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<?php |
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namespace Onoi\Remi\Ncbi; |
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use Onoi\Remi\FilteredHttpResponseParser; |
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use Onoi\Remi\FilteredRecord; |
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use DOMDocument; |
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/** |
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* @license GNU GPL v2+ |
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* @since 0.1 |
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* |
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* @author mwjames |
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*/ |
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class NcbiPubMedFilteredHttpResponseParser extends FilteredHttpResponseParser { |
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/** |
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* @see http://www.ncbi.nlm.nih.gov/books/NBK25501/ |
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* @see http://www.ncbi.nlm.nih.gov/books/NBK1058/ |
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*/ |
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const SUMMARY_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?"; |
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const FETCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"; |
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/** |
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* @since 0.1 |
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* |
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* {@inheritDoc} |
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*/ |
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public function getRawResponseById( $id ) { |
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$db = $this->filteredRecord->get( 'ncbi-dbtype' ); |
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return $this->requestSummaryResponseFor( $id, $db ) . $this->requestAbstractResponseFor( $id, $db ); |
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} |
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/** |
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* @since 0.1 |
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* |
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* {@inheritDoc} |
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*/ |
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public function doFilterResponseById( $id ) { |
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$db = $this->filteredRecord->get( 'ncbi-dbtype' ); |
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$text = $this->requestSummaryResponseFor( $id, $db ); |
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if ( $this->httpRequest->getLastError() !== '' ) { |
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return $this->addMessage( array( 'onoi-remi-request-error', $this->httpRequest->getLastError(), $id ) ); |
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} |
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$this->doProcessSummary( $text, $id, $db ); |
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if ( $this->getMessages() !== array() ) { |
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return null; |
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} |
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$this->doProcessAbstract( |
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$this->requestAbstractResponseFor( $id, $db ) |
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); |
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} |
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private function doProcessSummary( $text, $id, $db ) { |
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$result = json_decode( |
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$text, |
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true |
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); |
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if ( !isset( $result['result'][$id] ) ) { |
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return $this->addMessage( array( 'onoi-remi-response-empty', $id ) ); |
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} |
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$record = $result['result'][$id]; |
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if ( isset( $record['error'] ) ) { |
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return $this->addMessage( array( 'onoi-remi-request-error', $record['error'], $id ) ); |
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} |
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if ( isset( $record['pubtype'] ) ) { |
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foreach ( $record['pubtype'] as $type ) { |
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$this->filteredRecord->append( 'type', $type ); |
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} |
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} |
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foreach ( $record['articleids'] as $articleids ) { |
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if ( $articleids['idtype'] === 'doi' ) { |
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$this->filteredRecord->set( 'doi', $articleids['value'] ); |
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} |
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if ( $articleids['idtype'] === 'pmid' ) { |
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$this->filteredRecord->set( 'pmid', $articleids['value'] ); |
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} |
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if ( $articleids['idtype'] === 'pubmed' ) { |
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$this->filteredRecord->set( 'pmid', $articleids['value'] ); |
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} |
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if ( $articleids['idtype'] === 'pmcid' && $db === 'pmc' ) { |
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$this->filteredRecord->set( 'pmcid', $articleids['value'] ); |
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} |
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if ( $articleids['idtype'] === 'pmc' && $db === 'pubmed' ) { |
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$this->filteredRecord->set( 'pmcid', $articleids['value'] ); |
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} |
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} |
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foreach ( $record['authors'] as $author ) { |
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$this->filteredRecord->append( 'author', $author['name'] ); |
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} |
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$this->filteredRecord->set( 'title', $record['title'] ); |
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$this->filteredRecord->set( 'journal', $record['fulljournalname'] ); |
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$this->filteredRecord->set( 'pubdate', $record['pubdate'] ); |
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$this->filteredRecord->set( 'volume', $record['volume'] ); |
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$this->filteredRecord->set( 'issue', $record['issue'] ); |
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$this->filteredRecord->set( 'pages', $record['pages'] ); |
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$this->filteredRecord->set( 'retrieved-from', 'http://www.ncbi.nlm.nih.gov/' ); |
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} |
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private function doProcessAbstract( $xml ) { |
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$ncbiEntrezAbstractXMLProcessor = new NcbiEntrezAbstractXMLProcessor( |
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$this->filteredRecord |
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); |
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$ncbiEntrezAbstractXMLProcessor->doProcess( $xml ); |
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} |
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/** |
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* @param string $id |
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* |
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* @return string |
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*/ |
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public function requestSummaryResponseFor( $id, $type ) { |
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$this->httpRequest->setOption( CURLOPT_RETURNTRANSFER, true ); // put result into variable |
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$this->httpRequest->setOption( CURLOPT_FAILONERROR, true ); |
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$this->httpRequest->setOption( CURLOPT_URL, self::SUMMARY_URL ); |
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$this->httpRequest->setOption( CURLOPT_SSL_VERIFYPEER, false ); |
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$this->httpRequest->setOption( CURLOPT_HTTPHEADER, array( |
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'Accept: application/sparql-results+json, application/rdf+json, application/json', |
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'Content-Type: application/x-www-form-urlencoded;charset=UTF-8' |
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) ); |
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$this->httpRequest->setOption( CURLOPT_POST, true ); |
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$this->httpRequest->setOption( |
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CURLOPT_POSTFIELDS, |
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"db={$type}&retmode=json&id=" . $id |
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); |
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return $this->httpRequest->execute(); |
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} |
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/** |
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* @param string $id |
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* |
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* @return string |
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*/ |
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public function requestAbstractResponseFor( $id, $type ) { |
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// http://www.fredtrotter.com/2014/11/14/hacking-on-the-pubmed-api/ |
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$this->httpRequest->setOption( CURLOPT_RETURNTRANSFER, true ); // put result into variable |
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$this->httpRequest->setOption( CURLOPT_FAILONERROR, true ); |
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$this->httpRequest->setOption( CURLOPT_URL, self::FETCH_URL ); |
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$this->httpRequest->setOption( CURLOPT_SSL_VERIFYPEER, false ); |
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$this->httpRequest->setOption( CURLOPT_HTTPHEADER, array( |
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'Accept: application/sparql-results+xml, application/rdf+xml, application/xml', |
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'Content-Type: application/x-www-form-urlencoded;charset=UTF-8' |
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) ); |
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$this->httpRequest->setOption( CURLOPT_POST, true ); |
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$this->httpRequest->setOption( |
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CURLOPT_POSTFIELDS, |
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"db={$type}&rettype=abstract&retmode=xml&id=" . $id |
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); |
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return $this->httpRequest->execute(); |
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} |
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} |
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onoi /
remi
