/** parse directory of files */
function parse_dir()
{
$ignore = array("..", '.', '.DS_STORE', "0");
$this->setCheckPoint('dataset');
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$dataset_file = parent::getParameterValue("outdir") . parent::getBio2RDFReleaseFile();
$fp = fopen($dataset_file, "w");
if ($fp === FALSE) {
trigger_error("Unable to open {$dataset_file}", E_USER_ERROR);
return false;
}
$ids = explode(",", parent::getParameterValue('id_list'));
$indir = parent::getParameterValue('indir');
echo "Processing {$indir}\n";
$outfile = "clinicaltrials." . parent::getParameterValue('output_format');
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
parent::setWriteFile(parent::getParameterValue("outdir") . $outfile, $gz);
$files = glob($indir . "NCT*");
foreach ($files as $i => $file) {
if ($i % 10000 == 0) {
parent::clear();
}
$trial_id = basename($file, '.xml');
if (parent::getParameterValue('id_list') == '' || in_array($trial_id, $ids)) {
if (filesize($file) != 0) {
echo "Processing {$trial_id}" . PHP_EOL;
$this->process_file($file);
} else {
echo "Processing {$trial_id} -> Empty!" . PHP_EOL;
}
}
}
echo "Finished." . PHP_EOL;
parent::getWriteFile()->close();
// make the dataset description
parent::setGraphURI(parent::getDatasetURI());
$rfile = "http://clinicaltrials.gov/ct2/show/NCT_ID?resultsxml=true";
$source_version = parent::getDatasetVersion();
// dataset description
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("Clinicaltrials")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($file)))->setFormat("application/xml")->setPublisher("http://clinicaltrials.gov/")->setHomepage("http://clinicaltrials.gov/")->setRights("use")->setRights("by-attribution")->setLicense("http://clinicaltrials.gov/ct2/about-site/terms-conditions")->setDataset("http://identifiers.org/clinicaltrials/");
parent::writeToReleaseFile($source_file->toRDF());
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$outfile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} v{$source_version}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/clinicaltrials/clinicaltrials.php")->setCreateDate($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());
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
parent::writeToReleaseFile($output_file->toRDF());
parent::closeReleaseFile();
// write the dataset description file
fclose($fp);
}
function Run()
{
$indir = parent::getParameterValue('indir');
$outdir = parent::getParameterValue('outdir');
$download_url = parent::getParameterValue('download_url');
if (parent::getParameterValue('files') == 'all') {
$files = explode("|", parent::getParameterList('files'));
array_shift($files);
} else {
$files = explode("|", parent::getParameterValue('files'));
}
if (parent::getParameterValue("id_list")) {
$this->id_list = array_flip(explode(",", parent::getParameterValue('id_list')));
}
$dataset_description = '';
foreach ($files as $f) {
if ($f == 'drugbank') {
$file = 'drugbank.xml.zip';
$lname = 'drugbank';
}
$fnx = 'parse_' . $f;
$rfile = parent::getParameterValue('download_url') . $file;
$lfile = parent::getParameterValue('indir') . $file;
$cfile = $lname . "." . parent::getParameterValue('output_format');
// download
if (!file_exists($lfile) || parent::getParameterValue('download') == true) {
utils::downloadSingle($rfile, $lfile);
}
// setup the write
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
parent::setWriteFile($outdir . $cfile, $gz);
echo $outdir . $cfile;
if (file_exists($indir . $file)) {
// call the parser
echo "processing {$file} ..." . PHP_EOL;
$this->{$fnx}($indir, $file);
echo "done" . PHP_EOL;
parent::clear();
}
parent::getWriteFile()->close();
// dataset description
$ouri = parent::getGraphURI();
parent::setGraphURI(parent::getDatasetURI());
$source_version = parent::getDatasetVersion();
$bVersion = parent::getParameterValue('bio2rdf_release');
$prefix = parent::getPrefix();
$date = date("Y-m-d\\TH:i:sP");
// dataset description
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("DrugBank ({$file})")->setRetrievedDate(date("Y-m-d\\TH:i:sP", filemtime($indir . $file)))->setFormat("application/xml")->setFormat("application/zip")->setPublisher("http://drugbank.ca")->setHomepage("http://drugbank.ca")->setRights("use")->setRights("by-attribution")->setRights("no-commercial")->setLicense("http://www.drugbank.ca/about")->setDataset("http://identifiers.org/drugbank/");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$cfile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} v{$source_version}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/drugbank/drugbank.php")->setCreateDate($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());
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
parent::writeToReleaseFile($source_file->toRDF() . $output_file->toRDF());
parent::setGraphURI($ouri);
}
parent::closeReleaseFile();
}
