function Run()
{
$idir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$files = parent::getParameterValue('files');
// set the work
if ($files != 'all') {
// check if comma-separated, or hyphen-range
$list = explode(",", $files);
if (count($list) == 1) {
// try hyphen separated
$range = explode("-", $files);
if (count($range) == 2) {
for ($i = $range[0]; $i <= $range[1]; $i++) {
$myfiles[] = $i;
}
} else {
// must a single entry
$myfiles[] = $files;
}
} else {
$myfiles = $list;
}
}
$rest_uri = 'http://sabiork.h-its.org/sabioRestWebServices/';
$getReactionIds_url = $rest_uri . "suggestions/SABIOReactionIDs";
$reaction_list_file = $idir . "reactions.xml";
if (!file_exists($reaction_list_file) || parent::getParameterValue('download') == 'true') {
$xml = file_get_contents($getReactionIds_url);
if (FALSE === $reaction_list_file) {
exit;
}
$f = new FileFactory($reaction_list_file);
$f->Write($xml);
$f->Close();
}
$xml = simplexml_load_file($reaction_list_file);
$total = count($xml->SABIOReactionID);
if (isset($myfiles)) {
$total = count($myfiles);
}
$i = 0;
parent::setCheckpoint('dataset');
$graph_uri = parent::getGraphURI();
if (parent::getParameterValue('dataset_graph') == true) {
parent::setGraphURI(parent::getDatasetURI());
}
$suffix = parent::getParameterValue('output_format');
$ofile = "sabiork." . $suffix;
$gz = strstr(parent::getParameterValue('output_format'), "gz") ? true : false;
parent::setWriteFile($odir . $ofile, $gz);
foreach ($xml->SABIOReactionID as $rid) {
parent::setCheckpoint('file');
if (isset($myfiles)) {
if (!in_array($rid, $myfiles)) {
continue;
}
}
$i++;
echo "{$i} / {$total} : reaction {$rid}" . PHP_EOL;
$reaction_file = $idir . "reaction_" . $rid . ".owl.gz";
if (!file_exists($reaction_file) || $this->GetParameterValue('download') == 'true') {
$url = $rest_uri . 'searchKineticLaws/biopax?q=SabioReactionID:' . $rid;
$data = file_get_contents($url);
if ($data === FALSE) {
continue;
}
$f = new FileFactory($reaction_file, true);
$f->Write($data);
$f->Close();
}
$buf = file_get_contents("compress.zlib://" . $reaction_file);
// send for parsing
$p = new BioPAX2Bio2RDF($this);
$p->SetBuffer($buf)->SetBioPAXVersion(3)->SetBaseNamespace("http://sabio.h-its.org/biopax#")->SetBio2RDFNamespace("http://bio2rdf.org/sabiork:")->SetDatasetURI($this->GetDatasetURI());
$rdf = $p->Parse();
parent::getWriteFile()->Write($rdf);
}
parent::getWriteFile()->Close();
//generate dataset description
echo "Generating dataset description... ";
$source_file = (new DataResource($this))->setURI("http://sabiork.h-its.org/sabioRestWebServices/searchKineticLaws/biopax")->setTitle("SABIO-RK Biochemical Reaction Kinetics Database")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($odir . $ofile)))->setFormat("text/xml")->setPublisher("http://sabio.villa-bosch.de/")->setHomepage("http://sabio.villa-bosch.de/")->setRights("use-share-modify")->setRights("no-commercial")->setLicense("http://sabio.villa-bosch.de/layouts/content/termscondition.gsp")->setDataset("http://identifiers.org/sabiork.reaction/");
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/sabiork/sabiork.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description = $source_file->toRDF() . $output_file->toRDF();
//write dataset description to file
parent::setGraphURI($graph_uri);
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
}
/**
* parse an individual pubchem substance file
**/
function parse_substance_file($indir, $file)
{
$xml = new CXML($indir, $file);
while ($xml->Parse("PC-Substance") == TRUE) {
parent::setCheckpoint('record');
$this->parse_substance_record($xml);
}
}
function freq()
{
$cols = 10;
$i = 1;
parent::setCheckpoint('file');
while ($l = parent::getReadFile()->read()) {
$a = explode("\t", str_replace("%", "", $l));
if (count($a) != $cols) {
trigger_error("Expecting {$cols}, but found " . count($a) . " instead... skipping file!", E_USER_ERROR);
return false;
}
list($stitch_flat, $stitch_stereo, $cui, $placebo, $freq, $freq_lower, $freq_upper, $concept_type, $meddra_concept_id, $meddra_concept_label) = $a;
if ($concept_type == "LLT") {
continue;
}
$meddra_concept_label = trim($meddra_concept_label);
$id = "stitch_resource:" . md5("se_freq" . $l);
$stitch_flat = "stitch:{$stitch_flat}";
$label = "{$meddra_concept_label} frequency for {$stitch_flat}";
parent::addRDF(parent::describeIndividual($id, $label, parent::getVoc() . "Drug-Effect-Frequency") . parent::describeClass(parent::getVoc() . "Drug-Effect-Frequency", "SIDER Drug-Effect and Frequency") . parent::triplify($id, parent::getVoc() . "drug", $stitch_flat) . parent::triplify($id, parent::getVoc() . "effect", "umls:" . $meddra_concept_id));
if ($placebo) {
parent::addRDF(parent::triplifyString($id, parent::getVoc() . "placebo", "true", "xsd:boolean"));
}
$number = false;
if (is_numeric($freq)) {
$flabel = $freq . "%";
$ftype_label = "Exact-Frequency";
$ftype = parent::getVoc() . $ftype_label;
$number = true;
} else {
$flabel = $freq;
$ftype_label = "Qualitative-Frequency";
$ftype = parent::getVoc() . "{$ftype_label}";
}
if ($freq_lower != $freq_upper) {
$flabel .= "({$freq_lower}-{$freq_upper})";
$ftype_label = "Range-Frequency";
$ftype = parent::getVoc() . $ftype_label;
}
$fid = $id . md5($a[5] . $a[6] . $a[8]);
parent::addRDF(parent::triplify($id, parent::getVoc() . "frequency", $fid) . parent::describeIndividual($fid, $flabel, $ftype) . parent::describeClass($ftype, $ftype_label));
if ($number == true) {
parent::addRDF(parent::triplifyString($fid, parent::getVoc() . "frequency-value", $freq / 100));
} else {
parent::addRDF(parent::triplifyString($fid, parent::getVoc() . "frequency-value", $freq));
}
parent::addRDF(parent::triplifyString($fid, parent::getVoc() . "lower-frequency", sprintf("%.3f", $freq_lower)) . parent::triplifyString($fid, parent::getVoc() . "upper-frequency", sprintf("%.3f", $freq_upper)));
parent::setCheckpoint('record');
}
parent::setCheckpoint('file');
}