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Formatting JATS
as easy as 1-2-3
Tony Graham
Mentea
13 Kelly’s Bay Beach
Skerries, Co Dublin, Ireland
info@mentea.net
@MenteaXML
http://www.mentea.net
Version 1.0 – 2 April 2014
© 2014 Mentea
All rights reserved. The author grants the U.S. National Library of
Medicine permission to archive and post a copy of this paper on the
Journal Article Tag Suite Conference proceedings website.
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Help to Read and Extract Field Data from PDF with a Convenient C# Solution
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Html form output to pdf - VB.NET PDF Form Data Read library: extract form data from PDF in vb.net, ASP.NET, MVC, Ajax, WPF
Convenient VB.NET Solution to Read and Extract Field Data from PDF
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C# PDF Convert to HTML SDK: Convert PDF to html files in C#.net
Turn PDF form data to HTML form. Export PDF images to HTML images. ContextType. SVG ContextType.HTML. directory, The output file directory.
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VB.NET PDF Password Library: add, remove, edit PDF file password
' Define input and output file path. As String = Program.RootPath + "\\" 3_pw_a.pdf" ' Create a passwordSetting.IsAnnot = True ' Allow to fill form.
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Formatting JATS
as easy as 1-2-3
JATS Preview stylesheets
5
Aside: GitHub
11
XSLT 1.0: Government body
11
XSLT 2.0: PLOS ONE
15
XSLT 3.0: xslt3testbed
21
References
24
Appendix A – 
About
25
Formatting JATS
C# PDF Password Library: add, remove, edit PDF file password in C#
Define input and output file path. outputFilePath = Program.RootPath + "\\" 3_pw_a.pdf"; // Create a passwordSetting.IsAnnot = true; // Allow to fill form.
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C# PDF File Split Library: Split, seperate PDF into multiple files
also combine generated split PDF document files with other PDF files to form a new If your page number is set as 1, then the two output PDF files will contains
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Mentea
4
© 2014 Mentea
C# PDF File Merge Library: Merge, append PDF files in C#.net, ASP.
Microsoft Office Word, Excel and PowerPoint data to PDF form. 3.pdf"; String outputFilePath = Program.RootPath + "\\" Output.pdf"; String[] inputFilePaths
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C# Create PDF from Tiff Library to convert tif images to PDF in C#
String inputFilePath = Program.RootPath + "\\" 1.tif"; String outputFilePath = Program.RootPath + "\\" Output.pdf"; // Load a TIFF file.
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Formatting JATS: as easy as 1-2-3
1
• JATS Preview stylesheets
• XSLT 1.0
• XSLT 2.0
• XSLT 3.0
The 1-2-3 comes from using JATS with three versions of XSLT.
JATS Preview stylesheets
2
https://github.com/NCBITools/JATSPreviewStylesheets
• XSLT 1.0
• Public domain
• No copyright issues
• Developed for NCBI by Mulberry Technologies
JATS Preview with “selfie”
3
Paper for this talk formatted using JATS Preview stylesheet with picture of paper formatted
using JATS preview stylesheets.
(‘selfie’ was added to the OED in 2013 so maybe it doesn’t need quotes)
Formatting JATS
C# Create PDF from PowerPoint Library to convert pptx, ppt to PDF
String inputFilePath = Program.RootPath + "\\" 1.pptx"; String outputFilePath = Program.RootPath + "\\" Output.pdf"; // Load a PowerPoint (.pptx) file.
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C# Create PDF from Excel Library to convert xlsx, xls to PDF in C#
String inputFilePath = Program.RootPath + "\\" 1.xlsx"; String outputFilePath = Program.RootPath + "\\" Output.pdf"; // Load an Excel (.xlsx) file.
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Reconstructed timeline
4
2000
2010
2015
2005
XSLT 1.0
Initial design
NLM Preview
release
JATS Preview 1.0
XSLT 2.0
XSLT 3.0 ?
Reconstructed from comments in code, downloads, and emails with Kim Tryka and Tommie
Usdin.
Why still XSLT 1.0 in 2012?
5
• XSLT 1.0 still dominant on some platforms
• .NET
• Linux/Unix
• Also tested with XSLT 2.0
• NLM stylesheets developed circa 2006/2007
• One well-known XSLT 2.0 processor
• Java only
What does it do?
6
• Preprocessing
• Convert OASIS tables to HTML tables
• Massage citation format
• Some require XSLT 2.0
• Formatting
• XML to HTML
• XML to XSL-FO for formatting as PDF
• Post-processing
• HTML to XHTML for MathML
The only part that I’ve needed to use, and the only part being covered, is the transformation
to XSL-FO and formatting to PDF.
Mentea
6
© 2014 Mentea
C# Create PDF from Word Library to convert docx, doc to PDF in C#.
String inputFilePath = Program.RootPath + "\\" 1.docx"; String outputFilePath = Program.RootPath + "\\" Output.pdf"; // Load a Word (.docx) document.
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C# PDF Convert to Tiff SDK: Convert PDF to tiff images in C#.net
String inputFilePath = Program.RootPath + "\\" 1.pdf"; PDFDocument doc = new PDFDocument(inputFilePath); // Convert and output to a TIFF file.
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Customizability
7
“These stylesheets are provided as a point of entry for JATS users who may not have the
resources to create them from scratch. Because there are many varied implementations of JATS,
you should have no expectation that these stylesheets will create production ready files in any
arbitrary system. Instead, the stylesheets should be customized for your particular needs.”
“Because we view these stylesheets as a template for a customized solution, not the solution
itself, we will accept changes that fix an actual bug, but we will not merge in changes that we view
as “customization”. For example, we will accept changes that fix a problem which otherwise leads
to failure in creating a final output file, but we will not accept changes that focus on presentational
aspects of the final output (such as font changes, margin changes, graphics sizing, etc).”
Statement about customisation from JATSPreviewStylesheets README with added
emphasis.
XSLT features supporting customizability
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• Templates
• Modular stylesheets
• Named attribute sets
Templates
9
• match matches a context in source XML
• Content of xsl:template instantiated when template is applied
<xsl:template match="td">
<fo:table-cell xsl:use-attribute-sets="td">
<xsl:call-template name="process-table-cell"/>
</fo:table-cell>
</xsl:template>
Elements in the body of the template not in the XSLT namespace are copied to the result,
and elements and attributes in the XSLT namespace are acted on by the XSLT processor.
Formatting JATS
Modular stylesheets
10
<xsl:include
href = uri-reference />
• href refers to other stylesheet
• Children of other xsl:stylesheet replace xsl:include
<xsl:import
href = uri-reference />
• href refers to other stylesheet
• Imported definitions and template rules not part of importing stylesheet
• Have lower import precedence
Imports in JATS XSL-FO preview
11
xhtml-tables-fo.xsl
xsl:include
xsl:import
jats-xslfo.xsl
There are more interesting block diagrams later.
Overriding templates
12
• Template in importing stylesheet overrides same context in imported
• Good when overriding complete function of template
• Extra overhead if you just want to change one little thing
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© 2014 Mentea
Attribute sets
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• Named set of attribute definitions
• Use in multiple places
• Definitions evaluated in each context where used
<xsl:attribute-set name="fig">
<xsl:attribute name="keep-together.within-page"
>always</xsl:attribute>
<xsl:attribute name="id">
<xsl:value-of select="generate-id()" />
</xsl:attribute>
</xsl:attribute-set>
Since attribute definitions in attribute sets are evaluated each time the attribute set is used,
the value of the id attribute will be unique to each context.
JATS Preview supporting customizability
14
• Global variables
• Attribute sets
• Named templates
Formatting JATS
Example customization
15
• Add to attribute set from JATS stylesheets
<xsl:attribute-set name="td">
<xsl:attribute name="line-stacking-strategy"
>max-height</xsl:attribute>
</xsl:attribute-set>
• New attribute set reusing merged td attribute set
<xsl:attribute-set name="td-small"
use-attribute-sets="td">
<xsl:attribute name="line-height">10pt</xsl:attribute>
<xsl:attribute name="border">none</xsl:attribute>
<xsl:attribute name="padding-top">0pt</xsl:attribute>
<xsl:attribute name="padding-bottom">0pt</xsl:attribute>
</xsl:attribute-set>
• Override JATS stylesheet in more-specific context
<xsl:template
match="td[ancestor::table[@style = 'small']]">
<fo:table-cell xsl:use-attribute-sets="td-small">
<xsl:call-template name="process-table-cell"/>
</fo:table-cell>
</xsl:template>
The xsl:attribute-set extends the ‘td’ defined in the JATS Preview stylesheet.
The new ‘td-small’ attribute set includes the attribute definitions from all declarations for the
‘td’ attribute set plus the definitions contained in its definition.
The template matches on a more-specific context than the general-purpose template for td
in the JATS Preview stylesheets, so in those particular contexts, the XSLT processor uses this
template, which adds a different set of attributes to the generated fo:table-cell but
which still uses the ‘process-table-cell” named template from the JATS Preview stylesheets as
is used in the original template for td.
This illustrates in a nutshell how a customisation is able to extend, override, and reuse the
constructs in the core JATS Preview stylesheets.
Summary: JATS Preview
16
• XSLT 1.0
• Not accepting customisations into core
• Stylesheet structure facilitates customisations
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© 2014 Mentea
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