From 6ad486c3c3922e4ac7dd5710f69c3ccf623e92b4 Mon Sep 17 00:00:00 2001
From: John MacFarlane <jgm@berkeley.edu>
Date: Thu, 30 Mar 2017 16:43:17 +0200
Subject: [PATCH] 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.
---
COPYRIGHT | 5 +
data/jats.csl | 208 +++++++++++++++++++++++++++++++++++++++++
pandoc.cabal | 2 +
src/Text/Pandoc/App.hs | 10 +-
4 files changed, 223 insertions(+), 2 deletions(-)
create mode 100644 data/jats.csl
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}}<etal/>{{/jats}}</term>
+ </terms>
+ </locale>
+ <macro name="citation-number">
+ <text variable="citation-number" prefix="{{jats}}id="ref-{{/jats}}" suffix="{{jats}}">{{/jats}}"/>
+ </macro>
+ <macro name="author">
+ <names variable="author">
+ <name prefix="{{jats}}<name>{{/jats}}" suffix="{{jats}}</name>{{/jats}}" name-as-sort-order="all" sort-separator="">
+ <name-part name="family" text-case="capitalize-first" prefix="{{jats}}<surname>{{/jats}}" suffix="{{jats}}</surname>{{/jats}}"/>
+ <name-part name="given" text-case="capitalize-first" prefix="{{jats}}<given-names>{{/jats}}" suffix="{{jats}}</given-names>{{/jats}}"/>
+ </name>
+ <substitute>
+ <names variable="editor"/>
+ </substitute>
+ </names>
+ </macro>
+
+ <macro name="editor">
+ <names variable="editor" prefix="{{jats}}<person-group person-group-type="editor">{{/jats}}" suffix="{{jats}}</person-group>{{/jats}}">
+ <name prefix="{{jats}}<name>{{/jats}}" suffix="{{jats}}</name>{{/jats}}" name-as-sort-order="all" sort-separator="">
+ <name-part name="family" text-case="capitalize-first" prefix="{{jats}}<surname>{{/jats}}" suffix="{{jats}}</surname>{{/jats}}"/>
+ <name-part name="given" text-case="capitalize-first" prefix="{{jats}}<given-names>{{/jats}}" suffix="{{jats}}</given-names>{{/jats}}"/>
+ </name>
+ <substitute>
+ <names variable="editor"/>
+ </substitute>
+ </names>
+ </macro>
+
+ <macro name="editor">
+ <group delimiter=": ">
+ <names variable="editor">
+ <name prefix="{{jats}}<name>{{/jats}}" suffix="{{jats}}</name>{{/jats}}" name-as-sort-order="all" sort-separator="">
+ <name-part name="family" text-case="capitalize-first" prefix="{{jats}}<surname>{{/jats}}" suffix="{{jats}}</surname>{{/jats}}"/>
+ <name-part name="given" text-case="capitalize-first" prefix="{{jats}}<given-names>{{/jats}}" suffix="{{jats}}<given-names>{{/jats}}"/>
+ </name>
+ </names>
+ </group>
+ </macro>
+ <macro name="title">
+ <choose>
+ <if type="book" match="any">
+ <group prefix="{{jats}}<source>{{/jats}}" suffix="{{jats}}</source>{{/jats}}">
+ <text variable="title"/>
+ </group>
+ </if>
+ <else>
+ <group prefix="{{jats}}<article-title>{{/jats}}" suffix="{{jats}}</article-title>{{/jats}}">
+ <text variable="title"/>
+ </group>
+ </else>
+ </choose>
+ </macro>
+ <macro name="container-title">
+ <text variable="container-title" form="short" prefix="{{jats}}<source>{{/jats}}" suffix="{{jats}}</source>{{/jats}}"/>
+ </macro>
+ <macro name="publisher">
+ <text variable="publisher" prefix="{{jats}}<publisher-name>{{/jats}}" suffix="{{jats}}</publisher-name>{{/jats}}"/>
+ <text variable="publisher-place" prefix="{{jats}}<publisher-loc>{{/jats}}" suffix="{{jats}}</publisher-loc>{{/jats}}"/>
+ </macro>
+ <macro name="link">
+ <choose>
+ <if match="any" variable="DOI">
+ <group prefix="{{jats}}<pub-id pub-id-type="doi">{{/jats}}" suffix="{{jats}}</pub-id>{{/jats}}">
+ <text variable="DOI"/>
+ </group>
+ </if>
+ </choose>
+ <choose>
+ <if match="any" variable="PMID">
+ <group prefix="{{jats}}<ext-link ext-link-type="pmid" {{/jats}}" suffix="{{jats}}</ext-link>{{/jats}}">
+ <text variable="PMID" prefix="{{jats}}xlink:href="http://www.ncbi.nlm.nih.gov/pubmed/{{/jats}}" suffix="{{jats}}" xlink:type="simple">{{/jats}}"/>
+ <text variable="PMID"/>
+ </group>
+ </if>
+ </choose>
+ <choose>
+ <if variable="URL" match="any">
+ <group prefix="{{jats}}<ext-link ext-link-type="uri" {{/jats}}" suffix="{{jats}}</ext-link>{{/jats}}">
+ <text variable="URL" prefix="{{jats}}xlink:href="{{/jats}}" suffix="{{jats}}" xlink:type="simple">{{/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}}<date>{{/jats}}" suffix="{{jats}}</date>{{/jats}}">
+ <date variable="issued">
+ <date-part name="day" form="numeric-leading-zeros" prefix="{{jats}}<day>{{/jats}}" suffix="{{jats}}</day>{{/jats}}"/>
+ <date-part name="month" form="numeric-leading-zeros" prefix="{{jats}}<month>{{/jats}}" suffix="{{jats}}</month>{{/jats}}"/>
+ <date-part name="year" prefix="{{jats}}<year>{{/jats}}" suffix="{{jats}}</year>{{/jats}}"/>
+ </date>
+ </group>
+ </if>
+ <else>
+ <group prefix="{{jats}}<date-in-citation content-type="access-date"{{/jats}}" suffix="{{jats}}</date-in-citation>{{/jats}}">
+ <date variable="accessed" prefix="{{jats}} iso-8601-date="{{/jats}}" suffix="{{jats}}">{{/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}}<day>{{/jats}}" suffix="{{jats}}</day>{{/jats}}"/>
+ <date-part name="month" form="numeric-leading-zeros" prefix="{{jats}}<month>{{/jats}}" suffix="{{jats}}</month>{{/jats}}"/>
+ <date-part name="year" prefix="{{jats}}<year>{{/jats}}" suffix="{{jats}}</year>{{/jats}}"/>
+ </date>
+ </group>
+ </else>
+ </choose>
+ </macro>
+ <macro name="location">
+ <choose>
+ <if type="article-journal article-magazine" match="any">
+ <text variable="volume" prefix="{{jats}}<volume>{{/jats}}" suffix="{{jats}}</volume>{{/jats}}"/>
+ <text variable="issue" prefix="{{jats}}<issue>{{/jats}}" suffix="{{jats}}</issue>{{/jats}}"/>
+ </if>
+ </choose>
+ <choose>
+ <if type="article-journal article-magazine article-newspaper chapter" match="any">
+ <text variable="page-first" prefix="{{jats}}<fpage>{{/jats}}" suffix="{{jats}}</fpage>{{/jats}}"/>
+ </if>
+ </choose>
+ </macro>
+ <macro name="publication-type">
+ <group prefix="{{jats}} publication-type="{{/jats}}" suffix="{{jats}}">{{/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}}<xref ref-type="bibr" rid="{{/jats}}" suffix="{{jats}}</xref>{{/jats}}">
+ <text variable="citation-number" prefix="{{jats}}ref-{{/jats}}" suffix="{{jats}}">{{/jats}}"/>
+ <text variable="citation-number"/>
+ </group>
+ </layout>
+ </citation>
+ <bibliography sort-separator="">
+ <layout>
+ <group prefix="{{jats}}<ref {{/jats}}" suffix="{{jats}}</ref>{{/jats}}">
+ <text macro="citation-number"/>
+ <group prefix="{{jats}}<element-citation{{/jats}}" suffix="{{jats}}</element-citation>{{/jats}}">
+ <text macro="publication-type"/>
+ <text macro="author" prefix="{{jats}}<person-group person-group-type="author">{{/jats}}" suffix="{{jats}}</person-group>{{/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