function Run()
{
$idir = $this->GetParameterValue('indir');
$odir = $this->GetParameterValue('outdir');
$files = $this->GetParameterValue('files');
// set the work
if ($files != 'all') {
// check if comma-separated, or hyphen-range
$list = explode(",", $files);
if (count($list) == 1) {
// try hyphen separated
$range = explode("-", $files);
if (count($range) == 2) {
for ($i = $range[0]; $i <= $range[1]; $i++) {
$myfiles[] = $i;
}
} else {
// must a single entry
$myfiles[] = $files;
}
} else {
$myfiles = $list;
}
}
$rest_uri = 'http://sabiork.h-its.org/sabioRestWebServices/';
$getReactionIds_url = $rest_uri . "suggestions/SABIOReactionIDs";
$reaction_list_file = $idir . "reactions.xml";
if (!file_exists($reaction_list_file) || $this->GetParameterValue('download') == 'true') {
$xml = file_get_contents($getReactionIds_url);
if (FALSE === $reaction_ids) {
exit;
}
$f = new FileFactory($reaction_list_file);
$f->Write($xml);
$f->Close();
}
$xml = simplexml_load_file($reaction_list_file);
$total = count($xml->SABIOReactionID);
if (isset($myfiles)) {
$total = count($myfiles);
}
$i = 0;
foreach ($xml->SABIOReactionID as $rid) {
if (isset($myfiles)) {
if (!in_array($rid, $myfiles)) {
continue;
}
}
$i++;
echo "{$i} / {$total} : reaction {$rid}";
$reaction_file = $idir . "reaction_" . $rid . ".owl.gz";
if (!file_exists($reaction_file) || $this->GetParameterValue('download') == 'true') {
$url = $rest_uri . 'searchKineticLaws/biopax?q=SabioReactionID:' . $rid;
$data = file_get_contents($url);
if ($data === FALSE) {
continue;
}
$f = new FileFactory($reaction_file, true);
$f->Write($data);
$f->Close();
}
$buf = file_get_contents("compress.zlib://" . $reaction_file);
// send for parsing
$p = new BioPAX2Bio2RDF();
$p->SetBuffer($buf)->SetBioPAXVersion(3)->SetBaseNamespace("http://sabio.h-its.org/biopax#")->SetBio2RDFNamespace("http://bio2rdf.org/sabiork:")->SetDatasetURI($this->GetDatasetURI());
$rdf = $p->Parse();
$ofile = "sabiork_{$rid}.nt";
$gz = false;
if ($this->GetParameterValue("graph_uri")) {
$ofile = "sabiork_{$rid}.nq";
}
if ($this->GetParameterValue("gzip")) {
$gz = true;
$ofile .= ".gz";
}
$this->SetWriteFile($odir . $ofile, $gz);
$this->GetWriteFile()->Write($rdf);
$this->GetWriteFile()->Close();
$bio2rdf_download_files[] = $this->GetBio2RDFDownloadURL($this->GetNamespace()) . $ofile;
echo PHP_EOL;
}
// generate the release file
$desc = $this->GetBio2RDFDatasetDescription($this->GetNamespace(), "https://github.com/bio2rdf/bio2rdf-scripts/blob/master/sabiork/sabiork.php", $bio2rdf_download_files, "sabiork.h-its.org", array("use-share-modify", "no-commercial"), null, $this->GetParameterValue('download_url'), $this->version);
$this->SetWriteFile($odir . $this->GetBio2RDFReleaseFile($this->GetNamespace()));
$this->GetWriteFile()->Write($desc);
$this->GetWriteFile()->Close();
}
function Run()
{
$idir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$files = parent::getParameterValue('files');
// set the work
if ($files != 'all') {
// check if comma-separated, or hyphen-range
$list = explode(",", $files);
if (count($list) == 1) {
// try hyphen separated
$range = explode("-", $files);
if (count($range) == 2) {
for ($i = $range[0]; $i <= $range[1]; $i++) {
$myfiles[] = $i;
}
} else {
// must a single entry
$myfiles[] = $files;
}
} else {
$myfiles = $list;
}
}
$rest_uri = 'http://sabiork.h-its.org/sabioRestWebServices/';
$getReactionIds_url = $rest_uri . "suggestions/SABIOReactionIDs";
$reaction_list_file = $idir . "reactions.xml";
if (!file_exists($reaction_list_file) || parent::getParameterValue('download') == 'true') {
$xml = file_get_contents($getReactionIds_url);
if (FALSE === $reaction_list_file) {
exit;
}
$f = new FileFactory($reaction_list_file);
$f->Write($xml);
$f->Close();
}
$xml = simplexml_load_file($reaction_list_file);
$total = count($xml->SABIOReactionID);
if (isset($myfiles)) {
$total = count($myfiles);
}
$i = 0;
parent::setCheckpoint('dataset');
$graph_uri = parent::getGraphURI();
if (parent::getParameterValue('dataset_graph') == true) {
parent::setGraphURI(parent::getDatasetURI());
}
$suffix = parent::getParameterValue('output_format');
$ofile = "sabiork." . $suffix;
$gz = strstr(parent::getParameterValue('output_format'), "gz") ? true : false;
parent::setWriteFile($odir . $ofile, $gz);
foreach ($xml->SABIOReactionID as $rid) {
parent::setCheckpoint('file');
if (isset($myfiles)) {
if (!in_array($rid, $myfiles)) {
continue;
}
}
$i++;
echo "{$i} / {$total} : reaction {$rid}" . PHP_EOL;
$reaction_file = $idir . "reaction_" . $rid . ".owl.gz";
if (!file_exists($reaction_file) || $this->GetParameterValue('download') == 'true') {
$url = $rest_uri . 'searchKineticLaws/biopax?q=SabioReactionID:' . $rid;
$data = file_get_contents($url);
if ($data === FALSE) {
continue;
}
$f = new FileFactory($reaction_file, true);
$f->Write($data);
$f->Close();
}
$buf = file_get_contents("compress.zlib://" . $reaction_file);
// send for parsing
$p = new BioPAX2Bio2RDF($this);
$p->SetBuffer($buf)->SetBioPAXVersion(3)->SetBaseNamespace("http://sabio.h-its.org/biopax#")->SetBio2RDFNamespace("http://bio2rdf.org/sabiork:")->SetDatasetURI($this->GetDatasetURI());
$rdf = $p->Parse();
parent::getWriteFile()->Write($rdf);
}
parent::getWriteFile()->Close();
//generate dataset description
echo "Generating dataset description... ";
$source_file = (new DataResource($this))->setURI("http://sabiork.h-its.org/sabioRestWebServices/searchKineticLaws/biopax")->setTitle("SABIO-RK Biochemical Reaction Kinetics Database")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($odir . $ofile)))->setFormat("text/xml")->setPublisher("http://sabio.villa-bosch.de/")->setHomepage("http://sabio.villa-bosch.de/")->setRights("use-share-modify")->setRights("no-commercial")->setLicense("http://sabio.villa-bosch.de/layouts/content/termscondition.gsp")->setDataset("http://identifiers.org/sabiork.reaction/");
$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/sabiork/sabiork.php")->setCreateDate($date)->setHomepage("http://download.bio2rdf.org/release/{$bVersion}/{$prefix}/{$prefix}.html")->setPublisher("http://bio2rdf.org")->setRights("use-share-modify")->setRights("by-attribution")->setRights("restricted-by-source-license")->setLicense("http://creativecommons.org/licenses/by/3.0/")->setDataset(parent::getDatasetURI());
if ($gz) {
$output_file->setFormat("application/gzip");
}
if (strstr(parent::getParameterValue('output_format'), "nt")) {
$output_file->setFormat("application/n-triples");
} else {
$output_file->setFormat("application/n-quads");
}
$dataset_description = $source_file->toRDF() . $output_file->toRDF();
//write dataset description to file
parent::setGraphURI($graph_uri);
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
}
function Run()
{
// directory shortcuts
$ldir = $this->GetParameterValue('indir');
$odir = $this->GetParameterValue('outdir');
// get the work specified
$list = trim($this->GetParameterValue('files'));
if ($list == 'all') {
// call the getAllModelsId webservice
$file = $ldir . "all_models.json";
if (!file_exists($file)) {
try {
$x = @new SoapClient("http://www.ebi.ac.uk/biomodels-main/services/BioModelsWebServices?wsdl");
} catch (Exception $e) {
echo $e->getMessage();
}
$entries = $x->getAllModelsId();
file_put_contents($file, json_encode($entries));
} else {
$entries = json_decode(file_get_contents($file));
}
} elseif ($list == 'curated') {
// call the getAllCuratedModelsId webservice
$file = $ldir . "curated_models.json";
if (!file_exists($file)) {
try {
$x = @new SoapClient("http://www.ebi.ac.uk/biomodels-main/services/BioModelsWebServices?wsdl");
} catch (Exception $e) {
echo $e->getMessage();
}
$entries = $x->getAllCuratedModelsId();
file_put_contents($file, json_encode($entries));
} else {
$entries = json_decode(file_get_contents($file));
}
} else {
// check if a hyphenated list was provided
if (($pos = strpos($list, "-")) !== FALSE) {
$start_range = substr($list, 0, $pos);
$end_range = substr($list, $pos + 1);
for ($i = $start_range; $i <= $end_range; $i++) {
$entries[] = "BIOMD" . str_pad($i, 10, "0", STR_PAD_LEFT);
}
} else {
// for comma separated list
$b = explode(",", $this->GetParameterValue('files'));
foreach ($b as $e) {
$entries[] = "BIOMD" . str_pad($e, 10, "0", STR_PAD_LEFT);
}
}
}
// set the write file
$outfile = 'biomodels.nt';
$gz = false;
if ($this->GetParameterValue('graph_uri')) {
$outfile = 'biomodels.nq';
}
if ($this->GetParameterValue('gzip')) {
$outfile .= '.gz';
$gz = true;
}
$bio2rdf_download_files[] = $this->GetBio2RDFDownloadURL($this->GetNamespace()) . $outfile;
$this->SetWriteFile($odir . $outfile, $gz);
// iterate over the entries
$i = 0;
$total = count($entries);
foreach ($entries as $id) {
echo "processing " . ++$i . " of {$total} - biomodel# " . $id;
$download_file = $ldir . $id . ".owl.gz";
// download if the file doesn't exist or we are told to
if (!file_exists($download_file) || $this->GetParameterValue('download') == 'true') {
// download
echo " - downloading";
$url = $this->GetParameterValue('download_url') . "{$id}/{$id}-biopax3.owl";
$buf = file_get_contents($url);
if (strlen($buf) != 0) {
file_put_contents("compress.zlib://" . $download_file, $buf);
// usleep(500000); // limit of 4 requests per second
}
}
// load entry, parse and write to file
echo " - parsing";
// $this->SetReadFile($download_file,true);
$buf = file_get_contents("compress.zlib://" . $download_file);
$converter = new BioPAX2Bio2RDF();
$converter->SetBuffer($buf)->SetBioPAXVersion(3)->SetBaseNamespace("http://identifiers.org/biomodels.db/{$id}/")->SetBio2RDFNamespace("http://bio2rdf.org/biomodels:" . $id . "_")->SetDatasetURI($this->GetDatasetURI());
$this->AddRDF($converter->Parse());
$this->WriteRDFBufferToWriteFile();
echo PHP_EOL;
}
$this->GetWriteFile()->Close();
// generate the release file
$this->DeleteBio2RDFReleaseFiles($odir);
$desc = $this->GetBio2RDFDatasetDescription($this->GetNamespace(), "https://github.com/bio2rdf/bio2rdf-scripts/blob/master/biomodels/biomodels.php", $bio2rdf_download_files, "http://www.ebi.ac.uk/biomodels-main/", array("use-share-modify"), null, $this->GetParameterValue('download_url'), $this->version);
$this->SetWriteFile($odir . $this->GetBio2RDFReleaseFile($this->GetNamespace()));
$this->GetWriteFile()->Write($desc);
$this->GetWriteFile()->Close();
return true;
}
function Run()
{
// get the work
if ($this->GetParameterValue('files') == 'all') {
$sources = explode("|", parent::getParameterList('files'));
array_shift($sources);
} else {
// comma separated list
$sources = explode(",", parent::getParameterValue('files'));
}
$download_files = array("h**o-sapiens" => "Pathway%20Commons%202%20homo%20sapiens.BIOPAX.owl.gz", "hprd" => "Pathway%20Commons%202%20HPRD.BIOPAX.owl.gz", "humancyc" => "Pathway%20Commons%202%20HumanCyc.BIOPAX.owl.gz", "nci-nature" => "Pathway%20Commons%202%20NCI_Nature.BIOPAX.owl.gz", "panther-pathway" => "Pathway%20Commons%202%20PANTHER%20Pathway.BIOPAX.owl.gz", "phosphositeplus" => "Pathway%20Commons%202%20PhosphoSitePlus.BIOPAX.owl.gz", "reactome" => "Pathway%20Commons%202%20Reactome.BIOPAX.owl.gz");
$graph_uri = parent::getGraphURI();
if (parent::getParameterValue('dataset_graph') == true) {
parent::setGraphURI(parent::getDatasetURI());
}
$dataset_description = '';
// iterate over the requested data
foreach ($sources as $source) {
echo "processing {$source}... ";
$ldir = parent::getParameterValue('indir');
$odir = parent::getParameterValue('outdir');
$rdir = parent::getParameterValue('download_url');
// set the remote and input files
$file = $source . ".owl";
$zfile = $source . ".owl.gz";
$rfile = $rdir . $download_files[$source];
$lfile = $ldir . $zfile;
// download if if the file doesn't exist locally or we are told to
if (!file_exists($lfile) || $this->GetParameterValue('download') == 'true') {
// download
echo "downloading... ";
file_put_contents($lfile, file_get_contents($rfile));
}
// extract the file out of the ziparchive
// and load into a buffer
echo 'extracting... ';
if (($fpin = gzopen($lfile, "r")) === FALSE) {
trigger_error("Unable to open {$lfile}", E_USER_ERROR);
exit;
}
$data = '';
while (!gzeof($fpin)) {
$buffer = gzgets($fpin, 4096);
$data .= $buffer;
}
gzclose($fpin);
// set the output file
$suffix = parent::getParameterValue('output_format');
$outfile = $source . '.' . $suffix;
$gz = false;
if (strstr(parent::getParameterValue('output_format'), "gz")) {
$gz = true;
}
parent::setWriteFile($odir . $outfile, $gz);
// send for parsing
$p = new BioPAX2Bio2RDF($this);
$p->SetBuffer($data)->SetBioPAXVersion(3)->SetBaseNamespace("http://purl.org/pc2/3/")->SetBio2RDFNamespace("http://bio2rdf.org/pathwaycommons:")->SetDatasetURI(parent::getDatasetURI());
$rdf = $p->Parse();
parent::addRDF($rdf);
// write to output
parent::writeRDFBufferToWriteFile();
parent::getWriteFile()->Close();
echo "done!" . PHP_EOL;
//generate dataset description
echo "Generating dataset description for {$zfile}... ";
$source_file = (new DataResource($this))->setURI($rfile)->setTitle("Pathway Commons")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($lfile)))->setFormat("rdf/xml")->setPublisher("http://www.pathwaycommons.org/")->setHomepage("http://www.pathwaycommons.org/")->setRights("use")->setRights("restricted-by-source-license")->setLicense("http://www.pathwaycommons.org/pc2/home.html#data_sources")->setDataset("http://identifiers.org/pathwaycommons/");
$dataset_description .= $source_file->toRDF();
echo "done!" . PHP_EOL;
}
echo "Generating dataset description for Bio2RDF Pathways Commons 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}/")->setTitle("Bio2RDF v{$bVersion} RDF version of {$prefix} (generated at {$date})")->setSource($source_file->getURI())->setCreator("https://github.com/bio2rdf/bio2rdf-scripts/blob/master/pathwaycommons/pathwaycommons.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 .= $output_file->toRDF();
//write dataset description to file
parent::setGraphURI($graph_uri);
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 work specified
$list = trim(parent::getParameterValue('files'));
if ($list == 'all') {
// call the getAllModelsId webservice
$file = $ldir . "all_models.json";
if (!file_exists($file)) {
try {
$x = @new SoapClient("http://www.ebi.ac.uk/biomodels-main/services/BioModelsWebServices?wsdl");
} catch (Exception $e) {
echo $e->getMessage();
}
$entries = $x->getAllModelsId();
file_put_contents($file, json_encode($entries));
} else {
$entries = json_decode(file_get_contents($file));
}
} elseif ($list == 'curated') {
// call the getAllCuratedModelsId webservice
$file = $ldir . "curated_models.json";
if (!file_exists($file)) {
try {
$x = @new SoapClient("http://www.ebi.ac.uk/biomodels-main/services/BioModelsWebServices?wsdl");
} catch (Exception $e) {
echo $e->getMessage();
}
$entries = $x->getAllCuratedModelsId();
file_put_contents($file, json_encode($entries));
} else {
$entries = json_decode(file_get_contents($file));
}
} else {
// check if a hyphenated list was provided
if (($pos = strpos($list, "-")) !== FALSE) {
$start_range = substr($list, 0, $pos);
$end_range = substr($list, $pos + 1);
for ($i = $start_range; $i <= $end_range; $i++) {
$entries[] = "BIOMD" . str_pad($i, 10, "0", STR_PAD_LEFT);
}
} else {
// for comma separated list
$b = explode(",", $this->GetParameterValue('files'));
foreach ($b as $e) {
$entries[] = "BIOMD" . str_pad($e, 10, "0", STR_PAD_LEFT);
}
}
}
$graph_uri = parent::getGraphURI();
if (parent::getParameterValue('dataset_graph') == true) {
parent::setGraphURI(parent::getDatasetURI());
}
// set the write file
$suffix = parent::getParameterValue('output_format');
$outfile = 'biomodels' . '.' . $suffix;
$gz = false;
if (strstr(parent::getParameterValue('output_format'), "gz")) {
$gz = true;
}
$dataset_description = '';
parent::setWriteFile($odir . $outfile, $gz);
// iterate over the entries
$i = 0;
$total = count($entries);
foreach ($entries as $id) {
echo "processing " . ++$i . " of {$total} - biomodel# " . $id;
$download_file = $ldir . $id . ".owl.gz";
$url = parent::getParameterValue('download_url') . "publ/{$id}/{$id}-biopax3.owl";
// download if the file doesn't exist or we are told to
if (!file_exists($download_file) || $this->GetParameterValue('download') == 'true') {
// download
echo " - downloading";
$ret = utils::downloadsingle($url, 'compress.zlib://' . $download_file, true);
if ($ret === false) {
echo "\nTrying non-curated model";
$url = parent::getParametervalue('download_url') . "uncura_publ/{$id}/{$id}-biopax3.owl";
$ret = utils::downloadsingle($url, 'compress.zlib://' . $download_file, true);
if ($ret === false) {
continue;
}
}
echo " - downloaded";
}
// load entry, parse and write to file
echo " - parsing... ";
// $this->SetReadFile($download_file,true);
$buf = file_get_contents("compress.zlib://" . $download_file);
$converter = new BioPAX2Bio2RDF($this);
$converter->SetBuffer($buf)->SetBioPAXVersion(3)->SetBaseNamespace("http://identifiers.org/biomodels.db/{$id}/")->SetBio2RDFNamespace("http://bio2rdf.org/biomodels:" . $id . "_")->SetDatasetURI($this->GetDatasetURI());
$rdf = $converter->Parse();
parent::addRDF($rdf);
parent::writeRDFBufferToWriteFile();
//generate dataset description
$source_file = (new DataResource($this))->setURI($url)->setTitle("EBI BioModels Database - BioModel # {$id}")->setRetrievedDate(date("Y-m-d\\TG:i:s\\Z", filemtime($download_file)))->setFormat("rdf/xml")->setPublisher("http://www.ebi.ac.uk/")->setHomepage("http://www.ebi.ac.uk/biomodels-main/")->setRights("use-share-modify")->setLicense("http://www.ebi.ac.uk/biomodels-main/termsofuse")->setDataset("http://identifiers.org/biomodels.db/");
$dataset_description .= $source_file->toRDF();
echo "done!" . PHP_EOL;
}
//foreach
parent::getWriteFile()->close();
$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/biomodels/biomodels.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 .= $output_file->toRDF();
//write dataset description to file
parent::setGraphURI($graph_uri);
parent::setWriteFile($odir . parent::getBio2RDFReleaseFile());
parent::getWriteFile()->write($dataset_description);
parent::getWriteFile()->close();
echo "done!" . PHP_EOL;
}
