feat: Add user settings for NCBI API lookups with opt-out option

Author: jnton

content/content_script.js

@@ -371,6 +371,19 @@
         window._mdpiFilterRefFootnoteObserver = observer;
       }
 
+      // --- User Settings Container ---
+      if (!window.MDPIFilterSettings) window.MDPIFilterSettings = {};
+      // Load NCBI API enabled flag (default true)
+      chrome.storage.sync.get('ncbiApiEnabled', res => {
+        window.MDPIFilterSettings.ncbiApiEnabled = (res.ncbiApiEnabled !== false);
+      });
+      chrome.storage.onChanged.addListener(changes => {
+        if (changes.ncbiApiEnabled) {
+          window.MDPIFilterSettings.ncbiApiEnabled = changes.ncbiApiEnabled.newValue;
+          console.log("[MDPI Filter CS] NCBI API Enabled set to", changes.ncbiApiEnabled.newValue);
+        }
+      });
+
       if (chrome.runtime && chrome.runtime.id) {
         chrome.storage.sync.get({ 
           mode: 'highlight',
@@ -662,8 +675,8 @@
                 }
               }
 
-              // 2. NCBI API Check (if useNcbiApi is true and not already identified as MDPI)
-              if (!isMdpiResult && config.useNcbiApi) {
+              // 2. NCBI API Check (respect user setting for NCBI API lookups)
+              if (!isMdpiResult && window.MDPIFilterSettings?.ncbiApiEnabled !== false) {
                 // Try to find the primary link of the search result item.
                 // Common Google search result link structure:
                 let mainLinkElement = item.querySelector('div.yuRUbf > a[href]');
@@ -941,7 +954,7 @@
                 isMdpi = itemIsMdpiByDirectIdentification;
                 let itemIsMdpiByApi = false;
 
-                if (!isMdpi && activeConfig.useNcbiApi) {
+                if (!isMdpi && window.MDPIFilterSettings?.ncbiApiEnabled !== false) {
                   // console.log(`${logPrefix} Not MDPI by direct ID. Using NCBI API.`);
                   const pmidsToQuery = new Set();
                   const pmcidsToQuery = new Set();
@@ -1368,7 +1381,7 @@
                 }
 
                 // Log all current data-mdpi-filter-ref-id values for debugging
-                const allRefIds = Array.from(document.querySelectorAll('[data-mdpi-filter-ref-id]')).map(el => el.getAttribute('data-mdpi-filter-ref-id'));
+                const allRefIds = Array.from(document.querySelectorAll('[data-mdpi-filter-ref-id]')). map(el => el.getAttribute('data-mdpi-filter-ref-id'));
                 console.log('[MDPI Filter CS] All current data-mdpi-filter-ref-id values in DOM:', allRefIds);
 
                 if (target) {

content/google_content_checker.js

@@ -134,7 +134,10 @@ class GoogleContentChecker {
     console.log(`[MDPI Filter GoogleChecker DEBUG ${itemIdentifier}] No direct MDPI links found. Checking for potential indicators...`);
 
     // --- POTENTIAL MDPI CHECKS (Text or NCBI-confirmed IDs in links/text) ---
-    if (currentSettings.highlightPotentialMdpiSites) {
+    const ncbiEnabled = window.MDPIFilterSettings?.ncbiApiEnabled !== false;
+    if (ncbiEnabled && window.MDPIFilterNcbiApiHandler) {
+      console.log(`[MDPI Filter GoogleChecker DEBUG ${itemIdentifier}] NCBI API enabled by user, checking links and text...`);
+      
       const itemTextContent = item.textContent || '';
       let isPotential = false;
       let potentialDetailsArray = [];
@@ -153,7 +156,7 @@ class GoogleContentChecker {
       }
 
       // Check for NCBI-confirmed PMIDs/PMCIDs in links or text content
-      if (activeConfig.useNcbiApi && window.MDPIFilterNcbiApiHandler) {
+      if (ncbiEnabled && window.MDPIFilterNcbiApiHandler) {
         console.log(`[MDPI Filter GoogleChecker DEBUG ${itemIdentifier}] NCBI API enabled, checking links and text...`);
 
         // From links

content/ncbi_api_handler.js

@@ -7,6 +7,11 @@ if (typeof window.MDPIFilterNcbiApiHandler === 'undefined') {
   const MDPI_DOI_PREFIX = '10.3390'; // For identifying MDPI DOIs
 
   async function checkNcbiIdsForMdpi(ids, idType, runCache, ncbiApiCache) {
+    // Respect user opt-out for NCBI API
+    if (window.MDPIFilterSettings && window.MDPIFilterSettings.ncbiApiEnabled === false) {
+      console.log("[MDPI Filter NCBI API] Skipping lookup: user opt-out");
+      return false;
+    }
     // Filter out DOIs with fragments or invalid chars
     if (idType === 'doi') {
       ids = ids.map(id => id.split('#')[0].split('?')[0].trim())

options.html

@@ -36,6 +36,16 @@ <h2>Potential MDPI Site Highlighting (Google Search Only)</h2>
         <span>Enable Extension Logging</span>
       </label>
     </div>
+    <!-- Advanced Settings -->
+    <hr class="separator">
+    <p class="settings-title">Advanced Settings</p>
+    <div class="setting-item">
+      <label class="checkbox-label" for="ncbiApiEnabledOptions">
+        <input type="checkbox" id="ncbiApiEnabledOptions" name="ncbiApiEnabledOptions">
+        <span>Enable NCBI API lookups</span>
+        <span class="setting-warning">Disabling reduces accuracy, leading to missed or incorrect highlights.</span>
+      </label>
+    </div>
     <button id="save">Save</button>
     <div id="status"></div>
   </div>

options.js

@@ -12,22 +12,20 @@ function loadOptions() {
     mode: 'highlight',
     highlightPotentialMdpiSites: false,
     potentialMdpiHighlightColor: '#FFFF99',
-    loggingEnabled: false
+    loggingEnabled: false,
+    ncbiApiEnabled: true
   }, (settings) => {
     if (chrome.runtime.lastError) {
       console.error("Error loading options:", chrome.runtime.lastError);
       return;
     }
-    radios.forEach(r => r.checked = (r.value === settings.mode));
-    if (highlightPotentialMdpiCheckboxOptions) {
-      highlightPotentialMdpiCheckboxOptions.checked = settings.highlightPotentialMdpiSites;
-    }
-    if (potentialMdpiColorInputOptions) {
-      potentialMdpiColorInputOptions.value = settings.potentialMdpiHighlightColor;
-    }
-    if (loggingCheckboxOptions) {
-      loggingCheckboxOptions.checked = settings.loggingEnabled;
-    }
+    // populate UI
+    Array.from(radios).find(r => r.value === settings.mode).checked = true;
+    if (highlightPotentialMdpiCheckboxOptions) highlightPotentialMdpiCheckboxOptions.checked = settings.highlightPotentialMdpiSites;
+    if (potentialMdpiColorInputOptions) potentialMdpiColorInputOptions.value = settings.potentialMdpiHighlightColor;
+    if (loggingCheckboxOptions) loggingCheckboxOptions.checked = settings.loggingEnabled;
+    const ncbiCheckbox = document.getElementById('ncbiApiEnabledOptions');
+    if (ncbiCheckbox) ncbiCheckbox.checked = settings.ncbiApiEnabled;
   });
 }
 
@@ -36,12 +34,21 @@ function saveOptions() {
   const highlightPotential = highlightPotentialMdpiCheckboxOptions ? highlightPotentialMdpiCheckboxOptions.checked : false;
   const potentialColor = potentialMdpiColorInputOptions ? potentialMdpiColorInputOptions.value : '#FFFF99';
   const loggingEnabled = loggingCheckboxOptions ? loggingCheckboxOptions.checked : false;
+  const ncbiApiEnabled = document.getElementById('ncbiApiEnabledOptions')?.checked ?? true;
+  // Confirm if user is disabling NCBI API lookups
+  if (!ncbiApiEnabled) {
+    const proceed = confirm('Disabling NCBI API lookups will reduce detection accuracy and may miss or mislabel MDPI citations. Continue?');
+    if (!proceed) {
+      return; // Abort save
+    }
+  }
 
   chrome.storage.sync.set({
     mode: selectedMode,
     highlightPotentialMdpiSites: highlightPotential,
     potentialMdpiHighlightColor: potentialColor,
-    loggingEnabled
+    loggingEnabled,
+    ncbiApiEnabled
   }, () => {
     if (chrome.runtime.lastError) {
       status.textContent = 'Error saving options.';

popup.css

@@ -240,4 +240,11 @@ h2 {
   background-color: #fff; /* Ensure background for color swatch */
   margin-left: auto; /* Push color picker to the right if in flex container */
 }
+
+/* Warning text style */
+.setting-warning {
+  color: red;
+  font-size: 0.85em;
+  margin-left: 8px;
+}
 /* End Styles for new settings */

popup.html

@@ -69,6 +69,13 @@ <h1>MDPI Filter</h1>
           <input type="checkbox" id="loggingEnabled" name="loggingEnabled">
           <span>Enable Extension Logging</span>
         </label>
+      </div>
+      <div class="setting-item">
+        <label class="checkbox-label" for="ncbiApiEnabledPopup">
+          <input type="checkbox" id="ncbiApiEnabledPopup">
+          <span>Enable NCBI API lookups</span>
+          <span class="setting-warning">Disabling reduces accuracy, leading to missed or incorrect highlights.</span>
+        </label>
       </div>
        <!-- End New Settings -->
        <!-- Save button and status moved here -->

popup.js

@@ -56,18 +56,33 @@ document.addEventListener('DOMContentLoaded', () => {
     }
   });
 
-  // --- Save Mode Setting ---
+  // --- Load NCBI API setting ---
+  const ncbiPopupCheckbox = document.getElementById('ncbiApiEnabledPopup');
+  chrome.storage.sync.get({ ncbiApiEnabled: true }, settings => {
+    if (ncbiPopupCheckbox) ncbiPopupCheckbox.checked = settings.ncbiApiEnabled;
+  });
+
+  // --- Save all settings including NCBI API ---
   saveBtn.addEventListener('click', () => {
     const selectedMode = Array.from(radios).find(r => r.checked).value;
     const highlightPotential = highlightPotentialMdpiCheckbox ? highlightPotentialMdpiCheckbox.checked : false;
     const potentialColor = potentialMdpiColorInput ? potentialMdpiColorInput.value : '#FFFF99';
     const loggingEnabled = loggingEnabledCheckbox   ? loggingEnabledCheckbox.checked : false;
+    const ncbiEnabled = ncbiPopupCheckbox?.checked ?? true;
+    // Confirm if user is disabling NCBI API lookups
+    if (!ncbiEnabled) {
+      const proceed = confirm('Disabling NCBI API lookups will reduce detection accuracy and may miss or mislabel MDPI citations. Continue?');
+      if (!proceed) {
+        return; // Abort save
+      }
+    }
 
     chrome.storage.sync.set({
       mode: selectedMode,
       highlightPotentialMdpiSites: highlightPotential,
       potentialMdpiHighlightColor: potentialColor,
-      loggingEnabled
+      loggingEnabled,
+      ncbiApiEnabled: ncbiEnabled
     }, () => {
       if (chrome.runtime.lastError) {
         status.textContent = 'Error saving settings.';