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micheldumontiermicheldumontier
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Merge pull request #468 from bio2rdf/dailymed
Dailymed
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‎dailymed/dailymed.php

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<?php
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/**
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Copyright (C) 2013 Michel Dumontier
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Permission is hereby granted, free of charge, to any person obtaining a copy of
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this software and associated documentation files (the "Software"), to deal in
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the Software without restriction, including without limitation the rights to
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use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
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of the Software, and to permit persons to whom the Software is furnished to do
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so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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*/
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/**
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* An RDF generator for DailyMed
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* documentation: https://dailymed.nlm.nih.gov/
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* @version 1.0
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* @author Michel Dumontier
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*/
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require_once(__DIR__.'/../../php-lib/bio2rdfapi.php');
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class DailymedParser extends Bio2RDFizer
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{
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function __construct($argv) {
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parent::__construct($argv, "dailymed");
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parent::addParameter('files',true,'all|prescription|otc','all','all or comma-separated list of short names to process');
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parent::addParameter('download_url',false,null,'ftp://public.nlm.nih.gov/nlmdata/.dailymed/');
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parent::initialize();
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}
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var $filemap = array(
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"prescription" => array(
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"dm_spl_release_human_rx_part1.zip",
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"dm_spl_release_human_rx_part2.zip",
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"dm_spl_release_human_rx_part3.zip",
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"dm_spl_release_human_rx_part4.zip"),
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"otc" => array(
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"dm_spl_release_human_otc_part1.zip",
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"dm_spl_release_human_otc_part2.zip",
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"dm_spl_release_human_otc_part3.zip",
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"dm_spl_release_human_otc_part4.zip",
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"dm_spl_release_human_otc_part5.zip",
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"dm_spl_release_human_otc_part6.zip",
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"dm_spl_release_human_otc_part7.zip"
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)
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);
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function run()
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{
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$dd = '';
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$ldir = parent::getParameterValue('indir');
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$odir = parent::getParameterValue('outdir');
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$tdir = $ldir."tmp/";
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@mkdir ($tdir, 0777);
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$files = parent::getParameterValue('files');
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if($files == 'all') {
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$files = explode('|', parent::getParameterList('files'));
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array_shift($files);
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} else {
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$files = explode(',', parent::getParameterValue('files'));
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}
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foreach($files AS $filetype) {
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echo "processing $filetype ...";
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// download files
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$files_ = $this->filemap[$filetype];
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foreach($files_ AS $file) {
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$lfile = $ldir.$file;
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$rfile = parent::getParameterValue('download_url').$file;
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if(!file_exists($lfile) || parent::getParameterValue('download') == 'true') {
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$ret = utils::downloadSingle($rfile,$lfile);
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if($ret === false) {
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echo "unable to download $file ... skipping".PHP_EOL;
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continue;
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}
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}
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}
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/*
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$xmlfile = "c:/data/download/dailymed/tmp/8ae4a0c1-1424-47a9-9a59-7fe38bedc0c7.xml";
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$this->setReadFile($xmlfile);
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$this->$filetype($xmlfile);
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exit;
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*/
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// process files
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$z= 0;
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foreach($files_ AS $file) {
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$lfile = $ldir.$file;
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$zin1 = new ZipArchive();
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if ($zin1->open($lfile) === FALSE) {
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trigger_error("Unable to open $lfile");
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exit;
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}
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$suffix = parent::getParameterValue('output_format');
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$ofile = "dailymed-".substr($file,0,-4).'.'.$suffix;
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$gz = strstr(parent::getParameterValue('output_format'), "gz")?($gz=true):($gz=false);
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parent::setWriteFile($odir.$ofile, $gz);
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for($i = 0; $i < $zin1->count(); $i++) {
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//if(++$z == 20) break;
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$entry = $zin1->getNameIndex($i);
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echo "processing $entry".PHP_EOL;
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// extract the dailymed entry (zip file) as a temporary file
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$fileinfo = pathinfo($entry);
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$tfile = $tdir.$fileinfo['basename'];
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if(!file_exists($tfile)) {
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//break;
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copy("zip://".$lfile."#".$entry, $tfile);
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}
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// read the dailmed entry zip file
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$zin2 = new ZipArchive();
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if ($zin2->open($tfile) !== TRUE) {
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trigger_error("Unable to open $lfile2",E_USER_ERROR);
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exit;
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}
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// now find, extract, and process the xml file
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for($j = 0; $j < $zin2->count(); $j++) {
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$f = $zin2->getNameIndex($j);
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if(!strstr($f,".xml")) continue;
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$fileinfo = pathinfo($f);
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$xmlfile = $tdir.$fileinfo['basename'];
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$gzxml = $xmlfile.".gz";
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if(!file_exists($gzxml)) {
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copy("zip://".$tfile."#".$f, "compress.zlib://".$gzxml);
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}
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$this->setReadFile($gzxml);
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$this->$filetype($gzxml);
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$this->getReadFile()->close();
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$this->clear();
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//unlink($xmlfile);
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}
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$zin2->close();
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//unlink($tfile);
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}
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$zin1->close();
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parent::getWriteFile()->close();
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}
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// dataset description
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$source_file = (new DataResource($this))
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->setURI($rfile)
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->setTitle("Dailymed: $file")
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->setRetrievedDate(parent::getDate(filemtime($lfile)))
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->setFormat("application/xml")
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->setPublisher("https://dailymed.nlm.nih.gov")
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->setHomepage("https://dailymed.nlm.nih.gov")
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->setRights("use")
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->setLicense("http://creativecommons.org/licenses/by-nd/3.0/")
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->setDataset("http://identifiers.org/dailmed/");
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$prefix = parent::getPrefix();
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$bVersion = parent::getParameterValue('bio2rdf_release');
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$date = parent::getDate(filemtime($odir.$ofile));
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$output_file = (new DataResource($this))
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->setURI("http://download.bio2rdf.org/release/$bVersion/$prefix/$ofile")
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->setTitle("Bio2RDF v$bVersion RDF version of $prefix")
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->setSource($source_file->getURI())
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->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/dailymed/dailymed.php")
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->setCreateDate($date)
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->setHomepage("http://download.bio2rdf.org/release/$bVersion/$prefix/$prefix.html")
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->setPublisher("http://bio2rdf.org")
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->setRights("use-share-modify")
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->setRights("by-attribution")
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->setRights("restricted-by-source-license")
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->setLicense("http://creativecommons.org/licenses/by/3.0/")
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->setDataset(parent::getDatasetURI());
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$gz = (strstr(parent::getParameterValue('output_format'),".gz") === FALSE)?false:true;
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if($gz) $output_file->setFormat("application/gzip");
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if(strstr(parent::getParameterValue('output_format'),"nt")) $output_file->setFormat("application/n-triples");
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else $output_file->setFormat("application/n-quads");
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$dd .= $source_file->toRDF().$output_file->toRDF();
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}//foreach
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parent::writeToReleaseFile($dd);
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}
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function otc($file)
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{
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return $this->prescription($file);
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}
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function prescription($file)
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{
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$xml = new CXML($file);
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parent::addRDF(
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parent::describeClass(parent::getVoc()."Indication-Section", "FDA product label indication section")
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);
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while($xml->parse("document") == TRUE) {
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$x = $xml->getXMLRoot();
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$setid = $x->setId->attributes()->root;
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$id = parent::getNamespace().$setid;
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$title = addslashes(str_replace( array("\t", "\r","\n", '"'), array(" ","","",""), (string) $x->title));
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#@todo look elsewhere if empty
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$type_id = "loinc:".$x->code->attributes()->code;
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$type_label = $x->code->attributes()->displayName;
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parent::addRDF(
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parent::describeIndividual($id, $title, $type_id).
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parent::describeClass($type_id, $type_label)
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);
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$z = 1;
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foreach($x->component->structuredBody->component AS $c) {
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$section = $c->section;
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$code = (string) @$section->code->attributes()->code;
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if($code != "34067-9" and $code != "42229-5") continue; // indications
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$type_id = "loinc:$code";
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if(isset($section->text)) {
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$sid = parent::getRes().md5($section->text->asXML());
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$x = (string) $section->text->asXML();
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$x = preg_replace('/(?i)<[^>]*>/', ' ', $x);
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setlocale(LC_ALL, 'en_GB');
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$x = @iconv('UTF-8', 'ASCII//IGNORE', $x);
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$x = str_replace(array('"',"'",'\\','�'),'', $x);
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$x = trim(preg_replace("/\s+/",' ',$x));
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$x = addslashes($x);
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parent::addRDF(
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parent::describeIndividual($sid, "indication section", $type_id).
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parent::triplifyString($sid, "rdf:value", $x).
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parent::triplifyString($sid, parent::getVoc()."strlen", strlen($x)).
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parent::triplify($id, parent::getVoc()."indicationSection", $sid)
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);
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}
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/*
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if(isset($section->component->section)) {
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foreach($section->component as $component) {
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$component_code = (string) @$component->section->code->attributes()->code;
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$component_type_id = "loinc:$component_code";
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$component_label = (string) $component->title;
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$sid = parent::getRes().md5($id.$component->section->text->asXML());
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$content = addslashes(trim((string) $component->section->text->asXML()));
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if($content != "") {
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parent::addRDF(
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parent::describeIndividual($sid, "$component_label section $z for $id", $component_type_id).
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parent::triplifyString($sid, "rdf:value", $content).
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parent::triplifyString($sid, parent::getVoc()."order", $z++).
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parent::triplify($id, parent::getVoc()."indicationSection", $sid)
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);
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}
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}
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} else
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*/
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/* for processing individual paragraphs
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$n = 0;
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foreach($section->text->paragraph AS $paragraph) {
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$pid = parent::getRes().md5($paragraph->asXML());
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$content = trim((string) $paragraph);
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if($content == "") continue;
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parent::addRDF(
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parent::describeIndividual($pid, "indication section ".++$n." for $id", $type_id).
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parent::triplifyString($pid, "rdf:value", $content).
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parent::triplifyString($pid, parent::getVoc()."order", $n).
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parent::triplify($id, parent::getVoc()."indicationSection", $pid)
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);
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}
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*/
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}
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}
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unset($xml);
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parent::writeRDFBufferToWriteFile();
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}
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}
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?>

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