public function Run() { $dataset_description = ''; $ldir = parent::getParameterValue('indir'); $odir = parent::getParameterValue('outdir'); //first get the files that are to be processed $selectedPackage = trim(parent::getParameterValue('files')); if ($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]; } } } //download if ($this->getParameterValue('download')) { foreach ($files as $aP => $fn) { foreach ($fn as $aFn) { echo "downloading file {$aFn} :" . parent::getParameterValue('download_url') . $aFn . "..." . PHP_EOL; file_put_contents($ldir . $aFn, file_get_contents(parent::getParameterValue('download_url') . $aFn)); } } } //iterate over the files $paths = $this->getFilePaths($ldir, 'gz'); $lfile = null; foreach ($files as $k => $val) { foreach ($val as $fn) { if (in_array($fn, $paths)) { $lfile = $fn; $ofile = $odir . basename($fn, ".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($fn))->setTitle('International Protein Index filename: ' . basename($fn))->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($ldir . $lfile)))->setFormat('text/ipi-format')->setFormat('application/zip')->setPublisher('https://www.ebi.ac.uk')->setHomepage('https://www.ebi.ac.uk/IPI')->setRights('use')->setRights('attribution')->setLicense('https://www.ebi.ac.uk')->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/ipi/ipi.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() . $source_file->toRDF(); echo "processing {$fn} ..."; $this->{$k}(); echo "done!" . PHP_EOL; $this->setWriteFile($odir . $this->getBio2RDFReleaseFile()); $this->getWriteFile()->write($dataset_description); $this->getWriteFile()->close(); } } } }
function Run() { $file = "hgnc_complete_set.txt.gz"; $ldir = parent::getParameterValue('indir'); $odir = parent::getParameterValue('outdir'); $rdir = parent::getParameterValue('download_url'); $lfile = $ldir . $file; if (!file_exists($lfile) && parent::getParameterValue('download') == false) { trigger_error($lfile . " not found. Will attempt to download.", E_USER_NOTICE); parent::setParameterValue('download', true); } //download the hgnc file $rfile = null; if (parent::getParameterValue('download') == true) { $rfile = $rdir; echo "downloading {$file} ... "; Utils::DownloadSingle($rfile, $lfile); } $ofile = $odir . "hgnc." . parent::getParameterValue('output_format'); $gz = false; if (strstr(parent::getParameterValue('output_format'), "gz")) { $gz = true; } parent::setWriteFile($ofile, $gz); parent::setReadFile($lfile, true); echo "processing {$file}... "; $this->process(); echo "done!" . PHP_EOL; //close write file parent::getWriteFile()->close(); echo PHP_EOL; // generate the dataset release file echo "generating dataset release file... "; $dataset_description = ''; $source_file = (new DataResource($this))->setURI($rdir)->setTitle('HUGO Gene Nomenclature Committee (HGNC)')->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat('text/tab-separated-value')->setFormat('application/zip')->setPublisher('http://www.genenames.org/')->setHomepage('http://www.genenames.org/data/gdlw_columndef.html')->setRights('use')->setRights('attribution')->setLicense('http://www.genenames.org/about/overview')->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/hgnc/hgnc.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()); parent::getWriteFile()->close(); echo "done!" . PHP_EOL; 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(); $this->setWriteFile($odir . $this->getBio2RDFReleaseFile()); $this->getWriteFile()->write($dataset_description); $this->getWriteFile()->close(); }
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() { $idir = parent::getParameterValue('indir'); $odir = parent::getParameterValue('outdir'); $files = parent::getParameterValue('files'); if ($files == 'all') { $list = explode('|', parent::getParameterList('files')); array_shift($list); } else { $list = explode(',', parent::getParameterValue('files')); } $dataset_description = ''; foreach ($list as $item) { $lfile = $idir . $item . '.rpt'; $rfile = parent::getParameterValue('download_url') . $item . '.rpt'; if (!file_exists($lfile) || parent::getParameterValue('download') == 'true') { echo "downloading {$item}..."; $ret = Utils::DownloadSingle($rfile, $lfile); if ($ret != true) { continue; } } parent::setReadFile($lfile, true); echo "Processing {$item}..."; $ofile = $odir . $item . '.' . parent::getParameterValue('output_format'); $gz = strstr(parent::getParameterValue('output_format'), "gz") ? true : false; parent::setWriteFile($ofile, $gz); $this->{$item}(); parent::getWriteFile()->close(); parent::getReadFile()->close(); echo "Done" . PHP_EOL; parent::clear(); $source_file = (new DataResource($this))->setURI($rfile)->setTitle("MGI {$item}")->setRetrievedDate(date("Y-m-d\\TH:i:s", filemtime($lfile)))->setFormat("text")->setPublisher("http://www.informatics.jax.org")->setHomepage("http://www.informatics.jax.org")->setRights("use")->setLicense("http://www.informatics.jax.org/mgihome/other/copyright.shtml")->setDataset("http://identifiers.org/mgi/"); $prefix = parent::getPrefix(); $bVersion = parent::getParameterValue('bio2rdf_release'); $date = date("Y-m-d\\TH:i:s"); $output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$item} in {$prefix}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/mgi/mgi.php")->setCreateDate($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 // generate the dataset release file $this->setWriteFile($odir . parent::getBio2RDFReleaseFile()); $this->getWriteFile()->write($dataset_description); $this->getWriteFile()->close(); echo "done!" . PHP_EOL; }
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; }
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'); $odir = parent::GetParameterValue('outdir'); //download if ($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 }
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() { $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() { $idir = parent::getParameterValue('indir'); $odir = parent::getParameterValue('outdir'); $files = parent::getParameterValue('files'); $dataset_description = ''; if ($files == 'all') { $files = explode('|', parent::getParameterList('files')); array_shift($files); } else { $files = explode(',', parent::getParameterValue('files')); } foreach ($files as $file) { $f = $file; if ($file != "freq") { $f = "all_" . $file; } $f = "meddra_" . $f . ".tsv.gz"; $lfile = $idir . $f; $rfile = parent::getParameterValue('download_url') . $f; if (!file_exists($lfile) || parent::getParameterValue('download') == 'true') { echo "downloading {$file}... "; $ret = file_get_contents($rfile); if ($ret === FALSE) { trigger_error("Unable to get {$rfile}", E_USER_WARNING); continue; } $ret = file_put_contents($lfile, $ret); if ($ret === FALSE) { trigger_error("Unable to write {$lfile}", E_USER_ERROR); exit; } echo "done!" . PHP_EOL; } echo "Processing {$f}... "; parent::setReadFile($lfile, true); $suffix = parent::getParameterValue('output_format'); $ofile = "sider-" . $file . '.' . $suffix; $gz = false; if (strstr(parent::getParameterValue('output_format'), "gz")) { $gz = true; } parent::setWriteFile($odir . $ofile, $gz); $this->{$file}(); parent::getWriteFile()->Close(); parent::getReadFile()->Close(); echo "done!" . PHP_EOL; echo "Generating dataset description... "; $source_file = (new DataResource($this))->setURI($rfile)->setTitle("SIDER Side Effect resource ({$file}.tsv.gz")->setRetrievedDate(parent::getDate(filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/gzip")->setPublisher("http://sideeffects.embl.de/")->setHomepage("http://sideeffects.embl.de/")->setRights("use-share-modify")->setLicense("http://creativecommons.org/licenses/by-nc-sa/3.0/")->setDataset("http://identifiers.org/sider.effect/"); $prefix = parent::getPrefix(); $bVersion = parent::getParameterValue('bio2rdf_release'); $date = parent::getDate(filemtime($odir . $ofile)); $output_file = (new DataResource($this))->setURI("http://download.bio2df.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} - {$file}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/sider/sider.php")->setCreateDate($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() . $output_file->toRDF(); } //foreach parent::setWriteFile($odir . parent::getBio2RDFReleaseFile()); parent::getWriteFile()->write($dataset_description); parent::getWriteFile()->close(); echo "done!" . PHP_EOL; }
function Run() { // directory shortcuts $ldir = parent::getParameterValue('indir'); $odir = parent::getParameterValue('outdir'); // get the listings page $url = trim(parent::getParameterValue('download_url')); $listing_file = $ldir . "probeset_list.html"; if (!file_exists($listing_file) || parent::getParameterValue("download") == "true") { echo "Downloading {$listing_file}" . PHP_EOL; Utils::DownloadSingle($url, $listing_file); } $listings = file_get_contents($listing_file); // make a list of the csv.zip files preg_match_all("/\"([^\"]+)\\.csv\\.zip\"/", $listings, $m); if (count($m[1]) == 0) { trigger_error("could not find any .csv.zip files in {$url}"); exit; } if (parent::getParameterValue("files") == 'all') { $myfiles = $m[1]; } else { $a = explode(",", parent::getParameterValue("files")); foreach ($a as $f) { $found = false; foreach ($m[1] as $n) { if (strstr($n, $f)) { $found = true; $myfiles[] = $n; break; } } if ($found === false) { echo "cannot find {$f} in list" . PHP_EOL; } } } if (!isset($myfiles)) { exit; } // nothing to do $dataset_description = ''; // set the write file $gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true; $outfile = 'affymetrix.' . parent::getParameterValue('output_format'); $this->setWriteFile($odir . $outfile, $gz); // iterate over the files foreach ($myfiles as $rfile) { $base_file = substr($rfile, strrpos($rfile, "/") + 1); $base_url = substr($rfile, 0, strrpos($rfile, "/")); // get and set the dataset version if (parent::getDatasetVersion() == null) { preg_match("/\\.na([0-9]{2})\\.annot/", $base_file, $m); if (isset($m[1])) { $this->setDatasetVersion($m[1]); } } if (parent::getDatasetVersion() != parent::getParameterValue('version')) { $base_file = str_replace("na" . parent::getDatasetVersion(), "na" . parent::getParameterValue('version'), $base_file); } $csv_file = $base_file . ".csv"; $zip_file = $csv_file . ".zip"; $lfile = $ldir . $zip_file; if (!file_exists($lfile)) { echo "skipping: {$lfile} does not exist" . PHP_EOL; continue; } echo "processing {$lfile}" . PHP_EOL; // open the zip file $zin = new ZipArchive(); if ($zin->open($lfile) === FALSE) { trigger_error("Unable to open {$lfile}"); exit; } if (($fp = $zin->getStream($csv_file)) === FALSE) { trigger_error("Unable to get {$csv_file} in ziparchive {$lfile}"); return FALSE; } parent::setReadFile($lfile); parent::getReadFile()->setFilePointer($fp); $this->parse($base_file); parent::getReadFile()->close(); parent::clear(); // dataset description $source_file = (new DataResource($this))->setURI($rfile)->setTitle("Affymetrix Probeset: {$base_file}")->setRetrievedDate(parent::getDate(filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/zip")->setPublisher("http://affymetrix.com")->setHomepage("http://www.affymetrix.com/support/technical/annotationfilesmain.affx")->setRights("use")->setRights("no-commercial")->setRights("registration-required")->setLicense("http://www.affymetrix.com/about_affymetrix/legal/index.affx")->setDataset("http://identifiers.org/affy.probeset/"); $dataset_description .= $source_file->toRDF(); } $this->getWriteFile()->close(); // write the dataset description $prefix = parent::getPrefix(); $bVersion = parent::getParameterValue('bio2rdf_release'); $date = parent::getDate(filemtime($odir . $outfile)); $output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$outfile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/affymetrix/affymetrix.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 .= $output_file->toRDF(); // write the dataset description $this->setWriteFile($odir . $this->getBio2RDFReleaseFile()); $this->getWriteFile()->write($dataset_description); $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 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; }
public function run() { if (parent::getParameterValue('files') == 'all') { $files = explode("|", parent::getParameterList('files')); array_shift($files); } else { $files = explode(",", parent::getParameterValue('files')); } $release = parent::getParameterValue('release'); $releaseb = "WS249"; $remote_files = array("geneIDs" => "species/c_elegans/annotation/geneIDs/c_elegans.PRJNA13758." . $release . ".geneIDs.txt.gz", "functional_descriptions" => "species/c_elegans/annotation/functional_descriptions/c_elegans.PRJNA13758." . $release . ".functional_descriptions.txt.gz", "gene_interactions" => "species/c_elegans/annotation/gene_interactions/c_elegans.PRJNA13758." . $release . ".gene_interactions.txt.gz", "gene_associations" => "releases/current-production-release/ONTOLOGY/gene_association." . $releaseb . ".wb", "phenotype_associations" => "releases/current-production-release/ONTOLOGY/phenotype_association." . $releaseb . ".wb"); $local_files = array("geneIDs" => "wormbase." . parent::getParameterValue('release') . ".genes.txt.gz", "functional_descriptions" => "wormbase." . parent::getParameterValue('release') . ".functional_descriptions.txt.gz", "gene_interactions" => "wormbase." . parent::getParameterValue('release') . ".gene_interactions.txt.gz", "gene_associations" => "wormbase." . parent::getParameterValue('release') . ".gene_association.wb", "phenotype_associations" => "wormbase." . parent::getParameterValue('release') . ".phenotype_associations.wb"); $idir = 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 = $idir . $local_files[$file]; $rfile = $rdir . $remote_files[$file]; if (!file_exists($lfile) or parent::getParameterValue('download') == true) { trigger_error($lfile . " not found. Will attempt to download." . PHP_EOL, E_USER_WARNING); echo "Downloading {$rfile}... "; Utils::DownloadSingle($rfile, $lfile); echo "done!" . PHP_EOL; } if (strstr($lfile, "gz")) { parent::setReadFile($lfile, TRUE); } else { parent::setReadFile($lfile, FALSE); } $suffix = parent::getParameterValue('output_format'); $ofile = "wormbase." . $file . "." . $suffix; $gz = strstr(parent::getParameterValue('output_format'), "gz") ? true : false; parent::setWriteFile($odir . $ofile, $gz); echo "Processing {$file}... "; $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($rfile)->setTitle("WormBase Release " . parent::getParameterValue('release') . " subset ({$file})")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/gzip")->setPublisher("http://wormbase.org/")->setHomepage("http://wormbase.org/")->setRights("use")->setRights("restricted-by-source-license")->setLicense("http://www.wormbase.org/about/policies")->setDataset("http://identifiers.org/wormbase/"); $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 {$prefix} - {$file}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/wormbase/wormbase.php")->setCreateDate($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(); }
function run() { $ldir = parent::getParameterValue('indir'); $odir = parent::getParameterValue('outdir'); $dataset_description = ''; $files = parent::getParameterValue('files'); if ($files == 'all') { $files = explode('|', parent::getParameterList('files')); array_shift($files); } else { $files = explode(',', parent::getParameterValue('files')); } if (parent::getParameterValue('id_list') != '') { $this->idlist = explode(",", parent::getParameterValue("id_list")); } // handle genes separately if (in_array("genes", $files)) { $orgs = array("hsa"); //,"mmu","eco","dre","dme","ath","sce","ddi"); echo "processing genes" . PHP_EOL; $ofile = "kegg-genes." . parent::getParameterValue('output_format'); $gz = strstr(parent::getParameterValue('output_format'), "gz") ? true : false; parent::setWriteFile($odir . $ofile, $gz); // get the list of genomes $lfile = $ldir . "genome.txt"; $rfile = parent::getParameterValue("download_url") . "list/genome"; if (!file_exists($lfile) || parent::getParameterValue('download') == 'true') { $ret = utils::downloadSingle($rfile, $lfile); } $fp = fopen($lfile, "r"); while ($l = fgets($fp)) { $a = explode("\t", $l); $b = explode(", ", $a[1]); $org = $b[0]; if (!in_array($org, $orgs)) { continue; } // get the list of genes for this organims echo "processing {$org}" . PHP_EOL; $this->org = $org; // local variable $lfile = $ldir . $org . ".txt"; $rfile = parent::getParameterValue("download_url") . "list/{$org}"; if (!file_exists($lfile) || parent::getParameterValue('download') == 'true') { $ret = utils::downloadSingle($rfile, $lfile); } parent::setReadFile($lfile, false); $this->process("gene"); parent::getReadFile()->close(); parent::clear(); $this->org = null; // add dataset description $source_file = (new DataResource($this))->setURI($rfile)->setTitle("KEGG: Gene")->setRetrievedDate(parent::getDate(filemtime($lfile)))->setFormat("text/plain")->setPublisher("http://www.kegg.jp/")->setHomepage("http://www.kegg.jp/")->setRights("use")->setRights("no-commercial")->setLicense("http://www.kegg.jp/kegg/legal.html")->setDataset("http://identifiers.org/kegg/"); $dataset_description .= $source_file->toRDF(); } fclose($fp); parent::getWriteFile()->close(); echo "done" . PHP_EOL; $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 {$prefix} - Gene ")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/kegg/kegg.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 .= $output_file->toRDF(); } // all other files foreach ($files as $db) { if ($db == "genes") { continue; } echo "processing {$db}" . PHP_EOL; $lfile = $ldir . $db . ".txt"; $rfile = parent::getParameterValue("download_url") . "list/{$db}"; if (!file_exists($lfile) || parent::getParameterValue('download') == 'true') { echo "Downloading {$rfile} "; $ret = utils::downloadSingle($rfile, $lfile); if ($ret === false) { echo "unable to download {$file} ... skipping" . PHP_EOL; continue; } echo "done." . PHP_EOL; } // now for each list, get the individual entries $ofile = "kegg-{$db}." . parent::getParameterValue('output_format'); $gz = strstr(parent::getParameterValue('output_format'), "gz") ? true : false; parent::setReadFile($lfile, false); parent::setWriteFile($odir . $ofile, $gz); $this->process($db); parent::getWriteFile()->close(); parent::getReadFile()->close(); parent::clear(); echo "done!" . PHP_EOL; // add dataset description $source_file = (new DataResource($this))->setURI($rfile)->setTitle("KEGG: {$db}")->setRetrievedDate(parent::getDate(filemtime($lfile)))->setFormat("text/plain")->setPublisher("http://www.kegg.jp/")->setHomepage("http://www.kegg.jp/")->setRights("use")->setRights("no-commercial")->setLicense("http://www.kegg.jp/kegg/legal.html")->setDataset("http://identifiers.org/kegg/"); $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 {$prefix} - {$db} ")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/kegg/kegg.php")->setCreateDate($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(); } // write the dataset description $this->setWriteFile($odir . $this->getBio2RDFReleaseFile()); $this->getWriteFile()->write($dataset_description); $this->getWriteFile()->close(); }
function Run() { // get the file list if (parent::getParameterValue('files') == 'all') { $files = array('all'); } 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'); $version = parent::getParameterValue("version"); $zip_file = ucfirst($file) . ".mitab." . $version . ".txt.zip"; $lfile = $ldir . $zip_file; $gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true; $ofile = "irefindex-" . $file . "." . parent::getParameterValue('output_format'); if (!file_exists($lfile)) { trigger_error($lfile . " not found. Will attempt to download.", E_USER_NOTICE); $download = true; } $rfile = $rdir . $zip_file; if ($download == true) { echo "downloading {$rfile}" . PHP_EOL; if (FALSE === Utils::DownloadSingle($rfile, $lfile)) { trigger_error("Error in Download"); return FALSE; } } $zin = new ZipArchive(); if ($zin->open($lfile) === FALSE) { trigger_error("Unable to open {$lfile}"); exit; } if ($zin->numFiles != 1) { trigger_error("Found more than one file ... using first file"); } $f = $zin->statIndex(0); $base_file = $f['name']; if (($fp = $zin->getStream($base_file)) === FALSE) { trigger_error("Unable to get {$base_file} in ziparchive {$lfile}"); return FALSE; } parent::setReadFile($lfile); parent::getReadFile()->setFilePointer($fp); echo "Processing " . $file . " ..."; parent::setWriteFile($odir . $ofile, true); if ($this->Parse() === FALSE) { trigger_error("Parsing Error"); exit; } parent::writeRDFBufferToWriteFile(); parent::getWriteFile()->close(); $zin->close(); echo "Done!" . PHP_EOL; $graph_uri = parent::getGraphURI(); if (parent::getParameterValue('dataset_graph') == true) { parent::setGraphURI(parent::getDatasetURI()); } // dataset description $source_file = (new DataResource($this))->setURI($rfile)->setTitle("iRefIndex ({$zip_file}")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/zip")->setPublisher("http://irefindex.uio.no")->setHomepage("http://irefindex.uio.no")->setRights("use")->setRights("by-attribution")->setRights("no-commercial")->setLicense("http://irefindex.uio.no/wiki/README_MITAB2.6_for_iRefIndex#License")->setDataset("http://identifiers.org/irefindex/"); $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 {$prefix} - {$file}")->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(); return TRUE; }
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 process() { if (parent::getParameterValue('files') == 'all') { $files = explode("|", parent::getParameterList('files')); array_shift($files); } else { $files = explode(",", parent::getParameterValue('files')); } $ldir = parent::getParameterValue('indir'); $rdir = parent::getParameterValue('download_url'); $odir = parent::getParameterValue('outdir'); $rfiles = array("dbxref" => "curation/chromosomal_feature/dbxref.tab", "features" => "curation/chromosomal_feature/SGD_features.tab", "domains" => "curation/calculated_protein_info/domains/domains.tab", "protein" => "curation/calculated_protein_info/protein_properties.tab", "goa" => "curation/literature/gene_association.sgd.gz", "goslim" => "curation/literature/go_slim_mapping.tab", "complex" => "curation/literature/go_protein_complex_slim.tab", "interaction" => "curation/literature/interaction_data.tab", "phenotype" => "curation/literature/phenotype_data.tab", "pathways" => "curation/literature/biochemical_pathways.tab", "mapping" => "mapping"); $graph_uri = parent::getGraphURI(); if (parent::getParameterValue('dataset_graph') == true) { parent::setGraphURI(parent::getDatasetURI()); } $gz = false; if (strstr(parent::getParameterValue('output_format'), "gz")) { $gz = true; } if (parent::getParameterValue('one_file') == true) { $ofile = "sgd." . parent::getParameterValue('output_format'); parent::setWriteFile($odir . $ofile, $gz); } $dataset_description = ''; foreach ($files as $file) { $ext = substr(strrchr($rfiles[$file], '.'), 1); if ($ext == "tab") { $lfile = "sgd_" . $file . ".tab"; } elseif ($ext = "gz") { $lfile = "sgd_" . $file . ".tab.gz"; } $rfile = $rdir . $rfiles[$file]; if (!file_exists($ldir . $lfile) && parent::getParameterValue('download') == false && $file != 'mapping') { trigger_error($ldir . $lfile . " not found. Will attempt to download.", E_USER_NOTICE); Utils::DownloadSingle($rfile, $ldir . $lfile); } if (parent::getParameterValue('one_file') == false) { $ofile = "sgd_" . $file . '.' . parent::getParameterValue('output_format'); parent::setWriteFile($odir . $ofile, $gz); } //parse file parent::setReadFile($ldir . $lfile, $gz); $fnx = $file; echo "Processing {$file}... "; $this->{$fnx}(); echo PHP_EOL . "done!"; //write RDF to file parent::writeRDFBufferToWriteFile(); //close write file if (parent::getParameterValue('one_file') == false) { parent::getWriteFile()->close(); } echo PHP_EOL; // generate the dataset release file // dataset description $source_file = (new DataResource($this))->setURI($rfile)->setTitle("Saccharomyces Genome Database ({$file})")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($ldir . $lfile)))->setFormat("text/tab-separated-value")->setFormat("application/gzip")->setPublisher("http://www.yeastgenome.org/")->setHomepage("http://www.yeastgenome.org/")->setRights("use")->setLicense("http://www.stanford.edu/site/terms.html")->setDataset("http://identifiers.org/sgd/"); $dataset_description .= $source_file->toRDF(); if (parent::getParameterValue('one_file') == false) { $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 {$prefix} - {$file}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/sgd/sgd.php")->setCreateDate($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 .= $output_file->toRDF(); } } //foreach //set graph URI back to default parent::setGraphURI($graph_uri); if (parent::getParameterValue('one_file') == true) { $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 {$prefix} - {$file}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/sgd/sgd.php")->setCreateDate($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() . $output_file->toRDF(); } //write dataset description to file echo "Generating dataset description... " . PHP_EOL; parent::setWriteFile($odir . parent::getBio2RDFReleaseFile()); parent::getWriteFile()->write($dataset_description); parent::getWriteFile()->close(); echo "done!" . PHP_EOL; }
function process() { // get the file list if (parent::getParameterValue('files') == 'all') { $files = explode("|", parent::getParameterList('files')); array_shift($files); } else { $files = explode(",", parent::getParameterValue('files')); } $dataset_description = ''; //set directory values $ldir = parent::getParameterValue('indir'); $rdir = parent::getParameterValue('download_url'); $odir = parent::getParameterValue('outdir'); $graph_uri = parent::getGraphURI(); if (parent::getParameterValue('dataset_graph') == true) { parent::setGraphURI(parent::getDatasetURI()); } $gz_suffix = ".gz"; foreach ($files as $file) { if ($file == 'chem_gene_ixn_types') { $suffix = '.tsv'; } else { if ($file == 'exposure_ontology') { $suffix = '.obo'; } else { $suffix = ".tsv.gz"; } } $lfile = $ldir . $file . $gz_suffix; $rfile = $rdir . 'CTD_' . $file . $suffix; if (!file_exists($lfile)) { trigger_error($lfile . " not found. Will attempt to download.", E_USER_NOTICE); if ($suffix == ".tsv.gz") { Utils::DownloadSingle($rfile, $lfile); } else { Utils::DownloadSingle($rfile, "compress.zlib://" . $lfile); } } $out_suffix = parent::getParameterValue('output_format'); $ofile = "ctd_" . $file . "." . $out_suffix; $gz = false; if (strstr(parent::getParameterValue('output_format'), "gz")) { $gz = true; } echo "Processing " . $file . " ..."; parent::setWriteFile($odir . $ofile, $gz); //set read file parent::setReadFile($lfile, TRUE); $fnx = "CTD_" . $file; $this->{$fnx}(); //close write file parent::getWriteFile()->close(); parent::clear(); echo "done!" . PHP_EOL; // generate the dataset release file echo "Generating dataset description... "; if ($file == "chemicals") { $dataset = "http://identifiers.org/ctd.chemical/"; } else { if ($file == "diseases") { $dataset = "http://identifiers.org/ctd.disease/"; } else { if ($file == "genes") { $dataset = "http://identifiers.org/ctd.gene/"; } else { $dataset = null; } } } // dataset description $source_file = (new DataResource($this))->setURI($rfile)->setTitle("Comparative Toxicogenomics Database ({$file}.{$gz_suffix}")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/gzip")->setPublisher("http://ctdbase.org/")->setHomepage("http://ctdbase.org/")->setRights("use")->setRights("by-attribution")->setRights("no-commercial")->setLicense("http://ctdbase.org/about/legal.jsp")->setDataset($dataset); $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($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/ctd/ctd.php")->setCreateDate($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() { $dataset_description = ''; $idir = parent::getParameterValue('indir'); $odir = parent::getParameterValue('outdir'); if (parent::getParameterValue('ncbo_api_key')) { $apikey = "?apikey=" . parent::getParameterValue('ncbo_api_key'); } else { if (file_exists(parent::getParameterValue('ncbo_api_key_file'))) { $apikey = "?apikey=" . trim(file_get_contents(parent::getParameterValue('ncbo_api_key_file'))); } else { echo "You must provide an NCBO API key either as a file or as a parameter" . PHP_EOL; exit; } } // get the list of ontologies from bioportal $olist = $idir . "ontolist.json"; if (!file_exists($olist) || parent::getParameterValue('download') == 'true') { echo "downloading ontology list..."; $r_olist = parent::getParameterValue('download_url') . 'ontologies' . $apikey; file_put_contents($olist, file_get_contents($r_olist)); echo "done" . PHP_EOL; } // include if (parent::getParameterValue('files') == 'all') { $include_list = array('all'); } else { $include_list = explode(",", parent::getParameterValue('files')); } // exclude $exclude_list = array(); if (parent::getParameterValue('exclude') != '') { $exclude_list = explode(",", parent::getParameterValue('exclude')); } $continue_from = parent::getParameterValue('continue_from'); $go = true; if ($continue_from) { $go = false; } // now go through the list of ontologies $ontologies = json_decode(file_get_contents($olist), false); $total = count($ontologies); foreach ($ontologies as $i => $o) { $label = (string) $o->name; $abbv = (string) $o->acronym; if ($continue_from and $continue_from == $abbv) { $go = true; } if ($go == false) { continue; } if (array_search($abbv, $exclude_list) !== FALSE) { continue; } if ($include_list[0] != 'all') { // ignore if we don't find it in the include list OR we do find it in the exclude list if (array_search($abbv, $include_list) === FALSE) { continue; } } else { if (array_search($abbv, $exclude_list) !== FALSE) { continue; } } // get info on the latest submission $uri = $o->links->latest_submission; $ls = json_decode(file_get_contents($uri . $apikey), true); if (!isset($ls['hasOntologyLanguage'])) { echo 'insufficient metadata' . PHP_EOL; continue; } $format = strtolower($ls['hasOntologyLanguage']); if ($format != 'owl' and $format != 'obo') { continue; } echo "Processing ({$i}/{$total}) {$abbv} ... "; $version = $ls['version']; if (isset($ls['homepage'])) { $homepage = $ls['homepage']; } if (isset($ls['description'])) { $description = $ls['description']; } $rfile = $ls['ontology']['links']['download']; $lfile = $abbv . "." . $format . ".gz"; if (!file_exists($idir . $lfile) or parent::getParameterValue('download') == 'true') { echo "downloading ... "; $ch = curl_init(); // create cURL handle (ch) if (!$ch) { die("Couldn't initialize a cURL handle"); } $ret = curl_setopt($ch, CURLOPT_URL, $rfile . $apikey); $ret = curl_setopt($ch, CURLOPT_HEADER, 1); $ret = curl_setopt($ch, CURLOPT_FOLLOWLOCATION, 1); $ret = curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1); $ret = curl_setopt($ch, CURLOPT_TIMEOUT, 300); $ret = curl_exec($ch); if (!$ret) { echo "no content"; continue; } $header_size = curl_getinfo($ch, CURLINFO_HEADER_SIZE); $header = substr($ret, 0, $header_size); preg_match("/filename=\"([^\"]+)\"/", $header, $m); if (isset($m[1])) { $filename = $m[1]; if (strstr($filename, ".zip")) { continue; } } else { echo "error: no filename" . PHP_EOL; continue; } $body = substr($ret, $header_size); // now get the file suffix $path = pathinfo($filename); if (isset($path['extension'])) { $ext = $path['extension']; } else { echo "error: no extension" . PHP_EOL; continue; } $lz = "compress.zlib://" . $idir . $lfile; file_put_contents($lz, $body); echo "done" . PHP_EOL; } if (file_exists($idir . $lfile)) { parent::setReadFile($idir . $lfile, true); $gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true; $ofile = strtolower($abbv) . "." . parent::getParameterValue('output_format'); parent::setWriteFile($odir . $ofile, $gz); // process echo "converting ... "; set_time_limit(0); // let's double check the format $fp = gzopen($idir . $lfile, "r"); $l = gzgets($fp); if (strstr($l, "xml")) { $format = "owl"; } gzclose($fp); if ($format == 'obo') { $this->OBO2RDF($abbv); } else { if ($format == 'owl') { $this->OWL2RDF($abbv); if (isset($this->unmapped_uri)) { print_r($this->unmapped_uri); } unset($this->unmapped_uri); } else { echo "no processor for {$label} (format {$format})" . PHP_EOL; } } if (!file_exists($odir . $ofile)) { echo "no output" . PHP_EOL; continue; } parent::getWriteFile()->close(); parent::clear(); $bVersion = parent::getParameterValue('bio2rdf_release'); $source_file = (new DataResource($this))->setURI($rfile)->setTitle("{$label}")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($idir . $lfile)))->setFormat("obo")->setPublisher("http://www.bioontology.org")->setHomepage("http://bioportal.bioontology.org/")->setRights("use-share-modify")->setLicense("http://www.bioontology.org/terms")->setDataset("http://identifiers.org/{$abbv}"); $output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/bioportal/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$abbv}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/bioportal/bioportal.php")->setCreateDate(date("Y-m-d\\TG:i:s\\Z", filemtime($odir . $ofile)))->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/bioportal/bioportal.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 { $output_file->setFormat("application/n-quads"); } if (!isset($dd)) { $dd = fopen($odir . 'bio2rdf-bioportal.nq', "w"); } fwrite($dd, $source_file->toRDF() . $output_file->toRDF()); fflush($dd); echo "done!" . PHP_EOL; } } if (isset($dd)) { fclose($dd); } echo "done!" . PHP_EOL; }