Merge pull request #769 from elifesciences/pr-769

VOR - update RRID link in message text

src/final-JATS-schematron.sch

@@ -5435,7 +5435,7 @@
       <let name="link-strip-text" value="string-join(for $x in (*[not(matches(local-name(),'^ext-link$|^contrib-id$|^license_ref$|^institution-id$|^email$|^xref$|^monospace$'))]|text()) return $x,'')"/>
       <let name="url-text" value="string-join(for $x in tokenize($link-strip-text,' ')         return   if (matches($x,'^https?:..(www\.)?[-a-zA-Z0-9@:%._\+~#=]{2,256}\.[a-z]{2,6}([-a-zA-Z0-9@:%_\+.~#?&amp;//=]*)|^ftp://.|^git://.|^tel:.|^mailto:.|\.org[\p{Zs}]?|\.com[\p{Zs}]?|\.co.uk[\p{Zs}]?|\.us[\p{Zs}]?|\.net[\p{Zs}]?|\.edu[\p{Zs}]?|\.gov[\p{Zs}]?|\.io[\p{Zs}]?')) then $x         else (),'; ')"/>
 
-      <report see="https://elifeproduction.slab.com/posts/rri-ds-5k19v560#rrid-test" test="($text-count gt $count)" role="warning" id="rrid-test">[rrid-test] '<name/>' element contains what looks like <value-of select="$text-count - $count"/> unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID/RRID:'. Element begins with <value-of select="substring(.,1,15)"/>.</report>
+      <report see="https://elifeproduction.slab.com/posts/rri-ds-5k19v560#rrid-test" test="($text-count gt $count)" role="warning" id="rrid-test">[rrid-test] '<name/>' element contains what looks like <value-of select="$text-count - $count"/> unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID:'. Element begins with <value-of select="substring(.,1,15)"/>.</report>
 
       <report see="https://elifeproduction.slab.com/posts/house-style-yi0641ob#h6d61-org-test" test="matches($t,$org-regex) and not(descendant::italic[contains(.,e:org-conform($t))]) and not(descendant::element-citation)" role="warning" id="org-test">[org-test] <name/> element contains an organism - <value-of select="e:org-conform($t)"/> - but there is no italic element with that correct capitalisation or spacing. Is this correct? <name/> element begins with <value-of select="concat(.,substring(.,1,15))"/>.</report>
 

src/final-JATS-schematron.xsl

@@ -29521,7 +29521,7 @@
                <xsl:value-of select="name(.)"/>
                <xsl:text/>' element contains what looks like <xsl:text/>
                <xsl:value-of select="$text-count - $count"/>
-               <xsl:text/> unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID/RRID:'. Element begins with <xsl:text/>
+               <xsl:text/> unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID:'. Element begins with <xsl:text/>
                <xsl:value-of select="substring(.,1,15)"/>
                <xsl:text/>.</svrl:text>
          </svrl:successful-report>

src/final-package-JATS-schematron.sch

@@ -5441,7 +5441,7 @@
       <let name="link-strip-text" value="string-join(for $x in (*[not(matches(local-name(),'^ext-link$|^contrib-id$|^license_ref$|^institution-id$|^email$|^xref$|^monospace$'))]|text()) return $x,'')"/>
       <let name="url-text" value="string-join(for $x in tokenize($link-strip-text,' ')         return   if (matches($x,'^https?:..(www\.)?[-a-zA-Z0-9@:%._\+~#=]{2,256}\.[a-z]{2,6}([-a-zA-Z0-9@:%_\+.~#?&amp;//=]*)|^ftp://.|^git://.|^tel:.|^mailto:.|\.org[\p{Zs}]?|\.com[\p{Zs}]?|\.co.uk[\p{Zs}]?|\.us[\p{Zs}]?|\.net[\p{Zs}]?|\.edu[\p{Zs}]?|\.gov[\p{Zs}]?|\.io[\p{Zs}]?')) then $x         else (),'; ')"/>
 
-      <report see="https://elifeproduction.slab.com/posts/rri-ds-5k19v560#rrid-test" test="($text-count gt $count)" role="warning" id="rrid-test">'<name/>' element contains what looks like <value-of select="$text-count - $count"/> unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID/RRID:'. Element begins with <value-of select="substring(.,1,15)"/>.</report>
+      <report see="https://elifeproduction.slab.com/posts/rri-ds-5k19v560#rrid-test" test="($text-count gt $count)" role="warning" id="rrid-test">'<name/>' element contains what looks like <value-of select="$text-count - $count"/> unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID:'. Element begins with <value-of select="substring(.,1,15)"/>.</report>
 
       <report see="https://elifeproduction.slab.com/posts/house-style-yi0641ob#h6d61-org-test" test="matches($t,$org-regex) and not(descendant::italic[contains(.,e:org-conform($t))]) and not(descendant::element-citation)" role="warning" id="org-test"><name/> element contains an organism - <value-of select="e:org-conform($t)"/> - but there is no italic element with that correct capitalisation or spacing. Is this correct? <name/> element begins with <value-of select="concat(.,substring(.,1,15))"/>.</report>
 

src/pre-JATS-schematron.sch

@@ -5380,7 +5380,7 @@
       <let name="link-strip-text" value="string-join(for $x in (*[not(matches(local-name(),'^ext-link$|^contrib-id$|^license_ref$|^institution-id$|^email$|^xref$|^monospace$'))]|text()) return $x,'')"/>
       <let name="url-text" value="string-join(for $x in tokenize($link-strip-text,' ')         return   if (matches($x,'^https?:..(www\.)?[-a-zA-Z0-9@:%._\+~#=]{2,256}\.[a-z]{2,6}([-a-zA-Z0-9@:%_\+.~#?&amp;//=]*)|^ftp://.|^git://.|^tel:.|^mailto:.|\.org[\p{Zs}]?|\.com[\p{Zs}]?|\.co.uk[\p{Zs}]?|\.us[\p{Zs}]?|\.net[\p{Zs}]?|\.edu[\p{Zs}]?|\.gov[\p{Zs}]?|\.io[\p{Zs}]?')) then $x         else (),'; ')"/>
 
-      <report see="https://elifeproduction.slab.com/posts/rri-ds-5k19v560#rrid-test" test="($text-count gt $count)" role="warning" id="rrid-test">[rrid-test] '<name/>' element contains what looks like <value-of select="$text-count - $count"/> unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID/RRID:'. Element begins with <value-of select="substring(.,1,15)"/>.</report>
+      <report see="https://elifeproduction.slab.com/posts/rri-ds-5k19v560#rrid-test" test="($text-count gt $count)" role="warning" id="rrid-test">[rrid-test] '<name/>' element contains what looks like <value-of select="$text-count - $count"/> unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID:'. Element begins with <value-of select="substring(.,1,15)"/>.</report>
 
       <report see="https://elifeproduction.slab.com/posts/house-style-yi0641ob#h6d61-org-test" test="matches($t,$org-regex) and not(descendant::italic[contains(.,e:org-conform($t))]) and not(descendant::element-citation)" role="warning" id="org-test">[org-test] <name/> element contains an organism - <value-of select="e:org-conform($t)"/> - but there is no italic element with that correct capitalisation or spacing. Is this correct? <name/> element begins with <value-of select="concat(.,substring(.,1,15))"/>.</report>
 

src/pre-JATS-schematron.xsl

@@ -29267,7 +29267,7 @@
                <xsl:value-of select="name(.)"/>
                <xsl:text/>' element contains what looks like <xsl:text/>
                <xsl:value-of select="$text-count - $count"/>
-               <xsl:text/> unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID/RRID:'. Element begins with <xsl:text/>
+               <xsl:text/> unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID:'. Element begins with <xsl:text/>
                <xsl:value-of select="substring(.,1,15)"/>
                <xsl:text/>.</svrl:text>
          </svrl:successful-report>

src/schematron.sch

@@ -10055,7 +10055,7 @@ else self::*/local-name() = $allowed-p-blocks"
       <report see="https://elifeproduction.slab.com/posts/rri-ds-5k19v560#rrid-test" 
         test="($text-count gt $count)" 
         role="warning" 
-        id="rrid-test">'<name/>' element contains what looks like <value-of select="$text-count - $count"/> unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID/RRID:'. Element begins with <value-of select="substring(.,1,15)"/>.</report>
+        id="rrid-test">'<name/>' element contains what looks like <value-of select="$text-count - $count"/> unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID:'. Element begins with <value-of select="substring(.,1,15)"/>.</report>
 
       <report see="https://elifeproduction.slab.com/posts/house-style-yi0641ob#h6d61-org-test"  
         test="matches($t,$org-regex) and not(descendant::italic[contains(.,e:org-conform($t))]) and not(descendant::element-citation)" 

test/tests/gen/rrid-org-code/rrid-test/fail.xml

@@ -1,7 +1,7 @@
 <?oxygen SCHSchema="rrid-test.sch"?>
 <!--Context: p|td|th
 Test: report    ($text-count gt $count)
-Message: '' element contains what looks like  unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID/RRID:'. Element begins with . -->
+Message: '' element contains what looks like  unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID:'. Element begins with . -->
 <root xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:ali="http://www.niso.org/schemas/ali/1.0">
   <article>
     <p>RRID:AB_0001</p>

test/tests/gen/rrid-org-code/rrid-test/pass.xml

@@ -1,7 +1,7 @@
 <?oxygen SCHSchema="rrid-test.sch"?>
 <!--Context: p|td|th
 Test: report    ($text-count gt $count)
-Message: '' element contains what looks like  unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID/RRID:'. Element begins with . -->
+Message: '' element contains what looks like  unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID:'. Element begins with . -->
 <root xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:ali="http://www.niso.org/schemas/ali/1.0">
   <article>
     <p><ext-link xlink:href="https://identifiers.org/RRID/RRID:AB_0001">RRID:AB_0001</ext-link></p>

test/tests/gen/rrid-org-code/rrid-test/rrid-test.sch

@@ -1370,7 +1370,7 @@
       <let name="unequal-equal-text" value="string-join(for $x in tokenize(replace(.,'[&gt;&lt;]',''),' | ') return if (matches($x,'=$|^=') and not(matches($x,'^=$'))) then $x else (),'; ')"/>
       <let name="link-strip-text" value="string-join(for $x in (*[not(matches(local-name(),'^ext-link$|^contrib-id$|^license_ref$|^institution-id$|^email$|^xref$|^monospace$'))]|text()) return $x,'')"/>
       <let name="url-text" value="string-join(for $x in tokenize($link-strip-text,' ')         return   if (matches($x,'^https?:..(www\.)?[-a-zA-Z0-9@:%._\+~#=]{2,256}\.[a-z]{2,6}([-a-zA-Z0-9@:%_\+.~#?&amp;//=]*)|^ftp://.|^git://.|^tel:.|^mailto:.|\.org[\p{Zs}]?|\.com[\p{Zs}]?|\.co.uk[\p{Zs}]?|\.us[\p{Zs}]?|\.net[\p{Zs}]?|\.edu[\p{Zs}]?|\.gov[\p{Zs}]?|\.io[\p{Zs}]?')) then $x         else (),'; ')"/>
-      <report see="https://elifeproduction.slab.com/posts/rri-ds-5k19v560#rrid-test" test="($text-count gt $count)" role="warning" id="rrid-test">'<name/>' element contains what looks like <value-of select="$text-count - $count"/> unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID/RRID:'. Element begins with <value-of select="substring(.,1,15)"/>.</report>
+      <report see="https://elifeproduction.slab.com/posts/rri-ds-5k19v560#rrid-test" test="($text-count gt $count)" role="warning" id="rrid-test">'<name/>' element contains what looks like <value-of select="$text-count - $count"/> unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID:'. Element begins with <value-of select="substring(.,1,15)"/>.</report>
     </rule>
   </pattern>
   <pattern id="root-pattern">

test/xspec/schematron.sch

@@ -6995,7 +6995,7 @@
       <let name="link-strip-text" value="string-join(for $x in (*[not(matches(local-name(),'^ext-link$|^contrib-id$|^license_ref$|^institution-id$|^email$|^xref$|^monospace$'))]|text()) return $x,'')"/>
       <let name="url-text" value="string-join(for $x in tokenize($link-strip-text,' ')         return   if (matches($x,'^https?:..(www\.)?[-a-zA-Z0-9@:%._\+~#=]{2,256}\.[a-z]{2,6}([-a-zA-Z0-9@:%_\+.~#?&amp;//=]*)|^ftp://.|^git://.|^tel:.|^mailto:.|\.org[\p{Zs}]?|\.com[\p{Zs}]?|\.co.uk[\p{Zs}]?|\.us[\p{Zs}]?|\.net[\p{Zs}]?|\.edu[\p{Zs}]?|\.gov[\p{Zs}]?|\.io[\p{Zs}]?')) then $x         else (),'; ')"/>
 
-      <report see="https://elifeproduction.slab.com/posts/rri-ds-5k19v560#rrid-test" test="($text-count gt $count)" role="warning" id="rrid-test">'<name/>' element contains what looks like <value-of select="$text-count - $count"/> unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID/RRID:'. Element begins with <value-of select="substring(.,1,15)"/>.</report>
+      <report see="https://elifeproduction.slab.com/posts/rri-ds-5k19v560#rrid-test" test="($text-count gt $count)" role="warning" id="rrid-test">'<name/>' element contains what looks like <value-of select="$text-count - $count"/> unlinked RRID(s). These should always be linked using 'https://identifiers.org/RRID:'. Element begins with <value-of select="substring(.,1,15)"/>.</report>
 
       <report see="https://elifeproduction.slab.com/posts/house-style-yi0641ob#h6d61-org-test" test="matches($t,$org-regex) and not(descendant::italic[contains(.,e:org-conform($t))]) and not(descendant::element-citation)" role="warning" id="org-test">
         <name/> element contains an organism - <value-of select="e:org-conform($t)"/> - but there is no italic element with that correct capitalisation or spacing. Is this correct? <name/> element begins with <value-of select="concat(.,substring(.,1,15))"/>.</report>