From e16d5b1a5f6b11acb461afddd1eb82042e634d67 Mon Sep 17 00:00:00 2001
From: ziejd2
Date: Fri, 8 Oct 2021 13:48:41 -0500
Subject: Add files via upload

---
 sourcecodes/bn_genenet.php | 239 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 239 insertions(+)
 create mode 100644 sourcecodes/bn_genenet.php

(limited to 'sourcecodes/bn_genenet.php')

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>
+
+
-- 
cgit 1.4.1


From 31e40ec2d154eeee9ee3d85b1cb58905740e12de Mon Sep 17 00:00:00 2001
From: ziejd2
Date: Fri, 8 Oct 2021 13:53:10 -0500
Subject: Update bn_genenet.php

---
 sourcecodes/bn_genenet.php | 5 -----
 1 file changed, 5 deletions(-)

(limited to 'sourcecodes/bn_genenet.php')

diff --git a/sourcecodes/bn_genenet.php b/sourcecodes/bn_genenet.php
index de33e952..8fd5aea7 100644
--- a/sourcecodes/bn_genenet.php
+++ b/sourcecodes/bn_genenet.php
@@ -8,14 +8,9 @@ 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;
     }
 }
-- 
cgit 1.4.1