Automatically include URI-encoded jats.csl for jats output.

This way people can do

    pandoc -s -t jats --filter pandoc-citeproc

and it will just work.  If they want to specify a stylesheet,
they still can.

4 files changed, 223 insertions, 2 deletions

diff --git a/COPYRIGHT b/COPYRIGHT
index c7b0f58f7..9d6a78da5 100644
--- a/COPYRIGHT
+++ b/COPYRIGHT
@@ -110,3 +110,8 @@ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 ------------------------------------------------------------------------
 The template pandoc.jats is Copyright 2013--15 Martin Fenner,
 released under GPL version 2 or later.
+
+The file data/jats.csl is derived from a csl file by Martin Fenner,
+revised by Martin Paul Eve and then John MacFarlane.
+"This work is licensed under a Creative Commons Attribution-ShareAlike 3.0
+License. Originally by Martin Fenner."
diff --git a/data/jats.csl b/data/jats.csl
new file mode 100644
index 000000000..64872863c
--- /dev/null
+++ b/data/jats.csl
@@ -0,0 +1,208 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" default-locale="en-US">
+  <info>
+    <title>Journal Article Tag Suite</title>
+    <title-short>JATS</title-short>
+    <id>http://www.zotero.org/styles/journal-article-tag-suite</id>
+    <link href="https://github.com/MartinPaulEve/JATS-CSL/blob/master/jats.csl" rel="self"/>
+    <link rel="documentation" href="http://jats.nlm.nih.gov/archiving/tag-library/1.0/index.html"/>
+    <author>
+      <name>Martin Paul Eve</name>
+      <email>martin@martineve.com</email>
+    </author>
+    <category citation-format="numeric"/>
+    <category field="medicine"/>
+    <category field="biology"/>
+    <summary>Use this style to generate bibliographic data in Journal Article Tagging Suite (JATS) 1.0 XML format</summary>
+    <updated>2014-06-21T17:41:26+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License. Originally by Martin Fenner.</rights>
+  </info>
+  <locale xml:lang="en">
+    <terms>
+        <term name="et-al">{{jats}}&lt;etal/&gt;{{/jats}}</term>
+    </terms>
+  </locale>
+  <macro name="citation-number">
+    <text variable="citation-number" prefix="{{jats}}id=&quot;ref-{{/jats}}" suffix="{{jats}}&quot;&gt;{{/jats}}"/>
+  </macro>
+  <macro name="author">
+    <names variable="author">
+        <name prefix="{{jats}}&lt;name&gt;{{/jats}}" suffix="{{jats}}&lt;/name&gt;{{/jats}}" name-as-sort-order="all" sort-separator="">
+            <name-part name="family" text-case="capitalize-first" prefix="{{jats}}&lt;surname&gt;{{/jats}}" suffix="{{jats}}&lt;/surname&gt;{{/jats}}"/>
+            <name-part name="given" text-case="capitalize-first" prefix="{{jats}}&lt;given-names&gt;{{/jats}}" suffix="{{jats}}&lt;/given-names&gt;{{/jats}}"/>
+      </name>
+      <substitute>
+        <names variable="editor"/>
+      </substitute>
+    </names>
+  </macro>
+
+  <macro name="editor">
+    <names variable="editor" prefix="{{jats}}&lt;person-group person-group-type=&quot;editor&quot;&gt;{{/jats}}" suffix="{{jats}}&lt;/person-group&gt;{{/jats}}">
+      <name prefix="{{jats}}&lt;name&gt;{{/jats}}" suffix="{{jats}}&lt;/name&gt;{{/jats}}" name-as-sort-order="all" sort-separator="">
+        <name-part name="family" text-case="capitalize-first" prefix="{{jats}}&lt;surname&gt;{{/jats}}" suffix="{{jats}}&lt;/surname&gt;{{/jats}}"/>
+        <name-part name="given" text-case="capitalize-first" prefix="{{jats}}&lt;given-names&gt;{{/jats}}" suffix="{{jats}}&lt;/given-names&gt;{{/jats}}"/>
+      </name>
+      <substitute>
+        <names variable="editor"/>
+      </substitute>
+    </names>
+  </macro>
+
+  <macro name="editor">
+    <group delimiter=": ">
+      <names variable="editor">
+        <name prefix="{{jats}}&lt;name&gt;{{/jats}}" suffix="{{jats}}&lt;/name&gt;{{/jats}}" name-as-sort-order="all" sort-separator="">
+          <name-part name="family" text-case="capitalize-first" prefix="{{jats}}&lt;surname&gt;{{/jats}}" suffix="{{jats}}&lt;/surname&gt;{{/jats}}"/>
+          <name-part name="given" text-case="capitalize-first" prefix="{{jats}}&lt;given-names&gt;{{/jats}}" suffix="{{jats}}&lt;given-names&gt;{{/jats}}"/>
+        </name>
+      </names>
+    </group>
+  </macro>
+  <macro name="title">
+    <choose>
+      <if type="book" match="any">
+        <group prefix="{{jats}}&lt;source&gt;{{/jats}}" suffix="{{jats}}&lt;/source&gt;{{/jats}}">
+	        <text variable="title"/>
+				</group>			
+			</if>
+      <else>
+        <group prefix="{{jats}}&lt;article-title&gt;{{/jats}}" suffix="{{jats}}&lt;/article-title&gt;{{/jats}}">
+	        <text variable="title"/>
+				</group>
+      </else>
+    </choose>
+  </macro>
+  <macro name="container-title">
+    <text variable="container-title" form="short" prefix="{{jats}}&lt;source&gt;{{/jats}}" suffix="{{jats}}&lt;/source&gt;{{/jats}}"/>
+  </macro>
+  <macro name="publisher">
+    <text variable="publisher" prefix="{{jats}}&lt;publisher-name&gt;{{/jats}}" suffix="{{jats}}&lt;/publisher-name&gt;{{/jats}}"/>
+    <text variable="publisher-place" prefix="{{jats}}&lt;publisher-loc&gt;{{/jats}}" suffix="{{jats}}&lt;/publisher-loc&gt;{{/jats}}"/>
+  </macro>
+  <macro name="link">
+    <choose>
+      <if match="any" variable="DOI">
+        <group prefix="{{jats}}&lt;pub-id pub-id-type=&quot;doi&quot;&gt;{{/jats}}" suffix="{{jats}}&lt;/pub-id&gt;{{/jats}}">
+          <text variable="DOI"/>
+        </group>
+      </if>
+    </choose>
+    <choose>
+      <if match="any" variable="PMID">
+        <group prefix="{{jats}}&lt;ext-link ext-link-type=&quot;pmid&quot; {{/jats}}" suffix="{{jats}}&lt;/ext-link&gt;{{/jats}}">
+          <text variable="PMID" prefix="{{jats}}xlink:href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/{{/jats}}" suffix="{{jats}}&quot; xlink:type=&quot;simple&quot;&gt;{{/jats}}"/>
+          <text variable="PMID"/>
+        </group>
+      </if>
+    </choose>
+    <choose>
+      <if variable="URL" match="any">
+        <group prefix="{{jats}}&lt;ext-link ext-link-type=&quot;uri&quot; {{/jats}}" suffix="{{jats}}&lt;/ext-link&gt;{{/jats}}">
+          <text variable="URL" prefix="{{jats}}xlink:href=&quot;{{/jats}}" suffix="{{jats}}&quot; xlink:type=&quot;simple&quot;&gt;{{/jats}}"/>
+          <text variable="URL"/>
+        </group>
+      </if>
+    </choose>
+  </macro>
+  <macro name="date">
+    <choose>
+      <if type="article-journal article-magazine article-newspaper report patent book" match="any">
+        <group prefix="{{jats}}&lt;date&gt;{{/jats}}" suffix="{{jats}}&lt;/date&gt;{{/jats}}">
+          <date variable="issued">
+            <date-part name="day" form="numeric-leading-zeros" prefix="{{jats}}&lt;day&gt;{{/jats}}" suffix="{{jats}}&lt;/day&gt;{{/jats}}"/>
+            <date-part name="month" form="numeric-leading-zeros" prefix="{{jats}}&lt;month&gt;{{/jats}}" suffix="{{jats}}&lt;/month&gt;{{/jats}}"/>
+            <date-part name="year" prefix="{{jats}}&lt;year&gt;{{/jats}}" suffix="{{jats}}&lt;/year&gt;{{/jats}}"/>
+          </date>
+        </group>
+      </if>
+      <else>
+        <group prefix="{{jats}}&lt;date-in-citation content-type=&quot;access-date&quot;{{/jats}}" suffix="{{jats}}&lt;/date-in-citation&gt;{{/jats}}">
+          <date variable="accessed" prefix="{{jats}} iso-8601-date=&quot;{{/jats}}" suffix="{{jats}}&quot;&gt;{{/jats}}">
+            <date-part name="year"/>
+            <date-part name="month" form="numeric-leading-zeros" prefix="{{jats}}-{{/jats}}"/>
+            <date-part name="day" form="numeric-leading-zeros" prefix="{{jats}}-{{/jats}}"/>
+          </date>
+          <date variable="accessed">
+            <date-part name="day" prefix="{{jats}}&lt;day&gt;{{/jats}}" suffix="{{jats}}&lt;/day&gt;{{/jats}}"/>
+            <date-part name="month" form="numeric-leading-zeros" prefix="{{jats}}&lt;month&gt;{{/jats}}" suffix="{{jats}}&lt;/month&gt;{{/jats}}"/>
+            <date-part name="year" prefix="{{jats}}&lt;year&gt;{{/jats}}" suffix="{{jats}}&lt;/year&gt;{{/jats}}"/>
+          </date>
+        </group>
+      </else>
+    </choose>
+  </macro>
+  <macro name="location">
+    <choose>
+      <if type="article-journal article-magazine" match="any">
+        <text variable="volume" prefix="{{jats}}&lt;volume&gt;{{/jats}}" suffix="{{jats}}&lt;/volume&gt;{{/jats}}"/>
+        <text variable="issue" prefix="{{jats}}&lt;issue&gt;{{/jats}}" suffix="{{jats}}&lt;/issue&gt;{{/jats}}"/>
+      </if>
+    </choose>
+    <choose>
+      <if type="article-journal article-magazine article-newspaper chapter" match="any">
+        <text variable="page-first" prefix="{{jats}}&lt;fpage&gt;{{/jats}}" suffix="{{jats}}&lt;/fpage&gt;{{/jats}}"/>
+      </if>
+    </choose>
+  </macro>
+  <macro name="publication-type">
+    <group prefix="{{jats}} publication-type=&quot;{{/jats}}" suffix="{{jats}}&quot;&gt;{{/jats}}">
+      <choose>
+        <if type="article-journal article-magazine article-newspaper" match="any">
+          <text value="journal"/>
+        </if>
+        <else-if type="book" match="any">
+          <text value="book"/>
+        </else-if>
+        <else-if type="chapter" match="any">
+          <text value="bookchapter"/>
+        </else-if>
+        <else-if type="dataset" match="any">
+          <text value="dataset"/>
+        </else-if>
+        <else-if type="patent" match="any">
+          <text value="patent"/>
+        </else-if>
+        <else-if type="report" match="any">
+          <text value="report"/>
+        </else-if>
+        <else-if type="review" match="any">
+          <text value="review"/>
+        </else-if>
+        <else>
+          <text value="standard"/>
+        </else>
+      </choose>
+    </group>
+  </macro>
+  <citation collapse="citation-number">
+    <sort>
+      <key variable="citation-number"/>
+    </sort>
+    <layout delimiter=",">
+      <group prefix="{{jats}}&lt;xref ref-type=&quot;bibr&quot; rid=&quot;{{/jats}}" suffix="{{jats}}&lt;/xref&gt;{{/jats}}">
+        <text variable="citation-number" prefix="{{jats}}ref-{{/jats}}" suffix="{{jats}}&quot;&gt;{{/jats}}"/>
+        <text variable="citation-number"/>
+      </group>
+    </layout>
+  </citation>
+  <bibliography sort-separator="">
+    <layout>
+      <group prefix="{{jats}}&lt;ref {{/jats}}" suffix="{{jats}}&lt;/ref&gt;{{/jats}}">
+        <text macro="citation-number"/>
+        <group prefix="{{jats}}&lt;element-citation{{/jats}}" suffix="{{jats}}&lt;/element-citation&gt;{{/jats}}">
+          <text macro="publication-type"/>
+          <text macro="author" prefix="{{jats}}&lt;person-group person-group-type=&quot;author&quot;&gt;{{/jats}}" suffix="{{jats}}&lt;/person-group&gt;{{/jats}}"/>
+          <text macro="title" />
+          <text macro="container-title"/>
+          <text macro="editor"/>
+          <text macro="publisher"/>
+          <text macro="date"/>
+          <text macro="location"/>
+          <text macro="link"/>
+        </group>
+      </group>
+    </layout>
+  </bibliography>
+</style>
+
diff --git a/pandoc.cabal b/pandoc.cabal
index 33694dec0..1dfa74482 100644
--- a/pandoc.cabal
+++ b/pandoc.cabal
@@ -111,6 +111,8 @@ Data-Files:
                  data/pandoc.lua
                  -- bash completion template
                  data/bash_completion.tpl
+                 -- jats csl
+                 data/jats.csl
                  -- documentation
                  MANUAL.txt, COPYRIGHT
 Extra-Source-Files:
diff --git a/src/Text/Pandoc/App.hs b/src/Text/Pandoc/App.hs
index 0fc883792..e45d10254 100644
--- a/src/Text/Pandoc/App.hs
+++ b/src/Text/Pandoc/App.hs
@@ -73,7 +73,7 @@ import Text.Pandoc.Lua ( runLuaFilter )
 import Text.Pandoc.MediaBag (MediaBag, extractMediaBag, mediaDirectory)
 import Text.Pandoc.PDF (makePDF)
 import Text.Pandoc.Process (pipeProcess)
-import Text.Pandoc.SelfContained (makeSelfContained)
+import Text.Pandoc.SelfContained (makeSelfContained, makeDataURI)
 import Text.Pandoc.Shared (err, headerShift, openURL, readDataFile,
                            readDataFileUTF8, safeRead, tabFilter)
 import qualified Text.Pandoc.UTF8 as UTF8
@@ -386,10 +386,16 @@ convertWithOpts opts = do
                                  withMediaBag . r readerOpts) sources
                 return (mconcat (map fst pairs), mconcat (map snd pairs))
 
+  jatsCSL <- readDataFile datadir "jats.csl"
+  let jatsEncoded = makeDataURI ("application/xml", jatsCSL)
+  let metadata = if format == "jats"
+                    then ("csl", jatsEncoded) : optMetadata opts
+                    else optMetadata opts
+
   runIO' $ do
     (doc, media) <- sourceToDoc sources
     doc' <- (maybe return (extractMedia media) (optExtractMedia opts) >=>
-              return . flip (foldr addMetadata) (optMetadata opts) >=>
+              return . flip (foldr addMetadata) metadata >=>
               applyTransforms transforms >=>
               applyLuaFilters datadir (optLuaFilters opts) [format] >=>
               applyFilters datadir filters' [format]) doc