function process()
{
if (parent::getParameterValue('files') == 'all') {
$files = explode("|", parent::getParameterList('files'));
array_shift($files);
} else {
$files = explode(",", parent::getParameterValue('files'));
}
$remote_files = array("human" => "human_genes.zip", "models" => "models_genes.zip");
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$rdir = parent::getParameterValue('download_url');
$dataset_description = '';
$graph_uri = parent::getGraphURI();
if (parent::getParameterValue('dataset_graph') == true) {
parent::setGraphURI(parent::getDatasetURI());
}
foreach ($files as $file) {
$lfile = $ldir . $remote_files[$file];
$rfile = $rdir . $remote_files[$file];
if (!file_exists($lfile)) {
trigger_error($lfile . " not found. Will attempt to download." . PHP_EOL, E_USER_WARNING);
echo "Downloading {$rfile}... ";
Utils::DownloadSingle($rfile, $lfile);
echo "done!" . PHP_EOL;
}
$suffix = parent::getParameterValue('output_format');
$ofile = "genage_" . $file . '.' . $suffix;
if (strstr(parent::getParameterValue('output_format'), "gz")) {
$gz = true;
}
$zin = new ZipArchive();
if ($zin->open($lfile) === FALSE) {
trigger_error("Unable to open {$lfile}");
exit;
}
if ($file == "human") {
$zipentry = "genage_human.csv";
} else {
if ($file == "models") {
$zipentry = "genage_models.csv";
}
}
if (($fp = $zin->getStream($zipentry)) === FALSE) {
trigger_error("Unable to get {$zipentry} in ziparchive {$lfile}");
return FALSE;
}
parent::SetReadFile($lfile);
parent::GetReadFile()->SetFilePointer($fp);
// set the write file, parse, write and close
$suffix = parent::getParameterValue('output_format');
$outfile = "genage_" . $file . '.' . $suffix;
$gz = false;
if (strstr($suffix, "gz")) {
$gz = true;
}
parent::setWriteFile($odir . $ofile, $gz);
echo "Processing {$lfile}... ";
$fnx = $file;
$this->{$fnx}();
echo "done!" . PHP_EOL;
parent::getWriteFile()->close();
// generate the dataset release file
echo "Generating dataset description for {$ofile}... ";
// dataset description
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("Human Ageing Genomic Resources GenAge database (" . $remote_files[$file] . ")")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/comma-separated-value")->setFormat("application/gzip")->setPublisher("http://genomics.senescence.info/")->setHomepage("http://genomics.senescence.info/genes/")->setRights("use")->setLicense("http://genomics.senescence.info/legal.html")->setDataset("http://identifiers.org/genage/");
$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}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/genage/genage.php")->setCreateDate($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() . $output_file->toRDF();
echo "done!" . PHP_EOL;
}
parent::setGraphURI($graph_uri);
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
}
