LBMC » MyLabStocks

<?php

require_once("lib/seq.lib.php");

// a Trigger to display plsmid map image

$all = $this->myQuery("SELECT * FROM " . $this->tb . " WHERE id=" . $this->rec);

// reach the plasmid displayed

$plasmid = mysql_fetch_object($all);

if ($plasmid) {

  if ($_REQUEST["action"] == "REMOVE_FILE_SEQ") {

    if ($plasmid->Link_to_file != "") {

      $to_rem_file = "plasmid_files/" . $plasmid->Link_to_file;

      if (file_exists($to_rem_file)) {

        unlink($to_rem_file);

      }

    }

    $reqsql = "UPDATE  plasmids SET sequence='', Link_to_file=''  WHERE  id = $this->rec";

    mysql_query($reqsql);

    $all = $this->myQuery("SELECT * FROM " . $this->tb . " WHERE id=" . $this->rec);

    $plasmid = mysql_fetch_object($all);

  }

  if ($_REQUEST["action"] == "ADD_GB_GZ_FILE") {

    // echo"<pre>";

    // print_r($_FILES);

    // echo"</pre>";

    if ($_FILES["userfile"]["error"]) {

      exit("ERROR, your file is probably too big, maximum upload file size is "  . ini_get('upload_max_filesize') . ". <br/><a href='".$_SERVER["HTTP_REFERER"]."'>Back</a>");

    }

    $userfile = $_FILES["userfile"]["tmp_name"];

    $userfile_name = $_FILES["userfile"]["name"];

    if (stristr($userfile_name, ".gb.gz")) {

      $ext=".gb.gz";

    } else if (stristr($userfile_name, ".gb")) {

      $fp = fopen($userfile, "r");

      $data = fread ($fp, filesize($userfile));

      fclose($fp);

      $zp = gzopen($userfile, "w9");

      gzwrite($zp, $data);

      gzclose($zp);      

      $userfile_name = $userfile_name . ".gz";

      $ext=".gb.gz";

    } else {

      if(file_exists($userfile)) {

        unlink($userfile);

      }

      exit("ERROR 1, your file MUST have the extension .gb.gz (lowercase)). <br/><a href='".$_SERVER["HTTP_REFERER"]."'>Back</a>");

    }

    $dest_filename = str_replace(" ","_",substr($userfile_name, 0, strlen($userfile_name)-6)) . $ext;

    $dest_filepath = "plasmid_files/" . $dest_filename;

    if (file_exists($dest_filepath)) {

      if (file_exists($userfile)) {

        unlink($userfile);

      }

      exit("ERROR 2, this .gb.gz filename is already used. <br/><a href='".$_SERVER["HTTP_REFERER"]."'>Back</a>");

    }

    echo "<pre>$userfile $dest_filepath</pre>";

    if (!copy($userfile, $dest_filepath)){

      if (file_exists($userfile)) {

        unlink($userfile);

      }

      exit("ERROR 3, problem copying file. <br/><a href='".$_SERVER["HTTP_REFERER"]."'>Back</a>");

    }

    if(file_exists($userfile)) {

      unlink($userfile);

    }

    $url = "/var/www/labstocks/plasmid_files/" . $dest_filename;

    $handle = gzopen($url, 'r');

    if ($handle) {

      $content = "";

      while (!gzeof($handle)) {

         $buffer = gzgets($handle, 4096);

         $content .= $buffer;

      }

      gzclose($handle);

      preg_match('#ORIGIN(.*)//#sm', $content, $matches);

      $seq = $matches[0];

      $seq = preg_replace("#ORIGIN#", "", $seq);

      $seq = preg_replace("#[^a-zA-Z]#ms", "", $seq);

      $reqsql = "UPDATE  plasmids SET sequence='$seq', Link_to_file='$dest_filename'  WHERE  id = $this->rec";

      mysql_query($reqsql);

      $all = $this->myQuery("SELECT * FROM " . $this->tb . " WHERE id=" . $this->rec);

      $plasmid = mysql_fetch_object($all);

    }

  }

  /*

  * VIEW

  */

  $in_edit_mode = $_REQUEST["PME_sys_operation"] == "Change" || $_REQUEST["PME_sys_operation"] == "PME_op_Change";

  if ($plasmid->sequence) {

    if ($in_edit_mode) {  

      $remove_gbgz_form = <<<EOD

<form action='' method='post'>

  Remove file, filename and sequence for this plasmid: 

  <input type='hidden' name='PME_sys_operation' value='PME_op_Change'/>

  <input type='hidden' name='PME_sys_rec' value='$this->rec'/>

  <input type='hidden' name='action' value='REMOVE_FILE_SEQ'/>

  <input type='button' name='send' value='Remove' onclick='if(confirm("Are you sure that you want to remove file, filename and sequence for this plasmid?")){this.form.submit()}else{return false;}'/>

</form>

EOD;

    }

    $imgurl = seq2png($plasmid->sequence, PLASMAPPER_SERVER);

    $plasmapper_output = <<<EOD

<center>

<img src="$imgurl">

<br/>

<textarea readonly rows="10" cols="100">$plasmid->sequence</textarea></center>

</center>

EOD;

    $wwwblast_url = WWWBLAST_SERVER . "blast.cgi";

    $resp = post_vars($wwwblast_url, array(

      "DATALIB" => "plfeatstock_db", 

      "PROGRAM" => "blastn", 

      "EXPECT" => 10, 

      "OOF_ALIGN" => 0, 

      "OVERVIEW" => "on", 

      "ALIGNMENT_VIEW" => 0, 

      "DESCRIPTIONS" => 100, 

      "ALIGNMENTS" => 50, 

      "COLOR_SCHEMA" => 0,

      "SEQUENCE" => $plasmid->sequence

    ));

    $blast_output = preg_replace("/nph-viewgif.cgi/", WWWBLAST_SERVER . "nph-viewgif.cgi", $resp);

  } else {

    if ($in_edit_mode) {  

      $add_gbgz_form = <<<EOD

    <div class="centered_form">

      <i>Add a <b>.gb</b> or a <b>.gb.gz</b> file to this plasmid</i> 

      <br/>

      <br/>

      <form action='' method='post' enctype='multipart/form-data'>

        <fieldset>

          <legend>Upload .gb File</legend>

          <input type='hidden' name='action' value='ADD_GB_GZ_FILE'/>

          <input type='hidden' name='PME_sys_operation' value='PME_op_Change'/>

          <input type='hidden' name='PME_sys_rec' value='$this->rec'/>

          <input name='userfile' type='file' size='10'/>

          <input type='button' name='send' value='Upload' onclick='return this.form.submit();'/>

        </fieldset>

      </form>

    </div>

EOD;

    }

  }

}

  $to_be_post_list_content .= <<<EOD

    <div class="sheet">

    $remove_gbgz_form

    $add_gbgz_form

    $plasmapper_output

    </div>

EOD;

if ($blast_output != "") {

  $to_be_post_list_content .= <<<EOD

    <div class="sheet">

    $blast_output

    </div>

EOD;

}

?>