/usr/share/stacks/php/index.php is in stacks-web 2.0Beta8c+dfsg-1.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 | <?php
//
// Copyright 2010-2016, Julian Catchen <jcatchen@illinois.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
//
$query =
"SELECT id, date, description, type FROM batches";
if (!($db['batch_sth'] = $db['dbh']->prepare($query)))
write_db_error($db['dbh'], __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;
if (!$db['batch_sth']->execute())
write_db_error($db['batch_sth'], __FILE__, __LINE__);
$res = $db['batch_sth']->get_result();
while ($row = $res->fetch_assoc()) {
print
"<tr>\n" .
" <td class=\"s\"><a href=\"$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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