modelit/server/index.php

<?php
include_once("inc/settings.php");
session_start();

function is_valid_job_name($job_name) {
        return ereg('^[-0-9a-zA-Z_]+$', $job_name);
}

function is_valid_sequence($sequence) {
        return ereg('^[a-zA-Z]+$', $sequence);
}

function job_output_exists($job_name) {
        return file_exists(get_output_dir($job_name));
}

if (array_key_exists('_submit_check',$_POST)) {

        // save form input
        $seq = trim($_POST['sequence']);
        $seq = str_replace("\n", "", $seq);
        $seq = str_replace("\r", "", $seq);     
        $_SESSION['sequence'] = $_POST['sequence'];
        $_SESSION['job_name'] = substr($_POST['job_name'], 0, 50); # maximum job length is 50

        // check that job name is given
        if(!array_key_exists('job_name',$_POST) || $_POST['job_name'] == "") {
                $form_errors['no_job_name'] = 1;                
        } else {
                // check that job name is valid
                if(!is_valid_job_name($_POST['job_name'])) {
                        $form_errors["wrong_job_name"] = 1;
                } else {
                        // check that job name is not taken already
                        if(job_output_exists($_POST['job_name'])) {
                                $form_errors['job_name_exists'] = 1;
                        }
                }
        }
        
        // check that sequence exists
        if(!array_key_exists('sequence',$_POST) || $_POST['sequence'] == "") {
                $form_errors["no_sequence"] = 1;
        } else {
                // check that sequence is valid
                if(!is_valid_sequence($seq)) {
                        $form_errors['wrong_sequence'] = 1;
                } else {
                        $seqlen = strlen($seq);
                }
        }
        
        // check that sequence range is valid
        $seq_from = 1;
        $seq_to = $seqlen;
        // if start or end key exists
        if( (array_key_exists('seqfrom',$_POST) && $_POST['seqfrom'] != "") || 
            (array_key_exists('seqto',$_POST) && $_POST['seqto'] != "") ){
            // if start or end key is missing
                if(!array_key_exists('seqfrom',$_POST) || $_POST['seqfrom'] == "" ||
                   !array_key_exists('seqto',$_POST) || $_POST['seqto'] == "") {
                        $form_errors['wrong_seq_range'] = 1;
                } else {
                        $seq_from = (int) $_POST['seqfrom'];
                        $seq_to = (int) $_POST['seqto'];
                        if($seq_from < 1 || $seq_to > $seqlen || $seq_to < $seq_from) {
                                $form_errors['wrong_seq_range'] = 2;
                        }
                }
        } 
        
        // no errors -> redirect to template selection
        if(!isset($form_errors)) {
                $_SESSION['sequence'] = strtoupper($seq);
                $_SESSION['seqfrom'] = $seq_from;
                $_SESSION['seqto'] = $seq_to;
                header("Location: run_template_selection.php");
        }
}
?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">

<head>
  <title>Structure prediction server</title>
  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
  <link rel="stylesheet" type="text/css" href="css/default.css" />
  
    <script type="text/javascript">
    
    // performed if 'clear form' button is pressed
    function clearForm() {
        document.seqform.job_name.value='';
        document.seqform.sequence.value='';
        document.seqform.seqfrom.value='';
        document.seqform.seqto.value='';
        setSeqLen();
    }
        
        // show the current sequence length in the 'rescount' field
        function setSeqLen() {
                var seqLen = document.getElementById('sequence').value.length;
                var span = document.getElementById('rescount');
                span.innerHTML = seqLen;
        }
        
    // select part of text area
    function selectInTextArea(id, start, end){
    
        var textarea = document.getElementById(id);
        if(textarea.setSelectionRange){
                textarea.setSelectionRange(parseInt(start), parseInt(end));
        }
        else {
                var range = textarea.createTextRange();
                range.collapse(true);
        
                range.moveStart('character',parseInt(start) );
                range.moveEnd('character',(parseInt(end)-parseInt(start)+1));
                range.select();
        }
        }
        
        // highlight the subsequence chosen in the sequence range text fields
        function selectSubSequence() {
                var areaId='sequence';
                var fromId = 'seqfrom';
                var toId = 'seqto';
                
                var start = document.getElementById(fromId).value;
                var end = document.getElementById(toId).value;
                
                selectInTextArea(areaId, start-1, end);
        }
        
        // show the start and end indices of the selected sub sequence to the sequence range text fields
        function setRange() {
                var textarea=document.getElementById('sequence');
                document.getElementById('seqfrom').value=textarea.selectionStart+1;
                document.getElementById('seqto').value=textarea.selectionEnd;           
        }
        
        </script>
    
    
</head>
<body onload="setSeqLen();">
<?php include_once("inc/owl_header.inc.php") ?>
<h3>Protein Structure Prediction Server</h3>
<div style="width:800px">
<div class="roundedcornr_box_759934">
   <div class="roundedcornr_top_759934"><div></div></div>
      <div class="roundedcornr_content_759934">

<form name="seqform" action="<?php $_SERVER['PHP_SELF'] ?>" method="POST" enctype="multipart/form-data">
<input type="hidden" name="_submit_check" value="1"/>   
<table cellspacing=10>
  <tbody>
      <tr>
      <td valign="top">Job name:</td>
      <td><input type="text" name="job_name" size=30 maxlength="50" value="<? echo $_SESSION['job_name'] ?>">
      <?php 
        if(isset($form_errors['no_job_name'])) {
                echo '<br/><font color="red">Please provide a job name</font>';
        } 
        if(isset($form_errors['wrong_job_name'])) {
                echo '<br/><font color="red">Wrong job name: please use only letters, numbers and underscores</font>';
        }
        if(isset($form_errors['job_name_exists'])) {
                echo '<br/><font color="red">This job name exists already. Please choose a different one.<font>';
        }       
      ?>
      </td>
    </tr>
    <tr>
      <td valign="top">Protein sequence:</td> 
      <td><textarea style="width:600px; height:150px" id="sequence" name="sequence" wrap="soft" onselect="setRange();" onkeyup="setSeqLen();" onchange="setSeqLen();"><? echo $_SESSION['sequence'] ?></textarea>
      <?php 
        if(isset($form_errors['no_sequence'])) {
                echo '<br/><font color="red" size="2">Please provide a sequence</font>';
        } 
        if(isset($form_errors['wrong_sequence'])) {
                echo '<br/><font color="red" size="2">Illegal character in sequence: please provide a plain protein sequence without fasta header</font>';
        }       
      ?>       
      </td>
    </tr>
    <tr>
      <td>Sequence range:</td> 
      <td>
        <input type="text" name="seqfrom" id="seqfrom" value="<? echo $_SESSION['seqfrom'] ?>" size="4" maxlength="4" onkeyup="selectSubSequence()" onchange="selectSubSequence()" />
        to <input type="text" name="seqto" id="seqto" value="<? echo $_SESSION['seqto'] ?>" size="4" maxlength="4" onkeyup="selectSubSequence()" onchange="selectSubSequence()" />
        out of <span id="rescount">0</span>
        <?php
        if(isset($form_errors['wrong_seq_range'])) {
                echo '<br/><font color="red" size="2">Invalid sequence range</font>';
        } 
        ?>
      </td>
    
    </tr>
    <!-- tr>
      <td>Or upload file:</td>
      <td><INPUT type="file" name="seq_file"></td>
    </tr -->
    <tr>
      <td></td>
      <td><input type="submit" value="Submit" class="fancybutton"> <input type="button" class="fancybutton" value="Clear form" onClick="clearForm();"></td>
    </tr>
  </tbody>
</table>
</form>
</div>
      </div>
   <div class="roundedcornr_bottom_759934"><div></div></div>
</div>
<br/>
<div class="buttons">
<a href="results.php"><img src="images/application_view_list.png" alt="" /> View result list</a>
</div>
<div style="clear:both;"></div>
<p><b>Contact: </b>stehr@molgen.mpg.de</p>
</body>
</html>
Revision:	1299
Committed:	Tue Jan 11 17:38:33 2011 UTC (11 years, 5 months ago) by hstehr
Original Path:	*trunk/modelit/server/index.php*
File size:	7485 byte(s)
Log Message:	adding Model-It server files to repository
Line	File contents
1	<?php
2	include_once("inc/settings.php");
3	session_start();
4
5	function is_valid_job_name($job_name) {
6	return ereg('^[-0-9a-zA-Z_]+$', $job_name);
7	}
8
9	function is_valid_sequence($sequence) {
10	return ereg('^[a-zA-Z]+$', $sequence);
11	}
12
13	function job_output_exists($job_name) {
14	return file_exists(get_output_dir($job_name));
15	}
16
17	if (array_key_exists('_submit_check',$_POST)) {
18
19	// save form input
20	$seq = trim($_POST['sequence']);
21	$seq = str_replace("\n", "", $seq);
22	$seq = str_replace("\r", "", $seq);
23	$_SESSION['sequence'] = $_POST['sequence'];
24	$_SESSION['job_name'] = substr($_POST['job_name'], 0, 50); # maximum job length is 50
25
26	// check that job name is given
27	if(!array_key_exists('job_name',$_POST) \|\| $_POST['job_name'] == "") {
28	$form_errors['no_job_name'] = 1;
29	} else {
30	// check that job name is valid
31	if(!is_valid_job_name($_POST['job_name'])) {
32	$form_errors["wrong_job_name"] = 1;
33	} else {
34	// check that job name is not taken already
35	if(job_output_exists($_POST['job_name'])) {
36	$form_errors['job_name_exists'] = 1;
37	}
38	}
39	}
40
41	// check that sequence exists
42	if(!array_key_exists('sequence',$_POST) \|\| $_POST['sequence'] == "") {
43	$form_errors["no_sequence"] = 1;
44	} else {
45	// check that sequence is valid
46	if(!is_valid_sequence($seq)) {
47	$form_errors['wrong_sequence'] = 1;
48	} else {
49	$seqlen = strlen($seq);
50	}
51	}
52
53	// check that sequence range is valid
54	$seq_from = 1;
55	$seq_to = $seqlen;
56	// if start or end key exists
57	if( (array_key_exists('seqfrom',$_POST) && $_POST['seqfrom'] != "") \|\|
58	(array_key_exists('seqto',$_POST) && $_POST['seqto'] != "") ){
59	// if start or end key is missing
60	if(!array_key_exists('seqfrom',$_POST) \|\| $_POST['seqfrom'] == "" \|\|
61	!array_key_exists('seqto',$_POST) \|\| $_POST['seqto'] == "") {
62	$form_errors['wrong_seq_range'] = 1;
63	} else {
64	$seq_from = (int) $_POST['seqfrom'];
65	$seq_to = (int) $_POST['seqto'];
66	if($seq_from < 1 \|\| $seq_to > $seqlen \|\| $seq_to < $seq_from) {
67	$form_errors['wrong_seq_range'] = 2;
68	}
69	}
70	}
71
72	// no errors -> redirect to template selection
73	if(!isset($form_errors)) {
74	$_SESSION['sequence'] = strtoupper($seq);
75	$_SESSION['seqfrom'] = $seq_from;
76	$_SESSION['seqto'] = $seq_to;
77	header("Location: run_template_selection.php");
78	}
79	}
80	?>
81	<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
82	<html xmlns="http://www.w3.org/1999/xhtml">
83
84	<head>
85	<title>Structure prediction server</title>
86	<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
87	<link rel="stylesheet" type="text/css" href="css/default.css" />
88
89	<script type="text/javascript">
90
91	// performed if 'clear form' button is pressed
92	function clearForm() {
93	document.seqform.job_name.value='';
94	document.seqform.sequence.value='';
95	document.seqform.seqfrom.value='';
96	document.seqform.seqto.value='';
97	setSeqLen();
98	}
99
100	// show the current sequence length in the 'rescount' field
101	function setSeqLen() {
102	var seqLen = document.getElementById('sequence').value.length;
103	var span = document.getElementById('rescount');
104	span.innerHTML = seqLen;
105	}
106
107	// select part of text area
108	function selectInTextArea(id, start, end){
109
110	var textarea = document.getElementById(id);
111	if(textarea.setSelectionRange){
112	textarea.setSelectionRange(parseInt(start), parseInt(end));
113	}
114	else {
115	var range = textarea.createTextRange();
116	range.collapse(true);
117
118	range.moveStart('character',parseInt(start) );
119	range.moveEnd('character',(parseInt(end)-parseInt(start)+1));
120	range.select();
121	}
122	}
123
124	// highlight the subsequence chosen in the sequence range text fields
125	function selectSubSequence() {
126	var areaId='sequence';
127	var fromId = 'seqfrom';
128	var toId = 'seqto';
129
130	var start = document.getElementById(fromId).value;
131	var end = document.getElementById(toId).value;
132
133	selectInTextArea(areaId, start-1, end);
134	}
135
136	// show the start and end indices of the selected sub sequence to the sequence range text fields
137	function setRange() {
138	var textarea=document.getElementById('sequence');
139	document.getElementById('seqfrom').value=textarea.selectionStart+1;
140	document.getElementById('seqto').value=textarea.selectionEnd;
141	}
142
143	</script>
144
145
146	</head>
147	<body onload="setSeqLen();">
148	<?php include_once("inc/owl_header.inc.php") ?>
149	<h3>Protein Structure Prediction Server</h3>
150	<div style="width:800px">
151	<div class="roundedcornr_box_759934">
152	<div class="roundedcornr_top_759934"><div></div></div>
153	<div class="roundedcornr_content_759934">
154
155	<form name="seqform" action="<?php $_SERVER['PHP_SELF'] ?>" method="POST" enctype="multipart/form-data">
156	<input type="hidden" name="_submit_check" value="1"/>
157	<table cellspacing=10>
158	<tbody>
159	<tr>
160	<td valign="top">Job name:</td>
161	<td><input type="text" name="job_name" size=30 maxlength="50" value="<? echo $_SESSION['job_name'] ?>">
162	<?php
163	if(isset($form_errors['no_job_name'])) {
164	echo '<br/><font color="red">Please provide a job name</font>';
165	}
166	if(isset($form_errors['wrong_job_name'])) {
167	echo '<br/><font color="red">Wrong job name: please use only letters, numbers and underscores</font>';
168	}
169	if(isset($form_errors['job_name_exists'])) {
170	echo '<br/><font color="red">This job name exists already. Please choose a different one.<font>';
171	}
172	?>
173	</td>
174	</tr>
175	<tr>
176	<td valign="top">Protein sequence:</td>
177	<td><textarea style="width:600px; height:150px" id="sequence" name="sequence" wrap="soft" onselect="setRange();" onkeyup="setSeqLen();" onchange="setSeqLen();"><? echo $_SESSION['sequence'] ?></textarea>
178	<?php
179	if(isset($form_errors['no_sequence'])) {
180	echo '<br/><font color="red" size="2">Please provide a sequence</font>';
181	}
182	if(isset($form_errors['wrong_sequence'])) {
183	echo '<br/><font color="red" size="2">Illegal character in sequence: please provide a plain protein sequence without fasta header</font>';
184	}
185	?>
186	</td>
187	</tr>
188	<tr>
189	<td>Sequence range:</td>
190	<td>
191	<input type="text" name="seqfrom" id="seqfrom" value="<? echo $_SESSION['seqfrom'] ?>" size="4" maxlength="4" onkeyup="selectSubSequence()" onchange="selectSubSequence()" />
192	to <input type="text" name="seqto" id="seqto" value="<? echo $_SESSION['seqto'] ?>" size="4" maxlength="4" onkeyup="selectSubSequence()" onchange="selectSubSequence()" />
193	out of <span id="rescount">0</span>
194	<?php
195	if(isset($form_errors['wrong_seq_range'])) {
196	echo '<br/><font color="red" size="2">Invalid sequence range</font>';
197	}
198	?>
199	</td>
200
201	</tr>
202	<!-- tr>
203	<td>Or upload file:</td>
204	<td><INPUT type="file" name="seq_file"></td>
205	</tr -->
206	<tr>
207	<td></td>
208	<td><input type="submit" value="Submit" class="fancybutton"> <input type="button" class="fancybutton" value="Clear form" onClick="clearForm();"></td>
209	</tr>
210	</tbody>
211	</table>
212	</form>
213	</div>
214	</div>
215	<div class="roundedcornr_bottom_759934"><div></div></div>
216	</div>
217	<br/>
218	<div class="buttons">
219	<a href="results.php"><img src="images/application_view_list.png" alt="" /> View result list</a>
220	</div>
221	<div style="clear:both;"></div>
222	<p><b>Contact: </b>stehr@molgen.mpg.de</p>
223	</body>
224	</html>