PHP utils::DownloadSingle方法代码示例

 public function Run()
 {
     $file = "iproclass.tb.gz";
     $ldir = $this->GetParameterValue('indir');
     $odir = $this->GetParameterValue('outdir');
     $rdir = $this->GetParameterValue('download_url');
     $lfile = $ldir . $file;
     if (!file_exists($lfile)) {
         trigger_error($lfile . " not found. Will attempt to download.", E_USER_NOTICE);
         parent::setParameterValue('download', true);
     }
     //download all files
     $rfile = $rdir . $file;
     if ($this->GetParameterValue('download') == true) {
         echo "downloading {$file}... ";
         utils::DownloadSingle($rfile, $lfile);
         //			$cmd = "gzip -c $lfile | split -d -l 1000000 --filter='gzip > $FILE.gz' - iproclass-"
     }
     $ofile = "iproclass.nq";
     $gz = true;
     parent::setReadFile($lfile, true);
     echo "processing {$file}... ";
     $this->process();
     echo "done!" . PHP_EOL;
     parent::getWriteFile()->close();
     echo "generating dataset release file... ";
     $source_file = (new DataResource($this))->setURI($rfile)->setTitle("iProClass")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/gzip")->setPublisher("http://pir.georgetown.edu")->setHomepage("http://pir.georgetown.edu/iproclass")->setRights("use-share-modify")->setLicense("http://pir.georgetown.edu/pirwww/about/linkpir.shtml")->setDataset("http://identifiers.org/iproclass/");
     $prefix = parent::getPrefix();
     $bVersion = parent::getParameterValue('bio2rdf_release');
     $date = date("Y-m-d\\TG:i:s\\Z");
     $output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/iproclass/iproclass.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
     if ($gz) {
         $output_file->setFormat("application/gzip");
     }
     if (strstr(parent::getParameterValue('output_format'), "nt")) {
         $output_file->setFormat("application/n-triples");
     } else {
         $output_file->setFormat("application/n-quads");
     }
     $dataset_description = $source_file->toRDF() . $output_file->toRDF();
     parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
     parent::getWriteFile()->write($dataset_description);
     parent::getWriteFile()->close();
     echo "done!" . PHP_EOL;
 }

 function Run()
 {
     $dataset_description = '';
     $ldir = parent::getParameterValue('indir');
     $odir = parent::getParameterValue('outdir');
     $list_file = $ldir . "ftp_list.txt";
     if (!file_exists($list_file) || $this->getParameterValue('download') == true) {
         echo "Getting FTP file list ...";
         $list = $this->getFtpFileList('ftp.ncbi.nlm.nih.gov', '/refseq/release/complete/', '/(complete\\.[0-9]+\\.protein\\.gpff\\.gz)/');
         if (!isset($list) or count($list) == 0) {
             trigger_error("Unable to get list of files from FTP site. Check internet connection", E_USER_ERROR);
             exit(-1);
         }
         asort($list);
         $buf = implode("\n", $list);
         file_put_contents($list_file, $buf);
         echo "Done." . PHP_EOL;
     } else {
         echo "Using existing ftp list" . PHP_EOL;
         $list = explode("\n", file_get_contents($list_file));
     }
     $counter = 1;
     $total = count($list);
     foreach ($list as $f) {
         $lfile = $ldir . $f;
         echo "Processing " . $counter++ . "/{$total} {$f}. ";
         if (!file_exists($lfile) || $this->getParameterValue('download') == true) {
             $rfile = parent::getParameterValue('download_url') . $f;
             echo "Downloading ...";
             utils::DownloadSingle($rfile, $lfile);
             echo "done.";
         } else {
             echo "Using existing file.";
         }
         echo PHP_EOL;
     }
     //if download
     //iterate over the files
     $files = $this->getFilePaths($ldir, 'gz');
     asort($files);
     foreach ($files as $f) {
         $lfile = $ldir . $f;
         $ofile = $odir . basename($f, ".gz") . "." . parent::getParameterValue('output_format');
         $gz = strstr(parent::getParameterValue('output_format'), "gz") ? true : false;
         parent::setWriteFile($ofile, $gz);
         parent::setReadFile($lfile, true);
         echo "processing {$f} ...";
         $this->process();
         parent::clear();
         echo "done!" . PHP_EOL;
         $this->getReadFile()->close();
         $this->getWriteFile()->close();
         $source_file = (new DataResource($this))->setURI(parent::getParameterValue('download_url') . $lfile)->setTitle("NCBI RefSeq - {$f}")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat('text/refseq-format')->setFormat('application/zip')->setPublisher('http://www.ncbi.nlm.nih.gov')->setHomepage('http://www.ncbi.nlm.nih.gov/refseq')->setRights('use')->setRights('attribution')->setLicense('http://www.nlm.nih.gov/copyright.html')->setDataset(parent::getDatasetURI());
         $prefix = parent::getPrefix();
         $bVersion = parent::getParameterValue('bio2rdf_release');
         $date = date("Y-m-d\\TG:i:s\\Z");
         $output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} - {$f}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/refseq/refseq.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("restricted-by-source-license")->setLicense("http://creativecommons/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
         $dataset_description .= $output_file->toRDF() . $source_file->toRDF();
     }
     //for
     parent::writeToReleaseFile($dataset_description);
     parent::getWriteFile()->close();
 }

 function process()
 {
     $ldir = parent::getParameterValue('indir');
     $odir = parent::getParameterValue('outdir');
     $rdir = parent::getParameterValue('download_url');
     //which files are to be converted?
     $files = trim($this->GetParameterValue('files'));
     if ($files == 'all') {
         $files = $this->getPackageMap();
     } else {
         $sel_arr = explode(",", $files);
         $pm = $this->getPackageMap();
         $files = array();
         foreach ($sel_arr as $a) {
             if (array_key_exists($a, $pm)) {
                 $files[$a] = $pm[$a];
             }
         }
     }
     if ($this->getParameterValue('limit_organisms') == true) {
         $this->taxids = array_flip(explode(",", $this->getParameterValue('organisms')));
     }
     //set dataset graph to be dataset URI
     $graph_uri = parent::getGraphURI();
     if (parent::getParameterValue('dataset_graph') == true) {
         parent::setGraphURI(parent::getDatasetURI());
     }
     $dataset_description = '';
     //now iterate over the files array
     foreach ($files as $module => $rfilename) {
         $file = $module . ".gz";
         $lfile = $ldir . $file;
         $rfile = $rdir . $rfilename;
         // download
         if (!file_exists($lfile) || parent::getParameterValue('download') == true) {
             trigger_error("{$lfile} not found. Will attempt to download.", E_USER_NOTICE);
             $myfile = $lfile;
             if ($module == "gene2sts" || $module == "gene2unigene") {
                 $myfile = "compress.zlib://" . $lfile;
             }
             echo "downloading {$module} ...";
             utils::DownloadSingle($rfile, $myfile);
             echo "done" . PHP_EOL;
         }
     }
     foreach ($files as $module => $rfilename) {
         $file = $module . ".gz";
         $lfile = $ldir . $file;
         $rfile = $rdir . $rfilename;
         $ofile = $module . "." . parent::getParameterValue('output_format');
         $gz = false;
         if (strstr(parent::getParameterValue('output_format'), "gz")) {
             $gz = true;
         }
         echo "Processing {$module} ... ";
         parent::setReadFile($lfile, true);
         parent::setWriteFile($odir . $ofile, $gz);
         $fnx = $module;
         if ($module == 'gene2refseq') {
             $fnx = 'gene2accession';
         }
         $this->{$fnx}();
         parent::clear();
         echo 'done!' . PHP_EOL;
         parent::getReadFile()->close();
         parent::getWriteFile()->close();
         // generate the dataset release file
         // dataset description
         $source_file = (new DataResource($this))->setURI($rfile)->setTitle("NCBI Gene ({$module})")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/gzip")->setPublisher("http://www.ncbi.nlm.nih.gov")->setHomepage("http://www.ncbi.nlm.nih.gov/gene")->setRights("use-share-modify")->setLicense("http://www.ncbi.nlm.nih.gov/About/disclaimer.html")->setDataset("http://identifiers.org/ncbigene/");
         $prefix = parent::getPrefix();
         $bVersion = parent::getParameterValue('bio2rdf_release');
         $date = date("Y-m-d\\TG:i:s\\Z");
         $output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/ncbigene/ncbigene.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
         if ($gz) {
             $output_file->setFormat("application/gzip");
         }
         if (strstr(parent::getParameterValue('output_format'), "nt")) {
             $output_file->setFormat("application/n-triples");
         } else {
             $output_file->setFormat("application/n-quads");
         }
         $dataset_description .= $source_file->toRDF() . $output_file->toRDF();
     }
     //foreach
     //set graph URI back to default value
     parent::setGraphURI($graph_uri);
     //write dataset description to file
     echo "Generating dataset description... ";
     parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
     parent::getWriteFile()->write($dataset_description);
     parent::getWriteFile()->close();
     echo "done!" . PHP_EOL;
 }

 function run()
 {
     // get the file list
     if ($this->GetParameterValue('files') == 'all') {
         $files = explode("|", $this->GetParameterList('files'));
         array_shift($files);
     } else {
         $files = explode(",", $this->GetParameterValue('files'));
     }
     if ($this->getParameterValue('additional') != 'none') {
         $f = explode(",", $this->getParameterValue('additional'));
         $files = array_merge($files, $f);
     }
     $ldir = $this->GetParameterValue('indir');
     $odir = $this->GetParameterValue('outdir');
     $rdir = $this->GetParameterValue('download_url');
     $dataset_description = '';
     foreach ($files as $file) {
         $suffix = ".zip";
         $lfile = $ldir . $file . $suffix;
         $rfile = $rdir . $file . $suffix;
         if ($file == "offsides" and !file_exists($lfile)) {
             echo "downloading twosides...";
             $rfile = "http://www.pharmgkb.org/redirect.jsp?p=ftp%3A%2F%2Fftpuserd%3AGKB4ftp%40ftp.pharmgkb.org%2Fdownload%2Ftatonetti%2F3003377s-offsides.zip";
             utils::DownloadSingle($rfile, $lfile);
             echo "done" . PHP_EOL;
         } elseif ($file == "twosides" and !file_exists($lfile)) {
             echo "downloading {$file} ...";
             $rfile = "http://www.pharmgkb.org/redirect.jsp?p=ftp%3A%2F%2Fftpuserd%3AGKB4ftp%40ftp.pharmgkb.org%2Fdownload%2Ftatonetti%2F3003377s-twosides.zip";
             utils::DownloadSingle($rfile, $lfile);
             echo "done" . PHP_EOL;
         } elseif ($file == 'annotations' or $file == 'relationships') {
             if (!file_exists($lfile)) {
                 echo "Contact PharmGKB to get access to variants/clinical variants; save file as annotations.zip" . PHP_EOL;
                 continue;
             }
         } else {
             if (!file_exists($lfile) or parent::getParameterValue('download') == true) {
                 echo "Downloading {$lfile} ... ";
                 Utils::DownloadSingle('https://www.pharmgkb.org/download.do?objId=' . $file . '.zip&dlCls=common', $lfile);
                 echo "done" . PHP_EOL;
             }
         }
         // get a pointer to the file in the zip archive
         if (!file_exists($lfile)) {
             echo "no local copy of {$lfile} . skipping" . PHP_EOL;
             continue;
         }
         $zin = new ZipArchive();
         if ($zin->open($lfile) === FALSE) {
             trigger_error("Unable to open {$lfile}");
             exit;
         }
         $zipentries = array();
         if ($file == "annotations") {
             // exclude: 'clinical_ann.tsv','study_parameters.tsv'
             $zipentries = array('clinical_ann_metadata.tsv', 'var_drug_ann.tsv', 'var_pheno_ann.tsv', 'var_fa_ann.tsv');
         } else {
             if ($file == "pathways") {
                 for ($i = 0; $i < $zin->numFiles; $i++) {
                     $stat = $zin->statIndex($i);
                     $entry = $stat['name'];
                     $ext = pathinfo($entry, PATHINFO_EXTENSION);
                     if ($ext != "txt") {
                         $zipentries[] = $entry;
                     }
                 }
             } else {
                 if ($file == "relationships") {
                     $zipentries = array("relationships.tsv");
                 } else {
                     if ($file == 'offsides') {
                         $zipentries = array('3003377s-offsides.tsv');
                     } else {
                         if ($file == 'twosides') {
                             $zipentries = array('3003377s-twosides.tsv');
                         } else {
                             $zipentries = array($file . ".tsv");
                         }
                     }
                 }
             }
         }
         // set the write file, parse, write and close
         $suffix = parent::getParameterValue('output_format');
         $outfile = $file . '.' . $suffix;
         $gz = false;
         if (strstr(parent::getParameterValue('output_format'), "gz")) {
             $gz = true;
         }
         $this->SetWriteFile($odir . $outfile, $gz);
         foreach ($zipentries as $zipentry) {
             if (($fp = $zin->getStream($zipentry)) === FALSE) {
                 trigger_error("Unable to get {$file}.tsv in ziparchive {$lfile}");
                 return FALSE;
             }
             $this->SetReadFile($lfile);
             $this->GetReadFile()->SetFilePointer($fp);
             if ($file == "annotations") {
                 $fnx = substr($zipentry, 0, strpos($zipentry, ".tsv"));
//.........这里部分代码省略.........

 function run()
 {
     if (parent::getParameterValue('files') == 'all') {
         $files = explode("|", $this->GetParameterList('files'));
         array_shift($files);
     } else {
         $files = explode(",", parent::getParameterValue('files'));
     }
     $ldir = parent::getParameterValue('indir');
     $odir = parent::getParameterValue('outdir');
     $rdir = parent::getParameterValue('download_url');
     $dataset_description = '';
     foreach ($files as $file) {
         $download = parent::getParameterValue('download');
         $lfile = $ldir . "goa_" . $file . ".gz";
         if (!file_exists($lfile) && $download == false) {
             trigger_error($lfile . " not found. Will attempt to download.", E_USER_NOTICE);
             $download = true;
         }
         //download file
         $rfile = $rdir . strtoupper($file) . "/gene_association.goa_" . $file . ".gz";
         if ($download == true) {
             echo "downloading {$file} ... ";
             //file_put_contents($lfile,file_get_contents($rfile));
             utils::DownloadSingle($rfile, $lfile);
         }
         $gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
         $ofile = "goa_" . $file . "." . parent::getParameterValue('output_format');
         parent::setReadFile($lfile, TRUE);
         parent::setWriteFile($odir . $ofile, $gz);
         echo "processing {$file} ... ";
         $this->process($file);
         echo "done!";
         parent::clear();
         //close write file
         parent::getWriteFile()->close();
         echo PHP_EOL;
         // dataset description
         $graph_uri = parent::getGraphURI();
         if (parent::getParameterValue('dataset_graph') == true) {
             parent::setGraphURI(parent::getDatasetURI());
         }
         $source_file = (new DataResource($this))->setURI($rfile)->setTitle("Gene Ontology Annotation file {$file} ({$rfile}")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/gzip")->setPublisher("http://www.ebi.ac.uk/")->setHomepage("http://www.ebi.ac.uk/GOA/")->setRights("use")->setLicense("http://www.ebi.ac.uk/GOA/goaHelp.html")->setDataset("http://identifiers.org/goa/");
         $prefix = parent::getPrefix();
         $bVersion = parent::getParameterValue('bio2rdf_release');
         $date = date("Y-m-d\\TG:i:s\\Z");
         $output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/irefindex/irefindex.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
         if ($gz) {
             $output_file->setFormat("application/gzip");
         }
         if (strstr(parent::getParameterValue('output_format'), "nt")) {
             $output_file->setFormat("application/n-triples");
         } else {
             $output_file->setFormat("application/n-quads");
         }
         $dataset_description .= $source_file->toRDF() . $output_file->toRDF();
         parent::setGraphURI($graph_uri);
     }
     parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
     parent::getWriteFile()->write($dataset_description);
     parent::getWriteFile()->close();
     echo "done!" . PHP_EOL;
 }

 function run()
 {
     $ldir = parent::getParameterValue('indir');
     $odir = parent::getParameterValue('outdir');
     // get the snps from pharmgkb
     $snps = explode(",", parent::getParameterValue('files'));
     if ($snps[0] == 'all') {
         $snps = $this->getSNPs();
     } else {
         if ($snps[0] == 'clinical') {
             $snps = $this->getSNPs(true);
         } else {
             if ($snps[0] == 'omim') {
                 $lfile = $ldir . 'snp_omimvar.txt';
                 if (!file_exists($lfile) || parent::getParameterValue('download') == true) {
                     $ret = utils::DownloadSingle('ftp://ftp.ncbi.nlm.nih.gov/snp/Entrez/snp_omimvar.txt', $lfile);
                 }
                 $snps = $this->processOMIMVar($lfile);
             } else {
                 if ($snps[0] == 'pharmgkb') {
                     $lfile = $ldir . 'pharmgkb.snp.zip';
                     if (!file_exists($lfile) || parent::getParameterValue('download') == true) {
                         $ret = utils::DownloadSingle('http://www.pharmgkb.org/download.do?objId=rsid.zip&dlCls=common', $lfile);
                     }
                     $snps = $this->processPharmGKBSnps($lfile);
                 }
             }
         }
     }
     $outfile = $odir . "dbsnp." . parent::getParameterValue('output_format');
     $gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
     parent::setWriteFile($outfile, $gz);
     $n = count($snps);
     $z = 0;
     foreach ($snps as $i => $snp) {
         $file = $snp . '.xml.gz';
         $infile = $ldir . $file;
         $rfile = parent::getParameterValue('download_url') . $snp;
         //$outfile = $odir.$snp.".".parent::getParameterValue('output_format');
         // check if exists
         $download = false;
         if (!file_exists($infile)) {
             //trigger_error($lfile." not found. Will attempt to download. ", E_USER_NOTICE);
             parent::setParameterValue('download', true);
         }
         // download
         if (parent::getParameterValue('download') == true) {
             trigger_error("Downloading {$file}", E_USER_NOTICE);
             $ret = utils::downloadSingle($rfile, "compress.zlib://" . $infile, true);
             if ($ret === false) {
                 continue;
             }
         }
         // process
         echo "Processing {$snp} (" . ($i + 1) . "/{$n})" . PHP_EOL;
         $this->parse($infile);
         parent::writeRDFBufferToWriteFile();
         if ($z++ % 10000 == 0) {
             parent::clear();
         }
     }
     parent::getWriteFile()->close();
     // generate the dataset description file
     $source_file = (new DataResource($this))->setURI($rfile)->setTitle("dbSNP " . parent::getDatasetVersion())->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z"))->setFormat("application/xml")->setPublisher("http://www.ncbi.nlm.nih.gov")->setHomepage("http://www.ncbi.nlm.nih.gov/SNP/")->setRights("use-share-modify")->setLicense("http://www.ncbi.nlm.nih.gov/About/disclaimer.html")->setDataset("http://identifiers.org/dbsnp/");
     $prefix = parent::getPrefix();
     $bVersion = parent::getParameterValue('bio2rdf_release');
     $date = date("Y-m-d\\TG:i:s\\Z");
     $output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$outfile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/dbsnp/dbsnp.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
     if ($gz) {
         $output_file->setFormat("application/gzip");
     }
     if (strstr(parent::getParameterValue('output_format'), "nt")) {
         $output_file->setFormat("application/n-triples");
     } else {
         $output_file->setFormat("application/n-quads");
     }
     $dataset_description = $source_file->toRDF() . $output_file->toRDF();
     parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
     parent::getWriteFile()->write($dataset_description);
     parent::getWriteFile()->close();
 }