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.
This commit is contained in:
John MacFarlane
parent
2f19b5daac
commit
6ad486c3c3
4 changed files with 223 additions and 2 deletions
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@ -110,3 +110,8 @@ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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------------------------------------------------------------------------
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The template pandoc.jats is Copyright 2013--15 Martin Fenner,
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released under GPL version 2 or later.
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The file data/jats.csl is derived from a csl file by Martin Fenner,
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revised by Martin Paul Eve and then John MacFarlane.
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"This work is licensed under a Creative Commons Attribution-ShareAlike 3.0
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License. Originally by Martin Fenner."
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208
data/jats.csl
Normal file
208
data/jats.csl
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@ -0,0 +1,208 @@
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<?xml version="1.0" encoding="utf-8"?>
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<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" default-locale="en-US">
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<info>
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<title>Journal Article Tag Suite</title>
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<title-short>JATS</title-short>
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<id>http://www.zotero.org/styles/journal-article-tag-suite</id>
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<link href="https://github.com/MartinPaulEve/JATS-CSL/blob/master/jats.csl" rel="self"/>
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<link rel="documentation" href="http://jats.nlm.nih.gov/archiving/tag-library/1.0/index.html"/>
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<author>
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<name>Martin Paul Eve</name>
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<email>martin@martineve.com</email>
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</author>
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<category citation-format="numeric"/>
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<category field="medicine"/>
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<category field="biology"/>
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<summary>Use this style to generate bibliographic data in Journal Article Tagging Suite (JATS) 1.0 XML format</summary>
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<updated>2014-06-21T17:41:26+00:00</updated>
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<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>
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</info>
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<locale xml:lang="en">
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<terms>
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<term name="et-al">{{jats}}<etal/>{{/jats}}</term>
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</terms>
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</locale>
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<macro name="citation-number">
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<text variable="citation-number" prefix="{{jats}}id="ref-{{/jats}}" suffix="{{jats}}">{{/jats}}"/>
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</macro>
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<macro name="author">
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<names variable="author">
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<name prefix="{{jats}}<name>{{/jats}}" suffix="{{jats}}</name>{{/jats}}" name-as-sort-order="all" sort-separator="">
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<name-part name="family" text-case="capitalize-first" prefix="{{jats}}<surname>{{/jats}}" suffix="{{jats}}</surname>{{/jats}}"/>
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<name-part name="given" text-case="capitalize-first" prefix="{{jats}}<given-names>{{/jats}}" suffix="{{jats}}</given-names>{{/jats}}"/>
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</name>
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<substitute>
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<names variable="editor"/>
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</substitute>
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</names>
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</macro>
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<macro name="editor">
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<names variable="editor" prefix="{{jats}}<person-group person-group-type="editor">{{/jats}}" suffix="{{jats}}</person-group>{{/jats}}">
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<name prefix="{{jats}}<name>{{/jats}}" suffix="{{jats}}</name>{{/jats}}" name-as-sort-order="all" sort-separator="">
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<name-part name="family" text-case="capitalize-first" prefix="{{jats}}<surname>{{/jats}}" suffix="{{jats}}</surname>{{/jats}}"/>
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<name-part name="given" text-case="capitalize-first" prefix="{{jats}}<given-names>{{/jats}}" suffix="{{jats}}</given-names>{{/jats}}"/>
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</name>
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<substitute>
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<names variable="editor"/>
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</substitute>
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</names>
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</macro>
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<macro name="editor">
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<group delimiter=": ">
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<names variable="editor">
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<name prefix="{{jats}}<name>{{/jats}}" suffix="{{jats}}</name>{{/jats}}" name-as-sort-order="all" sort-separator="">
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<name-part name="family" text-case="capitalize-first" prefix="{{jats}}<surname>{{/jats}}" suffix="{{jats}}</surname>{{/jats}}"/>
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<name-part name="given" text-case="capitalize-first" prefix="{{jats}}<given-names>{{/jats}}" suffix="{{jats}}<given-names>{{/jats}}"/>
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</name>
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</names>
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</group>
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</macro>
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<macro name="title">
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<choose>
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<if type="book" match="any">
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<group prefix="{{jats}}<source>{{/jats}}" suffix="{{jats}}</source>{{/jats}}">
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<text variable="title"/>
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</group>
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</if>
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<else>
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<group prefix="{{jats}}<article-title>{{/jats}}" suffix="{{jats}}</article-title>{{/jats}}">
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<text variable="title"/>
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</group>
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</else>
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</choose>
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</macro>
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<macro name="container-title">
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<text variable="container-title" form="short" prefix="{{jats}}<source>{{/jats}}" suffix="{{jats}}</source>{{/jats}}"/>
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</macro>
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<macro name="publisher">
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<text variable="publisher" prefix="{{jats}}<publisher-name>{{/jats}}" suffix="{{jats}}</publisher-name>{{/jats}}"/>
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<text variable="publisher-place" prefix="{{jats}}<publisher-loc>{{/jats}}" suffix="{{jats}}</publisher-loc>{{/jats}}"/>
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</macro>
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<macro name="link">
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<choose>
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<if match="any" variable="DOI">
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<group prefix="{{jats}}<pub-id pub-id-type="doi">{{/jats}}" suffix="{{jats}}</pub-id>{{/jats}}">
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<text variable="DOI"/>
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</group>
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</if>
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</choose>
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<choose>
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<if match="any" variable="PMID">
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<group prefix="{{jats}}<ext-link ext-link-type="pmid" {{/jats}}" suffix="{{jats}}</ext-link>{{/jats}}">
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<text variable="PMID" prefix="{{jats}}xlink:href="http://www.ncbi.nlm.nih.gov/pubmed/{{/jats}}" suffix="{{jats}}" xlink:type="simple">{{/jats}}"/>
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<text variable="PMID"/>
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</group>
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</if>
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</choose>
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<choose>
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<if variable="URL" match="any">
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<group prefix="{{jats}}<ext-link ext-link-type="uri" {{/jats}}" suffix="{{jats}}</ext-link>{{/jats}}">
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<text variable="URL" prefix="{{jats}}xlink:href="{{/jats}}" suffix="{{jats}}" xlink:type="simple">{{/jats}}"/>
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<text variable="URL"/>
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</group>
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</if>
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</choose>
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</macro>
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<macro name="date">
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<choose>
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<if type="article-journal article-magazine article-newspaper report patent book" match="any">
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<group prefix="{{jats}}<date>{{/jats}}" suffix="{{jats}}</date>{{/jats}}">
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<date variable="issued">
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<date-part name="day" form="numeric-leading-zeros" prefix="{{jats}}<day>{{/jats}}" suffix="{{jats}}</day>{{/jats}}"/>
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<date-part name="month" form="numeric-leading-zeros" prefix="{{jats}}<month>{{/jats}}" suffix="{{jats}}</month>{{/jats}}"/>
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<date-part name="year" prefix="{{jats}}<year>{{/jats}}" suffix="{{jats}}</year>{{/jats}}"/>
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</date>
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</group>
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</if>
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<else>
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<group prefix="{{jats}}<date-in-citation content-type="access-date"{{/jats}}" suffix="{{jats}}</date-in-citation>{{/jats}}">
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<date variable="accessed" prefix="{{jats}} iso-8601-date="{{/jats}}" suffix="{{jats}}">{{/jats}}">
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<date-part name="year"/>
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<date-part name="month" form="numeric-leading-zeros" prefix="{{jats}}-{{/jats}}"/>
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<date-part name="day" form="numeric-leading-zeros" prefix="{{jats}}-{{/jats}}"/>
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</date>
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<date variable="accessed">
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<date-part name="day" prefix="{{jats}}<day>{{/jats}}" suffix="{{jats}}</day>{{/jats}}"/>
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<date-part name="month" form="numeric-leading-zeros" prefix="{{jats}}<month>{{/jats}}" suffix="{{jats}}</month>{{/jats}}"/>
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<date-part name="year" prefix="{{jats}}<year>{{/jats}}" suffix="{{jats}}</year>{{/jats}}"/>
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</date>
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</group>
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</else>
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</choose>
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</macro>
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<macro name="location">
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<choose>
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<if type="article-journal article-magazine" match="any">
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<text variable="volume" prefix="{{jats}}<volume>{{/jats}}" suffix="{{jats}}</volume>{{/jats}}"/>
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<text variable="issue" prefix="{{jats}}<issue>{{/jats}}" suffix="{{jats}}</issue>{{/jats}}"/>
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</if>
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</choose>
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<choose>
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<if type="article-journal article-magazine article-newspaper chapter" match="any">
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<text variable="page-first" prefix="{{jats}}<fpage>{{/jats}}" suffix="{{jats}}</fpage>{{/jats}}"/>
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</if>
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</choose>
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</macro>
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<macro name="publication-type">
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<group prefix="{{jats}} publication-type="{{/jats}}" suffix="{{jats}}">{{/jats}}">
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<choose>
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<if type="article-journal article-magazine article-newspaper" match="any">
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<text value="journal"/>
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</if>
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<else-if type="book" match="any">
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<text value="book"/>
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</else-if>
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<else-if type="chapter" match="any">
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<text value="bookchapter"/>
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</else-if>
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<else-if type="dataset" match="any">
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<text value="dataset"/>
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</else-if>
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<else-if type="patent" match="any">
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<text value="patent"/>
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</else-if>
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<else-if type="report" match="any">
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<text value="report"/>
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</else-if>
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<else-if type="review" match="any">
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<text value="review"/>
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</else-if>
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<else>
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<text value="standard"/>
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</else>
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</choose>
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</group>
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</macro>
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<citation collapse="citation-number">
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<sort>
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<key variable="citation-number"/>
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</sort>
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<layout delimiter=",">
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<group prefix="{{jats}}<xref ref-type="bibr" rid="{{/jats}}" suffix="{{jats}}</xref>{{/jats}}">
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<text variable="citation-number" prefix="{{jats}}ref-{{/jats}}" suffix="{{jats}}">{{/jats}}"/>
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<text variable="citation-number"/>
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</group>
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</layout>
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</citation>
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<bibliography sort-separator="">
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<layout>
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<group prefix="{{jats}}<ref {{/jats}}" suffix="{{jats}}</ref>{{/jats}}">
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<text macro="citation-number"/>
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<group prefix="{{jats}}<element-citation{{/jats}}" suffix="{{jats}}</element-citation>{{/jats}}">
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<text macro="publication-type"/>
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<text macro="author" prefix="{{jats}}<person-group person-group-type="author">{{/jats}}" suffix="{{jats}}</person-group>{{/jats}}"/>
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<text macro="title" />
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<text macro="container-title"/>
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<text macro="editor"/>
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<text macro="publisher"/>
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<text macro="date"/>
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<text macro="location"/>
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<text macro="link"/>
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</group>
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</group>
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</layout>
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</bibliography>
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</style>
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@ -111,6 +111,8 @@ Data-Files:
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data/pandoc.lua
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-- bash completion template
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data/bash_completion.tpl
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-- jats csl
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data/jats.csl
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-- documentation
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MANUAL.txt, COPYRIGHT
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Extra-Source-Files:
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@ -73,7 +73,7 @@ import Text.Pandoc.Lua ( runLuaFilter )
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import Text.Pandoc.MediaBag (MediaBag, extractMediaBag, mediaDirectory)
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import Text.Pandoc.PDF (makePDF)
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import Text.Pandoc.Process (pipeProcess)
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import Text.Pandoc.SelfContained (makeSelfContained)
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import Text.Pandoc.SelfContained (makeSelfContained, makeDataURI)
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import Text.Pandoc.Shared (err, headerShift, openURL, readDataFile,
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readDataFileUTF8, safeRead, tabFilter)
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import qualified Text.Pandoc.UTF8 as UTF8
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@ -386,10 +386,16 @@ convertWithOpts opts = do
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withMediaBag . r readerOpts) sources
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return (mconcat (map fst pairs), mconcat (map snd pairs))
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jatsCSL <- readDataFile datadir "jats.csl"
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let jatsEncoded = makeDataURI ("application/xml", jatsCSL)
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let metadata = if format == "jats"
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then ("csl", jatsEncoded) : optMetadata opts
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else optMetadata opts
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runIO' $ do
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(doc, media) <- sourceToDoc sources
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doc' <- (maybe return (extractMedia media) (optExtractMedia opts) >=>
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return . flip (foldr addMetadata) (optMetadata opts) >=>
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return . flip (foldr addMetadata) metadata >=>
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applyTransforms transforms >=>
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applyLuaFilters datadir (optLuaFilters opts) [format] >=>
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applyFilters datadir filters' [format]) doc
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