public function Run()
{
$dataset_description = '';
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
//first get the files that are to be processed
$selectedPackage = trim(parent::getParameterValue('files'));
if ($selectedPackage == 'all') {
$files = $this->getPackageMap();
} else {
$sel_arr = explode(",", $selectedPackage);
$pm = $this->getPackageMap();
$files = array();
foreach ($sel_arr as $a) {
if (array_key_exists($a, $pm)) {
$files[$a] = $pm[$a];
}
}
}
//download
if ($this->getParameterValue('download')) {
foreach ($files as $aP => $fn) {
foreach ($fn as $aFn) {
echo "downloading file {$aFn} :" . parent::getParameterValue('download_url') . $aFn . "..." . PHP_EOL;
file_put_contents($ldir . $aFn, file_get_contents(parent::getParameterValue('download_url') . $aFn));
}
}
}
//iterate over the files
$paths = $this->getFilePaths($ldir, 'gz');
$lfile = null;
foreach ($files as $k => $val) {
foreach ($val as $fn) {
if (in_array($fn, $paths)) {
$lfile = $fn;
$ofile = $odir . basename($fn, ".gz") . "." . parent::getParameterValue('output_format');
$gz = false;
if (strstr(parent::getParameterValue('output_format'), "gz")) {
$gz = true;
}
parent::setWriteFile($ofile, $gz);
parent::setReadFile($ldir . $lfile, true);
$source_file = (new DataResource($this))->setURI(parent::getParameterValue('download_url') . basename($fn))->setTitle('International Protein Index filename: ' . basename($fn))->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($ldir . $lfile)))->setFormat('text/ipi-format')->setFormat('application/zip')->setPublisher('https://www.ebi.ac.uk')->setHomepage('https://www.ebi.ac.uk/IPI')->setRights('use')->setRights('attribution')->setLicense('https://www.ebi.ac.uk')->setDataset(parent::getDatasetURI());
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/ipi/ipi.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("restricted-by-source-license")->setLicense("http://creativecommons/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
$dataset_description .= $output_file->toRDF() . $source_file->toRDF();
echo "processing {$fn} ...";
$this->{$k}();
echo "done!" . PHP_EOL;
$this->setWriteFile($odir . $this->getBio2RDFReleaseFile());
$this->getWriteFile()->write($dataset_description);
$this->getWriteFile()->close();
}
}
}
}
function Run()
{
$file = "hgnc_complete_set.txt.gz";
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$rdir = parent::getParameterValue('download_url');
$lfile = $ldir . $file;
if (!file_exists($lfile) && parent::getParameterValue('download') == false) {
trigger_error($lfile . " not found. Will attempt to download.", E_USER_NOTICE);
parent::setParameterValue('download', true);
}
//download the hgnc file
$rfile = null;
if (parent::getParameterValue('download') == true) {
$rfile = $rdir;
echo "downloading {$file} ... ";
Utils::DownloadSingle($rfile, $lfile);
}
$ofile = $odir . "hgnc." . parent::getParameterValue('output_format');
$gz = false;
if (strstr(parent::getParameterValue('output_format'), "gz")) {
$gz = true;
}
parent::setWriteFile($ofile, $gz);
parent::setReadFile($lfile, true);
echo "processing {$file}... ";
$this->process();
echo "done!" . PHP_EOL;
//close write file
parent::getWriteFile()->close();
echo PHP_EOL;
// generate the dataset release file
echo "generating dataset release file... ";
$dataset_description = '';
$source_file = (new DataResource($this))->setURI($rdir)->setTitle('HUGO Gene Nomenclature Committee (HGNC)')->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat('text/tab-separated-value')->setFormat('application/zip')->setPublisher('http://www.genenames.org/')->setHomepage('http://www.genenames.org/data/gdlw_columndef.html')->setRights('use')->setRights('attribution')->setLicense('http://www.genenames.org/about/overview')->setDataset(parent::getDatasetURI());
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/hgnc/hgnc.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("restricted-by-source-license")->setLicense("http://creativecommons/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description .= $source_file->toRDF() . $output_file->toRDF();
$this->setWriteFile($odir . $this->getBio2RDFReleaseFile());
$this->getWriteFile()->write($dataset_description);
$this->getWriteFile()->close();
}
function run()
{
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$dd = '';
$files = parent::getParameterValue('files');
if ($files == 'all') {
$files = explode('|', parent::getParameterList('files'));
array_shift($files);
} else {
$files = explode(',', parent::getParameterValue('files'));
}
foreach ($files as $file) {
echo "processing {$file} ...";
$lfile = $ldir . $this->filemap[$file];
$rfile = parent::getParameterValue('download_url') . $this->filemap[$file];
if (!file_exists($lfile) || parent::getParameterValue('download') == 'true') {
$ret = utils::downloadSingle($rfile, $lfile);
if ($ret === false) {
echo "unable to download {$file} ... skipping" . PHP_EOL;
continue;
}
}
parent::setReadFile($lfile, true);
$suffix = parent::getParameterValue('output_format');
$ofile = "orphanet-" . $file . '.' . $suffix;
$gz = strstr(parent::getParameterValue('output_format'), "gz") ? $gz = true : ($gz = false);
/* parent::setWriteFile($odir.$ofile, $gz);
$this->$file($lfile);
parent::getWriteFile()->close();
*/
parent::getReadFile()->close();
parent::clear();
echo "done!" . PHP_EOL;
// dataset description
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("Orphanet: {$file}")->setRetrievedDate(parent::getDate(filemtime($lfile)))->setFormat("application/xml")->setPublisher("http://www.orpha.net")->setHomepage("http://www.orpha.net/")->setRights("use")->setRights("sharing-modified-version-needs-permission")->setLicense("http://creativecommons.org/licenses/by-nd/3.0/")->setDataset("http://identifiers.org/orphanet/");
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = parent::getDate(filemtime($odir . $ofile));
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/orphanet/orphanet.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dd .= $source_file->toRDF() . $output_file->toRDF();
}
//foreach
parent::writeToReleaseFile($dd);
}
function Run()
{
$idir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$files = parent::getParameterValue('files');
if ($files == 'all') {
$list = explode('|', parent::getParameterList('files'));
array_shift($list);
} else {
$list = explode(',', parent::getParameterValue('files'));
}
$dataset_description = '';
foreach ($list as $item) {
$lfile = $idir . $item . '.rpt';
$rfile = parent::getParameterValue('download_url') . $item . '.rpt';
if (!file_exists($lfile) || parent::getParameterValue('download') == 'true') {
echo "downloading {$item}...";
$ret = Utils::DownloadSingle($rfile, $lfile);
if ($ret != true) {
continue;
}
}
parent::setReadFile($lfile, true);
echo "Processing {$item}...";
$ofile = $odir . $item . '.' . parent::getParameterValue('output_format');
$gz = strstr(parent::getParameterValue('output_format'), "gz") ? true : false;
parent::setWriteFile($ofile, $gz);
$this->{$item}();
parent::getWriteFile()->close();
parent::getReadFile()->close();
echo "Done" . PHP_EOL;
parent::clear();
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("MGI {$item}")->setRetrievedDate(date("Y-m-d\\TH:i:s", filemtime($lfile)))->setFormat("text")->setPublisher("http://www.informatics.jax.org")->setHomepage("http://www.informatics.jax.org")->setRights("use")->setLicense("http://www.informatics.jax.org/mgihome/other/copyright.shtml")->setDataset("http://identifiers.org/mgi/");
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TH:i:s");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$item} in {$prefix}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/mgi/mgi.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description .= $source_file->toRDF() . $output_file->toRDF();
}
//foreach
// generate the dataset release file
$this->setWriteFile($odir . parent::getBio2RDFReleaseFile());
$this->getWriteFile()->write($dataset_description);
$this->getWriteFile()->close();
echo "done!" . PHP_EOL;
}
function Run()
{
$file = "homologene.data";
$ldir = $this->GetParameterValue('indir');
$odir = $this->GetParameterValue('outdir');
$rdir = $this->GetParameterValue('download_url');
$lfile = $ldir . $file;
if (!file_exists($lfile)) {
trigger_error($file . " not found. Will attempt to download.", E_USER_NOTICE);
parent::setParameterValue('download', true);
}
//download
$rfile = $rdir . $file;
if ($this->GetParameterValue('download') == true) {
echo "downloading {$file} ... ";
utils::downloadSingle($rfile, $lfile);
}
$ofile = 'homologene.' . parent::getParameterValue('output_format');
$gz = strstr(parent::getParameterValue('output_format'), "gz") ? $gz = true : ($gz = false);
parent::setReadFile($lfile);
parent::setWriteFile($odir . $ofile, $gz);
echo "processing {$file}... ";
$this->process();
echo "done!" . PHP_EOL;
parent::getWriteFile()->close();
// generate the dataset release file
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("NCBI Homologene")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/tab-separated-value")->setPublisher("http://www.ncbi.nlm.nih.gov")->setHomepage("http://www.ncbi.nlm.nih.gov/homologene")->setRights("use-share-modify")->setLicense("http://www.ncbi.nlm.nih.gov/About/disclaimer.html")->setDataset("http://identifiers.org/homologene/");
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/homologene/homologene.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description = $source_file->toRDF() . $output_file->toRDF();
echo "Generating dataset description... ";
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
}
public function Run()
{
$file = "iproclass.tb.gz";
$ldir = $this->GetParameterValue('indir');
$odir = $this->GetParameterValue('outdir');
$rdir = $this->GetParameterValue('download_url');
$lfile = $ldir . $file;
if (!file_exists($lfile)) {
trigger_error($lfile . " not found. Will attempt to download.", E_USER_NOTICE);
parent::setParameterValue('download', true);
}
//download all files
$rfile = $rdir . $file;
if ($this->GetParameterValue('download') == true) {
echo "downloading {$file}... ";
utils::DownloadSingle($rfile, $lfile);
// $cmd = "gzip -c $lfile | split -d -l 1000000 --filter='gzip > $FILE.gz' - iproclass-"
}
$ofile = "iproclass.nq";
$gz = true;
parent::setReadFile($lfile, true);
echo "processing {$file}... ";
$this->process();
echo "done!" . PHP_EOL;
parent::getWriteFile()->close();
echo "generating dataset release file... ";
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("iProClass")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/gzip")->setPublisher("http://pir.georgetown.edu")->setHomepage("http://pir.georgetown.edu/iproclass")->setRights("use-share-modify")->setLicense("http://pir.georgetown.edu/pirwww/about/linkpir.shtml")->setDataset("http://identifiers.org/iproclass/");
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/iproclass/iproclass.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description = $source_file->toRDF() . $output_file->toRDF();
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
}
function run()
{
$dataset_description = '';
$ldir = parent::GetParameterValue('indir');
$odir = parent::GetParameterValue('outdir');
//download
if ($this->GetParameterValue('download') == true) {
$list = $this->getFtpFileList('ftp.ncbi.nih.gov');
$total = count($list);
$counter = 1;
foreach ($list as $f) {
echo "downloading file {$counter} out of {$total} :" . parent::getParameterValue('download_url') . $f . "... " . PHP_EOL;
file_put_contents($ldir . $f, file_get_contents(parent::GetParameterValue('download_url') . $f));
$counter++;
}
}
//if download
//iterate over the files
$paths = $this->getFilePaths($ldir, 'gz');
$lfile = null;
foreach ($paths as $aPath) {
$lfile = $aPath;
$ofile = $odir . basename($aPath, ".gz") . "." . parent::getParameterValue('output_format');
$gz = false;
if (strstr(parent::getParameterValue('output_format'), "gz")) {
$gz = true;
}
parent::setWriteFile($ofile, $gz);
parent::setReadFile($ldir . $lfile, true);
$source_file = (new DataResource($this))->setURI(parent::getParameterValue('download_url') . basename($aPath))->setTitle('NCBI UniSTS filename: ' . basename($aPath))->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($ldir . $lfile)))->setFormat('xml/unists-format')->setFormat('application/zip')->setPublisher('https://www.ncbi.nlm.nih.gov')->setHomepage('https://www.ncbi.nlm.nih.gov/unists')->setRights('use')->setRights('attribution')->setLicense('https://www.nlm.nih.gov/copyright.html')->setDataset(parent::getDatasetURI());
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/unists/unists.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("restricted-by-source-license")->setLicense("http://creativecommons/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
$dataset_description .= $output_file->toRDF() . $source_file->toRDF();
echo "processing {$aPath} ...";
$this->process();
echo "done!" . PHP_EOL;
$this->setWriteFile($odir . $this->getBio2RDFReleaseFile());
$this->getWriteFile()->write($dataset_description);
$this->getWriteFile()->close();
}
//foreach
}
function Run()
{
echo "processing miriam database";
// directory shortcuts
$ldir = $this->getParameterValue('indir');
$odir = $this->getParameterValue('outdir');
// download and set the read file
$file = 'miriam.xml';
$rfile = $this->getParameterValue("download_url");
$lfile = $ldir . $file;
if (!file_exists($lfile) || $this->getParameterValue("download") == "true") {
utils::downloadSingle($rfile, $lfile);
}
parent::setReadFile($lfile);
// set the write file
$outfile = "miriam." . parent::getParameterValue('output_format');
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
parent::setWriteFile(parent::getParameterValue("outdir") . $outfile, $gz);
$this->parse();
parent::WriteRDFBufferToWriteFile();
$this->getWriteFile()->Close();
return true;
}
function Run()
{
$dataset_description = '';
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$list_file = $ldir . "ftp_list.txt";
if (!file_exists($list_file) || $this->getParameterValue('download') == true) {
echo "Getting FTP file list ...";
$list = $this->getFtpFileList('ftp.ncbi.nlm.nih.gov', '/refseq/release/complete/', '/(complete\\.[0-9]+\\.protein\\.gpff\\.gz)/');
if (!isset($list) or count($list) == 0) {
trigger_error("Unable to get list of files from FTP site. Check internet connection", E_USER_ERROR);
exit(-1);
}
asort($list);
$buf = implode("\n", $list);
file_put_contents($list_file, $buf);
echo "Done." . PHP_EOL;
} else {
echo "Using existing ftp list" . PHP_EOL;
$list = explode("\n", file_get_contents($list_file));
}
$counter = 1;
$total = count($list);
foreach ($list as $f) {
$lfile = $ldir . $f;
echo "Processing " . $counter++ . "/{$total} {$f}. ";
if (!file_exists($lfile) || $this->getParameterValue('download') == true) {
$rfile = parent::getParameterValue('download_url') . $f;
echo "Downloading ...";
utils::DownloadSingle($rfile, $lfile);
echo "done.";
} else {
echo "Using existing file.";
}
echo PHP_EOL;
}
//if download
//iterate over the files
$files = $this->getFilePaths($ldir, 'gz');
asort($files);
foreach ($files as $f) {
$lfile = $ldir . $f;
$ofile = $odir . basename($f, ".gz") . "." . parent::getParameterValue('output_format');
$gz = strstr(parent::getParameterValue('output_format'), "gz") ? true : false;
parent::setWriteFile($ofile, $gz);
parent::setReadFile($lfile, true);
echo "processing {$f} ...";
$this->process();
parent::clear();
echo "done!" . PHP_EOL;
$this->getReadFile()->close();
$this->getWriteFile()->close();
$source_file = (new DataResource($this))->setURI(parent::getParameterValue('download_url') . $lfile)->setTitle("NCBI RefSeq - {$f}")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat('text/refseq-format')->setFormat('application/zip')->setPublisher('http://www.ncbi.nlm.nih.gov')->setHomepage('http://www.ncbi.nlm.nih.gov/refseq')->setRights('use')->setRights('attribution')->setLicense('http://www.nlm.nih.gov/copyright.html')->setDataset(parent::getDatasetURI());
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} - {$f}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/refseq/refseq.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("restricted-by-source-license")->setLicense("http://creativecommons/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
$dataset_description .= $output_file->toRDF() . $source_file->toRDF();
}
//for
parent::writeToReleaseFile($dataset_description);
parent::getWriteFile()->close();
}
function process()
{
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$rdir = parent::getParameterValue('download_url');
//which files are to be converted?
$files = trim($this->GetParameterValue('files'));
if ($files == 'all') {
$files = $this->getPackageMap();
} else {
$sel_arr = explode(",", $files);
$pm = $this->getPackageMap();
$files = array();
foreach ($sel_arr as $a) {
if (array_key_exists($a, $pm)) {
$files[$a] = $pm[$a];
}
}
}
if ($this->getParameterValue('limit_organisms') == true) {
$this->taxids = array_flip(explode(",", $this->getParameterValue('organisms')));
}
//set dataset graph to be dataset URI
$graph_uri = parent::getGraphURI();
if (parent::getParameterValue('dataset_graph') == true) {
parent::setGraphURI(parent::getDatasetURI());
}
$dataset_description = '';
//now iterate over the files array
foreach ($files as $module => $rfilename) {
$file = $module . ".gz";
$lfile = $ldir . $file;
$rfile = $rdir . $rfilename;
// download
if (!file_exists($lfile) || parent::getParameterValue('download') == true) {
trigger_error("{$lfile} not found. Will attempt to download.", E_USER_NOTICE);
$myfile = $lfile;
if ($module == "gene2sts" || $module == "gene2unigene") {
$myfile = "compress.zlib://" . $lfile;
}
echo "downloading {$module} ...";
utils::DownloadSingle($rfile, $myfile);
echo "done" . PHP_EOL;
}
}
foreach ($files as $module => $rfilename) {
$file = $module . ".gz";
$lfile = $ldir . $file;
$rfile = $rdir . $rfilename;
$ofile = $module . "." . parent::getParameterValue('output_format');
$gz = false;
if (strstr(parent::getParameterValue('output_format'), "gz")) {
$gz = true;
}
echo "Processing {$module} ... ";
parent::setReadFile($lfile, true);
parent::setWriteFile($odir . $ofile, $gz);
$fnx = $module;
if ($module == 'gene2refseq') {
$fnx = 'gene2accession';
}
$this->{$fnx}();
parent::clear();
echo 'done!' . PHP_EOL;
parent::getReadFile()->close();
parent::getWriteFile()->close();
// generate the dataset release file
// dataset description
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("NCBI Gene ({$module})")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/gzip")->setPublisher("http://www.ncbi.nlm.nih.gov")->setHomepage("http://www.ncbi.nlm.nih.gov/gene")->setRights("use-share-modify")->setLicense("http://www.ncbi.nlm.nih.gov/About/disclaimer.html")->setDataset("http://identifiers.org/ncbigene/");
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/ncbigene/ncbigene.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description .= $source_file->toRDF() . $output_file->toRDF();
}
//foreach
//set graph URI back to default value
parent::setGraphURI($graph_uri);
//write dataset description to file
echo "Generating dataset description... ";
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
}
function run()
{
$idir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$files = parent::getParameterValue('files');
$dataset_description = '';
if ($files == 'all') {
$files = explode('|', parent::getParameterList('files'));
array_shift($files);
} else {
$files = explode(',', parent::getParameterValue('files'));
}
foreach ($files as $file) {
$f = $file;
if ($file != "freq") {
$f = "all_" . $file;
}
$f = "meddra_" . $f . ".tsv.gz";
$lfile = $idir . $f;
$rfile = parent::getParameterValue('download_url') . $f;
if (!file_exists($lfile) || parent::getParameterValue('download') == 'true') {
echo "downloading {$file}... ";
$ret = file_get_contents($rfile);
if ($ret === FALSE) {
trigger_error("Unable to get {$rfile}", E_USER_WARNING);
continue;
}
$ret = file_put_contents($lfile, $ret);
if ($ret === FALSE) {
trigger_error("Unable to write {$lfile}", E_USER_ERROR);
exit;
}
echo "done!" . PHP_EOL;
}
echo "Processing {$f}... ";
parent::setReadFile($lfile, true);
$suffix = parent::getParameterValue('output_format');
$ofile = "sider-" . $file . '.' . $suffix;
$gz = false;
if (strstr(parent::getParameterValue('output_format'), "gz")) {
$gz = true;
}
parent::setWriteFile($odir . $ofile, $gz);
$this->{$file}();
parent::getWriteFile()->Close();
parent::getReadFile()->Close();
echo "done!" . PHP_EOL;
echo "Generating dataset description... ";
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("SIDER Side Effect resource ({$file}.tsv.gz")->setRetrievedDate(parent::getDate(filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/gzip")->setPublisher("http://sideeffects.embl.de/")->setHomepage("http://sideeffects.embl.de/")->setRights("use-share-modify")->setLicense("http://creativecommons.org/licenses/by-nc-sa/3.0/")->setDataset("http://identifiers.org/sider.effect/");
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = parent::getDate(filemtime($odir . $ofile));
$output_file = (new DataResource($this))->setURI("http://download.bio2df.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} - {$file}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/sider/sider.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description .= $source_file->toRDF() . $output_file->toRDF();
}
//foreach
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
}
function Run()
{
// directory shortcuts
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
// get the listings page
$url = trim(parent::getParameterValue('download_url'));
$listing_file = $ldir . "probeset_list.html";
if (!file_exists($listing_file) || parent::getParameterValue("download") == "true") {
echo "Downloading {$listing_file}" . PHP_EOL;
Utils::DownloadSingle($url, $listing_file);
}
$listings = file_get_contents($listing_file);
// make a list of the csv.zip files
preg_match_all("/\"([^\"]+)\\.csv\\.zip\"/", $listings, $m);
if (count($m[1]) == 0) {
trigger_error("could not find any .csv.zip files in {$url}");
exit;
}
if (parent::getParameterValue("files") == 'all') {
$myfiles = $m[1];
} else {
$a = explode(",", parent::getParameterValue("files"));
foreach ($a as $f) {
$found = false;
foreach ($m[1] as $n) {
if (strstr($n, $f)) {
$found = true;
$myfiles[] = $n;
break;
}
}
if ($found === false) {
echo "cannot find {$f} in list" . PHP_EOL;
}
}
}
if (!isset($myfiles)) {
exit;
}
// nothing to do
$dataset_description = '';
// set the write file
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
$outfile = 'affymetrix.' . parent::getParameterValue('output_format');
$this->setWriteFile($odir . $outfile, $gz);
// iterate over the files
foreach ($myfiles as $rfile) {
$base_file = substr($rfile, strrpos($rfile, "/") + 1);
$base_url = substr($rfile, 0, strrpos($rfile, "/"));
// get and set the dataset version
if (parent::getDatasetVersion() == null) {
preg_match("/\\.na([0-9]{2})\\.annot/", $base_file, $m);
if (isset($m[1])) {
$this->setDatasetVersion($m[1]);
}
}
if (parent::getDatasetVersion() != parent::getParameterValue('version')) {
$base_file = str_replace("na" . parent::getDatasetVersion(), "na" . parent::getParameterValue('version'), $base_file);
}
$csv_file = $base_file . ".csv";
$zip_file = $csv_file . ".zip";
$lfile = $ldir . $zip_file;
if (!file_exists($lfile)) {
echo "skipping: {$lfile} does not exist" . PHP_EOL;
continue;
}
echo "processing {$lfile}" . PHP_EOL;
// open the zip file
$zin = new ZipArchive();
if ($zin->open($lfile) === FALSE) {
trigger_error("Unable to open {$lfile}");
exit;
}
if (($fp = $zin->getStream($csv_file)) === FALSE) {
trigger_error("Unable to get {$csv_file} in ziparchive {$lfile}");
return FALSE;
}
parent::setReadFile($lfile);
parent::getReadFile()->setFilePointer($fp);
$this->parse($base_file);
parent::getReadFile()->close();
parent::clear();
// dataset description
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("Affymetrix Probeset: {$base_file}")->setRetrievedDate(parent::getDate(filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/zip")->setPublisher("http://affymetrix.com")->setHomepage("http://www.affymetrix.com/support/technical/annotationfilesmain.affx")->setRights("use")->setRights("no-commercial")->setRights("registration-required")->setLicense("http://www.affymetrix.com/about_affymetrix/legal/index.affx")->setDataset("http://identifiers.org/affy.probeset/");
$dataset_description .= $source_file->toRDF();
}
$this->getWriteFile()->close();
// write the dataset description
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = parent::getDate(filemtime($odir . $outfile));
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$outfile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/affymetrix/affymetrix.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description .= $output_file->toRDF();
// write the dataset description
$this->setWriteFile($odir . $this->getBio2RDFReleaseFile());
$this->getWriteFile()->write($dataset_description);
$this->getWriteFile()->close();
return true;
}
function Run()
{
$sp = trim(parent::getParameterValue('files'));
if ($sp == 'all') {
$files = $this->getPackageMap();
} else {
$s_a = explode(",", $sp);
$pm = $this->getPackageMap();
$files = array();
foreach ($s_a as $a) {
if (array_key_exists($a, $pm)) {
$files[$a] = $pm[$a];
}
}
}
//else
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$dd = '';
//now iterate over the files array
$year = parent::getParameterValue('year');
foreach ($files as $k => $fpattern) {
$file = str_replace("YEAR", $year, $fpattern);
$lfile = $ldir . $file;
$rfile = parent::getParameterValue("download_url") . $file;
// download if necessary
if (!file_exists($lfile) || parent::getParameterValue('download') == "true") {
echo "Downloading {$file} ... ";
$ret = utils::downloadSingle($rfile, $lfile);
if ($ret === FALSE) {
trigger_error("Unable to get {$file}", E_USER_ERROR);
continue;
}
echo "done!" . PHP_EOL;
}
//set the outfile
$ofile = "mesh_" . $k . "." . parent::getParameterValue('output_format');
$gz = strstr(parent::getParameterValue('output_format'), "gz") ? true : false;
echo "processing {$k} ...";
parent::setReadFile($lfile, FALSE);
parent::setWriteFile($odir . $ofile, $gz);
$fnx = $k;
$this->{$fnx}();
parent::writeRDFBufferToWriteFile();
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("MeSH")->setRetrievedDate(parent::getDate(filemtime($lfile)))->setFormat("text/x-mesh-record")->setPublisher("http://www.nlm.nih.gov")->setHomepage("http://www.nlm.nih.gov/mesh/")->setRights("use")->setLicense("http://www.nlm.nih.gov/databases/download.html")->setDataset("http://identifiers.org/mesh/");
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = parent::getDate(filemtime($odir . $ofile));
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/mesh/mesh.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dd .= $source_file->toRDF() . $output_file->toRDF();
}
//foreach
parent::setWriteFile($odir . $this->getBio2RDFReleaseFile($this->getNamespace()));
parent::getWriteFile()->write($dd);
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
}
function run()
{
if (parent::getParameterValue('files') == 'all') {
$files = explode("|", $this->GetParameterList('files'));
array_shift($files);
} else {
$files = explode(",", parent::getParameterValue('files'));
}
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$rdir = parent::getParameterValue('download_url');
$dataset_description = '';
foreach ($files as $file) {
$download = parent::getParameterValue('download');
$lfile = $ldir . "goa_" . $file . ".gz";
if (!file_exists($lfile) && $download == false) {
trigger_error($lfile . " not found. Will attempt to download.", E_USER_NOTICE);
$download = true;
}
//download file
$rfile = $rdir . strtoupper($file) . "/gene_association.goa_" . $file . ".gz";
if ($download == true) {
echo "downloading {$file} ... ";
//file_put_contents($lfile,file_get_contents($rfile));
utils::DownloadSingle($rfile, $lfile);
}
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
$ofile = "goa_" . $file . "." . parent::getParameterValue('output_format');
parent::setReadFile($lfile, TRUE);
parent::setWriteFile($odir . $ofile, $gz);
echo "processing {$file} ... ";
$this->process($file);
echo "done!";
parent::clear();
//close write file
parent::getWriteFile()->close();
echo PHP_EOL;
// dataset description
$graph_uri = parent::getGraphURI();
if (parent::getParameterValue('dataset_graph') == true) {
parent::setGraphURI(parent::getDatasetURI());
}
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("Gene Ontology Annotation file {$file} ({$rfile}")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/gzip")->setPublisher("http://www.ebi.ac.uk/")->setHomepage("http://www.ebi.ac.uk/GOA/")->setRights("use")->setLicense("http://www.ebi.ac.uk/GOA/goaHelp.html")->setDataset("http://identifiers.org/goa/");
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/irefindex/irefindex.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description .= $source_file->toRDF() . $output_file->toRDF();
parent::setGraphURI($graph_uri);
}
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
}
public function run()
{
if (parent::getParameterValue('files') == 'all') {
$files = explode("|", parent::getParameterList('files'));
array_shift($files);
} else {
$files = explode(",", parent::getParameterValue('files'));
}
$release = parent::getParameterValue('release');
$releaseb = "WS249";
$remote_files = array("geneIDs" => "species/c_elegans/annotation/geneIDs/c_elegans.PRJNA13758." . $release . ".geneIDs.txt.gz", "functional_descriptions" => "species/c_elegans/annotation/functional_descriptions/c_elegans.PRJNA13758." . $release . ".functional_descriptions.txt.gz", "gene_interactions" => "species/c_elegans/annotation/gene_interactions/c_elegans.PRJNA13758." . $release . ".gene_interactions.txt.gz", "gene_associations" => "releases/current-production-release/ONTOLOGY/gene_association." . $releaseb . ".wb", "phenotype_associations" => "releases/current-production-release/ONTOLOGY/phenotype_association." . $releaseb . ".wb");
$local_files = array("geneIDs" => "wormbase." . parent::getParameterValue('release') . ".genes.txt.gz", "functional_descriptions" => "wormbase." . parent::getParameterValue('release') . ".functional_descriptions.txt.gz", "gene_interactions" => "wormbase." . parent::getParameterValue('release') . ".gene_interactions.txt.gz", "gene_associations" => "wormbase." . parent::getParameterValue('release') . ".gene_association.wb", "phenotype_associations" => "wormbase." . parent::getParameterValue('release') . ".phenotype_associations.wb");
$idir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$rdir = parent::getParameterValue('download_url');
$dataset_description = '';
$graph_uri = parent::getGraphURI();
if (parent::getParameterValue('dataset_graph') == true) {
parent::setGraphURI(parent::getDatasetURI());
}
foreach ($files as $file) {
$lfile = $idir . $local_files[$file];
$rfile = $rdir . $remote_files[$file];
if (!file_exists($lfile) or parent::getParameterValue('download') == true) {
trigger_error($lfile . " not found. Will attempt to download." . PHP_EOL, E_USER_WARNING);
echo "Downloading {$rfile}... ";
Utils::DownloadSingle($rfile, $lfile);
echo "done!" . PHP_EOL;
}
if (strstr($lfile, "gz")) {
parent::setReadFile($lfile, TRUE);
} else {
parent::setReadFile($lfile, FALSE);
}
$suffix = parent::getParameterValue('output_format');
$ofile = "wormbase." . $file . "." . $suffix;
$gz = strstr(parent::getParameterValue('output_format'), "gz") ? true : false;
parent::setWriteFile($odir . $ofile, $gz);
echo "Processing {$file}... ";
$fnx = $file;
$this->{$fnx}();
echo "done!" . PHP_EOL;
parent::getWriteFile()->close();
// generate the dataset release file
echo "Generating dataset description for {$ofile}... ";
// dataset description
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("WormBase Release " . parent::getParameterValue('release') . " subset ({$file})")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/gzip")->setPublisher("http://wormbase.org/")->setHomepage("http://wormbase.org/")->setRights("use")->setRights("restricted-by-source-license")->setLicense("http://www.wormbase.org/about/policies")->setDataset("http://identifiers.org/wormbase/");
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} - {$file}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/wormbase/wormbase.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description .= $source_file->toRDF() . $output_file->toRDF();
echo "done!" . PHP_EOL;
}
parent::setGraphURI($graph_uri);
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
}
function run()
{
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$dataset_description = '';
$files = parent::getParameterValue('files');
if ($files == 'all') {
$files = explode('|', parent::getParameterList('files'));
array_shift($files);
} else {
$files = explode(',', parent::getParameterValue('files'));
}
if (parent::getParameterValue('id_list') != '') {
$this->idlist = explode(",", parent::getParameterValue("id_list"));
}
// handle genes separately
if (in_array("genes", $files)) {
$orgs = array("hsa");
//,"mmu","eco","dre","dme","ath","sce","ddi");
echo "processing genes" . PHP_EOL;
$ofile = "kegg-genes." . parent::getParameterValue('output_format');
$gz = strstr(parent::getParameterValue('output_format'), "gz") ? true : false;
parent::setWriteFile($odir . $ofile, $gz);
// get the list of genomes
$lfile = $ldir . "genome.txt";
$rfile = parent::getParameterValue("download_url") . "list/genome";
if (!file_exists($lfile) || parent::getParameterValue('download') == 'true') {
$ret = utils::downloadSingle($rfile, $lfile);
}
$fp = fopen($lfile, "r");
while ($l = fgets($fp)) {
$a = explode("\t", $l);
$b = explode(", ", $a[1]);
$org = $b[0];
if (!in_array($org, $orgs)) {
continue;
}
// get the list of genes for this organims
echo "processing {$org}" . PHP_EOL;
$this->org = $org;
// local variable
$lfile = $ldir . $org . ".txt";
$rfile = parent::getParameterValue("download_url") . "list/{$org}";
if (!file_exists($lfile) || parent::getParameterValue('download') == 'true') {
$ret = utils::downloadSingle($rfile, $lfile);
}
parent::setReadFile($lfile, false);
$this->process("gene");
parent::getReadFile()->close();
parent::clear();
$this->org = null;
// add dataset description
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("KEGG: Gene")->setRetrievedDate(parent::getDate(filemtime($lfile)))->setFormat("text/plain")->setPublisher("http://www.kegg.jp/")->setHomepage("http://www.kegg.jp/")->setRights("use")->setRights("no-commercial")->setLicense("http://www.kegg.jp/kegg/legal.html")->setDataset("http://identifiers.org/kegg/");
$dataset_description .= $source_file->toRDF();
}
fclose($fp);
parent::getWriteFile()->close();
echo "done" . PHP_EOL;
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = parent::getDate(filemtime($odir . $ofile));
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} - Gene ")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/kegg/kegg.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description .= $output_file->toRDF();
}
// all other files
foreach ($files as $db) {
if ($db == "genes") {
continue;
}
echo "processing {$db}" . PHP_EOL;
$lfile = $ldir . $db . ".txt";
$rfile = parent::getParameterValue("download_url") . "list/{$db}";
if (!file_exists($lfile) || parent::getParameterValue('download') == 'true') {
echo "Downloading {$rfile} ";
$ret = utils::downloadSingle($rfile, $lfile);
if ($ret === false) {
echo "unable to download {$file} ... skipping" . PHP_EOL;
continue;
}
echo "done." . PHP_EOL;
}
// now for each list, get the individual entries
$ofile = "kegg-{$db}." . parent::getParameterValue('output_format');
$gz = strstr(parent::getParameterValue('output_format'), "gz") ? true : false;
parent::setReadFile($lfile, false);
parent::setWriteFile($odir . $ofile, $gz);
$this->process($db);
parent::getWriteFile()->close();
parent::getReadFile()->close();
parent::clear();
echo "done!" . PHP_EOL;
// add dataset description
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("KEGG: {$db}")->setRetrievedDate(parent::getDate(filemtime($lfile)))->setFormat("text/plain")->setPublisher("http://www.kegg.jp/")->setHomepage("http://www.kegg.jp/")->setRights("use")->setRights("no-commercial")->setLicense("http://www.kegg.jp/kegg/legal.html")->setDataset("http://identifiers.org/kegg/");
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = parent::getDate(filemtime($odir . $ofile));
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} - {$db} ")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/kegg/kegg.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description .= $source_file->toRDF() . $output_file->toRDF();
}
// write the dataset description
$this->setWriteFile($odir . $this->getBio2RDFReleaseFile());
$this->getWriteFile()->write($dataset_description);
$this->getWriteFile()->close();
}
function Run()
{
// get the file list
if (parent::getParameterValue('files') == 'all') {
$files = array('all');
} else {
$files = explode(",", parent::getParameterValue('files'));
}
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$rdir = parent::getParameterValue('download_url');
$dataset_description = '';
foreach ($files as $file) {
$download = parent::getParameterValue('download');
$version = parent::getParameterValue("version");
$zip_file = ucfirst($file) . ".mitab." . $version . ".txt.zip";
$lfile = $ldir . $zip_file;
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
$ofile = "irefindex-" . $file . "." . parent::getParameterValue('output_format');
if (!file_exists($lfile)) {
trigger_error($lfile . " not found. Will attempt to download.", E_USER_NOTICE);
$download = true;
}
$rfile = $rdir . $zip_file;
if ($download == true) {
echo "downloading {$rfile}" . PHP_EOL;
if (FALSE === Utils::DownloadSingle($rfile, $lfile)) {
trigger_error("Error in Download");
return FALSE;
}
}
$zin = new ZipArchive();
if ($zin->open($lfile) === FALSE) {
trigger_error("Unable to open {$lfile}");
exit;
}
if ($zin->numFiles != 1) {
trigger_error("Found more than one file ... using first file");
}
$f = $zin->statIndex(0);
$base_file = $f['name'];
if (($fp = $zin->getStream($base_file)) === FALSE) {
trigger_error("Unable to get {$base_file} in ziparchive {$lfile}");
return FALSE;
}
parent::setReadFile($lfile);
parent::getReadFile()->setFilePointer($fp);
echo "Processing " . $file . " ...";
parent::setWriteFile($odir . $ofile, true);
if ($this->Parse() === FALSE) {
trigger_error("Parsing Error");
exit;
}
parent::writeRDFBufferToWriteFile();
parent::getWriteFile()->close();
$zin->close();
echo "Done!" . PHP_EOL;
$graph_uri = parent::getGraphURI();
if (parent::getParameterValue('dataset_graph') == true) {
parent::setGraphURI(parent::getDatasetURI());
}
// dataset description
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("iRefIndex ({$zip_file}")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/zip")->setPublisher("http://irefindex.uio.no")->setHomepage("http://irefindex.uio.no")->setRights("use")->setRights("by-attribution")->setRights("no-commercial")->setLicense("http://irefindex.uio.no/wiki/README_MITAB2.6_for_iRefIndex#License")->setDataset("http://identifiers.org/irefindex/");
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} - {$file}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/irefindex/irefindex.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description .= $source_file->toRDF() . $output_file->toRDF();
parent::setGraphURI($graph_uri);
}
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
return TRUE;
}
public function Run()
{
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
// make sure we have the zip archive
//which files are to be converted?
$selectedPackage = trim(parent::getParameterValue('files'));
if ($selectedPackage == 'all') {
$files = $this->getPackageMap();
} else {
$sel_arr = explode(",", $selectedPackage);
$pm = $this->getPackageMap();
$files = array();
foreach ($sel_arr as $a) {
if (array_key_exists($a, $pm)) {
$files[$a] = $pm[$a];
}
}
}
$dataset_description = '';
foreach ($files as $key => $value) {
$lfile = $ldir . $value['filename'];
if (!file_exists($lfile) && parent::getParameterValue('download') == false) {
trigger_error($lfile . " not found. Will attempt to download.", E_USER_NOTICE);
$this->SetParameterValue('download', true);
}
//download all files [except mapping file]
if ($this->GetParameterValue('download') == true) {
$rfile = $value["file_url"];
echo "downloading " . var_dump($value["file_url"]) . " ... ";
utils::downloadSingle($rfile, $lfile);
}
if ($key == "taxdmp" || $key == "gi2taxid_protein" || $key == "gi2taxid_nucleotide") {
//get the name of the zip archive
$lfile = $value["filename"];
// make sure we have the zip archive
$zinfile = $ldir . $lfile;
$zin = new ZipArchive();
if ($zin->open($zinfile) === FALSE) {
trigger_error("Unable to open {$zinfile}");
exit;
}
//now iterate over the files in the ziparchive
$source_file = (new DataResource($this))->setURI($value['file_url'])->setTitle('NCBI Taxonomy - ' . $key)->setRetrievedDate(date("Y-m-d\\TH:i:sP", filemtime($ldir . $lfile)))->setFormat('text/tab-separated-value')->setFormat('application/zip')->setPublisher('http://www.ncbi.nlm.nih.gov')->setHomepage('http://www.ncbi.nlm.nih.gov/taxonomy')->setRights('use')->setRights('attribution')->setLicense('https://www.nlm.nih.gov/copyright.html')->setDataset(parent::getDatasetURI());
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TH:i:sP");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} - {$key}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/taxonomy/taxonomy.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("restricted-by-source-license")->setLicense("http://creativecommons/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
$dataset_description .= $output_file->toRDF() . $source_file->toRDF();
foreach ($value["contents"] as $k => $fn) {
if ($k == "names" || $k == "nodes" || $k == "citations" || $k == "gencode" || $k == "division" || $k == "gi_taxid_prot" || $k == "gi_taxid_nucl") {
//if($k !== 'citations') continue;
$fpin = $zin->getStream($fn);
if (!$fpin) {
trigger_error("Unable to get pointer to {$fn} in {$zinfile}");
exit("failed\n");
}
$gzoutfile = $odir . "taxonomy-{$k}" . "." . parent::getParameterValue('output_format');
//set the write file
$gz = strstr(parent::getParameterValue('output_format'), 'gz') ? true : false;
parent::setReadFile($ldir . $lfile);
parent::getReadFile()->SetFilePointer($fpin);
parent::setWriteFile($gzoutfile, $gz);
echo "processing {$fn}...\n";
$this->{$k}();
$this->GetWriteFile()->Close();
echo "done!" . PHP_EOL;
parent::clear();
}
//if $k
}
//foreach
}
//if key taxdmp
$this->setWriteFile($odir . $this->getBio2RDFReleaseFile());
$this->getWriteFile()->write($dataset_description);
$this->getWriteFile()->close();
}
}
function process()
{
if (parent::getParameterValue('files') == 'all') {
$files = explode("|", parent::getParameterList('files'));
array_shift($files);
} else {
$files = explode(",", parent::getParameterValue('files'));
}
$ldir = parent::getParameterValue('indir');
$rdir = parent::getParameterValue('download_url');
$odir = parent::getParameterValue('outdir');
$rfiles = array("dbxref" => "curation/chromosomal_feature/dbxref.tab", "features" => "curation/chromosomal_feature/SGD_features.tab", "domains" => "curation/calculated_protein_info/domains/domains.tab", "protein" => "curation/calculated_protein_info/protein_properties.tab", "goa" => "curation/literature/gene_association.sgd.gz", "goslim" => "curation/literature/go_slim_mapping.tab", "complex" => "curation/literature/go_protein_complex_slim.tab", "interaction" => "curation/literature/interaction_data.tab", "phenotype" => "curation/literature/phenotype_data.tab", "pathways" => "curation/literature/biochemical_pathways.tab", "mapping" => "mapping");
$graph_uri = parent::getGraphURI();
if (parent::getParameterValue('dataset_graph') == true) {
parent::setGraphURI(parent::getDatasetURI());
}
$gz = false;
if (strstr(parent::getParameterValue('output_format'), "gz")) {
$gz = true;
}
if (parent::getParameterValue('one_file') == true) {
$ofile = "sgd." . parent::getParameterValue('output_format');
parent::setWriteFile($odir . $ofile, $gz);
}
$dataset_description = '';
foreach ($files as $file) {
$ext = substr(strrchr($rfiles[$file], '.'), 1);
if ($ext == "tab") {
$lfile = "sgd_" . $file . ".tab";
} elseif ($ext = "gz") {
$lfile = "sgd_" . $file . ".tab.gz";
}
$rfile = $rdir . $rfiles[$file];
if (!file_exists($ldir . $lfile) && parent::getParameterValue('download') == false && $file != 'mapping') {
trigger_error($ldir . $lfile . " not found. Will attempt to download.", E_USER_NOTICE);
Utils::DownloadSingle($rfile, $ldir . $lfile);
}
if (parent::getParameterValue('one_file') == false) {
$ofile = "sgd_" . $file . '.' . parent::getParameterValue('output_format');
parent::setWriteFile($odir . $ofile, $gz);
}
//parse file
parent::setReadFile($ldir . $lfile, $gz);
$fnx = $file;
echo "Processing {$file}... ";
$this->{$fnx}();
echo PHP_EOL . "done!";
//write RDF to file
parent::writeRDFBufferToWriteFile();
//close write file
if (parent::getParameterValue('one_file') == false) {
parent::getWriteFile()->close();
}
echo PHP_EOL;
// generate the dataset release file
// dataset description
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("Saccharomyces Genome Database ({$file})")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($ldir . $lfile)))->setFormat("text/tab-separated-value")->setFormat("application/gzip")->setPublisher("http://www.yeastgenome.org/")->setHomepage("http://www.yeastgenome.org/")->setRights("use")->setLicense("http://www.stanford.edu/site/terms.html")->setDataset("http://identifiers.org/sgd/");
$dataset_description .= $source_file->toRDF();
if (parent::getParameterValue('one_file') == false) {
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} - {$file}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/sgd/sgd.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description .= $output_file->toRDF();
}
}
//foreach
//set graph URI back to default
parent::setGraphURI($graph_uri);
if (parent::getParameterValue('one_file') == true) {
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} - {$file}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/sgd/sgd.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description .= $source_file->toRDF() . $output_file->toRDF();
}
//write dataset description to file
echo "Generating dataset description... " . PHP_EOL;
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
}
function process()
{
// get the file list
if (parent::getParameterValue('files') == 'all') {
$files = explode("|", parent::getParameterList('files'));
array_shift($files);
} else {
$files = explode(",", parent::getParameterValue('files'));
}
$dataset_description = '';
//set directory values
$ldir = parent::getParameterValue('indir');
$rdir = parent::getParameterValue('download_url');
$odir = parent::getParameterValue('outdir');
$graph_uri = parent::getGraphURI();
if (parent::getParameterValue('dataset_graph') == true) {
parent::setGraphURI(parent::getDatasetURI());
}
$gz_suffix = ".gz";
foreach ($files as $file) {
if ($file == 'chem_gene_ixn_types') {
$suffix = '.tsv';
} else {
if ($file == 'exposure_ontology') {
$suffix = '.obo';
} else {
$suffix = ".tsv.gz";
}
}
$lfile = $ldir . $file . $gz_suffix;
$rfile = $rdir . 'CTD_' . $file . $suffix;
if (!file_exists($lfile)) {
trigger_error($lfile . " not found. Will attempt to download.", E_USER_NOTICE);
if ($suffix == ".tsv.gz") {
Utils::DownloadSingle($rfile, $lfile);
} else {
Utils::DownloadSingle($rfile, "compress.zlib://" . $lfile);
}
}
$out_suffix = parent::getParameterValue('output_format');
$ofile = "ctd_" . $file . "." . $out_suffix;
$gz = false;
if (strstr(parent::getParameterValue('output_format'), "gz")) {
$gz = true;
}
echo "Processing " . $file . " ...";
parent::setWriteFile($odir . $ofile, $gz);
//set read file
parent::setReadFile($lfile, TRUE);
$fnx = "CTD_" . $file;
$this->{$fnx}();
//close write file
parent::getWriteFile()->close();
parent::clear();
echo "done!" . PHP_EOL;
// generate the dataset release file
echo "Generating dataset description... ";
if ($file == "chemicals") {
$dataset = "http://identifiers.org/ctd.chemical/";
} else {
if ($file == "diseases") {
$dataset = "http://identifiers.org/ctd.disease/";
} else {
if ($file == "genes") {
$dataset = "http://identifiers.org/ctd.gene/";
} else {
$dataset = null;
}
}
}
// dataset description
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("Comparative Toxicogenomics Database ({$file}.{$gz_suffix}")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("text/tab-separated-value")->setFormat("application/gzip")->setPublisher("http://ctdbase.org/")->setHomepage("http://ctdbase.org/")->setRights("use")->setRights("by-attribution")->setRights("no-commercial")->setLicense("http://ctdbase.org/about/legal.jsp")->setDataset($dataset);
$prefix = parent::getPrefix();
$bVersion = parent::getParameterValue('bio2rdf_release');
$date = date("Y-m-d\\TG:i:s\\Z");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/ctd/ctd.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description .= $source_file->toRDF() . $output_file->toRDF();
}
parent::setGraphURI($graph_uri);
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
}
function Run()
{
$dataset_description = '';
$idir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
if (parent::getParameterValue('ncbo_api_key')) {
$apikey = "?apikey=" . parent::getParameterValue('ncbo_api_key');
} else {
if (file_exists(parent::getParameterValue('ncbo_api_key_file'))) {
$apikey = "?apikey=" . trim(file_get_contents(parent::getParameterValue('ncbo_api_key_file')));
} else {
echo "You must provide an NCBO API key either as a file or as a parameter" . PHP_EOL;
exit;
}
}
// get the list of ontologies from bioportal
$olist = $idir . "ontolist.json";
if (!file_exists($olist) || parent::getParameterValue('download') == 'true') {
echo "downloading ontology list...";
$r_olist = parent::getParameterValue('download_url') . 'ontologies' . $apikey;
file_put_contents($olist, file_get_contents($r_olist));
echo "done" . PHP_EOL;
}
// include
if (parent::getParameterValue('files') == 'all') {
$include_list = array('all');
} else {
$include_list = explode(",", parent::getParameterValue('files'));
}
// exclude
$exclude_list = array();
if (parent::getParameterValue('exclude') != '') {
$exclude_list = explode(",", parent::getParameterValue('exclude'));
}
$continue_from = parent::getParameterValue('continue_from');
$go = true;
if ($continue_from) {
$go = false;
}
// now go through the list of ontologies
$ontologies = json_decode(file_get_contents($olist), false);
$total = count($ontologies);
foreach ($ontologies as $i => $o) {
$label = (string) $o->name;
$abbv = (string) $o->acronym;
if ($continue_from and $continue_from == $abbv) {
$go = true;
}
if ($go == false) {
continue;
}
if (array_search($abbv, $exclude_list) !== FALSE) {
continue;
}
if ($include_list[0] != 'all') {
// ignore if we don't find it in the include list OR we do find it in the exclude list
if (array_search($abbv, $include_list) === FALSE) {
continue;
}
} else {
if (array_search($abbv, $exclude_list) !== FALSE) {
continue;
}
}
// get info on the latest submission
$uri = $o->links->latest_submission;
$ls = json_decode(file_get_contents($uri . $apikey), true);
if (!isset($ls['hasOntologyLanguage'])) {
echo 'insufficient metadata' . PHP_EOL;
continue;
}
$format = strtolower($ls['hasOntologyLanguage']);
if ($format != 'owl' and $format != 'obo') {
continue;
}
echo "Processing ({$i}/{$total}) {$abbv} ... ";
$version = $ls['version'];
if (isset($ls['homepage'])) {
$homepage = $ls['homepage'];
}
if (isset($ls['description'])) {
$description = $ls['description'];
}
$rfile = $ls['ontology']['links']['download'];
$lfile = $abbv . "." . $format . ".gz";
if (!file_exists($idir . $lfile) or parent::getParameterValue('download') == 'true') {
echo "downloading ... ";
$ch = curl_init();
// create cURL handle (ch)
if (!$ch) {
die("Couldn't initialize a cURL handle");
}
$ret = curl_setopt($ch, CURLOPT_URL, $rfile . $apikey);
$ret = curl_setopt($ch, CURLOPT_HEADER, 1);
$ret = curl_setopt($ch, CURLOPT_FOLLOWLOCATION, 1);
$ret = curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
$ret = curl_setopt($ch, CURLOPT_TIMEOUT, 300);
$ret = curl_exec($ch);
if (!$ret) {
echo "no content";
continue;
}
$header_size = curl_getinfo($ch, CURLINFO_HEADER_SIZE);
$header = substr($ret, 0, $header_size);
preg_match("/filename=\"([^\"]+)\"/", $header, $m);
if (isset($m[1])) {
$filename = $m[1];
if (strstr($filename, ".zip")) {
continue;
}
} else {
echo "error: no filename" . PHP_EOL;
continue;
}
$body = substr($ret, $header_size);
// now get the file suffix
$path = pathinfo($filename);
if (isset($path['extension'])) {
$ext = $path['extension'];
} else {
echo "error: no extension" . PHP_EOL;
continue;
}
$lz = "compress.zlib://" . $idir . $lfile;
file_put_contents($lz, $body);
echo "done" . PHP_EOL;
}
if (file_exists($idir . $lfile)) {
parent::setReadFile($idir . $lfile, true);
$gz = strstr(parent::getParameterValue('output_format'), ".gz") === FALSE ? false : true;
$ofile = strtolower($abbv) . "." . parent::getParameterValue('output_format');
parent::setWriteFile($odir . $ofile, $gz);
// process
echo "converting ... ";
set_time_limit(0);
// let's double check the format
$fp = gzopen($idir . $lfile, "r");
$l = gzgets($fp);
if (strstr($l, "xml")) {
$format = "owl";
}
gzclose($fp);
if ($format == 'obo') {
$this->OBO2RDF($abbv);
} else {
if ($format == 'owl') {
$this->OWL2RDF($abbv);
if (isset($this->unmapped_uri)) {
print_r($this->unmapped_uri);
}
unset($this->unmapped_uri);
} else {
echo "no processor for {$label} (format {$format})" . PHP_EOL;
}
}
if (!file_exists($odir . $ofile)) {
echo "no output" . PHP_EOL;
continue;
}
parent::getWriteFile()->close();
parent::clear();
$bVersion = parent::getParameterValue('bio2rdf_release');
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("{$label}")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($idir . $lfile)))->setFormat("obo")->setPublisher("http://www.bioontology.org")->setHomepage("http://bioportal.bioontology.org/")->setRights("use-share-modify")->setLicense("http://www.bioontology.org/terms")->setDataset("http://identifiers.org/{$abbv}");
$output_file = (new DataResource($this))->setURI("http://download.bio2rdf.org/release/{$bVersion}/bioportal/{$ofile}")->setTitle("Bio2RDF v{$bVersion} RDF version of {$abbv}")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/bioportal/bioportal.php")->setCreateDate(date("Y-m-d\\TG:i:s\\Z", filemtime($odir . $ofile)))->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/bioportal/bioportal.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
if (!isset($dd)) {
$dd = fopen($odir . 'bio2rdf-bioportal.nq', "w");
}
fwrite($dd, $source_file->toRDF() . $output_file->toRDF());
fflush($dd);
echo "done!" . PHP_EOL;
}
}
if (isset($dd)) {
fclose($dd);
}
echo "done!" . PHP_EOL;
}
