-
Notifications
You must be signed in to change notification settings - Fork 6
/
Copy pathpanel.genome.php
executable file
·203 lines (196 loc) · 9.56 KB
/
panel.genome.php
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
<?php
session_start();
if (isset($_SESSION['logged_on'])) { $user = $_SESSION['user']; } else { $user = 'default'; }
?>
<style type="text/css">
html * {
font-family: arial !important;
}
</style>
<font size='3'>Install new reference genomes for use in sequence analysis.</font>
<p><font size='2'>
<b>IMPORTANT:</b>
<ol>
<li>Ymap only supports .fasta file extensions (which can be compressed with gzip or zip - ending with .gz and .zip, respectively). If your files end with .fa or .fna, you should rename them appropriately.</li>
<li>Small chromosomes and mitochodnrial DNA (less than 100 kbp) will not be displayed well, and you should remove them from the reference before uploading.</li>
</ol>
</font></p>
<?php
if(isset($_SESSION['logged_on']))
{
require_once 'sharedFunctions.php';
// getting the current size of the user folder in Gigabytes
$currentSize = getUserUsageSize($user);
// getting user quota in Gigabytes
$quota = getUserQuota($user);
// Setting boolean variable that will indicate whether the user has exceeded it's allocated space, if true the button to add new dataset will not appear
$exceededSpace = $quota > $currentSize ? FALSE : TRUE;
if ($exceededSpace)
echo "<span style='color:#FF0000; font-weight: bold;'>You have exceeded your quota (" . $quota . "G) please clear space and then reload to install new genome</span><br><br>";
}
?>
<table width="100%" cellpadding="0"><tr>
<td width="50%">
<?php
// .-----------------.
// | Make new genome |
// '-----------------'
if (isset($_SESSION['logged_on'])) {
// show Install new genome button only if user has space
if (!$exceededSpace)
echo "<input name=\"button_InstallNewGenome\" type=\"button\" value=\"Install New Genome\" onclick=\"parent.show_hidden('Hidden_InstallNewGenome')\"><br>\n\t\t\t\t";
$_SESSION['pending_install_genome_count'] = 0;
?>
<b><font size='2'>Genomes Pending:</font></b><br>
<div class='tab' style='color:#CC0000; font-size:10pt;' id='newly_installed_list' name='newly_installed_list'></div><br>
<div style='color:#CC0000; font-size:10pt; visibility:hidden; text-align:center;' id='pending_comment' name='pending_comment'>(Reload page after current uploads have completed to prepare these
for upload.)</div>
<div style='color:#CC0000; font-size:10pt; visibility:hidden; text-align:center;' id='name_error_comment' name='name_error_comment'>(Entered genome name is already in use.)</div>
<?php
}
// .--------------.
// | User genomes |
// '--------------'
$userGenomeCount = 0;
if (isset($_SESSION['logged_on'])) {
$genomesDir = "users/".$user."/genomes/";
$genomeFolders = array_diff(glob($genomesDir."*"), array('..', '.'));
// Sort directories by date, newest first.
array_multisort(array_map('filemtime', $genomeFolders), SORT_DESC, $genomeFolders);
// Trim path from each folder string.
foreach($genomeFolders as $key=>$folder) { $genomeFolders[$key] = str_replace($genomesDir,"",$folder); }
// Split genome list into ready/working/starting lists for sequential display.
$genomeFolders_complete = array();
$genomeFolders_working = array();
$genomeFolders_starting = array();
foreach($genomeFolders as $key=>$genome) {
if (file_exists("users/".$user."/genomes/".$genome."/complete.txt")) {
array_push($genomeFolders_complete,$genome);
} else if (file_exists("users/".$user."/genomes/".$genome."/working.txt")) {
array_push($genomeFolders_working, $genome);
} else {
array_push($genomeFolders_starting,$genome);
}
}
$userGenomeCount_starting = count($genomeFolders_starting);
$userGenomeCount_working = count($genomeFolders_working);
$userGenomeCount_complete = count($genomeFolders_complete);
// Sort complete and working genomes alphabetically.
array_multisort($genomeFolders_working, SORT_ASC, $genomeFolders_working);
array_multisort($genomeFolders_complete, SORT_ASC, $genomeFolders_complete);
// Build new 'genomeFolders' array;
$genomeFolders = array();
$genomeFolders = array_merge($genomeFolders_starting, $genomeFolders_working, $genomeFolders_complete);
$userGenomeCount = count($genomeFolders);
// displaying size if it's bigger then 0
if ($currentSize > 0 )
echo "<b><font size='2'>User Installed Genomes: (currently using " . $currentSize . "G of " . $quota . "G)</font></b>\n\t\t\t\t";
else
echo "<b><font size='2'>User Installed Genomes:</font></b>\n\t\t\t\t";
echo "<br>\n\t\t\t\t";
foreach($genomeFolders_starting as $key_=>$genome) {
printGenomeInfo("3", $key_, "CC0000", $user, $genome);
}
foreach($genomeFolders_working as $key_=>$genome) {
printGenomeInfo("2", $key_ + $userGenomeCount_starting, "BB9900", $user, $genome);
}
foreach($genomeFolders_complete as $key_=>$genome) {
printGenomeInfo("1", $key_ + $userGenomeCount_starting + $userGenomeCount_working, "00AA00", $user, $genome);
}
}
function printGenomeInfo($frameContainerIx, $key, $labelRgbColor, $user, $genome) {
$genomeNameString = file_get_contents("users/".$user."/genomes/".$genome."/name.txt");
$genomeNameString = trim($genomeNameString);
echo "<span id='g_label_".$key."' style='color:#".$labelRgbColor.";'>\n\t\t\t\t";
echo "<font size='2'>".($key+1).".";
echo "<button id='genome_delete_".$key."' type='button' onclick=\"parent.deleteGenomeConfirmation('".$user."','".$genome."','".$key."')\">Delete</button>";
echo $genomeNameString;
// display total size of files only if the genome is finished processeing
if ($frameContainerIx == "1")
{
$totalSizeFile = "users/".$user."/genomes/". $genome ."/totalSize.txt";
// display total genome size
// first checking if size already calculated and is stored in totalSize.txt
if (file_exists($totalSizeFile))
{
$handle = fopen($totalSizeFile,'r');
$genomeSizeStr = trim(fgets($handle));
fclose($handle);
}
else // calculate size and store in totalSize.txt to avoid calculating again
{
// calculating size
$genomeSizeStr = trim(shell_exec("du -sh " . "users/".$user."/genomes/". $genome . "/ | cut -f1"));
// saving to file
$output = fopen($totalSizeFile, 'w');
fwrite($output, $genomeSizeStr);
fclose($output);
}
// printing total size
echo " <font color='black' size='1'>(". $genomeSizeStr .")</font>";
}
echo "</font></span>\n\t\t\t\t";
echo "<span id='g_delete_".$key."'></span>\n\t\t";
echo "\n\t\t\t\t";
echo "<div id='frameContainer.g".$frameContainerIx."_".$key."'></div>";
}
?>
</td><td width="50%" valign="top">
<?php
//.----------------.
//| System genomes |
//'----------------'
$genomesDir = "users/default/genomes/";
$systemGenomeFolders = array_diff(glob($genomesDir."*"), array('..', '.'));
// Sort directories by date, newest first.
array_multisort(array_map('filemtime', $systemGenomeFolders), SORT_DESC, $systemGenomeFolders);
// Trim path from each folder string.
foreach($systemGenomeFolders as $key=>$folder) { $systemGenomeFolders[$key] = str_replace($genomesDir,"",$folder); }
$systemGenomeCount = count($systemGenomeFolders);
echo "<b><font size='2'>Installed Reference Genomes:</font></b><br>\n";
foreach ($systemGenomeFolders as $key=>$genome) {
$genomeNameString = file_get_contents("users/default/genomes/".$genome."/name.txt");
$genomeNameString = trim($genomeNameString);
echo "\t\t\t\t<font size='2'>".$genomeNameString."</font><br>\n";
}
?>
</td></tr></table>
<script type="text/javascript">
// Javascript which needs to be run.
var userGenomeCount = "<?php echo $userGenomeCount; ?>";
var systemGenomeCount = "<?php echo $systemGenomeCount; ?>";
<?php
if (isset($_SESSION['logged_on'])) {
foreach($genomeFolders_starting as $key_=>$genome) {
$key = $key_;
$genome = $genomeFolders[$key];
echo "\n\t// javascript for genome #".$key.", '".$genome."'\n\t";
echo "var el_g = document.getElementById('frameContainer.g3_".$key."');\n\t";
echo "el_g.innerHTML = '<iframe id=\"g_".$key."\" name=\"g_".$key."\" class=\"upload\" style=\"height:38px\" ";
echo "src=\"uploader.1.php\" marginwidth=\"0\" marginheight=\"0\" vspace=\"0\" hspace=\"0\" width=\"100%\" frameborder=\"0\"></iframe>';\n\t";
echo "var g_iframe = document.getElementById('g_".$key."');\n\t";
echo "var g_js = g_iframe.contentWindow;\n\t";
echo "g_js.display_string = new Array();\n\t";
echo "g_js.display_string[0] = \"Add : Genome reference FASTA file...\";\n\t";
echo "g_js.target_dir = \"../../users/".$user."/genomes/".$genome."/\";\n\t";
echo "g_js.conclusion_script = \"scripts_genomes/genome.install_1.php\";\n\t";
echo "g_js.user = \"".$user."\";\n\t";
echo "g_js.genome = \"".$genome."\";\n\t";
echo "g_js.key = \"g_".$key."\";\n";
}
foreach($genomeFolders_working as $key_=>$genome) {
$key = $key_ + $userGenomeCount_starting;
$genome = $genomeFolders[$key];
echo "\n\t// javascript for genome #".$key.", '".$genome."'\n\t";
echo "var el_g = document.getElementById('frameContainer.g2_".$key."');\n\t";
echo "el_g.innerHTML = '<iframe id=\"g_".$key."\" name=\"g_".$key."\" class=\"upload\" style=\"height:76px\" ";
echo "src=\"genome.working.php\" marginwidth=\"0\" marginheight=\"0\" vspace=\"0\" hspace=\"0\" width=\"100%\" frameborder=\"0\"></iframe>';\n\t";
echo "var g_iframe = document.getElementById('g_".$key."');\n\t";
echo "var g_js = g_iframe.contentWindow;\n\t";
echo "g_js.user = \"".$user."\";\n\t";
echo "g_js.genome = \"".$genome."\";\n\t";
echo "g_js.key = \"g_".$key."\";\n";
}
}
?>
</script>