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Diffstat (limited to 'sourcecodes/bn_file_load_gom.php')
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1 files changed, 401 insertions, 0 deletions
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($searchID)?> </textarea> +</td> +</tr> +<tr> +<td> +<INPUT TYPE="submit" value=" Load example data of immune responses to infection with Chlamydia psittaci " onclick="return demochl();">    +<INPUT TYPE="hidden" NAME="My_key" value=<?php print($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();">    +<INPUT TYPE="hidden" NAME="My_key" value=<?php print($keyval) ?> > +</td> +</tr> +<tr> +<td> +<INPUT TYPE="submit" value=" Load example data of immune-related gene in the spleens of BXD mice " onclick="return demospnl();">    +<INPUT TYPE="hidden" NAME="My_key" value=<?php print($keyval) ?> > +</td> +</tr> +<tr> +<td> +<INPUT TYPE="submit" value=" Load the ksl dataset from deal " onclick="return demoksl();">    +<INPUT TYPE="hidden" NAME="My_key" value=<?php print($keyval) ?> > +</td> +</tr> +<tr> +<td> +<INPUT TYPE="submit" value=" Load the rat dataset from deal " onclick="return demorat();">    +<INPUT TYPE="hidden" NAME="My_key" value=<?php print($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> + + |