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; }