Merge pull request #819 from elifesciences/pr-819

Pr 819

src/final-JATS-schematron.sch

@@ -2256,7 +2256,7 @@
 
       <assert see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-related-object-7" test="@xlink:href[not(matches(.,'\p{Zs}'))]" role="error" id="clintrial-related-object-7">[clintrial-related-object-7] <name/> must have an @xlink:href with a value that does not contain a space character.</assert>
 
-      <assert see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-related-object-8" test="contains(.,@document-id/string())" role="warning" id="clintrial-related-object-8">[clintrial-related-object-8] <name/> has an @document-id '<value-of select="@document-id"/>'. But this is not in the text, which is likely incorrect - <value-of select="."/>.</assert>
+      <assert see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-related-object-8" test="@document-id = ." role="warning" id="clintrial-related-object-8">[clintrial-related-object-8] <name/> has an @document-id '<value-of select="@document-id"/>'. But this is not the text of the related-object, which is likely incorrect - <value-of select="."/>.</assert>
 
       <assert see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-related-object-9" test="matches(@id,'^RO[1-9]')" role="error" id="clintrial-related-object-9">[clintrial-related-object-9] <name/> must have an @id in the format 'RO1'. '<value-of select="@id"/>' does not conform to this convention.</assert>
 

src/final-JATS-schematron.xsl

@@ -11110,9 +11110,9 @@
       </xsl:choose>
       <!--ASSERT warning-->
       <xsl:choose>
-         <xsl:when test="contains(.,@document-id/string())"/>
+         <xsl:when test="@document-id = ."/>
          <xsl:otherwise>
-            <svrl:failed-assert xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="contains(.,@document-id/string())">
+            <svrl:failed-assert xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="@document-id = .">
                <xsl:attribute name="id">clintrial-related-object-8</xsl:attribute>
                <xsl:attribute name="see">https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-related-object-8</xsl:attribute>
                <xsl:attribute name="role">warning</xsl:attribute>
@@ -11123,7 +11123,7 @@
                   <xsl:value-of select="name(.)"/>
                   <xsl:text/> has an @document-id '<xsl:text/>
                   <xsl:value-of select="@document-id"/>
-                  <xsl:text/>'. But this is not in the text, which is likely incorrect - <xsl:text/>
+                  <xsl:text/>'. But this is not the text of the related-object, which is likely incorrect - <xsl:text/>
                   <xsl:value-of select="."/>
                   <xsl:text/>.</svrl:text>
             </svrl:failed-assert>

src/final-package-JATS-schematron.sch

@@ -2262,7 +2262,7 @@
 
       <assert see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-related-object-7" test="@xlink:href[not(matches(.,'\p{Zs}'))]" role="error" id="clintrial-related-object-7"><name/> must have an @xlink:href with a value that does not contain a space character.</assert>
 
-      <assert see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-related-object-8" test="contains(.,@document-id/string())" role="warning" id="clintrial-related-object-8"><name/> has an @document-id '<value-of select="@document-id"/>'. But this is not in the text, which is likely incorrect - <value-of select="."/>.</assert>
+      <assert see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-related-object-8" test="@document-id = ." role="warning" id="clintrial-related-object-8"><name/> has an @document-id '<value-of select="@document-id"/>'. But this is not the text of the related-object, which is likely incorrect - <value-of select="."/>.</assert>
 
       <assert see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-related-object-9" test="matches(@id,'^RO[1-9]')" role="error" id="clintrial-related-object-9"><name/> must have an @id in the format 'RO1'. '<value-of select="@id"/>' does not conform to this convention.</assert>
 

src/pre-JATS-schematron.sch

@@ -2201,7 +2201,7 @@
 
       <assert see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-related-object-7" test="@xlink:href[not(matches(.,'\p{Zs}'))]" role="error" id="clintrial-related-object-7">[clintrial-related-object-7] <name/> must have an @xlink:href with a value that does not contain a space character.</assert>
 
-      <assert see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-related-object-8" test="contains(.,@document-id/string())" role="warning" id="clintrial-related-object-8">[clintrial-related-object-8] <name/> has an @document-id '<value-of select="@document-id"/>'. But this is not in the text, which is likely incorrect - <value-of select="."/>.</assert>
+      <assert see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-related-object-8" test="@document-id = ." role="warning" id="clintrial-related-object-8">[clintrial-related-object-8] <name/> has an @document-id '<value-of select="@document-id"/>'. But this is not the text of the related-object, which is likely incorrect - <value-of select="."/>.</assert>
 
       <assert see="https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-related-object-9" test="matches(@id,'^RO[1-9]')" role="error" id="clintrial-related-object-9">[clintrial-related-object-9] <name/> must have an @id in the format 'RO1'. '<value-of select="@id"/>' does not conform to this convention.</assert>
 

src/pre-JATS-schematron.xsl

@@ -10957,9 +10957,9 @@
       </xsl:choose>
       <!--ASSERT warning-->
       <xsl:choose>
-         <xsl:when test="contains(.,@document-id/string())"/>
+         <xsl:when test="@document-id = ."/>
          <xsl:otherwise>
-            <svrl:failed-assert xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="contains(.,@document-id/string())">
+            <svrl:failed-assert xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="@document-id = .">
                <xsl:attribute name="id">clintrial-related-object-8</xsl:attribute>
                <xsl:attribute name="see">https://elifeproduction.slab.com/posts/abstracts-digests-and-impact-statements-tiau2k6x#clintrial-related-object-8</xsl:attribute>
                <xsl:attribute name="role">warning</xsl:attribute>
@@ -10970,7 +10970,7 @@
                   <xsl:value-of select="name(.)"/>
                   <xsl:text/> has an @document-id '<xsl:text/>
                   <xsl:value-of select="@document-id"/>
-                  <xsl:text/>'. But this is not in the text, which is likely incorrect - <xsl:text/>
+                  <xsl:text/>'. But this is not the text of the related-object, which is likely incorrect - <xsl:text/>
                   <xsl:value-of select="."/>
                   <xsl:text/>.</svrl:text>
             </svrl:failed-assert>

src/preprint-changes.xsl

@@ -1239,6 +1239,13 @@
     <!-- Fixes mistagged and all caps source elements -->
      <xsl:template xml:id="ref-source-fixes" match="mixed-citation//source">
          <xsl:choose>
+             <!-- Fix casing for eLife -->
+             <xsl:when test="matches(lower-case(.),'^\s*elife\s*$') and not(matches(.,'^\s*eLife\s*$'))">
+                    <xsl:copy>
+                        <xsl:apply-templates select="@*"/>
+                        <xsl:text>eLife</xsl:text>
+                    </xsl:copy>
+                </xsl:when>
                 <xsl:when test="matches(lower-case(.),'^in\s')">
                     <xsl:choose>
                         <xsl:when test="(ancestor::mixed-citation/@publication-type=('preprint','journal','other')) and upper-case(.)=.">

src/rp-schematron-base.sch

@@ -579,6 +579,10 @@
         <report test="text()[matches(.,'\p{L}') and not(matches(lower-case(.),'^[\p{Z}\p{P}]+(doi|pmid|and|pp?)[:\.]?'))]" 
         role="warning" 
         id="preprint-ref-text-content">This preprint 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|and|pp?)[:\.]?'))],'; ')"/>. Is it tagged correctly?</report>
+
+       <report test="volume" 
+        role="error" 
+        id="preprint-ref-volume">This preprint reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has a volume - <value-of select="volume"/>. That information is either tagged incorrectly, or the publication-type is wrong.</report>
      </rule>
 
       <rule context="mixed-citation[@publication-type='preprint']/source" id="preprint-source-checks">
@@ -784,6 +788,10 @@
         <report test="ancestor::mixed-citation[@publication-type='web']" 
           role="error" 
           id="pub-id-check-5">Web reference (with id <value-of select="ancestor::ref/@id"/>) has a <name/> <value-of select="if (@pub-id-type) then concat('with a pub-id-type ',@pub-id-type) else 'with no pub-id-type'"/> (<value-of select="."/>). This must be incorrect. Either the publication-type for the reference needs changing, or the pub-id should be changed to another element.</report>
+
+        <report test="@pub-id-type='doi' and ancestor::mixed-citation[@publication-type=('journal','book','preprint')] and matches(following-sibling::text()[1],'^[\.\s]?[\.\s]?[/&lt;&gt;:\d\+\-]')" 
+          role="warning" 
+          id="pub-id-check-6">doi in <value-of select="ancestor::mixed-citation/@publication-type"/> ref is followd by text - '<value-of select="following-sibling::text()[1]"/>'. Should that text be part of the DOI or tagged in some other way?</report>
      </rule>
 
       <rule context="ref//pub-id[@pub-id-type='isbn']|isbn" id="isbn-conformity">
@@ -2022,9 +2030,9 @@
         role="error" 
         id="clintrial-related-object-7"><name/> must have an @xlink:href with a value that does not contain a space character.</assert>
 
-      <assert test="contains(.,@document-id/string())" 
+      <assert test="@document-id = ." 
         role="warning" 
-        id="clintrial-related-object-8"><name/> has an @document-id '<value-of select="@document-id"/>'. But this is not in the text, which is likely incorrect - <value-of select="."/>.</assert>
+        id="clintrial-related-object-8"><name/> has an @document-id '<value-of select="@document-id"/>'. But this is not the text of the related-object, which is likely incorrect - <value-of select="."/>.</assert>
 
       <assert test="some $x in document($registries)/registries/registry satisfies ($x/subtitle/string()=@source-id)" 
         role="warning" 

src/rp-schematron.sch

@@ -363,6 +363,8 @@
         <assert test="article-title" role="error" id="preprint-ref-article-title">[preprint-ref-article-title] This preprint 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|and|pp?)[:\.]?'))]" role="warning" id="preprint-ref-text-content">[preprint-ref-text-content] This preprint 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|and|pp?)[:\.]?'))],'; ')"/>. Is it tagged correctly?</report>
+
+       <report test="volume" role="error" id="preprint-ref-volume">[preprint-ref-volume] This preprint reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has a volume - <value-of select="volume"/>. That information is either tagged incorrectly, or the publication-type is wrong.</report>
      </rule></pattern><pattern id="preprint-source-checks-pattern"><rule context="mixed-citation[@publication-type='preprint']/source" id="preprint-source-checks">
         <report test="matches(lower-case(.),'^(\.\s*)?in[^a-z]')" role="warning" id="preprint-source">[preprint-source] Preprint reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has a source that starts with 'In ', '<value-of select="."/>'. Should that text be moved out of the source? And is it a different type of reference?</report>
 
@@ -462,6 +464,8 @@
         <report test="ancestor::mixed-citation[@publication-type='preprint'] and not(@pub-id-type=('doi','pmid','pmcid','arxiv'))" role="error" id="pub-id-check-4">[pub-id-check-4] <name/> is within a journal reference, but it does not have one of the following permitted @pub-id-type values: 'doi','pmid','pmcid','arxiv'.</report>
 
         <report test="ancestor::mixed-citation[@publication-type='web']" role="error" id="pub-id-check-5">[pub-id-check-5] Web reference (with id <value-of select="ancestor::ref/@id"/>) has a <name/> <value-of select="if (@pub-id-type) then concat('with a pub-id-type ',@pub-id-type) else 'with no pub-id-type'"/> (<value-of select="."/>). This must be incorrect. Either the publication-type for the reference needs changing, or the pub-id should be changed to another element.</report>
+
+        <report test="@pub-id-type='doi' and ancestor::mixed-citation[@publication-type=('journal','book','preprint')] and matches(following-sibling::text()[1],'^[\.\s]?[\.\s]?[/&lt;&gt;:\d\+\-]')" role="warning" id="pub-id-check-6">[pub-id-check-6] doi in <value-of select="ancestor::mixed-citation/@publication-type"/> ref is followd by text - '<value-of select="following-sibling::text()[1]"/>'. Should that text be part of the DOI or tagged in some other way?</report>
      </rule></pattern><pattern id="isbn-conformity-pattern"><rule context="ref//pub-id[@pub-id-type='isbn']|isbn" id="isbn-conformity">
         <let name="t" value="translate(.,'-','')"/>
         <let name="sum" value="e:isbn-sum($t)"/>
@@ -1069,7 +1073,7 @@
 
       <assert test="@xlink:href[not(matches(.,'\p{Zs}'))]" role="error" id="clintrial-related-object-7">[clintrial-related-object-7] <name/> must have an @xlink:href with a value that does not contain a space character.</assert>
 
-      <assert test="contains(.,@document-id/string())" role="warning" id="clintrial-related-object-8">[clintrial-related-object-8] <name/> has an @document-id '<value-of select="@document-id"/>'. But this is not in the text, which is likely incorrect - <value-of select="."/>.</assert>
+      <assert test="@document-id = ." role="warning" id="clintrial-related-object-8">[clintrial-related-object-8] <name/> has an @document-id '<value-of select="@document-id"/>'. But this is not the text of the related-object, which is likely incorrect - <value-of select="."/>.</assert>
 
       <assert test="some $x in document($registries)/registries/registry satisfies ($x/subtitle/string()=@source-id)" role="warning" id="clintrial-related-object-11">[clintrial-related-object-11] <name/> @source-id value should almost always be one of the subtitles of the Crossref clinical trial registries. "<value-of select="@source-id"/>" is not one of the following <value-of select="string-join(for $x in document($registries)/registries/registry return concat('&quot;',$x/subtitle/string(),'&quot; (',$x/doi/string(),')'),', ')"/>. Is that correct?</assert>
 

src/rp-schematron.xsl

@@ -2885,6 +2885,21 @@
                <xsl:text/>. Is it tagged correctly?</svrl:text>
          </svrl:successful-report>
       </xsl:if>
+      <!--REPORT error-->
+      <xsl:if test="volume">
+         <svrl:successful-report xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="volume">
+            <xsl:attribute name="id">preprint-ref-volume</xsl:attribute>
+            <xsl:attribute name="role">error</xsl:attribute>
+            <xsl:attribute name="location">
+               <xsl:apply-templates select="." mode="schematron-select-full-path"/>
+            </xsl:attribute>
+            <svrl:text>[preprint-ref-volume] This preprint reference (<xsl:text/>
+               <xsl:value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>
+               <xsl:text/>) has a volume - <xsl:text/>
+               <xsl:value-of select="volume"/>
+               <xsl:text/>. That information is either tagged incorrectly, or the publication-type is wrong.</svrl:text>
+         </svrl:successful-report>
+      </xsl:if>
       <xsl:apply-templates select="*" mode="M35"/>
    </xsl:template>
    <xsl:template match="text()" priority="-1" mode="M35"/>
@@ -3611,6 +3626,21 @@
                <xsl:text/>). This must be incorrect. Either the publication-type for the reference needs changing, or the pub-id should be changed to another element.</svrl:text>
          </svrl:successful-report>
       </xsl:if>
+      <!--REPORT warning-->
+      <xsl:if test="@pub-id-type='doi' and ancestor::mixed-citation[@publication-type=('journal','book','preprint')] and matches(following-sibling::text()[1],'^[\.\s]?[\.\s]?[/&lt;&gt;:\d\+\-]')">
+         <svrl:successful-report xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="@pub-id-type='doi' and ancestor::mixed-citation[@publication-type=('journal','book','preprint')] and matches(following-sibling::text()[1],'^[\.\s]?[\.\s]?[/&lt;&gt;:\d\+\-]')">
+            <xsl:attribute name="id">pub-id-check-6</xsl:attribute>
+            <xsl:attribute name="role">warning</xsl:attribute>
+            <xsl:attribute name="location">
+               <xsl:apply-templates select="." mode="schematron-select-full-path"/>
+            </xsl:attribute>
+            <svrl:text>[pub-id-check-6] doi in <xsl:text/>
+               <xsl:value-of select="ancestor::mixed-citation/@publication-type"/>
+               <xsl:text/> ref is followd by text - '<xsl:text/>
+               <xsl:value-of select="following-sibling::text()[1]"/>
+               <xsl:text/>'. Should that text be part of the DOI or tagged in some other way?</svrl:text>
+         </svrl:successful-report>
+      </xsl:if>
       <xsl:apply-templates select="*" mode="M50"/>
    </xsl:template>
    <xsl:template match="text()" priority="-1" mode="M50"/>
@@ -7630,9 +7660,9 @@
       </xsl:choose>
       <!--ASSERT warning-->
       <xsl:choose>
-         <xsl:when test="contains(.,@document-id/string())"/>
+         <xsl:when test="@document-id = ."/>
          <xsl:otherwise>
-            <svrl:failed-assert xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="contains(.,@document-id/string())">
+            <svrl:failed-assert xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="@document-id = .">
                <xsl:attribute name="id">clintrial-related-object-8</xsl:attribute>
                <xsl:attribute name="role">warning</xsl:attribute>
                <xsl:attribute name="location">
@@ -7642,7 +7672,7 @@
                   <xsl:value-of select="name(.)"/>
                   <xsl:text/> has an @document-id '<xsl:text/>
                   <xsl:value-of select="@document-id"/>
-                  <xsl:text/>'. But this is not in the text, which is likely incorrect - <xsl:text/>
+                  <xsl:text/>'. But this is not the text of the related-object, which is likely incorrect - <xsl:text/>
                   <xsl:value-of select="."/>
                   <xsl:text/>.</svrl:text>
             </svrl:failed-assert>