From 794e62efb8ac7b90b1627b88e0989931bcc2442f Mon Sep 17 00:00:00 2001
From: Fred Atherden <43879983+fred-atherden@users.noreply.github.com>
Date: Tue, 26 Nov 2024 13:23:19 +0000
Subject: [PATCH 1/2] RP - tweak regex in journal-source-3

---
 src/rp-schematron-base.sch                                    | 2 +-
 src/rp-schematron.sch                                         | 2 +-
 src/rp-schematron.xsl                                         | 4 ++--
 test/tests/rp/journal-source-checks/journal-source-3/fail.xml | 2 +-
 .../journal-source-3/journal-source-3.sch                     | 2 +-
 test/tests/rp/journal-source-checks/journal-source-3/pass.xml | 2 +-
 test/xspec/rp-schematron.sch                                  | 2 +-
 7 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/rp-schematron-base.sch b/src/rp-schematron-base.sch
index c2c40c57b1..37d88986fc 100644
--- a/src/rp-schematron-base.sch
+++ b/src/rp-schematron-base.sch
@@ -468,7 +468,7 @@
         role="warning" 
         id="journal-source-2">Journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has a source that starts with a roman numeral. Is part of the article-title captured in source? Source = <value-of select="."/>.</report>
 
-       <report test="matches(lower-case(.),'^(symposium|conference|proc\.?|proceeding|meeting|workshop)|\s?(symposium|conference|proc\.?|proceeding|meeting|workshop)\s?|(symposium|conference|proc\.?|proceeding|meeting|workshop)$')" 
+       <report test="matches(lower-case(.),'^(symposium|conference|meeting|workshop)|\s?(symposium|conference|meeting|workshop)\s?|(symposium|conference|meeting|workshop)$')" 
         role="warning" 
         id="journal-source-3">Journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has the following source, '<value-of select="."/>'. Should it be captured as a conference proceeding instead?</report>
      </rule>
diff --git a/src/rp-schematron.sch b/src/rp-schematron.sch
index 4b078586c6..84748073d7 100644
--- a/src/rp-schematron.sch
+++ b/src/rp-schematron.sch
@@ -304,7 +304,7 @@
 
        <report test="matches(lower-case(.),'^i{1,3}\.\s') and parent::*/article-title" role="warning" id="journal-source-2">[journal-source-2] Journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has a source that starts with a roman numeral. Is part of the article-title captured in source? Source = <value-of select="."/>.</report>
 
-       <report test="matches(lower-case(.),'^(symposium|conference|proc\.?|proceeding|meeting|workshop)|\s?(symposium|conference|proc\.?|proceeding|meeting|workshop)\s?|(symposium|conference|proc\.?|proceeding|meeting|workshop)$')" role="warning" id="journal-source-3">[journal-source-3] Journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has the following source, '<value-of select="."/>'. Should it be captured as a conference proceeding instead?</report>
+       <report test="matches(lower-case(.),'^(symposium|conference|meeting|workshop)|\s?(symposium|conference|meeting|workshop)\s?|(symposium|conference|meeting|workshop)$')" role="warning" id="journal-source-3">[journal-source-3] Journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has the following source, '<value-of select="."/>'. Should it be captured as a conference proceeding instead?</report>
      </rule></pattern>
 
     <pattern id="preprint-ref-checks-pattern"><rule context="mixed-citation[@publication-type='preprint']" id="preprint-ref-checks">
diff --git a/src/rp-schematron.xsl b/src/rp-schematron.xsl
index 669ba4509e..745a35c428 100644
--- a/src/rp-schematron.xsl
+++ b/src/rp-schematron.xsl
@@ -2271,8 +2271,8 @@
          </svrl:successful-report>
       </xsl:if>
       <!--REPORT warning-->
-      <xsl:if test="matches(lower-case(.),'^(symposium|conference|proc\.?|proceeding|meeting|workshop)|\s?(symposium|conference|proc\.?|proceeding|meeting|workshop)\s?|(symposium|conference|proc\.?|proceeding|meeting|workshop)$')">
-         <svrl:successful-report xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="matches(lower-case(.),'^(symposium|conference|proc\.?|proceeding|meeting|workshop)|\s?(symposium|conference|proc\.?|proceeding|meeting|workshop)\s?|(symposium|conference|proc\.?|proceeding|meeting|workshop)$')">
+      <xsl:if test="matches(lower-case(.),'^(symposium|conference|meeting|workshop)|\s?(symposium|conference|meeting|workshop)\s?|(symposium|conference|meeting|workshop)$')">
+         <svrl:successful-report xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="matches(lower-case(.),'^(symposium|conference|meeting|workshop)|\s?(symposium|conference|meeting|workshop)\s?|(symposium|conference|meeting|workshop)$')">
             <xsl:attribute name="id">journal-source-3</xsl:attribute>
             <xsl:attribute name="role">warning</xsl:attribute>
             <xsl:attribute name="location">
diff --git a/test/tests/rp/journal-source-checks/journal-source-3/fail.xml b/test/tests/rp/journal-source-checks/journal-source-3/fail.xml
index 98bf626335..d10c485f66 100644
--- a/test/tests/rp/journal-source-checks/journal-source-3/fail.xml
+++ b/test/tests/rp/journal-source-checks/journal-source-3/fail.xml
@@ -1,6 +1,6 @@
 <?oxygen SCHSchema="journal-source-3.sch"?>
 <!--Context: mixed-citation[@publication-type='journal']/source
-Test: report    matches(lower-case(.),'^(symposium|conference|proc\.?|proceeding|meeting|workshop)|\s?(symposium|conference|proc\.?|proceeding|meeting|workshop)\s?|(symposium|conference|proc\.?|proceeding|meeting|workshop)$')
+Test: report    matches(lower-case(.),'^(symposium|conference|meeting|workshop)|\s?(symposium|conference|meeting|workshop)\s?|(symposium|conference|meeting|workshop)$')
 Message: Journal reference () has the following source, ''. Should it be captured as a conference proceeding instead? -->
 <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>
diff --git a/test/tests/rp/journal-source-checks/journal-source-3/journal-source-3.sch b/test/tests/rp/journal-source-checks/journal-source-3/journal-source-3.sch
index 16c8f6d797..e668fa9ac5 100644
--- a/test/tests/rp/journal-source-checks/journal-source-3/journal-source-3.sch
+++ b/test/tests/rp/journal-source-checks/journal-source-3/journal-source-3.sch
@@ -147,7 +147,7 @@
   <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'"/>
-      <report test="matches(lower-case(.),'^(symposium|conference|proc\.?|proceeding|meeting|workshop)|\s?(symposium|conference|proc\.?|proceeding|meeting|workshop)\s?|(symposium|conference|proc\.?|proceeding|meeting|workshop)$')" role="warning" id="journal-source-3">[journal-source-3] Journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has the following source, '<value-of select="."/>'. Should it be captured as a conference proceeding instead?</report>
+      <report test="matches(lower-case(.),'^(symposium|conference|meeting|workshop)|\s?(symposium|conference|meeting|workshop)\s?|(symposium|conference|meeting|workshop)$')" role="warning" id="journal-source-3">[journal-source-3] Journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has the following source, '<value-of select="."/>'. Should it be captured as a conference proceeding instead?</report>
     </rule>
   </pattern>
   <pattern id="root-pattern">
diff --git a/test/tests/rp/journal-source-checks/journal-source-3/pass.xml b/test/tests/rp/journal-source-checks/journal-source-3/pass.xml
index 96fc998fa0..11085f30ca 100644
--- a/test/tests/rp/journal-source-checks/journal-source-3/pass.xml
+++ b/test/tests/rp/journal-source-checks/journal-source-3/pass.xml
@@ -1,6 +1,6 @@
 <?oxygen SCHSchema="journal-source-3.sch"?>
 <!--Context: mixed-citation[@publication-type='journal']/source
-Test: report    matches(lower-case(.),'^(symposium|conference|proc\.?|proceeding|meeting|workshop)|\s?(symposium|conference|proc\.?|proceeding|meeting|workshop)\s?|(symposium|conference|proc\.?|proceeding|meeting|workshop)$')
+Test: report    matches(lower-case(.),'^(symposium|conference|meeting|workshop)|\s?(symposium|conference|meeting|workshop)\s?|(symposium|conference|meeting|workshop)$')
 Message: Journal reference () has the following source, ''. Should it be captured as a conference proceeding instead? -->
 <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>
diff --git a/test/xspec/rp-schematron.sch b/test/xspec/rp-schematron.sch
index c4399ada0f..6f344b5adc 100644
--- a/test/xspec/rp-schematron.sch
+++ b/test/xspec/rp-schematron.sch
@@ -352,7 +352,7 @@
 
        <report test="matches(lower-case(.),'^i{1,3}\.\s') and parent::*/article-title" role="warning" id="journal-source-2">Journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has a source that starts with a roman numeral. Is part of the article-title captured in source? Source = <value-of select="."/>.</report>
 
-       <report test="matches(lower-case(.),'^(symposium|conference|proc\.?|proceeding|meeting|workshop)|\s?(symposium|conference|proc\.?|proceeding|meeting|workshop)\s?|(symposium|conference|proc\.?|proceeding|meeting|workshop)$')" role="warning" id="journal-source-3">Journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has the following source, '<value-of select="."/>'. Should it be captured as a conference proceeding instead?</report>
+       <report test="matches(lower-case(.),'^(symposium|conference|meeting|workshop)|\s?(symposium|conference|meeting|workshop)\s?|(symposium|conference|meeting|workshop)$')" role="warning" id="journal-source-3">Journal reference (<value-of select="if (ancestor::ref/@id) then concat('id ',ancestor::ref/@id) else 'no id'"/>) has the following source, '<value-of select="."/>'. Should it be captured as a conference proceeding instead?</report>
      </rule>
   </pattern>
 

From 7030d29fa46b7c5daec4c623ac890864d067751f Mon Sep 17 00:00:00 2001
From: Fred Atherden <43879983+fred-atherden@users.noreply.github.com>
Date: Tue, 26 Nov 2024 13:32:13 +0000
Subject: [PATCH 2/2] RP - ignore Editor affs in aff-has-wrap-no-id

---
 src/rp-schematron-base.sch                                    | 2 +-
 src/rp-schematron.sch                                         | 2 +-
 src/rp-schematron.xsl                                         | 4 ++--
 .../aff-has-wrap-no-id/aff-has-wrap-no-id.sch                 | 2 +-
 test/tests/rp/affiliation-checks/aff-has-wrap-no-id/fail.xml  | 2 +-
 test/tests/rp/affiliation-checks/aff-has-wrap-no-id/pass.xml  | 2 +-
 test/xspec/rp-schematron.sch                                  | 2 +-
 7 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/rp-schematron-base.sch b/src/rp-schematron-base.sch
index 37d88986fc..d48ab3ce7d 100644
--- a/src/rp-schematron-base.sch
+++ b/src/rp-schematron-base.sch
@@ -389,7 +389,7 @@
         role="warning" 
         id="aff-no-wrap">Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?</report>
       
-      <report test="institution-wrap[not(institution-id)]" 
+      <report test="institution-wrap[not(institution-id)] and not(ancestor::contrib-group[@content-type='section']) and not(ancestor::sub-article)" 
         role="error" 
         id="aff-has-wrap-no-id">aff contains institution-wrap, but that institution-wrap does not have a child institution-id. institution-wrap should only be used when there is an institution-id for the institution.</report>
       
diff --git a/src/rp-schematron.sch b/src/rp-schematron.sch
index 84748073d7..13d372e985 100644
--- a/src/rp-schematron.sch
+++ b/src/rp-schematron.sch
@@ -263,7 +263,7 @@
       
       <report test="ancestor::article/journal-meta/lower-case(journal-id[1])='elife' and count(institution-wrap) = 0" role="warning" id="aff-no-wrap">[aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?</report>
       
-      <report test="institution-wrap[not(institution-id)]" role="error" id="aff-has-wrap-no-id">[aff-has-wrap-no-id] aff contains institution-wrap, but that institution-wrap does not have a child institution-id. institution-wrap should only be used when there is an institution-id for the institution.</report>
+      <report test="institution-wrap[not(institution-id)] and not(ancestor::contrib-group[@content-type='section']) and not(ancestor::sub-article)" role="error" id="aff-has-wrap-no-id">[aff-has-wrap-no-id] aff contains institution-wrap, but that institution-wrap does not have a child institution-id. institution-wrap should only be used when there is an institution-id for the institution.</report>
       
       <report test="institution-wrap[not(institution)]" role="error" id="aff-has-wrap-no-inst">[aff-has-wrap-no-inst] aff contains institution-wrap, but that institution-wrap does not have a child institution.</report>
       
diff --git a/src/rp-schematron.xsl b/src/rp-schematron.xsl
index 745a35c428..4f8f58eac4 100644
--- a/src/rp-schematron.xsl
+++ b/src/rp-schematron.xsl
@@ -2013,8 +2013,8 @@
          </svrl:successful-report>
       </xsl:if>
       <!--REPORT error-->
-      <xsl:if test="institution-wrap[not(institution-id)]">
-         <svrl:successful-report xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="institution-wrap[not(institution-id)]">
+      <xsl:if test="institution-wrap[not(institution-id)] and not(ancestor::contrib-group[@content-type='section']) and not(ancestor::sub-article)">
+         <svrl:successful-report xmlns:svrl="http://purl.oclc.org/dsdl/svrl" test="institution-wrap[not(institution-id)] and not(ancestor::contrib-group[@content-type='section']) and not(ancestor::sub-article)">
             <xsl:attribute name="id">aff-has-wrap-no-id</xsl:attribute>
             <xsl:attribute name="role">error</xsl:attribute>
             <xsl:attribute name="location">
diff --git a/test/tests/rp/affiliation-checks/aff-has-wrap-no-id/aff-has-wrap-no-id.sch b/test/tests/rp/affiliation-checks/aff-has-wrap-no-id/aff-has-wrap-no-id.sch
index a329cc3a8b..82c5b39db0 100644
--- a/test/tests/rp/affiliation-checks/aff-has-wrap-no-id/aff-has-wrap-no-id.sch
+++ b/test/tests/rp/affiliation-checks/aff-has-wrap-no-id/aff-has-wrap-no-id.sch
@@ -147,7 +147,7 @@
   <pattern id="affiliation-checks-pattern">
     <rule context="aff" id="affiliation-checks">
       <let name="country-count" value="count(descendant::country)"/>
-      <report test="institution-wrap[not(institution-id)]" role="error" id="aff-has-wrap-no-id">[aff-has-wrap-no-id] aff contains institution-wrap, but that institution-wrap does not have a child institution-id. institution-wrap should only be used when there is an institution-id for the institution.</report>
+      <report test="institution-wrap[not(institution-id)] and not(ancestor::contrib-group[@content-type='section']) and not(ancestor::sub-article)" role="error" id="aff-has-wrap-no-id">[aff-has-wrap-no-id] aff contains institution-wrap, but that institution-wrap does not have a child institution-id. institution-wrap should only be used when there is an institution-id for the institution.</report>
     </rule>
   </pattern>
   <pattern id="root-pattern">
diff --git a/test/tests/rp/affiliation-checks/aff-has-wrap-no-id/fail.xml b/test/tests/rp/affiliation-checks/aff-has-wrap-no-id/fail.xml
index f97d649b84..e1c0aeb90e 100644
--- a/test/tests/rp/affiliation-checks/aff-has-wrap-no-id/fail.xml
+++ b/test/tests/rp/affiliation-checks/aff-has-wrap-no-id/fail.xml
@@ -1,6 +1,6 @@
 <?oxygen SCHSchema="aff-has-wrap-no-id.sch"?>
 <!--Context: aff
-Test: report    institution-wrap[not(institution-id)]
+Test: report    institution-wrap[not(institution-id)] and not(ancestor::contrib-group[@content-type='section']) and not(ancestor::sub-article)
 Message: aff contains institution-wrap, but that institution-wrap does not have a child institution-id. institution-wrap should only be used when there is an institution-id for the institution. -->
 <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>
diff --git a/test/tests/rp/affiliation-checks/aff-has-wrap-no-id/pass.xml b/test/tests/rp/affiliation-checks/aff-has-wrap-no-id/pass.xml
index 50cbe209fd..0f3447b3ab 100644
--- a/test/tests/rp/affiliation-checks/aff-has-wrap-no-id/pass.xml
+++ b/test/tests/rp/affiliation-checks/aff-has-wrap-no-id/pass.xml
@@ -1,6 +1,6 @@
 <?oxygen SCHSchema="aff-has-wrap-no-id.sch"?>
 <!--Context: aff
-Test: report    institution-wrap[not(institution-id)]
+Test: report    institution-wrap[not(institution-id)] and not(ancestor::contrib-group[@content-type='section']) and not(ancestor::sub-article)
 Message: aff contains institution-wrap, but that institution-wrap does not have a child institution-id. institution-wrap should only be used when there is an institution-id for the institution. -->
 <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>
diff --git a/test/xspec/rp-schematron.sch b/test/xspec/rp-schematron.sch
index 6f344b5adc..d5722eeba0 100644
--- a/test/xspec/rp-schematron.sch
+++ b/test/xspec/rp-schematron.sch
@@ -298,7 +298,7 @@
       
       <report test="ancestor::article/journal-meta/lower-case(journal-id[1])='elife' and count(institution-wrap) = 0" role="warning" id="aff-no-wrap">Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?</report>
       
-      <report test="institution-wrap[not(institution-id)]" role="error" id="aff-has-wrap-no-id">aff contains institution-wrap, but that institution-wrap does not have a child institution-id. institution-wrap should only be used when there is an institution-id for the institution.</report>
+      <report test="institution-wrap[not(institution-id)] and not(ancestor::contrib-group[@content-type='section']) and not(ancestor::sub-article)" role="error" id="aff-has-wrap-no-id">aff contains institution-wrap, but that institution-wrap does not have a child institution-id. institution-wrap should only be used when there is an institution-id for the institution.</report>
       
       <report test="institution-wrap[not(institution)]" role="error" id="aff-has-wrap-no-inst">aff contains institution-wrap, but that institution-wrap does not have a child institution.</report>