Moved bibliography processing into readers.

Previously this was done in src/pandoc.hs, which made it difficult
for library users.

* Removed readerCitations in ReaderOptions.
* Added readerReferences and readerCitationStyle to ReaderOptions.
* Moved use of processBiblio from main program to the
  markdown and LaTeX readers.

4 files changed, 43 insertions, 33 deletions

diff --git a/src/Text/Pandoc/Options.hs b/src/Text/Pandoc/Options.hs
index 834810859..27661ecd4 100644
--- a/src/Text/Pandoc/Options.hs
+++ b/src/Text/Pandoc/Options.hs
@@ -44,6 +44,7 @@ import Data.Set (Set)
 import qualified Data.Set as Set
 import Data.Default
 import Text.Pandoc.Highlighting (Style, pygments)
+import qualified Text.CSL as CSL
 
 -- | Individually selectable syntax extensions.
 data Extension =
@@ -141,11 +142,12 @@ data ReaderOptions = ReaderOptions{
        , readerOldDashes       :: Bool -- ^ Use pandoc <= 1.8.2.1 behavior
                                        --   in parsing dashes; -- is em-dash;
                                        --   - before numerial is en-dash
-       , readerCitations       :: [String] -- ^ List of available citations
+       , readerReferences      :: [CSL.Reference]  -- ^ Bibliographic references
+       , readerCitationStyle   :: Maybe CSL.Style -- ^ Citation style
        , readerApplyMacros     :: Bool -- ^ Apply macros to TeX math
        , readerIndentedCodeClasses :: [String] -- ^ Default classes for
                                        -- indented code blocks
-} deriving (Show, Read)
+} deriving (Show {- TODO need update in citeproc-hs , Read -})
 
 instance Default ReaderOptions
   where def = ReaderOptions{
@@ -157,7 +159,8 @@ instance Default ReaderOptions
                , readerColumns             = 80
                , readerTabStop             = 4
                , readerOldDashes           = False
-               , readerCitations           = []
+               , readerReferences          = []
+               , readerCitationStyle       = Nothing
                , readerApplyMacros         = True
                , readerIndentedCodeClasses = []
                }
diff --git a/src/Text/Pandoc/Readers/LaTeX.hs b/src/Text/Pandoc/Readers/LaTeX.hs
index bdbf8f100..458c114ff 100644
--- a/src/Text/Pandoc/Readers/LaTeX.hs
+++ b/src/Text/Pandoc/Readers/LaTeX.hs
@@ -36,6 +36,7 @@ module Text.Pandoc.Readers.LaTeX ( readLaTeX,
 import Text.Pandoc.Definition
 import Text.Pandoc.Shared
 import Text.Pandoc.Options
+import Text.Pandoc.Biblio (processBiblio)
 import Text.Pandoc.Parsing hiding ((<|>), many, optional, space)
 import qualified Text.Pandoc.UTF8 as UTF8
 import Data.Char ( chr, ord )
@@ -63,7 +64,10 @@ parseLaTeX = do
   let title' = stateTitle st
   let authors' = stateAuthors st
   let date' = stateDate st
-  return $ Pandoc (Meta title' authors' date') $ toList bs
+  refs <- getOption readerReferences
+  mbsty <- getOption readerCitationStyle
+  return $ processBiblio mbsty refs
+         $ Pandoc (Meta title' authors' date') $ toList bs
 
 type LP = Parser [Char] ParserState
 
diff --git a/src/Text/Pandoc/Readers/Markdown.hs b/src/Text/Pandoc/Readers/Markdown.hs
index 7ac68c856..ab8069a75 100644
--- a/src/Text/Pandoc/Readers/Markdown.hs
+++ b/src/Text/Pandoc/Readers/Markdown.hs
@@ -45,6 +45,8 @@ import Text.Pandoc.Readers.LaTeX ( rawLaTeXInline, rawLaTeXBlock )
 import Text.Pandoc.Readers.HTML ( htmlTag, htmlInBalanced, isInlineTag, isBlockTag,
                                   isTextTag, isCommentTag )
 import Text.Pandoc.XML ( fromEntities )
+import Text.Pandoc.Biblio (processBiblio)
+import qualified Text.CSL as CSL
 import Data.Monoid (mconcat, mempty)
 import Control.Applicative ((<$>), (<*), (*>), (<$))
 import Control.Monad
@@ -216,7 +218,10 @@ parseMarkdown = do
   (title, authors, date) <- option (mempty,return [],mempty) titleBlock
   blocks <- parseBlocks
   st <- getState
-  return $ B.setTitle (runF title st)
+  mbsty <- getOption readerCitationStyle
+  refs <- getOption readerReferences
+  return $ processBiblio mbsty refs
+         $ B.setTitle (runF title st)
          $ B.setAuthors (runF authors st)
          $ B.setDate (runF date st)
          $ B.doc $ runF blocks st
@@ -1542,7 +1547,7 @@ rawHtmlInline = do
 cite :: Parser [Char] ParserState (F Inlines)
 cite = do
   guardEnabled Ext_citations
-  getOption readerCitations >>= guard . not . null
+  getOption readerReferences >>= guard . not . null
   citations <- textualCite <|> normalCite
   return $ flip B.cite mempty <$> citations
 
@@ -1591,7 +1596,7 @@ citeKey = try $ do
   let internal p = try $ p >>~ lookAhead (letter <|> digit)
   rest <- many $ letter <|> digit <|> internal (oneOf ":.#$%&-_?<>~")
   let key = first:rest
-  citations' <- getOption readerCitations
+  citations' <- map CSL.refId <$> getOption readerReferences
   guard $ key `elem` citations'
   return (suppress_author, key)
 
diff --git a/src/pandoc.hs b/src/pandoc.hs
index 406469598..dfba4093d 100644
--- a/src/pandoc.hs
+++ b/src/pandoc.hs
@@ -52,7 +52,6 @@ import qualified Control.Exception as E
 import Control.Exception.Extensible ( throwIO )
 import qualified Text.Pandoc.UTF8 as UTF8
 import qualified Text.CSL as CSL
-import Text.Pandoc.Biblio
 import Control.Monad (when, unless, liftM)
 import Network.HTTP (simpleHTTP, mkRequest, getResponseBody, RequestMethod(..))
 import Network.URI (parseURI, isURI, URI(..))
@@ -924,6 +923,24 @@ main = do
           reffiles >>=
            return . map unescapeRefId . concat
 
+  mbsty <- if citeMethod == Citeproc && not (null refs)
+              then do
+                csl <- CSL.parseCSL =<<
+                        case mbCsl of
+                            Nothing      -> readDataFile datadir "default.csl"
+                            Just cslfile -> do
+                                  exists <- doesFileExist cslfile
+                                  if exists
+                                     then UTF8.readFile cslfile
+                                     else do
+                                       csldir <- getAppUserDataDirectory "csl"
+                                       print csldir
+                                       readDataFile datadir (replaceDirectory
+                                        (replaceExtension cslfile "csl") csldir)
+                abbrevs <- maybe (return []) CSL.readJsonAbbrevFile cslabbrevs
+                return $ Just csl { CSL.styleAbbrevs = abbrevs }
+              else return Nothing
+
   let sourceDir = if null sources
                      then "."
                      else takeDirectory (head sources)
@@ -935,7 +952,8 @@ main = do
                       , readerColumns = columns
                       , readerTabStop = tabStop
                       , readerOldDashes = oldDashes
-                      , readerCitations = map CSL.refId refs
+                      , readerReferences = refs
+                      , readerCitationStyle = mbsty
                       , readerIndentedCodeClasses = codeBlockClasses
                       , readerApplyMacros = not laTeXOutput
                       }
@@ -1004,26 +1022,6 @@ main = do
              then bottomUpM rtfEmbedImage doc0
              else return doc0
 
-  doc2 <- do
-          if citeMethod == Citeproc && not (null refs)
-             then do
-               csl <- CSL.parseCSL =<<
-                       case mbCsl of
-                            Nothing      -> readDataFile datadir "default.csl"
-                            Just cslfile -> do
-                                  exists <- doesFileExist cslfile
-                                  if exists
-                                     then UTF8.readFile cslfile
-                                     else do
-                                       csldir <- getAppUserDataDirectory "csl"
-                                       print csldir
-                                       readDataFile datadir (replaceDirectory
-                                                (replaceExtension cslfile "csl") csldir)
-               abbrevs <- maybe (return []) CSL.readJsonAbbrevFile cslabbrevs
-               let csl' = csl { CSL.styleAbbrevs = abbrevs }
-               return $ processBiblio csl' refs doc1
-             else return doc1
-
   let writeBinary :: B.ByteString -> IO ()
       writeBinary = B.writeFile (UTF8.encodePath outputFile)
 
@@ -1033,15 +1031,15 @@ main = do
 
   case getWriter writerName' of
     Left e -> err 9 e
-    Right (IOStringWriter f) -> f writerOptions doc2 >>= writerFn outputFile
-    Right (IOByteStringWriter f) -> f writerOptions doc2 >>= writeBinary
+    Right (IOStringWriter f) -> f writerOptions doc1 >>= writerFn outputFile
+    Right (IOByteStringWriter f) -> f writerOptions doc1 >>= writeBinary
     Right (PureStringWriter f)
       | pdfOutput -> do
-              res <- tex2pdf latexEngine $ f writerOptions doc2
+              res <- tex2pdf latexEngine $ f writerOptions doc1
               case res of
                    Right pdf -> writeBinary pdf
                    Left err' -> err 43 $ UTF8.toStringLazy err'
-      | otherwise -> selfcontain (f writerOptions doc2 ++
+      | otherwise -> selfcontain (f writerOptions doc1 ++
                                   ['\n' | not standalone'])
                       >>= writerFn outputFile . handleEntities
           where htmlFormat = writerName' `elem`