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| -rw-r--r-- | sourcecodes/bn_genenet.php | 239 |
1 files changed, 239 insertions, 0 deletions
diff --git a/sourcecodes/bn_genenet.php b/sourcecodes/bn_genenet.php new file mode 100644 index 00000000..de33e952 --- /dev/null +++ b/sourcecodes/bn_genenet.php @@ -0,0 +1,239 @@ +<meta charset="utf-8"> +<script src="./scripts/d3.v4.min.js"></script> +<script src="./scripts/create_table.js"></script> + + +<script> +function genenetwork_data() +{ + with(window.document.key_search) + { + //searchkey.value="<?php echo $_POST['My_Genenet'] ?>"; + genenet_str = "<?php echo $_POST['My_Genenet'] ?>"; + //genenet_str = genenet_str.slice(0,-1); + //console.log(genenet_str); + genenet_str = genenet_str.replace(/,/g, '\t'); + genenet_str = genenet_str.replace(/;/g,'\n'); + //console.log(genenet_str); + //genenet_str = genenet_str + "\n\n"; + searchkey.value=genenet_str; + } +} +</script> + + + + +<?php + //Going to modify this so it just writes the uploaded data to a file. + //Standardization and determining other factors will be performed in + // a Matlab/Octave script. +//<link rel="stylesheet" href="./scripts/table.css" type="text/css"> +include("header_new.inc"); +include("header_batchsearch.inc"); +include("runtime_check.php"); +include("input_validate.php"); +$searchID=""; +$UploadValue="NO"; +$TextFile=$_FILES["MyFile"]["name"]; + + +/////////////Generate a random key///////////////////// +$alphas=array(); +$alphas = array_merge(range('A', 'Z'), range('a', 'z')); + +$al1=rand(0,51); +$al2=rand(0,51); +$al3=rand(0,51); + +$alpha="$alphas[$al1]"."$alphas[$al2]"."$alphas[$al3]"; +$keyval=$alpha; + + +if($_POST["My_key"]!="") + $keyval=$_POST["My_key"]; + $keyval=valid_keyval($keyval); + +$sid=$keyval."continuous_input"; +//$dir="./data/"; +//$dir="/tmp/bnw/"; +$dir="/var/lib/genenet/bnw/"; +//$input_table_file="./data/".$keyval."input_table.txt"; +$input_table_file=$dir.$keyval."input_table.txt"; + +$TextinFile=$dir.$sid."_orig.txt"; + + +if(isset($_POST["searchkey"])) +{ + $searchID=$_POST["searchkey"]; + $searchID = str_replace(',', "\t", $searchID); + $searchID = str_replace(';', "\n", $searchID); +} + +if($searchID=="") +{ +?> + +<!-- Site navigation menu --> +<ul class="navbar2"> + <li><a href="sample_input.php" target="_blank">View sample input file</a> + <li><a href="help.php#file_format" target="_blank">Data formatting guidelines</a> + <li><a href="about_this_page.php#file_upload" target="_blank">About this page</a> + <li><a href="help.php" target="_blank">Help</a> + <li><a href="home.php">Home</a> +</ul> +<?php +} + + +if(isset($_POST["MyUpload"])) +{ + $UploadValue=$_POST["MyUpload"]; + if ($UploadValue=="YES") + { + if($TextFile!="") + { + // $TextFile = valid_input($TextFile); + $sta=move_uploaded_file($_FILES['MyFile']['tmp_name'],$TextinFile); + if(!$sta) + { + echo "<script type='text/javascript'> window.alert ('Sorry, error uploading $TextFile.')</script>"; + flush(); + exit(); + } + else + { + $searchID=file_get_contents("$TextinFile"); + //unlink($TextinFile); + + } + + } + + else + { + echo "<script type='text/javascript'> window.alert ('Sorry, please select upload file.')</script>"; + } + } +} + +?> +<div id="outernew"> +<br> +<FORM name="key_search" id="in_form" enctype="multipart/form-data" ACTION="bn_genenet.php" METHOD=POST> + +<INPUT style="background-color:#FFFFFF;" type="file" name="MyFile" id="MyFile_id" class="inputfile" onchange="upload_submit()" > +<label for="MyFile_id"> Loading data from GeneNetwork </label> +<INPUT TYPE="hidden" NAME="My_key" value=<?php print($keyval) ?> > +<INPUT TYPE="hidden" name="MyUpload" value="NO"> +<textarea name="searchkey" style="display:none;"><?PHP print($searchID)?> </textarea> + +<?php +if(isset($_POST["My_Genenet"])) +{?> +<INPUT TYPE="submit" id="genenet" style="display: none;" onclick="return genenetwork_data();"> +<INPUT TYPE="hidden" NAME="My_key" value=<?php print($keyval) ?> > +<?php +}?> + +</FORM> +</div> + +<script> + function upload_submit() { + Upload(); + document.getElementById("in_form").submit(); + } +</script> + +<?php +if(isset($_POST["My_Genenet"])) +{?> +<script type="text/javascript"> + document.getElementById("genenet").click(); +</script> +<?php +}?> + + + + +<?php + +if($searchID!="") +{ + if ($UploadValue=="NO") + { + $fpdata = fopen($dir.$keyval."continuous_input_orig.txt","w"); + fwrite($fpdata,$searchID); + fclose($fpdata); + } + $keyval = valid_keyval($keyval); + shell_exec('./run_scripts/run_prep_input '.$keyval); + $parent_number=4; + $k_number=1; + $runtime=exe_time($keyval,$parent_number,$k_number); +?> +<ul class="navbar2"> +<li><a href="about_this_page.php#file_upload" target="_blank">About this page</a> +<li><a href="help.php" target="_blank">Help</a> +<li><a href="home.php">Home</a> +</ul> +<div id="outernew_load"> +<br> + <a class=button3 href="executionprogress_default.php?My_key=<?php print($keyval);?>">Perform Bayesian network modeling using default settings. Estimated runtime: <?php print($runtime);?> seconds</a> +<br> +<a class=button3 href="create_tiers_gom_part1.php?My_key=<?php print($keyval);?>">Go to structure learning settings and the BNW structural constraint interface</a> +<br> +<a class=button3 href="remove_variables.php?My_key=<?php print($keyval);?>">Remove variables from data set</a> +<br> +<br> +<p><h3>The uploaded data file has the following properties: +<br></h3> +<?php +$table_text = json_encode(file("file://".$input_table_file)); +?> + <div class="d3_table" id="table_div1"> + <script type="text/javascript"> + d3.text("", function(error, raw_temp){ + var dsv = d3.dsvFormat("\t") + var data1 = <?php echo $table_text?> + var data2 = data1.join("") + var data = dsv.parse(data2) + var caption_text = data.pop() + if (error) throw error; + tabulate_caption("#table_div1",data,caption_text.Variable); + }); +</script> +</div> +<br><br><br></h3> +</p> +<br> +<br> +<br> +<br> +<br> +<br> +<br> +<br> +<br> +<br> +<br> +<br> +<br> +<br> +<br> +<br> +<br> +<br> +<br> +</div> +<?php +} +?> + +</body> +</html> + + |