xml_jats_resolver 0.1.0 → 0.2.0

checksums.yaml

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data/CHANGELOG.md

@@ -1,3 +1,7 @@
+## 0.2.0
+
+* Add Atypon DTDs: 3.0.1, 3.0.4 and 3.0.5
+
 ## 0.1.0
 
 * Initial project to resolve DTD with XMLs

data/lib/dtd/atypon/3.0.1/dtd/XHTMLtablesetup3.ent

@@ -0,0 +1,284 @@
+<!-- ============================================================= -->
+<!--  MODULE:    XHTML Table Setup Module                          -->
+<!--  VERSION:   3.0.1                                             -->
+<!--  DATE:      Apr 2009                                          -->
+<!--                                                               -->
+<!-- ============================================================= -->
+
+<!-- ============================================================= -->
+<!--                    PUBLIC DOCUMENT TYPE DEFINITION            -->
+<!--                        TYPICAL INVOCATION                     -->
+<!--
+"-//Atypon//DTD Atypon Systems Archival NLM DTD XHTML Table Setup Module v3.0.1 20100714//EN"
+     Delivered as file "XHTMLtablesetup3.ent"                      -->
+<!-- ============================================================= -->
+
+<!-- ============================================================= -->
+<!-- SYSTEM:     Archiving and Interchange DTD Suite               -->
+<!--                                                               -->
+<!-- PURPOSE:    Provides the organization for using the XHTML 1.1 -->
+<!--             table model                                       -->
+<!--                                                               -->
+<!-- CONTAINS:   1) Invokes the inline style attribute module      -->
+<!--                  to pick up the "style" attribute             -->
+<!--             2) Overrides to standard parameter entities used  -->
+<!--                in the XHTML 1.1 table model                   -->
+<!--             3) Invokes the XHTML 1.1 table model              -->
+<!--                                                               -->
+<!-- MODULES REQUIRED:                                             -->
+<!--             1) XHTML inline style module                      -->
+<!--                  (-%xhtml-inlstyle-1.mod;)                    -->
+<!--             2) XHTML 1.1 table model (-%xhtml-table-1.mod;)   -->
+<!--                                                               -->
+<!-- CREATED FOR:                                                  -->
+<!--             Digital archives and publishers who wish to       -->
+<!--             create a custom XML DTD for original markup of    -->
+<!--             journal literature, books, and related material,  -->
+<!--             or for archiving and transferring such material   -->
+<!--             between archives.                                 -->
+<!--                                                               -->
+<!--             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 Archiving and     -->
+<!--                Interchange 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 Archiving and Interchange DTD Suite."  -->
+<!--                                                               -->
+<!--             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 Archiving and Interchange DTD    --> 
+<!--                    Suite."                                    -->
+<!--                                                               -->
+<!--             Suggestions for refinements and enhancements to   -->
+<!--             the DTD suite should be sent in email to:         -->
+<!--                 archive-dtd@ncbi.nlm.nih.gov                  -->
+<!--                                                               -->
+<!-- ORIGINAL CREATION DATE:                                       -->
+<!--             December 2002                                     -->
+<!--                                                               -->
+<!-- CREATED BY: Jeff Beck       (NCBI)                            -->
+<!--             Deborah Lapeyre (Mulberry Technologies, Inc.)     -->
+<!--             Bruce Rosenblum (Inera Inc.)                      -->
+<!--                                                               -->
+<!--             NLM thanks the Harvard University Libraries, both -->
+<!--             for proposing that a draft archiving NLM DTD for  --> 
+<!--             life sciences journals be extended to accommodate -->
+<!--             journals in all disciplines and for sponsoring    -->
+<!--             Bruce Rosenblum's collaboration with other DTD    -->
+<!--             authors in completing Version 1.0. The Andrew W.  --> 
+<!--             Mellon Foundation provided support for these      --> 
+<!--             important contributions.                          -->
+<!--                                                               -->
+<!-- ============================================================= -->
+
+
+<!-- ============================================================= -->
+<!--                    DTD VERSION/CHANGE HISTORY                 -->
+<!-- ============================================================= -->
+<!--
+     =============================================================
+
+Version  Reason/Occasion                   (who) vx.x (yyyy-mm-dd)
+
+     =============================================================
+     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"              -->
+
+                                                                   
+<!-- ============================================================= -->
+<!--                    SET UP FOR THE XHTML 1.1 TABLE MODULE      -->
+<!-- ============================================================= -->
+ 
+
+<!-- ============================================================= -->
+<!--                    THE XHTML TABLE STYLE ATTRIBUTE MODULE     -->
+<!-- ============================================================= -->
+
+
+<!--                    XHTML TABLE INLINE STYLE MODULE            -->
+<!--                    This module declares the 'style' attribute, 
+                        used to support inline style markup for the
+                        <td> and <tr> elements. Copyright 1998-2005 
+                        W3C (MIT, ERCIM, Keio), All Rights Reserved.
+                        Revision: $Id: xhtml-inlstyle-1.mod,v 4.0 
+                        2001/04/02 22:42:49 altheim Exp $
+                        PUBLIC identifier
+                        "-//W3C//ENTITIES XHTML Inline Style 1.0//EN"
+                        SYSTEM identifier
+                "http://www.w3.org/MarkUp/DTD/xhtml-inlstyle-1.mod"-->
+%xhtml-inlstyle-1.mod;
+                                                                   
+                                                                   
+<!-- ============================================================= -->
+<!--                    DEFAULTS FOR TABLE ELEMENT NAMES           -->
+<!-- ============================================================= -->
+
+
+<!ENTITY % table.qname  "table"                                      >
+<!ENTITY % caption.qname  
+                        "caption"                                    >
+<!ENTITY % thead.qname  "thead"                                      >
+<!ENTITY % tfoot.qname  "tfoot"                                      >
+<!ENTITY % tbody.qname  "tbody"                                      >
+<!ENTITY % colgroup.qname  
+                        "colgroup"                                   >
+<!ENTITY % col.qname    "col"                                        >
+<!ENTITY % tr.qname     "tr"                                         >
+<!ENTITY % th.qname     "th"                                         >
+<!ENTITY % td.qname     "td"                                         >
+                                                                   
+                                                                   
+<!-- ============================================================= -->
+<!--                    DEFAULTS FOR DATATYPE PARAMETER ENTITIES   -->
+<!-- ============================================================= -->
+
+
+<!ENTITY % Text.datatype  
+                        "CDATA"                                      >
+
+
+<!ENTITY % Number.datatype  
+                        "CDATA"                                      >
+
+
+<!ENTITY % MultiLength.datatype
+                        "CDATA"                                      >
+
+
+<!ENTITY % Length.datatype
+                        "CDATA"                                      >
+
+
+<!ENTITY % Pixels.datatype
+                        "CDATA"                                      >
+
+
+<!ENTITY % Character.datatype
+                        "CDATA"                                      >
+                                                                   
+                                                                   
+<!-- ============================================================= -->
+<!--                    DEFAULTS FOR ATTRIBUTE PARAMETER ENTITIES  -->
+<!-- ============================================================= -->
+
+
+<!--         style      Defined in the PE -%Core.extra.attrib; and
+                        used to support inline style markup. This
+                        attribute is defined in the XHTML Table
+                        Inline Style Module called in with the PE:
+                           -%xhtml-inlstyle-1.mod
+                        which must be invoked before the attribute
+                        PE is used.                                -->
+<!ENTITY % Common.attrib
+              "id       ID                                #IMPLIED
+               content-type
+                        CDATA                             #IMPLIED
+               %Core.extra.attrib;"                                  >
+                                                                   
+                                                                   
+<!-- ============================================================= -->
+<!--                    OVER-RIDES TO REMOVE CAPTION               -->
+<!-- ============================================================= -->
+
+
+<!--                   CAPTION FOR A TABLE                         -->
+<!--                   Modification of the standard XHMTL model    
+                       Removed the definition of caption, so the
+                       element would not be multiply defined       -->
+<!ENTITY % caption.element  
+                       "IGNORE"                                      >
+                                                                   
+                                                                   
+<!-- ============================================================= -->
+<!--                    OVER-RIDES FOR CONTENT PARAMETER ENTITIES  -->
+<!-- ============================================================= -->
+
+
+<!--                   INLINE ELEMENTS                             -->
+<!--                   Modification of the standard XHMTL model     
+                       for inline elements used in the <caption>
+                       Set to the null because the <caption>
+                       element is now inside the table wrapper,
+                       not inside the table, as the original XHTML
+                       table intended                              -->
+<!ENTITY % Inline.mix  ""                                            >
+
+
+<!--                   CONTENTS OF A TABLE CELL                    -->
+<!--                   Modification of the standard XHMTL model
+                       used for the content of tables cells <th>
+                       and <td>                                    -->
+<!ENTITY % Flow.mix    "%inside-cell;"                               >
+
+
+<!--                   CONTENTS OF A TABLE                         -->
+<!--                   Modification of the standard XHMTL model    
+                       This has been modified from the XHTML model
+                       to remove the <caption> element from the
+                       <table> model, since in the Archiving and
+                       Interchange DTD Suite modular library, the 
+                       <caption> element is part  of the Table Wrapper 
+                       <table-wrap> element. No other changes were 
+                       made to the XHTML table content model.      -->
+<!ENTITY % table.content
+     "( ( %col.qname;* | %colgroup.qname;* ),
+        ( ( %thead.qname;?, %tfoot.qname;?, %tbody.qname;+ ) | 
+          ( %tr.qname;+ ) 
+        ) 
+      )"                                                             >
+ 
+
+<!-- ============================================================= -->
+<!--                    THE XHTML V1.1 TABLE INVOCATION            -->
+<!-- ============================================================= -->
+
+
+<!--                    XHTML TABLE MODEL                          -->
+<!--                    This module declares element types and 
+                        attributes used to provide table markup 
+                        similar to HTML 4, including features that 
+                        enable better accessibility for non-visual 
+                        user agents. This is the XHTML reformulation 
+                        of HTML as a modular XML application. 
+                        Copyright 1998-2005 W3C (MIT, ERCIM, Keio), 
+                        All Rights Reserved.
+                        Revision: $Id: xhtml-table-1.mod,v 4.1 
+                        2001/04/10 09:42:30 altheim Exp $ SMI
+                        PUBLIC identifier
+                        "-//W3C//ELEMENTS XHTML Tables 1.0//EN"
+                        SYSTEM identifier:
+                  "http://www.w3.org/MarkUp/DTD/xhtml-table-1.mod" -->
+%xhtml-table-1.mod;
+
+
+<!-- ================== End XHTML Table Setup Module ============= -->

data/lib/dtd/atypon/3.0.1/dtd/annotation3.ent

@@ -0,0 +1,266 @@
+<!-- ============================================================= -->
+<!--  MODULE:    Historical Book DTD Annotation Elements           -->
+<!--  VERSION:   3.0.1                                             -->
+<!--  DATE:      Apr 2009                                          -->
+<!--                                                               -->
+<!-- ============================================================= -->
+
+<!-- ============================================================= -->
+<!--                    PUBLIC DOCUMENT TYPE DEFINITION            -->
+<!--                        TYPICAL INVOCATION                     -->
+<!--
+"-//Atypon//DTD Atypon Systems Archival NLM DTD Annotation Elements v3.0.1 20100714//EN"
+Delivered as file "annotation3.ent"                                -->
+<!-- ============================================================= -->
+
+
+<!-- ============================================================= -->
+<!-- SYSTEM:     NCBI BOOK DTD of the                              -->
+<!--             Archiving and Interchange DTD Suite               -->
+<!--                                                               -->
+<!-- PURPOSE:    Defines elements that describe the variety of     -->
+<!--             added material seen in older books and historical -->
+<!--             editions, for example editorial emendations and   -->
+<!--             additions as well as the need to record the page  -->
+<!--             numbers.                                          -->
+<!--                                                               -->
+<!-- CONTAINS:   1) Page start elements                            -->
+<!--             2) Alternative terms                              -->
+<!--                                                               -->
+<!-- CREATED FOR:                                                  -->
+<!--             NLM Bookshelf                                     -->
+<!--             National Center for Biotechnology Information     -->
+<!--                (NCBI)                                         -->
+<!--             National Library of Medicine (NLM)                -->
+<!--                                                               -->
+<!-- ORIGINAL CREATION DATE:                                       -->
+<!--             December 2004                                     -->
+<!--                                                               -->
+<!-- CREATED BY: Bart Trawick    (NCBI)                            -->
+<!--             Jeff Beck       (NCBI)                            -->
+<!--             Michael North   (NLM)                             -->
+<!--             Deborah Lapeyre (Mulberry Technologies, Inc.)     -->
+<!--             B. Tommie Usdin (Mulberry Technologies, Inc.)     -->
+<!--                                                               -->
+<!--             Suggestions for refinements and enhancements to   -->
+<!--             this DTD should be sent in email to:              -->
+<!--                 archive-dtd@ncbi.nlm.nih.gov                  -->
+<!-- ============================================================= -->
+
+
+<!-- ============================================================= -->
+<!--                    DTD VERSION\CHANGE HISTORY                 -->
+<!-- ============================================================= -->
+<!--
+     =============================================================
+
+Version  Reason/Occasion                   (who) vx.x (yyyy-mm-dd)
+
+     =============================================================
+     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"              -->
+
+
+<!-- ============================================================= -->
+<!--                    Design Note: HISTORICAL ANNOTATIONS        -->
+<!-- ============================================================= -->
+
+<!--                    For the purposes of this DTD, annotations of 
+                        historical material are considered to be of
+                        two types: those with content, that is, those 
+                        which add words to the text (for example, a
+                        penciled marginal note) and those that merely
+                        decorate words already in the text, for 
+                        example, a phrase underlined in pencil.
+                          Text-bearing annotations, whether inline
+                        or block-level, use the <annotation> or the
+                        <alt-text> elements. Decorations use the
+                        <named-content> element with the attribute
+                        "content-type" taking values like "underline"
+                        and "yellow highlighter".
+                           The <annotation> and <named-content>
+                        elements are not defined in this module, since
+                        they were already part of the NLM Archiving 
+                        and Interchange DTD Suite when this DTD was
+                        was written. No changes were needed to the
+                        <named-content> element except that it is
+                        allowed in a few more places through the
+                        modification of the %phrase.class; and
+                        %emphasis.class; Parameter Entities.
+                           In the Suite, however, the <annotation>
+                        element is only used within citations. In 
+                        this DTD, it is a block-level element at the 
+                        same level as a paragraph (%para-level;) as 
+                        well as an inline-element inside textual 
+                        passages (%emphasis.class;). New attributes 
+                        were  added to <annotation> to describe some 
+                        of these new roles/purposes.               -->
+                        
+
+<!-- ============================================================= -->
+<!--                    PAGE NUMBER ELEMENTS                       -->
+<!-- ============================================================= -->
+
+
+<!--                    PAGE START ATTRIBUTES                      -->
+<!--                    Milestone element that marks the start of a 
+                        physical page in the printed edition of a
+                        historical work. For display on the web,
+                        a typical behavior for this element would be
+                        to cause the display of a horizontal rule and
+                        display the page number, so that print page 
+                        breaks may be seen in flowing webpages.
+                           The identifier attribute allows cross
+                        references <xref> to the page to be made.
+                                                                   -->
+<!ENTITY % page-start-atts
+            "id         ID                                 #IMPLIED" >
+
+
+<!--                    PAGE START GROUP                           -->
+<!--                    Milestone element that marks the start of a 
+                        physical page in the printed edition of a
+                        historical work. 
+                           This element may also hold any running
+                        heads, catchwords, or the page number(s) 
+                        that are present on the printed page, whatever 
+                        their physical location. Page numbers may be 
+                        printed, hand-written, perfed, etc., and 
+                        there may be more than one number per page.
+                        Remarks: 
+                        A typical behavior for this element would be
+                        to cause the display of a horizontal rule and
+                        the page number, so that print page breaks 
+                        may be seen in flowing webpages.
+                           This information may be physically located
+                        almost anywhere on a page, so this element
+                        can be placed within or between most
+                        paragraph-level elements.                  -->
+<!ELEMENT  page-start   ((page-num | running-head)* )                >
+<!--         id         Identifier for the container, to provide a
+                        target so that references to the page may be
+                        made into live links in the electronic form.
+                        This reference can be made even to blank pages
+                        which contain no page number.              -->
+<!ATTLIST  page-start    
+             %page-start-atts;                                       >
+
+
+<!--                    PAGE NUMBER ATTRIBUTES                     -->
+<!--                    The page number type is a hook for book-
+                        specific processing, for example, to allow one
+                        page number to be marked as primary; to 
+                        distinguish between printed numbers provided
+                        by the publisher and penciled numbers added
+                        by a library; or to make other pagination
+                        distinctions.                              -->
+<!ENTITY % page-num-atts
+            "page-num-type
+                        CDATA                              #IMPLIED" >
+
+
+<!--                    PAGE NUMBER                                -->
+<!--                    A pagination number (potentially one of many)
+                        present on a physical page.                -->
+<!ELEMENT  page-num     (#PCDATA)                                    >
+<!--         page-num-type          
+                        The page number type is a hook for book-
+                        specific processing, for example, to allow one
+                        page number to be marked as primary; to 
+                        distinguish between printed numbers provided
+                        by the publisher and penciled numbers added
+                        by a library; or to make other pagination
+                        distinctions.                              -->
+<!ATTLIST  page-num    
+             %page-num-atts;                                         >
+
+
+<!--                    RUNNING HEAD TEXT                          -->
+<!--                    The contents of a running head or foot
+                        when those have content other than the
+                        ordinary metadata for the book
+                        Remarks: In most modern editions, the
+                        running heads and feet can be derived from
+                        the book's metadata, for example the title
+                        of the work, the publication date, the
+                        publisher, the heading of the most
+                        recently encountered section. ent. In some
+                        historical material, new information, not
+                        derivable from the metadata, is presented in
+                        the running head, and this element can be
+                        used to preserve it.                       -->
+<!ELEMENT  running-head (#PCDATA)                                    >
+
+
+<!-- ============================================================= -->
+<!--                    SEARCHABLE WORD ELEMENTS                   -->
+<!-- ============================================================= -->
+
+
+<!--                    ALTERNATIVE TERM ATTRIBUTES                -->
+<!--                    Attribute list for the element that holds
+                        words placed into the text to provide
+                        complete words for searching, modernized
+                        versions for searching, or other
+                        interpolations.
+                           The words may be displayed with the
+                        text, in which case they would be visually set
+                        apart, for example in square brackets. The
+                        "display" attribute controls whether or not the
+                        term shows to the user.
+                            The "alt-term-type" attribute is used to
+                        provide a reason/explanation for the
+                        added word, for example, if a word in text
+                        was "small-pox", the modern spelling might
+                        be added, tagged as
+                           <alt-term display="yes" 
+                            alt-term-type="modernization">
+                            smallpox</alt-term>
+                        to provide both the older form and the
+                        modern equivalent to a search engine.      -->
+<!ENTITY % alt-term-atts
+            "display    (yes | no)                         'yes'
+             alt-term-type
+                        CDATA                              #IMPLIED" >
+
+
+<!--                    ALTERNATIVE VERSION OF A TERM              -->
+<!--                    An element that offers a second version 
+                        of a word or phrase in the text, for example, 
+                        a more modern version of an out-dated 
+                        historical term. The word is added to the
+                        historical text for searching and may also be
+                        displayed next to the term, possibly pointed
+                        out by a mechanism such as square brackets,
+                        as an aid to the reader. For example, to 
+                        show the modern spelling of a disease name
+                             small-pox [smallpox]
+                        and to make sure that searches for the modern
+                        term find the page, the following tagging 
+                        could be used:
+                           ...small-pox <alt-term display="yes">
+                              smallpox</alt-term>
+                           Another use for <alt-term> is to complete
+                        words that are elided, illegible, or
+                        hyphenated across structural boundaries in the
+                        text. The shortened word can be displayed with
+                        the page, but the full term can also be 
+                        provided for search engines and increased 
+                        user understanding.                        -->
+<!ELEMENT  alt-term     (#PCDATA)                                    >
+<!ATTLIST  alt-term    
+             %alt-term-atts;                                         >
+
+
+<!-- ================== End Annotation Elements  ================= -->