Issue warning for duplicate header identifiers.

As noted in the previous commit, an autogenerated identifier
may still coincide with an explicit identifier that is given
for a header later in the document, or with an identifier on
a div, span, link, or image. This commit adds a warning
in this case, so users can supply an explicit identifier.

* Added `DuplicateIdentifier` to LogMessage.
* Modified HTML, Org, MediaWiki readers so their custom
  state type is an instance of HasLogMessages.  This is necessary
  for `registerHeader` to issue warnings.

See #1745.

6 files changed, 46 insertions, 8 deletions

diff --git a/src/Text/Pandoc/Logging.hs b/src/Text/Pandoc/Logging.hs
index ba836b91a..3d2cc2287 100644
--- a/src/Text/Pandoc/Logging.hs
+++ b/src/Text/Pandoc/Logging.hs
@@ -62,6 +62,7 @@ data LogMessage =
   | CouldNotParseYamlMetadata String SourcePos
   | DuplicateLinkReference String SourcePos
   | DuplicateNoteReference String SourcePos
+  | DuplicateIdentifier String SourcePos
   | ReferenceNotFound String SourcePos
   | CircularReference String SourcePos
   | ParsingUnescaped String SourcePos
@@ -106,6 +107,11 @@ instance ToJSON LogMessage where
             "source" .= Text.pack (sourceName pos),
             "line" .= toJSON (sourceLine pos),
             "column" .= toJSON (sourceColumn pos)]
+      DuplicateIdentifier s pos ->
+           ["contents" .= Text.pack s,
+            "source" .= Text.pack (sourceName pos),
+            "line" .= toJSON (sourceLine pos),
+            "column" .= toJSON (sourceColumn pos)]
       ReferenceNotFound s pos ->
            ["contents" .= Text.pack s,
             "source" .= Text.pack (sourceName pos),
@@ -184,6 +190,8 @@ showLogMessage msg =
          "Duplicate link reference '" ++ s ++ "' at " ++ showPos pos
        DuplicateNoteReference s pos ->
          "Duplicate note reference '" ++ s ++ "' at " ++ showPos pos
+       DuplicateIdentifier s pos ->
+         "Duplicate identifier '" ++ s ++ "' at " ++ showPos pos
        ReferenceNotFound s pos ->
          "Reference not found for '" ++ s ++ "' at " ++ showPos pos
        CircularReference s pos ->
@@ -233,6 +241,7 @@ messageVerbosity msg =
        CouldNotParseYamlMetadata{}  -> WARNING
        DuplicateLinkReference{}     -> WARNING
        DuplicateNoteReference{}     -> WARNING
+       DuplicateIdentifier{}        -> WARNING
        ReferenceNotFound{}          -> WARNING
        CircularReference{}          -> WARNING
        CouldNotLoadIncludeFile{}    -> WARNING
@@ -249,4 +258,4 @@ messageVerbosity msg =
        CouldNotParseCSS{}           -> WARNING
        Fetching{}                   -> INFO
        NoTitleElement{}             -> WARNING
-       NoLangSpecified              -> INFO
\ No newline at end of file
+       NoLangSpecified              -> INFO
diff --git a/src/Text/Pandoc/Parsing.hs b/src/Text/Pandoc/Parsing.hs
index a616058bb..3058185da 100644
--- a/src/Text/Pandoc/Parsing.hs
+++ b/src/Text/Pandoc/Parsing.hs
@@ -1112,8 +1112,11 @@ type SubstTable = M.Map Key Inlines
 --  with its associated identifier.  If the identifier is null
 --  and the auto_identifers extension is set, generate a new
 --  unique identifier, and update the list of identifiers
---  in state.
-registerHeader :: (Stream s m a, HasReaderOptions st, HasHeaderMap st, HasIdentifierList st)
+--  in state.  Issue a warning if an explicit identifier
+--  is encountered that duplicates an earlier identifier
+--  (explict or automatically generated).
+registerHeader :: (Stream s m a, HasReaderOptions st,
+                    HasHeaderMap st, HasLogMessages st, HasIdentifierList st)
                => Attr -> Inlines -> ParserT s st m Attr
 registerHeader (ident,classes,kvs) header' = do
   ids <- extractIdentifierList <$> getState
@@ -1131,6 +1134,9 @@ registerHeader (ident,classes,kvs) header' = do
        return (id'',classes,kvs)
      else do
         unless (null ident) $ do
+          when (ident `Set.member` ids) $ do
+            pos <- getPosition
+            logMessage $ DuplicateIdentifier ident pos
           updateState $ updateIdentifierList $ Set.insert ident
           updateState $ updateHeaderMap $ insert' header' ident
         return (ident,classes,kvs)
diff --git a/src/Text/Pandoc/Readers/HTML.hs b/src/Text/Pandoc/Readers/HTML.hs
index 7e7d505ac..0af369469 100644
--- a/src/Text/Pandoc/Readers/HTML.hs
+++ b/src/Text/Pandoc/Readers/HTML.hs
@@ -83,14 +83,15 @@ readHtml opts inp = do
         blocks <- (fixPlains False) . mconcat <$> manyTill block eof
         meta <- stateMeta . parserState <$> getState
         bs' <- replaceNotes (B.toList blocks)
+        reportLogMessages
         return $ Pandoc meta bs'
       getError (errorMessages -> ms) = case ms of
                                          []    -> ""
                                          (m:_) -> messageString m
   result <- flip runReaderT def $
-         runParserT parseDoc
-         (HTMLState def{ stateOptions = opts } [] Nothing Set.empty M.empty)
-         "source" tags
+       runParserT parseDoc
+       (HTMLState def{ stateOptions = opts } [] Nothing Set.empty M.empty [])
+       "source" tags
   case result of
     Right doc -> return doc
     Left  err -> throwError $ PandocParseError $ getError err
@@ -110,7 +111,8 @@ data HTMLState =
      noteTable   :: [(String, Blocks)],
      baseHref    :: Maybe URI,
      identifiers :: Set.Set String,
-     headerMap   :: M.Map Inlines String
+     headerMap   :: M.Map Inlines String,
+     logMessages :: [LogMessage]
   }
 
 data HTMLLocal = HTMLLocal { quoteContext :: QuoteContext
@@ -376,7 +378,7 @@ ignore raw = do
   -- raw can be null for tags like <!DOCTYPE>; see paRawTag
   -- in this case we don't want a warning:
   unless (null raw) $
-    report $ SkippedContent raw pos
+    logMessage $ SkippedContent raw pos
   return mempty
 
 pHtmlBlock :: PandocMonad m => String -> TagParser m String
@@ -1092,6 +1094,10 @@ instance HasHeaderMap HTMLState where
   extractHeaderMap = headerMap
   updateHeaderMap  f s = s{ headerMap = f (headerMap s) }
 
+instance HasLogMessages HTMLState where
+  addLogMessage m s = s{ logMessages = m : logMessages s }
+  getLogMessages = reverse . logMessages
+
 -- This signature should be more general
 -- MonadReader HTMLLocal m => HasQuoteContext st m
 instance PandocMonad m => HasQuoteContext HTMLState (ReaderT HTMLLocal m) where
diff --git a/src/Text/Pandoc/Readers/MediaWiki.hs b/src/Text/Pandoc/Readers/MediaWiki.hs
index fa20ade07..b35f39aad 100644
--- a/src/Text/Pandoc/Readers/MediaWiki.hs
+++ b/src/Text/Pandoc/Readers/MediaWiki.hs
@@ -73,6 +73,7 @@ readMediaWiki opts s = do
                                             , mwCategoryLinks = []
                                             , mwHeaderMap = M.empty
                                             , mwIdentifierList = Set.empty
+                                            , mwLogMessages = []
                                             }
             (s ++ "\n")
   case parsed of
@@ -85,6 +86,7 @@ data MWState = MWState { mwOptions         :: ReaderOptions
                        , mwCategoryLinks   :: [Inlines]
                        , mwHeaderMap       :: M.Map Inlines String
                        , mwIdentifierList  :: Set.Set String
+                       , mwLogMessages     :: [LogMessage]
                        }
 
 type MWParser m = ParserT [Char] MWState m
@@ -100,6 +102,10 @@ instance HasIdentifierList MWState where
   extractIdentifierList     = mwIdentifierList
   updateIdentifierList f st = st{ mwIdentifierList = f $ mwIdentifierList st }
 
+instance HasLogMessages MWState where
+  addLogMessage m s = s{ mwLogMessages = m : mwLogMessages s }
+  getLogMessages = reverse . mwLogMessages
+
 --
 -- auxiliary functions
 --
@@ -187,6 +193,7 @@ parseMediaWiki = do
   let categories = if null categoryLinks
                       then mempty
                       else B.para $ mconcat $ intersperse B.space categoryLinks
+  reportLogMessages
   return $ B.doc $ bs <> categories
 
 --
diff --git a/src/Text/Pandoc/Readers/Org.hs b/src/Text/Pandoc/Readers/Org.hs
index cc3ed6003..5e509178d 100644
--- a/src/Text/Pandoc/Readers/Org.hs
+++ b/src/Text/Pandoc/Readers/Org.hs
@@ -35,6 +35,7 @@ import Text.Pandoc.Class (PandocMonad)
 import Text.Pandoc.Definition
 import Text.Pandoc.Error
 import Text.Pandoc.Options
+import Text.Pandoc.Parsing (reportLogMessages)
 
 import Control.Monad.Except (throwError)
 import Control.Monad.Reader (runReaderT)
@@ -59,4 +60,5 @@ parseOrg :: PandocMonad m => OrgParser m Pandoc
 parseOrg = do
   blocks' <- blockList
   meta'   <- meta
+  reportLogMessages
   return $ Pandoc meta' blocks'
diff --git a/src/Text/Pandoc/Readers/Org/ParserState.hs b/src/Text/Pandoc/Readers/Org/ParserState.hs
index 0bbe27991..6bed2a547 100644
--- a/src/Text/Pandoc/Readers/Org/ParserState.hs
+++ b/src/Text/Pandoc/Readers/Org/ParserState.hs
@@ -60,7 +60,9 @@ import qualified Data.Set as Set
 import Text.Pandoc.Builder (Blocks, Inlines, trimInlines)
 import Text.Pandoc.Definition (Meta (..), nullMeta)
 import Text.Pandoc.Options (ReaderOptions (..))
+import Text.Pandoc.Logging
 import Text.Pandoc.Parsing (HasHeaderMap (..), HasIdentifierList (..),
+                            HasLogMessages (..),
                             HasLastStrPosition (..), HasQuoteContext (..),
                             HasReaderOptions (..), ParserContext (..),
                             QuoteContext (..), SourcePos)
@@ -104,6 +106,7 @@ data OrgParserState = OrgParserState
   , orgStateOptions              :: ReaderOptions
   , orgStateParserContext        :: ParserContext
   , orgStateTodoSequences        :: [TodoSequence]
+  , orgLogMessages               :: [LogMessage]
   }
 
 data OrgParserLocal = OrgParserLocal { orgLocalQuoteContext :: QuoteContext }
@@ -130,6 +133,10 @@ instance HasHeaderMap OrgParserState where
   extractHeaderMap = orgStateHeaderMap
   updateHeaderMap  f s = s{ orgStateHeaderMap = f (orgStateHeaderMap s) }
 
+instance HasLogMessages OrgParserState where
+  addLogMessage msg st = st{ orgLogMessages = msg : orgLogMessages st }
+  getLogMessages st = reverse $ orgLogMessages st
+
 instance Default OrgParserState where
   def = defaultOrgParserState
 
@@ -150,6 +157,7 @@ defaultOrgParserState = OrgParserState
   , orgStateOptions = def
   , orgStateParserContext = NullState
   , orgStateTodoSequences = []
+  , orgLogMessages = []
   }
 
 optionsToParserState :: ReaderOptions -> OrgParserState