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()
{
// 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()
{
$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()
{
$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;
}
