function Run()
{
// directory shortcuts
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
// get the listings page
$rfile = trim(parent::getParameterValue('download_url'));
$file = "interpro.xml.gz";
$lfile = $ldir . $file;
if (!file_exists($lfile) || parent::getParameterValue("download") == "true") {
echo "Downloading {$lfile}" . PHP_EOL;
$ret = file_get_contents($rfile);
if ($ret === FALSE) {
trigger_error("unable to download {$rfile}");
exit;
}
file_put_contents($lfile, $ret);
}
echo "Loading XML file...";
$cxml = new CXML($lfile);
$cxml->Parse();
$xml = $cxml->GetXMLRoot();
echo "Done" . PHP_EOL;
// set the write file
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
$outfile = "interpro." . parent::getParameterValue('output_format');
parent::setWriteFile($odir . $outfile, $gz);
echo "Parsing interpro xml file" . PHP_EOL;
$this->parse($xml);
parent::writeRDFBufferToWriteFile();
parent::getWriteFile()->close();
echo "Done!" . PHP_EOL;
// let's make an nq file
parent::setGraphURI(parent::getDatasetURI());
// dataset description
$source_version = parent::getDatasetVersion();
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("InterPro v{$source_version}")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("application/xml")->setFormat("application/g-zip")->setPublisher("http://www.ebi.ac.uk/")->setHomepage("http://www.ebi.ac.uk/interpro/")->setRights("InterPro - Integrated Resource Of Protein Domains And Functional Sites. Copyright (C) 2001 The InterPro Consortium")->setLicense("http://www.ebi.ac.uk/interpro/faqs.html")->setDataset("http://identifiers.org/interpro/");
$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 {$prefix} v{$source_version}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/interpro/interpro.php")->setCreateDate($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();
return true;
}
/** parse directory of files */
function parse_dir()
{
$ignore = array("..", '.', '.DS_STORE', "0");
$this->setCheckPoint('dataset');
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$dataset_file = parent::getParameterValue("outdir") . parent::getBio2RDFReleaseFile();
$fp = fopen($dataset_file, "w");
if ($fp === FALSE) {
trigger_error("Unable to open {$dataset_file}", E_USER_ERROR);
return false;
}
$ids = explode(",", parent::getParameterValue('id_list'));
$indir = parent::getParameterValue('indir');
echo "Processing {$indir}\n";
$outfile = "clinicaltrials." . parent::getParameterValue('output_format');
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
parent::setWriteFile(parent::getParameterValue("outdir") . $outfile, $gz);
$files = glob($indir . "NCT*");
foreach ($files as $i => $file) {
if ($i % 10000 == 0) {
parent::clear();
}
$trial_id = basename($file, '.xml');
if (parent::getParameterValue('id_list') == '' || in_array($trial_id, $ids)) {
if (filesize($file) != 0) {
echo "Processing {$trial_id}" . PHP_EOL;
$this->process_file($file);
} else {
echo "Processing {$trial_id} -> Empty!" . PHP_EOL;
}
}
}
echo "Finished." . PHP_EOL;
parent::getWriteFile()->close();
// make the dataset description
parent::setGraphURI(parent::getDatasetURI());
$rfile = "http://clinicaltrials.gov/ct2/show/NCT_ID?resultsxml=true";
$source_version = parent::getDatasetVersion();
// dataset description
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("Clinicaltrials")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($file)))->setFormat("application/xml")->setPublisher("http://clinicaltrials.gov/")->setHomepage("http://clinicaltrials.gov/")->setRights("use")->setRights("by-attribution")->setLicense("http://clinicaltrials.gov/ct2/about-site/terms-conditions")->setDataset("http://identifiers.org/clinicaltrials/");
parent::writeToReleaseFile($source_file->toRDF());
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$outfile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} v{$source_version}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/clinicaltrials/clinicaltrials.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
parent::writeToReleaseFile($output_file->toRDF());
parent::closeReleaseFile();
// write the dataset description file
fclose($fp);
}
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()
{
// directory shortcuts
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
if (parent::getParameterValue('omim_api_key') == '') {
$key_file = parent::getParameterValue('omim_api_key_file');
if (file_exists($key_file)) {
$key = trim(file_get_contents($key_file));
if ($key) {
parent::setParameterValue('omim_api_key', $key);
} else {
trigger_error("No API key found in the specified omim key file {$key_file}", E_USER_WARNING);
}
} else {
trigger_error("No OMIM key has been provided either by commmand line or in the expected omim key file {$key_file}", E_USER_WARNING);
}
}
// get the list of mim2gene entries
$entries = $this->GetListOfEntries($ldir);
// get the work specified
$list = trim(parent::getParameterValue('files'));
if ($list != 'all') {
// check if a hyphenated list was provided
if (($pos = strpos($list, "-")) !== FALSE) {
$start_range = substr($list, 0, $pos);
$end_range = substr($list, $pos + 1);
// get the whole list
$full_list = $this->GetListOfEntries($ldir);
// now intersect
foreach ($full_list as $e => $type) {
if ($e >= $start_range && $e <= $end_range) {
$myentries[$e] = $type;
}
}
$entries = $myentries;
} else {
// for comma separated list
$b = explode(",", parent::getParameterValue('files'));
foreach ($b as $e) {
$myentries[$e] = '';
}
$entries = array_intersect_key($entries, $myentries);
}
}
// set the write file
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
$outfile = 'omim.' . parent::getParameterValue('output_format');
parent::setWriteFile($odir . $outfile, $gz);
// declare the mapping method types
$this->get_method_type(null, true);
// iterate over the entries
$i = 0;
$total = count($entries);
foreach ($entries as $omim_id => $type) {
echo "processing " . ++$i . " of {$total} - omim# ";
$download_file = $ldir . $omim_id . ".json.gz";
$gzfile = "compress.zlib://{$download_file}";
// download if the file doesn't exist or we are told to
if (!file_exists($download_file) || parent::getParameterValue('download') == true) {
// download using the api
$url = parent::getParameterValue('omim_api_url') . '&apiKey=' . parent::getParameterValue('omim_api_key') . '&mimNumber=' . $omim_id;
$buf = file_get_contents($url);
if (strlen($buf) != 0) {
file_put_contents($download_file, $buf);
usleep(500000);
// limit of 4 requests per second
}
}
// load entry, parse and write to file
$entry = json_decode(file_get_contents($gzfile), true);
$omim_id = trim((string) $entry["omim"]["entryList"][0]["entry"]['mimNumber']);
echo $omim_id;
$this->ParseEntry($entry, $type);
parent::writeRDFBufferToWriteFile();
echo PHP_EOL;
}
parent::writeRDFBufferToWriteFile();
parent::getWriteFile()->close();
// generate the dataset description file
$source_file = (new DataResource($this))->setURI(parent::getParameterValue('omim_api_url'))->setTitle("OMIM " . parent::getDatasetVersion())->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z"))->setFormat("application/json")->setPublisher("http://omim.org")->setHomepage("http://omim.org")->setRights("use")->setRights("no-commercial")->setRights("registration-required")->setLicense("http://www.omim.org/help/agreement")->setDataset("http://identifiers.org/omim/");
$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($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/omim/omim.php")->setCreateDate($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();
return TRUE;
}
function Run()
{
$indir = parent::getParameterValue('indir');
$outdir = parent::getParameterValue('outdir');
$download_url = parent::getParameterValue('download_url');
if (parent::getParameterValue('files') == 'all') {
$files = explode("|", parent::getParameterList('files'));
array_shift($files);
} else {
$files = explode("|", parent::getParameterValue('files'));
}
if (parent::getParameterValue("id_list")) {
$this->id_list = array_flip(explode(",", parent::getParameterValue('id_list')));
}
$dataset_description = '';
foreach ($files as $f) {
if ($f == 'drugbank') {
$file = 'drugbank.xml.zip';
$lname = 'drugbank';
}
$fnx = 'parse_' . $f;
$rfile = parent::getParameterValue('download_url') . $file;
$lfile = parent::getParameterValue('indir') . $file;
$cfile = $lname . "." . parent::getParameterValue('output_format');
// download
if (!file_exists($lfile) || parent::getParameterValue('download') == true) {
utils::downloadSingle($rfile, $lfile);
}
// setup the write
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
parent::setWriteFile($outdir . $cfile, $gz);
echo $outdir . $cfile;
if (file_exists($indir . $file)) {
// call the parser
echo "processing {$file} ..." . PHP_EOL;
$this->{$fnx}($indir, $file);
echo "done" . PHP_EOL;
parent::clear();
}
parent::getWriteFile()->close();
// dataset description
$ouri = parent::getGraphURI();
parent::setGraphURI(parent::getDatasetURI());
$source_version = parent::getDatasetVersion();
$bVersion = parent::getParameterValue('bio2rdf_release');
$prefix = parent::getPrefix();
$date = date("Y-m-d\\TH:i:sP");
// dataset description
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("DrugBank ({$file})")->setRetrievedDate(date("Y-m-d\\TH:i:sP", filemtime($indir . $file)))->setFormat("application/xml")->setFormat("application/zip")->setPublisher("http://drugbank.ca")->setHomepage("http://drugbank.ca")->setRights("use")->setRights("by-attribution")->setRights("no-commercial")->setLicense("http://www.drugbank.ca/about")->setDataset("http://identifiers.org/drugbank/");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$cfile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} v{$source_version}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/drugbank/drugbank.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
parent::writeToReleaseFile($source_file->toRDF() . $output_file->toRDF());
parent::setGraphURI($ouri);
}
parent::closeReleaseFile();
}
function run()
{
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
// get the snps from pharmgkb
$snps = explode(",", parent::getParameterValue('files'));
if ($snps[0] == 'all') {
$snps = $this->getSNPs();
} else {
if ($snps[0] == 'clinical') {
$snps = $this->getSNPs(true);
} else {
if ($snps[0] == 'omim') {
$lfile = $ldir . 'snp_omimvar.txt';
if (!file_exists($lfile) || parent::getParameterValue('download') == true) {
$ret = utils::DownloadSingle('ftp://ftp.ncbi.nlm.nih.gov/snp/Entrez/snp_omimvar.txt', $lfile);
}
$snps = $this->processOMIMVar($lfile);
} else {
if ($snps[0] == 'pharmgkb') {
$lfile = $ldir . 'pharmgkb.snp.zip';
if (!file_exists($lfile) || parent::getParameterValue('download') == true) {
$ret = utils::DownloadSingle('http://www.pharmgkb.org/download.do?objId=rsid.zip&dlCls=common', $lfile);
}
$snps = $this->processPharmGKBSnps($lfile);
}
}
}
}
$outfile = $odir . "dbsnp." . parent::getParameterValue('output_format');
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
parent::setWriteFile($outfile, $gz);
$n = count($snps);
$z = 0;
foreach ($snps as $i => $snp) {
$file = $snp . '.xml.gz';
$infile = $ldir . $file;
$rfile = parent::getParameterValue('download_url') . $snp;
//$outfile = $odir.$snp.".".parent::getParameterValue('output_format');
// check if exists
$download = false;
if (!file_exists($infile)) {
//trigger_error($lfile." not found. Will attempt to download. ", E_USER_NOTICE);
parent::setParameterValue('download', true);
}
// download
if (parent::getParameterValue('download') == true) {
trigger_error("Downloading {$file}", E_USER_NOTICE);
$ret = utils::downloadSingle($rfile, "compress.zlib://" . $infile, true);
if ($ret === false) {
continue;
}
}
// process
echo "Processing {$snp} (" . ($i + 1) . "/{$n})" . PHP_EOL;
$this->parse($infile);
parent::writeRDFBufferToWriteFile();
if ($z++ % 10000 == 0) {
parent::clear();
}
}
parent::getWriteFile()->close();
// generate the dataset description file
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("dbSNP " . parent::getDatasetVersion())->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z"))->setFormat("application/xml")->setPublisher("http://www.ncbi.nlm.nih.gov")->setHomepage("http://www.ncbi.nlm.nih.gov/SNP/")->setRights("use-share-modify")->setLicense("http://www.ncbi.nlm.nih.gov/About/disclaimer.html")->setDataset("http://identifiers.org/dbsnp/");
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$outfile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/dbsnp/dbsnp.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description = $source_file->toRDF() . $output_file->toRDF();
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
}
