function run() { $dataset_description = ''; $ldir = parent::GetParameterValue('indir'); $odir = parent::GetParameterValue('outdir'); //download if ($this->GetParameterValue('download') == true) { $list = $this->getFtpFileList('ftp.ncbi.nih.gov'); $total = count($list); $counter = 1; foreach ($list as $f) { echo "downloading file {$counter} out of {$total} :" . parent::getParameterValue('download_url') . $f . "... " . PHP_EOL; file_put_contents($ldir . $f, file_get_contents(parent::GetParameterValue('download_url') . $f)); $counter++; } } //if download //iterate over the files $paths = $this->getFilePaths($ldir, 'gz'); $lfile = null; foreach ($paths as $aPath) { $lfile = $aPath; $ofile = $odir . basename($aPath, ".gz") . "." . parent::getParameterValue('output_format'); $gz = false; if (strstr(parent::getParameterValue('output_format'), "gz")) { $gz = true; } parent::setWriteFile($ofile, $gz); parent::setReadFile($ldir . $lfile, true); $source_file = (new DataResource($this))->setURI(parent::getParameterValue('download_url') . basename($aPath))->setTitle('NCBI UniSTS filename: ' . basename($aPath))->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($ldir . $lfile)))->setFormat('xml/unists-format')->setFormat('application/zip')->setPublisher('https://www.ncbi.nlm.nih.gov')->setHomepage('https://www.ncbi.nlm.nih.gov/unists')->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\\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/unists/unists.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() . $source_file->toRDF(); echo "processing {$aPath} ..."; $this->process(); echo "done!" . PHP_EOL; $this->setWriteFile($odir . $this->getBio2RDFReleaseFile()); $this->getWriteFile()->write($dataset_description); $this->getWriteFile()->close(); } //foreach }