ref_paper.inc.php

<?php

define( 'PLUGIN_PAPER_DIR', 'papers' );
define( 'PDF_ICON_FILE_PATH', 'image/pdf_alt.png' );

function ref_paper_get_paper_filename( $pubmed_id )
{
	return PLUGIN_PAPER_DIR . '/' . $pubmed_id . '.xml';
}

function ref_paper_get_pubmed_url( $pubmed_id )
{
	return'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=' . $pubmed_id;
}

function ref_paper_get_pdf_filename( $pubmed_id )
{
	return PLUGIN_PAPER_DIR . '/' . $pubmed_id . '.pdf';
}

function ref_paper_store_paper_info( $pubmed_id )
{
        $xml_filename = ref_paper_get_paper_filename( $pubmed_id );
        if ( file_exists( $xml_filename ) ) {
                return;
        }
       
        $entrez_eutils_url = 'https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&rettype=abstract&id=' . $pubmed_id;
        
        //XXX: http_request doesn't work with HTTPS. Use cUrl instead.
        // $paper_info = http_request( $entrez_eutils_url );
        // file_put_contents( $xml_filename, $paper_info[ 'data' ] );

        //XXX: The following code doesn't care about proxy.
        $ch = curl_init();
        curl_setopt( $ch, CURLOPT_URL, $entrez_eutils_url );
        curl_setopt( $ch, CURLOPT_RETURNTRANSFER, true );
        $response = curl_exec( $ch );
        curl_close( $ch );
        file_put_contents( $xml_filename, $response );
}

function ref_paper_read_paper_info( $pubmed_id )
{
	$xml_filename = ref_paper_get_paper_filename( $pubmed_id );

	$simple_xml = simplexml_load_file( $xml_filename );
	if ( !$simple_xml ) {
		return false;
	}
	
	$paper_info = array();
	
	$article_node = $simple_xml->PubmedArticle[ 0 ]->MedlineCitation->Article;
	
	// AuthorList
	$paper_info[ 'AuthorList' ] = array();
	foreach ( $article_node->AuthorList->Author as $author_item ) {
		array_push( $paper_info[ 'AuthorList' ], htmlspecialchars( (string) $author_item->LastName . ' ' . (string) $author_item->Initials ) );
	}
	
	// ArticleTitle
	$paper_info[ 'ArticleTitle' ] = htmlspecialchars( (string) $article_node->ArticleTitle );
	
	// Journal
	$paper_info[ 'Journal' ] = htmlspecialchars( (string) $simple_xml->PubmedArticle[ 0 ]->MedlineCitation->MedlineJournalInfo->MedlineTA );
	
	// PubDate
	$paper_info[ 'PubDateYear' ] = htmlspecialchars( (string) $article_node->Journal->JournalIssue->PubDate[ 0 ]->Year[ 0 ] );
	$paper_info[ 'PubDateMonth' ] = htmlspecialchars( (string) $article_node->Journal->JournalIssue->PubDate[ 0 ]->Month[ 0 ] );
	$paper_info[ 'PubDateDay' ] = htmlspecialchars( (string) $article_node->Journal->JournalIssue->PubDate[ 0 ]->Day[ 0 ] );
	
	// Volume
	$paper_info[ 'Volume' ] = htmlspecialchars( (string) $article_node->Journal->JournalIssue->Volume[ 0 ] );
	
	// Issue
	$paper_info[ 'Issue' ] = htmlspecialchars( (string) $article_node->Journal->JournalIssue->Issue[ 0 ] );
	
	// Pagination
	$paper_info[ 'Pagination' ] = htmlspecialchars( (string) $article_node->Pagination->MedlinePgn[ 0 ] );
	
	// Abstract
	$paper_info[ 'Abstract' ] = htmlspecialchars( (string) $article_node->Abstract[ 0 ]->AbstractText[ 0 ] );
	
	return $paper_info;
}

function ref_paper_format_paper_info( &$paper_info )
{
	// Author
	if ( array_key_exists( 'AuthorList', $paper_info ) ) {
		$paper_info[ 'Author' ] = join( ', ', $paper_info[ 'AuthorList' ] ) . '.';
	}
	else {
		$paper_info[ 'Author' ] = '';
	}

	// PubDate
	if ( array_key_exists( 'PubDateYear', $paper_info ) and ( $paper_info[ 'PubDateYear' ] != '' ) ) {
		$paper_info[ 'PubDate' ] = $paper_info[ 'PubDateYear' ];
		
		if ( array_key_exists( 'PubDateMonth', $paper_info ) and ( $paper_info[ 'PubDateMonth' ] != '' ) ) {
			$paper_info[ 'PubDate' ] = $paper_info[ 'PubDate' ] . ' ' . $paper_info[ 'PubDateMonth' ];
		
			if ( array_key_exists( 'PubDateDay', $paper_info ) and ( $paper_info[ 'PubDateDay' ] != '' ) ) {
				$paper_info[ 'PubDate' ] = $paper_info[ 'PubDate' ] . ' ' .  $paper_info[ 'PubDateDay' ];
			}
		}
	}
	else {
		$paper_info[ 'PubDate' ] = '';
	}
	
	// FormattedVolume
	if ( array_key_exists( 'Volume', $paper_info ) and ( $paper_info[ 'Volume' ] != '' ) ) {
		$paper_info[ 'FormattedVolume' ] = $paper_info[ 'Volume' ];
		if ( array_key_exists( 'Issue', $paper_info ) and ( $paper_info[ 'Issue' ] != '' ) ) {
			$paper_info[ 'FormattedVolume' ] = $paper_info[ 'FormattedVolume' ] . '(' . $paper_info[ 'Issue' ] . ')';
		}
	}
	else {
		$paper_info[ 'FormattedVolume' ] = '';
	}
}

function plugin_ref_paper_inline( $pubmed_id )
{
	ref_paper_store_paper_info( $pubmed_id );

	$paper_info = ref_paper_read_paper_info( $pubmed_id );
	if ( !$paper_info ) {
		return 'ERROR: Unable to read a stored XML file.';
	}

	ref_paper_format_paper_info( $paper_info );
	
	$pubmed_url = ref_paper_get_pubmed_url( $pubmed_id );

	$paper_info_str = '<a href="' . $pubmed_url . '">' . $paper_info[ 'Author' ] . '</a>, ' . $paper_info[ 'ArticleTitle' ] . ', ' . $paper_info[ 'Journal' ] . '. ' . $paper_info[ 'PubDate' ] . ';' . $paper_info[ 'FormattedVolume' ] . ':' . $paper_info[ 'Pagination' ] . '.';
	
	$paper_pdf_filename = ref_paper_get_pdf_filename( $pubmed_id );
	if ( file_exists( $paper_pdf_filename ) ) {
		$paper_info_str = '<a href="' . $paper_pdf_filename . '"><img src="' . PDF_ICON_FILE_PATH . '" /></a>' . $paper_info_str;
	}
	
	return $paper_info_str;
}

function plugin_ref_paper_convert( $pubmed_id )
{
	ref_paper_store_paper_info( $pubmed_id );

	$paper_info = ref_paper_read_paper_info( $pubmed_id );
	if ( !$paper_info ) {
		return 'ERROR: Unable to read a stored XML file.';
	}

	ref_paper_format_paper_info( $paper_info );
	
	$pubmed_url = ref_paper_get_pubmed_url( $pubmed_id );

	$paper_info_str = '<p>';

	$paper_pdf_filename = ref_paper_get_pdf_filename( $pubmed_id );
	if ( file_exists( $paper_pdf_filename ) ) {
		$paper_info_str .= '<a href="' . $paper_pdf_filename . '"><img src="' . PDF_ICON_FILE_PATH . '" /></a>';
	}

	$paper_info_str .= '<a href="' . $pubmed_url . '">' . $paper_info[ 'Author' ] . '</a></p>';

	$paper_info_str .= '<p>' . $paper_info[ 'ArticleTitle' ] . '</p>';
	$paper_info_str .= '<p>' . $paper_info[ 'Journal' ] . '. ' . $paper_info[ 'PubDate' ] . ';' . $paper_info[ 'FormattedVolume' ] . ':' . $paper_info[ 'Pagination' ] . '.</p>';
	$paper_info_str .= '<p>' . $paper_info[ 'Abstract' ] . '</p>';
	$paper_info_str .= '<p>PMID: ' . htmlspecialchars( (string) $pubmed_id ) . ' [PubMed - indexed for MEDLINE]</p>';
	
	return $paper_info_str;
}

?>