public function Run()
{
$file = "iproclass.tb.gz";
$ldir = $this->GetParameterValue('indir');
$odir = $this->GetParameterValue('outdir');
$rdir = $this->GetParameterValue('download_url');
$lfile = $ldir . $file;
if (!file_exists($lfile)) {
trigger_error($lfile . " not found. Will attempt to download.", E_USER_NOTICE);
parent::setParameterValue('download', true);
}
//download all files
$rfile = $rdir . $file;
if ($this->GetParameterValue('download') == true) {
echo "downloading {$file}... ";
utils::DownloadSingle($rfile, $lfile);
// $cmd = "gzip -c $lfile | split -d -l 1000000 --filter='gzip > $FILE.gz' - iproclass-"
}
$ofile = "iproclass.nq";
$gz = true;
parent::setReadFile($lfile, true);
echo "processing {$file}... ";
$this->process();
echo "done!" . PHP_EOL;
parent::getWriteFile()->close();
echo "generating dataset release file... ";
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("iProClass")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/gzip")->setPublisher("http://pir.georgetown.edu")->setHomepage("http://pir.georgetown.edu/iproclass")->setRights("use-share-modify")->setLicense("http://pir.georgetown.edu/pirwww/about/linkpir.shtml")->setDataset("http://identifiers.org/iproclass/");
$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($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/iproclass/iproclass.php")->setCreateDate($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() . $output_file->toRDF();
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
}
function Run()
{
$dataset_description = '';
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$list_file = $ldir . "ftp_list.txt";
if (!file_exists($list_file) || $this->getParameterValue('download') == true) {
echo "Getting FTP file list ...";
$list = $this->getFtpFileList('ftp.ncbi.nlm.nih.gov', '/refseq/release/complete/', '/(complete\\.[0-9]+\\.protein\\.gpff\\.gz)/');
if (!isset($list) or count($list) == 0) {
trigger_error("Unable to get list of files from FTP site. Check internet connection", E_USER_ERROR);
exit(-1);
}
asort($list);
$buf = implode("\n", $list);
file_put_contents($list_file, $buf);
echo "Done." . PHP_EOL;
} else {
echo "Using existing ftp list" . PHP_EOL;
$list = explode("\n", file_get_contents($list_file));
}
$counter = 1;
$total = count($list);
foreach ($list as $f) {
$lfile = $ldir . $f;
echo "Processing " . $counter++ . "/{$total} {$f}. ";
if (!file_exists($lfile) || $this->getParameterValue('download') == true) {
$rfile = parent::getParameterValue('download_url') . $f;
echo "Downloading ...";
utils::DownloadSingle($rfile, $lfile);
echo "done.";
} else {
echo "Using existing file.";
}
echo PHP_EOL;
}
//if download
//iterate over the files
$files = $this->getFilePaths($ldir, 'gz');
asort($files);
foreach ($files as $f) {
$lfile = $ldir . $f;
$ofile = $odir . basename($f, ".gz") . "." . parent::getParameterValue('output_format');
$gz = strstr(parent::getParameterValue('output_format'), "gz") ? true : false;
parent::setWriteFile($ofile, $gz);
parent::setReadFile($lfile, true);
echo "processing {$f} ...";
$this->process();
parent::clear();
echo "done!" . PHP_EOL;
$this->getReadFile()->close();
$this->getWriteFile()->close();
$source_file = (new DataResource($this))->setURI(parent::getParameterValue('download_url') . $lfile)->setTitle("NCBI RefSeq - {$f}")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat('text/refseq-format')->setFormat('application/zip')->setPublisher('http://www.ncbi.nlm.nih.gov')->setHomepage('http://www.ncbi.nlm.nih.gov/refseq')->setRights('use')->setRights('attribution')->setLicense('http://www.nlm.nih.gov/copyright.html')->setDataset(parent::getDatasetURI());
$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} - {$f}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/refseq/refseq.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("restricted-by-source-license")->setLicense("http://creativecommons/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
$dataset_description .= $output_file->toRDF() . $source_file->toRDF();
}
//for
parent::writeToReleaseFile($dataset_description);
parent::getWriteFile()->close();
}
function process()
{
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$rdir = parent::getParameterValue('download_url');
//which files are to be converted?
$files = trim($this->GetParameterValue('files'));
if ($files == 'all') {
$files = $this->getPackageMap();
} else {
$sel_arr = explode(",", $files);
$pm = $this->getPackageMap();
$files = array();
foreach ($sel_arr as $a) {
if (array_key_exists($a, $pm)) {
$files[$a] = $pm[$a];
}
}
}
if ($this->getParameterValue('limit_organisms') == true) {
$this->taxids = array_flip(explode(",", $this->getParameterValue('organisms')));
}
//set dataset graph to be dataset URI
$graph_uri = parent::getGraphURI();
if (parent::getParameterValue('dataset_graph') == true) {
parent::setGraphURI(parent::getDatasetURI());
}
$dataset_description = '';
//now iterate over the files array
foreach ($files as $module => $rfilename) {
$file = $module . ".gz";
$lfile = $ldir . $file;
$rfile = $rdir . $rfilename;
// download
if (!file_exists($lfile) || parent::getParameterValue('download') == true) {
trigger_error("{$lfile} not found. Will attempt to download.", E_USER_NOTICE);
$myfile = $lfile;
if ($module == "gene2sts" || $module == "gene2unigene") {
$myfile = "compress.zlib://" . $lfile;
}
echo "downloading {$module} ...";
utils::DownloadSingle($rfile, $myfile);
echo "done" . PHP_EOL;
}
}
foreach ($files as $module => $rfilename) {
$file = $module . ".gz";
$lfile = $ldir . $file;
$rfile = $rdir . $rfilename;
$ofile = $module . "." . parent::getParameterValue('output_format');
$gz = false;
if (strstr(parent::getParameterValue('output_format'), "gz")) {
$gz = true;
}
echo "Processing {$module} ... ";
parent::setReadFile($lfile, true);
parent::setWriteFile($odir . $ofile, $gz);
$fnx = $module;
if ($module == 'gene2refseq') {
$fnx = 'gene2accession';
}
$this->{$fnx}();
parent::clear();
echo 'done!' . PHP_EOL;
parent::getReadFile()->close();
parent::getWriteFile()->close();
// generate the dataset release file
// dataset description
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("NCBI Gene ({$module})")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/gzip")->setPublisher("http://www.ncbi.nlm.nih.gov")->setHomepage("http://www.ncbi.nlm.nih.gov/gene")->setRights("use-share-modify")->setLicense("http://www.ncbi.nlm.nih.gov/About/disclaimer.html")->setDataset("http://identifiers.org/ncbigene/");
$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($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/ncbigene/ncbigene.php")->setCreateDate($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() . $output_file->toRDF();
}
//foreach
//set graph URI back to default value
parent::setGraphURI($graph_uri);
//write dataset description to file
echo "Generating dataset description... ";
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
}
function run()
{
// get the file list
if ($this->GetParameterValue('files') == 'all') {
$files = explode("|", $this->GetParameterList('files'));
array_shift($files);
} else {
$files = explode(",", $this->GetParameterValue('files'));
}
if ($this->getParameterValue('additional') != 'none') {
$f = explode(",", $this->getParameterValue('additional'));
$files = array_merge($files, $f);
}
$ldir = $this->GetParameterValue('indir');
$odir = $this->GetParameterValue('outdir');
$rdir = $this->GetParameterValue('download_url');
$dataset_description = '';
foreach ($files as $file) {
$suffix = ".zip";
$lfile = $ldir . $file . $suffix;
$rfile = $rdir . $file . $suffix;
if ($file == "offsides" and !file_exists($lfile)) {
echo "downloading twosides...";
$rfile = "http://www.pharmgkb.org/redirect.jsp?p=ftp%3A%2F%2Fftpuserd%3AGKB4ftp%40ftp.pharmgkb.org%2Fdownload%2Ftatonetti%2F3003377s-offsides.zip";
utils::DownloadSingle($rfile, $lfile);
echo "done" . PHP_EOL;
} elseif ($file == "twosides" and !file_exists($lfile)) {
echo "downloading {$file} ...";
$rfile = "http://www.pharmgkb.org/redirect.jsp?p=ftp%3A%2F%2Fftpuserd%3AGKB4ftp%40ftp.pharmgkb.org%2Fdownload%2Ftatonetti%2F3003377s-twosides.zip";
utils::DownloadSingle($rfile, $lfile);
echo "done" . PHP_EOL;
} elseif ($file == 'annotations' or $file == 'relationships') {
if (!file_exists($lfile)) {
echo "Contact PharmGKB to get access to variants/clinical variants; save file as annotations.zip" . PHP_EOL;
continue;
}
} else {
if (!file_exists($lfile) or parent::getParameterValue('download') == true) {
echo "Downloading {$lfile} ... ";
Utils::DownloadSingle('https://www.pharmgkb.org/download.do?objId=' . $file . '.zip&dlCls=common', $lfile);
echo "done" . PHP_EOL;
}
}
// get a pointer to the file in the zip archive
if (!file_exists($lfile)) {
echo "no local copy of {$lfile} . skipping" . PHP_EOL;
continue;
}
$zin = new ZipArchive();
if ($zin->open($lfile) === FALSE) {
trigger_error("Unable to open {$lfile}");
exit;
}
$zipentries = array();
if ($file == "annotations") {
// exclude: 'clinical_ann.tsv','study_parameters.tsv'
$zipentries = array('clinical_ann_metadata.tsv', 'var_drug_ann.tsv', 'var_pheno_ann.tsv', 'var_fa_ann.tsv');
} else {
if ($file == "pathways") {
for ($i = 0; $i < $zin->numFiles; $i++) {
$stat = $zin->statIndex($i);
$entry = $stat['name'];
$ext = pathinfo($entry, PATHINFO_EXTENSION);
if ($ext != "txt") {
$zipentries[] = $entry;
}
}
} else {
if ($file == "relationships") {
$zipentries = array("relationships.tsv");
} else {
if ($file == 'offsides') {
$zipentries = array('3003377s-offsides.tsv');
} else {
if ($file == 'twosides') {
$zipentries = array('3003377s-twosides.tsv');
} else {
$zipentries = array($file . ".tsv");
}
}
}
}
}
// set the write file, parse, write and close
$suffix = parent::getParameterValue('output_format');
$outfile = $file . '.' . $suffix;
$gz = false;
if (strstr(parent::getParameterValue('output_format'), "gz")) {
$gz = true;
}
$this->SetWriteFile($odir . $outfile, $gz);
foreach ($zipentries as $zipentry) {
if (($fp = $zin->getStream($zipentry)) === FALSE) {
trigger_error("Unable to get {$file}.tsv in ziparchive {$lfile}");
return FALSE;
}
$this->SetReadFile($lfile);
$this->GetReadFile()->SetFilePointer($fp);
if ($file == "annotations") {
$fnx = substr($zipentry, 0, strpos($zipentry, ".tsv"));
echo "processing {$zipentry}..";
} else {
if ($file == 'pathways') {
$fnx = 'pathways';
echo "processing {$fnx} ({$zipentry})... ";
} else {
$fnx = $file;
echo "processing {$fnx} ... ";
}
}
$this->{$fnx}();
parent::writeRDFBufferToWriteFile();
parent::clear();
echo "done!" . PHP_EOL;
// generate the dataset release file
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("Pharmacogenomics Knowledge Base ({$zipentry})")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/zip")->setPublisher("http://www.pharmgkb.org/")->setHomepage("http://www.pharmgkb.org/")->setRights("use")->setRights("no-commercial")->setLicense("http://www.pharmgkb.org/page/policies")->setDataset("http://identifiers.org/pharmgkb/");
$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}/{$outfile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} {$file} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/pharmgkb/pharmgkb.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();
}
$this->GetWriteFile()->Close();
}
// foreach
echo "Generating dataset description... ";
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
}
function run()
{
if (parent::getParameterValue('files') == 'all') {
$files = explode("|", $this->GetParameterList('files'));
array_shift($files);
} else {
$files = explode(",", parent::getParameterValue('files'));
}
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$rdir = parent::getParameterValue('download_url');
$dataset_description = '';
foreach ($files as $file) {
$download = parent::getParameterValue('download');
$lfile = $ldir . "goa_" . $file . ".gz";
if (!file_exists($lfile) && $download == false) {
trigger_error($lfile . " not found. Will attempt to download.", E_USER_NOTICE);
$download = true;
}
//download file
$rfile = $rdir . strtoupper($file) . "/gene_association.goa_" . $file . ".gz";
if ($download == true) {
echo "downloading {$file} ... ";
//file_put_contents($lfile,file_get_contents($rfile));
utils::DownloadSingle($rfile, $lfile);
}
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
$ofile = "goa_" . $file . "." . parent::getParameterValue('output_format');
parent::setReadFile($lfile, TRUE);
parent::setWriteFile($odir . $ofile, $gz);
echo "processing {$file} ... ";
$this->process($file);
echo "done!";
parent::clear();
//close write file
parent::getWriteFile()->close();
echo PHP_EOL;
// dataset description
$graph_uri = parent::getGraphURI();
if (parent::getParameterValue('dataset_graph') == true) {
parent::setGraphURI(parent::getDatasetURI());
}
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("Gene Ontology Annotation file {$file} ({$rfile}")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/gzip")->setPublisher("http://www.ebi.ac.uk/")->setHomepage("http://www.ebi.ac.uk/GOA/")->setRights("use")->setLicense("http://www.ebi.ac.uk/GOA/goaHelp.html")->setDataset("http://identifiers.org/goa/");
$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($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/irefindex/irefindex.php")->setCreateDate($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() . $output_file->toRDF();
parent::setGraphURI($graph_uri);
}
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
}
function run()
{
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
// get the snps from pharmgkb
$snps = explode(",", parent::getParameterValue('files'));
if ($snps[0] == 'all') {
$snps = $this->getSNPs();
} else {
if ($snps[0] == 'clinical') {
$snps = $this->getSNPs(true);
} else {
if ($snps[0] == 'omim') {
$lfile = $ldir . 'snp_omimvar.txt';
if (!file_exists($lfile) || parent::getParameterValue('download') == true) {
$ret = utils::DownloadSingle('ftp://ftp.ncbi.nlm.nih.gov/snp/Entrez/snp_omimvar.txt', $lfile);
}
$snps = $this->processOMIMVar($lfile);
} else {
if ($snps[0] == 'pharmgkb') {
$lfile = $ldir . 'pharmgkb.snp.zip';
if (!file_exists($lfile) || parent::getParameterValue('download') == true) {
$ret = utils::DownloadSingle('http://www.pharmgkb.org/download.do?objId=rsid.zip&dlCls=common', $lfile);
}
$snps = $this->processPharmGKBSnps($lfile);
}
}
}
}
$outfile = $odir . "dbsnp." . parent::getParameterValue('output_format');
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
parent::setWriteFile($outfile, $gz);
$n = count($snps);
$z = 0;
foreach ($snps as $i => $snp) {
$file = $snp . '.xml.gz';
$infile = $ldir . $file;
$rfile = parent::getParameterValue('download_url') . $snp;
//$outfile = $odir.$snp.".".parent::getParameterValue('output_format');
// check if exists
$download = false;
if (!file_exists($infile)) {
//trigger_error($lfile." not found. Will attempt to download. ", E_USER_NOTICE);
parent::setParameterValue('download', true);
}
// download
if (parent::getParameterValue('download') == true) {
trigger_error("Downloading {$file}", E_USER_NOTICE);
$ret = utils::downloadSingle($rfile, "compress.zlib://" . $infile, true);
if ($ret === false) {
continue;
}
}
// process
echo "Processing {$snp} (" . ($i + 1) . "/{$n})" . PHP_EOL;
$this->parse($infile);
parent::writeRDFBufferToWriteFile();
if ($z++ % 10000 == 0) {
parent::clear();
}
}
parent::getWriteFile()->close();
// generate the dataset description file
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("dbSNP " . parent::getDatasetVersion())->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z"))->setFormat("application/xml")->setPublisher("http://www.ncbi.nlm.nih.gov")->setHomepage("http://www.ncbi.nlm.nih.gov/SNP/")->setRights("use-share-modify")->setLicense("http://www.ncbi.nlm.nih.gov/About/disclaimer.html")->setDataset("http://identifiers.org/dbsnp/");
$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}/{$outfile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/dbsnp/dbsnp.php")->setCreateDate($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() . $output_file->toRDF();
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
}
