本文整理汇总了PHP中Utils::DownloadSingle方法的典型用法代码示例。如果您正苦于以下问题：PHP Utils::DownloadSingle方法的具体用法？PHP Utils::DownloadSingle怎么用？PHP Utils::DownloadSingle使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Utils的用法示例。
在下文中一共展示了Utils::DownloadSingle方法的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的PHP代码示例。
示例1: Run
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;
}示例2: Run
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();
}示例3: Run
function Run()
{
$file = "hgnc.tab";
$ldir = $this->GetParameterValue('indir');
$odir = $this->GetParameterValue('outdir');
$rdir = $this->GetParameterValue('download_url');
//make sure directories end with slash
if (substr($ldir, -1) !== "/") {
$ldir = $ldir . "/";
}
if (substr($odir, -1) !== "/") {
$odir = $odir . "/";
}
$lfile = $ldir . $file;
if (!file_exists($lfile) && $this->GetParameterValue('download') == false) {
trigger_error($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 = $rdir;
echo "downloading {$file} ... ";
Utils::DownloadSingle($rfile, $lfile);
}
$ofile = $odir . $file . '.nt';
$gz = false;
if ($this->GetParameterValue('graph_uri')) {
$ofile = $odir . $file . '.nq';
}
if ($this->GetParameterValue('gzip')) {
$ofile .= '.gz';
$gz = true;
}
$this->SetWriteFile($ofile, $gz);
$this->SetReadFile($lfile);
echo "processing {$file}... ";
$this->process();
echo "done!";
//close write file
$this->GetWriteFile()->Close();
echo PHP_EOL;
// generate the dataset release file
echo "generating dataset release file... ";
$desc = $this->GetBio2RDFDatasetDescription($this->GetNamespace(), "https://github.com/bio2rdf/bio2rdf-scripts/blob/master/hgnc/hgnc.php", $this->GetBio2RDFDownloadURL($this->GetNamespace()), "http://www.genenames.org", array("use"), "http://www.genenames.org/about/overview", $this->GetParameterValue('download_url'), $this->version);
$this->SetWriteFile($odir . $this->GetBio2RDFReleaseFile($this->GetNamespace()));
$this->GetWriteFile()->Write($desc);
$this->GetWriteFile()->Close();
echo "done!" . PHP_EOL;
}示例4: Run
function Run()
{
// get the file list
if ($this->GetParameterValue('files') == 'all') {
$files = explode("|", $this->GetParameterList('files'));
array_shift($files);
} else {
$files = explode("|", $this->GetParameterValue('files'));
}
$ldir = $this->GetParameterValue('indir');
$odir = $this->GetParameterValue('outdir');
$rdir = $this->GetParameterValue('download_url');
// check if exists
$file = $files[0];
$lfile = $ldir . $file;
if (!file_exists($lfile)) {
trigger_error($lfile . " not found. Will attempt to download.", E_USER_NOTICE);
$this->SetParameterValue('download', true);
}
// download
if ($this->GetParameterValue('download') == true) {
$rfile = $rdir . $file;
trigger_error("Downloading {$file} from {$rfile}", E_USER_NOTICE);
Utils::DownloadSingle($rfile, $lfile);
}
// set the write file, parse, write and close
$ofile = 'drugbank.nt';
$gz = false;
if ($this->GetParameterValue('graph_uri')) {
$ofile = 'drugbank.nq';
}
if ($this->GetParameterValue('gzip')) {
$ofile .= '.gz';
$gz = true;
}
$this->SetWriteFile($odir . $ofile, $gz);
$this->Parse($ldir, $file);
$this->GetWriteFile()->Close();
// generate the release file
$desc = $this->GetBio2RDFDatasetDescription($this->GetNamespace(), "https://github.com/bio2rdf/bio2rdf-scripts/blob/master/drugbank/drugbank.php", $this->GetBio2RDFDownloadURL($this->GetNamespace()) . $ofile, "http://drugbank.ca", array("use", "no-commercial"), "http://www.drugbank.ca/about", $this->GetParameterValue('download_url'), $this->version);
$this->SetWriteFile($odir . $this->GetBio2RDFReleaseFile($this->GetNamespace()));
$this->GetWriteFile()->Write($desc);
$this->GetWriteFile()->Close();
return TRUE;
}示例5: Run
function Run()
{
$idir = $this->GetParameterValue('indir');
$odir = $this->GetParameterValue('outdir');
$files = $this->GetParameterValue('files');
if ($files == 'all') {
$list = explode('|', $this->GetParameterList('files'));
array_shift($list);
} else {
$list = explode('|', $this->GetParameterValue('files'));
}
foreach ($list as $item) {
$lfile = $idir . $item . '.rpt';
$rfile = $this->GetParameterValue('download_url') . $item . '.rpt';
if (!file_exists($lfile) || $this->GetParameterValue('download') == 'true') {
echo "downloading {$item}...";
Utils::DownloadSingle($rfile, $lfile);
}
$this->SetReadFile($lfile, true);
echo "Processing {$item}...";
$ofile = $odir . "mgi-" . $item . '.nt';
$gz = false;
if ($this->GetParameterValue('graph_uri')) {
$ofile = $odir . "mgi-" . $item . '.nq';
}
if ($this->GetParameterValue('gzip')) {
$ofile .= '.gz';
$gz = true;
}
$this->SetWriteFile($ofile, $gz);
$this->{$item}();
$this->GetWriteFile()->Close();
$this->GetReadFile()->Close();
echo "Done" . PHP_EOL;
}
}示例6: run
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();
}示例7: Run
function Run()
{
$ldir = $this->GetParameterValue('indir');
$odir = $this->GetParameterValue('outdir');
$rdir = $this->GetParameterValue('download_url');
//which files are to be converted?
$selectedPackage = trim($this->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];
}
}
}
//now iterate over the files array
foreach ($files as $id => $file) {
echo "Processing {$id} ...";
$lfile = $ldir . $id . ".gz";
// download
if (!file_exists($lfile) || $this->GetParameterValue('download') == true) {
echo "downloading ... ";
//don't use subdirectory GENE_INFO for saving local version of All_data.gene_info.gz
if ($id == "gene2sts" || $id == "gene2unigene") {
$rfile = "compress.zlib://" . $rdir . $file;
} else {
$rfile = $rdir . $file;
}
Utils::DownloadSingle($rfile, $lfile);
}
$writefile = $odir . $id . ".nt";
$gz = false;
if ($this->GetParameterValue('graph_uri')) {
$writefile = $odir . $id . ".nq";
}
if ($this->GetParameterValue('gzip')) {
$writefile .= '.gz';
$gz = true;
}
$this->SetReadFile($lfile, true);
$this->SetWriteFile($writefile, $gz);
echo 'parsing ...';
$this->{$id}();
echo 'done.' . PHP_EOL;
$this->GetReadFile()->Close();
$this->GetWriteFile()->Close();
$bio2rdf_download_files[] = $this->GetBio2RDFDownloadURL($this->GetNamespace()) . $writefile;
}
//foreach
// generate the release file
$desc = $this->GetBio2RDFDatasetDescription($this->GetNamespace(), "https://github.com/bio2rdf/bio2rdf-scripts/blob/master/gene/entrez_gene.php", $bio2rdf_download_files, "http://www.ncbi.nlm.nih.gov/gene", array("use-share-modify"), "http://www.ncbi.nlm.nih.gov/About/disclaimer.html", "ftp://ftp.ncbi.nih.gov/gene/", $this->version);
$this->SetWriteFile($odir . $this->GetBio2RDFReleaseFile($this->GetNamespace()));
$this->GetWriteFile()->Write($desc);
$this->GetWriteFile()->Close();
return TRUE;
}示例8: Run
function Run()
{
$ldir = $this->GetParameterValue('indir');
$odir = $this->GetParameterValue('outdir');
$rfile = $this->GetParameterValue('download_url');
$lfile = substr($rfile, strrpos($rfile, "/") + 1);
// check if exists
if (!file_exists($ldir . $lfile) or parent::getParameterValue('download') == 'true') {
echo "dowloading {$rfile} ...";
trigger_error("Will attempt to download ", E_USER_NOTICE);
Utils::DownloadSingle($rfile, $ldir . $lfile);
echo "done" . PHP_EOL;
}
// make sure we have the zip archive
$zin = new ZipArchive();
if ($zin->open($ldir . $lfile) === FALSE) {
trigger_error("Unable to open {$ldir}{$lfile}");
exit;
}
// get the work
if ($this->GetParameterValue('files') == 'all') {
$files = explode("|", $this->GetParameterList('files'));
array_shift($files);
} else {
$files = explode("|", $this->GetParameterValue('files'));
}
$gz = false;
if (strstr(parent::getParameterValue('output_format'), "gz")) {
$gz = true;
}
$outfile = "ndc." . parent::getParameterValue('output_format');
parent::setWriteFile($odir . $outfile, $gz);
// now go through each item in the zip file and process
foreach ($files as $file) {
echo "Processing {$file}... ";
$fpin = $zin->getStream($file . ".txt");
if (!$fpin) {
trigger_error("Unable to get pointer to {$file} in {$ldir}{$lfile}", E_USER_ERROR);
return FALSE;
}
$this->{$file}($fpin);
parent::writeRDFBufferToWriteFile();
echo "done!" . PHP_EOL;
}
parent::getWriteFile()->close();
echo "Generating dataset description for {$outfile}... ";
//start generating dataset description file
$dataset_description = '';
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("FDA National Drug Code Directory")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($ldir . $lfile)))->setFormat("text/tab-separated-value")->setFormat("application/zip")->setPublisher("http://www.fda.gov")->setHomepage("http://www.fda.gov/Drugs/InformationOnDrugs/ucm142438.htm")->setRights("use-share")->setLicense(null)->setDataset("http://identifiers.org/ndc/");
$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 {$prefix}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/ndc/ndc.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() . $output_file->toRDF();
//write dataset description to file
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
}示例9: Run
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;
}示例10: Run
function Run()
{
$ldir = $this->GetParameterValue('indir');
$odir = $this->GetParameterValue('outdir');
$rfile = $this->GetParameterValue('download_url');
$lfile = substr($rfile, strrpos($rfile, "/") + 1);
// check if exists
if (!file_exists($ldir . $lfile)) {
trigger_error($ldir . $lfile . " not found. Will attempt to download. ", E_USER_NOTICE);
$this->SetParameterValue('download', true);
}
// download
if ($this->GetParameterValue('download') == true) {
trigger_error("Downloading {$rfile}", E_USER_NOTICE);
Utils::DownloadSingle($rfile, $ldir . $lfile);
}
// make sure we have the zip archive
$zin = new ZipArchive();
if ($zin->open($ldir . $lfile) === FALSE) {
trigger_error("Unable to open {$ldir}{$lfile}");
exit;
}
// get the work
if ($this->GetParameterValue('files') == 'all') {
$files = explode("|", $this->GetParameterList('files'));
array_shift($files);
} else {
$files = explode("|", $this->GetParameterValue('files'));
}
// now go through each item in the zip file and process
foreach ($files as $file) {
echo "Processing {$file} ...";
// the file name in the zip archive is Product not product
if ($file == "product") {
$file = ucfirst($file);
}
$fpin = $zin->getStream($file . ".txt");
if (!$fpin) {
trigger_error("Unable to get pointer to {$file} in {$ldir}{$lfile}", E_USER_ERROR);
exit("failed\n");
}
// set the write file
$outfile = $file . '.nt';
$gz = false;
if ($this->GetParameterValue('graph_uri')) {
$outfile = $file . '.nq';
}
if ($this->GetParameterValue('gzip')) {
$outfile .= '.gz';
$gz = true;
}
$bio2rdf_download_files[] = $this->GetBio2RDFDownloadURL($this->GetNamespace()) . $outfile;
$this->SetWriteFile($odir . $outfile, $gz);
// process
$this->{$file}($fpin);
// write to file
$this->WriteRDFBufferToWriteFile();
$this->GetWriteFile()->Close();
echo "done!" . PHP_EOL;
}
// generate the release file
$this->DeleteBio2RDFReleaseFiles($odir);
$desc = $this->GetBio2RDFDatasetDescription($this->GetNamespace(), "https://github.com/bio2rdf/bio2rdf-scripts/blob/master/ndc/ndc.php", $bio2rdf_download_files, "http://www.fda.gov/Drugs/InformationOnDrugs/ucm142438.htm", array("use-share"), null, $this->GetParameterValue('download_url'), $this->version);
$this->SetWriteFile($odir . $this->GetBio2RDFReleaseFile($this->GetNamespace()));
$this->GetWriteFile()->Write($desc);
$this->GetWriteFile()->Close();
}示例11: process
function process()
{
if (parent::getParameterValue('files') == 'all') {
$files = explode("|", parent::getParameterList('files'));
array_shift($files);
} else {
$files = explode(",", parent::getParameterValue('files'));
}
$remote_files = array("human" => "human_genes.zip", "models" => "models_genes.zip");
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$rdir = parent::getParameterValue('download_url');
$dataset_description = '';
$graph_uri = parent::getGraphURI();
if (parent::getParameterValue('dataset_graph') == true) {
parent::setGraphURI(parent::getDatasetURI());
}
foreach ($files as $file) {
$lfile = $ldir . $remote_files[$file];
$rfile = $rdir . $remote_files[$file];
if (!file_exists($lfile)) {
trigger_error($lfile . " not found. Will attempt to download." . PHP_EOL, E_USER_WARNING);
echo "Downloading {$rfile}... ";
Utils::DownloadSingle($rfile, $lfile);
echo "done!" . PHP_EOL;
}
$suffix = parent::getParameterValue('output_format');
$ofile = "genage_" . $file . '.' . $suffix;
if (strstr(parent::getParameterValue('output_format'), "gz")) {
$gz = true;
}
$zin = new ZipArchive();
if ($zin->open($lfile) === FALSE) {
trigger_error("Unable to open {$lfile}");
exit;
}
if ($file == "human") {
$zipentry = "genage_human.csv";
} else {
if ($file == "models") {
$zipentry = "genage_models.csv";
}
}
if (($fp = $zin->getStream($zipentry)) === FALSE) {
trigger_error("Unable to get {$zipentry} in ziparchive {$lfile}");
return FALSE;
}
parent::SetReadFile($lfile);
parent::GetReadFile()->SetFilePointer($fp);
// set the write file, parse, write and close
$suffix = parent::getParameterValue('output_format');
$outfile = "genage_" . $file . '.' . $suffix;
$gz = false;
if (strstr($suffix, "gz")) {
$gz = true;
}
parent::setWriteFile($odir . $ofile, $gz);
echo "Processing {$lfile}... ";
$fnx = $file;
$this->{$fnx}();
echo "done!" . PHP_EOL;
parent::getWriteFile()->close();
// generate the dataset release file
echo "Generating dataset description for {$ofile}... ";
// dataset description
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("Human Ageing Genomic Resources GenAge database (" . $remote_files[$file] . ")")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/comma-separated-value")->setFormat("application/gzip")->setPublisher("http://genomics.senescence.info/")->setHomepage("http://genomics.senescence.info/genes/")->setRights("use")->setLicense("http://genomics.senescence.info/legal.html")->setDataset("http://identifiers.org/genage/");
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/genage/genage.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description .= $source_file->toRDF() . $output_file->toRDF();
echo "done!" . PHP_EOL;
}
parent::setGraphURI($graph_uri);
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
}示例12: Run
function Run()
{
// get the file list
if ($this->GetParameterValue('files') == 'all') {
$files = explode("|", $this->GetParameterList('files'));
array_shift($files);
} else {
$files = explode(",", $this->GetParameterValue('files'));
}
$ldir = $this->GetParameterValue('indir');
$odir = $this->GetParameterValue('outdir');
$rdir = $this->GetParameterValue('download_url');
$gz_suffix = ".gz";
foreach ($files as $file) {
$lfile = $ldir . $file . $gz_suffix;
$ofile = $file . ".nt";
$gz = false;
if ($this->GetParameterValue('graph_uri')) {
$ofile = $file . '.nq';
}
if ($this->GetParameterValue('gzip')) {
$ofile .= '.gz';
$gz = true;
}
$bio2rdf_download_files[] = $this->GetBio2RDFDownloadURL($this->GetNamespace()) . $ofile;
if (!file_exists($lfile)) {
trigger_error($lfile . " not found. Will attempt to download.", E_USER_NOTICE);
$this->SetParameterValue('download', true);
}
if ($this->GetParameterValue('download') == true) {
if ($file == 'chem_gene_ixn_types') {
$suffix = '.tsv';
} else {
if ($file == 'exposure_ontology') {
$suffix = '.obo';
} else {
$suffix = ".tsv.gz";
}
}
$rfile = $rdir . 'CTD_' . $file . $suffix;
if ($suffix == ".tsv.gz") {
Utils::DownloadSingle($rfile, $lfile);
} else {
Utils::DownloadSingle($rfile, "compress.zlib://" . $lfile);
}
}
echo "Processing " . $file . " ...";
$this->SetReadFile($lfile, true);
$this->SetWriteFile($odir . $ofile, $gz);
$fnx = "CTD_" . $file;
if ($this->{$fnx}() === FALSE) {
trigger_error("Error in {$fnx}");
exit;
}
$this->WriteRDFBufferToWriteFile();
$this->GetWriteFile()->Close();
echo "Done!" . PHP_EOL;
}
// generate the release file
$desc = $this->GetBio2RDFDatasetDescription($this->GetNamespace(), "https://github.com/bio2rdf/bio2rdf-scripts/blob/master/ctd/ctd.php", $bio2rdf_download_files, "http://ctdbase.org", array("use", "no-commercial"), "http://ctdbase.org/about/legal.jsp", $this->GetParameterValue('download_url'), $this->version);
$this->SetWriteFile($odir . $this->GetBio2RDFReleaseFile($this->GetNamespace()));
$this->GetWriteFile()->Write($desc);
$this->GetWriteFile()->Close();
return TRUE;
}示例13: Run
function Run()
{
// get the file list
if ($this->GetParameterValue('files') == 'all') {
$files = explode("|", $this->GetParameterList('files'));
array_shift($files);
} else {
$files = explode(",", $this->GetParameterValue('files'));
}
$ldir = $this->GetParameterValue('indir');
$odir = $this->GetParameterValue('outdir');
$rdir = $this->GetParameterValue('download_url');
foreach ($files as $file) {
if ($file == 'variant_annotations') {
$lfile = $ldir . "annotations.zip";
if (!file_exists($lfile)) {
echo "Contact PharmGKB to get access to variants/clinical variants; save file as annotations.zip" . PHP_EOL;
continue;
}
} else {
// check if exists
$lfile = $ldir . $file . ".zip";
if (!file_exists($lfile)) {
trigger_error($lfile . " not found. Will attempt to download.", E_USER_NOTICE);
$this->SetParameterValue('download', true);
}
}
// download
if ($this->GetParameterValue('download') == true) {
$rfile = $rdir . $file . ".zip";
echo "downloading {$file}...";
if ($file == 'offsides') {
Utils::DownloadSingle('http://www.pharmgkb.org/redirect.jsp?p=ftp%3A%2F%2Fftpuserd%3AGKB4ftp%40ftp.pharmgkb.org%2Fdownload%2Ftatonetti%2F3003377s-offsides.zip', $lfile);
} elseif ($file == 'twosides') {
Utils::DownloadSingle('http://www.pharmgkb.org/redirect.jsp?p=ftp%3A%2F%2Fftpuserd%3AGKB4ftp%40ftp.pharmgkb.org%2Fdownload%2Ftatonetti%2F3003377s-twosides.zip', $lfile);
} elseif ($file == 'pathways') {
Utils::DownloadSingle('http://www.pharmgkb.org/commonFileDownload.action?filename=' . $file . '-tsv.zip', $lfile);
} else {
Utils::DownloadSingle('http://www.pharmgkb.org/commonFileDownload.action?filename=' . $file . '.zip', $lfile);
}
}
// get a pointer to the file in the zip archive
$zin = new ZipArchive();
if ($zin->open($lfile) === FALSE) {
trigger_error("Unable to open {$lfile}");
exit;
}
if ($file == "variant_annotations") {
$zipentries = array('clinical_ann_metadata.tsv', 'var_drug_ann.tsv', 'var_pheno_ann.tsv', 'var_fa_ann.tsv');
} else {
if ($file == "relationships") {
$zipentries = array("relationships.tsv");
} else {
if ($file == 'offsides') {
$zipentries = array('3003377s-offsides.tsv');
} else {
if ($file == 'twosides') {
$zipentries = array('3003377s-twosides.tsv');
} else {
$zipentries = array($file . ".tsv");
}
}
}
}
// set the write file, parse, write and close
$outfile = $odir . $file . '.nt';
$gz = false;
if ($this->GetParameterValue('graph_uri')) {
$outfile = $odir . $file . '.nq';
}
if ($this->GetParameterValue('gzip')) {
$outfile .= '.gz';
$gz = true;
}
$this->SetWriteFile($outfile, $gz);
$bio2rdf_download_files[] = $this->GetBio2RDFDownloadURL($this->GetNamespace()) . $outfile;
foreach ($zipentries as $zipentry) {
if (($fp = $zin->getStream($zipentry)) === FALSE) {
trigger_error("Unable to get {$file}.tsv in ziparchive {$lfile}");
return FALSE;
}
$this->SetReadFile($lfile);
$this->GetReadFile()->SetFilePointer($fp);
if ($file == "variant_annotations") {
if ($zipentry == "clinical_ann_metadata.tsv") {
$fnx = "clinical_ann_metadata";
} else {
$fnx = 'variant_annotation';
}
echo "processing {$zipentry}..";
} else {
$fnx = $file;
echo "processing {$fnx}..";
}
$this->{$fnx}();
$this->WriteRDFBufferToWriteFile();
echo PHP_EOL;
}
$this->GetWriteFile()->Close();
}
//.........这里部分代码省略.........
示例14: process
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;
}示例15: Run
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");
//.........这里部分代码省略.........