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15 changes: 8 additions & 7 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -22,18 +22,19 @@ The following command should work in a `bash` shell.
git clone https://github.com/Klortho/JATS-to-Mediawiki.git
cd JATS-to-Mediawiki
# Get the JATS dtd
mkdir dtd
cd dtd
wget ftp://ftp.ncbi.nlm.nih.gov/pub/jats/archiving/1.0/jats-archiving-dtd-1.0.zip
unzip *.zip
cd ..
# Make sure you have xsltproc
which xsltproc # should return with the location of your xsltproc command
# Set up XML catalog file
export XML_CATALOG_FILES=`pwd`/dtd/catalog-test-jats-v1.xml
# (Optional) Check the JATS dtd Version
wget http://ftp.ncbi.nlm.nih.gov/pub/jats/archiving/1.0/ | grep "jats-archiving-dtd-1.0.zip"
# if date modified is after "10/11/12 5:00:00 pm" then,
rm -rf dtd/*
cd dtd
wget ftp://ftp.ncbi.nlm.nih.gov/pub/jats/archiving/1.0/jats-archiving-dtd-1.0.zip
unzip *.zip
```

## Convert an article
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342 changes: 342 additions & 0 deletions dtd/JATS-XHTMLtablesetup1.ent

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734 changes: 734 additions & 0 deletions dtd/JATS-archive-oasis-article1.dtd

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271 changes: 271 additions & 0 deletions dtd/JATS-archive-oasis-custom-classes1.ent
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<!-- ============================================================= -->
<!-- MODULE: Journal Archiving DTD Customize Classes Module -->
<!-- VERSION: ANSI/NISO JATS Version 1.0 (Z39.96-2012) -->
<!-- DATE: March 2012 -->
<!-- -->
<!-- ============================================================= -->

<!-- ============================================================= -->
<!-- PUBLIC DOCUMENT TYPE DEFINITION -->
<!-- TYPICAL INVOCATION -->
<!--
"-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables Customize Classes Module v1.0 20120330//EN"
Delivered as file "JATS-archivecustom-classes1.ent" -->
<!-- ============================================================= -->


<!-- ============================================================= -->
<!-- SYSTEM: Journal Archiving and Interchange DTD with -->
<!-- OASIS Tables of the JATS DTD Suite -->
<!-- -->
<!-- PURPOSE: To declare the Parameter Entities (PEs) used to -->
<!-- over-ride the JATS DTD Suite default named -->
<!-- element classes. -->
<!-- -->
<!-- Note: Since PEs must be declared before they -->
<!-- are used, this module must be called before the -->
<!-- content modules that declare elements, and before -->
<!-- the default classes module. -->
<!-- -->
<!-- TAG SET SPONSOR -->
<!-- National Center for Biotechnology -->
<!-- Information (NCBI) -->
<!-- National Library of Medicine (NLM) -->
<!-- -->
<!-- CREATED FOR: -->
<!-- This DTD was created from the JATS DTD Suite. -->
<!-- Digital archives and publishers may use the -->
<!-- DTD as is for markup of journal literature or -->
<!-- related material for archiving and transferring -->
<!-- such material between archives or create a -->
<!-- custom XML DTD from the Suite for -->
<!-- these purposes. -->
<!-- -->
<!-- This DTD is in the public domain. An organization -->
<!-- that wishes to create its own DTD from the suite -->
<!-- may do so without permission from NLM. -->
<!-- -->
<!-- The suite has been set up to be extended using a -->
<!-- new DTD file and a new DTD-specific customization -->
<!-- module to redefine the many Parameter Entities. -->
<!-- Do not modify the suite directly or redistribute -->
<!-- modified versions of the suite. -->
<!-- -->
<!-- In the interest of maintaining consistency and -->
<!-- clarity for potential users, NLM requests: -->
<!-- -->
<!-- 1. If you create a DTD from the JATS DTD Suite -->
<!-- and intend to stay compatible with the suite, -->
<!-- then please include the following statement -->
<!-- as a comment in all of your DTD modules: -->
<!-- "Created from, and fully compatible with, -->
<!-- the ANSI/NISO Z39.96 Journal Article Tag -->
<!-- Suite (JATS)." -->
<!-- -->
<!-- 2. If you alter one or more modules of the suite, -->
<!-- then please rename your version and all its -->
<!-- modules to avoid any confusion with the -->
<!-- original suite. Also, please include the -->
<!-- following statement as a comment in all your -->
<!-- DTD modules: -->
<!-- "Based in part on, but not fully compatible -->
<!-- with, the ANSI/NISO Z39.96 Journal Article -->
<!-- Tag Suite (JATS)." -->
<!-- -->
<!-- ORIGINAL CREATION DATE: -->
<!-- August 2004 -->
<!-- -->
<!-- CREATED BY: Mulberry Technologies, Inc. for the NISO Z39.96 -->
<!-- Working Group. Mulberry Technologies was -->
<!-- supported by National Center for Biotechnology -->
<!-- Information (NCBI), a center of the US National -->
<!-- Library of Medicine (NLM). -->
<!-- -->
<!-- The Journal Archiving and Interchange DTD is -->
<!-- built from the JATS DTD Suite. -->
<!-- -->
<!-- Suggestions for refinements and enhancements to -->
<!-- this DTD should be sent in email to: -->
<!-- [email protected] -->
<!-- ============================================================= -->


<!-- ============================================================= -->
<!-- DTD VERSION/CHANGE HISTORY -->
<!-- ============================================================= -->
<!--

Version Reason/Occasion (who) vx.x (yyyy-mm-dd)

=============================================================
NISO JATS Version 1.0 (DAL/BTU) v1.0 (2012-xx-xx)

ANSI/NISO Z39.96-2012 (Version 1.0)

Details concerning ANSI/NISO Z39.96-2012 JATS-based DTDs, XSDs,
RNGs and supporting documentation are available at
http://jats.nlm.nih.gov/1.0/

5. CITATION ALTERNATIVES - Added a new element
<citation-alternatives> to the citation.class. The element
will hold, for example, a single citation in multiple
languages or a single citation tagged as a <mixed-citation>
complete with punctuation and spacing and also as an
<element-citation> with all punctuation and spacing removed.

=============================================================
Version 0.4 (DAL/BTU) v0.4 (2011-01-31)

This Tag Set is in the process of becoming a NISO standard.
The version numbers are starting over from 0.4", as a Trial
Use Draft, to be made into "Version 1.0" when the Tag Suite
becomes a NISO standard. Thus, the version number that would
have been "NLM Version 3.1 Draft" has become NISO JATS
"Version 0.4".

Details on NISO Trial Use Draft Version 0.4 are available at
http://jats.nlm.nih.gov/JATS-0.4.

4. Updated the DTD-version attribute to "0.4"

3. Updated the public identifier to "v0.4 20110131",
modified the formal public identifier to include "JATS (Z39.96)",
and the filename as delivered to include "JATS" and the
new version number "0". Also included the phrase
"(OASIS Tables)" in the formal name.

2. AFFILIATION ALTERNATIVES - Added the element <aff-alternatives>
to contrib-info.class to hold multiple <aff>s that are
representations of a single affiliation, for example, the name
of an institution in two languages or two scripts.

=============================================================
Version 3.0 (DAL/BTU) v3.0 (2007-10-31)

Version 3.0 is the first non-backward-compatible release.
In addition to the usual incremental changes, some
elements and attributes have been renamed and/or remodeled
to better meet user needs and to increase tag set consistency.
All module change histories are available through the Tag Suite
web site at http://dtd.nlm.nih.gov.

Details on version 3.0 are available at
http://dtd.nlm.nih.gov/3.0.

1. Updated public identifier to "v3.0 20080202//EN" -->


<!-- ============================================================= -->
<!-- METADATA CLASSES (articlemeta.ent) -->
<!-- ============================================================= -->


<!-- CONTRIBUTOR INFORMATION CLASS -->
<!-- Metadata about a contributor
Added <fn> -->
<!ENTITY % contrib-info.class
"address | aff | aff-alternatives |
author-comment | bio | email | etal |
ext-link | fn | on-behalf-of | role |
uri | xref" >


<!-- ============================================================= -->
<!-- CITATION CLASSES (references.ent) -->
<!-- ============================================================= -->


<!-- CITATION CLASS ELEMENTS -->
<!-- Reference to an external document, as used
within, for example, the text of a
paragraph -->
<!ENTITY % citation.class
"citation-alternatives | element-citation |
mixed-citation | nlm-citation" >


<!-- CITATION MINUS ALTERNATIVES CLASS ELEMENTS -->
<!-- All the citation elements except the
<citation-alternatives> element. -->
<!ENTITY % citation-minus-alt.class
"element-citation | mixed-citation |
nlm-citation" >


<!ENTITY % citation-additions.class
"string-date" >

<!-- ============================================================= -->
<!-- PRESENTATION INFO CLASSES -->
<!-- ============================================================= -->


<!-- X-GENERATED PUNCTUATION CLASS -->
<!-- Class containing a single element that will
hold generated punctuation or other
generatable text, for example, the commas or
semicolons between keywords.
This textual material element has been
created:
- to match existing input DTDs
- to identify such material, so that it
can be processed (such as removed)
- to try to remove look-and-feel material
from semantic material such as keywords.
-->
<!ENTITY % x.class "x" >


<!-- ============================================================= -->
<!-- STRUCTURAL ELEMENT CLASSES -->
<!-- ============================================================= -->


<!-- REST OF PARAGRAPH CLASS -->
<!-- Information for the reader that is at the
same structural level as a Paragraph.
Contains all paragraph-level objects that are
not also used inside tables and excepting
also the paragraph element itself. -->
<!ENTITY % rest-of-para.class
"ack | disp-quote | speech | statement |
verse-group" >


<!-- ============================================================= -->
<!-- TABLE CLASSES -->
<!-- ============================================================= -->


<!-- ALTERNATIVES DISPLAY CLASS ELEMENTS -->
<!-- Display elements that can be alternatives to
each other inside an alternatives element.
XHTML Table Model table
OASIS CALS Table oasis:table -->
<!ENTITY % alternatives-display.class
"array | chem-struct | graphic |
inline-graphic |
inline-supplementary-material |
media | preformat | private-char |
supplementary-material |
table | %otable.qname; |
textual-form" >


<!-- TABLE CLASS ELEMENTS -->
<!-- Elements that will be used to contain the
rows and columns inside the Table Wrapper
element <tbl>. The following elements can
be set up for inclusion:
XHTML Table Model table
OASIS CALS Table oasis:table -->
<!ENTITY % table.class "table | %otable.qname;" >


<!-- TABLE BODY CLASS -->
<!-- To include just a table body <tbody>
element. Both XHTML and OASIS table types. -->
<!ENTITY % tbody.class "tbody | %otbody.qname;" >


<!-- ================== End Archiving Classes Customization ====== -->
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