"; if(!isset($_POST['Upload']) and !isset($_POST['generate']) and !isset($_POST['generateFit']) and !isset($_POST['UploadData']) and !isset($_POST['UploadSpec'])){ echo "

modelMaGe web interface (preliminary)

"; echo "This web interface is designed only for testing modelMaGe.
Please download and install modelMaGe on your local machine,
in case you plan to generate large number of files.
Especially, the 'Generate+Fit'-option should be used only
for a small number of models.

This service only runs smoothly with Firefox,
whereas with Internet Explorer we experienced some problems.

"; echo "

modelMaGe specifications:

"; uploadFormular(); echo "
Note: In case you upload a Copasi-file, with a defined parameter estimation task,
the corresponding data file should be defined to be loacted in the same directory as the model file."; } elseif (isset($_POST['Upload']) and !isset($_POST['UploadSpec'])){ $offerDataUpload = uploading(); if ($offerDataUpload == 1){ uploadFormularData(); } generateFormular(); } elseif (isset($_POST['UploadData']) and !isset($_POST['UploadSpec'])){ $outputPathName = showResult2(); transferData(); generateFormular(); } elseif (isset($_POST['UploadSpec']) and !isset($_POST['generate']) and !isset($_POST['generateFit'])) { $outputPathName = showResult2(); transferSpec(); generateFormular(); } elseif (isset($_POST['generateFit'])){ generateFit(); } elseif (isset($_POST['generate'])){ generate(); } echo " "; footer('webVersion.php'); ################################### function definitions ######################################### function getTime(){ $timestamp = time(); $datum = date("Y.m.d",$timestamp); $uhrzeit = date("H:i",$timestamp); #echo $datum," - ",$uhrzeit," Uhr"; return $datum."-".$uhrzeit."-"; } function uploadFormular(){ echo " "; } function uploading(){ global $modelPath, $sbmlPath, $LD_LIBRARY_PATH, $PYTHONPATH, $ndatafiles; putenv('HOME='.$sbmlPath); putenv('LD_LIBRARY_PATH='.$LD_LIBRARY_PATH); putenv('PYTHONPATH='.$PYTHONPATH); $outputResult = 0; $b = 0; #$server = $_SERVER['DOCUMENT_ROOT']; #$currentDir = getcwd(); #echo "the dir: $currentDir

"; $filename = $_FILES['mastermodel']['name']; #$type = $_FILES['mastermodel']['type']; #$tmpName = $_FILES['mastermodel']['tmp_name']; $jobTime = getTime(); $_SESSION['jobTime'] = $jobTime; $offerDataUpload = 0; if (preg_match('/\.cps$/',$filename)){ $outputPathName = $sbmlPath."/".$jobTime."job.cps"; $offerDataUpload = 1; }else{ $outputPathName = $sbmlPath."/".$jobTime."job.xml"; } #copy ( $sbmlfile, "$modelPath/xxx.xml") or die ("Couldn't copy"); $result = move_uploaded_file($_FILES['mastermodel']['tmp_name'], $outputPathName); if ($result == 1) echo "

Uploaded file: $filename

"; else echo "

There was a problem by uploading $filename.

"; if ($offerDataUpload == 1){ ## for check data file $modelCommand = "python $modelPath/modelmage.py -e $outputPathName"; #echo $modelCommand; exec($modelCommand, $outputResult, $b); if ($b == 0) { # if everything ok # echo "b : $b

"; $length = count($outputResult); #echo "length: $length

"; $ndatafiles = $length-2; #echo "ndatafiles: $ndatafiles

"; #$tt = $outputResult[$length-1]; #echo "$tt

"; if ( $outputResult[0] == " with no defined experimental data

"){ $offerDataUpload = 0; } ## producing the master model and the graph $modelCommand = "python $modelPath/modelmage.py -w $outputPathName"; #unset($outputResult); exec($modelCommand, $outputResult, $b); showResult($outputPathName, $outputResult); return $offerDataUpload; } else { echo "

Output: $outputResult

"; echo " There was a problem executing $modelCommand

. Please refer to the documentation or send an email to adminmodelmage.org

."; } } } function showResult($outputPathName, $outputResult){ global $sbmlPath; ### open file for save result ### $tmpFile = $sbmlPath."/".$_SESSION['jobTime']."a.text"; if(file_exists($tmpFile)){ unlink($tmpFile); } $fp = fopen($tmpFile,'w') or die("can't open file"); fwrite($fp, $outputPathName.""); foreach ( $outputResult as $ele){ echo "$ele"; fwrite($fp, $ele); } fclose($fp); } function showResult2(){ global $sbmlPath; $tmpFile = $sbmlPath."/".$_SESSION['jobTime']."a.text"; $fp = fopen($tmpFile, 'r') or die("can't open file"); $content = fread($fp, filesize($tmpFile)); fclose($fp); $parts = split('', $content); echo $parts[1]; return $parts[0]; } function getOutPutPathName(){ global $sbmlPath; $tmpFile = $sbmlPath."/".$_SESSION['jobTime']."a.text"; $fp = fopen($tmpFile, 'r') or die("can't open file"); $content = fread($fp, filesize($tmpFile)); fclose($fp); $parts = split('', $content); #echo $parts[1]; return $parts[0]; } function generate(){ global $modelPath, $sbmlPath, $LD_LIBRARY_PATH, $PYTHONPATH, $outputPathName, $specfile; putenv('HOME='.$sbmlPath); putenv('LD_LIBRARY_PATH='.$LD_LIBRARY_PATH); putenv('PYTHONPATH='.$PYTHONPATH); $outputResult = 0; $b = 0; $outputPathName = $_POST['outputPathName']; if ($outputPathName == ''){ $outputPathName = getOutPutPathName(); } if (isset($_POST['specfile'])){ $specfile = $_POST['specfile']; #echo "spec: $specfile"; $filename = $sbmlPath."/".$specfile; $modelCommand = "python $modelPath/modelmage.py -w -i $filename $outputPathName"; } else { $species_Id = $_POST['species_Id']; $kinetics_Id = $_POST['kinetics_Id']; #echo "

outputPathName: $outputPathName

"; #echo "species_id: ".$species_Id."

"; #echo "kinetics_id: ".$kinetics_Id."

"; if($species_Id != ''){ $modelCommand = "python $modelPath/modelmage.py -r '$species_Id' $outputPathName -w"; #echo "enter species

"; } if($kinetics_Id != ''){ #echo "enter kinetics

"; $modelCommand = "python $modelPath/modelmage.py -k '$kinetics_Id' $outputPathName -w"; } if($kinetics_Id != '' & $species_Id != ''){ #echo "enter both

"; $modelCommand = "python $modelPath/modelmage.py -r '$species_Id' -k '$kinetics_Id' $outputPathName -w"; } if($kinetics_Id == '' & $species_Id == '') $modelCommand = "python $modelPath/modelmage.py $outputPathName -w"; } exec($modelCommand, $outputResult, $b); if ($b > 0) { errorMessage($modelCommand,$outputResult); } else { foreach ($outputResult as $ele) echo "$ele"; } unset($_SESSION['jobTime']); } function generateFit(){ global $modelPath, $sbmlPath, $LD_LIBRARY_PATH, $PYTHONPATH, $outputPathName, $discriminate, $specfile; putenv('HOME='.$sbmlPath); putenv('LD_LIBRARY_PATH='.$LD_LIBRARY_PATH); putenv('PYTHONPATH='.$PYTHONPATH); $outputResult = 0; $b = 0; $outputPathName = $_POST['outputPathName']; if ($outputPathName == ''){ $outputPathName = getOutPutPathName(); } $discriminate = $_POST['discriminate']; #echo "dis: $discriminate"; if ($discriminate == 1){ if (isset($_POST['specfile'])){ $specfile = $_POST['specfile']; #echo "spec: $specfile"; $filename = $sbmlPath."/".$specfile; $modelCommand = "python $modelPath/modelmage.py -p -w -i $filename $outputPathName"; } else { $species_Id = $_POST['species_Id']; $kinetics_Id = $_POST['kinetics_Id']; if($species_Id != ''){ $modelCommand = "python $modelPath/modelmage.py -p -w -r '$species_Id' $outputPathName"; #echo "enter species

"; } if($kinetics_Id != ''){ #echo "enter kinetics

"; $modelCommand = "python $modelPath/modelmage.py -p -w -k '$kinetics_Id' $outputPathName"; } if($kinetics_Id != '' & $species_Id != ''){ #echo "enter both

"; $modelCommand = "python $modelPath/modelmage.py -p -w -r '$species_Id' -k '$kinetics_Id' $outputPathName"; } if($kinetics_Id == '' & $species_Id == ''){ $modelCommand = "python $modelPath/modelmage.py -p -w $outputPathName"; } } exec($modelCommand, $outputResult, $b); if ($b > 0) { errorMessage($modelCommand,$outputResult); } else { foreach ($outputResult as $ele){ echo "$ele"; } } } else{ print "

Sorry, you haven't uploaded corresponding exprimental data for the parameter estimation task

"; } unset($_SESSION['jobTime']); } function errorMessage($modelCommand,$outputResult){ echo "There was a problem executing $modelCommand.
"; $length = count($outputResult); #echo "length: $length

"; if ($length > 0) { foreach ($outputResult as $ele) echo "$ele"; echo "

If you have problems interpreting this error message,
please refer to the documentation or send an email to adminmodelmage.org

."; } else echo "

No output was generated.
Please refer to the documentation or send an email to adminmodelmage.org.

"; } function transferSpec(){ global $sbmlPath, $specfile, $discriminate; $discriminate = $_POST['discriminate']; #echo "dis: $discriminate"; $specfile = $_FILES['SpecData']['name']; $result = move_uploaded_file($_FILES['SpecData']['tmp_name'], $sbmlPath."/".$specfile); if ($result == 1) echo "

Uploaded file: $specfile

"; else echo "

There was a problem uploading the spec-file '$specfile'.

"; } function transferData(){ global $sbmlPath, $discriminate; while(list($key,$value) = each($_FILES['expData']['name'])){ if(!empty($value)){ // this will check if any blank field is entered $filename = $value; // filename stores the value $result = move_uploaded_file($_FILES['expData']['tmp_name'][$key], $sbmlPath."/".$filename); if ($result == 1) { $discriminate = 1; echo "

Uploaded file: $filename

"; } else { $discriminate = 0; echo "

There was a problem uploading $filename.

"; } } } } function uploadFormularData(){ global $outputPathName, $ndatafiles; echo "
"; } function generateFormular(){ global $outputPathName, $discriminate, $specfile; # echo " "; #echo "dis: $discriminate"; echo "

"; echo "

"; if (!isset($_POST['UploadSpec'])){ echo " Upload generate-specifications as a file OR specify them here: Remove Kinetics
OR
	After pressing this button the interface might take while to return. Therefore, if you are using a proxy with a 'timeout-option', you might not get any results at all. In this case, please use the stand-alone version.

"; } if (isset($_POST['UploadSpec'])){ echo "