From c4f926438dcb8abe805e910399940f79ff643c4b Mon Sep 17 00:00:00 2001
From: ziejd2
Date: Thu, 14 Sep 2017 15:39:41 -0500
Subject: Add files via upload

---
 sourcecodes/bn_file_load_gom.php | 401 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 401 insertions(+)
 create mode 100644 sourcecodes/bn_file_load_gom.php

(limited to 'sourcecodes/bn_file_load_gom.php')

diff --git a/sourcecodes/bn_file_load_gom.php b/sourcecodes/bn_file_load_gom.php
new file mode 100644
index 00000000..342afe02
--- /dev/null
+++ b/sourcecodes/bn_file_load_gom.php
@@ -0,0 +1,401 @@
+<?php
+////////////////This code load a data file and creates input file for continuous global optimal search (our modification). execute_bn_gom.php link is for execution of structure learning and create_tiers_gom.php is for adding restrictions///////////////////////////////////
+
+include("header_new.inc");
+include("header_batchsearch.inc");
+include("runtime_check.php");
+$searchID="";
+$UploadValue="NO";
+$TextFile=$HTTP_POST_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"];
+
+
+////////////////////max parent/////////////////////////
+
+
+$type_n=array();
+
+//Get number of parent data and key value for changes in number of parent
+$type_n=explode("|",$_POST["nm_parent"]);
+if($keyval=="")
+   $keyval=$type_n[0];
+
+$sid=$keyval."continuous_input";
+$dir="./data/";
+
+$TextinFileFinal=$dir.$sid.".txt";
+$TextinFile=$dir.$sid."_temp.txt";
+$TextinFilenamelist=$dir.$keyval."name.txt";
+
+//print default number of parents
+$parent_number=4;
+$pfile=$dir.$keyval."parent.txt";
+$parentf=fopen($pfile,"w");
+fwrite($parentf,"$parent_number\n");
+
+//print default number of k for model averaging
+$k_number=1;
+$kfile=$dir.$keyval."k.txt";
+$kf=fopen($kfile,"w");
+fwrite($kf,"$k_number\n");
+
+//print default threshold for model averaging
+$thrfile=$dir.$keyval."thr.txt";
+$kf=fopen($thrfile,"w");
+fwrite($kf,"0.5\n");
+
+if(isset($HTTP_POST_VARS["searchkey"]))
+{
+   $searchID=$HTTP_POST_VARS["searchkey"];
+
+}
+
+if($searchID!="")
+{
+?>
+
+<!-- Site navigation menu -->
+<ul class="navbar2">
+  <li><a href="executionprogress.php?My_key=<?php print($keyval);?>">Perform Bayesian network modeling using default settings</a>
+  <li><a href="create_tiers_gom.php?My_key=<?php print($keyval);?>">Go to structure learning settings and the BNW structural constraint interface</a>  
+</ul>
+<ul class="navbar">
+  <li><a href="help.php#file_format" target="_blank">Data formatting guidelines</a> 
+  <li><a href="help.php" target="_blank">Help</a>
+  <li><a href="home.php">Home</a>
+</ul>
+<?php
+}
+else
+{
+
+?>
+<!-- Site navigation menu -->
+<ul class="navbar">
+  <li><a href="help.php#file_format" target="_blank">Data formatting guidelines</a> 
+  <li><a href="help.php" target="_blank">Help</a>
+  <li><a href="home.php">Home</a>
+</ul>
+<?php
+}
+
+
+if(isset($HTTP_POST_VARS["MyUpload"]))
+{
+   $UploadValue=$HTTP_POST_VARS["MyUpload"];
+   if ($UploadValue=="YES")
+   {
+        if($TextFile!="")
+        {
+            $sta=move_uploaded_file($HTTP_POST_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($TextinFile);
+
+            }
+
+        }
+
+       else
+       {
+           echo "<script type='text/javascript'> window.alert ('Sorry, please select upload file.')</script>";
+       }
+   }
+}
+
+?>
+<div id="outernew">
+<h2><font color=#33339f>Upload data file for structure learning search</font></h2>
+<FORM name="key_search" enctype="multipart/form-data" ACTION="bn_file_load_gom.php" METHOD=POST>
+
+<table align="left" cellspacing="3" cellpadding="1" border="0"  width="60%">
+<tr>
+<td>
+<INPUT style="background-color:#FFFFFF;color:#0000FF" type="file" name="MyFile" size=45 > 
+<INPUT TYPE="submit" value="  Upload  " onclick="return Upload();">
+<INPUT TYPE="hidden" NAME="My_key" value=<?php print($keyval) ?> >
+<INPUT TYPE="hidden" name="MyUpload" value="NO"> 
+</td>
+</tr>
+<tr>
+<td align="left"><font color=#33339f><br>Content of uploaded data file:</font><br>
+          <textarea name="searchkey" rows="10" cols="100"><?PHP print($searchID)?> </textarea>
+</td>
+</tr>
+<tr>
+<td>
+<INPUT TYPE="submit" value="  Load example data of immune responses to infection with Chlamydia psittaci  " onclick="return demochl();">&nbsp&nbsp&nbsp
+<INPUT TYPE="hidden" NAME="My_key" value=<?php print($keyval) ?> >
+</td>
+</tr>
+<tr>
+<td>
+<INPUT TYPE="submit" value="  Load example data of a synthetic genetic network with 2 genotypes and 6 traits  " onclick="return demo8nodes();">&nbsp&nbsp&nbsp
+<INPUT TYPE="hidden" NAME="My_key" value=<?php print($keyval) ?> >
+</td>
+</tr>
+<tr>
+<td>
+<INPUT TYPE="submit" value="  Load example data of immune-related gene in the spleens of BXD mice  " onclick="return demospnl();">&nbsp&nbsp&nbsp
+<INPUT TYPE="hidden" NAME="My_key" value=<?php print($keyval) ?> >
+</td>
+</tr>
+<tr>
+<td>
+<INPUT TYPE="submit" value="  Load the ksl dataset from deal  " onclick="return demoksl();">&nbsp&nbsp&nbsp
+<INPUT TYPE="hidden" NAME="My_key" value=<?php print($keyval) ?> >
+</td>
+</tr>
+<tr>
+<td>
+<INPUT TYPE="submit" value="  Load the rat dataset from deal  " onclick="return demorat();">&nbsp&nbsp&nbsp
+<INPUT TYPE="hidden" NAME="My_key" value=<?php print($keyval) ?> >
+</td>
+</tr>
+</table>
+</FORM>
+</div>
+<?php
+//////////////////Format data for Structure learning "C" code////////
+
+  $str_arr=array();
+  $searchID=trim($searchID);
+  $str_arr=explode("\n",$searchID);
+  $data=array();
+
+   
+  $fph = fopen($TextinFilenamelist,"w");
+  $fpmain = fopen($TextinFileFinal,"w");
+
+  $cont_arr=array();
+  $cont_arr_tmp=array();
+
+
+  $data_type=array();
+  $level_arr=array();
+
+//Who is discrete? Who is continuous?
+  $i=0;
+  $lc=0;
+  foreach($str_arr as $line)
+  {
+    $line=trim($line); 
+    if($lc==0)
+      {
+       fwrite($fph, "$line\n");
+	fprintf($fpmain, "$line\n");
+       $name_t=$line;
+
+	fclose($fph); 
+       $data=explode("\t",$line);
+	$j=0;
+       foreach($data as $d_c)
+	  {
+           $d_c=trim($d_c);
+           $level_arr[$j][0]=$d_c;  //variable name y for 
+            
+	    $data_type[$j]=0;
+            $j++;
+          }
+          $lcc=$j;  //$lcc=number of column in the input file 
+      }        
+    else
+      { 
+        
+        $strline=""; 
+        $data=explode("\t",$line);
+	 $j=0;
+        foreach($data as $d_c) 
+        {
+            $d_c=trim($d_c);
+	     $cont_arr[$i][$j]=$d_c; 
+            $cont_arr_tmp[$i][$j]=$d_c; 
+
+            $mystring = $d_c;
+	     $findme   = '.';
+	     $pos = strpos($mystring, $findme);
+            $strline.="1\t";
+  
+            if ($pos != false)
+            {
+                $data_type[$j]=1;
+            }
+            $j++;
+         }
+	 $i++; 
+    
+      }
+     $lc++;
+     
+  }
+$lc--; //$lc=number of rows in the input file
+//Now count number of labels for discrete variables and populate the $data_type[$j] 
+$data_count=0;
+$l_type="";
+for($j=0;$j<$lcc;$j++)
+{
+
+       if($data_type[$j]!=1)
+	{
+	  $data_count=0;
+	  for($i=0;$i<$lc;$i++)
+	  {
+              $vi=$i+1;
+	       for($ii=$vi;$ii<$lc;$ii++)
+	       {
+                 if($cont_arr[$i][$j]==$cont_arr[$ii][$j] && $cont_arr[$i][$j]!=-9999)
+		   {
+		       $cont_arr[$ii][$j]=-9999; 
+               
+		   } 
+	       }
+               
+              
+         }
+	  for($i=0;$i<$lc;$i++)
+	     {
+	       if($cont_arr[$i][$j]!=-9999 && $cont_arr[$i][$j]!="")
+		{
+                  // $data_count_l=$data_count+2;
+                  $data_count++;
+                  $level_arr[$j][$data_count]=$cont_arr[$i][$j];
+              }
+	     }
+	  $data_type[$j]=$data_count;
+	    
+	   
+	}
+       if($j==0)
+         $l_type.=$data_type[$j];
+       else
+	 $l_type.="\t".$data_type[$j];  
+      
+    }
+
+///////////////////Write data to files/////////////////
+$fptype = fopen($dir.$keyval."type.txt","w");
+$fpnode= fopen($dir.$keyval."nnode.txt","w");
+fwrite($fpnode,"$lcc\n");
+$fprows = fopen($dir.$keyval."nrows.txt","w");
+fwrite($fprows,"$lc\n");
+$flevel = fopen($dir.$keyval."nlevels.txt","w");
+
+//print in level mapping file for discrete variables
+for($j=0;$j<$lcc;$j++)
+{
+  if($data_type[$j]>1)
+  {  
+      fprintf($flevel,"%s",$level_arr[$j][0]);
+      $m=$data_type[$j];
+      for($jj=1;$jj<=$m;$jj++)
+      {
+         fprintf($flevel,"\t%s",$level_arr[$j][$jj]);
+      }
+
+      fprintf($flevel,"\n");  
+  }   
+}
+
+
+fwrite($fptype,"$name_t\n");
+for($j=0;$j<$lcc;$j++)
+{
+  fprintf($fptype,"$data_type[$j]\t");
+}
+fwrite($fptype,"\n");
+
+  
+fwrite($fpmain, "$l_type\n");
+$l_c=0;
+
+//perform discrete level replacement 
+for($m=0;$m<$lcc;$m++)  //column
+{
+  if($data_type[$m]>1)
+  {
+     $r=$data_type[$m];
+     for($j=1;$j<=$r;$j++)
+     {  
+         $search=$level_arr[$m][$j];
+         $replace=$j."#";
+         for($n=0;$n<$lc;$n++)  //row
+         { 
+           $val=$cont_arr_tmp[$n][$m];
+           if($val==$search)
+               $cont_arr_tmp[$n][$m]=$replace;  //alter levels 
+         }
+     }
+     for($n=0;$n<$lc;$n++)  //row
+          $cont_arr_tmp[$n][$m]=str_replace('#','',$cont_arr_tmp[$n][$m]);
+  }
+}
+
+//write data to output file
+for($j=0;$j<$lc;$j++)
+{
+  fprintf($fpmain,"%s",$cont_arr_tmp[$j][0]);
+  for($jj=1;$jj<$lcc;$jj++)
+    fprintf($fpmain,"\t%s",$cont_arr_tmp[$j][$jj]);
+  fprintf($fpmain, "\n");
+}
+
+fclose($fpmain);
+
+////////////////empty ban and white list/////////////////////////////
+
+$sid1=$keyval."ban";
+$sid2=$keyval."white";
+$wdir="./data/"; 
+
+$Textban=$wdir.$sid1.".txt";
+$Textwhite=$wdir.$sid2.".txt";
+
+$fpb = fopen($Textban,"w");
+$fpw = fopen($Textwhite,"w");
+
+$datpost="From\tTo\n";
+
+fwrite($fpb,"$datpost");
+fwrite($fpw,"$datpost");
+if($searchID!="")
+{
+
+$runtime=exe_time($keyval,$parent_number,$k_number);
+?>
+<div id="outernew">
+<p><h3><?php 
+print("Estimated run time for current dataset using default settings: $runtime seconds");
+?>
+<br><br></h3>
+</p>
+<br>
+</div>
+<?php
+}
+?>
+
+</body>
+</html>
+
+
-- 
cgit 1.4.1