Also recognize links that are linked back to as footnote links

src/calibre/ebooks/oeb/display/extract.coffee

@@ -40,12 +40,14 @@ get_epub_type = (node, possible_values) ->
                 break
     return epub_type
 
-is_footnote_link = (node, url) ->
+is_footnote_link = (node, url, linked_to_anchors) ->
     if not url or url.substr(0, 'file://'.length).toLowerCase() != 'file://'
         return false  # Ignore non-local links
     epub_type = get_epub_type(node, ['noteref'])
     if epub_type and epub_type.toLowerCase() == 'noteref'
         return true
+    if epub_type and epub_type == 'link'
+        return false
 
     # Check if node or any of its first few parents have vertical-align set
     [x, num] = [node, 3]
@@ -63,6 +65,12 @@ is_footnote_link = (node, url) ->
         if style.verticalAlign in ['sub', 'super']
             return true
 
+    eid = node.getAttribute('id') or node.getAttribute('name')
+    if eid and linked_to_anchors.hasOwnProperty(eid)
+        # An <a href="..." id="..."> link that is linked back from some other
+        # file in the spine, most likely a footnote
+        return true
+
     return false
 
 is_epub_footnote = (node) ->
@@ -112,14 +120,8 @@ class CalibreExtract
         cnode = inline_styles(node)
         return cnode.outerHTML
 
-    get_footnote_data: () =>
-        ans = {}
-        for a in document.querySelectorAll('a[href]')
-            url = a.href  # .href returns the full URL while getAttribute() returns the value of the attribute
-            if not is_footnote_link(a, url)
-                continue
-            ans[url] = 1
-        return JSON.stringify(ans)
+    is_footnote_link: (a) ->
+        return is_footnote_link(a, a.href, py_bridge.value)
 
     show_footnote: (target, known_targets) ->
         if not target

src/calibre/ebooks/oeb/iterator/book.py

@@ -24,6 +24,7 @@ from calibre import (guess_type, prepare_string_for_xml,
 from calibre.ebooks.oeb.transforms.cover import CoverManager
 from calibre.ebooks.oeb.iterator.spine import (SpineItem, create_indexing_data)
 from calibre.ebooks.oeb.iterator.bookmarks import BookmarksMixin
+from calibre.ebooks.oeb.base import urlparse, urlunquote
 
 TITLEPAGE = CoverManager.SVG_TEMPLATE.decode('utf-8').replace(
         '__ar__', 'none').replace('__viewbox__', '0 0 600 800'
@@ -75,7 +76,7 @@ class EbookIterator(BookmarksMixin):
                     return i
 
     def __enter__(self, processed=False, only_input_plugin=False,
-                  run_char_count=True, read_anchor_map=True, view_kepub=False):
+                  run_char_count=True, read_anchor_map=True, view_kepub=False, read_links=True):
         ''' Convert an ebook file into an exploded OEB book suitable for
         display in viewers/preprocessing etc. '''
 
@@ -124,7 +125,7 @@ class EbookIterator(BookmarksMixin):
         ordered = [i for i in self.opf.spine if i.is_linear] + \
                   [i for i in self.opf.spine if not i.is_linear]
         self.spine = []
-        Spiny = partial(SpineItem, read_anchor_map=read_anchor_map,
+        Spiny = partial(SpineItem, read_anchor_map=read_anchor_map, read_links=read_links,
                 run_char_count=run_char_count, from_epub=self.book_format == 'EPUB')
         is_comic = plumber.input_fmt.lower() in {'cbc', 'cbz', 'cbr', 'cb7'}
         for i in ordered:
@@ -175,10 +176,29 @@ class EbookIterator(BookmarksMixin):
         if read_anchor_map:
             create_indexing_data(self.spine, self.toc)
 
+        self.verify_links()
+
         self.read_bookmarks()
 
         return self
 
+    def verify_links(self):
+        spine_paths = {s:s for s in self.spine}
+        for item in self.spine:
+            base = os.path.dirname(item)
+            for link in item.all_links:
+                try:
+                    p = urlparse(urlunquote(link))
+                except Exception:
+                    continue
+                if not p.scheme and not p.netloc and p.path:
+                    try:
+                        path = spine_paths[os.path.abspath(os.path.join(base, p.path))]
+                    except Exception:
+                        continue
+                    if not p.fragment or p.fragment in path.anchor_map:
+                        item.verified_links.add((path, p.fragment))
+
     def __exit__(self, *args):
         self._tdir.__exit__(*args)
         for x in self.delete_on_exit:

src/calibre/ebooks/oeb/iterator/spine.py

@@ -13,7 +13,7 @@ from functools import partial
 from operator import attrgetter
 from collections import namedtuple
 
-from calibre import guess_type
+from calibre import guess_type, replace_entities
 from calibre.ebooks.chardet import xml_to_unicode
 
 def character_count(html):
@@ -33,10 +33,18 @@ def anchor_map(html):
         ans[anchor] = ans.get(anchor, match.start())
     return ans
 
+def all_links(html):
+    ''' Return set of all links in the file '''
+    ans = set()
+    for match in re.finditer(
+            r'''<\s*[Aa]\s+.*?[hH][Rr][Ee][Ff]\s*=\s*(['"])(.+?)\1''', html, re.MULTILINE|re.DOTALL):
+        ans.add(replace_entities(match.group(2)))
+    return ans
+
 class SpineItem(unicode):
 
     def __new__(cls, path, mime_type=None, read_anchor_map=True,
-            run_char_count=True, from_epub=False):
+            run_char_count=True, from_epub=False, read_links=True):
         ppath = path.partition('#')[0]
         if not os.path.exists(path) and os.path.exists(ppath):
             path = ppath
@@ -62,6 +70,8 @@ class SpineItem(unicode):
             raw, obj.encoding = xml_to_unicode(raw)
         obj.character_count = character_count(raw) if run_char_count else 10000
         obj.anchor_map = anchor_map(raw) if read_anchor_map else {}
+        obj.all_links = all_links(raw) if read_links else set()
+        obj.verified_links = set()
         obj.start_page = -1
         obj.pages      = -1
         obj.max_page   = -1

src/calibre/gui2/viewer/documentview.py

@@ -1316,9 +1316,10 @@ class DocumentView(QWebView):  # {{{
         return QWebView.event(self, ev)
 
     def mouseReleaseEvent(self, ev):
-        url = self.document.mainFrame().hitTestContent(ev.pos()).linkUrl()
-        if url.isValid() and self.manager is not None:
-            fd = self.footnotes.get_footnote_data(url)
+        r = self.document.mainFrame().hitTestContent(ev.pos())
+        a, url = r.linkElement(), r.linkUrl()
+        if url.isValid() and not a.isNull() and self.manager is not None:
+            fd = self.footnotes.get_footnote_data(a, url)
             if fd:
                 self.footnotes.show_footnote(fd)
                 self.manager.show_footnote_view()

src/calibre/gui2/viewer/footnote.py

@@ -98,7 +98,6 @@ class Footnotes(object):
         settings.setUserStyleSheetUrl(source.userStyleSheetUrl())
 
     def clear(self):
-        self.footnote_data_cache = {}
         self.known_footnote_targets = defaultdict(set)
         self.showing_url = None
 
@@ -109,33 +108,22 @@ class Footnotes(object):
         except (AttributeError, ValueError):
             pass
 
-    def load_footnote_data(self, current_url):
-        fd = self.footnote_data_cache[current_url] = {}
-        try:
-            raw = self.view.document.javascript('window.calibre_extract.get_footnote_data()', typ='string')
-            for x in json.loads(raw or '{}'):
-                if x not in fd:
-                    qu = QUrl(x)
-                    path = qu.toLocalFile()
-                    spath = self.spine_path(path)
-                    if spath is not None:
-                        target = qu.fragment(QUrl.FullyDecoded)
-                        fd[qu.toString()] = (spath, target, qu)
-                        self.known_footnote_targets[spath].add(target)
-        except Exception:
-            prints('Failed to get footnote data, with error:')
-            import traceback
-            traceback.print_exc()
-        return fd
-
-    def get_footnote_data(self, qurl):
-        current_url = unicode(self.view.document.mainFrame().baseUrl().toLocalFile())
-        if not current_url:
+    def get_footnote_data(self, a, qurl):
+        current_path = unicode(self.view.document.mainFrame().baseUrl().toLocalFile())
+        if not current_path:
             return  # Not viewing a local file
-        fd = self.footnote_data_cache.get(current_url)
-        if fd is None:
-            fd = self.load_footnote_data(current_url)
-        return fd.get(qurl.toString())
+        dest_path = self.spine_path(qurl.toLocalFile())
+        if dest_path is not None:
+            linked_to_anchors = {anchor:0 for path, anchor in dest_path.verified_links if path == current_path}
+            self.view.document.bridge_value = linked_to_anchors
+            if a.evaluateJavaScript('calibre_extract.is_footnote_link(this)'):
+                if dest_path not in self.known_footnote_targets:
+                    self.known_footnote_targets[dest_path] = s = set()
+                    for item in self.view.manager.iterator.spine:
+                        for path, target in item.verified_links:
+                            if target and path == dest_path:
+                                s.add(target)
+                return (dest_path, qurl.fragment(QUrl.FullyDecoded), qurl)
 
     def show_footnote(self, fd):
         path, target, self.showing_url = fd