/usr/share/stacks/php/index.php is in stacks-web 1.35-1ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | <?php
//
// Copyright 2010, Julian Catchen <jcatchen@uoregon.edu>
//
// This file is part of Stacks.
//
// Stacks is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// Stacks is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with Stacks. If not, see <http://www.gnu.org/licenses/>.
//
require_once("header.php");
$database = isset($_GET['db']) ? $_GET['db'] : "";
if (strlen($database) == 0)
write_database_list($database);
else
write_database($database);
function write_database_list($database) {
global $db_user, $db_pass, $db_host, $root_path, $img_path, $mysql_bin;
$databases = array();
exec("$mysql_bin --user=$db_user --password=$db_pass -h $db_host -N -B -e \"SHOW DATABASES LIKE '%_radtags'\"", $databases);
$page_title = "Stacks Databases";
write_header($page_title);
echo <<< EOQ
<h4 class="info_head">
<img id="sources_img" src="$img_path/caret-d.png" />
<a onclick="toggle_div('sources', '$img_path', 'page_state');">Stacks Databases</a>
</h4>
<a name="results_top"></a>
<table class="db" style="width: 35%;">
<tr>
<th style="width: 100%;">Database</th>
</tr>
EOQ;
foreach ($databases as $dbase) {
print
"<tr>\n" .
" <td><a href=\"$root_path/index.php?db=" . $dbase . "\">$dbase</a></td>\n" .
"</tr>\n";
}
echo <<< EOQ
</table>
EOQ;
write_footer();
}
function write_database($database) {
global $root_path, $img_path;
//
// Connect to the database
//
$db = db_connect($database);
//
// Prepare some SQL queries
//
$query =
"SELECT id, date, description, type FROM batches";
$db['batch_sth'] = $db['dbh']->prepare($query);
check_db_error($db['batch_sth'], __FILE__, __LINE__);
$page_title = "RAD-Tag Analyses";
write_header($page_title);
echo <<< EOQ
<h4 class="info_head">
<img id="sources_img" src="$img_path/caret-d.png" />
<a onclick="toggle_div('sources', '$img_path', 'page_state');">RAD-Tag Samples</a>
</h4>
<a name="results_top"></a>
<table class="db" style="width: 75%;">
<tr>
<th style="width: 10%;"> </th>
<th style="width: 10%;"> </th>
<th style="width: 10%;">Batch ID</th>
<th style="width: 10%;">Date</th>
<th style="width: 10%;">Type</th>
<th style="width: 50%;">Description</th>
</tr>
EOQ;
$result = $db['batch_sth']->execute();
check_db_error($result, __FILE__, __LINE__);
while ($row = $result->fetchRow()) {
print
"<tr>\n" .
" <td class=\"s\"><a href=\"$root_path/catalog.php?db=$database&id=$row[id]\">Catalog</a></td>\n" .
" <td class=\"s\"><a href=\"$root_path/samples.php?db=$database&id=$row[id]\">Samples</a></td>\n" .
" <td>" . $row['id'] . "</td>\n" .
" <td>" . $row['date'] . "</td>\n" .
" <td>" . $row['type'] . "</td>\n" .
" <td>" . $row['description'] . "</td>\n" .
"</tr>\n";
}
echo <<< EOQ
</table>
EOQ;
write_footer();
}
?>
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