $authorList = @self::field_decode($row['http://purl.org/ontology/bibo/authorList']);
     $editorList = @self::field_decode($row['http://purl.org/ontology/bibo/editorList']);
     $created = @self::field_decode($row['http://purl.org/dc/terms/created']);
     $language = Language::find_or_create_for_parser(@self::field_decode($row['http://purl.org/dc/terms/language']));
     $uri = @self::field_decode($row['http://purl.org/ontology/bibo/uri']);
     $doi = @self::field_decode($row['http://purl.org/ontology/bibo/doi']);
     $params = array("provider_mangaed_id" => $reference_id, "full_reference" => $full_reference, "title" => $title, "pages" => $pages, "page_start" => $pageStart, "page_end" => $pageEnd, "volume" => $volume, "edition" => $edition, "publisher" => $publisher, "authors" => $authorList, "editors" => $editorList, "publication_created_at" => @$created ?: '0000-00-00 00:00:00', "language_id" => @$language->id ?: 0, "editors" => $editorList);
     $reference = Reference::find_or_create($params);
     if ($uri) {
         $type = RefIdentifierType::find_or_create_by_label('uri');
         $reference->add_ref_identifier(@$type->id ?: 0, $uri);
     }
     if ($doi) {
         $type = RefIdentifierType::find_or_create_by_label('doi');
         $reference->add_ref_identifier(@$type->id ?: 0, $doi);
     }
     if (isset($this->taxon_reference_ids[$reference_id])) {
         foreach ($this->taxon_reference_ids[$reference_id] as $hierarchy_entry_id => $val) {
             $this->mysqli->insert("INSERT IGNORE INTO hierarchy_entries_refs (hierarchy_entry_id, ref_id) VALUES ({$hierarchy_entry_id}, {$reference->id})");
             $this->mysqli->query("UPDATE refs SET published=1, visibility_id=" . Visibility::visible()->id . " WHERE id={$reference->id}");
             // TODO: find_or_create doesn't work here because of the dual primary key
             // HierarchyEntriesRef::find_or_create(array(
             //     'hierarchy_entry_id'    => $hierarchy_entry_id,
             //     'ref_id'                => $reference->id));
         }
     }
     if (isset($this->media_reference_ids[$reference_id])) {
         foreach ($this->media_reference_ids[$reference_id] as $data_object_id => $data_object_guid) {
             $this->mysqli->insert("INSERT IGNORE INTO data_objects_refs (data_object_id, ref_id) VALUES ({$data_object_id}, {$reference->id})");
             $this->mysqli->query("UPDATE refs SET published=1, visibility_id=" . Visibility::visible()->id . " WHERE id={$reference->id}");
             // TODO: find_or_create doesn't work here because of the dual primary key - same as above with entries
         }
     }
     foreach ($reference_taxon_info as $taxon_info) {
         $he_id = $taxon_info['hierarchy_entry_id'];
         $this->mysqli->insert("INSERT IGNORE INTO hierarchy_entries_refs (hierarchy_entry_id, ref_id) VALUES ({$he_id}, {$reference->id})");
         $this->mysqli->query("UPDATE refs SET published=1, visibility_id=" . Visibility::visible()->id . " WHERE id={$reference->id}");
         // TODO: find_or_create doesn't work here because of the dual primary key - same as above with entries
     }
     $this->insert_data($row, $parameters);
 }
예제 #2
0
 public static function read_taxon_xml($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;
 }