Merge pull request #760 from elifesciences/pr-760

PR 760

src/rp-schematron-base.sch

@@ -235,6 +235,14 @@
         <report test="not(@corresp='yes') and (email or xref[@ref-type='corresp'])" 
           role="error" 
           id="author-email-no-corresp">Author <value-of select="e:get-name(name[1])"/> does not have the attribute corresp="yes", but they have a child email element or an xref with the attribute ref-type="corresp".</report>
+
+        <report test="(xref/@rid = ancestor::article-meta/author-notes/fn[@fn-type='equal']/@id) and not(@equal-contrib='yes')" 
+          role="error" 
+          id="author-equal-contrib-1">Author <value-of select="e:get-name(name[1])"/> does not have the attribute equal-contrib="yes", but they have a child xref element that points to a footnote with the fn-type 'equal'.</report>
+
+        <report test="not(xref/@rid = ancestor::article-meta/author-notes/fn[@fn-type='equal']/@id) and @equal-contrib='yes'" 
+          role="error" 
+          id="author-equal-contrib-2">Author <value-of select="e:get-name(name[1])"/> has the attribute equal-contrib="yes", but they do not have a child xref element that points to a footnote with the fn-type 'equal'.</report>
      </rule>
 
      <rule context="contrib-group//name" id="name-tests">
@@ -454,6 +462,10 @@
         <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|epub|vol|and|pp?|in|is[sb]n)[:\.]?'))],'; ')"/>. Is it tagged correctly?</report>
+
+       <report test="person-group[@person-group-type='editor']" 
+        role="warning" 
+        id="journal-ref-editor">This journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has an editor person-group. This info isn;t typically included in journal refs. Is it really a journal ref? Does it really contain editors?</report>
      </rule>
 
      <rule context="mixed-citation[@publication-type='journal']/source" id="journal-source-checks">
@@ -1630,6 +1642,50 @@
         role="error" 
         id="license-p-test-4">If a license contains an ali:license_ref element, there must be a link in license-p that matches the link in the ali:license_ref element. ali:license_ref link: <value-of select="$ali-ref"/>. Links in the license-p: <value-of select="string-join(ext-link/@xlink:href,'; ')"/>.</assert>
     </rule>
+
+      <rule context="fig[not(descendant::permissions)]|media[@mimetype='video' and not(descendant::permissions)]|table-wrap[not(descendant::permissions)]|supplementary-material[not(descendant::permissions)]" id="fig-permissions-check">
+      <let name="label" value="replace(label[1],'\.','')"/>
+
+      <report see="https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#reproduce-test-1" 
+        test="matches(caption[1],'[Rr]eproduced from')" 
+        role="warning" 
+        id="reproduce-test-1">The caption for <value-of select="$label"/> contains the text 'reproduced from', but has no permissions. Is this correct?</report>
+
+      <report see="https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#reproduce-test-2" 
+        test="matches(caption[1],'[Rr]eproduced [Ww]ith [Pp]ermission')" 
+        role="warning" 
+        id="reproduce-test-2">The caption for <value-of select="$label"/> contains the text 'reproduced with permission', but has no permissions. Is this correct?</report>
+
+      <report see="https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#reproduce-test-3" 
+        test="matches(caption[1],'[Aa]dapted from|[Aa]dapted with')" 
+        role="warning" 
+        id="reproduce-test-3">The caption for <value-of select="$label"/> contains the text 'adapted from ...', but has no permissions. Is this correct?</report>
+
+      <report see="https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#reproduce-test-4" 
+        test="matches(caption[1],'[Rr]eprinted from')" 
+        role="warning" 
+        id="reproduce-test-4">The caption for <value-of select="$label"/> contains the text 'reprinted from', but has no permissions. Is this correct?</report>
+
+      <report see="https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#reproduce-test-5" 
+        test="matches(caption[1],'[Rr]eprinted [Ww]ith [Pp]ermission')" 
+        role="warning" 
+        id="reproduce-test-5">The caption for <value-of select="$label"/> contains the text 'reprinted with permission', but has no permissions. Is this correct?</report>
+
+      <report see="https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#reproduce-test-6" 
+        test="matches(caption[1],'[Mm]odified from')" 
+        role="warning" 
+        id="reproduce-test-6">The caption for <value-of select="$label"/> contains the text 'modified from', but has no permissions. Is this correct?</report>
+
+      <report see="https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#reproduce-test-7"
+        test="matches(caption[1],'[Mm]odified [Ww]ith')" 
+        role="warning" 
+        id="reproduce-test-7">The caption for <value-of select="$label"/> contains the text 'modified with', but has no permissions. Is this correct?</report>
+
+      <report see="https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#reproduce-test-8" 
+        test="matches(caption[1],'[Uu]sed [Ww]ith [Pp]ermission')" 
+        role="warning" 
+        id="reproduce-test-8">The caption for <value-of select="$label"/> contains the text 'used with permission', but has no permissions. Is this correct?</report>
+    </rule>
     </pattern>
 
     <pattern id="digest">

src/rp-schematron.sch

@@ -187,6 +187,10 @@
         <report test="@corresp='yes' and not(email) and not(xref[@ref-type='corresp'])" role="error" id="author-corresp-no-email">[author-corresp-no-email] Author <value-of select="e:get-name(name[1])"/> has the attribute corresp="yes", but they do not have a child email element or an xref with the attribute ref-type="corresp".</report>
 
         <report test="not(@corresp='yes') and (email or xref[@ref-type='corresp'])" role="error" id="author-email-no-corresp">[author-email-no-corresp] Author <value-of select="e:get-name(name[1])"/> does not have the attribute corresp="yes", but they have a child email element or an xref with the attribute ref-type="corresp".</report>
+
+        <report test="(xref/@rid = ancestor::article-meta/author-notes/fn[@fn-type='equal']/@id) and not(@equal-contrib='yes')" role="error" id="author-equal-contrib-1">[author-equal-contrib-1] Author <value-of select="e:get-name(name[1])"/> does not have the attribute equal-contrib="yes", but they have a child xref element that points to a footnote with the fn-type 'equal'.</report>
+
+        <report test="not(xref/@rid = ancestor::article-meta/author-notes/fn[@fn-type='equal']/@id) and @equal-contrib='yes'" role="error" id="author-equal-contrib-2">[author-equal-contrib-2] Author <value-of select="e:get-name(name[1])"/> has the attribute equal-contrib="yes", but they do not have a child xref element that points to a footnote with the fn-type 'equal'.</report>
      </rule></pattern><pattern id="name-tests-pattern"><rule context="contrib-group//name" id="name-tests">
     	<assert test="count(surname) = 1" role="error" id="surname-test-1">[surname-test-1] Each name must contain only one surname.</assert>
 
@@ -296,6 +300,8 @@
         <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|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>
+
+       <report test="person-group[@person-group-type='editor']" role="warning" id="journal-ref-editor">[journal-ref-editor] This journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has an editor person-group. This info isn;t typically included in journal refs. Is it really a journal ref? Does it really contain editors?</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'"/>
 
@@ -876,6 +882,24 @@
       <let name="ali-ref" value="parent::license/ali:license_ref"/>
 
       <assert test="some $x in ext-link satisfies $x/@xlink:href = $ali-ref" role="error" id="license-p-test-4">[license-p-test-4] If a license contains an ali:license_ref element, there must be a link in license-p that matches the link in the ali:license_ref element. ali:license_ref link: <value-of select="$ali-ref"/>. Links in the license-p: <value-of select="string-join(ext-link/@xlink:href,'; ')"/>.</assert>
+    </rule></pattern><pattern id="fig-permissions-check-pattern"><rule context="fig[not(descendant::permissions)]|media[@mimetype='video' and not(descendant::permissions)]|table-wrap[not(descendant::permissions)]|supplementary-material[not(descendant::permissions)]" id="fig-permissions-check">
+      <let name="label" value="replace(label[1],'\.','')"/>
+
+      <report see="https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#reproduce-test-1" test="matches(caption[1],'[Rr]eproduced from')" role="warning" id="reproduce-test-1">[reproduce-test-1] The caption for <value-of select="$label"/> contains the text 'reproduced from', but has no permissions. Is this correct?</report>
+
+      <report see="https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#reproduce-test-2" test="matches(caption[1],'[Rr]eproduced [Ww]ith [Pp]ermission')" role="warning" id="reproduce-test-2">[reproduce-test-2] The caption for <value-of select="$label"/> contains the text 'reproduced with permission', but has no permissions. Is this correct?</report>
+
+      <report see="https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#reproduce-test-3" test="matches(caption[1],'[Aa]dapted from|[Aa]dapted with')" role="warning" id="reproduce-test-3">[reproduce-test-3] The caption for <value-of select="$label"/> contains the text 'adapted from ...', but has no permissions. Is this correct?</report>
+
+      <report see="https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#reproduce-test-4" test="matches(caption[1],'[Rr]eprinted from')" role="warning" id="reproduce-test-4">[reproduce-test-4] The caption for <value-of select="$label"/> contains the text 'reprinted from', but has no permissions. Is this correct?</report>
+
+      <report see="https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#reproduce-test-5" test="matches(caption[1],'[Rr]eprinted [Ww]ith [Pp]ermission')" role="warning" id="reproduce-test-5">[reproduce-test-5] The caption for <value-of select="$label"/> contains the text 'reprinted with permission', but has no permissions. Is this correct?</report>
+
+      <report see="https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#reproduce-test-6" test="matches(caption[1],'[Mm]odified from')" role="warning" id="reproduce-test-6">[reproduce-test-6] The caption for <value-of select="$label"/> contains the text 'modified from', but has no permissions. Is this correct?</report>
+
+      <report see="https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#reproduce-test-7" test="matches(caption[1],'[Mm]odified [Ww]ith')" role="warning" id="reproduce-test-7">[reproduce-test-7] The caption for <value-of select="$label"/> contains the text 'modified with', but has no permissions. Is this correct?</report>
+
+      <report see="https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#reproduce-test-8" test="matches(caption[1],'[Uu]sed [Ww]ith [Pp]ermission')" role="warning" id="reproduce-test-8">[reproduce-test-8] The caption for <value-of select="$label"/> contains the text 'used with permission', but has no permissions. Is this correct?</report>
     </rule></pattern>
 
     <pattern id="digest-title-checks-pattern"><rule context="title" id="digest-title-checks">