Merge pull request #816 from elifesciences/pr-816

RP XSL changes

src/preprint-changes.xsl

@@ -756,15 +756,22 @@
                     </xsl:choose>
                     <xsl:element name="p">
                         <xsl:choose>
+                            <xsl:when test="./@notes-type='competing-interest-statement'">
+                                <xsl:text>Competing interests: </xsl:text>
+                                <xsl:choose>
+                                    <xsl:when test="count(p) = 1 and ./p[1]='The authors have declared no competing interest.'">
+                                        <xsl:text>No competing interests declared</xsl:text>
+                                    </xsl:when>
+                                    <xsl:otherwise>
+                                        <xsl:apply-templates select="./p/(*|text())"/>
+                                    </xsl:otherwise>
+                                </xsl:choose>
+                            </xsl:when>
                             <xsl:when test="./title">
                                 <xsl:value-of select="./title"/>
                                 <xsl:text>: </xsl:text>
                                 <xsl:apply-templates select="./p/(*|text())"/>
                             </xsl:when>
-                            <xsl:when test="./@notes-type='competing-interest-statement'">
-                                <xsl:text>Competing interests: </xsl:text>
-                                <xsl:apply-templates select="./p/(*|text())"/>
-                            </xsl:when>
                             <xsl:otherwise>
                                 <xsl:apply-templates select="./p/(*|text())"/>
                             </xsl:otherwise>
@@ -1376,6 +1383,20 @@
             <xsl:apply-templates select="*|text()|comment()|processing-instruction()"/>
         </xsl:copy>
     </xsl:template>
+
+     <!-- Add sec-type="ethics-statement" -->
+    <xsl:template xml:id="sec-ethics" match="sec[(not(@sec-type)) and matches(lower-case(title[1]),'ethics') and not(matches(lower-case(title[1]),'data') and matches(lower-case(title[1]),'ava[il][il]ability|access|sharing')) and not(ancestor::sec[matches(lower-case(title[1]),'ethics')])]">
+        <xsl:copy>
+            <xsl:apply-templates select="@*"/>
+            <xsl:attribute name="sec-type">ethics-statement</xsl:attribute>
+            <xsl:if test="not(@id)">
+                <xsl:attribute name="id">
+                    <xsl:value-of select="generate-id(.)"/>
+                </xsl:attribute>
+            </xsl:if>
+            <xsl:apply-templates select="*|text()|comment()|processing-instruction()"/>
+        </xsl:copy>
+    </xsl:template>
 
     <!-- Strip unnecessary bolding and italicisation from inside citations -->
     <xsl:template xml:id="strip-bold-italic-around-xref" match="xref/bold[italic[not(xref)]]

src/rp-schematron-base.sch

@@ -1218,7 +1218,7 @@
           role="error" 
           id="sec-empty">sec element is not populated with any content. Either there's a mistake or the section should be removed.</assert>
 
-        <report test="@sec-type='data-availability' and preceding::sec[@sec-type='data-availability']" 
+        <report test="@sec-type='data-availability' and (preceding::sec[@sec-type='data-availability'] or ancestor::sec[@sec-type='data-availability'])" 
           role="warning" 
           id="sec-data-availability">sec has the sec-type 'data-availability', but there is one or more other secs with this same sec-type. Are they duplicates?</report>
 
@@ -1230,6 +1230,10 @@
           role="warning" 
           id="sec-coi-2">sec has a title suggesting it's a competing interest statement. COI statements should be captured within author-notes, so this content should be moved into fn with the fn-type="coi-statement" within author-notes.</report>
 
+        <report test="@sec-type='ethics-statement' and (preceding::sec[@sec-type='ethics-statement'] or ancestor::sec[@sec-type='ethics-statement'])" 
+          role="error" 
+          id="sec-ethics">sec has the sec-type 'ethics-statement', but there is one or more other secs with this same sec-type. Are they duplicates? There can only be one section with this sec-type (although it can have subsections with further distinctions that have separate 'ethics-...' sec-types - e.g. "ethics-approval-human", "ethics-approval-animal" etc.)</report>
+
         <report test="def-list and not(*[not(name()=('label','title','sec-meta','def-list'))])" 
           role="error" 
           id="sec-def-list">sec element only contains a child def-list. This is therefore a glossary, not a sec.</report>

src/rp-schematron.sch

@@ -675,12 +675,14 @@
 
         <assert test="*[not(name()=('label','title','sec-meta'))]" role="error" id="sec-empty">[sec-empty] sec element is not populated with any content. Either there's a mistake or the section should be removed.</assert>
 
-        <report test="@sec-type='data-availability' and preceding::sec[@sec-type='data-availability']" role="warning" id="sec-data-availability">[sec-data-availability] sec has the sec-type 'data-availability', but there is one or more other secs with this same sec-type. Are they duplicates?</report>
+        <report test="@sec-type='data-availability' and (preceding::sec[@sec-type='data-availability'] or ancestor::sec[@sec-type='data-availability'])" role="warning" id="sec-data-availability">[sec-data-availability] sec has the sec-type 'data-availability', but there is one or more other secs with this same sec-type. Are they duplicates?</report>
 
         <report test="title[1][matches(lower-case(.),'(compete?t?ing|conflicts?[\s-]of)[\s-]interest|disclosure|declaration|disclaimer')] and ancestor::article//article-meta/author-notes/fn[@fn-type='coi-statement']" role="warning" id="sec-coi">[sec-coi] sec has a title suggesting it's a competing interest statement, but there is also a competing interest statement in author-notes. Are they duplicates? COI statements should be captured within author-notes, so this section should likely be deleted.</report>
 
         <report test="title[1][matches(lower-case(.),'(compete?t?ing|conflicts?[\s-]of)[\s-]interest|disclosure|declaration|disclaimer')] and not(ancestor::article//article-meta/author-notes/fn[@fn-type='coi-statement'])" role="warning" id="sec-coi-2">[sec-coi-2] sec has a title suggesting it's a competing interest statement. COI statements should be captured within author-notes, so this content should be moved into fn with the fn-type="coi-statement" within author-notes.</report>
 
+        <report test="@sec-type='ethics-statement' and (preceding::sec[@sec-type='ethics-statement'] or ancestor::sec[@sec-type='ethics-statement'])" role="error" id="sec-ethics">[sec-ethics] sec has the sec-type 'ethics-statement', but there is one or more other secs with this same sec-type. Are they duplicates? There can only be one section with this sec-type (although it can have subsections with further distinctions that have separate 'ethics-...' sec-types - e.g. "ethics-approval-human", "ethics-approval-animal" etc.)</report>
+
         <report test="def-list and not(*[not(name()=('label','title','sec-meta','def-list'))])" role="error" id="sec-def-list">[sec-def-list] sec element only contains a child def-list. This is therefore a glossary, not a sec.</report>
 
         <report test="glossary and not(*[not(name()=('label','title','sec-meta','glossary'))])" role="warning" id="sec-glossary">[sec-glossary] sec element only contains a child glossary. Is it a redundant sec (which should be deleted)? Or perhaps it indicates the structure/hierarchy has been incorrectly captured.</report>

src/rp-schematron.xsl

@@ -5066,8 +5066,8 @@
          </xsl:otherwise>
       </xsl:choose>
       <!--REPORT warning-->
-      <xsl:if test="@sec-type='data-availability' and preceding::sec[@sec-type='data-availability']">
-         <svrl:successful-report xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="@sec-type='data-availability' and preceding::sec[@sec-type='data-availability']">
+      <xsl:if test="@sec-type='data-availability' and (preceding::sec[@sec-type='data-availability'] or ancestor::sec[@sec-type='data-availability'])">
+         <svrl:successful-report xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="@sec-type='data-availability' and (preceding::sec[@sec-type='data-availability'] or ancestor::sec[@sec-type='data-availability'])">
             <xsl:attribute name="id">sec-data-availability</xsl:attribute>
             <xsl:attribute name="role">warning</xsl:attribute>
             <xsl:attribute name="location">
@@ -5099,6 +5099,17 @@
          </svrl:successful-report>
       </xsl:if>
       <!--REPORT error-->
+      <xsl:if test="@sec-type='ethics-statement' and (preceding::sec[@sec-type='ethics-statement'] or ancestor::sec[@sec-type='ethics-statement'])">
+         <svrl:successful-report xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="@sec-type='ethics-statement' and (preceding::sec[@sec-type='ethics-statement'] or ancestor::sec[@sec-type='ethics-statement'])">
+            <xsl:attribute name="id">sec-ethics</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>[sec-ethics] sec has the sec-type 'ethics-statement', but there is one or more other secs with this same sec-type. Are they duplicates? There can only be one section with this sec-type (although it can have subsections with further distinctions that have separate 'ethics-...' sec-types - e.g. "ethics-approval-human", "ethics-approval-animal" etc.)</svrl:text>
+         </svrl:successful-report>
+      </xsl:if>
+      <!--REPORT error-->
       <xsl:if test="def-list and not(*[not(name()=('label','title','sec-meta','def-list'))])">
          <svrl:successful-report xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="def-list and not(*[not(name()=('label','title','sec-meta','def-list'))])">
             <xsl:attribute name="id">sec-def-list</xsl:attribute>

test/tests/preprint-changes/all/output.xml

@@ -68,7 +68,7 @@
 <fn id="n2" fn-type="present-address"><label>‡</label><p><bold>Present address</bold>: Department of Biochemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland</p></fn>
 <fn id="n3" fn-type="present-address"><label>§</label><p>Present address: Massachusetts <italic>Institute</italic> of <bold>Technology</bold>, Picower Institute for Learning and Memory, 43 Vassar St, Cambridge, MA 02139, United States</p></fn>
 <fn id="n4" fn-type="present-address"><label>¶</label><p>Present address: Vertex Pharmaceuticals, 50 Northern Avenue, Boston, Mass. 02210, United States</p></fn>
-<fn fn-type="coi-statement"><p>Competing Interest Statement: The authors have declared no competing interest.</p></fn>
+<fn fn-type="coi-statement"><p>Competing interests: No competing interests declared</p></fn>
 </author-notes>
 <permissions>
 <ali:free_to_read/>

test/tests/preprint-changes/article-meta-changes/output.xml

@@ -50,7 +50,7 @@
 </contrib>
 </contrib-group>
 <author-notes>
-<fn fn-type="coi-statement"><p>Competing Interest Statement: The authors have declared no competing interest.</p></fn>
+<fn fn-type="coi-statement"><p>Competing interests: No competing interests declared</p></fn>
 </author-notes>
 <pub-date pub-type="epub"><year>2024</year></pub-date>
 <volume>13</volume>

test/tests/preprint-changes/author-notes-notes-handling/output.xml

@@ -3,7 +3,7 @@
 <front>
 <article-meta><author-notes>
 <fn/>
-<fn fn-type="coi-statement"><p>Competing Interest Statement: The authors have declared no competing interest.</p></fn>
+<fn fn-type="coi-statement"><p>Competing interests: No competing interests declared</p></fn>
 </author-notes>
 <related-object content-type="" source-id="" source-id-type="registry-name" source-type="clinical-trials-registry" document-id="" document-id-type="clinical-trial-number" xlink:href="">DRKS00021419</related-object>
 <custom-meta-group>

test/tests/preprint-changes/rearrange-back/output.xml

@@ -16,7 +16,7 @@
 <title>Something else</title>
 <p>...</p>
 </ack>
-<sec id="d545e19" sec-type="additional-information">
+<sec id="d556e19" sec-type="additional-information">
 <title>Additional information</title>
 <sec id="s5">
 <title>Funding</title>
@@ -41,9 +41,9 @@
 <p>All code and software needed to generate the results is available as part of public resources: LD score regression (<ext-link ext-link-type="uri" xlink:href="https://github.com/bulik/ldsc">https://github.com/bulik/ldsc</ext-link>), FUMA (<ext-link ext-link-type="uri" xlink:href="https://fuma.ctglab.nl/">https://fuma.ctglab.nl/</ext-link>), MiXeR (<ext-link ext-link-type="uri" xlink:href="https://github.com/precimed/mixer">https://github.com/precimed/mixer</ext-link>), BM location (simulation, training, and model) <italic>[made public upon acceptance]</italic>.</p>
 </sec>
 </sec>
-<sec id="suppd545e19" sec-type="supplementary-material">
+<sec id="suppd556e19" sec-type="supplementary-material">
 <title>Additional files</title>
-<supplementary-material id="d545e10">
+<supplementary-material id="d556e10">
 <label>Supplementary materials</label>
 <media xlink:href="supplements/278950_file02.docx"/>
 </supplementary-material>

test/tests/preprint-changes/sec-ethics/input.xml

@@ -0,0 +1,13 @@
+<!--Testing template with id: sec-ethics-->
+<sec id="s4">
+<title>ETHICS STATEMENT</title>
+<sec>
+<title>Human</title>
+</sec>
+<sec>
+<title>Monkey</title>
+</sec>
+<sec>
+<title>Machine</title>
+</sec>
+</sec>

test/tests/preprint-changes/sec-ethics/output.xml

@@ -0,0 +1,13 @@
+<!--Testing template with id: sec-ethics-->
+<sec id="s4" sec-type="ethics-statement">
+<title>ETHICS STATEMENT</title>
+<sec>
+<title>Human</title>
+</sec>
+<sec>
+<title>Monkey</title>
+</sec>
+<sec>
+<title>Machine</title>
+</sec>
+</sec>

test/tests/rp/sec-checks/sec-data-availability/fail.xml

@@ -1,6 +1,6 @@
 <?oxygen SCHSchema="sec-data-availability.sch"?>
 <!--Context: sec
-Test: report    @sec-type='data-availability' and preceding::sec[@sec-type='data-availability']
+Test: report    @sec-type='data-availability' and (preceding::sec[@sec-type='data-availability'] or ancestor::sec[@sec-type='data-availability'])
 Message: sec has the sec-type 'data-availability', but there is one or more other secs with this same sec-type. Are they duplicates? -->
 <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/sec-checks/sec-data-availability/pass.xml

@@ -1,6 +1,6 @@
 <?oxygen SCHSchema="sec-data-availability.sch"?>
 <!--Context: sec
-Test: report    @sec-type='data-availability' and preceding::sec[@sec-type='data-availability']
+Test: report    @sec-type='data-availability' and (preceding::sec[@sec-type='data-availability'] or ancestor::sec[@sec-type='data-availability'])
 Message: sec has the sec-type 'data-availability', but there is one or more other secs with this same sec-type. Are they duplicates? -->
 <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/sec-checks/sec-data-availability/sec-data-availability.sch

@@ -146,7 +146,7 @@
   </xsl:function>
   <pattern id="sec-checks-pattern">
     <rule context="sec" id="sec-checks">
-      <report test="@sec-type='data-availability' and preceding::sec[@sec-type='data-availability']" role="warning" id="sec-data-availability">[sec-data-availability] sec has the sec-type 'data-availability', but there is one or more other secs with this same sec-type. Are they duplicates?</report>
+      <report test="@sec-type='data-availability' and (preceding::sec[@sec-type='data-availability'] or ancestor::sec[@sec-type='data-availability'])" role="warning" id="sec-data-availability">[sec-data-availability] sec has the sec-type 'data-availability', but there is one or more other secs with this same sec-type. Are they duplicates?</report>
     </rule>
   </pattern>
   <pattern id="root-pattern">

test/tests/rp/sec-checks/sec-ethics/fail.xml

@@ -0,0 +1,17 @@
+<?oxygen SCHSchema="sec-ethics.sch"?>
+<!--Context: sec
+Test: report    @sec-type='ethics-statement' and (preceding::sec[@sec-type='ethics-statement'] or ancestor::sec[@sec-type='ethics-statement'])
+Message: sec has the sec-type 'ethics-statement', but there is one or more other secs with this same sec-type. Are they duplicates? There can only be one section with this sec-type (although it can have subsections with further distinctions that have separate 'ethics-...' sec-types - e.g. "ethics-approval-human", "ethics-approval-animal" etc.) -->
+<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>
+        <sec id="s6" sec-type="ethics-statement">
+            <title>Ethics</title>
+            <sec sec-type="ethics-statement">
+                <p>Human subjects: Fresh tissue samples were obtained upon informed consent from patients undergoing surgery at the Gynecology Division of the European Institute of Oncology (Milan). Sample collection was performed under the protocol number R789-IEO approved by the Ethics Committee of the European Institute of Oncology.</p>
+            </sec>
+            <sec sec-type="ethics-statement">
+                <p>Animal experimentation: All animal studies were performed following a  protocol approved by the fully authorized animal facility of European Institute of Oncology and by the Italian Ministry of Health (as required by the Italian Law) (IACUCs number 1256/2015) and in accordance to EU directive 2010/63. Mouse tissues were obtained from Karolinska Institutet (Stockholm, Sweden) and IRCCS San Raffaele Scientific Institute (Milan, Italy), in accordance with Institutional Animal Care and Use Committees.</p>
+            </sec>
+        </sec>
+    </article>
+</root>

test/tests/rp/sec-checks/sec-ethics/pass.xml

@@ -0,0 +1,17 @@
+<?oxygen SCHSchema="sec-ethics.sch"?>
+<!--Context: sec
+Test: report    @sec-type='ethics-statement' and (preceding::sec[@sec-type='ethics-statement'] or ancestor::sec[@sec-type='ethics-statement'])
+Message: sec has the sec-type 'ethics-statement', but there is one or more other secs with this same sec-type. Are they duplicates? There can only be one section with this sec-type (although it can have subsections with further distinctions that have separate 'ethics-...' sec-types - e.g. "ethics-approval-human", "ethics-approval-animal" etc.) -->
+<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>
+        <sec id="s6" sec-type="ethics-statement">
+            <title>Ethics</title>
+            <sec sec-type="ethics-approval-human">
+                <p>Human subjects: Fresh tissue samples were obtained upon informed consent from patients undergoing surgery at the Gynecology Division of the European Institute of Oncology (Milan). Sample collection was performed under the protocol number R789-IEO approved by the Ethics Committee of the European Institute of Oncology.</p>
+            </sec>
+            <sec sec-type="ethics-approval-animal">
+                <p>Animal experimentation: All animal studies were performed following a  protocol approved by the fully authorized animal facility of European Institute of Oncology and by the Italian Ministry of Health (as required by the Italian Law) (IACUCs number 1256/2015) and in accordance to EU directive 2010/63. Mouse tissues were obtained from Karolinska Institutet (Stockholm, Sweden) and IRCCS San Raffaele Scientific Institute (Milan, Italy), in accordance with Institutional Animal Care and Use Committees.</p>
+            </sec>
+        </sec>
+    </article>
+</root>