Merge pull request #752 from elifesciences/pr-752

RP -exclude epub text from journal-ref-text-content

src/rp-schematron-base.sch

@@ -443,9 +443,9 @@
         role="error" 
         id="journal-ref-article-title">This journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has no article-title element.</assert>
 
-        <report test="text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|vol|and|pp?|in|is[sb]n)[:\.]?'))]" 
+        <report test="text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|epub|vol|and|pp?|in|is[sb]n)[:\.]?'))]" 
         role="warning" 
-        id="journal-ref-text-content">This journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has untagged textual content - <value-of select="string-join(text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|vol|and|pp?|in|is[sb]n)[:\.]?'))],'; ')"/>. Is it tagged correctly?</report>
+        id="journal-ref-text-content">This journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has untagged textual content - <value-of select="string-join(text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|epub|vol|and|pp?|in|is[sb]n)[:\.]?'))],'; ')"/>. Is it tagged correctly?</report>
      </rule>
 
      <rule context="mixed-citation[@publication-type='journal']/source" id="journal-source-checks">

src/rp-schematron.sch

@@ -291,7 +291,7 @@
 
         <assert test="article-title" role="error" id="journal-ref-article-title">[journal-ref-article-title] This journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has no article-title element.</assert>
 
-        <report test="text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|vol|and|pp?|in|is[sb]n)[:\.]?'))]" role="warning" id="journal-ref-text-content">[journal-ref-text-content] This journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has untagged textual content - <value-of select="string-join(text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|vol|and|pp?|in|is[sb]n)[:\.]?'))],'; ')"/>. Is it tagged correctly?</report>
+        <report test="text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|epub|vol|and|pp?|in|is[sb]n)[:\.]?'))]" role="warning" id="journal-ref-text-content">[journal-ref-text-content] This journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has untagged textual content - <value-of select="string-join(text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|epub|vol|and|pp?|in|is[sb]n)[:\.]?'))],'; ')"/>. Is it tagged correctly?</report>
      </rule></pattern><pattern id="journal-source-checks-pattern"><rule context="mixed-citation[@publication-type='journal']/source" id="journal-source-checks">
       <let name="preprint-regex" value="'biorxiv|africarxiv|arxiv|cell\s+sneak\s+peak|chemrxiv|chinaxiv|eartharxiv|medrxiv|osf\s+preprints|paleorxiv|peerj\s+preprints|preprints|preprints\.org|psyarxiv|research\s+square|scielo\s+preprints|ssrn|vixra'"/>
 

src/rp-schematron.xsl

@@ -2194,8 +2194,8 @@
          </xsl:otherwise>
       </xsl:choose>
       <!--REPORT warning-->
-      <xsl:if test="text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|vol|and|pp?|in|is[sb]n)[:\.]?'))]">
-         <svrl:successful-report xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|vol|and|pp?|in|is[sb]n)[:\.]?'))]">
+      <xsl:if test="text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|epub|vol|and|pp?|in|is[sb]n)[:\.]?'))]">
+         <svrl:successful-report xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|epub|vol|and|pp?|in|is[sb]n)[:\.]?'))]">
             <xsl:attribute name="id">journal-ref-text-content</xsl:attribute>
             <xsl:attribute name="role">warning</xsl:attribute>
             <xsl:attribute name="location">
@@ -2204,7 +2204,7 @@
             <svrl:text>[journal-ref-text-content] This journal reference (<xsl:text/>
                <xsl:value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>
                <xsl:text/>) has untagged textual content - <xsl:text/>
-               <xsl:value-of select="string-join(text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|vol|and|pp?|in|is[sb]n)[:\.]?'))],'; ')"/>
+               <xsl:value-of select="string-join(text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|epub|vol|and|pp?|in|is[sb]n)[:\.]?'))],'; ')"/>
                <xsl:text/>. Is it tagged correctly?</svrl:text>
          </svrl:successful-report>
       </xsl:if>

test/tests/rp/journal-ref-checks/journal-ref-text-content/fail.xml

@@ -1,6 +1,6 @@
 <?oxygen SCHSchema="journal-ref-text-content.sch"?>
 <!--Context: mixed-citation[@publication-type='journal']
-Test: report    text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|vol|and|pp?|in|is[sb]n)[:\.]?'))]
+Test: report    text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|epub|vol|and|pp?|in|is[sb]n)[:\.]?'))]
 Message: This journal reference () has untagged textual content - . Is it tagged correctly? -->
 <root xmlns:ali="http://www.niso.org/schemas/ali/1.0/" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">
     <article>

test/tests/rp/journal-ref-checks/journal-ref-text-content/journal-ref-text-content.sch

@@ -146,7 +146,7 @@
   </xsl:function>
   <pattern id="journal-ref-checks-pattern">
     <rule context="mixed-citation[@publication-type='journal']" id="journal-ref-checks">
-      <report test="text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|vol|and|pp?|in|is[sb]n)[:\.]?'))]" role="warning" id="journal-ref-text-content">[journal-ref-text-content] This journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has untagged textual content - <value-of select="string-join(text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|vol|and|pp?|in|is[sb]n)[:\.]?'))],'; ')"/>. Is it tagged correctly?</report>
+      <report test="text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|epub|vol|and|pp?|in|is[sb]n)[:\.]?'))]" role="warning" id="journal-ref-text-content">[journal-ref-text-content] This journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has untagged textual content - <value-of select="string-join(text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|epub|vol|and|pp?|in|is[sb]n)[:\.]?'))],'; ')"/>. Is it tagged correctly?</report>
     </rule>
   </pattern>
   <pattern id="root-pattern">

test/tests/rp/journal-ref-checks/journal-ref-text-content/pass.xml

@@ -1,6 +1,6 @@
 <?oxygen SCHSchema="journal-ref-text-content.sch"?>
 <!--Context: mixed-citation[@publication-type='journal']
-Test: report    text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|vol|and|pp?|in|is[sb]n)[:\.]?'))]
+Test: report    text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|epub|vol|and|pp?|in|is[sb]n)[:\.]?'))]
 Message: This journal reference () has untagged textual content - . Is it tagged correctly? -->
 <root xmlns:ali="http://www.niso.org/schemas/ali/1.0/" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">
     <article>