Alexandre
536 lines
22 KiB
PHP
536 lines
22 KiB
PHP
<?php
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/* Basic input sanitation */
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$_GET = filter_input_array(INPUT_GET, FILTER_SANITIZE_STRING) ?: [];
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$_POST = filter_input_array(INPUT_POST, FILTER_SANITIZE_STRING) ?: [];
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require_once __DIR__ . '/common.php';
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ensure_authenticated();
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$home = get_home();
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/* ---------- disk species counts (AJAX endpoint) ---------- */
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if (isset($_GET['diskcounts'])) {
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header('Content-Type: application/json');
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$script = __DIR__ . '/disk_species_count.sh';
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$cmd = 'HOME=' . escapeshellarg($home) . ' bash ' . escapeshellarg($script) . ' 2>&1';
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$output = @shell_exec($cmd);
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$counts = [];
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if ($output !== null) {
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foreach (preg_split('/\\r?\\n/', $output) as $line) {
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$line = trim($line);
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if ($line === '') continue;
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if (preg_match('/^([0-9]+(?:\\.[0-9]+)?)(k?)\\s*:\\s*(.+)$/i', $line, $m)) {
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$num = (float)$m[1];
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if (strtolower($m[2]) === 'k') $num *= 1000;
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$counts[$m[3]] = (int)round($num);
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}
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}
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}
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echo json_encode($counts, JSON_UNESCAPED_UNICODE);
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exit;
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}
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/* ---------- DB open (RO unless deleting) ---------- */
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$flags = isset($_GET['delete']) ? SQLITE3_OPEN_READWRITE : SQLITE3_OPEN_READONLY;
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$db = new SQLite3(__DIR__ . '/birds.db', $flags);
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$db->busyTimeout(1000);
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$db->exec("
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PRAGMA journal_mode=WAL; -- safe read concurrency
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PRAGMA synchronous=NORMAL; -- cheaper fsyncs (read-mostly)
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PRAGMA temp_store=MEMORY; -- temp data stays in RAM
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PRAGMA cache_size=-80000; -- ~80MB page cache (tune to your RAM)
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PRAGMA mmap_size=268435456; -- 256MB mmap (set 0 if kernel disallows)
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");
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/* Paths / lists */
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$base_symlink = $home . '/BirdSongs/Extracted/By_Date';
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$base = realpath($base_symlink); // safety checks
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$confirm_file = __DIR__ . '/confirmed_species_list.txt';
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$exclude_file = __DIR__ . '/exclude_species_list.txt';
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$whitelist_file = __DIR__ . '/whitelist_species_list.txt';
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foreach ([$confirm_file, $exclude_file, $whitelist_file] as $file) {
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if (!file_exists($file)) touch($file);
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}
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$confirmed_species = file_exists($confirm_file) ? file($confirm_file, FILE_IGNORE_NEW_LINES | FILE_SKIP_EMPTY_LINES) : [];
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$excluded_species = file_exists($exclude_file) ? file($exclude_file, FILE_IGNORE_NEW_LINES | FILE_SKIP_EMPTY_LINES) : [];
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$whitelisted_species = file_exists($whitelist_file) ? file($whitelist_file, FILE_IGNORE_NEW_LINES | FILE_SKIP_EMPTY_LINES) : [];
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$config = get_config();
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$sf_thresh = isset($config['SF_THRESH']) ? (float)$config['SF_THRESH'] : 0.0;
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/* ---------- helpers ---------- */
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function join_path(...$parts): string { return preg_replace('#/+#', '/', implode('/', $parts)); }
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function can_unlink(string $p): bool { return is_link($p) || is_file($p); }
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function under_base(string $path, string $base): bool {
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if ($base === false) return false;
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$baseReal = rtrim(realpath($base) ?: $base, DIRECTORY_SEPARATOR);
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$resolved = realpath($path);
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if ($resolved === false) {
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$parent = realpath(dirname($path));
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if ($parent === false) return false;
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$resolved = $parent . DIRECTORY_SEPARATOR . basename($path);
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}
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return $resolved === $baseReal || strpos($resolved, $baseReal . DIRECTORY_SEPARATOR) === 0;
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}
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/* Collect files/dirs for a species */
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function collect_species_targets(SQLite3 $db, string $species, string $home, $base): array {
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$stmt = $db->prepare('SELECT Date, Com_Name, Sci_Name, File_Name FROM detections WHERE Com_Name = :name');
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ensure_db_ok($stmt);
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$stmt->bindValue(':name', $species, SQLITE3_TEXT);
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$res = $stmt->execute();
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$count = 0; $files = []; $dirs = []; $sci = null;
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while ($row = $res->fetchArray(SQLITE3_ASSOC)) {
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$count++; if ($sci === null) $sci = $row['Sci_Name'];
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$dir = str_replace([' ', "'"], ['_', ''], $row['Com_Name']);
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$candidates = [
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join_path($home, 'BirdSongs/Extracted/By_Date', $row['Date'], $dir, $row['File_Name']),
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join_path($home, 'BirdSongs/Extracted/By_Date/shifted', $row['Date'], $dir, $row['File_Name']),
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];
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foreach ($candidates as $c) {
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if (can_unlink($c) && under_base($c, $base)) { $files[$c] = true; $dirs[] = dirname($c); continue; }
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$d = realpath(dirname($c));
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if ($d !== false) {
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$alt = $d . DIRECTORY_SEPARATOR . basename($c);
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if (can_unlink($alt) && under_base($alt, $base)) { $files[$alt] = true; $dirs[] = dirname($alt); }
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}
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}
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}
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return ['count'=>$count, 'files'=>array_keys($files), 'dirs'=>array_values(array_unique($dirs)), 'sci'=>$sci];
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}
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/* ---------- toggle exclude/whitelist/confirmed ---------- */
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if (isset($_GET['toggle'], $_GET['species'], $_GET['action'])) {
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$list = $_GET['toggle'];
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$species = htmlspecialchars_decode($_GET['species'], ENT_QUOTES);
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if ($list === 'exclude') { $file = $exclude_file; }
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elseif ($list === 'whitelist') { $file = $whitelist_file; }
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elseif ($list === 'confirmed') { $file = $confirm_file; }
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else { header('Content-Type: text/plain'); echo 'Invalid list type'; exit; }
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$lines = file_exists($file) ? file($file, FILE_IGNORE_NEW_LINES | FILE_SKIP_EMPTY_LINES) : [];
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if ($_GET['action'] === 'add') {
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if (!in_array($species, $lines, true)) $lines[] = $species;
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} else {
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$lines = array_values(array_filter($lines, fn($l) => $l !== $species));
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}
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file_put_contents($file, implode("\n", $lines) . (empty($lines) ? "" : "\n"));
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header('Content-Type: text/plain'); echo 'OK'; exit;
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}
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/* ---------- count ---------- */
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if (isset($_GET['getcounts'])) {
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header('Content-Type: application/json');
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if ($base === false) { http_response_code(500); exit(json_encode(['error' => 'Base directory not found'])); }
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$species = htmlspecialchars_decode($_GET['getcounts'], ENT_QUOTES);
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$info = collect_species_targets($db, $species, $home, $base);
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echo json_encode(['count' => $info['count'], 'files' => count($info['files'])]); exit;
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}
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/* ---------- delete ---------- */
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if (isset($_GET['delete'])) {
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header('Content-Type: application/json');
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if ($base === false) { http_response_code(500); exit(json_encode(['error' => 'Base directory not found'])); }
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$species = htmlspecialchars_decode($_GET['delete'], ENT_QUOTES);
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$info = collect_species_targets($db, $species, $home, $base);
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$deleted = 0;
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foreach ($info['files'] as $fp) {
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if (!under_base($fp, $base)) continue;
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if (can_unlink($fp) && @unlink($fp)) {
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$deleted++;
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foreach ([$fp . '.png', preg_replace('/\.[^.]+$/', '.png', $fp)] as $png) {
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if (can_unlink($png)) @unlink($png);
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}
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}
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}
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foreach ($info['dirs'] as $dir) { if (under_base($dir, $base)) @rmdir($dir); }
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$del = $db->prepare('DELETE FROM detections WHERE Com_Name = :name');
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ensure_db_ok($del);
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$del->bindValue(':name', $species, SQLITE3_TEXT);
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$del->execute();
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$lines_deleted = $db->changes();
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if ($info['sci'] !== null && file_exists($confirm_file)) {
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$identifier = str_replace("'", '', $info['sci']);
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$lines = array_values(array_filter($confirmed_species, fn($l) => $l !== $identifier));
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file_put_contents($confirm_file, implode("\n", $lines) . (empty($lines) ? "" : "\n"));
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}
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echo json_encode(['lines' => $lines_deleted, 'files' => $deleted]); exit;
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}
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/* ---------- query species aggregates ---------- */
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$sql = <<<SQL
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SELECT Com_Name, Sci_Name, COUNT(*) AS Count, MAX(Confidence) AS MaxConfidence, MAX(Date) AS LastSeen
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FROM detections
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GROUP BY Com_Name, Sci_Name;
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SQL;
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$result = $db->query($sql);
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?>
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<style>
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.circle-icon{display:inline-block;width:12px;height:12px;border:1px solid #777;border-radius:50%;cursor:pointer;}
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.centered{max-width:1100px;margin:0 auto}
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#speciesTable th{cursor:pointer}
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.toolbar{display:flex;gap:8px;align-items:center;margin:8px 0}
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.toolbar input[type="text"]{padding:6px 8px;min-width:260px}
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#speciesTable a,
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#speciesTable a:visited,
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#speciesTable a:active {
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color: black;
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text-decoration: none;
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}
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</style>
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<div class="centered">
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<!-- Search with persistence -->
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<div class="toolbar">
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<input id="q" type="text" placeholder="Filter species… (name, scientific)" title="Type to filter; persists across reloads">
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<small id="matchCount"></small>
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</div>
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<table id="speciesTable">
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<thead>
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<tr>
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<th onclick="sortTable(0)">Common Name</th>
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<th onclick="sortTable(1)">Scientific Name</th>
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<th>Stats</th>
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<th onclick="sortTable(3)">Count</th>
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<th onclick="sortTable(4)">Max Confidence</th>
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<th onclick="sortTable(5)">Last Seen</th>
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<th onclick="sortTable(6)">Probability</th>
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<th onclick="sortTable(7)">Confirmed</th>
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<th onclick="sortTable(8)">Excluded</th>
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<th onclick="sortTable(9)">Whitelisted</th>
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<th>Delete</th>
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</tr>
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</thead>
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<tbody>
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<?php while ($row = $result->fetchArray(SQLITE3_ASSOC)) {
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$common = htmlspecialchars($row['Com_Name'], ENT_QUOTES);
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$scient = htmlspecialchars($row['Sci_Name'], ENT_QUOTES);
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$count = (int)$row['Count'];
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$max_confidence = round((float)$row['MaxConfidence'] * 100, 1);
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$identifier = str_replace("'", '', $row['Sci_Name'].'_'.$row['Com_Name']);
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$identifier_sci = str_replace("'", '', $row['Sci_Name']);
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$lastSeen = $row['LastSeen'] ?? '';
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$lastSeenSort = $lastSeen ? (strtotime($lastSeen) ?: 0) : 0;
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$lastSeenDisplay = htmlspecialchars($lastSeen, ENT_QUOTES);
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$common_link = "<a href='views.php?view=Recordings&species=" . rawurlencode($row['Sci_Name']) . "'>{$common}</a>";
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$is_confirmed = in_array($identifier_sci, $confirmed_species, true);
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$is_excluded = in_array($identifier, $excluded_species, true);
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$is_whitelisted = in_array($identifier, $whitelisted_species, true);
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$comnamegraph = str_replace("'", "\'", $row['Com_Name']);
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$chart_cell = sprintf("<img style='height: 1em;cursor:pointer;float:unset;display:inline' title='View species stats' onclick=\"generateMiniGraph(this, '%s', 180)\" width=25 src='images/chart.svg'>", $comnamegraph);
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$confirm_cell = $is_confirmed
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? "<img style='cursor:pointer;max-width:12px;max-height:12px' src='images/check.svg' onclick=\"toggleSpecies('confirmed','".str_replace("'", '', $identifier_sci)."','del')\">"
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: "<span class='circle-icon' onclick=\"toggleSpecies('confirmed','".str_replace("'", '', $identifier_sci)."','add')\"></span>";
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$excl_cell = $is_excluded
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? "<img style='cursor:pointer;max-width:12px;max-height:12px' src='images/check.svg' onclick=\"toggleSpecies('exclude','".str_replace("'", '', $identifier)."','del')\">"
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: "<span class='circle-icon' onclick=\"toggleSpecies('exclude','".str_replace("'", '', $identifier)."','add')\"></span>";
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$white_cell = $is_whitelisted
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? "<img style='cursor:pointer;max-width:12px;max-height:12px' src='images/check.svg' onclick=\"toggleSpecies('whitelist','".str_replace("'", '', $identifier)."','del')\">"
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: "<span class='circle-icon' onclick=\"toggleSpecies('whitelist','".str_replace("'", '', $identifier)."','add')\"></span>";
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$sciname_raw = $row['Sci_Name'];
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$info_url = get_info_url($sciname_raw);
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if (!empty($info_url)) {
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$url = $info_url['URL'] ?? $info_url;
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$url_esc = htmlspecialchars($url, ENT_QUOTES);
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$scient_link = "<a href=\"{$url_esc}\" target=\"_blank\"><i>{$scient}</i></a>";
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} else {
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$scient_link = "<i>{$scient}</i>";
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}
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echo "<tr data-comname=\"{$common}\">"
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. "<td>{$common_link}</td>"
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. "<td>{$scient_link}</td>"
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. "<td>{$chart_cell}</td>"
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. "<td>{$count}</td>"
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. "<td data-sort='{$max_confidence}'>{$max_confidence}%</td>"
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. "<td data-sort=\"{$lastSeenSort}\">{$lastSeenDisplay}</td>"
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. "<td class='threshold' data-sort='0'>0.0000</td>"
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. "<td data-sort='".($is_confirmed?0:1)."'>".$confirm_cell."</td>"
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. "<td data-sort='".($is_excluded?0:1)."'>".$excl_cell."</td>"
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. "<td data-sort='".($is_whitelisted?0:1)."'>".$white_cell."</td>"
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. "<td><img style='cursor:pointer;max-width:20px' src='images/delete.svg' onclick=\"deleteSpecies('".addslashes($row['Com_Name'])."')\"></td>"
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. "</tr>";
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} ?>
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</tbody>
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</table>
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</div>
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<script src="static/Chart.bundle.js"></script>
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<script>
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const scriptsBase = 'scripts/';
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const sfThresh = <?php echo json_encode($sf_thresh, JSON_UNESCAPED_UNICODE); ?>;
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const get = (url) => fetch(url, {cache:'no-store'}).then(r => r.text());
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/* ---------- Probability (thresholds) auto-load ---------- */
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function loadThresholds() {
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return get(scriptsBase + 'config.php?threshold=0').then(text => {
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const lines = (text || '').split(/\r?\n/);
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const map = Object.create(null);
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for (const line of lines) {
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const m = line.match(/^(.*)\s-\s([0-9.]+)\s*$/);
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if (!m) continue;
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const left = m[1].trim();
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const val = parseFloat(m[2]);
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if (Number.isNaN(val)) continue;
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const u = left.lastIndexOf('_');
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const common = u >= 0 ? left.slice(u + 1) : left;
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map[common] = val; map[left] = val;
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}
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const decoder = document.createElement('textarea');
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document.querySelectorAll('#speciesTable tbody tr').forEach(row => {
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decoder.innerHTML = row.getAttribute('data-comname') || '';
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const commonName = decoder.value;
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if (Object.prototype.hasOwnProperty.call(map, commonName)) {
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const v = map[commonName];
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const cell = row.querySelector('td.threshold');
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cell.textContent = v.toFixed(4);
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cell.style.color = v >= sfThresh ? 'green' : 'red';
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cell.dataset.sort = v.toFixed(4);
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}
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});
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}).catch(() => {
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console.warn('Probability load failed.');
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});
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}
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/* ---------- Files on Disk column auto-load ---------- */
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function addDiskCounts() {
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return get(scriptsBase + 'species_tools.php?diskcounts=1').then(t => {
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let counts; try { counts = JSON.parse(t); } catch { console.warn('Could not parse disk counts'); return; }
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const table = document.getElementById('speciesTable');
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const headerRow = table.tHead.rows[0];
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// Insert header before last column (Delete)
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const deleteHeader = headerRow.lastElementChild;
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const th = document.createElement('th');
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th.textContent = 'Files on Disk';
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headerRow.insertBefore(th, deleteHeader);
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const colIndex = headerRow.cells.length - 2; // new column index
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th.addEventListener('click', () => sortTable(colIndex));
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const decoder = document.createElement('textarea');
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document.querySelectorAll('#speciesTable tbody tr').forEach(tr => {
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decoder.innerHTML = tr.getAttribute('data-comname') || '';
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const name = decoder.value;
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const lookup = name.replace(/'/g, '');
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const count = counts[lookup] || 0;
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const td = document.createElement('td');
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td.textContent = count;
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td.dataset.sort = count;
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tr.insertBefore(td, tr.lastElementChild); // before Delete cell
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});
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}).catch(() => {
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console.warn('Disk counts load failed.');
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});
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}
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function generateMiniGraph(elem, comname, days = 30) {
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var xhr = new XMLHttpRequest();
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xhr.open('GET', '/todays_detections.php?comname=' + encodeURIComponent(comname) + '&days=' + days);
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xhr.onload = function() {
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if (xhr.status === 200) {
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var detections = JSON.parse(xhr.responseText);
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if (typeof(window.chartWindow) !== 'undefined') {
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document.body.removeChild(window.chartWindow);
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window.chartWindow = undefined;
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}
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var chartWindow = document.createElement('div');
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chartWindow.className = 'chartdiv';
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document.body.appendChild(chartWindow);
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var canvas = document.createElement('canvas');
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canvas.width = chartWindow.offsetWidth;
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canvas.height = chartWindow.offsetHeight - 40;
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chartWindow.appendChild(canvas);
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var ctx = canvas.getContext('2d');
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var chart = new Chart(ctx, {
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type: 'line',
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data: {
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labels: detections.map(function(item){ return item.date; }),
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datasets: [{
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label: 'Detections',
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data: detections.map(function(item){ return item.count; }),
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backgroundColor: '#9fe29b',
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borderColor: '#77c487',
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borderWidth: 1,
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lineTension: 0.3,
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pointRadius: 1,
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pointHitRadius: 10,
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trendlineLinear: {
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style: 'rgba(55, 99, 64, 0.5)',
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lineStyle: 'solid',
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width: 1.5
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}
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}]
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},
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options: {
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layout: { padding: { right: 10 } },
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title: { display: true, text: 'Detections Over ' + days + 'd' },
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legend: { display: false },
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scales: {
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xAxes: [{
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display: true,
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gridLines: { display: true },
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ticks: {
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autoSkip: true,
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maxTicksLimit: 6,
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callback: function(value) { return value.substring(5); }
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}
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}],
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yAxes: [{
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gridLines: { display: false },
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ticks: { beginAtZero: true, precision: 0, maxTicksLimit: 5 }
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}]
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}
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}
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});
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var buttonRect = elem.getBoundingClientRect();
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var chartRect = chartWindow.getBoundingClientRect();
|
|
if (window.innerWidth < 700) {
|
|
chartWindow.style.left = 'calc(75% - ' + (chartRect.width / 2) + 'px)';
|
|
} else {
|
|
chartWindow.style.left = (buttonRect.right + 10) + 'px';
|
|
}
|
|
|
|
var buttonCenter = buttonRect.top + (buttonRect.height / 2);
|
|
var chartHeight = chartWindow.offsetHeight;
|
|
var chartTop = buttonCenter - (chartHeight / 2);
|
|
chartWindow.style.top = chartTop + 'px';
|
|
|
|
var closeButton = document.createElement('button');
|
|
closeButton.id = 'chartcb';
|
|
closeButton.innerText = 'X';
|
|
closeButton.style.position = 'absolute';
|
|
closeButton.style.top = '5px';
|
|
closeButton.style.right = '5px';
|
|
closeButton.addEventListener('click', function() {
|
|
document.body.removeChild(chartWindow);
|
|
window.chartWindow = undefined;
|
|
});
|
|
chartWindow.appendChild(closeButton);
|
|
|
|
var selector = document.createElement('select');
|
|
[30, 180, 360, 720, 1080].forEach(function(opt) {
|
|
var option = document.createElement('option');
|
|
option.value = opt;
|
|
option.text = opt + 'd';
|
|
if (opt === days) option.selected = true;
|
|
selector.appendChild(option);
|
|
});
|
|
selector.addEventListener('change', function() {
|
|
generateMiniGraph(elem, comname, parseInt(this.value));
|
|
});
|
|
selector.style.position = 'absolute';
|
|
selector.style.bottom = '5px';
|
|
selector.style.left = '5px';
|
|
chartWindow.appendChild(selector);
|
|
|
|
window.chartWindow = chartWindow;
|
|
}
|
|
};
|
|
xhr.send();
|
|
}
|
|
|
|
window.addEventListener('scroll', function() {
|
|
var charts = document.querySelectorAll('.chartdiv');
|
|
charts.forEach(function(chart) {
|
|
chart.parentNode.removeChild(chart);
|
|
window.chartWindow = undefined;
|
|
});
|
|
});
|
|
|
|
/* ---------- toggles / delete ---------- */
|
|
function toggleSpecies(list, species, action) {
|
|
get(scriptsBase + 'species_tools.php?toggle=' + list + '&species=' + encodeURIComponent(species) + '&action=' + action)
|
|
.then(t => { if (t.trim() === 'OK') location.reload(); });
|
|
}
|
|
function deleteSpecies(species) {
|
|
get(scriptsBase + 'species_tools.php?getcounts=' + encodeURIComponent(species)).then(t => {
|
|
let info; try { info = JSON.parse(t); } catch { alert('Could not parse count response'); return; }
|
|
if (!confirm('Delete ' + info.count + ' detections and local audio and png files for ' + species + '?')) return;
|
|
get(scriptsBase + 'species_tools.php?delete=' + encodeURIComponent(species)).then(t2 => {
|
|
try { const res = JSON.parse(t2); alert('Deleted ' + res.lines + ' detections and ' + res.files + ' files for ' + species); }
|
|
catch { alert('Deletion complete'); }
|
|
location.reload();
|
|
});
|
|
});
|
|
}
|
|
|
|
/* ---------- Sorting with persistence ---------- */
|
|
function sortTable(n) {
|
|
const table = document.getElementById('speciesTable');
|
|
const tbody = table.tBodies[0];
|
|
const rows = Array.from(tbody.rows);
|
|
const asc = table.getAttribute('data-sort-' + n) !== 'asc';
|
|
rows.sort((a, b) => {
|
|
let x = a.cells[n].dataset.sort ?? a.cells[n].innerText.toLowerCase();
|
|
let y = b.cells[n].dataset.sort ?? b.cells[n].innerText.toLowerCase();
|
|
const nx = parseFloat(x), ny = parseFloat(y);
|
|
if (!Number.isNaN(nx) && !Number.isNaN(ny)) { x = nx; y = ny; }
|
|
return (x < y ? (asc ? -1 : 1) : (x > y ? (asc ? 1 : -1) : 0));
|
|
});
|
|
rows.forEach(r => tbody.appendChild(r));
|
|
table.setAttribute('data-sort-' + n, asc ? 'asc' : 'desc');
|
|
try { localStorage.setItem('speciesSortCol', String(n)); localStorage.setItem('speciesSortAsc', asc ? '1' : '0'); } catch(e){}
|
|
}
|
|
function applySavedSort() {
|
|
const table = document.getElementById('speciesTable');
|
|
const col = parseInt(localStorage.getItem('speciesSortCol') || '', 10);
|
|
const asc = localStorage.getItem('speciesSortAsc');
|
|
if (!Number.isFinite(col)) return;
|
|
sortTable(col);
|
|
const isAscNow = table.getAttribute('data-sort-' + col) === 'asc';
|
|
if ((asc === '1') !== isAscNow) sortTable(col);
|
|
}
|
|
|
|
/* ---------- Search with persistence ---------- */
|
|
const q = document.getElementById('q');
|
|
const matchCount = document.getElementById('matchCount');
|
|
function applyFilter() {
|
|
const needle = (q.value || '').trim().toLowerCase();
|
|
let shown = 0, total = 0;
|
|
document.querySelectorAll('#speciesTable tbody tr').forEach(tr => {
|
|
total++;
|
|
const txt = tr.innerText.toLowerCase();
|
|
const vis = txt.includes(needle);
|
|
tr.style.display = vis ? '' : 'none';
|
|
if (vis) shown++;
|
|
});
|
|
matchCount.textContent = total ? `${shown} / ${total}` : '';
|
|
try { localStorage.setItem('speciesFilter', q.value); } catch(e){}
|
|
}
|
|
q.addEventListener('input', applyFilter);
|
|
|
|
/* ---------- boot ---------- */
|
|
document.addEventListener('DOMContentLoaded', () => {
|
|
try { const saved = localStorage.getItem('speciesFilter'); if (saved !== null) q.value = saved; } catch(e){}
|
|
applyFilter();
|
|
applySavedSort();
|
|
// Auto-load both heavy enrichments
|
|
loadThresholds();
|
|
addDiskCounts();
|
|
});
|
|
</script>
|