From 2169bc4975e154eb3ba002fcd82fa4db9ed7695b Mon Sep 17 00:00:00 2001
From: Alexandre <44178713+alexbelgium@users.noreply.github.com>
Date: Tue, 26 Aug 2025 08:45:57 +0200
Subject: [PATCH] Add species_tools.php for species management

---
 scripts/species_tools.php | 284 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 284 insertions(+)
 create mode 100644 scripts/species_tools.php

diff --git a/scripts/species_tools.php b/scripts/species_tools.php
new file mode 100644
index 0000000..ddeec81
--- /dev/null
+++ b/scripts/species_tools.php
@@ -0,0 +1,284 @@
+<?php
+/* Basic input sanitation */
+$_GET  = filter_input_array(INPUT_GET, FILTER_SANITIZE_STRING)  ?: [];
+$_POST = filter_input_array(INPUT_POST, FILTER_SANITIZE_STRING) ?: [];
+
+require_once __DIR__ . '/common.php';
+ensure_authenticated();
+
+$home = get_home();
+$db   = new SQLite3(__DIR__ . '/birds.db', SQLITE3_OPEN_READWRITE);
+$db->busyTimeout(1000);
+
+/* Paths / lists */
+$base_symlink   = $home . '/BirdSongs/Extracted/By_Date';
+$base           = realpath($base_symlink); // used only for safety checks
+
+$exclude_file   = __DIR__ . '/exclude_species_list.txt';
+$whitelist_file = __DIR__ . '/whitelist_species_list.txt';
+
+$excluded_species    = file_exists($exclude_file)   ? file($exclude_file,   FILE_IGNORE_NEW_LINES | FILE_SKIP_EMPTY_LINES) : [];
+$whitelisted_species = file_exists($whitelist_file) ? file($whitelist_file, FILE_IGNORE_NEW_LINES | FILE_SKIP_EMPTY_LINES) : [];
+
+$config    = get_config();
+$sf_thresh = isset($config['SF_THRESH']) ? (float)$config['SF_THRESH'] : 0.0;
+
+/* ---------- helpers (tiny, single-purpose) ---------- */
+function join_path(...$parts): string {
+  return preg_replace('#/+#', '/', implode('/', $parts));
+}
+function can_unlink(string $p): bool {
+  // unlink-able: symlink (even dangling) or regular file
+  return is_link($p) || is_file($p);
+}
+function under_base(string $path, string $base): bool {
+  if ($base === false) return false;
+  $baseReal = rtrim(realpath($base) ?: $base, DIRECTORY_SEPARATOR);
+
+  $resolved = realpath($path);
+  if ($resolved === false) {
+    $parent = realpath(dirname($path));
+    if ($parent === false) return false;
+    $resolved = $parent . DIRECTORY_SEPARATOR . basename($path);
+  }
+  return $resolved === $baseReal || strpos($resolved, $baseReal . DIRECTORY_SEPARATOR) === 0;
+}
+
+/**
+ * Collect detection count, files to delete (unique), first scientific name,
+ * and dirs to try rmdir later — for a given species.
+ */
+function collect_species_targets(SQLite3 $db, string $species, string $home, $base): array {
+  $stmt = $db->prepare('SELECT Date, Com_Name, Sci_Name, File_Name FROM detections WHERE Com_Name = :name');
+  ensure_db_ok($stmt);
+  $stmt->bindValue(':name', $species, SQLITE3_TEXT);
+  $res = $stmt->execute();
+
+  $count = 0;
+  $files = [];
+  $dirs  = [];
+  $sci   = null;
+
+  while ($row = $res->fetchArray(SQLITE3_ASSOC)) {
+    $count++;
+    if ($sci === null) $sci = $row['Sci_Name'];
+    $dir = str_replace([' ', "'"], ['_', ''], $row['Com_Name']);
+
+    $candidates = [
+      join_path($home, 'BirdSongs/Extracted/By_Date',        $row['Date'], $dir, $row['File_Name']),
+      join_path($home, 'BirdSongs/Extracted/By_Date/shifted', $row['Date'], $dir, $row['File_Name']),
+    ];
+
+    foreach ($candidates as $c) {
+      if (can_unlink($c) && under_base($c, $base)) {
+        $files[$c] = true; $dirs[] = dirname($c); continue;
+      }
+      $d = realpath(dirname($c));
+      if ($d !== false) {
+        $alt = $d . DIRECTORY_SEPARATOR . basename($c);
+        if (can_unlink($alt) && under_base($alt, $base)) {
+          $files[$alt] = true; $dirs[] = dirname($alt);
+        }
+      }
+    }
+  }
+  return [
+    'count' => $count,
+    'files' => array_keys($files),
+    'dirs'  => array_values(array_unique($dirs)),
+    'sci'   => $sci,
+  ];
+}
+
+/* ---------- toggle exclude/whitelist ---------- */
+if (isset($_GET['toggle'], $_GET['species'], $_GET['action'])) {
+  $list    = $_GET['toggle'];
+  $species = htmlspecialchars_decode($_GET['species'], ENT_QUOTES);
+  
+  if ($list === 'exclude') {
+    $file = $exclude_file;
+  } elseif ($list === 'whitelist') {
+    $file = $whitelist_file;
+  } else {
+    header('Content-Type: text/plain'); echo 'Invalid list type'; exit;
+  }
+
+  $lines = file_exists($file) ? file($file, FILE_IGNORE_NEW_LINES | FILE_SKIP_EMPTY_LINES) : [];
+  if ($_GET['action'] === 'add') {
+    if (!in_array($species, $lines, true)) $lines[] = $species;
+  } else {
+    $lines = array_values(array_filter($lines, fn($l) => $l !== $species));
+  }
+  file_put_contents($file, implode("\n", $lines) . (empty($lines) ? "" : "\n"));
+  header('Content-Type: text/plain'); echo 'OK'; exit;
+}
+
+/* ---------- count (keeps your old "getcounts=" API) ---------- */
+if (isset($_GET['getcounts'])) {
+  header('Content-Type: application/json');
+  if ($base === false) { http_response_code(500); exit(json_encode(['error' => 'Base directory not found'])); }
+  $species = htmlspecialchars_decode($_GET['getcounts'], ENT_QUOTES);
+  $info = collect_species_targets($db, $species, $home, $base);
+  echo json_encode(['count' => $info['count'], 'files' => count($info['files'])]); exit;
+}
+
+/* ---------- delete (keeps your old "delete=" API) ---------- */
+if (isset($_GET['delete'])) {
+  header('Content-Type: application/json');
+  if ($base === false) { http_response_code(500); exit(json_encode(['error' => 'Base directory not found'])); }
+  $species = htmlspecialchars_decode($_GET['delete'], ENT_QUOTES);
+  $info = collect_species_targets($db, $species, $home, $base);
+
+  $deleted = 0;
+  foreach ($info['files'] as $fp) {
+    if (!under_base($fp, $base)) continue;
+    if (can_unlink($fp) && @unlink($fp)) {
+      $deleted++;
+      // thumbnails: "file.wav.png" and "file.png"
+      foreach ([$fp . '.png', preg_replace('/\.[^.]+$/', '.png', $fp)] as $png) {
+        if (can_unlink($png)) @unlink($png);
+      }
+    }
+  }
+  foreach ($info['dirs'] as $dir) {
+    if (under_base($dir, $base)) @rmdir($dir); // best effort
+  }
+
+  // DB rows
+  $del = $db->prepare('DELETE FROM detections WHERE Com_Name = :name');
+  ensure_db_ok($del);
+  $del->bindValue(':name', $species, SQLITE3_TEXT);
+  $del->execute();
+  $lines_deleted = $db->changes();
+
+  echo json_encode(['lines' => $lines_deleted, 'files' => $deleted]); exit;
+}
+
+/* ---------- page (unchanged semantics; minor tidy) ---------- */
+$result = fetch_species_array('alphabetical');
+?>
+<style>
+  .circle-icon{display:inline-block;width:12px;height:12px;border:1px solid #777;border-radius:50%;cursor:pointer;}
+  .centered{max-width:1100px;margin:0 auto}
+  #speciesTable th{cursor:pointer}
+</style>
+
+<div class="centered">
+<table id="speciesTable">
+  <thead>
+    <tr>
+      <th onclick="sortTable(0)">Common Name</th>
+      <th onclick="sortTable(1)">Scientific Name</th>
+      <th onclick="sortTable(2)">Identifications</th>
+      <th onclick="sortTable(3)">Max Confidence</th>
+      <th onclick="sortTable(4)">Threshold</th>
+      <th onclick="sortTable(5)">Excluded</th>
+      <th onclick="sortTable(6)">Whitelisted</th>
+      <th>Delete</th>
+    </tr>
+  </thead>
+  <tbody>
+<?php while ($row = $result->fetchArray(SQLITE3_ASSOC)) {
+  $common = htmlspecialchars($row['Com_Name'], ENT_QUOTES);
+  $scient = htmlspecialchars($row['Sci_Name'], ENT_QUOTES);
+  $count  = (int)$row['Count'];
+  $max_confidence = round((float)$row['MaxConfidence'] * 100, 1);
+  $identifier = str_replace("'", '', $row['Sci_Name'].'_'.$row['Com_Name']);
+
+  $common_link = "<a href='views.php?view=Recordings&species="
+    . rawurlencode($row['Sci_Name']) . "'>{$common}</a>";
+
+  $is_excluded    = in_array($identifier, $excluded_species, true);
+  $is_whitelisted = in_array($identifier, $whitelisted_species, true);
+
+  $excl_cell = $is_excluded
+    ? "<img style='cursor:pointer;max-width:12px;max-height:12px' src='images/check.svg' onclick=\"toggleSpecies('exclude','".str_replace("'", '', $identifier)."','del')\">"
+    : "<span class='circle-icon' onclick=\"toggleSpecies('exclude','".str_replace("'", '', $identifier)."','add')\"></span>";
+
+  $white_cell = $is_whitelisted
+    ? "<img style='cursor:pointer;max-width:12px;max-height:12px' src='images/check.svg' onclick=\"toggleSpecies('whitelist','".str_replace("'", '', $identifier)."','del')\">"
+    : "<span class='circle-icon' onclick=\"toggleSpecies('whitelist','".str_replace("'", '', $identifier)."','add')\"></span>";
+
+  echo "<tr data-comname=\"{$common}\"><td>{$common_link}</td><td><i>{$scient}</i></td><td>{$count}</td>"
+     . "<td data-sort='{$max_confidence}'>{$max_confidence}%</td>"
+     . "<td class='threshold' data-sort='0'>0.0000</td>"
+     . "<td data-sort='".($is_excluded?0:1)."'>".$excl_cell."</td>"
+     . "<td data-sort='".($is_whitelisted?0:1)."'>".$white_cell."</td>"
+     . "<td><img style='cursor:pointer;max-width:20px' src='images/delete.svg' onclick=\"deleteSpecies('".addslashes($row['Com_Name'])."')\"></td></tr>";
+} ?>
+  </tbody>
+</table>
+</div>
+
+<script>
+const scriptsBase = 'scripts/';
+const sfThresh = <?php echo json_encode($sf_thresh, JSON_UNESCAPED_UNICODE); ?>;
+
+// tiny fetch helper
+const get = (url) => fetch(url, {cache:'no-store'}).then(r => r.text());
+
+function loadThresholds() {
+  get(scriptsBase + 'config.php?threshold=0').then(text => {
+    const lines = (text || '').split(/\r?\n/);
+    const map = Object.create(null);
+    for (const line of lines) {
+      const m = line.match(/^(.*)\s-\s([0-9.]+)\s*$/);
+      if (!m) continue;
+      const left = m[1].trim();
+      const val  = parseFloat(m[2]);
+      if (Number.isNaN(val)) continue;
+      const u = left.lastIndexOf('_');
+      const common = u >= 0 ? left.slice(u + 1) : left;
+      map[common] = val; map[left] = val;
+    }
+    const decoder = document.createElement('textarea');
+    document.querySelectorAll('#speciesTable tbody tr').forEach(row => {
+      decoder.innerHTML = row.getAttribute('data-comname') || '';
+      const commonName = decoder.value;
+      if (Object.prototype.hasOwnProperty.call(map, commonName)) {
+        const v = map[commonName];
+        const cell = row.querySelector('td.threshold');
+        cell.textContent = v.toFixed(4);
+        cell.style.color = v >= sfThresh ? 'green' : 'red';
+        cell.dataset.sort = v.toFixed(4);
+      }
+    });
+  });
+}
+document.addEventListener('DOMContentLoaded', loadThresholds);
+
+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 ' + info.files + ' 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();
+    });
+  });
+}
+
+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');
+}
+</script>