PHP utils::downloadSingle方法代码示例

 function run()
 {
     $ldir = parent::getParameterValue('indir');
     $odir = parent::getParameterValue('outdir');
     $dd = '';
     $files = parent::getParameterValue('files');
     if ($files == 'all') {
         $files = explode('|', parent::getParameterList('files'));
         array_shift($files);
     } else {
         $files = explode(',', parent::getParameterValue('files'));
     }
     foreach ($files as $file) {
         echo "processing {$file} ...";
         $lfile = $ldir . $this->filemap[$file];
         $rfile = parent::getParameterValue('download_url') . $this->filemap[$file];
         if (!file_exists($lfile) || parent::getParameterValue('download') == 'true') {
             $ret = utils::downloadSingle($rfile, $lfile);
             if ($ret === false) {
                 echo "unable to download {$file} ... skipping" . PHP_EOL;
                 continue;
             }
         }
         parent::setReadFile($lfile, true);
         $suffix = parent::getParameterValue('output_format');
         $ofile = "orphanet-" . $file . '.' . $suffix;
         $gz = strstr(parent::getParameterValue('output_format'), "gz") ? $gz = true : ($gz = false);
         /*			parent::setWriteFile($odir.$ofile, $gz);
         			$this->$file($lfile);
         			parent::getWriteFile()->close();
         */
         parent::getReadFile()->close();
         parent::clear();
         echo "done!" . PHP_EOL;
         // dataset description
         $source_file = (new DataResource($this))->setURI($rfile)->setTitle("Orphanet: {$file}")->setRetrievedDate(parent::getDate(filemtime($lfile)))->setFormat("application/xml")->setPublisher("http://www.orpha.net")->setHomepage("http://www.orpha.net/")->setRights("use")->setRights("sharing-modified-version-needs-permission")->setLicense("http://creativecommons.org/licenses/by-nd/3.0/")->setDataset("http://identifiers.org/orphanet/");
         $prefix = parent::getPrefix();
         $bVersion = parent::getParameterValue('bio2rdf_release');
         $date = parent::getDate(filemtime($odir . $ofile));
         $output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/orphanet/orphanet.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");
         }
         $dd .= $source_file->toRDF() . $output_file->toRDF();
     }
     //foreach
     parent::writeToReleaseFile($dd);
 }

 function Run()
 {
     $file = "homologene.data";
     $ldir = $this->GetParameterValue('indir');
     $odir = $this->GetParameterValue('outdir');
     $rdir = $this->GetParameterValue('download_url');
     $lfile = $ldir . $file;
     if (!file_exists($lfile)) {
         trigger_error($file . " not found. Will attempt to download.", E_USER_NOTICE);
         parent::setParameterValue('download', true);
     }
     //download
     $rfile = $rdir . $file;
     if ($this->GetParameterValue('download') == true) {
         echo "downloading {$file} ... ";
         utils::downloadSingle($rfile, $lfile);
     }
     $ofile = 'homologene.' . parent::getParameterValue('output_format');
     $gz = strstr(parent::getParameterValue('output_format'), "gz") ? $gz = true : ($gz = false);
     parent::setReadFile($lfile);
     parent::setWriteFile($odir . $ofile, $gz);
     echo "processing {$file}... ";
     $this->process();
     echo "done!" . PHP_EOL;
     parent::getWriteFile()->close();
     // generate the dataset release file
     $source_file = (new DataResource($this))->setURI($rfile)->setTitle("NCBI Homologene")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/tab-separated-value")->setPublisher("http://www.ncbi.nlm.nih.gov")->setHomepage("http://www.ncbi.nlm.nih.gov/homologene")->setRights("use-share-modify")->setLicense("http://www.ncbi.nlm.nih.gov/About/disclaimer.html")->setDataset("http://identifiers.org/homologene/");
     $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 {$prefix}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/homologene/homologene.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() . $output_file->toRDF();
     echo "Generating dataset description... ";
     parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
     parent::getWriteFile()->write($dataset_description);
     parent::getWriteFile()->close();
     echo "done!" . PHP_EOL;
 }

 function Run()
 {
     echo "processing miriam database";
     // directory shortcuts
     $ldir = $this->getParameterValue('indir');
     $odir = $this->getParameterValue('outdir');
     // download and set the read file
     $file = 'miriam.xml';
     $rfile = $this->getParameterValue("download_url");
     $lfile = $ldir . $file;
     if (!file_exists($lfile) || $this->getParameterValue("download") == "true") {
         utils::downloadSingle($rfile, $lfile);
     }
     parent::setReadFile($lfile);
     // set the write file
     $outfile = "miriam." . parent::getParameterValue('output_format');
     $gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
     parent::setWriteFile(parent::getParameterValue("outdir") . $outfile, $gz);
     $this->parse();
     parent::WriteRDFBufferToWriteFile();
     $this->getWriteFile()->Close();
     return true;
 }

 function Run()
 {
     $sp = trim(parent::getParameterValue('files'));
     if ($sp == 'all') {
         $files = $this->getPackageMap();
     } else {
         $s_a = explode(",", $sp);
         $pm = $this->getPackageMap();
         $files = array();
         foreach ($s_a as $a) {
             if (array_key_exists($a, $pm)) {
                 $files[$a] = $pm[$a];
             }
         }
     }
     //else
     $ldir = parent::getParameterValue('indir');
     $odir = parent::getParameterValue('outdir');
     $dd = '';
     //now iterate over the files array
     $year = parent::getParameterValue('year');
     foreach ($files as $k => $fpattern) {
         $file = str_replace("YEAR", $year, $fpattern);
         $lfile = $ldir . $file;
         $rfile = parent::getParameterValue("download_url") . $file;
         // download if necessary
         if (!file_exists($lfile) || parent::getParameterValue('download') == "true") {
             echo "Downloading {$file} ... ";
             $ret = utils::downloadSingle($rfile, $lfile);
             if ($ret === FALSE) {
                 trigger_error("Unable to get {$file}", E_USER_ERROR);
                 continue;
             }
             echo "done!" . PHP_EOL;
         }
         //set the outfile
         $ofile = "mesh_" . $k . "." . parent::getParameterValue('output_format');
         $gz = strstr(parent::getParameterValue('output_format'), "gz") ? true : false;
         echo "processing {$k} ...";
         parent::setReadFile($lfile, FALSE);
         parent::setWriteFile($odir . $ofile, $gz);
         $fnx = $k;
         $this->{$fnx}();
         parent::writeRDFBufferToWriteFile();
         parent::getWriteFile()->close();
         echo "done!" . PHP_EOL;
         $source_file = (new DataResource($this))->setURI($rfile)->setTitle("MeSH")->setRetrievedDate(parent::getDate(filemtime($lfile)))->setFormat("text/x-mesh-record")->setPublisher("http://www.nlm.nih.gov")->setHomepage("http://www.nlm.nih.gov/mesh/")->setRights("use")->setLicense("http://www.nlm.nih.gov/databases/download.html")->setDataset("http://identifiers.org/mesh/");
         $prefix = parent::getPrefix();
         $bVersion = parent::getParameterValue('bio2rdf_release');
         $date = parent::getDate(filemtime($odir . $ofile));
         $output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/mesh/mesh.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");
         }
         $dd .= $source_file->toRDF() . $output_file->toRDF();
     }
     //foreach
     parent::setWriteFile($odir . $this->getBio2RDFReleaseFile($this->getNamespace()));
     parent::getWriteFile()->write($dd);
     parent::getWriteFile()->close();
     echo "done!" . PHP_EOL;
 }

 function process($db)
 {
     $ldir = parent::getParameterValue('indir');
     $odir = parent::getParameterValue('outdir');
     while ($l = parent::getReadFile()->read()) {
         list($nsid, $name) = explode("\t", $l);
         list($ns, $id) = explode(":", $nsid);
         if (isset($this->idlist) and !in_array($id, $this->idlist)) {
             continue;
         }
         if (isset($this->org)) {
             $id = $ns . "_" . $id;
         }
         $uri = $this->getNamespace() . $id;
         parent::addRDF(parent::describeIndividual($uri, $name, parent::getVoc() . ucfirst($db)) . parent::describeClass(parent::getVoc() . ucfirst($db), "KEGG {$db}") . parent::triplifyString($uri, parent::getVoc() . "internal-id", $nsid));
         // now get the entries for each
         $lfile = $ldir . $id . ".txt";
         $rfile = parent::getParameterValue("download_url") . "get/{$nsid}";
         if (!file_exists($lfile) || parent::getParameterValue('download') == 'true') {
             echo "downloading {$nsid} ";
             $ret = utils::downloadSingle($rfile, $lfile);
             if ($ret === false) {
                 echo "unable to download " . $nsid . " ... skipping" . PHP_EOL;
                 continue;
             }
             echo "done. ";
         }
         echo "parsing {$nsid} ... ";
         $this->parseEntry($lfile);
         parent::writeRDFBufferToWriteFile();
         if ($db === "pathway") {
             $ko = str_replace("map", "ko", $id);
             $lfile = $ldir . $id . ".kgml";
             $rfile = "http://www.kegg.jp/kegg-bin/download?entry=" . $ko . "&format=kgml";
             if (!file_exists($lfile) || parent::getParameterValue('download') == 'true') {
                 echo "downloading KGML for {$nsid} ";
                 $ret = utils::downloadSingle($rfile, $lfile);
                 if ($ret === false) {
                     echo "unable to download " . $nsid . " ... skipping" . PHP_EOL;
                     continue;
                 }
                 echo "done. ";
             }
             $this->parseKGML($lfile);
             parent::writeRDFBufferToWriteFile();
         }
         echo "done!" . PHP_EOL;
     }
 }

 public function Run()
 {
     $ldir = parent::getParameterValue('indir');
     $odir = parent::getParameterValue('outdir');
     // make sure we have the zip archive
     //which files are to be converted?
     $selectedPackage = trim(parent::getParameterValue('files'));
     if ($selectedPackage == 'all') {
         $files = $this->getPackageMap();
     } else {
         $sel_arr = explode(",", $selectedPackage);
         $pm = $this->getPackageMap();
         $files = array();
         foreach ($sel_arr as $a) {
             if (array_key_exists($a, $pm)) {
                 $files[$a] = $pm[$a];
             }
         }
     }
     $dataset_description = '';
     foreach ($files as $key => $value) {
         $lfile = $ldir . $value['filename'];
         if (!file_exists($lfile) && parent::getParameterValue('download') == false) {
             trigger_error($lfile . " not found. Will attempt to download.", E_USER_NOTICE);
             $this->SetParameterValue('download', true);
         }
         //download all files [except mapping file]
         if ($this->GetParameterValue('download') == true) {
             $rfile = $value["file_url"];
             echo "downloading " . var_dump($value["file_url"]) . " ... ";
             utils::downloadSingle($rfile, $lfile);
         }
         if ($key == "taxdmp" || $key == "gi2taxid_protein" || $key == "gi2taxid_nucleotide") {
             //get the name of the zip archive
             $lfile = $value["filename"];
             // make sure we have the zip archive
             $zinfile = $ldir . $lfile;
             $zin = new ZipArchive();
             if ($zin->open($zinfile) === FALSE) {
                 trigger_error("Unable to open {$zinfile}");
                 exit;
             }
             //now iterate over the files in the ziparchive
             $source_file = (new DataResource($this))->setURI($value['file_url'])->setTitle('NCBI Taxonomy - ' . $key)->setRetrievedDate(date("Y-m-d\\TH:i:sP", filemtime($ldir . $lfile)))->setFormat('text/tab-separated-value')->setFormat('application/zip')->setPublisher('http://www.ncbi.nlm.nih.gov')->setHomepage('http://www.ncbi.nlm.nih.gov/taxonomy')->setRights('use')->setRights('attribution')->setLicense('https://www.nlm.nih.gov/copyright.html')->setDataset(parent::getDatasetURI());
             $prefix = parent::getPrefix();
             $bVersion = parent::getParameterValue('bio2rdf_release');
             $date = date("Y-m-d\\TH:i:sP");
             $output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} - {$key}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/taxonomy/taxonomy.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() . $source_file->toRDF();
             foreach ($value["contents"] as $k => $fn) {
                 if ($k == "names" || $k == "nodes" || $k == "citations" || $k == "gencode" || $k == "division" || $k == "gi_taxid_prot" || $k == "gi_taxid_nucl") {
                     //if($k !== 'citations') continue;
                     $fpin = $zin->getStream($fn);
                     if (!$fpin) {
                         trigger_error("Unable to get pointer to {$fn} in {$zinfile}");
                         exit("failed\n");
                     }
                     $gzoutfile = $odir . "taxonomy-{$k}" . "." . parent::getParameterValue('output_format');
                     //set the write file
                     $gz = strstr(parent::getParameterValue('output_format'), 'gz') ? true : false;
                     parent::setReadFile($ldir . $lfile);
                     parent::getReadFile()->SetFilePointer($fpin);
                     parent::setWriteFile($gzoutfile, $gz);
                     echo "processing {$fn}...\n";
                     $this->{$k}();
                     $this->GetWriteFile()->Close();
                     echo "done!" . PHP_EOL;
                     parent::clear();
                 }
                 //if $k
             }
             //foreach
         }
         //if key taxdmp
         $this->setWriteFile($odir . $this->getBio2RDFReleaseFile());
         $this->getWriteFile()->write($dataset_description);
         $this->getWriteFile()->close();
     }
 }

 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();
 }

 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();
 }