public function __construct()
{
$this->headerFooter = HeaderFooterFactory::createHeaderFooter();
$this->pageHome = PageFactory::createHome();
$this->database = DatabaseFactory::createDatabase();
$this->file = FileFactory::setFile();
}
public function countWords($files)
{
if (!is_array($files)) {
$files = array($files);
}
$factory = new FileFactory();
$result = 0;
foreach ($files as $file) {
$result += $factory->getFile($file)->getWordCount();
}
return $result;
}
/**
* @covers FileFactory::GetFile
*/
public function testParameterPass()
{
$file = $this->object->GetFile("Andris Bērziņš");
$this->assertequals("Andris Bērziņš", $file->studentName);
}
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);
$this->GetWriteFile()->Close();
}
<?php
require_once "./classes/gradefile.class.php";
require_once "./classes/pdfgradefile.class.php";
require_once "./classes/rtfgradefile.class.php";
require_once "./classes/filefactory.class.php";
if (isset($_GET["type"])) {
$file = FileFactory::GetFile("Kārlis Zummeris", $_GET["type"]);
} else {
$file = FileFactory::GetFile("Kārlis Zummeris");
}
$file->add_grade("2008-10-13", "Matemātika", "8");
$file->add_grade("2008-09-11", "Literatūra", "7");
$file->Generate_Content();
$file->Write_To_Client();
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;
}
} else {
//uncomment for debug
/*
$action = $_GET['action'];
$filename = $_GET['filename'];
$description = $_GET['description'];
global $gl_loglevel;
$gl_loglevel = 1;
*/
}
if (application_userisvalid()) {
$usr = application_getvaliduser();
if ($usr != null) {
$df = new DirectoryFactory();
$ff = new FileFactory();
global $gl_filedir;
//msg_updatefilelist
//TODO delete file from db if the file does not exist in directory
if ($action == msg_updatefilelist) {
//$ff->updateFiles($usr->getUid());
$ff->setInvalid($usr->getUid());
$lst1 = $df->listFiles_Dir($usr->getUid(), $gl_filedir, array("gpx", "xml"));
if ($lst1 != null) {
for ($i = 0; $i < count($lst1); $i++) {
$fn = $lst1[$i];
if (!$ff->fileExists($usr->getUid(), basename($fn))) {
$path = dirname($fn) . "/";
$filename = basename($fn);
$ff->createFile($usr->getUid(), $path, $filename, NULL);
} else {
/**
*
*/
function getGroupItems($aUserid, $aParentGroupId)
{
$items = array();
$pois = array();
$files = array();
$qry = "SELECT * FROM `tab_grp_item` WHERE ((usrid = {$aUserid}) AND (itemid = {$aParentGroupId}))";
$result = $this->executeQuery($qry);
if ($result != NULL) {
while ($row = mysql_fetch_row($result)) {
if ($row != null) {
$itemtype = strtolower($row[3]);
switch ($itemtype) {
case "file":
$fl1 = new File();
$this->parse_ItemLink($fl1, $row, $result);
array_push($files, $fl1);
break;
case "poi":
$poi = new Poi();
$this->parse_ItemLink($poi, $row, $result);
array_push($pois, $poi);
break;
}
}
}
if (count($pois) > 0) {
$pf = new PoiFactory();
$pf->addPois($aUserid, $pois, $items);
}
if (count($files) > 0) {
$ff = new FileFactory();
$ff->addFiles($aUserid, $files, $items);
}
}
return $items;
}
