diff --git a/RA-sec-titles.xq b/RA-sec-titles.xq
new file mode 100644
index 0000000..736349a
--- /dev/null
+++ b/RA-sec-titles.xq
@@ -0,0 +1,2 @@
+distinct-values(for $x in collection('articles')//*:article[(descendant::*:subject[text() = ('Research Article', 'Short Report', 'Tools and Resources', 'Research Advance', 'Registered Report', 'Replication Study', 'Research Communication')])]/*:body/*:sec/*:title
+return normalize-space($x))
\ No newline at end of file
diff --git a/acceptance-summaries.xq b/acceptance-summaries.xq
new file mode 100644
index 0000000..45bd62f
--- /dev/null
+++ b/acceptance-summaries.xq
@@ -0,0 +1,87 @@
+for $x in collection('articles')//*:article/*:sub-article[1]//*:p
+let $no := substring-before(substring-after($x/base-uri(),'/articles/elife-'),'-v')
+return
+if (matches($x,'^[Aa]cceptance summary[:]?$')) then
+ if (matches($x/following-sibling::*:p[2],'^Decision letter after peer review[:]?$'))
+ then (
+ ($no||' - '||('https://elifesciences.org/articles/'||$no||'#'||$x/ancestor::*:sub-article/@id)),
+ '
',
+ $x/following-sibling::*:p[1]/data(),
+ '
',
+ ' ---- ',
+ '
'
+ )
+ else if (matches($x/following-sibling::*:p[3],'^Decision letter after peer review[:]?$'))
+ then (
+ ($no||' - '||('https://elifesciences.org/articles/'||$no||'#'||$x/ancestor::*:sub-article/@id)),
+ '
',
+ $x/following-sibling::*:p[1]/data(),
+ $x/following-sibling::*:p[2]/data(),
+ '
',
+ ' ---- ',
+ '
'
+ )
+ else if (matches($x/following-sibling::*:p[4],'^Decision letter after peer review[:]?$'))
+ then (
+ ($no||' - '||('https://elifesciences.org/articles/'||$no||'#'||$x/ancestor::*:sub-article/@id)),
+ '
',
+ $x/following-sibling::*:p[1]/data(),
+ $x/following-sibling::*:p[2]/data(),
+ $x/following-sibling::*:p[3]/data(),
+ '
',
+ ' ---- ',
+ '
'
+ )
+ else if (matches($x/following-sibling::*:p[5],'^Decision letter after peer review[:]?$'))
+ then (
+ ($no||' - '||('https://elifesciences.org/articles/'||$no||'#'||$x/ancestor::*:sub-article/@id)),
+ '
',
+ $x/following-sibling::*:p[1]/data(),
+ $x/following-sibling::*:p[2]/data(),
+ $x/following-sibling::*:p[3]/data(),
+ $x/following-sibling::*:p[4]/data(),
+ '
',
+ ' ---- ',
+ '
'
+ )
+
+ else if (matches($x/following-sibling::*:p[6],'^Decision letter after peer review[:]?$'))
+ then (
+ ($no||' - '||('https://elifesciences.org/articles/'||$no||'#'||$x/ancestor::*:sub-article/@id)),
+ '
',
+ $x/following-sibling::*:p[1]/data(),
+ $x/following-sibling::*:p[2]/data(),
+ $x/following-sibling::*:p[3]/data(),
+ $x/following-sibling::*:p[4]/data(),
+ $x/following-sibling::*:p[5]/data(),
+ '
',
+ ' ---- ',
+ '
'
+ )
+ else if (matches($x/following-sibling::*:p[7],'^Decision letter after peer review[:]?$'))
+ then (
+ ($no||' - '||('https://elifesciences.org/articles/'||$no||'#'||$x/ancestor::*:sub-article/@id)),
+ '
',
+ $x/following-sibling::*:p[1]/data(),
+ $x/following-sibling::*:p[2]/data(),
+ $x/following-sibling::*:p[3]/data(),
+ $x/following-sibling::*:p[4]/data(),
+ $x/following-sibling::*:p[5]/data(),
+ $x/following-sibling::*:p[6]/data(),
+ '
',
+ ' ---- ',
+ '
'
+ )
+ else if (count($x/following-sibling::*:p)lt 3)
+ then (
+ ($no||' - '||('https://elifesciences.org/articles/'||$no||'#'||$x/ancestor::*:sub-article/@id)),
+ '
',
+ for $y in $x/following-sibling::*:p
+ return $y/data(),
+ '
',
+ ' ---- ',
+ '
'
+ )
+ else (($no||' - '||'ERROR'))
+else ()
+
\ No newline at end of file
diff --git a/add-ids-to-support.xq b/add-ids-to-support.xq
new file mode 100644
index 0000000..1828cbe
--- /dev/null
+++ b/add-ids-to-support.xq
@@ -0,0 +1,18 @@
+let $x := doc('/Users/fredatherden/Documents/GitHub/jats-support/src/support.sch')
+
+return copy $copy := $x
+modify(
+
+ for $x in $copy//(*:assert|*:report)
+ let $r := $x/ancestor::*:pattern/@id
+ let $pos := count($x/ancestor::*:pattern//*[local-name() = $x/local-name()]) - count($x/following::*[(local-name() = $x/local-name()) and (ancestor::*:pattern/@id = $r)])
+ return
+ insert node attribute id {concat($x/ancestor::*:pattern/@id,'-',$x/local-name(),'-',$pos)} as last into $x
+
+
+
+)
+
+return
+
+file:write('/Users/fredatherden/Desktop/support.sch',$copy, map{'indent':'no'})
\ No newline at end of file
diff --git a/add-org-name-tests.xq b/add-org-name-tests.xq
new file mode 100644
index 0000000..2780af3
--- /dev/null
+++ b/add-org-name-tests.xq
@@ -0,0 +1,59 @@
+declare variable $sch := doc('/Users/fredatherden/Documents/GitHub/eLife-JATS-schematron/schematron.sch');
+declare variable $base-uri := substring-before(base-uri($sch),'/schematron.sch');
+
+for $x in $sch//*:pattern[@id="org-pattern"]//(*:report|*:assert)
+let $org-name := substring-before(substring-after($x,"an organism - '"),"' - but there is n")
+let $rule-id := $x/parent::*:rule/@id
+let $path := concat($base-uri,'/tests/',$rule-id,'/',$x/@id,'/')
+let $pass := concat($path,'pass.xml')
+let $fail := concat($path,'fail.xml')
+let $pass-element := if ($rule-id = 'org-ref-article-book-title') then
+
+ test {$org-name} test
+
+ else
+
+
+ test {$org-name} test
+
+
+
+let $fail-element := if ($rule-id = 'org-ref-article-book-title') then
+
+ {concat(' test ',lower-case($org-name),' test ')}
+
+ else
+
+
+ {concat(' test ',lower-case($org-name),' test ')}
+
+
+
+let $pi-content := ('SCHSchema="'||$x/@id||'.sch'||'"')
+let $comment := comment{concat('Context: ',$x/parent::*:rule/@context/string(),'
+Test: ',normalize-space($x/@test/string()))}
+
+let $pass-new :=
+(processing-instruction {'oxygen'}{$pi-content},
+$comment,
+
+
+ {$pass-element}
+
+)
+
+let $fail-new :=
+(processing-instruction {'oxygen'}{$pi-content},
+$comment,
+
+
+ {$fail-element}
+
+
+)
+return
+(
+ file:write($pass,$pass-new),
+ file:write($fail,$fail-new)
+)
+
diff --git a/aff-edit-test.xq b/aff-edit-test.xq
new file mode 100644
index 0000000..3ee597e
--- /dev/null
+++ b/aff-edit-test.xq
@@ -0,0 +1,16 @@
+let $xml := doc('/Users/fredatherden/Desktop/elife-49920-vor-r2/elife-49920.xml')
+
+let $new-xml := copy $copy := $xml
+modify(
+ for $x in $copy//*:contrib-group[not(@content-type)]//*:aff
+ let $dept := $x/*:institution[@content-type="dept"]
+ let $inst := $x/*:institution[not(@content-type)]
+ return if ($inst = 'University of Kentucky') then (
+ replace node $inst with {concat($dept,', ',$inst)},
+ delete node $dept
+ )
+ else ()
+)
+return $copy
+
+return file:write('Desktop/elife-49920.xml',$new-xml,map{'indent':'no'})
\ No newline at end of file
diff --git a/aff-tests.xq b/aff-tests.xq
new file mode 100644
index 0000000..926b5be
--- /dev/null
+++ b/aff-tests.xq
@@ -0,0 +1,12 @@
+for $x in collection('articles')//*:contrib-group[not(@content-type)]
+let $list :=
+{
+ for $aff in $x/*:aff
+ let $i := $aff/*:institution[not(@content-type)]
+ return
+ if ($i=$aff/preceding-sibling::*:aff/institution[not(@content-type)]) then {$aff}
+ else ()
+}
+return
+if (count($list//*:item)>4) then $x/base-uri()
+else ()
\ No newline at end of file
diff --git a/alt-group-markup.xq b/alt-group-markup.xq
new file mode 100644
index 0000000..21dbadb
--- /dev/null
+++ b/alt-group-markup.xq
@@ -0,0 +1,24 @@
+let $xml := doc('/Users/fredatherden/Desktop/elife-42463-v1.xml')
+
+let $copy := copy $copy1 := $xml
+modify(
+ for $x in $copy1//*:contrib-group[@content-type="collab-list"]//*:aff
+ let $id := generate-id($x)
+ return insert node attribute id {$id} as first into $x
+)
+
+
+return copy $copy2 := $copy1
+modify(
+ for $x in $copy2//*:contrib-group[@content-type="collab-list"]//*:contrib
+ return replace value of node $x/@contrib-type with 'collaborator',
+
+ for $y in $copy2//*:contrib-group[@content-type="collab-list"]//*:contrib//*:aff
+ return
+ (replace node $y with ,
+ insert node $y as last into $y/ancestor::*:contrib-group[@content-type="collab-list"])
+
+)
+return $copy2
+
+return $copy
\ No newline at end of file
diff --git a/article.xq b/article.xq
new file mode 100644
index 0000000..db3af97
--- /dev/null
+++ b/article.xq
@@ -0,0 +1,2 @@
+for $x in collection('articles')//*:article[(descendant::*:article-id[@pub-id-type="publisher-id"]= '42955') and descendant::*:body]
+return $x
\ No newline at end of file
diff --git a/award-ids.xq b/award-ids.xq
new file mode 100644
index 0000000..a6db566
--- /dev/null
+++ b/award-ids.xq
@@ -0,0 +1,28 @@
+declare function local:get-doi($a){
+ let $id := $a/ancestor::*:article/descendant::*:article-id[@pub-id-type="publisher-id"][1]
+ let $version := substring-before(substring-after($a/base-uri(),concat($id,'-')),'.xml')
+ let $url := concat('https://elifesciences.org/articles/',$id,$version)
+ return copy $copy := $a
+ modify(
+ for $x in $copy/descendant-or-self::*:award-group
+ return insert node attribute {'url'}{$url} as last into $x
+ )
+ return $copy
+};
+
+
+
+
+{
+for $x in collection('articles')//*:article//*:funding-group//*:award-group[*:award-id]
+let $id := $x/*:award-id
+let $y := replace($id,'[\p{P}\p{N}]|[Gg]rant','')
+let $new-x := local:get-doi($x)
+return
+if (matches($id,'\p{Ll}')) then (
+ if (string-length($y) < 10) then ()
+ else $new-x)
+else ()
+}
+
+
diff --git a/batch-biorxiv-tranformation-2.xq b/batch-biorxiv-tranformation-2.xq
new file mode 100644
index 0000000..2a3f833
--- /dev/null
+++ b/batch-biorxiv-tranformation-2.xq
@@ -0,0 +1,78 @@
+declare namespace xlink="http://www.w3.org/1999/xlink";
+declare namespace mml="http://www.w3.org/1998/Math/MathML";
+
+
+declare variable $dir := '/Users/fredatherden/Desktop/biorxiv-tranformed/';
+declare variable $xsl := doc('/Users/fredatherden/Documents/xsl/biorxiv.xsl');
+
+
+for $x in collection('biorxiv-xml')//*:article[not(descendant::*:media[@mimetype="video"]) and not(descendant::mml:math) and not(descendant::table) and not(descendant::fig-group) and not(descendant::disp-quote) and (count(descendant::*:mixed-citation[@publication-type!='journal']) le 3)]
+let $filename := concat(substring-after($x//*:article-meta/*:article-id[@pub-id-type="doi"],'10.1101/'),'.xml')
+let $file := xslt:transform($x, $xsl)
+
+let $file2 :=
+copy $copy := $file
+modify(
+
+ for $x in $copy//*:fig
+ let $label := if (ends-with($x/*:label,'.')) then concat($x/*:label/text(),' ')
+ else if (ends-with($x/*:label,'.')) then concat($x/*:label/text(),' ')
+ else concat($x/*:label,'. ')
+ return
+ replace node $x with
+
+
+ {$label,
+ $x/*:caption/*:p/(*|text())}
+
+
+ ,
+
+ for $x in $copy//*:table-wrap
+ let $label := if (ends-with($x/*:label,'.')) then $x/*:label/text()
+ else concat($x/*:label,'. ')
+ return
+ replace node $x with
+
+
+ {$label,
+ $x/*:caption/*:p/(*|text())}
+
+
+ ,
+
+ for $x in $copy//*:sec[(@sec-type="supplementary-material") and not(child::*[local-name()!='title' and local-name()!='supplementary-material'])]
+ return
+ delete node $x,
+
+ for $x in $copy//*:article-meta//*:contrib//*:xref[@ref-type="aff"]
+ let $a := $x/ancestor::*:article-meta//*:aff[@id = $x/@rid]
+ let $aff := {
+ for $y in $a/(*|text())
+ return
+ if ($y/local-name()='label') then ()
+ else $y/data()
+ }
+ return
+ replace node $x with $aff,
+
+ for $x in $copy//*:article-meta//*:aff
+ return delete node $x,
+
+ for $x in $copy//*:back/*:ack
+ return
+ if ($x/*:title) then (delete node $x,
+ insert node {$x/*} as last into $x/preceding::body[1])
+ else (delete node $x,
+ insert node Acknowledgements{$x/*} as last into $x/preceding::body[1]),
+
+ for $x in $copy//*:abstract
+ return
+ (delete node $x,
+ insert node {$x/*} as first into $x/following::body[1])
+
+)
+return $copy
+
+return file:write(concat($dir,$filename),$file2, map {'indent':'no'})
+
diff --git a/batch-biorxiv-transform.xq b/batch-biorxiv-transform.xq
new file mode 100644
index 0000000..704a5da
--- /dev/null
+++ b/batch-biorxiv-transform.xq
@@ -0,0 +1,14 @@
+declare namespace xlink="http://www.w3.org/1999/xlink";
+declare namespace mml="http://www.w3.org/1998/Math/MathML";
+
+
+declare variable $dir := '/Users/fredatherden/Desktop/biorxiv-tranformed/';
+declare variable $xsl := doc('/Users/fredatherden/Documents/xsl/mixed-2-element-citation.xsl');
+
+
+
+for $x in collection('biorxiv-xml')//*:article
+let $filename := concat(substring-after($x//*:article-meta/*:article-id[@pub-id-type="doi"],'10.1101/'),'.xml')
+let $file := xslt:transform($x, $xsl)
+return file:write(concat($dir,$filename),$file, map {'indent':'no'})
+
diff --git a/batch-normalise-test.xq b/batch-normalise-test.xq
new file mode 100644
index 0000000..c44eaf7
--- /dev/null
+++ b/batch-normalise-test.xq
@@ -0,0 +1,8 @@
+let $xsl := doc('/Users/fredatherden/Documents/xsl/normalise.xsl')
+
+for $x in collection('ijm-xml')//*:article
+let $t := xslt:transform($x,$xsl)
+let $name := for $y in tokenize($x/base-uri(),'/')[last()]
+ return $y
+
+return file:write(concat('/Users/fredatherden/Desktop/output/',$name),$t)
diff --git a/batch-rdf-test.xq b/batch-rdf-test.xq
new file mode 100644
index 0000000..6d0436c
--- /dev/null
+++ b/batch-rdf-test.xq
@@ -0,0 +1,8 @@
+let $xsl := doc('/Users/fredatherden/Documents/xsl/jats2rdf.xsl')
+
+for $x in collection('ijm-xml')//*:article
+let $t := xslt:transform($x,$xsl)
+let $name := for $y in tokenize($x/base-uri(),'/')[last()]
+ return $y
+
+return file:write(concat('/Users/fredatherden/Desktop/output/',$name),$t)
\ No newline at end of file
diff --git a/batch-validate-test.xq b/batch-validate-test.xq
new file mode 100644
index 0000000..7e7121d
--- /dev/null
+++ b/batch-validate-test.xq
@@ -0,0 +1,15 @@
+import module namespace schematron = "http://github.com/Schematron/schematron-basex";
+
+declare variable $sch := schematron:compile(doc('/Users/fredatherden/Documents/GitHub/eLife-JATS-schematron/src/final-JATS-schematron.sch'));
+
+for $x in collection('articles')//*:article[matches(descendant::*:article-id[@pub-id-type="publisher-id"],'^4222')]
+let $article-id := $x//*:article-id[@pub-id-type="publisher-id"]/text()
+let $folder := concat('/articles/elife-',$article-id,'-v')
+let $v-no := number(substring-before(substring-after($x/base-uri(),$folder),'.xml'))
+let $count := count(collection('articles')//*:article[descendant::*:article-id[@pub-id-type="publisher-id"]/text() = $article-id])
+return if ($count != $v-no) then ()
+else
+
+let $svrl := schematron:validate($x, $sch)
+return if ($svrl//*:successful-report[@id="unlinked-url-2"]) then $x/base-uri()
+else ()
diff --git a/batch-validate.xq b/batch-validate.xq
new file mode 100644
index 0000000..2e3b8d2
--- /dev/null
+++ b/batch-validate.xq
@@ -0,0 +1,32 @@
+import module namespace schematron = "http://github.com/Schematron/schematron-basex";
+
+(: Compile schematron - need to account for gen-country-test which basex is unable to resolve :)
+let $s := doc('/Users/fredatherden/Documents/github/elife-JATS-schematron/src/final-JATS-schematron.sch')
+let $s2 := copy $copy:=$s
+modify(
+ for $x in $copy//*:assert[@id='gen-country-test']
+ return delete node $x
+)
+return $copy
+let $sch := schematron:compile($s2)
+
+for $x in collection('articles')//*:article
+let $article-id := $x//*:article-id[@pub-id-type="publisher-id"]/text()
+let $folder := concat('/articles/elife-',$article-id,'-v')
+let $v-no := number(substring-before(substring-after($x/base-uri(),$folder),'.xml'))
+let $count := count(collection('articles')//*:article[descendant::*:article-id[@pub-id-type="publisher-id"]/text() = $article-id])
+
+return
+(: Define a subset of articles based on regex against tracking number :)
+if (not(matches($article-id,'^444'))) then ()
+(: Only pick out latest version :)
+else if ($count != $v-no) then ()
+else
+
+ let $svrl := schematron:validate($x, $sch)
+ return
+ (: Only return invalid articles :)
+ if (schematron:is-valid($svrl) = true()) then ()
+ else $x/base-uri()
+
+
diff --git a/biorxiv-edits.xq b/biorxiv-edits.xq
new file mode 100644
index 0000000..3b25e22
--- /dev/null
+++ b/biorxiv-edits.xq
@@ -0,0 +1,76 @@
+declare namespace xlink="http://www.w3.org/1999/xlink";
+declare namespace mml="http://www.w3.org/1998/Math/MathML";
+
+
+declare variable $dir := '/Users/fredatherden/Desktop/biorxiv-tranformed/';
+
+
+
+for $x in collection('biorxiv-xml')//*:article[not(descendant::*:media[@mimetype="video"]) and not(descendant::mml:math) and not(descendant::table) and not(descendant::fig-group) and not(descendant::disp-quote) and (count(descendant::*:mixed-citation[@publication-type!='journal']) le 3)]
+let $filename := concat(substring-after($x//*:article-meta/*:article-id[@pub-id-type="doi"],'10.1101/'),'.xml')
+let $file2 :=
+copy $copy := $x
+modify(
+
+ for $x in $copy//*:fig
+ let $label := if (ends-with($x/*:label,'.')) then concat($x/*:label/text(),' ')
+ else if (ends-with($x/*:label,'.')) then concat($x/*:label/text(),' ')
+ else concat($x/*:label,'. ')
+ return
+ replace node $x with
+
+
+ {$label,
+ $x/*:caption/*:p/(*|text())}
+
+
+ ,
+
+ for $x in $copy//*:table-wrap
+ let $label := if (ends-with($x/*:label,'.')) then $x/*:label/text()
+ else concat($x/*:label,'. ')
+ return
+ replace node $x with
+
+
+ {$label,
+ $x/*:caption/*:p/(*|text())}
+
+
+ ,
+
+ for $x in $copy//*:sec[(@sec-type="supplementary-material") and not(child::*[local-name()!='title' and local-name()!='supplementary-material'])]
+ return
+ delete node $x,
+
+ for $x in $copy//*:article-meta//*:contrib//*:xref[@ref-type="aff"]
+ let $a := $x/ancestor::*:article-meta//*:aff[@id = $x/@rid]
+ let $aff := {
+ for $y in $a/(*|text())
+ return
+ if ($y/local-name()='label') then ()
+ else $y/data()
+ }
+ return
+ replace node $x with $aff,
+
+ for $x in $copy//*:article-meta//*:aff
+ return delete node $x,
+
+ for $x in $copy//*:back/*:ack
+ return
+ if ($x/*:title) then (delete node $x,
+ insert node {$x/*} as last into $x/preceding::body[1])
+ else (delete node $x,
+ insert node Acknowledgements{$x/*} as last into $x/preceding::body[1]),
+
+ for $x in $copy//*:abstract
+ return
+ (delete node $x,
+ insert node {$x/*} as first into $x/following::body[1])
+
+)
+return $copy
+
+return file:write(concat($dir,$filename),$file2, map {'indent':'no'})
+
diff --git a/biorxiv-mixed-2-element-citation.xq b/biorxiv-mixed-2-element-citation.xq
new file mode 100644
index 0000000..73541fd
--- /dev/null
+++ b/biorxiv-mixed-2-element-citation.xq
@@ -0,0 +1,13 @@
+declare namespace xlink="http://www.w3.org/1999/xlink";
+declare namespace mml="http://www.w3.org/1998/Math/MathML";
+
+declare variable $filename := 'xsl-test.xml';
+declare variable $dir := '/Users/fredatherden/Desktop/';
+declare variable $xsl := doc('/Users/fredatherden/Documents/xsl/mixed-2-element-citation.xsl');
+
+
+
+for $x in collection('biorxiv-xml')//*:article[base-uri() = '/biorxiv-xml/686329.xml']
+let $file := xslt:transform($x, $xsl)
+return file:write(concat($dir,$filename),$file, map {'indent':'no'})
+
diff --git a/collab1.xq b/collab1.xq
new file mode 100644
index 0000000..6adefd9
--- /dev/null
+++ b/collab1.xq
@@ -0,0 +1,5 @@
+for $x in //*:article-meta//*:collab//*:contrib[*:aff]
+let $n := (count($x/parent::*:contrib-group/*:contrib) - count($x/following-sibling::*:contrib)) + 1
+let $aff := $x/*:aff
+return (insert node {$n} as last into $x,
+ insert node attribute id {('aff'||$n)} as first into $aff)
\ No newline at end of file
diff --git a/collab2.xq b/collab2.xq
new file mode 100644
index 0000000..84ca1ba
--- /dev/null
+++ b/collab2.xq
@@ -0,0 +1,3 @@
+for $x in //*:article-meta//*:collab//*:contrib/*:aff
+let $d := $x/ancestor::article-meta/*:contrib-group
+return insert node $x as last into $d
\ No newline at end of file
diff --git a/collab3.xq b/collab3.xq
new file mode 100644
index 0000000..1ac4be6
--- /dev/null
+++ b/collab3.xq
@@ -0,0 +1,3 @@
+for $x in //*:article-meta/*:contrib-group/*:aff[not(child::*:label)]
+let $n := substring-after($x/@id,'aff')
+return insert node as first into $x
diff --git a/collab4.xq b/collab4.xq
new file mode 100644
index 0000000..746c400
--- /dev/null
+++ b/collab4.xq
@@ -0,0 +1,2 @@
+for $x in //*:article-meta//*:collab//*:contrib/*:aff
+return delete node $x
\ No newline at end of file
diff --git a/colour-check.xq b/colour-check.xq
new file mode 100644
index 0000000..f4bc499
--- /dev/null
+++ b/colour-check.xq
@@ -0,0 +1,2 @@
+distinct-values(for $x in collection('articles')//*:article[((descendant::*:named-content[starts-with(@content-type,'author-callout')]) or (descendant::*:td[starts-with(@style,'author-callout')]) or (descendant::*:th[starts-with(@style,'author-callout')]) )]
+return $x//article-id[@pub-id-type="publisher-id"]/text())
\ No newline at end of file
diff --git a/component-dois.xq b/component-dois.xq
new file mode 100644
index 0000000..89f8740
--- /dev/null
+++ b/component-dois.xq
@@ -0,0 +1,11 @@
+let $c :=
+
+{for $x in collection('articles')//*:article[@article-type="research-article"][descendant::*:body]
+let $id := $x/descendant::*:article-id[@pub-id-type="publisher-id"]/text()
+let $type := normalize-space($x/descendant::*:article-categories/*:subj-group[@subj-group-type="display-channel"]/data())
+let $count := count($x//*:object-id[@pub-id-type="doi"])
+return
+{$id}{$type}{$count}
+}
+
+return file:write('/Users/fredatherden/Desktop/component-dois.csv',$c, map { "method": "csv", "item-separator": "," })
\ No newline at end of file
diff --git a/copy-edit-test.xq b/copy-edit-test.xq
new file mode 100644
index 0000000..acc2b51
--- /dev/null
+++ b/copy-edit-test.xq
@@ -0,0 +1,36 @@
+declare variable $us-uk-list := doc('/Users/fredatherden/Documents/GitHub/eLife-JATS-schematron/src/us-uk-list.xml');
+
+
+for $xml in collection('articles')//*:article[*:body]
+let $article-id := $xml//*:article-id[@pub-id-type="publisher-id"]/text()
+return
+if (matches($article-id,'^44')) then
+ (
+let $text := replace(string-join(
+ for $x in $xml/(*:front/*:article-meta//(*:article-title|*:abstract//*:p|*:custom-meta/*:meta-value)|
+ *:body//(*:p|*:title|*:th|*:td)|
+ *:back//(*:ack//*:p|*:app//*:p|*:title|*:th|*:td)
+ )
+ return $x/data()
+ ,' '),'[^\p{L}\s]','')
+
+let $tokens := tokenize($text,' ')
+
+let $style-list := {
+ for $x in $tokens
+ return
+ if ($x = $us-uk-list//*:item/@us/string()) then {$x}
+ else if ($x = $us-uk-list//*:item/@uk/string()) then {$x}
+ else ()
+ }
+
+let $us := count($style-list//*:us)
+let $uk := count($style-list//*:uk)
+
+ return
+ if (($us gt 0) and ($uk gt 0)) then $xml/base-uri()
+ else ()
+
+)
+
+else ()
\ No newline at end of file
diff --git a/count-dois.xq b/count-dois.xq
new file mode 100644
index 0000000..e3bca05
--- /dev/null
+++ b/count-dois.xq
@@ -0,0 +1,4 @@
+count(for $x in collection('articles')//*:element-citation
+return
+if ($x//pub-id[@pub-id-type="doi"]) then $x
+else ()) div count(collection('articles')//*:element-citation) * 100
\ No newline at end of file
diff --git a/display-subject.xq b/display-subject.xq
new file mode 100644
index 0000000..b541541
--- /dev/null
+++ b/display-subject.xq
@@ -0,0 +1,2 @@
+distinct-values(for $x in collection('articles')//*:article[(descendant::*:subject[text() = 'Replication Study']) and descendant::*:body]
+return $x//*:article-id[@pub-id-type="publisher-id"]/text())
\ No newline at end of file
diff --git a/element-and-atribute-construct.xq b/element-and-atribute-construct.xq
new file mode 100644
index 0000000..c9a14c7
--- /dev/null
+++ b/element-and-atribute-construct.xq
@@ -0,0 +1,10 @@
+declare namespace x="http://www.jenitennison.com/xslt/xspec";
+
+
+{let $x := doc('/Users/fredatherden/xspec/jats-support/support.sch')
+
+for $y in $x//*:pattern//(*:report|*:assert)
+let $name := concat('x:expect-not-',$y/local-name())
+return element {$name} {attribute {'id'} {$y/@id}, attribute {'role'} {$y/@role}}}
+
+
diff --git a/encoda-check.xq b/encoda-check.xq
new file mode 100644
index 0000000..7876852
--- /dev/null
+++ b/encoda-check.xq
@@ -0,0 +1,6 @@
+ for $x in collection('articles')//*:article[*:body and descendant::*:article-meta/*:contrib-group//*:collab]
+ let $base := $x/base-uri()
+ let $version := replace(substring-before(substring-after($base,'/articles/elife-'),'.xml'),'-','')
+ let $cmd := ('encoda convert https://elifesciences.org/articles/'||$version||' encoda-test/'||$version||'.xml --to jats')
+ return
+ $cmd
\ No newline at end of file
diff --git a/ext-link-test.xq b/ext-link-test.xq
new file mode 100644
index 0000000..336761b
--- /dev/null
+++ b/ext-link-test.xq
@@ -0,0 +1,9 @@
+declare namespace xlink="http://www.w3.org/1999/xlink";
+
+let $list :=
+{for $x in collection('articles')//*:ext-link
+return if (matches($x/@xlink:href,'^ftp|^http')) then ()
+else $x}
+
+
+return file:write('/Users/fredatherden/Desktop/link-list.xml',$list, map {'indent':'yes'})
\ No newline at end of file
diff --git a/feature-kwd-sub.xq b/feature-kwd-sub.xq
new file mode 100644
index 0000000..4727de3
--- /dev/null
+++ b/feature-kwd-sub.xq
@@ -0,0 +1,14 @@
+for $x in collection('articles')//*:article
+let $type := $x//*:subj-group[@subj-group-type="display-channel"]/*:subject/lower-case(.)
+let $sub := $x//*:subj-group[@subj-group-type="sub-display-channel"]/*:subject/lower-case(.)
+let $kwds := $x//*:kwd-group[@kwd-group-type="author-keywords"]
+return
+if ($type = ('feature article', 'insight')) then (
+ let $match := for $x in $kwds/*:kwd
+ return if (lower-case($x) = $sub) then $x
+ else ()
+ return
+ if (matches($match,'[a-z]')) then concat($x/base-uri(),' ------ ',$match)
+ else ()
+ )
+else ()
\ No newline at end of file
diff --git a/fetch-xml.xq b/fetch-xml.xq
new file mode 100644
index 0000000..80ffd65
--- /dev/null
+++ b/fetch-xml.xq
@@ -0,0 +1,690 @@
+let $list :=
+ https://wellcomeopenresearch.org/articles/1-1/v1/xml
+ https://wellcomeopenresearch.org/articles/1-1/v2/xml
+ https://wellcomeopenresearch.org/articles/1-10/v1/xml
+ https://wellcomeopenresearch.org/articles/1-10/v2/xml
+ https://wellcomeopenresearch.org/articles/1-11/v1/xml
+ https://wellcomeopenresearch.org/articles/1-12/v1/xml
+ https://wellcomeopenresearch.org/articles/1-13/v1/xml
+ https://wellcomeopenresearch.org/articles/1-14/v1/xml
+ https://wellcomeopenresearch.org/articles/1-15/v1/xml
+ https://wellcomeopenresearch.org/articles/1-16/v1/xml
+ https://wellcomeopenresearch.org/articles/1-16/v2/xml
+ https://wellcomeopenresearch.org/articles/1-17/v1/xml
+ https://wellcomeopenresearch.org/articles/1-18/v1/xml
+ https://wellcomeopenresearch.org/articles/1-18/v2/xml
+ https://wellcomeopenresearch.org/articles/1-19/v1/xml
+ https://wellcomeopenresearch.org/articles/1-19/v2/xml
+ https://wellcomeopenresearch.org/articles/1-19/v3/xml
+ https://wellcomeopenresearch.org/articles/1-2/v1/xml
+ https://wellcomeopenresearch.org/articles/1-2/v2/xml
+ https://wellcomeopenresearch.org/articles/1-20/v1/xml
+ https://wellcomeopenresearch.org/articles/1-21/v1/xml
+ https://wellcomeopenresearch.org/articles/1-22/v1/xml
+ https://wellcomeopenresearch.org/articles/1-22/v2/xml
+ https://wellcomeopenresearch.org/articles/1-23/v1/xml
+ https://wellcomeopenresearch.org/articles/1-23/v2/xml
+ https://wellcomeopenresearch.org/articles/1-24/v1/xml
+ https://wellcomeopenresearch.org/articles/1-25/v1/xml
+ https://wellcomeopenresearch.org/articles/1-25/v2/xml
+ https://wellcomeopenresearch.org/articles/1-26/v1/xml
+ https://wellcomeopenresearch.org/articles/1-27/v1/xml
+ https://wellcomeopenresearch.org/articles/1-27/v2/xml
+ https://wellcomeopenresearch.org/articles/1-28/v1/xml
+ https://wellcomeopenresearch.org/articles/1-28/v2/xml
+ https://wellcomeopenresearch.org/articles/1-29/v1/xml
+ https://wellcomeopenresearch.org/articles/1-3/v1/xml
+ https://wellcomeopenresearch.org/articles/1-3/v2/xml
+ https://wellcomeopenresearch.org/articles/1-30/v1/xml
+ https://wellcomeopenresearch.org/articles/1-30/v2/xml
+ https://wellcomeopenresearch.org/articles/1-31/v1/xml
+ https://wellcomeopenresearch.org/articles/1-32/v1/xml
+ https://wellcomeopenresearch.org/articles/1-32/v2/xml
+ https://wellcomeopenresearch.org/articles/1-32/v3/xml
+ https://wellcomeopenresearch.org/articles/1-33/v1/xml
+ https://wellcomeopenresearch.org/articles/1-4/v1/xml
+ https://wellcomeopenresearch.org/articles/1-5/v1/xml
+ https://wellcomeopenresearch.org/articles/1-6/v1/xml
+ https://wellcomeopenresearch.org/articles/1-6/v2/xml
+ https://wellcomeopenresearch.org/articles/1-7/v1/xml
+ https://wellcomeopenresearch.org/articles/1-7/v2/xml
+ https://wellcomeopenresearch.org/articles/1-8/v1/xml
+ https://wellcomeopenresearch.org/articles/1-9/v1/xml
+ https://wellcomeopenresearch.org/articles/2-1/v1/xml
+ https://wellcomeopenresearch.org/articles/2-10/v1/xml
+ https://wellcomeopenresearch.org/articles/2-10/v2/xml
+ https://wellcomeopenresearch.org/articles/2-100/v1/xml
+ https://wellcomeopenresearch.org/articles/2-100/v2/xml
+ https://wellcomeopenresearch.org/articles/2-101/v1/xml
+ https://wellcomeopenresearch.org/articles/2-102/v1/xml
+ https://wellcomeopenresearch.org/articles/2-103/v1/xml
+ https://wellcomeopenresearch.org/articles/2-104/v1/xml
+ https://wellcomeopenresearch.org/articles/2-105/v1/xml
+ https://wellcomeopenresearch.org/articles/2-105/v2/xml
+ https://wellcomeopenresearch.org/articles/2-105/v3/xml
+ https://wellcomeopenresearch.org/articles/2-106/v1/xml
+ https://wellcomeopenresearch.org/articles/2-107/v1/xml
+ https://wellcomeopenresearch.org/articles/2-107/v2/xml
+ https://wellcomeopenresearch.org/articles/2-108/v1/xml
+ https://wellcomeopenresearch.org/articles/2-109/v1/xml
+ https://wellcomeopenresearch.org/articles/2-109/v2/xml
+ https://wellcomeopenresearch.org/articles/2-11/v1/xml
+ https://wellcomeopenresearch.org/articles/2-110/v1/xml
+ https://wellcomeopenresearch.org/articles/2-110/v2/xml
+ https://wellcomeopenresearch.org/articles/2-111/v1/xml
+ https://wellcomeopenresearch.org/articles/2-112/v1/xml
+ https://wellcomeopenresearch.org/articles/2-113/v1/xml
+ https://wellcomeopenresearch.org/articles/2-114/v1/xml
+ https://wellcomeopenresearch.org/articles/2-114/v2/xml
+ https://wellcomeopenresearch.org/articles/2-114/v3/xml
+ https://wellcomeopenresearch.org/articles/2-115/v1/xml
+ https://wellcomeopenresearch.org/articles/2-115/v2/xml
+ https://wellcomeopenresearch.org/articles/2-116/v1/xml
+ https://wellcomeopenresearch.org/articles/2-116/v2/xml
+ https://wellcomeopenresearch.org/articles/2-117/v1/xml
+ https://wellcomeopenresearch.org/articles/2-117/v2/xml
+ https://wellcomeopenresearch.org/articles/2-117/v3/xml
+ https://wellcomeopenresearch.org/articles/2-118/v1/xml
+ https://wellcomeopenresearch.org/articles/2-118/v2/xml
+ https://wellcomeopenresearch.org/articles/2-119/v1/xml
+ https://wellcomeopenresearch.org/articles/2-119/v2/xml
+ https://wellcomeopenresearch.org/articles/2-12/v1/xml
+ https://wellcomeopenresearch.org/articles/2-120/v1/xml
+ https://wellcomeopenresearch.org/articles/2-120/v2/xml
+ https://wellcomeopenresearch.org/articles/2-120/v3/xml
+ https://wellcomeopenresearch.org/articles/2-121/v1/xml
+ https://wellcomeopenresearch.org/articles/2-121/v2/xml
+ https://wellcomeopenresearch.org/articles/2-121/v3/xml
+ https://wellcomeopenresearch.org/articles/2-13/v1/xml
+ https://wellcomeopenresearch.org/articles/2-13/v2/xml
+ https://wellcomeopenresearch.org/articles/2-14/v2/xml
+ https://wellcomeopenresearch.org/articles/2-15/v1/xml
+ https://wellcomeopenresearch.org/articles/2-16/v1/xml
+ https://wellcomeopenresearch.org/articles/2-16/v2/xml
+ https://wellcomeopenresearch.org/articles/2-17/v1/xml
+ https://wellcomeopenresearch.org/articles/2-17/v2/xml
+ https://wellcomeopenresearch.org/articles/2-18/v1/xml
+ https://wellcomeopenresearch.org/articles/2-19/v1/xml
+ https://wellcomeopenresearch.org/articles/2-2/v1/xml
+ https://wellcomeopenresearch.org/articles/2-2/v2/xml
+ https://wellcomeopenresearch.org/articles/2-20/v1/xml
+ https://wellcomeopenresearch.org/articles/2-20/v2/xml
+ https://wellcomeopenresearch.org/articles/2-21/v1/xml
+ https://wellcomeopenresearch.org/articles/2-21/v2/xml
+ https://wellcomeopenresearch.org/articles/2-22/v1/xml
+ https://wellcomeopenresearch.org/articles/2-22/v2/xml
+ https://wellcomeopenresearch.org/articles/2-22/v3/xml
+ https://wellcomeopenresearch.org/articles/2-22/v4/xml
+ https://wellcomeopenresearch.org/articles/2-23/v1/xml
+ https://wellcomeopenresearch.org/articles/2-23/v2/xml
+ https://wellcomeopenresearch.org/articles/2-23/v3/xml
+ https://wellcomeopenresearch.org/articles/2-24/v1/xml
+ https://wellcomeopenresearch.org/articles/2-25/v1/xml
+ https://wellcomeopenresearch.org/articles/2-25/v2/xml
+ https://wellcomeopenresearch.org/articles/2-26/v1/xml
+ https://wellcomeopenresearch.org/articles/2-27/v1/xml
+ https://wellcomeopenresearch.org/articles/2-28/v1/xml
+ https://wellcomeopenresearch.org/articles/2-28/v2/xml
+ https://wellcomeopenresearch.org/articles/2-28/v3/xml
+ https://wellcomeopenresearch.org/articles/2-29/v1/xml
+ https://wellcomeopenresearch.org/articles/2-29/v2/xml
+ https://wellcomeopenresearch.org/articles/2-3/v1/xml
+ https://wellcomeopenresearch.org/articles/2-3/v2/xml
+ https://wellcomeopenresearch.org/articles/2-30/v1/xml
+ https://wellcomeopenresearch.org/articles/2-31/v1/xml
+ https://wellcomeopenresearch.org/articles/2-31/v2/xml
+ https://wellcomeopenresearch.org/articles/2-32/v1/xml
+ https://wellcomeopenresearch.org/articles/2-32/v2/xml
+ https://wellcomeopenresearch.org/articles/2-33/v1/xml
+ https://wellcomeopenresearch.org/articles/2-34/v1/xml
+ https://wellcomeopenresearch.org/articles/2-34/v2/xml
+ https://wellcomeopenresearch.org/articles/2-35/v1/xml
+ https://wellcomeopenresearch.org/articles/2-36/v1/xml
+ https://wellcomeopenresearch.org/articles/2-36/v2/xml
+ https://wellcomeopenresearch.org/articles/2-37/v1/xml
+ https://wellcomeopenresearch.org/articles/2-37/v2/xml
+ https://wellcomeopenresearch.org/articles/2-38/v1/xml
+ https://wellcomeopenresearch.org/articles/2-39/v1/xml
+ https://wellcomeopenresearch.org/articles/2-39/v2/xml
+ https://wellcomeopenresearch.org/articles/2-4/v1/xml
+ https://wellcomeopenresearch.org/articles/2-4/v2/xml
+ https://wellcomeopenresearch.org/articles/2-40/v1/xml
+ https://wellcomeopenresearch.org/articles/2-40/v2/xml
+ https://wellcomeopenresearch.org/articles/2-41/v1/xml
+ https://wellcomeopenresearch.org/articles/2-41/v2/xml
+ https://wellcomeopenresearch.org/articles/2-42/v1/xml
+ https://wellcomeopenresearch.org/articles/2-43/v1/xml
+ https://wellcomeopenresearch.org/articles/2-43/v2/xml
+ https://wellcomeopenresearch.org/articles/2-44/v1/xml
+ https://wellcomeopenresearch.org/articles/2-44/v2/xml
+ https://wellcomeopenresearch.org/articles/2-45/v1/xml
+ https://wellcomeopenresearch.org/articles/2-45/v2/xml
+ https://wellcomeopenresearch.org/articles/2-46/v1/xml
+ https://wellcomeopenresearch.org/articles/2-47/v1/xml
+ https://wellcomeopenresearch.org/articles/2-47/v2/xml
+ https://wellcomeopenresearch.org/articles/2-48/v1/xml
+ https://wellcomeopenresearch.org/articles/2-48/v2/xml
+ https://wellcomeopenresearch.org/articles/2-49/v1/xml
+ https://wellcomeopenresearch.org/articles/2-5/v1/xml
+ https://wellcomeopenresearch.org/articles/2-50/v1/xml
+ https://wellcomeopenresearch.org/articles/2-50/v2/xml
+ https://wellcomeopenresearch.org/articles/2-51/v1/xml
+ https://wellcomeopenresearch.org/articles/2-52/v1/xml
+ https://wellcomeopenresearch.org/articles/2-52/v2/xml
+ https://wellcomeopenresearch.org/articles/2-53/v1/xml
+ https://wellcomeopenresearch.org/articles/2-53/v2/xml
+ https://wellcomeopenresearch.org/articles/2-54/v1/xml
+ https://wellcomeopenresearch.org/articles/2-55/v1/xml
+ https://wellcomeopenresearch.org/articles/2-55/v2/xml
+ https://wellcomeopenresearch.org/articles/2-56/v1/xml
+ https://wellcomeopenresearch.org/articles/2-57/v1/xml
+ https://wellcomeopenresearch.org/articles/2-58/v1/xml
+ https://wellcomeopenresearch.org/articles/2-59/v1/xml
+ https://wellcomeopenresearch.org/articles/2-6/v1/xml
+ https://wellcomeopenresearch.org/articles/2-6/v2/xml
+ https://wellcomeopenresearch.org/articles/2-60/v1/xml
+ https://wellcomeopenresearch.org/articles/2-60/v2/xml
+ https://wellcomeopenresearch.org/articles/2-61/v1/xml
+ https://wellcomeopenresearch.org/articles/2-62/v1/xml
+ https://wellcomeopenresearch.org/articles/2-63/v1/xml
+ https://wellcomeopenresearch.org/articles/2-64/v1/xml
+ https://wellcomeopenresearch.org/articles/2-64/v2/xml
+ https://wellcomeopenresearch.org/articles/2-65/v1/xml
+ https://wellcomeopenresearch.org/articles/2-66/v1/xml
+ https://wellcomeopenresearch.org/articles/2-66/v2/xml
+ https://wellcomeopenresearch.org/articles/2-66/v3/xml
+ https://wellcomeopenresearch.org/articles/2-67/v1/xml
+ https://wellcomeopenresearch.org/articles/2-68/v1/xml
+ https://wellcomeopenresearch.org/articles/2-69/v1/xml
+ https://wellcomeopenresearch.org/articles/2-69/v2/xml
+ https://wellcomeopenresearch.org/articles/2-7/v1/xml
+ https://wellcomeopenresearch.org/articles/2-70/v1/xml
+ https://wellcomeopenresearch.org/articles/2-71/v1/xml
+ https://wellcomeopenresearch.org/articles/2-72/v1/xml
+ https://wellcomeopenresearch.org/articles/2-72/v2/xml
+ https://wellcomeopenresearch.org/articles/2-73/v1/xml
+ https://wellcomeopenresearch.org/articles/2-73/v2/xml
+ https://wellcomeopenresearch.org/articles/2-74/v1/xml
+ https://wellcomeopenresearch.org/articles/2-75/v1/xml
+ https://wellcomeopenresearch.org/articles/2-76/v1/xml
+ https://wellcomeopenresearch.org/articles/2-76/v2/xml
+ https://wellcomeopenresearch.org/articles/2-77/v1/xml
+ https://wellcomeopenresearch.org/articles/2-77/v2/xml
+ https://wellcomeopenresearch.org/articles/2-78/v1/xml
+ https://wellcomeopenresearch.org/articles/2-78/v2/xml
+ https://wellcomeopenresearch.org/articles/2-79/v1/xml
+ https://wellcomeopenresearch.org/articles/2-8/v1/xml
+ https://wellcomeopenresearch.org/articles/2-80/v1/xml
+ https://wellcomeopenresearch.org/articles/2-80/v2/xml
+ https://wellcomeopenresearch.org/articles/2-81/v1/xml
+ https://wellcomeopenresearch.org/articles/2-82/v1/xml
+ https://wellcomeopenresearch.org/articles/2-83/v1/xml
+ https://wellcomeopenresearch.org/articles/2-83/v2/xml
+ https://wellcomeopenresearch.org/articles/2-84/v1/xml
+ https://wellcomeopenresearch.org/articles/2-84/v2/xml
+ https://wellcomeopenresearch.org/articles/2-85/v1/xml
+ https://wellcomeopenresearch.org/articles/2-86/v1/xml
+ https://wellcomeopenresearch.org/articles/2-87/v1/xml
+ https://wellcomeopenresearch.org/articles/2-87/v2/xml
+ https://wellcomeopenresearch.org/articles/2-88/v1/xml
+ https://wellcomeopenresearch.org/articles/2-89/v1/xml
+ https://wellcomeopenresearch.org/articles/2-89/v2/xml
+ https://wellcomeopenresearch.org/articles/2-9/v1/xml
+ https://wellcomeopenresearch.org/articles/2-90/v1/xml
+ https://wellcomeopenresearch.org/articles/2-91/v1/xml
+ https://wellcomeopenresearch.org/articles/2-92/v1/xml
+ https://wellcomeopenresearch.org/articles/2-93/v1/xml
+ https://wellcomeopenresearch.org/articles/2-93/v2/xml
+ https://wellcomeopenresearch.org/articles/2-93/v3/xml
+ https://wellcomeopenresearch.org/articles/2-94/v1/xml
+ https://wellcomeopenresearch.org/articles/2-95/v1/xml
+ https://wellcomeopenresearch.org/articles/2-95/v2/xml
+ https://wellcomeopenresearch.org/articles/2-96/v1/xml
+ https://wellcomeopenresearch.org/articles/2-97/v1/xml
+ https://wellcomeopenresearch.org/articles/2-97/v2/xml
+ https://wellcomeopenresearch.org/articles/2-98/v1/xml
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+ https://wellcomeopenresearch.org/articles/4-58/v1/xml
+ https://wellcomeopenresearch.org/articles/4-58/v2/xml
+ https://wellcomeopenresearch.org/articles/4-59/v1/xml
+ https://wellcomeopenresearch.org/articles/4-6/v1/xml
+ https://wellcomeopenresearch.org/articles/4-60/v1/xml
+ https://wellcomeopenresearch.org/articles/4-61/v1/xml
+ https://wellcomeopenresearch.org/articles/4-61/v2/xml
+ https://wellcomeopenresearch.org/articles/4-62/v1/xml
+ https://wellcomeopenresearch.org/articles/4-62/v2/xml
+ https://wellcomeopenresearch.org/articles/4-63/v1/xml
+ https://wellcomeopenresearch.org/articles/4-64/v1/xml
+ https://wellcomeopenresearch.org/articles/4-64/v2/xml
+ https://wellcomeopenresearch.org/articles/4-65/v1/xml
+ https://wellcomeopenresearch.org/articles/4-65/v2/xml
+ https://wellcomeopenresearch.org/articles/4-66/v1/xml
+ https://wellcomeopenresearch.org/articles/4-66/v2/xml
+ https://wellcomeopenresearch.org/articles/4-67/v1/xml
+ https://wellcomeopenresearch.org/articles/4-67/v2/xml
+ https://wellcomeopenresearch.org/articles/4-68/v1/xml
+ https://wellcomeopenresearch.org/articles/4-68/v2/xml
+ https://wellcomeopenresearch.org/articles/4-69/v1/xml
+ https://wellcomeopenresearch.org/articles/4-7/v1/xml
+ https://wellcomeopenresearch.org/articles/4-70/v1/xml
+ https://wellcomeopenresearch.org/articles/4-71/v1/xml
+ https://wellcomeopenresearch.org/articles/4-72/v1/xml
+ https://wellcomeopenresearch.org/articles/4-73/v1/xml
+ https://wellcomeopenresearch.org/articles/4-74/v1/xml
+ https://wellcomeopenresearch.org/articles/4-75/v1/xml
+ https://wellcomeopenresearch.org/articles/4-75/v2/xml
+ https://wellcomeopenresearch.org/articles/4-76/v1/xml
+ https://wellcomeopenresearch.org/articles/4-76/v2/xml
+ https://wellcomeopenresearch.org/articles/4-77/v1/xml
+ https://wellcomeopenresearch.org/articles/4-77/v2/xml
+ https://wellcomeopenresearch.org/articles/4-78/v1/xml
+ https://wellcomeopenresearch.org/articles/4-79/v1/xml
+ https://wellcomeopenresearch.org/articles/4-8/v1/xml
+ https://wellcomeopenresearch.org/articles/4-80/v1/xml
+ https://wellcomeopenresearch.org/articles/4-81/v1/xml
+ https://wellcomeopenresearch.org/articles/4-82/v1/xml
+ https://wellcomeopenresearch.org/articles/4-83/v1/xml
+ https://wellcomeopenresearch.org/articles/4-84/v1/xml
+ https://wellcomeopenresearch.org/articles/4-84/v2/xml
+ https://wellcomeopenresearch.org/articles/4-85/v1/xml
+ https://wellcomeopenresearch.org/articles/4-86/v1/xml
+ https://wellcomeopenresearch.org/articles/4-87/v1/xml
+ https://wellcomeopenresearch.org/articles/4-87/v2/xml
+ https://wellcomeopenresearch.org/articles/4-88/v1/xml
+ https://wellcomeopenresearch.org/articles/4-89/v1/xml
+ https://wellcomeopenresearch.org/articles/4-9/v1/xml
+ https://wellcomeopenresearch.org/articles/4-90/v1/xml
+ https://wellcomeopenresearch.org/articles/4-91/v1/xml
+ https://wellcomeopenresearch.org/articles/4-92/v1/xml
+ https://wellcomeopenresearch.org/articles/4-93/v1/xml
+ https://wellcomeopenresearch.org/articles/4-94/v1/xml
+ https://wellcomeopenresearch.org/articles/4-95/v1/xml
+ https://wellcomeopenresearch.org/articles/4-96/v1/xml
+ https://wellcomeopenresearch.org/articles/4-97/v1/xml
+ https://wellcomeopenresearch.org/articles/4-98/v1/xml
+ https://wellcomeopenresearch.org/articles/4-99/v1/xml
+ https://wellcomeopenresearch.org/articles/4-99/v2/xml
+
+
+for $x in $list//*:item
+let $txt := fetch:text($x/text())
+let $name := replace(concat('wellcomeopenresearch','-',substring-before(substring-after($x,'/articles/'),'/xml'),'.xml'),'/','-')
+let $file-path := concat('/Users/fredatherden/Documents/f1000-xml/',$name)
+
+return
+if ($txt = '') then ()
+else
+let $xml := fetch:xml($x/text())
+return file:write($file-path,$xml)
+
diff --git a/find-articles-with-book-ref.xq b/find-articles-with-book-ref.xq
new file mode 100644
index 0000000..0883108
--- /dev/null
+++ b/find-articles-with-book-ref.xq
@@ -0,0 +1,2 @@
+distinct-values(for $x in collection('articles')//*:article[descendant::*:element-citation[@publication-type="book"]]
+return $x//*:article-id[@pub-id-type="publisher-id"]/text())
\ No newline at end of file
diff --git a/find-equal-authors.xq b/find-equal-authors.xq
new file mode 100644
index 0000000..470657a
--- /dev/null
+++ b/find-equal-authors.xq
@@ -0,0 +1,14 @@
+distinct-values(
+ for $x in collection('articles')//*:article
+ let $authors := $x//*:article-meta//*:contrib-group[not(@*)]
+ let $count := count($authors/*:contrib)
+ let $eq-count := count($authors/*:contrib[@equal-contrib='yes'])
+ let $auth1 := $authors/*:contrib[1]
+ let $auth2 := $authors/*:contrib[2]
+ let $auth3 := $authors/*:contrib[3]
+ let $auth4 := $authors/*:contrib[4]
+ return
+ if ($count < 3) then ()
+ else if ($auth1[@equal-contrib='yes'] and $auth2[@equal-contrib='yes'] and $auth3[@equal-contrib='yes']) then substring-before($x/base-uri(),'-v')
+ else ()
+)
\ No newline at end of file
diff --git a/find-fundref.xq b/find-fundref.xq
new file mode 100644
index 0000000..9859aac
--- /dev/null
+++ b/find-fundref.xq
@@ -0,0 +1,2 @@
+distinct-values(for $x in collection('articles')//*:article//*:funding-group//*:award-group[descendant::*:institution = 'Seventh Framework Programme']
+return $x//*:institution-id/text())
\ No newline at end of file
diff --git a/find-numerous-versions.xq b/find-numerous-versions.xq
new file mode 100644
index 0000000..ca14b45
--- /dev/null
+++ b/find-numerous-versions.xq
@@ -0,0 +1,13 @@
+let $list :=
+{
+for $x in collection('articles')//*:article
+let $no := $x//*:article-meta/*:article-id[@pub-id-type="publisher-id"]/data()
+let $doi := ('http://doi.org/'||$x//*:article-meta/*:article-id[@pub-id-type="doi"]/data())
+return {$x//*:article-meta//*:article-title}
+}
+
+for $x in $list//*:item
+let $no := $x/@no
+order by $no
+return if (count($x/preceding::*:item[@no=$no])>3) then $x
+else ()
\ No newline at end of file
diff --git a/find-unique-atts.xq b/find-unique-atts.xq
new file mode 100644
index 0000000..1a8aa51
--- /dev/null
+++ b/find-unique-atts.xq
@@ -0,0 +1,19 @@
+let $base := '/Users/fredatherden/Desktop/lists/'
+let $ijm := doc(concat($base,'ijm-att-list.xml'))/*:list
+
+let $elife := doc(concat($base,'elife-att-list.xml'))/*:list
+let $biorxiv := doc(concat($base,'biorxiv-att-list.xml'))/*:list
+let $wellcome := doc(concat($base,'wellcome-att-list.xml'))/*:list
+let $gates := doc(concat($base,'gates-att-list.xml'))/*:list
+let $f1000 := doc(concat($base,'f1000-att-list.xml'))/*:list
+
+for $x in $biorxiv//*:attribute
+let $t := $x/text()
+return
+if ($t = $ijm//*:attribute/text()) then ()
+else if ($t = $wellcome//*:attribute/text()) then ()
+else if ($t = $gates//*:attribute/text()) then ()
+else if ($t = $f1000//*:attribute/text()) then ()
+else $x
+
+
diff --git a/find-xml-from-urls.xq b/find-xml-from-urls.xq
new file mode 100644
index 0000000..bfa4296
--- /dev/null
+++ b/find-xml-from-urls.xq
@@ -0,0 +1,12 @@
+let $list := doc('/Users/fredatherden/Desktop/list.xml')
+
+for $x in $list//*:item
+let $url := concat('https://gatesopenresearch.org/articles/3-',$x/text(),'/v1/xml')
+let $type := fetch:content-type($url)
+
+let $name := concat('gatesopenresearch','-',concat('3-',$x/text()),'.xml')
+let $file-path := concat('/Users/fredatherden/Documents/gates-xml/',$name)
+
+return
+if (substring-before($type,';') = 'application/xml') then $url
+else ()
\ No newline at end of file
diff --git a/first-author-check.xq b/first-author-check.xq
new file mode 100644
index 0000000..835267a
--- /dev/null
+++ b/first-author-check.xq
@@ -0,0 +1,5 @@
+distinct-values(for $x in collection('articles')//*:article
+let $c := $x//*:article-meta/*:contrib-group[not(@*)][1]/*:contrib[1]
+return
+if (matches($c,'Seidel')) then $x//article-id[@pub-id-type="publisher-id"]/text()
+else ())
\ No newline at end of file
diff --git a/funders-not-in-author-list.xq b/funders-not-in-author-list.xq
new file mode 100644
index 0000000..a2f633e
--- /dev/null
+++ b/funders-not-in-author-list.xq
@@ -0,0 +1,28 @@
+declare function local:translate($input)
+{
+ replace(replace(translate($input,'àáâãäåçčèéêěëħìíîïłñňòóôõöőøřšśşùúûüýÿž','aaaaaacceeeeehiiiilnnooooooorsssuuuuyyz'),'æ','ae'),'ß','ss')
+
+};
+
+for $x in collection('articles')//*:article
+
+
+let $a-list := {
+ for $y in $x//*:article-meta//*:contrib[@contrib-type="author"]
+ return
+ for $c in $y//*:surname
+ return {local:translate(lower-case($c))}
+}
+
+
+let $f-list := {
+ for $f in $x//*:article-meta/*:funding-group//*:surname
+ return {local:translate(lower-case($f))}
+}
+
+return
+ for $z in $f-list//*:item
+ return
+ if (not($a-list//*:item)) then ()
+ else if ($z = $a-list//*:item) then ()
+ else $x/base-uri()
\ No newline at end of file
diff --git a/gene-sequence.xq b/gene-sequence.xq
new file mode 100644
index 0000000..5332b80
--- /dev/null
+++ b/gene-sequence.xq
@@ -0,0 +1,2 @@
+for $x in collection('articles')//*:article[descendant::*:p//named-content[@content-type="sequence"]]
+return $x//article-id[@pub-id-type="publisher-id"]
\ No newline at end of file
diff --git a/generate-manifest.xq b/generate-manifest.xq
new file mode 100644
index 0000000..c9d7c16
--- /dev/null
+++ b/generate-manifest.xq
@@ -0,0 +1,23 @@
+declare namespace xlink="http://www.w3.org/1999/xlink";
+
+let $file-loc := '/Users/fredatherden/Desktop/elife-52628-vor-r1/elife-52628.xml'
+let $filename := tokenize($file-loc,'/')[last()]
+let $file := doc($file-loc)
+
+let $manifest :=
+
+
+
+
+ {(
+ for $asset in $file//(*:fig|*:supplementary-material|*:media[@mimemtype="video"])
+ let $name := $asset/name()
+ return
+ if ($name='fig') then
+ else if ($name='supplementary-material') then
+ else
+ )}
+
+
+
+return $manifest
\ No newline at end of file
diff --git a/get-all-ref-links.xq b/get-all-ref-links.xq
new file mode 100644
index 0000000..d465fb1
--- /dev/null
+++ b/get-all-ref-links.xq
@@ -0,0 +1,32 @@
+let $xml := doc('/Users/fredatherden/Documents/GitHub/reference-manuscripts/manuscripts/00002/elife-00002.xml')
+
+for $x in $xml//*:ref
+let $year := $x/descendant::*:year[1]
+let $cite :=
+ if ((count($year/ancestor::element-citation/person-group[1]/*) = 1) and $year/ancestor::element-citation/person-group[1]/name)
+ then concat($year/ancestor::element-citation/person-group[1]/name/surname,', ',$year)
+
+else if ((count($year/ancestor::element-citation/person-group[1]/*) = 1) and $year/ancestor::element-citation/person-group[1]/collab)
+ then concat($year/ancestor::element-citation/person-group[1]/collab,', ',$year)
+
+else if ((count($year/ancestor::element-citation/person-group[1]/*) = 2) and (count($year/ancestor::element-citation/person-group[1]/name) = 1) and $year/ancestor::element-citation/person-group[1]/*[1]/local-name() = 'collab')
+ then concat($year/ancestor::element-citation/person-group[1]/collab,' and ',$year/ancestor::element-citation/person-group[1]/name/surname,', ',$year)
+
+else if ((count($year/ancestor::element-citation/person-group[1]/*) = 2) and (count($year/ancestor::element-citation/person-group[1]/name) = 1) and $year/ancestor::element-citation/person-group[1]/*[1]/local-name() = 'name')
+ then concat($year/ancestor::element-citation/person-group[1]/name/surname,' and ',$year/ancestor::element-citation/person-group[1]/collab,', ',$year)
+
+else if ((count($year/ancestor::element-citation/person-group[1]/*) = 2) and (count($year/ancestor::element-citation/person-group[1]/name) = 2))
+ then concat($year/ancestor::element-citation/person-group[1]/name[1]/surname,' and ',$year/ancestor::element-citation/person-group[1]/name[2]/surname,', ',$year)
+
+else if ((count($year/ancestor::element-citation/person-group[1]/*) = 2) and (count($year/ancestor::element-citation/person-group[1]/collab) = 2))
+ then concat($year/ancestor::element-citation/person-group[1]/collab[1],' and ',$year/ancestor::element-citation/person-group[1]/collab[2],', ',$year)
+
+else if ((count($year/ancestor::element-citation/person-group[1]/*) ge 2) and $year/ancestor::element-citation/person-group[1]/*[1]/local-name() = 'collab')
+ then concat($year/ancestor::element-citation/person-group[1]/collab[1], ' et al., ',$year)
+
+else if ((count($year/ancestor::element-citation/person-group[1]/*) ge 2) and $year/ancestor::element-citation/person-group[1]/*[1]/local-name() = 'name')
+ then concat($year/ancestor::element-citation/person-group[1]/name[1]/surname, ' et al., ',$year)
+
+ else ()
+
+ return {$cite}
\ No newline at end of file
diff --git a/get-formatting-elements.xq b/get-formatting-elements.xq
new file mode 100644
index 0000000..dc610b7
--- /dev/null
+++ b/get-formatting-elements.xq
@@ -0,0 +1,9 @@
+let $formatting := ('bold','fixed-case','italic','monospace','overline','overline-start','overline-end','roman','sans-serif','sc','strike','underline','underline-start','underline-end','ruby','sub','sup')
+
+return distinct-values(
+ for $x in collection('f1000')//*
+ let $name := $x/name()
+ return
+ if ($name = $formatting) then $name
+ else ()
+)
\ No newline at end of file
diff --git a/group-authors.xq b/group-authors.xq
new file mode 100644
index 0000000..b760ae4
--- /dev/null
+++ b/group-authors.xq
@@ -0,0 +1,11 @@
+distinct-values(for $x in collection('articles')//*:article
+ let $m := $x//*:article-meta
+ let $id:= $x//*:article-id[@pub-id-type="publisher-id"]
+ return
+ for $y in $m//*:contrib
+ return
+ if (matches($y,'[Rr]eproducibility [Pp]roject')) then ()
+ else if ($y/*:collab) then $id
+ else if ($y//*:contrib) then $id
+ else ()
+ )
\ No newline at end of file
diff --git a/hindawi-manipulation.xq b/hindawi-manipulation.xq
new file mode 100644
index 0000000..ac5879a
--- /dev/null
+++ b/hindawi-manipulation.xq
@@ -0,0 +1,33 @@
+declare namespace xlink="http://www.w3.org/1999/xlink";
+declare namespace mml="http://www.w3.org/1998/Math/MathML";
+
+declare variable $filename := '8093192.xml';
+declare variable $dir := '/Users/fredatherden/Desktop/';
+declare variable $file := doc(concat('/Users/fredatherden/Desktop/CRID_8093192_Final_1 copy/',$filename));
+
+
+for $x in $file//*:article
+let $y :=
+
+copy $copy := $x
+modify(
+
+ for $x in $copy//*:fig
+ let $label := if (ends-with($x/*:label,'.')) then $x/*:label/text()
+ else concat($x/*:label,'. ')
+ return
+ replace node $x with
+
+
+ {$label,
+ $x/*:caption/*:p/(*|text())}
+
+
+
+
+
+)
+return $copy
+
+
+return file:write(concat($dir,$filename),$y, map {'indent':'no'})
\ No newline at end of file
diff --git a/hindawi-simple-content.xq b/hindawi-simple-content.xq
new file mode 100644
index 0000000..5475ab5
--- /dev/null
+++ b/hindawi-simple-content.xq
@@ -0,0 +1,11 @@
+declare namespace xlink="http://www.w3.org/1999/xlink";
+declare namespace mml="http://www.w3.org/1998/Math/MathML";
+
+for $x in collection('hindawi-xml')//*:article[not(descendant::table-wrap) and (count(descendant::*:fig-group) le 2)]
+let $c := count($x//*:article-meta/*:contrib-group[not(@*)]/*:contrib)
+let $a := count($x//*:article-meta/*:contrib-group[not(@*)]/*:aff)
+return
+if ($c ge 8) then ()
+else if ($a ge 3) then ()
+else if ($x//*:fig[descendant::*:supplementary-material]) then ()
+else $x//*:article-id[@pub-id-type="publisher-id"]/text()
diff --git a/html2markdown.xq b/html2markdown.xq
new file mode 100644
index 0000000..b8e6a25
--- /dev/null
+++ b/html2markdown.xq
@@ -0,0 +1,113 @@
+declare function local:ul-list($ul){
+ {
+ for $x in $ul//*:li
+ let $c := count($x/ancestor::*:ul)
+ let $y := count($x/following-sibling::*:li)
+ return
+ if ($c = 1) then
+ if ($y=0) then concat('- ',$x/data())
+ else concat('- ',$x/data(),'
')
+ else if ($c = 2) then concat(' - ',$x/data(),'
')
+ else if ($c = 3) then concat(' - ',$x/data(),'
')
+ else if ($c = 4) then concat(' - ',$x/data(),'
')
+ else concat(' - ',$x/data(),'
+')
+ }
+
+};
+
+declare function local:ol-list($ol){
+ {
+ for $x in $ol//*:li
+ let $pos := string(count($x/preceding-sibling::*:li) + 1)
+ return
+ if ($x/following-sibling::*:li) then concat($pos,'. ',$x/data(),'
')
+ else concat ($pos,'. ',$x/data())
+ }
+};
+
+declare function local:edit-issue($issue){
+ copy $copy := $issue
+ modify(
+ for $x in $copy//*:div[@class="comment"]
+ let $c := count($x/preceding-sibling::*:div[@class="comment"])
+ return
+ if ($c = 0) then ()
+ else delete node $x,
+
+ for $x in $copy//*:pre
+ return replace node $x with $x/(*|text()),
+
+ for $x in $copy//*:div[@class="body"]
+ let $url := $x/ancestor::*:div[@class="container"]//*:header//*:span[@class="url"]//*:a/@href/string()
+ return insert node
{concat('Taken from: ',$url)}
as last into $x,
+
+ for $x in $copy//*:h3[parent::*:li]
+ return
+ (delete node $x/parent::li,
+ insert node $x before $x/ancestor::*:ul)
+ )
+ return copy $copy2 := $copy
+ modify(
+ for $x in $copy2/*:header
+ return delete node $x,
+
+ for $x in $copy2//*:div[@class="meta"]
+ return delete node $x,
+
+ for $x in $copy2//*:div[@class="body"]/*:ul
+ let $pos := count($x/preceding-sibling::*:ul)
+ return
+ if ($pos=0) then delete node $x
+ else replace node $x with local:ul-list($x),
+
+ for $x in $copy2//*:div[@class="body"]/*:ol
+ return replace node $x with local:ol-list($x),
+
+ for $x in $copy2//*:code
+ return
+ if ($x/@class="lang-xml") then replace node $x with {concat('```xml
+ ',$x/data(),'
```')}
+ else replace node $x with concat('`',$x/data(),'`'),
+
+ for $x in $copy2//*:a
+ return replace node $x with {concat('[',$x/data(),']','(',$x/@href/string(),')')},
+
+ for $x in $copy2//*:h2
+ return replace node $x with {concat('## ',$x/data())},
+
+ for $x in $copy2//*:h3
+ return replace node $x with {concat('### ',$x/data())},
+
+ for $x in $copy2//*:h4
+ return replace node $x with {concat('#### ',$x/data())},
+
+ for $x in $copy2//*:h5
+ return replace node $x with {concat('##### ',$x/data())}
+
+ )
+ return copy $copy3 := $copy2
+ modify(
+
+ for $x in $copy3//*:div[@class="body"]/text()[1]
+ return delete node $x,
+
+ for $x in $copy3//(*:p|*:placeholder)
+ return replace node $x with $x/text(),
+
+ for $x in $copy3//*:div[@class="body"]/descendant::p[last()]/preceding-sibling::text()[1]
+ return replace node $x with '
'
+
+ )
+ return $copy3//*:div[@class="body"]/text()
+};
+
+
+for $x in collection('issue-test')/*:html//*:div[@class="container"]
+let $name := $x/ancestor::body//*:h1/text()
+let $filename := concat(substring-before(substring-after($x/base-uri(),'/issue-test/'),'html'),'md')
+let $ticket := (concat($name,'
'),
+ local:edit-issue($x))
+return
+file:write(concat('/Users/fredatherden/Desktop/issue-test/',$filename),$ticket,map{'method':'text','indent':'no'})
+
diff --git a/human-animal-ethics.xq b/human-animal-ethics.xq
new file mode 100644
index 0000000..96a8ac6
--- /dev/null
+++ b/human-animal-ethics.xq
@@ -0,0 +1,6 @@
+distinct-values(for $x in collection('articles')//*:article[descendant::*:fn-group[@content-type="ethics-information"]]
+let $fn := $x//*:fn-group[@content-type="ethics-information"]
+let $d := $fn/data()
+return if (contains($d,'Human subjects:') and contains($d,'Animal experimentation:') )
+ then $x//article-id[@pub-id-type="publisher-id"]/text()
+ else ())
\ No newline at end of file
diff --git a/ijm-batch-validate.xq b/ijm-batch-validate.xq
new file mode 100644
index 0000000..7034c4d
--- /dev/null
+++ b/ijm-batch-validate.xq
@@ -0,0 +1,12 @@
+import module namespace schematron = "http://github.com/Schematron/schematron-basex";
+
+declare variable $sch := schematron:compile(doc('/Users/fredatherden/Documents/GitHub/jats-support-2/src/support.sch'));
+
+for $x in collection('ijm')//*:article
+let $svrl := schematron:validate($x, $sch)
+let $ids := ('table_parent-assert-1','table-assert-1','table-wrap-assert-1','tbody_parent-assert-1','td_child-assert-1','th_child-assert-1','thead_parent-assert-1','tr_parent-assert-1')
+return
+{
+ if ($svrl//(*:successful-report[@id=$ids]|*:failed-assert[@id=$ids])) then $svrl//(*:successful-report[@id=$ids]|*:failed-assert[@id=$ids])
+ else ()}
+
\ No newline at end of file
diff --git a/ijm-simple-content.xq b/ijm-simple-content.xq
new file mode 100644
index 0000000..69bea35
--- /dev/null
+++ b/ijm-simple-content.xq
@@ -0,0 +1,12 @@
+declare namespace xlink="http://www.w3.org/1999/xlink";
+declare namespace mml="http://www.w3.org/1998/Math/MathML";
+
+for $x in collection('ijm-xml')//*:article[@article-type="research-article" and descendant::*:body and not(descendant::*:media[@mimetype="video"]) and not(descendant::mml:math) and not(descendant::table-wrap) and not(descendant::fig-group) and not(descendant::disp-quote)]
+let $c := count($x//*:article-meta/*:contrib-group[not(@*)]/*:contrib)
+let $a := count($x//*:article-meta/*:contrib-group[not(@*)]/*:aff)
+return
+if ($c ge 8) then ()
+else if ($a ge 3) then ()
+else if ($x//*:fig[descendant::*:supplementary-material]) then ()
+else if ($x//*:sec[child::*:label]) then ()
+else $x//*:article-id[@pub-id-type="publisher-id"]/text()
diff --git a/ijm-v-elife-elems.xq b/ijm-v-elife-elems.xq
new file mode 100644
index 0000000..557edd8
--- /dev/null
+++ b/ijm-v-elife-elems.xq
@@ -0,0 +1,278 @@
+let $e-list :=
+
+front
+journal-meta
+journal-id
+journal-title-group
+journal-title
+issn
+publisher
+publisher-name
+article-meta
+article-id
+article-categories
+subj-group
+subject
+title-group
+article-title
+contrib-group
+contrib
+name
+surname
+given-names
+xref
+contrib-id
+email
+aff
+label
+institution
+addr-line
+named-content
+country
+role
+author-notes
+fn
+p
+pub-date
+day
+month
+year
+volume
+elocation-id
+history
+date
+permissions
+copyright-statement
+copyright-year
+copyright-holder
+free_to_read
+license
+license_ref
+license-p
+ext-link
+self-uri
+abstract
+object-id
+bold
+title
+kwd-group
+kwd
+funding-group
+award-group
+funding-source
+institution-wrap
+institution-id
+award-id
+principal-award-recipient
+funding-statement
+custom-meta-group
+custom-meta
+meta-name
+meta-value
+body
+sec
+italic
+fig-group
+fig
+caption
+graphic
+sup
+table-wrap
+table
+thead
+tr
+th
+tbody
+td
+table-wrap-foot
+supplementary-material
+media
+break
+sub
+back
+ack
+fn-group
+element-citation
+person-group
+data-title
+source
+pub-id
+ref-list
+ref
+fpage
+lpage
+collab
+sub-article
+front-stub
+boxed-text
+disp-quote
+corresp
+comment
+disp-formula
+math
+inline-formula
+publisher-loc
+edition
+chapter-title
+conf-name
+conf-loc
+bio
+inline-graphic
+suffix
+sc
+related-article
+underline
+date-in-citation
+version
+app-group
+app
+patent
+monospace
+list
+list-item
+code
+related-object
+styled-content
+strike
+attrib
+
+let $i-list := front
+journal-meta
+journal-id
+journal-title-group
+journal-title
+issn
+publisher
+publisher-name
+article-meta
+article-id
+article-categories
+subj-group
+subject
+title-group
+article-title
+contrib-group
+contrib
+name
+surname
+given-names
+email
+xref
+aff
+label
+institution
+addr-line
+country
+pub-date
+day
+month
+year
+volume
+issue
+fpage
+lpage
+permissions
+copyright-statement
+copyright-year
+copyright-holder
+free_to_read
+license
+license_ref
+license-p
+ext-link
+self-uri
+body
+sec
+title
+p
+italic
+fig
+caption
+graphic
+back
+ref-list
+ref
+element-citation
+person-group
+source
+date-in-citation
+publisher-loc
+ack
+author-notes
+fn
+target
+sup
+sub
+fn-group
+abstract
+kwd-group
+kwd
+disp-formula
+math
+table-wrap
+table
+tbody
+tr
+td
+thead
+th
+break
+bold
+string-name
+string-date
+comment
+chapter-title
+edition
+collab
+app-group
+app
+list
+list-item
+named-content
+corresp
+etal
+version
+suffix
+elocation-id
+disp-quote
+series
+conf-name
+conf-loc
+conf-date
+table-wrap-foot
+product
+isbn
+price
+inline-formula
+code
+boxed-text
+sc
+monospace
+x
+season
+role
+fig-group
+def-list
+def-item
+term
+def
+underline
+conf-sponsor
+phone
+fax
+uri
+conf-data
+subtitle
+mixed-citation
+pub-id
+glossary
+array
+colgroup
+col
+statement
+attrib
+table-wrap-group
+
+for $x in $i-list//*:item
+return if ($x = $e-list//*:item) then ()
+else $x
\ No newline at end of file
diff --git a/inline-tables.xq b/inline-tables.xq
new file mode 100644
index 0000000..f83c5c2
--- /dev/null
+++ b/inline-tables.xq
@@ -0,0 +1,8 @@
+
+{for $x in collection('articles')//*:article
+let $id := $x//*:article-id[@pub-id-type="publisher-id"]
+let $type := $x/@article-type
+let $subj := $x//*:subj-group[@subj-group-type="display-channel"]/*:subject
+return if ($x//*:table-wrap[not(child::*:label)]) then ()
+else ()
+}
\ No newline at end of file
diff --git a/insert-pmid-links.xq b/insert-pmid-links.xq
new file mode 100644
index 0000000..6c1f444
--- /dev/null
+++ b/insert-pmid-links.xq
@@ -0,0 +1,18 @@
+declare namespace xlink="http://www.w3.org/1999/xlink";
+
+
+let $file := doc('/Users/fredatherden/Documents/GitHub/XML-mapping/elife-00666.xml')
+
+for $x in $file
+let $c := copy $copy := $file
+modify(
+ for $y in $copy//*:table-wrap[@id="keyresource"]//*:td[matches(.,'PMID:')]
+ let $id := substring-after($y,'PMID:')
+ let $url := concat('https://www.ncbi.nlm.nih.gov/pubmed/',$id)
+ return
+ replace node $y with
PMID:{$id}
+
+)
+return $copy
+
+return file:write('/Users/fredatherden/Desktop/elife-00666.xml',$c,map{'indent':'no'})
\ No newline at end of file
diff --git a/latest-version.xq b/latest-version.xq
new file mode 100644
index 0000000..015f774
--- /dev/null
+++ b/latest-version.xq
@@ -0,0 +1,14 @@
+let $list-1 := {
+ for $x in collection('articles')//*:article
+ let $b := $x/base-uri()
+ order by $b
+ return {$b}
+ }
+
+return (
+ for $x in $list-1/*:item
+ let $id := substring-before(substring-after($x,'/articles/elife-'),'-v')
+ return
+ if (substring-before(substring-after($x/following-sibling::*:item[1],'/articles/elife-'),'-v') = $id) then ()
+ else $x/string()
+)
\ No newline at end of file
diff --git a/libero-edits.xq b/libero-edits.xq
new file mode 100644
index 0000000..af2ee51
--- /dev/null
+++ b/libero-edits.xq
@@ -0,0 +1,20 @@
+declare namespace xlink="http://www.w3.org/1999/xlink";
+declare namespace mml="http://www.w3.org/1998/Math/MathML";
+
+declare variable $dir := '/Users/fredatherden/Desktop/edits-done/';
+
+for $x in collection('edits')//*:article
+let $filename := substring-after($x/base-uri(),'/edits/')
+let $y :=
+
+copy $copy := $x
+modify(
+
+ for $y in $copy//*:article-meta//*:abstract
+ return (insert node Abstract{$y/*} as first into $y/following::body[1],
+ delete node $y)
+
+)
+return $copy
+
+return file:write(concat($dir,$filename),$y, map {'indent':'no'})
\ No newline at end of file
diff --git a/libero-manipulation.xq b/libero-manipulation.xq
new file mode 100644
index 0000000..0d6fa14
--- /dev/null
+++ b/libero-manipulation.xq
@@ -0,0 +1,34 @@
+declare namespace xlink="http://www.w3.org/1999/xlink";
+declare namespace mml="http://www.w3.org/1998/Math/MathML";
+
+declare variable $filename := 'elife-25480.xml';
+declare variable $dir := '/Users/fredatherden/Desktop/';
+declare variable $file := doc(concat('/Users/fredatherden/Desktop/elife-25480-vor-r1/',$filename));
+
+
+for $x in $file//*:article
+let $y :=
+
+copy $copy := $x
+modify(
+
+ for $x in $copy//*:ack
+ return (insert node {$x/*} as last into $x/preceding::body,
+ delete node $x),
+
+ for $x in $copy//*:label
+ return
+ if ($x/parent::*:aff) then ()
+ else if ($x/parent::*:fig) then
+ insert node concat($x/text(),' ') as first into $x/following-sibling::caption[1]/*:title
+ else if ($x/parent::*:sec) then
+ insert node concat($x/text(),' ') as first into $x/following-sibling::*:title[1]
+ else if ($x/parent::*:fn) then
+ insert node concat($x/text(),' ') as first into $x/following-sibling::p[1]
+ else ()
+
+)
+return $copy
+
+
+return file:write(concat($dir,$filename),$y, map {'indent':'no'})
\ No newline at end of file
diff --git a/libero-publisher/article-categories.xq b/libero-publisher/article-categories.xq
new file mode 100644
index 0000000..7fe25c9
--- /dev/null
+++ b/libero-publisher/article-categories.xq
@@ -0,0 +1,4 @@
+count(for $x in (collection('pmc1')//*:article[descendant::*:article-categories[*:subj-group/child::*:subject[2]]],
+ collection('pmc2')//*:article[descendant::*:article-categories[*:subj-group/child::*:subject[2]]],
+ collection('pmc3')//*:article[descendant::*:article-categories[*:subj-group/child::*:subject[2]]])
+return $x)
\ No newline at end of file
diff --git a/libero-publisher/change-elife-article-categories.xq b/libero-publisher/change-elife-article-categories.xq
new file mode 100644
index 0000000..1273372
--- /dev/null
+++ b/libero-publisher/change-elife-article-categories.xq
@@ -0,0 +1,18 @@
+declare variable $outputDir := '/Users/fredatherden/Desktop/categories/';
+
+for $x in collection('articles')//*:article
+let $filename := substring-after($x/base-uri(),'articles/')
+let $new :=
+copy $copy := $x
+modify(
+ for $y in $copy//*:article-meta//*:subj-group[@subj-group-type="heading"]/@subj-group-type
+ return
+ replace value of node $y with 'subject',
+
+ for $d in $copy//*:article-meta//*:subj-group[@subj-group-type="display-channel"]/@subj-group-type
+ return
+ replace value of node $d with 'heading'
+)
+return $copy
+
+return file:write(concat($outputDir,$filename),$new,map{'indent':'no'})
diff --git a/list-all-report-refs.xq b/list-all-report-refs.xq
new file mode 100644
index 0000000..1d16e68
--- /dev/null
+++ b/list-all-report-refs.xq
@@ -0,0 +1,2 @@
+{for $x in collection('articles')//*:article//*:element-citation[@publication-type="report"][*:ext-link]
+return $x}
\ No newline at end of file
diff --git a/mathml2latex.xsl b/mathml2latex.xsl
new file mode 100644
index 0000000..accab83
--- /dev/null
+++ b/mathml2latex.xsl
@@ -0,0 +1,167 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Presentation MathML
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
status:
+
+
Reference image:
+
+
+
+
TeX Rendering:
+
+
+
MathML:
+
+ <![CDATA[
+
+ ]]>
+
+
+
+
+
+
+
+
+
+ bad bvar
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/namespaces-in-use.xq b/namespaces-in-use.xq
new file mode 100644
index 0000000..77c424d
--- /dev/null
+++ b/namespaces-in-use.xq
@@ -0,0 +1,9 @@
+declare namespace functx = "http://www.functx.com";
+declare function functx:namespaces-in-use
+ ( $root as node()? ) as xs:anyURI* {
+
+ distinct-values(
+ $root/descendant-or-self::*/(.|@*)/namespace-uri(.))
+ } ;
+
+collection('ijm-xml')//*:article/functx:namespaces-in-use(.)
\ No newline at end of file
diff --git a/no-das-pub-date-check.xq b/no-das-pub-date-check.xq
new file mode 100644
index 0000000..7a5299a
--- /dev/null
+++ b/no-das-pub-date-check.xq
@@ -0,0 +1,16 @@
+for $x in collection('articles')//*:article[(@article-type="research-article") and *:body and not(descendant::*:sec[@sec-type="data-availability"])]
+let $p := $x//*:article-meta//*:pub-date[(@date-type='pub') or (@date-type='publication')]
+let $iso-date := concat($p/year,'-',$p/month,'-',$p/day)
+let $subj := $x//*:article-meta//*:subj-group[@subj-group-type="display-channel"]/*:subject
+order by $iso-date
+return
+(substring-after($x/base-uri(),'elife-')
+||
+' --- '
+||
+$subj
+||
+' --- '
+||
+$iso-date
+)
diff --git a/non-corr-email-2.xq b/non-corr-email-2.xq
new file mode 100644
index 0000000..f1c782e
--- /dev/null
+++ b/non-corr-email-2.xq
@@ -0,0 +1,19 @@
+let $list :=
+{
+ for $x in collection('articles')//*:article
+let $article-id := $x//*:article-id[@pub-id-type="publisher-id"]/text()
+let $folder := concat('/articles/elife-',$article-id,'-v')
+let $v-no := number(substring-before(substring-after($x/base-uri(),$folder),'.xml'))
+let $count := count(collection('articles')//*:article[descendant::*:article-id[@pub-id-type="publisher-id"]/text() = $article-id])
+return if ($count = $v-no) then
+else ()
+}
+
+for $x in collection('articles')//*:article
+let $b := $x/base-uri()
+let $c := count($x//*:contrib-group[not(@content-type="section")]/*:contrib)
+return if ($b = $list//*:item/@id) then
+ if ($c = 1) then ()
+ else if ($x//*:contrib[not(@corresp="yes")and not(descendant::*:xref[@ref-type="corresp"])]//*:email) then $x//article-id[@pub-id-type="publisher-id"]/text()
+ else ()
+else ()
\ No newline at end of file
diff --git a/non-corr-email-as-csv.xq b/non-corr-email-as-csv.xq
new file mode 100644
index 0000000..66b876f
--- /dev/null
+++ b/non-corr-email-as-csv.xq
@@ -0,0 +1,1819 @@
+let $list :=
+09693
+12572
+12792
+13546
+15828
+17915
+20178
+21114
+21992
+22199
+22225
+22425
+22599
+22626
+22901
+23279
+23435
+23612
+23625
+23647
+23649
+23708
+23770
+24192
+24196
+24260
+24271
+24340
+24502
+24578
+24656
+24779
+24820
+24994
+25008
+25012
+25060
+25141
+25165
+25197
+25269
+25281
+25301
+25423
+25462
+25496
+25606
+25607
+25726
+25727
+25752
+25784
+25787
+25819
+25843
+25844
+25861
+25884
+25923
+25950
+26002
+26014
+26016
+26022
+26039
+26067
+26106
+26116
+26129
+26148
+26161
+26163
+26231
+26255
+26278
+26280
+26349
+26376
+26423
+26424
+26435
+26439
+26476
+26487
+26517
+26556
+26607
+26642
+26653
+26686
+26693
+26724
+26726
+26738
+26759
+26796
+26832
+26839
+26845
+26851
+26856
+26866
+26876
+26898
+26910
+26944
+26945
+26947
+26952
+26956
+26957
+26973
+26985
+26990
+27000
+27024
+27049
+27057
+27069
+27082
+27119
+27131
+27155
+27157
+27159
+27166
+27167
+27192
+27203
+27215
+27237
+27293
+27344
+27346
+27356
+27362
+27364
+27369
+27388
+27396
+27402
+27417
+27420
+27421
+27430
+27434
+27441
+27443
+27444
+27445
+27451
+27454
+27455
+27469
+27480
+27518
+27529
+27574
+27576
+27592
+27601
+27602
+27679
+27694
+27696
+27701
+27702
+27706
+27713
+27744
+27746
+27793
+27798
+27814
+27819
+27826
+27827
+27842
+27854
+27860
+27861
+27868
+27872
+27873
+27891
+27955
+27991
+27995
+28020
+28023
+28040
+28046
+28070
+28074
+28075
+28081
+28083
+28086
+28111
+28118
+28123
+28132
+28141
+28166
+28197
+28199
+28202
+28270
+28275
+28295
+28298
+28307
+28324
+28329
+28342
+28366
+28377
+28383
+28384
+28387
+28409
+28415
+28477
+28482
+28505
+28507
+28534
+28560
+28563
+28590
+28606
+28619
+28625
+28626
+28629
+28635
+28662
+28671
+28672
+28673
+28680
+28683
+28685
+28716
+28723
+28728
+28751
+28755
+28766
+28768
+28802
+28804
+28811
+28836
+28842
+28844
+28865
+28875
+28877
+28889
+28899
+28909
+28921
+28927
+28932
+28935
+28974
+29002
+29005
+29013
+29023
+29044
+29053
+29061
+29086
+29087
+29088
+29100
+29106
+29112
+29118
+29123
+29132
+29144
+29145
+29150
+29154
+29156
+29176
+29178
+29198
+29213
+29215
+29222
+29224
+29226
+29236
+29276
+29280
+29285
+29292
+29303
+29307
+29312
+29315
+29328
+29329
+29330
+29353
+29365
+29384
+29388
+29391
+29425
+29430
+29494
+29495
+29507
+29510
+29511
+29515
+29518
+29538
+29539
+29546
+29550
+29555
+29566
+29593
+29594
+29595
+29605
+29626
+29630
+29639
+29648
+29677
+29702
+29718
+29736
+29738
+29742
+29744
+29750
+29754
+29793
+29795
+29797
+29808
+29809
+29815
+29820
+29830
+29834
+29845
+29854
+29865
+29878
+29880
+29887
+29893
+29905
+29908
+29913
+29915
+29917
+29929
+29939
+29944
+29953
+29959
+29968
+29988
+29996
+30000
+30015
+30018
+30051
+30054
+30057
+30058
+30084
+30094
+30120
+30126
+30127
+30134
+30135
+30150
+30178
+30187
+30189
+30198
+30201
+30203
+30212
+30224
+30233
+30241
+30244
+30246
+30274
+30278
+30281
+30286
+30292
+30294
+30325
+30333
+30334
+30352
+30373
+30387
+30388
+30391
+30395
+30425
+30433
+30442
+30457
+30463
+30473
+30474
+30483
+30490
+30493
+30496
+30498
+30503
+30506
+30523
+30543
+30552
+30560
+30577
+30590
+30637
+30640
+30647
+30649
+30657
+30668
+30688
+30693
+30697
+30703
+30756
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+
+
+let $csv :=
+
+{for $x in collection('articles')//*:article[descendant::*:body]
+let $id := $x//*:article-id[@pub-id-type="publisher-id"]/text()
+let $d := string-join(for $y in $x//*:pub-date[@date-type="publication"]/* return $y,'-')
+return
+if (matches($d,'\d')) then
+ if ($id = $list//*:item/text()) then
+{$id}{$d}
+ else ()
+ else ()
+}
+
+let $csv2 :=
+copy $copy := $csv
+modify(
+for $x in $copy//*:record
+let $id := $x/*:entry[1]/text()
+return if ($x/following-sibling::*:record/*:entry[1] = $id) then delete node $x
+else ())
+return $copy
+
+return file:write('/Users/fredatherden/Desktop/non-corr-email.csv',$csv2, map { "method": "csv", "item-separator": "," })
\ No newline at end of file
diff --git a/non-corr-email.xq b/non-corr-email.xq
new file mode 100644
index 0000000..8b75cee
--- /dev/null
+++ b/non-corr-email.xq
@@ -0,0 +1,6 @@
+distinct-values(for $x in collection('articles')//*:article[descendant::*:body]
+let $c := count($x//*:contrib-group[not(@content-type="section")]/*:contrib)
+return
+if ($c = 1) then ()
+else if ($x//*:contrib[not(@corresp="yes")and not(descendant::*:xref[@ref-type="corresp"])]//*:email) then $x//article-id[@pub-id-type="publisher-id"]/text()
+else ())
\ No newline at end of file
diff --git a/non-credit-contributions.xq b/non-credit-contributions.xq
new file mode 100644
index 0000000..d35b4a5
--- /dev/null
+++ b/non-credit-contributions.xq
@@ -0,0 +1,15 @@
+distinct-values(let $regex := 'conceptualization[;,]?|data curation[;,]?|formal analysis[;,]?|funding acquisition[;,]?|investigation[;,]?|methodology[;,]?|project administration[;,]?|resources[;,]?|software[;,]?|supervision[;,]?|validation[;,]?|visualization[;,]?|writing—review and editing[;,]?|writing—original draft[;,]?'
+
+
+for $x in collection('articles')//*:article//*:contrib[@contrib-type="author"]
+let $name := concat($x/*:name/*:given-names,' ',$x/*:name/*:surname)
+let $doi := $x/ancestor::*:article//*:article-meta//*:article-id[@pub-id-type="doi"]/text()
+let $y := $x/*:xref[matches(@rid,'^con[\d]{1,2}$')]/@rid/string()
+let $list := {for $z in $x/ancestor::article/descendant::*:fn[@id/string() = $y]/*:p[1] return $z}
+return
+if ($list = '') then ()
+else if (matches(lower-case($list/*:p[1]),$regex)) then ()
+else concat($list/*:p[1]/data(),' ---- ',$name,' ---- ',$doi)
+
+
+)
\ No newline at end of file
diff --git a/old-elife2dar.xq b/old-elife2dar.xq
new file mode 100644
index 0000000..51d54da
--- /dev/null
+++ b/old-elife2dar.xq
@@ -0,0 +1,417 @@
+declare namespace xlink="http://www.w3.org/1999/xlink";
+declare namespace mml="http://www.w3.org/1998/Math/MathML";
+
+(:
+Assumes that the local instance of Texture is running from files in the following directory '/Users/fredatherden/Documents/GitHub/texture/data/kitchen-sink'.
+This currently runs on one file (currently 20178-v3), but could be adjusted to run/output numerous files with ease/processing power.
+ :)
+
+declare variable $outputDir := '/Users/fredatherden/Documents/GitHub/texture/data/kitchen-sink/manuscript.xml';
+
+for $x in collection('articles')//*:article[base-uri() = '/articles/elife-10015-v2.xml']
+let $y :=
+copy $copy := $x
+modify(
+ for $a in $copy//*:sub-article
+ return delete node $a,
+
+ for $y in $copy//*:back/*:ack
+ return (delete node $y,
+ insert node {$y/*} as last into $y/preceding::*:body),
+
+ for $z in $copy//*:article-meta/*:author-notes
+ return delete node $z,
+
+ for $s in $copy//*:sec[@sec-type="additional-information"]/*:fn-group
+ return delete node $s,
+
+ for $s in $copy//*:back/*:fn-group
+ return delete node $s,
+
+ for $x in $copy//*:front//*:xref[@ref-type="fn"]
+ return delete node $x,
+
+ for $e in $copy//*:object-id
+ return delete node $e,
+
+ for $d in $copy//*:funding-group/*:funding-statement
+ return delete node $d,
+
+ for $t in $copy//*:kwd-group/*:title
+ return delete node $t,
+
+ for $r in $copy//*:ref-list[*:title = 'Acknowledgements']
+ return delete node $r,
+
+ for $f in $copy//*:collab[not(descendant::*)]
+ return delete node $f,
+
+ for $x in $copy//*:article-meta
+ let $count := count($x/contrib-group[@content-type="section"])
+ return if ($count > 1) then
+ (insert node {for $c in $x/*:contrib-group[@content-type="section"] return $c/*} after $x/*:contrib-group[not(@*)],
+ for $c in $x/*:contrib-group[@content-type="section"] return delete node $c)
+ else (),
+
+for $x in $copy//*:supplementary-material
+let $m := $x/*:media
+let $ms := $m/@mime-subtype
+let $mt := $m/@mimetype
+let $xl := $m/@xlink:href
+return (insert node attribute mime-subtype {$ms} into $x,
+ insert node attribute mimetype {$mt} into $x,
+ insert node attribute xlink:href {$xl} into $x,
+ delete node $m),
+
+ for $f in $copy//*:related-article
+ return delete node $f,
+
+ for $f in $copy//*:related-object
+ return delete node $f,
+
+ for $x in $copy//*:p//*:disp-formula
+ return
+ if ($x/ancestor::caption) then delete node $x
+ else if ($x/ancestor::list/ancestor::*:p) then
+ (insert node $x after $x/ancestor::*:list/ancestor::*:p,
+ delete node $x)
+ else if ($x/ancestor::list) then
+ (insert node $x after $x/ancestor::*:list[1],
+ delete node $x)
+ else (insert node $x after $x/ancestor::*:p[1],
+ delete node $x),
+
+ for $o in $copy//*:abstract[@abstract-type="executive-summary"]
+ return delete node $o,
+
+ for $x in $copy//*:element-citation//*:xref
+ return delete node $x,
+
+ for $x in $copy//*:fig/*:attrib
+ return delete node $x,
+
+ for $x in $copy//*:body
+ return
+ if ($x/following-sibling::*:back) then ()
+ else insert node after $x,
+
+ for $i in $copy//*:table-wrap[count(descendant::*:table)>1]
+ return (delete node $i,
+ for $t in $i//*:table
+ let $count := count($i/descendant::*:table)
+ let $pos := $count - count($t/following-sibling::*:table)
+ return
+ if ($pos = 1) then insert node {$i/*:label}{$t} after $i
+ else insert node {$t} after $i),
+
+ for $x in $copy//*:fig/*:graphic
+ let $count := count($x/ancestor::*:article//*:fig)
+ let $pos := $count - count($x/following::*:fig)
+ return
+ if (($pos mod 4) = 0) then replace node $x with
+ else if (($pos mod 3) = 0) then replace node $x with
+ else if (($pos mod 2) = 0) then replace node $x with
+ else replace node $x with
+
+)
+return
+copy $copy2 := $copy
+modify(
+for $x in $copy2//*:addr-line[*:named-content]
+return replace node $x with {$x/(*:named-content/*|*:named-content/text())},
+
+for $x in $copy2//*:back/*:sec
+ return if ($x/@sec-type="additional-information" and $x/preceding::*:body) then (insert node $x as last into $x/preceding::*:body, delete node $x)
+ else if ($x/@sec-type="supplementary-material" and $x/preceding::*:body) then (insert node $x as last into $x/preceding::*:body, delete node $x)
+ else delete node $x,
+
+ for $x in $copy2//*:underline/*:named-content[@content-type="sequence"]
+ return replace node $x with $x/(text()|*),
+
+ for $x in $copy2//*:fn-group[@content-type="author-contribution"]
+ return delete node $x,
+
+ for $x in $copy2//*:table-wrap-foot/*:fn
+ return replace node $x with {$x},
+
+ for $x in $copy2//*:styled-content
+ return delete node $x,
+
+ for $x in $copy2//*:p//*:list
+ return (delete node $x, insert node $x after $x/ancestor::*:p[position() = last()]),
+
+ for $x in $copy2//*:code
+ let $c := $x/data()
+ return
+ if (count($x/parent::*:p/child::*) = 1) then replace node $x/parent::*:p with {$c}
+ else replace node $x with {$c},
+
+ for $x in $copy2//*:article-meta/*:contrib-group[@content-type="section"]/following-sibling::*:contrib-group
+ return delete node $x,
+
+ for $x in $copy2//*:app//*:sec[@sec-type="appendix"]
+ return delete node $x/@sec-type,
+
+ for $x in $copy2//*:article-meta/*:contrib-group/*:contrib[not(child::*:name)]
+ return if ($x//*:contrib-group) then delete node $x
+ else insert node Placeholder as first into $x,
+
+ for $x in $copy2//(*:td|*:th)/*:p
+ return replace node $x with $x/(*|text())
+ )
+return
+copy $copy3 := $copy2
+modify(
+
+ for $x in $copy3//*:contrib-group[@content-type="section"]/*//*:aff
+ let $id := replace(generate-id($x),'id','aff')
+ return (replace node $x with , insert node {$x/*} after $x/ancestor::*:contrib-group),
+
+ for $x in $copy3//*:contrib-group[not(@content-type="section")]/*:aff
+ return (insert node $x after $x/parent::*:contrib-group, delete node $x),
+
+ for $x in $copy3//*:contrib-group[@content-type="section"]/*:aff
+ let $id := replace(generate-id($x),'id','aff')
+ return (
+ delete node $x,
+ for $y in $x/preceding-sibling::*:contrib return insert node as last into $y,
+ insert node {$x/*} after $x/ancestor::*:contrib-group
+ ),
+
+ for $x in $copy3//*:self-uri
+ return delete node $x,
+
+ for $x in $copy3//*:custom-meta-group
+ return delete node $x,
+
+ for $x in $copy3//*:ref//*:ext-link
+ return replace node $x with {$x/text()},
+
+ for $x in $copy3//*:xref[@ref-type="video"]
+ return delete node $x,
+
+ for $x in $copy3//*:sec[@sec-type="data-availability"]
+ return delete node $x,
+
+ for $x in $copy3//*:sec[@sec-type="datasets"]
+ return delete node $x,
+
+ for $x in $copy3//*:app
+ return (delete node $x, insert node {$x/*[not(local-name() = 'object-id')]} as last into $x/preceding::*:body),
+
+ for $x in $copy3//*:p//*:list
+ return (delete node $x, insert node $x after $x/ancestor::*:p[position() = last()])
+
+)
+return
+copy $copy4 := $copy3
+modify(
+
+ for $x in $copy4//*:article-meta/*:contrib-group[@content-type="section"]
+ return
+ (delete node $x,
+ insert node $x after $x/parent::*:article-meta/*:contrib-group[not(@*)][1]),
+
+ for $x in $copy4//*:p//*:fig
+ return (delete node $x, insert node $x after $x/ancestor::*:p[position() = last()]),
+
+ for $x in $copy4//*:p//*:fig-group
+ return (delete node $x, insert node $x after $x/ancestor::*:p[position() = last()]),
+
+ for $x in $copy4//*:p//*:table-wrap
+ return (delete node $x, insert node $x after $x/ancestor::*:p[position() = last()]),
+
+ for $x in $copy4//*:p/*:related-object
+ return delete node $x,
+
+ for $x in $copy4//*:app-group
+ return delete node $x,
+
+ for $x in $copy4//*:element-citation[@publication-type="web"]
+ return replace value of node $x/@publication-type with 'webpage',
+
+ for $x in $copy4//*:element-citation[@publication-type="preprint"]
+ return replace value of node $x/@publication-type with 'journal',
+
+ for $x in $copy4//*:element-citation[@publication-type="other"]
+ return replace value of node $x/@publication-type with 'software',
+
+ for $x in $copy4//*:element-citation[@publication-type="journal" or @publication-type="book"]
+ return if (count($x/*:volume) > 1) then (for $y in $x/*:volume return delete node $y,
+ insert node $x/*:volume[1] after $x/*:source)
+ else ()
+)
+return
+copy $copy5 := $copy4
+modify(
+
+ for $x in $copy5//*:ext-link
+ let $p := $x/parent::*
+ let $p-name := $p/local-name()
+ let $form := ('bold','fixed-case','italic','monospace','overline','overline-start','overline-end','roman','sans-serif','sc','strike','underline','underline-start','underline-end','ruby','sub','sup')
+ let $new-x := {$x/(*|text())}
+ return
+ if ($p-name = $form) then (delete node $p, insert node $new-x after $p)
+ else if ($x/@ext-link-type) then
+ if ($x/@ext-link-type='uri') then ()
+ else replace value of node $x/@ext-link-type with 'uri'
+ else insert node attribute ext-link {'uri'} into $x,
+
+ for $x in $copy5//(*:table[not(@id)]|*:td[not(@id)]|*:tr[not(@id)]|*:th[not(@id)])
+ let $id := generate-id($x)
+ return insert node attribute id {$id} into $x,
+
+ for $x in $copy5//*[*:inline-formula]
+ let $n := $x/local-name()
+ return
+ if ($n = ('sup','sub','italic','bold','underline')) then replace node $x with $x/(*|text())
+ else (),
+
+ for $x in $copy5//*:aff/*:institution
+ return if ($x/@content-type) then replace value of node $x/@content-type with 'orgdiv1'
+ else insert node attribute content-type {'orgname'} into $x,
+
+ for $x in $copy5//*:p//*:list
+ return (delete node $x, insert node $x after $x/ancestor::*:p[position() = last()])
+
+)
+return
+copy $copy6 := $copy5
+modify(
+
+ for $m in $copy6//mml:math
+ return replace node $m with e=mc^2,
+
+ for $x in $copy6//*:ext-link[child::*]
+ return replace node $x with {$x/data()},
+
+ for $x in $copy6//*:xref
+ let $form := ('bold','fixed-case','italic','monospace','overline','overline-start','overline-end','roman','sans-serif','sc','strike','underline','underline-start','underline-end','ruby','sub','sup')
+ return if ($x/ancestor::*[local-name() = $form]) then
+ (insert node $x after $x/ancestor::*[local-name() = $form][position() = last()],
+ delete node $x)
+ else if ($x/*[local-name() = $form]) then
+ replace node $x with {$x/data()}
+ else (),
+
+ for $x in $copy6//*:collab/*
+ let $bad-children := ('bold','fixed-case','italic','monospace','overline','overline-start','overline-end','roman','sans-serif','sc','strike','underline','underline-start','underline-end','ruby','sub','sup')
+ return if ($x/local-name() = $bad-children) then
+ replace node $x with $x/(*|text())
+ else ()
+
+)
+return
+copy $copy7 := $copy6
+modify(
+
+ for $x in $copy7//*:p//*:table-wrap
+ return (insert node $x after $x/ancestor::*:p,
+ delete node $x/ancestor::*:p),
+
+ for $x in $copy7//*:fig/*:graphic[preceding-sibling::*:graphic]
+ return delete node $x
+
+)
+return
+copy $copy8 := $copy7
+modify(
+
+ for $x in $copy8//*:table-wrap-foot[count(fn-group)>1]
+ return (for $c in $x/descendant::*:fn-group
+ let $count := count($c/ancestor::*:table-wrap-foot//*:fn-group)
+ let $pos := $count - count($c/following-sibling::*:fn-group)
+ return if ($pos > 1) then (for $y in $c/*:fn return insert node $y as last into $y/ancestor::table-wrap-foot/descendant::*:fn-group[1], delete node $c)
+ else ()),
+
+ for $x in $copy8//*:inline-formula
+ let $form := ('bold','fixed-case','italic','monospace','overline','overline-start','overline-end','roman','sans-serif','sc','strike','underline','underline-start','underline-end','ruby','sub','sup')
+ return
+ if ($x//ancestor::*[local-name() = $form]) then
+ (insert node $x before $x//ancestor::*[local-name() = $form][position() = last()],
+ delete node $x)
+ else (),
+
+ for $y in $copy8//*:conf-name/*:italic
+ return replace node $y with $y/data(),
+
+ for $y in $copy8//*:element-citation/*:year[preceding-sibling::*:year]
+ return delete node $y,
+
+ for $y in $copy8//*:element-citation/*:fpage[preceding-sibling::*:fpage]
+ return delete node $y,
+
+ for $y in $copy8//*:element-citation/*:lpage[preceding-sibling::*:lpage]
+ return delete node $y,
+
+ for $y in $copy8//*:element-citation/*:elocation-id[preceding-sibling::*:elocation-id]
+ return delete node $y,
+
+ for $y in $copy8//*:element-citation/*:article-title[preceding-sibling::*:article-title]
+ return delete node $y,
+
+ for $y in $copy8//*:element-citation/*:source[preceding-sibling::*:source]
+ return delete node $y,
+
+ for $y in $copy8//*:element-citation/*:conf-date
+ return delete node $y,
+
+ for $y in $copy8//*:volume//(*:sup|*:bold|*:italic)
+ return replace node $y with $x/text(),
+
+ for $x in $copy8//*:uri/*:uri
+ return
+ if ($x/ancestor::*:ref) then
+ if ($x/parent::*:uri/@xlink:href) then replace node $x with $x/text()
+ else if ($x/@xlink:href) then replace node $x/parent::*:uri with $x
+ else delete node $x/parent::*:uri
+ else if ($x/parent::*:uri/@xlink:href) then replace node $x/parent::*:uri with {$x/text()}
+ else if ($x/@xlink:href) then replace node $x/parent::*:uri with {$x/text()}
+ else delete node $x/parent::*:uri,
+
+ for $x in $copy8//*:uri[ancestor::*:body]
+ return replace node $x with {$x/text()},
+
+ for $y in $copy8//*:aff/*:label[preceding-sibling::*:label]
+ return delete node $y,
+
+ for $x in $copy8//*:contrib/*:email[preceding-sibling::*:email]
+ return delete node $x,
+
+ for $x in $copy8//*:fig/*:p
+ return
+ if ($x/parent::*:fig/*:caption) then
+ (delete node $x,
+ insert node $x as last into $x/parent::*:fig/*:caption[1])
+ else if ($x/parent::*:fig/*:label) then
+ (delete node $x,
+ insert node
{$x}
after $x/parent::*:fig/*:label[1])
+ else delete node $x,
+
+ for $x in $copy8//*:media[@mimetype="video"]
+ return delete node $x,
+
+ for $x in $copy8//*:break
+ return delete node $x,
+
+ for $x in $copy8//*:named-content
+ return
+ if (starts-with($x/@content-type,'author-callout-style')) then delete node $x
+ else ()
+
+)
+
+return
+copy $copy9 := $copy8
+modify(
+
+
+ for $x in $copy9//*:boxed-text
+ return replace node $x with $x/*[local-name() = ('sec','p')],
+
+ for $x in $copy9//*:contrib-group/*:on-behalf-of
+ return delete node $x
+
+)
+return $copy9
+return file:write($outputDir,$y)
\ No newline at end of file
diff --git a/pmc-award-ids.xq b/pmc-award-ids.xq
new file mode 100644
index 0000000..b116581
--- /dev/null
+++ b/pmc-award-ids.xq
@@ -0,0 +1,32 @@
+declare function local:get-doi($a){
+ if ($a/ancestor::*:article/descendant::*:article-id[@pub-id-type="doi"][1])
+ then (
+ let $doi := $a/ancestor::*:article/descendant::*:article-id[@pub-id-type="doi"][1]
+ let $url := concat('http://doi.org/',$doi)
+ return copy $copy := $a
+ modify(
+ for $x in $copy/descendant-or-self::*:award-group
+ return insert node attribute {'url'}{$url} as last into $x
+ )
+ return $copy)
+
+ else $a
+};
+
+
+
+
+{
+for $x in collection('pmc1')//*:article//*:funding-group//*:award-group[*:award-id]
+let $id := $x/*:award-id[1]
+let $y := replace($id,'[\p{P}\p{N}]|[Gg]rant','')
+let $new-x := local:get-doi($x)
+return
+if (matches($id,'[Nn]o\. ')) then ()
+else if (matches($id,'\p{Ll}')) then (
+ if (string-length($y) < 10) then ()
+ else $new-x)
+else ()
+}
+
+
diff --git a/pmc-no-authors.xq b/pmc-no-authors.xq
new file mode 100644
index 0000000..be0f7b7
--- /dev/null
+++ b/pmc-no-authors.xq
@@ -0,0 +1,15 @@
+let $list := {
+
+ for $x in (
+ collection('pmc1')//*:article-meta[not(descendant::*:contrib[@contrib-type="author"])],
+ collection('pmc2')//*:article-meta[not(descendant::*:contrib[@contrib-type="author"])],
+ collection('pmc3')//*:article-meta[not(descendant::*:contrib[@contrib-type="author"])]
+ )
+ let $url := ('https://www.ncbi.nlm.nih.gov/pmc/articles/PMC'||$x/article-id[@pub-id-type="pmc"]||'/')
+ return {$url}
+
+}
+
+for $x in distinct-values($list//*:item/@publisher)
+let $count := count($list//*:item[@publisher = $x])
+return ($x||' --- '||$count)
\ No newline at end of file
diff --git a/pmc-style-check.xq b/pmc-style-check.xq
new file mode 100644
index 0000000..18acc1f
--- /dev/null
+++ b/pmc-style-check.xq
@@ -0,0 +1,8 @@
+declare variable $xsl := doc('/Users/fredatherden/Documents/pmc-style-check/nlm-style-5.23/nlm-stylechecker.xsl');
+
+for $x in collection('articles')//*:article[not(descendant::subj-group[@subj-group-type="heading"])]
+let $output := xslt:transform($x,$xsl)
+let $errors := {for $y in $output//*:error
+ return $y}
+
+return $errors
\ No newline at end of file
diff --git a/pmc-weird-ids.xq b/pmc-weird-ids.xq
new file mode 100644
index 0000000..342ca11
--- /dev/null
+++ b/pmc-weird-ids.xq
@@ -0,0 +1,9 @@
+distinct-values(for $x in collection('pmc')//*:article//*:article-id
+let $t := $x/@pub-id-type
+return
+if ($t = 'pmc') then ()
+else if ($t = 'pmid') then ()
+else if ($t = 'publisher-id') then ()
+else if ($t = 'doi') then ()
+else $t
+)
\ No newline at end of file
diff --git a/ras-w-fig-sups.xq b/ras-w-fig-sups.xq
new file mode 100644
index 0000000..fefd0ef
--- /dev/null
+++ b/ras-w-fig-sups.xq
@@ -0,0 +1,2 @@
+distinct-values(for $x in collection('articles')//*:article[(descendant::*:subject[text() = 'Research Article']) and (descendant::*:body) and (descendant::*:fig[matches(*:label,'[Ss]upplement')])]
+return $x//*:article-id[@pub-id-type="publisher-id"]/text())
\ No newline at end of file
diff --git a/re-order-ref-list.xq b/re-order-ref-list.xq
new file mode 100644
index 0000000..dc76aef
--- /dev/null
+++ b/re-order-ref-list.xq
@@ -0,0 +1,459 @@
+declare namespace xlink = 'http://www.w3.org/1999/xlink';
+
+let $ref-list :=
+ References
+
+
+
+
+ Srinivasan
+ S
+
+
+ Kaplan
+ C Nadir
+
+
+ Mahadevan
+ L
+
+
+ 2019
+ A multiphase theory for spreadingmicrobial swarms and films
+ eLife
+ 8
+ e42697
+ 10.7554/eLife.42697
+ 31038122
+ PMC12345
+
+
+
+
+
+
+ Srinivasan
+ S
+
+
+ Kaplan
+ C Nadir
+
+
+ Mahadevan
+ L
+
+
+ 2019
+ A multiphase theory for spreadingmicrobial swarms and films
+ eLife
+ 8
+ e42697
+ 10.7554/eLife.42697
+ 31038122
+ PMC12345
+
+
+
+
+
+ BerkV
+ FongJC
+ DempseyGT
+ DeveliogluON
+ ZhuangX
+ LiphardtJ
+ YildizFH
+ ChuS
+
+ 2012
+ Molecular architecture and assembly principles of Vibrio cholerae biofilms
+ Science
+ 337
+ 236
+ 239
+
+
+
+
+
+
+ Feyerabend
+ PK
+
+
+ 2010
+ Against Method
+ 4th Edition
+ London
+ Verso
+ 978-1844674428
+
+
+
+
+
+
+ Hogarth
+ KM
+
+
+ Jaroszz
+ J
+
+
+ Butler
+ P
+
+
+ 2012
+ The skull and brain
+
+
+ Butler
+ P
+
+
+ Mitchell
+ A
+
+
+ Healy
+ JC
+
+
+ Applied Radiological Anatomy
+ 1
+ 2nd Edition
+ Cambridge, United Kingdom
+ Cambridge University Press
+ 1
+ 32
+ 10.1017/CBO9780511977930.001
+ 9780511977930
+
+
+
+
+
+
+ Spangler
+ S
+
+
+ 2014
+ Automated hypothesis generation based on mining scientific literature
+ Proceedings of the 20th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining
+ 1877
+ 1886
+ 10.1145/2623330.2623667
+
+
+
+
+
+
+ Miller
+ MA
+
+
+ Pfeiffer
+ W
+
+
+ Schwartz
+ T
+
+
+ 2011
+ The CIPRES science gateway: a community resource for phylogenetic analyses
+ Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery
+ Salt Lake City, Utah
+ New York, USA
+ ACM
+ 1
+ 8
+ https://dl.acm.org/citation.cfm?doid=2016741.2016785
+
+
+
+
+
+
+ Gavrilov
+ S
+
+
+ Harvey
+ RP
+
+
+ Papaioannou
+ VE
+
+
+ 2014
+ Mus musculus T-box 2 (Tbx2), mRNA
+ NCBI Nucleotide
+ NM_009324
+ NM_009324.2
+
+
+
+
+
+
+ Mulvihill
+ DP
+
+
+ 2010
+ TORC2 dependent phosphorylation modulates calcium regulation of fission yeast myosin
+ Kent Data Repository
+ 60
+
+
+
+
+
+
+ Read
+ K
+
+
+ Sizing the Problem of Improving Discovery and Access to NIH-funded Data: A Preliminary Study (Datasets)
+ Figshare
+ 2015
+ https://doi.org/10.6084/m9.figshare.1285515
+
+
+
+
+
+
+ Kok
+ K
+
+
+ Ay
+ A
+
+
+ Li
+ L
+
+
+ Genome-wide errant targeting by Hairy
+ Dryad Digital Repository
+ 2015
+ https://doi.org/10.5061/dryad.cv323
+
+
+
+
+
+
+ Wahls
+ WP
+
+
+ October3, 2016
+ Send my tax dollars to Mississippi
+ ASBMB Today
+ 15
+ 24
+ 25
+ https://www.asbmb.org/asbmbtoday/201610/Essay/
+
+
+
+
+
+
+ Schwartz
+ J
+
+
+ September9, 1993
+ Obesity affects economic, social status
+ The Washington Post
+ A1
+ A4
+
+
+
+
+
+
+ Murray
+ D
+
+ ...
+
+ 2019
+ Gender and international diversity improves equity in peer review
+ bioRxiv
+ 400515
+ 10.1101/400515
+
+
+
+
+
+
+ LiH
+
+
+ 2013
+ Aligning sequence reads clone sequences and assembly contigs with BWA-MEM
+ arXiv
+ https://arxiv.org/abs/1303.3997
+
+
+
+
+
+ World Health Organization
+
+ 2015
+ World Malaria Report 2015
+ Geneva
+ World Health Organization
+ http://www.who.int/malaria/publications/world-malaria-report-2015/en/
+
+
+
+
+
+
+ FoleyB
+
+
+ LeitnerT
+
+
+ ApetreiC
+
+
+ HahnB
+
+
+ MizrachiI
+
+
+ MullinsJ
+
+
+ RambautA
+
+
+ WolinskyS
+
+
+ KorberB
+
+
+ 2018
+ Hiv Sequence Compendium 2018
+ US Department of Energy
+ 10.2172/1458915
+
+
+
+
+
+
+ OnodaT
+
+ ...
+
+ 2015
+ Imidazopyridine Derivative
+ World Intellectual Property Organization
+ 2015087996
+ https://patents.google.com/patent/WO2015087996A1/en
+
+
+
+
+
+
+ LinaresD
+
+
+ 2019
+ Data and Code for 'Decoupling Sensory From Decisional Choice Biases in Perceptual Decision Making'
+ 3e48e64
+ GitHub
+ https://github.com/danilinares/2018LinaresAguilarLopezmoliner
+
+
+
+
+
+ R Development Core Team
+
+ 2014
+ R: A Language and Environment for Statistical Computing
+ Vienna, Austria
+ R Foundation for Statistical Computing
+ http://www.R-project.org/
+
+
+
+
+
+
+ HarmonA
+
+
+ 2019
+ James Watson had a chance to salvage his reputation on race. He made things worse
+ The New York Times
+ https://www.nytimes.com/2019/01/01/science/watson-dna-genetics-race.html
+ January 1, 2019
+
+
+
+
+
+ HeisslerSM
+ SellersJR
+
+ 2016a
+ Various Themes of Myosin Regulation
+ Journal of Molecular Biology
+ 428
+ 1927
+ 1946
+ 10.1016/j.jmb.2016.01.022
+
+
+
+
+
+ HeisslerSM
+ SellersJR
+
+ 2016b
+ Kinetic Adaptations of Myosins for Their Diverse Cellular Functions
+ Traffic
+ 17
+ 839
+ 859
+ 10.1111/tra.12388
+
+
+
+
+return {
+ for $ref in $ref-list//*:ref
+ let $count := count($ref//*:person-group[@person-group-type=("author","inventor")]/*)
+ let $cite :=
+ if ($ref//*:collab) then ($ref//*:collab||' , '||$ref//*:year)
+ else if ($count = 1) then ($ref//person-group[@person-group-type=("author","inventor")]/*:name[1]/*:surname||' , '||$ref//*:year)
+ else if ($count =2) then ($ref//person-group[@person-group-type=("author","inventor")]/*:name[1]/*:surname||' and '||$ref//person-group[@person-group-type=("author","inventor")]/*:name[2]/*:surname||' , '||$ref//*:year)
+ else (($ref//person-group[@person-group-type=("author","inventor")]/*:name[1]/*:surname||' et al., '||$ref//*:year))
+ order by $cite
+ return $ref
+ }
\ No newline at end of file
diff --git a/ref-journal-children.xq b/ref-journal-children.xq
new file mode 100644
index 0000000..12dd089
--- /dev/null
+++ b/ref-journal-children.xq
@@ -0,0 +1,2 @@
+distinct-values(for $x in collection('articles')//*:element-citation[@publication-type="journal"]
+return $x/*/local-name())
\ No newline at end of file
diff --git a/remove-old-versions.xq b/remove-old-versions.xq
new file mode 100644
index 0000000..fd706d3
--- /dev/null
+++ b/remove-old-versions.xq
@@ -0,0 +1,8 @@
+for $x in collection('articles')//*:article
+let $article-id := $x//*:article-id[@pub-id-type="publisher-id"]/text()
+let $filename := substring-after($x/base-uri(),'/articles/')
+let $folder := concat('/articles/elife-',$article-id,'-v')
+let $v-no := number(substring-before(substring-after($x/base-uri(),$folder),'.xml'))
+let $count := count(collection('articles')//*:article[descendant::*:article-id[@pub-id-type="publisher-id"]/text() = $article-id])
+return if ($count = $v-no) then ()
+else (db:delete('articles',$filename))
\ No newline at end of file
diff --git a/replace-xrefs-with-afss.xq b/replace-xrefs-with-afss.xq
new file mode 100644
index 0000000..f39b529
--- /dev/null
+++ b/replace-xrefs-with-afss.xq
@@ -0,0 +1,26 @@
+declare namespace xlink="http://www.w3.org/1999/xlink";
+declare namespace mml="http://www.w3.org/1998/Math/MathML";
+
+declare variable $filename := 'elife-46962.xml';
+declare variable $dir := '/Users/fredatherden/Desktop/';
+declare variable $file := doc(concat('/Users/fredatherden/Desktop/elife-46962-vor-r1/',$filename));
+
+
+for $x in $file//*:article
+let $y :=
+
+copy $copy := $x
+modify(
+
+ for $x in $copy//*:contrib//*:xref[@ref-type="aff"]
+ let $aff := $x/ancestor::*:article-meta//*:aff[@id = $x/@rid]
+ return (replace node $x with {$aff/data()}),
+
+ for $x in $copy//*:aff[not(parent::*:contrib)]
+ return delete node $x
+
+)
+return $copy
+
+
+return file:write(concat($dir,$filename),$y, map {'indent':'no'})
\ No newline at end of file
diff --git a/rewrite-test-cases.xq b/rewrite-test-cases.xq
new file mode 100644
index 0000000..9f04310
--- /dev/null
+++ b/rewrite-test-cases.xq
@@ -0,0 +1,39 @@
+import module namespace schematron = "http://github.com/Schematron/schematron-basex";
+declare namespace svrl = 'xmlns="http://purl.oclc.org/dsdl/schematron';
+
+declare variable $dir := '/Users/fredatherden/Documents/GitHub/jats-support-2/tests/cases/';
+declare variable $sch := schematron:compile(doc('/Users/fredatherden/Desktop/backup/support.sch'));
+
+
+let $list :=
+{
+for $x in file:list($dir)
+return
+if ($x='.DS_Store') then ()
+else if (ends-with($x,'/')) then for $y in file:list($dir||$x) return {doc($dir||$x||$y)}
+else {doc($dir||$x)}
+}
+
+for $x in $list//*:item
+let $svrl := schematron:validate($x/descendant::*[1], $sch)
+let $new :=
+copy $copy := $x
+modify(
+ for $m in $copy//processing-instruction('expected-error')
+ return delete node $m,
+
+ for $z in $svrl//(*:failed-assert|*:successful-report)
+ let $t := normalize-space($z/*:text)
+ return insert node
+ processing-instruction{'expected-error'}{('message="'||$t||'" node="'||$z/@location||'"')}
+ before $copy/descendant::*[1],
+
+ for $n in $copy/descendant::*[1]
+ return insert node '
' before $n
+)
+return $copy
+return $new/(*|text()|processing-instruction())
+
+
+
+
diff --git a/run-test.xq b/run-test.xq
new file mode 100644
index 0000000..06dfced
--- /dev/null
+++ b/run-test.xq
@@ -0,0 +1,46 @@
+import module namespace schematron = "http://github.com/Schematron/schematron-basex";
+declare namespace svrl = 'xmlns="http://purl.oclc.org/dsdl/schematron';
+
+declare variable $dir := '/Users/fredatherden/Documents/GitHub/jats-support-2/tests/cases/';
+declare variable $sch := schematron:compile(doc('/Users/fredatherden/Desktop/backup/support.sch'));
+
+
+let $list :=
+{
+for $x in file:list($dir)
+return
+if ($x='.DS_Store') then ()
+else if (ends-with($x,'/')) then for $y in file:list($dir||$x) return {doc($dir||$x||$y)}
+else {doc($dir||$x)}
+}
+
+for $x in $list//*:item
+
+let $p-list :=
+{
+ for $y in $x//processing-instruction('expected-error')
+ let $m := substring-before(
+ substring-after($y,'message="')
+ , '" node="'
+ )
+ order by $m
+ return {$m}
+}
+
+let $svrl := schematron:validate($x/descendant::*[1], $sch)
+
+let $svrl-list :=
+{
+ for $y in $svrl//(*:failed-assert|*:successful-report)
+ let $t := normalize-space($y/*:text)
+ order by $t
+ return {$t}
+}
+
+return
+if ($p-list = $svrl-list) then ()
+else ({$svrl-list,$p-list})
+
+
+
+
diff --git a/same-award-multiple-funders.xq b/same-award-multiple-funders.xq
new file mode 100644
index 0000000..6af7f73
--- /dev/null
+++ b/same-award-multiple-funders.xq
@@ -0,0 +1,16 @@
+distinct-values(for $x in collection('articles')//*:article[(descendant::*:body) and descendant::*:article-meta/*:funding-group]
+let $article-id := $x//*:article-id[@pub-id-type="publisher-id"]/text()
+let $f := $x//*:article-meta/*:funding-group
+
+
+return
+ for $y in $f/*:award-group
+ let $i := $y//*:institution/data()
+ let $i-id := $y//*:institution-id/data()
+ let $a-id := $y/*:award-id/data()
+ return
+ if ($y/following-sibling::*:award-group[descendant::*:institution/data() != $i]//*:award-id/data() = $a-id)
+
+ then $article-id
+ else ()
+)
\ No newline at end of file
diff --git a/same-funder-multiple-awards.xq b/same-funder-multiple-awards.xq
new file mode 100644
index 0000000..671074d
--- /dev/null
+++ b/same-funder-multiple-awards.xq
@@ -0,0 +1,16 @@
+distinct-values(for $x in collection('articles')//*:article[(descendant::*:body) and descendant::*:article-meta/*:funding-group]
+let $article-id := $x//*:article-id[@pub-id-type="publisher-id"]/text()
+let $f := $x//*:article-meta/*:funding-group
+
+
+return
+ for $y in $f/*:award-group
+ let $i := $y//*:institution/data()
+ let $i-id := $y//*:institution-id/data()
+ let $a-id := $y/*:award-id/data()
+ return
+ if ($y/following-sibling::*:award-group[descendant::*:institution/data() = $i]//*:award-id/data() != $a-id)
+
+ then $article-id
+ else ()
+)
\ No newline at end of file
diff --git a/schematron2xspex.xq b/schematron2xspex.xq
new file mode 100644
index 0000000..8f68bdd
--- /dev/null
+++ b/schematron2xspex.xq
@@ -0,0 +1,25 @@
+declare namespace x="http://www.jenitennison.com/xslt/xspec";
+declare namespace sch="http://purl.oclc.org/dsdl/schematron";
+declare variable $sch := doc('../xspec/schematron.sch');
+
+declare function local:get-id($rule){
+ if ($rule/@id) then $rule/@id
+ else if ($rule/parent::sch:pattern/@id) then
+ let $p := $rule/parent::sch:pattern[@id]
+ let $pos := count($p/sch:rule) - count($rule/following-sibling::sch:rule)
+ return concat($rule/parent::sch:pattern/@id,$pos)
+ else generate-id($rule)
+};
+
+
+
+ {
+ for $x in $sch//sch:rule
+ let $id := local:get-id($x)
+ return
+
+
+
+ }
+
+
diff --git a/sec-id-non-conformity.xq b/sec-id-non-conformity.xq
new file mode 100644
index 0000000..e76d2f4
--- /dev/null
+++ b/sec-id-non-conformity.xq
@@ -0,0 +1,9 @@
+distinct-values(for $x in collection('articles')//*:article/(*:body|*:back)/*:sec[@id]
+let $c := $x/ancestor::*:article//*:article-id[@pub-id-type="publisher-id"]
+let $pos := if ($x/parent::*/local-name() = 'body') then count($x/parent::*/*:sec) - count($x/following-sibling::*:sec)
+else count($x/ancestor::*:article/*:body/*:sec) + count($x/parent::*:back/*:sec) - count($x/following-sibling::*:sec)
+return
+if ($x[@sec-type="data-availability"]) then ()
+else if (contains($x/@id,'-')) then ($c)
+else if ($x/@id = ('s'||$pos)) then ()
+else ($c))
\ No newline at end of file
diff --git a/simple-content-2.xq b/simple-content-2.xq
new file mode 100644
index 0000000..644fcd7
--- /dev/null
+++ b/simple-content-2.xq
@@ -0,0 +1,13 @@
+declare namespace xlink="http://www.w3.org/1999/xlink";
+declare namespace mml="http://www.w3.org/1998/Math/MathML";
+
+for $x in collection('articles')//*:article[descendant::*:body and not(descendant::*:media[@mimetype="video"]) and not(descendant::mml:math) and not(descendant::table-wrap) and not(descendant::fig-group)]
+let $c := count($x//*:article-meta/*:contrib-group[not(@*)]/*:contrib)
+let $a := count($x//*:article-meta/*:contrib-group[not(@*)]/*:aff)
+return
+if ($c ge 8) then ()
+else if ($a ge 3) then ()
+else if ($x//*:fig[descendant::*:supplementary-material]) then ()
+else if ($x//*:element-citation[not(@publication-type="journal")]) then ()
+else if ($x/@article-type != ('research-article')) then ()
+else concat('https://elifesciences.org/articles/',$x/base-uri())
diff --git a/simple-content.xq b/simple-content.xq
new file mode 100644
index 0000000..dcb5f4e
--- /dev/null
+++ b/simple-content.xq
@@ -0,0 +1,10 @@
+declare namespace xlink="http://www.w3.org/1999/xlink";
+declare namespace mml="http://www.w3.org/1998/Math/MathML";
+
+for $x in collection('articles')//*:article[@article-type="research-article" and descendant::*:body and not(descendant::*:media[@mimetype="video"]) and not(descendant::mml:math) and not(descendant::table-wrap)]
+let $c := count($x//*:article-meta/*:contrib-group[not(@*)]/*:contrib)
+let $a := count($x//*:article-meta/*:contrib-group[not(@*)]/*:aff)
+return
+if ($c ge 8) then ()
+else if ($a ge 3) then ()
+else concat('https://elifesciences.org/articles/',$x//*:article-id[@pub-id-type="publisher-id"]/text())
diff --git a/special-issue-2.xq b/special-issue-2.xq
new file mode 100644
index 0000000..fc604b1
--- /dev/null
+++ b/special-issue-2.xq
@@ -0,0 +1,152 @@
+let $list :=
+
+/articles/elife-00065-v1.xml
+/articles/elife-00286-v1.xml
+/articles/elife-00306-v1.xml
+/articles/elife-00515-v1.xml
+/articles/elife-00518-v1.xml
+/articles/elife-00537-v1.xml
+/articles/elife-01098-v1.xml
+/articles/elife-01730-v1.xml
+/articles/elife-01883-v1.xml
+/articles/elife-02077-v1.xml
+/articles/elife-03504-v2.xml
+/articles/elife-03706-v1.xml
+/articles/elife-03790-v1.xml
+/articles/elife-05505-v2.xml
+/articles/elife-05949-v1.xml
+/articles/elife-06003-v2.xml
+/articles/elife-06184-v1.xml
+/articles/elife-06197-v1.xml
+/articles/elife-06259-v1.xml
+/articles/elife-07836-v3.xml
+/articles/elife-08186-v1.xml
+/articles/elife-08527-v2.xml
+/articles/elife-08833-v2.xml
+/articles/elife-09221-v2.xml
+/articles/elife-09594-v2.xml
+/articles/elife-09709-v2.xml
+/articles/elife-10161-v1.xml
+/articles/elife-10181-v1.xml
+/articles/elife-10956-v2.xml
+/articles/elife-12010-v2.xml
+/articles/elife-13943-v3.xml
+/articles/elife-16351-v2.xml
+/articles/elife-16843-v1.xml
+/articles/elife-16923-v1.xml
+/articles/elife-17185-v1.xml
+/articles/elife-17214-v1.xml
+/articles/elife-17915-v1.xml
+/articles/elife-18459-v1.xml
+/articles/elife-18648-v2.xml
+/articles/elife-19130-v2.xml
+/articles/elife-19264-v2.xml
+/articles/elife-19358-v1.xml
+/articles/elife-19484-v2.xml
+/articles/elife-19493-v2.xml
+/articles/elife-20340-v3.xml
+/articles/elife-20851-v1.xml
+/articles/elife-20914-v2.xml
+/articles/elife-21491-v2.xml
+/articles/elife-21690-v2.xml
+/articles/elife-22978-v2.xml
+/articles/elife-23493-v3.xml
+/articles/elife-24059-v2.xml
+/articles/elife-24506-v1.xml
+/articles/elife-24662-v2.xml
+/articles/elife-26424-v2.xml
+/articles/elife-26464-v2.xml
+/articles/elife-26652-v4.xml
+/articles/elife-26952-v3.xml
+/articles/elife-27014-v1.xml
+/articles/elife-27345-v2.xml
+/articles/elife-27692-v1.xml
+/articles/elife-27842-v2.xml
+/articles/elife-28129-v4.xml
+/articles/elife-28329-v2.xml
+/articles/elife-28877-v1.xml
+/articles/elife-29815-v3.xml
+/articles/elife-29908-v2.xml
+/articles/elife-31126-v1.xml
+/articles/elife-31157-v2.xml
+/articles/elife-31268-v2.xml
+/articles/elife-32018-v2.xml
+/articles/elife-32127-v2.xml
+/articles/elife-32421-v2.xml
+/articles/elife-33670-v1.xml
+/articles/elife-33781-v1.xml
+/articles/elife-34081-v1.xml
+/articles/elife-34427-v1.xml
+/articles/elife-34701-v2.xml
+/articles/elife-34836-v2.xml
+/articles/elife-34970-v2.xml
+/articles/elife-34985-v2.xml
+/articles/elife-35330-v2.xml
+/articles/elife-35368-v3.xml
+/articles/elife-35551-v1.xml
+/articles/elife-35685-v1.xml
+/articles/elife-35878-v2.xml
+/articles/elife-36095-v2.xml
+/articles/elife-36157-v2.xml
+/articles/elife-37316-v1.xml
+/articles/elife-37344-v2.xml
+/articles/elife-37462-v2.xml
+/articles/elife-38635-v2.xml
+/articles/elife-39856-v2.xml
+/articles/elife-39911-v3.xml
+/articles/elife-40314-v1.xml
+/articles/elife-40675-v2.xml
+/articles/elife-41046-v2.xml
+/articles/elife-41258-v1.xml
+/articles/elife-41548-v1.xml
+/articles/elife-41792-v2.xml
+/articles/elife-42650-v2.xml
+/articles/elife-42976-v1.xml
+/articles/elife-43059-v2.xml
+/articles/elife-44219-v1.xml
+/articles/elife-44425-v1.xml
+/articles/elife-44745-v2.xml
+/articles/elife-45415-v1.xml
+/articles/elife-45974-v1.xml
+/articles/elife-46174-v2.xml
+/articles/elife-46413-v2.xml
+/articles/elife-46418-v2.xml
+/articles/elife-47047-v1.xml
+/articles/elife-47156-v3.xml
+/articles/elife-48186-v2.xml
+/articles/elife-49154-v2.xml
+/articles/elife-49158-v2.xml
+/articles/elife-50140-v1.xml
+/articles/elife-47156-v4.xml
+/articles/elife-48240-v1.xml
+/articles/elife-49132-v2.xml
+/articles/elife-49874-v1.xml
+
+
+
+let $csv :=
+{
+ for $x in collection('articles')//*:article[*:body]
+ let $subj1 := $x//*:article-meta/descendant::*:subj-group[@subj-group-type="heading"][1]/*:subject
+ let $subj2 := $x//*:article-meta/descendant::*:subj-group[@subj-group-type="heading"][2]/*:subject
+ let $base := $x/base-uri()
+ let $meta := $x/*:front/*:article-meta
+ let $title := $meta//*:article-title
+ let $kwds := $meta/*:kwd-group[@kwd-group-type="author-keywords"]
+ let $doi := ('http://doi.org/'||$meta/*:article-id[@pub-id-type="doi"])
+ let $unallowed-subjs := ('neuroscience','plant biology','evolutionary biology')
+ return
+ if ($base = $list//*:item/string()) then
+ if ((lower-case($subj1)=$unallowed-subjs) and not($subj2)) then ()
+ else (
+
+ {$doi}
+ {$title/data()}
+ {for $z in ($subj1|$subj2) return {$z/data()}}
+ {for $y in $kwds/*:kwd return {$y/data()}}
+ )
+}
+
+
+
+ return $csv
\ No newline at end of file
diff --git a/special-issue-3.xq b/special-issue-3.xq
new file mode 100644
index 0000000..0135b81
--- /dev/null
+++ b/special-issue-3.xq
@@ -0,0 +1,40 @@
+let $values := distinct-values(
+ for $x in collection('articles')//*:article[*:body]//*:article-meta//(*:article-title|*:kwd)
+ let $l := lower-case($x)
+ let $doi := $x/ancestor::*:article-meta/*:article-id[@pub-id-type="doi"]
+ return
+ if (matches($l,' aging| ageing| longevity| lifespan| geroscience|^aging|^ageing|^longevity|^lifespan|^geroscience')) then $x/base-uri()
+ else ()
+)
+
+let $list :=
+{for $y in $values
+return {$y}}
+
+
+let $csv :=
+{
+ for $x in collection('articles')//*:article[*:body]
+ let $subj1 := $x//*:article-meta/descendant::*:subj-group[@subj-group-type="heading"][1]/*:subject
+ let $subj2 := $x//*:article-meta/descendant::*:subj-group[@subj-group-type="heading"][2]/*:subject
+ let $base := $x/base-uri()
+ let $meta := $x/*:front/*:article-meta
+ let $title := $meta//*:article-title
+ let $kwds := $meta/*:kwd-group[@kwd-group-type="author-keywords"]
+ let $doi := ('http://doi.org/'||$meta/*:article-id[@pub-id-type="doi"])
+ let $unallowed-subjs := ('neuroscience','plant biology','evolutionary biology')
+ return
+ if ($base = $list//*:item/string()) then
+ if ((lower-case($subj1)=$unallowed-subjs) and not($subj2)) then ()
+ else (
+
+ {$doi}
+ {$title/data()}
+ {for $z in ($subj1|$subj2) return {$z/data()}}
+ {for $y in $kwds/*:kwd return {$y/data()}}
+ )
+}
+
+
+
+ return $csv
\ No newline at end of file
diff --git a/special-issue-4.xq b/special-issue-4.xq
new file mode 100644
index 0000000..f2781c5
--- /dev/null
+++ b/special-issue-4.xq
@@ -0,0 +1,52 @@
+let $list-1 :=
+{
+ for $x in collection('articles')//*:article
+ let $b := $x/base-uri()
+ order by $b
+ return {$b}
+}
+
+let $latest-list :=
+{
+ for $x in $list-1/*:item
+ let $id := substring-before(substring-after($x,'/articles/elife-'),'-v')
+ return
+ if (substring-before(substring-after($x/following-sibling::*:item[1],'/articles/elife-'),'-v') = $id) then ()
+ else {$x}
+}
+
+
+let $values := distinct-values(
+ for $x in collection('articles')//*:article[base-uri()=$latest-list//*:item/data()]//*:article-meta//(*:article-title|*:kwd)
+ let $l := lower-case($x)
+ return
+ if (matches($l,' aging| ageing| longevity| lifespan| geroscience|^aging|^ageing|^longevity|^lifespan|^geroscience')) then $x/base-uri()
+ else ()
+)
+
+let $list-2 :=
+{for $y in $values
+return {$y}}
+
+let $final-ids :=
+for $article in collection('articles')//*:article
+ let $base := $article/base-uri()
+ return
+ if ($base = $list-2//*:item/string()) then
+ let $subj1 := $article//*:article-meta/descendant::*:subj-group[@subj-group-type="heading"][1]/*:subject
+ let $subj2 := $article//*:article-meta/descendant::*:subj-group[@subj-group-type="heading"][2]/*:subject
+ let $id := $article/*:front/*:article-meta/*:article-id[@pub-id-type="publisher-id"]
+ let $unallowed-subjs := ('neuroscience','plant biology','evolutionary biology')
+ order by $id
+ return (
+ if ((lower-case($subj1)=$unallowed-subjs) and not($subj2)) then ()
+ else $id
+ )
+ else ()
+
+
+
+ for $id in $final-ids
+ order by $id
+ return ('- '||$id)
+
\ No newline at end of file
diff --git a/special-issue-as-csv.xq b/special-issue-as-csv.xq
new file mode 100644
index 0000000..f4c0c36
--- /dev/null
+++ b/special-issue-as-csv.xq
@@ -0,0 +1,146 @@
+let $list :=
+
+/articles/elife-00065-v1.xml
+/articles/elife-00286-v1.xml
+/articles/elife-00306-v1.xml
+/articles/elife-00515-v1.xml
+/articles/elife-00518-v1.xml
+/articles/elife-00537-v1.xml
+/articles/elife-01098-v1.xml
+/articles/elife-01730-v1.xml
+/articles/elife-01883-v1.xml
+/articles/elife-02077-v1.xml
+/articles/elife-03504-v2.xml
+/articles/elife-03706-v1.xml
+/articles/elife-03790-v1.xml
+/articles/elife-05505-v2.xml
+/articles/elife-05949-v1.xml
+/articles/elife-06003-v2.xml
+/articles/elife-06184-v1.xml
+/articles/elife-06197-v1.xml
+/articles/elife-06259-v1.xml
+/articles/elife-07836-v3.xml
+/articles/elife-08186-v1.xml
+/articles/elife-08527-v2.xml
+/articles/elife-08833-v2.xml
+/articles/elife-09221-v2.xml
+/articles/elife-09594-v2.xml
+/articles/elife-09709-v2.xml
+/articles/elife-10161-v1.xml
+/articles/elife-10181-v1.xml
+/articles/elife-10956-v2.xml
+/articles/elife-12010-v2.xml
+/articles/elife-13943-v3.xml
+/articles/elife-16351-v2.xml
+/articles/elife-16843-v1.xml
+/articles/elife-16923-v1.xml
+/articles/elife-17185-v1.xml
+/articles/elife-17214-v1.xml
+/articles/elife-17915-v1.xml
+/articles/elife-18459-v1.xml
+/articles/elife-18648-v2.xml
+/articles/elife-19130-v2.xml
+/articles/elife-19264-v2.xml
+/articles/elife-19358-v1.xml
+/articles/elife-19484-v2.xml
+/articles/elife-19493-v2.xml
+/articles/elife-20340-v3.xml
+/articles/elife-20851-v1.xml
+/articles/elife-20914-v2.xml
+/articles/elife-21491-v2.xml
+/articles/elife-21690-v2.xml
+/articles/elife-22978-v2.xml
+/articles/elife-23493-v3.xml
+/articles/elife-24059-v2.xml
+/articles/elife-24506-v1.xml
+/articles/elife-24662-v2.xml
+/articles/elife-26424-v2.xml
+/articles/elife-26464-v2.xml
+/articles/elife-26652-v4.xml
+/articles/elife-26952-v3.xml
+/articles/elife-27014-v1.xml
+/articles/elife-27345-v2.xml
+/articles/elife-27692-v1.xml
+/articles/elife-27842-v2.xml
+/articles/elife-28129-v4.xml
+/articles/elife-28329-v2.xml
+/articles/elife-28877-v1.xml
+/articles/elife-29815-v3.xml
+/articles/elife-29908-v2.xml
+/articles/elife-31126-v1.xml
+/articles/elife-31157-v2.xml
+/articles/elife-31268-v2.xml
+/articles/elife-32018-v2.xml
+/articles/elife-32127-v2.xml
+/articles/elife-32421-v2.xml
+/articles/elife-33670-v1.xml
+/articles/elife-33781-v1.xml
+/articles/elife-34081-v1.xml
+/articles/elife-34427-v1.xml
+/articles/elife-34701-v2.xml
+/articles/elife-34836-v2.xml
+/articles/elife-34970-v2.xml
+/articles/elife-34985-v2.xml
+/articles/elife-35330-v2.xml
+/articles/elife-35368-v3.xml
+/articles/elife-35551-v1.xml
+/articles/elife-35685-v1.xml
+/articles/elife-35878-v2.xml
+/articles/elife-36095-v2.xml
+/articles/elife-36157-v2.xml
+/articles/elife-37316-v1.xml
+/articles/elife-37344-v2.xml
+/articles/elife-37462-v2.xml
+/articles/elife-38635-v2.xml
+/articles/elife-39856-v2.xml
+/articles/elife-39911-v3.xml
+/articles/elife-40314-v1.xml
+/articles/elife-40675-v2.xml
+/articles/elife-41046-v2.xml
+/articles/elife-41258-v1.xml
+/articles/elife-41548-v1.xml
+/articles/elife-41792-v2.xml
+/articles/elife-42650-v2.xml
+/articles/elife-42976-v1.xml
+/articles/elife-43059-v2.xml
+/articles/elife-44219-v1.xml
+/articles/elife-44425-v1.xml
+/articles/elife-44745-v2.xml
+/articles/elife-45415-v1.xml
+/articles/elife-45974-v1.xml
+/articles/elife-46174-v2.xml
+/articles/elife-46413-v2.xml
+/articles/elife-46418-v2.xml
+/articles/elife-47047-v1.xml
+/articles/elife-47156-v3.xml
+/articles/elife-48186-v2.xml
+/articles/elife-49154-v2.xml
+/articles/elife-49158-v2.xml
+/articles/elife-50140-v1.xml
+/articles/elife-47156-v4.xml
+/articles/elife-48240-v1.xml
+/articles/elife-49132-v2.xml
+/articles/elife-49874-v1.xml
+
+
+
+let $csv :=
+{
+ for $x in collection('articles')//*:article[*:body]
+ let $base := $x/base-uri()
+ let $meta := $x/*:front/*:article-meta
+ let $title := $meta//*:article-title
+ let $kwds := $meta/*:kwd-group[@kwd-group-type="author-keywords"]
+ let $doi := ('http://doi.org/'||$meta/*:article-id[@pub-id-type="doi"])
+ return
+ if ($base = $list//*:item/string()) then
+
+ {$doi}
+ {$title/data()}
+ {for $y in $kwds/*:kwd return {$y/data()}}
+
+}
+
+
+
+ return file:write('/Users/fredatherden/Desktop/special-issue.csv',$csv, map{'method':'csv'})
\ No newline at end of file
diff --git a/special-issue-check.xq b/special-issue-check.xq
new file mode 100644
index 0000000..32847ac
--- /dev/null
+++ b/special-issue-check.xq
@@ -0,0 +1,8 @@
+distinct-values(
+ for $x in collection('articles')//*:article[*:body]//*:article-meta//(*:article-title|*:kwd)
+ let $l := lower-case($x)
+ let $doi := $x/ancestor::*:article-meta/*:article-id[@pub-id-type="doi"]
+ return
+ if (matches($l,' aging| ageing| longevity| lifespan| geroscience|^aging|^ageing|^longevity|^lifespan|^geroscience')) then ('- http://doi.org/'||$doi)
+ else ()
+)
\ No newline at end of file
diff --git a/subject-change-across-version.xq b/subject-change-across-version.xq
new file mode 100644
index 0000000..edb60b4
--- /dev/null
+++ b/subject-change-across-version.xq
@@ -0,0 +1,23 @@
+let $list := {
+for $x in collection('articles')//*:article
+let $article-id := $x//*:article-id[@pub-id-type="publisher-id"]/text()
+let $b := $x/base-uri()
+let $count := count(collection('articles')//*:article[descendant::*:article-id[@pub-id-type="publisher-id"]/text() = $article-id])
+let $subj := {
+ for $y in $x//*:article-categories//*:subj-group[@subj-group-type="heading"]
+ return
+ {$y/*:subject/data()}
+ }
+
+return if ($count = 1) then ()
+else if ($subj = '') then ()
+else {$subj}
+}
+
+return {
+ for $x in $list//*:item
+ let $id := $x/@article-id
+ return
+ if ($list//*:item[@article-id = $id]/*:subjects != $x/*:subjects) then $x
+ else ()
+}
\ No newline at end of file
diff --git a/texture-article-check.xq b/texture-article-check.xq
new file mode 100644
index 0000000..79ce026
--- /dev/null
+++ b/texture-article-check.xq
@@ -0,0 +1,190 @@
+declare namespace xlink="http://www.w3.org/1999/xlink";
+declare namespace mml="http://www.w3.org/1998/Math/MathML";
+
+declare variable $outputDir := '/Users/fredatherden/Documents/GitHub/texture/data/kitchen-sink/manuscript.xml';
+
+for $x in collection('articles')//*:article[(descendant::*:article-id[@pub-id-type="publisher-id"]= '42955') and descendant::*:body]
+let $y :=
+copy $copy := $x
+modify(
+ for $a in $copy//*:sub-article
+ return delete node $a,
+
+ for $y in $copy//*:back/*:ack
+ return (delete node $y,
+ insert node {$y/*} as last into $y/preceding::*:body),
+
+ for $z in $copy//*:article-meta/*:author-notes
+ return delete node $z,
+
+ for $s in $copy//*:sec[@sec-type="additional-information"]/*:fn-group
+ return delete node $s,
+
+ for $x in $copy//*:front//*:xref[@ref-type="fn"]
+ return delete node $x,
+
+ for $e in $copy//*:object-id[ancestor::*:abstract or ancestor::*:supplementary-material]
+ return delete node $e,
+
+ for $d in $copy//*:funding-group/*:funding-statement
+ return delete node $d,
+
+ for $t in $copy//*:kwd-group/*:title
+ return delete node $t,
+
+ for $f in $copy//*:collab[not(descendant::*)]
+ return delete node $f,
+
+ for $x in $copy//*:contrib-group[@content-type="section"]//*:aff
+let $id := if ($x/ancestor::contrib[@contrib-type="editor"]) then 'aff100'
+ else 'aff200'
+return (replace node $x with , insert node {$x/*} after $x/ancestor::*:contrib-group),
+
+for $x in $copy//*:contrib-group/*:aff
+return (insert node $x after $x/parent::*:contrib-group, delete node $x),
+
+for $x in $copy//*:supplementary-material
+let $m := $x/*:media
+let $ms := $m/@mime-subtype
+let $mt := $m/@mimetype
+let $xl := $m/@xlink:href
+return (insert node attribute mime-subtype {$ms} into $x,
+ insert node attribute mimetype {$mt} into $x,
+ insert node attribute xlink:href {$xl} into $x,
+ delete node $m),
+
+ for $f in $copy//*:related-article
+ return delete node $f,
+
+ for $x in $copy//*:p//*:disp-formula
+ return (insert node $x after $x/ancestor::*:p,
+ delete node $x),
+
+ for $o in $copy//*:abstract[@abstract-type="executive-summary"]
+ return delete node $o,
+
+ for $x in $copy//*:fig/*:attrib
+ return delete node $x,
+
+ for $x in $copy//*:body
+ return
+ if ($x/following-sibling::*:back) then ()
+ else insert node after $x,
+
+ for $i in $copy//*:table-wrap[count(descendant::*:table)>1]
+ return (delete node $i,
+ for $t in $i//*:table
+ let $count := count($i/descendant::*:table)
+ let $pos := $count - count($t/following-sibling::*:table)
+ return
+ if ($pos = 1) then insert node {$i/*:label}{$t} after $i
+ else insert node {$t} after $i),
+
+ for $x in $copy//*:fig/*:graphic
+ let $count := count($x/ancestor::*:article//*:fig)
+ let $pos := $count - count($x/following::*:fig)
+ return
+ if (($pos mod 4) = 0) then replace node $x with
+ else if (($pos mod 3) = 0) then replace node $x with
+ else if (($pos mod 2) = 0) then replace node $x with
+ else replace node $x with
+
+)
+return
+copy $copy2 := $copy
+modify(
+for $x in $copy2//*:addr-line/*:named-content
+return replace node $x with $x/(*|text()),
+
+for $x in $copy2//*:back/*:sec
+ return if ($x/@sec-type="additional-information") then (insert node $x as last into $x/preceding::*:body, delete node $x)
+ else if ($x/@sec-type="supplementary-material") then (insert node $x as last into $x/preceding::*:body, delete node $x)
+ else delete node $x,
+
+ for $m in $copy2//mml:math
+ return delete node $m,
+
+ for $x in $copy2//*:inline-formula
+ return insert node e=mc^2 as last into $x,
+
+ for $x in $copy2//*:disp-formula
+ return insert node e=mc^2 as last into $x,
+
+ for $x in $copy2//*:underline/*:named-content[@content-type="sequence"]
+ return replace node $x with $x/(text()|*),
+
+ for $x in $copy2//*:fn-group[@content-type="author-contribution"]
+ return delete node $x
+)
+return
+copy $copy3 := $copy2
+modify(
+
+for $v in $copy3//*:contrib-group[@content-type="section"]
+ return (delete node $v,insert node $v after $v/preceding-sibling::*:contrib-group),
+
+ for $x in $copy3//*:self-uri
+ return delete node $x,
+
+ for $x in $copy3//*:custom-meta-group
+ return delete node $x,
+
+ for $x in $copy3//*:aff/*:institution
+ return if ($x/@content-type) then replace value of node $x/@content-type with 'orgdiv1'
+ else insert node attribute content-type {'orgname'} into $x,
+
+ for $x in $copy3//*:ref//*:ext-link
+ return replace node $x with {$x/text()},
+
+ for $x in $copy3//*:table-wrap-foot/*:fn
+ return replace node $x with {$x},
+
+ for $x in $copy3//*:break
+ return delete node $x,
+
+ for $x in $copy3//*:media[@mimetype="video"]
+ return delete node $x,
+
+ for $x in $copy3//*:xref[@ref-type="video"]
+ return delete node $x,
+
+ for $x in $copy3//*:sec[@sec-type="data-availability"]
+ return delete node $x,
+
+ for $x in $copy3//*:app
+ return (delete node $x, insert node {$x/*[not(local-name() = 'object-id')]} as last into $x/preceding::*:body)
+
+)
+return
+copy $copy4 := $copy3
+modify(
+ for $x in $copy4//*:p/*:fig
+ return (delete node $x, insert node $x after $x/parent::*:p),
+
+ for $x in $copy4//*:p/*:fig-group
+ return (delete node $x, insert node $x after $x/parent::*:p),
+
+ for $x in $copy4//*:p/*:table-wrap
+ return (delete node $x, insert node $x after $x/parent::*:p),
+
+ for $x in $copy4//*:p/*:related-object
+ return delete node $x,
+
+ for $x in $copy4//*:app-group
+ return delete node $x,
+
+ for $x in $copy4//*:table-wrap-foot[count(fn-group)>1]
+ return (for $c in $x/descendant::*:fn-group
+ let $count := count($c/ancestor::*:table-wrap-foot//*:fn-group)
+ let $pos := $count - count($c/following-sibling::*:fn-group)
+ return if ($pos > 1) then (for $y in $c/*:fn return insert node $y as last into $y/ancestor::table-wrap-foot/descendant::*:fn-group[1], delete node $c)
+ else ()),
+
+ for $x in $copy4//*:boxed-text
+ return replace node $x with $x/*,
+
+ for $x in $copy4//*:element-citation[@publication-type="web"]
+ return replace value of node $x/@publication-type with 'webpage'
+)
+return $copy4
+return file:write($outputDir,$y)
\ No newline at end of file
diff --git a/texture-manipulation-backup.xq b/texture-manipulation-backup.xq
new file mode 100644
index 0000000..a69685c
--- /dev/null
+++ b/texture-manipulation-backup.xq
@@ -0,0 +1,196 @@
+declare namespace xlink="http://www.w3.org/1999/xlink";
+declare namespace mml="http://www.w3.org/1998/Math/MathML";
+
+declare variable $outputDir := '/Users/fredatherden/Documents/GitHub/texture/data/kitchen-sink/manuscript.xml';
+
+for $x in collection('articles')//*:article[(descendant::*:article-id[@pub-id-type="publisher-id"]= '42955') and descendant::*:body]
+let $y :=
+copy $copy := $x
+modify(
+ for $a in $copy//*:sub-article
+ return delete node $a,
+
+ for $y in $copy//*:back/*:ack
+ return (delete node $y,
+ insert node {$y/*} as last into $y/preceding::*:body),
+
+ for $z in $copy//*:article-meta/*:author-notes
+ return delete node $z,
+
+ for $s in $copy//*:sec[@sec-type="additional-information"]/*:fn-group
+ return delete node $s,
+
+ for $x in $copy//*:front//*:xref[@ref-type="fn"]
+ return delete node $x,
+
+ for $e in $copy//*:object-id[ancestor::*:abstract or ancestor::*:supplementary-material]
+ return delete node $e,
+
+ for $d in $copy//*:funding-group/*:funding-statement
+ return delete node $d,
+
+ for $t in $copy//*:kwd-group/*:title
+ return delete node $t,
+
+ for $f in $copy//*:collab[not(descendant::*)]
+ return delete node $f,
+
+ for $x in $copy//*:contrib-group[@content-type="section"]//*:aff
+let $id := if ($x/ancestor::contrib[@contrib-type="editor"]) then 'aff100'
+ else 'aff200'
+return (replace node $x with , insert node {$x/*} after $x/ancestor::*:contrib-group),
+
+for $x in $copy//*:contrib-group/*:aff
+return (insert node $x after $x/parent::*:contrib-group, delete node $x),
+
+for $x in $copy//*:supplementary-material
+let $m := $x/*:media
+let $ms := $m/@mime-subtype
+let $mt := $m/@mimetype
+let $xl := $m/@xlink:href
+return (insert node attribute mime-subtype {$ms} into $x,
+ insert node attribute mimetype {$mt} into $x,
+ insert node attribute xlink:href {$xl} into $x,
+ delete node $m),
+
+ for $f in $copy//*:related-article
+ return delete node $f,
+
+ for $x in $copy//*:p//*:disp-formula
+ return (insert node $x after $x/ancestor::*:p,
+ delete node $x),
+
+ for $o in $copy//*:abstract[@abstract-type="executive-summary"]
+ return delete node $o,
+
+ for $x in $copy//*:fig/*:attrib
+ return delete node $x,
+
+ for $x in $copy//*:body
+ return
+ if ($x/following-sibling::*:back) then ()
+ else insert node after $x,
+
+ for $i in $copy//*:table-wrap[count(descendant::*:table)>1]
+ return (delete node $i,
+ for $t in $i//*:table
+ let $count := count($i/descendant::*:table)
+ let $pos := $count - count($t/following-sibling::*:table)
+ return
+ if ($pos = 1) then insert node {$i/*:label}{$t} after $i
+ else insert node {$t} after $i),
+
+ for $x in $copy//*:fig/*:graphic
+ let $count := count($x/ancestor::*:article//*:fig)
+ let $pos := $count - count($x/following::*:fig)
+ return
+ if (($pos mod 4) = 0) then replace node $x with
+ else if (($pos mod 3) = 0) then replace node $x with
+ else if (($pos mod 2) = 0) then replace node $x with
+ else replace node $x with
+
+)
+return
+copy $copy2 := $copy
+modify(
+for $x in $copy2//*:addr-line/*:named-content
+return replace node $x with $x/(*|text()),
+
+for $x in $copy2//*:back/*:sec
+ return if ($x/@sec-type="additional-information") then (insert node $x as last into $x/preceding::*:body, delete node $x)
+ else if ($x/@sec-type="supplementary-material") then (insert node $x as last into $x/preceding::*:body, delete node $x)
+ else delete node $x,
+
+ for $m in $copy2//mml:math
+ return delete node $m,
+
+ for $x in $copy2//*:inline-formula
+ return insert node e=mc^2 as last into $x,
+
+ for $x in $copy2//*:disp-formula
+ return insert node e=mc^2 as last into $x,
+
+ for $x in $copy2//*:underline/*:named-content[@content-type="sequence"]
+ return replace node $x with $x/(text()|*),
+
+ for $x in $copy2//*:fn-group[@content-type="author-contribution"]
+ return delete node $x,
+
+ for $x in $copy2//*:table-wrap-foot/*:fn
+ return replace node $x with {$x},
+
+ for $x in $copy2//*:break
+ return delete node $x,
+
+ for $x in $copy2//*:code
+ let $c := $x/data()
+ return
+ if (count($x/parent::*:p/child::*) = 1) then replace node $x/parent::*:p with {$c}
+ else replace node $x with {$c}
+)
+return
+copy $copy3 := $copy2
+modify(
+
+for $v in $copy3//*:contrib-group[@content-type="section"]
+ return (delete node $v,insert node $v after $v/preceding-sibling::*:contrib-group),
+
+ for $x in $copy3//*:self-uri
+ return delete node $x,
+
+ for $x in $copy3//*:custom-meta-group
+ return delete node $x,
+
+ for $x in $copy3//*:aff/*:institution
+ return if ($x/@content-type) then replace value of node $x/@content-type with 'orgdiv1'
+ else insert node attribute content-type {'orgname'} into $x,
+
+ for $x in $copy3//*:ref//*:ext-link
+ return replace node $x with {$x/text()},
+
+ for $x in $copy3//*:media[@mimetype="video"]
+ return delete node $x,
+
+ for $x in $copy3//*:xref[@ref-type="video"]
+ return delete node $x,
+
+ for $x in $copy3//*:sec[@sec-type="data-availability"]
+ return delete node $x,
+
+ for $x in $copy3//*:app
+ return (delete node $x, insert node {$x/*[not(local-name() = 'object-id')]} as last into $x/preceding::*:body)
+
+)
+return
+copy $copy4 := $copy3
+modify(
+ for $x in $copy4//*:p/*:fig
+ return (delete node $x, insert node $x after $x/parent::*:p),
+
+ for $x in $copy4//*:p/*:fig-group
+ return (delete node $x, insert node $x after $x/parent::*:p),
+
+ for $x in $copy4//*:p/*:table-wrap
+ return (delete node $x, insert node $x after $x/parent::*:p),
+
+ for $x in $copy4//*:p/*:related-object
+ return delete node $x,
+
+ for $x in $copy4//*:app-group
+ return delete node $x,
+
+ for $x in $copy4//*:table-wrap-foot[count(fn-group)>1]
+ return (for $c in $x/descendant::*:fn-group
+ let $count := count($c/ancestor::*:table-wrap-foot//*:fn-group)
+ let $pos := $count - count($c/following-sibling::*:fn-group)
+ return if ($pos > 1) then (for $y in $c/*:fn return insert node $y as last into $y/ancestor::table-wrap-foot/descendant::*:fn-group[1], delete node $c)
+ else ()),
+
+ for $x in $copy4//*:boxed-text
+ return replace node $x with $x/*,
+
+ for $x in $copy4//*:element-citation[@publication-type="web"]
+ return replace value of node $x/@publication-type with 'webpage'
+)
+return $copy4
+return file:write($outputDir,$y)
\ No newline at end of file
diff --git a/uk-us-spelling-generate.xq b/uk-us-spelling-generate.xq
new file mode 100644
index 0000000..3e308e6
--- /dev/null
+++ b/uk-us-spelling-generate.xq
@@ -0,0 +1,3490 @@
+let $list1 :=
+accessorise
+accessorised
+accessorises
+accessorising
+acclimatisation
+acclimatise
+acclimatised
+acclimatises
+acclimatising
+accoutrements
+aeon
+aeons
+aerogramme
+aerogrammes
+aeroplane
+aeroplanes
+aesthete
+aesthetes
+aesthetic
+aesthetically
+aesthetics
+aetiology
+ageing
+aggrandisement
+agonise
+agonised
+agonises
+agonising
+agonisingly
+almanack
+almanacks
+aluminium
+amortisable
+amortisation
+amortisations
+amortise
+amortised
+amortises
+amortising
+amphitheatre
+amphitheatres
+anaemia
+anaemic
+anaesthesia
+anaesthetic
+anaesthetics
+anaesthetise
+anaesthetised
+anaesthetises
+anaesthetising
+anaesthetist
+anaesthetists
+anaesthetize
+anaesthetized
+anaesthetizes
+anaesthetizing
+analogue
+analogues
+analyse
+analysed
+analyses
+analysing
+anglicise
+anglicised
+anglicises
+anglicising
+annualised
+antagonise
+antagonised
+antagonises
+antagonising
+apologise
+apologised
+apologises
+apologising
+appal
+appals
+appetiser
+appetisers
+appetising
+appetisingly
+arbour
+arbours
+archaeological
+archaeologically
+archaeologist
+archaeologists
+archaeology
+ardour
+armour
+armoured
+armourer
+armourers
+armouries
+armoury
+artefact
+artefacts
+authorise
+authorised
+authorises
+authorising
+axe
+backpedalled
+backpedalling
+bannister
+bannisters
+baptise
+baptised
+baptises
+baptising
+bastardise
+bastardised
+bastardises
+bastardising
+battleaxe
+baulk
+baulked
+baulking
+baulks
+bedevilled
+bedevilling
+behaviour
+behavioural
+behaviourism
+behaviourist
+behaviourists
+behaviours
+behove
+behoved
+behoves
+bejewelled
+belabour
+belaboured
+belabouring
+belabours
+bevelled
+bevvies
+bevvy
+biassed
+biassing
+bingeing
+bougainvillaea
+bougainvillaeas
+bowdlerise
+bowdlerised
+bowdlerises
+bowdlerising
+breathalyse
+breathalysed
+breathalyser
+breathalysers
+breathalyses
+breathalysing
+brutalise
+brutalised
+brutalises
+brutalising
+buses
+busing
+caesarean
+caesareans
+calibre
+calibres
+calliper
+callipers
+callisthenics
+canalise
+canalised
+canalises
+canalising
+cancellation
+cancellations
+cancelled
+cancelling
+candour
+cannibalise
+cannibalised
+cannibalises
+cannibalising
+canonise
+canonised
+canonises
+canonising
+capitalise
+capitalised
+capitalises
+capitalising
+caramelise
+caramelised
+caramelises
+caramelising
+carbonise
+carbonised
+carbonises
+carbonising
+carolled
+carolling
+catalogue
+catalogued
+catalogues
+cataloguing
+catalyse
+catalysed
+catalyses
+catalysing
+categorise
+categorised
+categorises
+categorising
+cauterise
+cauterised
+cauterises
+cauterising
+cavilled
+cavilling
+centigramme
+centigrammes
+centilitre
+centilitres
+centimetre
+centimetres
+centralise
+centralised
+centralises
+centralising
+centre
+centred
+centrefold
+centrefolds
+centrepiece
+centrepieces
+centres
+channelled
+channelling
+characterise
+characterised
+characterises
+characterising
+cheque
+chequebook
+chequebooks
+chequered
+cheques
+chilli
+chimaera
+chimaeras
+chiselled
+chiselling
+circularise
+circularised
+circularises
+circularising
+civilise
+civilised
+civilises
+civilising
+clamour
+clamoured
+clamouring
+clamours
+clangour
+clarinettist
+clarinettists
+collectivise
+collectivised
+collectivises
+collectivising
+colonisation
+colonise
+colonised
+coloniser
+colonisers
+colonises
+colonising
+colour
+colourant
+colourants
+coloured
+coloureds
+colourful
+colourfully
+colouring
+colourize
+colourized
+colourizes
+colourizing
+colourless
+colours
+commercialise
+commercialised
+commercialises
+commercialising
+compartmentalise
+compartmentalised
+compartmentalises
+compartmentalising
+computerise
+computerised
+computerises
+computerising
+conceptualise
+conceptualised
+conceptualises
+conceptualising
+connexion
+connexions
+contextualise
+contextualised
+contextualises
+contextualising
+cosier
+cosies
+cosiest
+cosily
+cosiness
+cosy
+councillor
+councillors
+counselled
+counselling
+counsellor
+counsellors
+crenellated
+criminalise
+criminalised
+criminalises
+criminalising
+criticise
+criticised
+criticises
+criticising
+crueller
+cruellest
+crystallisation
+crystallise
+crystallised
+crystallises
+crystallising
+cudgelled
+cudgelling
+customise
+customised
+customises
+customising
+cypher
+cyphers
+decentralisation
+decentralise
+decentralised
+decentralises
+decentralising
+decriminalisation
+decriminalise
+decriminalised
+decriminalises
+decriminalising
+defence
+defenceless
+defences
+dehumanisation
+dehumanise
+dehumanised
+dehumanises
+dehumanising
+demeanour
+demilitarisation
+demilitarise
+demilitarised
+demilitarises
+demilitarising
+demobilisation
+demobilise
+demobilised
+demobilises
+demobilising
+democratisation
+democratise
+democratised
+democratises
+democratising
+demonise
+demonised
+demonises
+demonising
+demoralisation
+demoralise
+demoralised
+demoralises
+demoralising
+denationalisation
+denationalise
+denationalised
+denationalises
+denationalising
+deodorise
+deodorised
+deodorises
+deodorising
+depersonalise
+depersonalised
+depersonalises
+depersonalising
+deputise
+deputised
+deputises
+deputising
+desensitisation
+desensitise
+desensitised
+desensitises
+desensitising
+destabilisation
+destabilise
+destabilised
+destabilises
+destabilising
+dialled
+dialling
+dialogue
+dialogues
+diarrhoea
+digitise
+digitised
+digitises
+digitising
+disc
+discolour
+discoloured
+discolouring
+discolours
+discs
+disembowelled
+disembowelling
+disfavour
+dishevelled
+dishonour
+dishonourable
+dishonourably
+dishonoured
+dishonouring
+dishonours
+disorganisation
+disorganised
+distil
+distils
+dramatisation
+dramatisations
+dramatise
+dramatised
+dramatises
+dramatising
+draught
+draughtboard
+draughtboards
+draughtier
+draughtiest
+draughts
+draughtsman
+draughtsmanship
+draughtsmen
+draughtswoman
+draughtswomen
+draughty
+drivelled
+drivelling
+duelled
+duelling
+economise
+economised
+economises
+economising
+edoema
+editorialise
+editorialised
+editorialises
+editorialising
+empathise
+empathised
+empathises
+empathising
+emphasise
+emphasised
+emphasises
+emphasising
+enamelled
+enamelling
+enamoured
+encyclopaedia
+encyclopaedias
+encyclopaedic
+endeavour
+endeavoured
+endeavouring
+endeavours
+energise
+energised
+energises
+energising
+enrol
+enrols
+enthral
+enthrals
+epaulette
+epaulettes
+epicentre
+epicentres
+epilogue
+epilogues
+epitomise
+epitomised
+epitomises
+epitomising
+equalisation
+equalise
+equalised
+equaliser
+equalisers
+equalises
+equalising
+eulogise
+eulogised
+eulogises
+eulogising
+evangelise
+evangelised
+evangelises
+evangelising
+exorcise
+exorcised
+exorcises
+exorcising
+extemporisation
+extemporise
+extemporised
+extemporises
+extemporising
+externalisation
+externalisations
+externalise
+externalised
+externalises
+externalising
+factorise
+factorised
+factorises
+factorising
+faecal
+faeces
+familiarisation
+familiarise
+familiarised
+familiarises
+familiarising
+fantasise
+fantasised
+fantasises
+fantasising
+favour
+favourable
+favourably
+favoured
+favouring
+favourite
+favourites
+favouritism
+favours
+feminise
+feminised
+feminises
+feminising
+fertilisation
+fertilise
+fertilised
+fertiliser
+fertilisers
+fertilises
+fertilising
+fervour
+fibre
+fibreglass
+fibres
+fictionalisation
+fictionalisations
+fictionalise
+fictionalised
+fictionalises
+fictionalising
+fillet
+filleted
+filleting
+fillets
+finalisation
+finalise
+finalised
+finalises
+finalising
+flautist
+flautists
+flavour
+flavoured
+flavouring
+flavourings
+flavourless
+flavours
+flavoursome
+flyer / flier
+foetal
+foetid
+foetus
+foetuses
+formalisation
+formalise
+formalised
+formalises
+formalising
+fossilisation
+fossilise
+fossilised
+fossilises
+fossilising
+fraternisation
+fraternise
+fraternised
+fraternises
+fraternising
+fulfil
+fulfilment
+fulfils
+funnelled
+funnelling
+galvanise
+galvanised
+galvanises
+galvanising
+gambolled
+gambolling
+gaol
+gaolbird
+gaolbirds
+gaolbreak
+gaolbreaks
+gaoled
+gaoler
+gaolers
+gaoling
+gaols
+gases
+gauge
+gauged
+gauges
+gauging
+generalisation
+generalisations
+generalise
+generalised
+generalises
+generalising
+ghettoise
+ghettoised
+ghettoises
+ghettoising
+gipsies
+glamorise
+glamorised
+glamorises
+glamorising
+glamour
+globalisation
+globalise
+globalised
+globalises
+globalising
+glueing
+goitre
+goitres
+gonorrhoea
+gramme
+grammes
+gravelled
+grey
+greyed
+greying
+greyish
+greyness
+greys
+grovelled
+grovelling
+groyne
+groynes
+gruelling
+gruellingly
+gryphon
+gryphons
+gynaecological
+gynaecologist
+gynaecologists
+gynaecology
+haematological
+haematologist
+haematologists
+haematology
+haemoglobin
+haemophilia
+haemophiliac
+haemophiliacs
+haemorrhage
+haemorrhaged
+haemorrhages
+haemorrhaging
+haemorrhoids
+harbour
+harboured
+harbouring
+harbours
+harmonisation
+harmonise
+harmonised
+harmonises
+harmonising
+homoeopath
+homoeopathic
+homoeopaths
+homoeopathy
+homogenise
+homogenised
+homogenises
+homogenising
+honour
+honourable
+honourably
+honoured
+honouring
+honours
+hospitalisation
+hospitalise
+hospitalised
+hospitalises
+hospitalising
+humanise
+humanised
+humanises
+humanising
+humour
+humoured
+humouring
+humourless
+humours
+hybridise
+hybridised
+hybridises
+hybridising
+hypnotise
+hypnotised
+hypnotises
+hypnotising
+hypothesise
+hypothesised
+hypothesises
+hypothesising
+idealisation
+idealise
+idealised
+idealises
+idealising
+idolise
+idolised
+idolises
+idolising
+immobilisation
+immobilise
+immobilised
+immobiliser
+immobilisers
+immobilises
+immobilising
+immortalise
+immortalised
+immortalises
+immortalising
+immunisation
+immunise
+immunised
+immunises
+immunising
+impanelled
+impanelling
+imperilled
+imperilling
+individualise
+individualised
+individualises
+individualising
+industrialise
+industrialised
+industrialises
+industrialising
+inflexion
+inflexions
+initialise
+initialised
+initialises
+initialising
+initialled
+initialling
+instal
+instalment
+instalments
+instals
+instil
+instils
+institutionalisation
+institutionalise
+institutionalised
+institutionalises
+institutionalising
+intellectualise
+intellectualised
+intellectualises
+intellectualising
+internalisation
+internalise
+internalised
+internalises
+internalising
+internationalisation
+internationalise
+internationalised
+internationalises
+internationalising
+ionisation
+ionise
+ionised
+ioniser
+ionisers
+ionises
+ionising
+italicise
+italicised
+italicises
+italicising
+itemise
+itemised
+itemises
+itemising
+jeopardise
+jeopardised
+jeopardises
+jeopardising
+jewelled
+jeweller
+jewellers
+jewellery
+judgement
+kilogramme
+kilogrammes
+kilometre
+kilometres
+labelled
+labelling
+labour
+laboured
+labourer
+labourers
+labouring
+labours
+lacklustre
+legalisation
+legalise
+legalised
+legalises
+legalising
+legitimise
+legitimised
+legitimises
+legitimising
+leukaemia
+levelled
+leveller
+levellers
+levelling
+libelled
+libelling
+libellous
+liberalisation
+liberalise
+liberalised
+liberalises
+liberalising
+licence
+licenced
+licences
+licencing
+likeable
+lionisation
+lionise
+lionised
+lionises
+lionising
+liquidise
+liquidised
+liquidiser
+liquidisers
+liquidises
+liquidising
+litre
+litres
+localise
+localised
+localises
+localising
+louvre
+louvred
+louvres
+lustre
+magnetise
+magnetised
+magnetises
+magnetising
+manoeuvrability
+manoeuvrable
+manoeuvre
+manoeuvred
+manoeuvres
+manoeuvring
+manoeuvrings
+marginalisation
+marginalise
+marginalised
+marginalises
+marginalising
+marshalled
+marshalling
+marvelled
+marvelling
+marvellous
+marvellously
+materialisation
+materialise
+materialised
+materialises
+materialising
+maximisation
+maximise
+maximised
+maximises
+maximising
+meagre
+mechanisation
+mechanise
+mechanised
+mechanises
+mechanising
+mediaeval
+memorialise
+memorialised
+memorialises
+memorialising
+memorise
+memorised
+memorises
+memorising
+mesmerise
+mesmerised
+mesmerises
+mesmerising
+metabolise
+metabolised
+metabolises
+metabolising
+metre
+metres
+micrometre
+micrometres
+militarise
+militarised
+militarises
+militarising
+milligramme
+milligrammes
+millilitre
+millilitres
+millimetre
+millimetres
+miniaturisation
+miniaturise
+miniaturised
+miniaturises
+miniaturising
+minibuses
+minimise
+minimised
+minimises
+minimising
+misbehaviour
+misdemeanour
+misdemeanours
+misspelt
+mitre
+mitres
+mobilisation
+mobilise
+mobilised
+mobilises
+mobilising
+modelled
+modeller
+modellers
+modelling
+modernise
+modernised
+modernises
+modernising
+moisturise
+moisturised
+moisturiser
+moisturisers
+moisturises
+moisturising
+monologue
+monologues
+monopolisation
+monopolise
+monopolised
+monopolises
+monopolising
+moralise
+moralised
+moralises
+moralising
+motorised
+mould
+moulded
+moulder
+mouldered
+mouldering
+moulders
+mouldier
+mouldiest
+moulding
+mouldings
+moulds
+mouldy
+moult
+moulted
+moulting
+moults
+moustache
+moustached
+moustaches
+moustachioed
+multicoloured
+nationalisation
+nationalisations
+nationalise
+nationalised
+nationalises
+nationalising
+naturalisation
+naturalise
+naturalised
+naturalises
+naturalising
+neighbour
+neighbourhood
+neighbourhoods
+neighbouring
+neighbourliness
+neighbourly
+neighbours
+neutralisation
+neutralise
+neutralised
+neutralises
+neutralising
+normalisation
+normalise
+normalised
+normalises
+normalising
+odour
+odourless
+odours
+oesophagus
+oesophaguses
+oestrogen
+offence
+offences
+omelette
+omelettes
+optimise
+optimised
+optimises
+optimising
+organisation
+organisational
+organisations
+organise
+organised
+organiser
+organisers
+organises
+organising
+orthopaedic
+orthopaedics
+ostracise
+ostracised
+ostracises
+ostracising
+outmanoeuvre
+outmanoeuvred
+outmanoeuvres
+outmanoeuvring
+overemphasise
+overemphasised
+overemphasises
+overemphasising
+oxidisation
+oxidise
+oxidised
+oxidises
+oxidising
+paederast
+paederasts
+paediatric
+paediatrician
+paediatricians
+paediatrics
+paedophile
+paedophiles
+paedophilia
+palaeolithic
+palaeontologist
+palaeontologists
+palaeontology
+panelled
+panelling
+panellist
+panellists
+paralyse
+paralysed
+paralyses
+paralysing
+parcelled
+parcelling
+parlour
+parlours
+particularise
+particularised
+particularises
+particularising
+passivisation
+passivise
+passivised
+passivises
+passivising
+pasteurisation
+pasteurise
+pasteurised
+pasteurises
+pasteurising
+patronise
+patronised
+patronises
+patronising
+patronisingly
+pedalled
+pedalling
+pedestrianisation
+pedestrianise
+pedestrianised
+pedestrianises
+pedestrianising
+penalise
+penalised
+penalises
+penalising
+pencilled
+pencilling
+personalise
+personalised
+personalises
+personalising
+pharmacopoeia
+pharmacopoeias
+philosophise
+philosophised
+philosophises
+philosophising
+philtre
+philtres
+phoney
+plagiarise
+plagiarised
+plagiarises
+plagiarising
+plough
+ploughed
+ploughing
+ploughman
+ploughmen
+ploughs
+ploughshare
+ploughshares
+polarisation
+polarise
+polarised
+polarises
+polarising
+politicisation
+politicise
+politicised
+politicises
+politicising
+popularisation
+popularise
+popularised
+popularises
+popularising
+pouffe
+pouffes
+practise
+practised
+practises
+practising
+praesidium
+praesidiums
+pressurisation
+pressurise
+pressurised
+pressurises
+pressurising
+pretence
+pretences
+primaeval
+prioritisation
+prioritise
+prioritised
+prioritises
+prioritising
+privatisation
+privatisations
+privatise
+privatised
+privatises
+privatising
+professionalisation
+professionalise
+professionalised
+professionalises
+professionalising
+programme
+programmes
+prologue
+prologues
+propagandise
+propagandised
+propagandises
+propagandising
+proselytise
+proselytised
+proselytiser
+proselytisers
+proselytises
+proselytising
+psychoanalyse
+psychoanalysed
+psychoanalyses
+psychoanalysing
+publicise
+publicised
+publicises
+publicising
+pulverisation
+pulverise
+pulverised
+pulverises
+pulverising
+pummelled
+pummelling
+pyjama
+pyjamas
+pzazz
+quarrelled
+quarrelling
+radicalise
+radicalised
+radicalises
+radicalising
+rancour
+randomise
+randomised
+randomises
+randomising
+rationalisation
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+milligrams
+milliliter
+milliliters
+millimeter
+millimeters
+miniaturization
+miniaturize
+miniaturized
+miniaturizes
+miniaturizing
+minibusses
+minimize
+minimized
+minimizes
+minimizing
+misbehavior
+misdemeanor
+misdemeanors
+misspelled
+miter
+miters
+mobilization
+mobilize
+mobilized
+mobilizes
+mobilizing
+modeled
+modeler
+modelers
+modeling
+modernize
+modernized
+modernizes
+modernizing
+moisturize
+moisturized
+moisturizer
+moisturizers
+moisturizes
+moisturizing
+monolog
+monologs
+monopolization
+monopolize
+monopolized
+monopolizes
+monopolizing
+moralize
+moralized
+moralizes
+moralizing
+motorized
+mold
+molded
+molder
+moldered
+moldering
+molders
+moldier
+moldiest
+molding
+moldings
+molds
+moldy
+molt
+molted
+molting
+molts
+mustache
+mustached
+mustaches
+mustachioed
+multicolored
+nationalization
+nationalizations
+nationalize
+nationalized
+nationalizes
+nationalizing
+naturalization
+naturalize
+naturalized
+naturalizes
+naturalizing
+neighbor
+neighborhood
+neighborhoods
+neighboring
+neighborliness
+neighborly
+neighbors
+neutralization
+neutralize
+neutralized
+neutralizes
+neutralizing
+normalization
+normalize
+normalized
+normalizes
+normalizing
+odor
+odorless
+odors
+esophagus
+esophaguses
+estrogen
+offense
+offenses
+omelet
+omelets
+optimize
+optimized
+optimizes
+optimizing
+organization
+organizational
+organizations
+organize
+organized
+organizer
+organizers
+organizes
+organizing
+orthopedic
+orthopedics
+ostracize
+ostracized
+ostracizes
+ostracizing
+outmaneuver
+outmaneuvered
+outmaneuvers
+outmaneuvering
+overemphasize
+overemphasized
+overemphasizes
+overemphasizing
+oxidization
+oxidize
+oxidized
+oxidizes
+oxidizing
+pederast
+pederasts
+pediatric
+pediatrician
+pediatricians
+pediatrics
+pedophile
+pedophiles
+pedophilia
+paleolithic
+paleontologist
+paleontologists
+paleontology
+paneled
+paneling
+panelist
+panelists
+paralyze
+paralyzed
+paralyzes
+paralyzing
+parceled
+parceling
+parlor
+parlors
+particularize
+particularized
+particularizes
+particularizing
+passivization
+passivize
+passivized
+passivizes
+passivizing
+pasteurization
+pasteurize
+pasteurized
+pasteurizes
+pasteurizing
+patronize
+patronized
+patronizes
+patronizing
+patronizingly
+pedaled
+pedaling
+pedestrianization
+pedestrianize
+pedestrianized
+pedestrianizes
+pedestrianizing
+penalize
+penalized
+penalizes
+penalizing
+penciled
+penciling
+personalize
+personalized
+personalizes
+personalizing
+pharmacopeia
+pharmacopeias
+philosophize
+philosophized
+philosophizes
+philosophizing
+filter
+filters
+phony
+plagiarize
+plagiarized
+plagiarizes
+plagiarizing
+plow
+plowed
+plowing
+plowman
+plowmen
+plows
+plowshare
+plowshares
+polarization
+polarize
+polarized
+polarizes
+polarizing
+politicization
+politicize
+politicized
+politicizes
+politicizing
+popularization
+popularize
+popularized
+popularizes
+popularizing
+pouf
+poufs
+practice
+practiced
+practices
+practicing
+presidium
+presidiums
+pressurization
+pressurize
+pressurized
+pressurizes
+pressurizing
+pretense
+pretenses
+primeval
+prioritization
+prioritize
+prioritized
+prioritizes
+prioritizing
+privatization
+privatizations
+privatize
+privatized
+privatizes
+privatizing
+professionalization
+professionalize
+professionalized
+professionalizes
+professionalizing
+program
+programs
+prolog
+prologs
+propagandize
+propagandized
+propagandizes
+propagandizing
+proselytize
+proselytized
+proselytizer
+proselytizers
+proselytizes
+proselytizing
+psychoanalyze
+psychoanalyzed
+psychoanalyzes
+psychoanalyzing
+publicize
+publicized
+publicizes
+publicizing
+pulverization
+pulverize
+pulverized
+pulverizes
+pulverizing
+pummel
+pummeled
+pajama
+pajamas
+pizzazz
+quarreled
+quarreling
+radicalize
+radicalized
+radicalizes
+radicalizing
+rancor
+randomize
+randomized
+randomizes
+randomizing
+rationalization
+rationalizations
+rationalize
+rationalized
+rationalizes
+rationalizing
+raveled
+raveling
+realizable
+realization
+realizations
+realize
+realized
+realizes
+realizing
+recognizable
+recognizably
+recognizance
+recognize
+recognized
+recognizes
+recognizing
+reconnoiter
+reconnoitered
+reconnoiters
+reconnoitering
+refueled
+refueling
+regularization
+regularize
+regularized
+regularizes
+regularizing
+remodeled
+remodeling
+remold
+remolded
+remolding
+remolds
+reorganization
+reorganizations
+reorganize
+reorganized
+reorganizes
+reorganizing
+reveled
+reveler
+revelers
+reveling
+revitalize
+revitalized
+revitalizes
+revitalizing
+revolutionize
+revolutionized
+revolutionizes
+revolutionizing
+rhapsodize
+rhapsodized
+rhapsodizes
+rhapsodizing
+rigor
+rigors
+ritualized
+rivaled
+rivaling
+romanticize
+romanticized
+romanticizes
+romanticizing
+rumor
+rumored
+rumors
+saber
+sabers
+saltpeter
+sanitize
+sanitized
+sanitizes
+sanitizing
+satirize
+satirized
+satirizes
+satirizing
+savior
+saviors
+savor
+savored
+savories
+savoring
+savors
+savory
+scandalize
+scandalized
+scandalizes
+scandalizing
+skeptic
+skeptical
+skeptically
+skepticism
+skeptics
+scepter
+scepters
+scrutinize
+scrutinized
+scrutinizes
+scrutinizing
+secularization
+secularize
+secularized
+secularizes
+secularizing
+sensationalize
+sensationalized
+sensationalizes
+sensationalizing
+sensitize
+sensitized
+sensitizes
+sensitizing
+sentimentalize
+sentimentalized
+sentimentalizes
+sentimentalizing
+sepulcher
+sepulchers
+serialization
+serializations
+serialize
+serialized
+serializes
+serializing
+sermonize
+sermonized
+sermonizes
+sermonizing
+sheik
+shoveled
+shoveling
+shriveled
+shriveling
+signalize
+signalized
+signalizes
+signalizing
+signaled
+signaling
+smolder
+smoldered
+smoldering
+smolders
+sniveled
+sniveling
+snorkeled
+snorkeling
+snowplow
+snowplow
+socialization
+socialize
+socialized
+socializes
+socializing
+sodomize
+sodomized
+sodomizes
+sodomizing
+solemnize
+solemnized
+solemnizes
+solemnizing
+somber
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+specializations
+specialize
+specialized
+specializes
+specializing
+specter
+specters
+spiraled
+spiraling
+splendor
+splendors
+squirreled
+squirreling
+stabilization
+stabilize
+stabilized
+stabilizer
+stabilizers
+stabilizes
+stabilizing
+standardization
+standardize
+standardized
+standardizes
+standardizing
+stenciled
+stenciling
+sterilization
+sterilizations
+sterilize
+sterilized
+sterilizer
+sterilizers
+sterilizes
+sterilizing
+stigmatization
+stigmatize
+stigmatized
+stigmatizes
+stigmatizing
+story
+stories
+subsidization
+subsidize
+subsidized
+subsidizer
+subsidizers
+subsidizes
+subsidizing
+succor
+succored
+succoring
+succors
+sulfate
+sulfates
+sulfide
+sulfides
+sulfur
+sulfurous
+summarize
+summarized
+summarizes
+summarizing
+swiveled
+swiveling
+symbolize
+symbolized
+symbolizes
+symbolizing
+sympathize
+sympathized
+sympathizer
+sympathizers
+sympathizes
+sympathizing
+synchronization
+synchronize
+synchronized
+synchronizes
+synchronizing
+synthesize
+synthesized
+synthesizer
+synthesizers
+synthesizes
+synthesizing
+siphon
+siphoned
+siphoning
+siphons
+systematization
+systematize
+systematized
+systematizes
+systematizing
+tantalize
+tantalized
+tantalizes
+tantalizing
+tantalizingly
+tasseled
+technicolor
+temporize
+temporized
+temporizes
+temporizing
+tenderize
+tenderized
+tenderizes
+tenderizing
+terrorize
+terrorized
+terrorizes
+terrorizing
+theater
+theatergoer
+theatergoers
+theaters
+theorize
+theorized
+theorizes
+theorizing
+ton
+tons
+toweled
+toweling
+toxemia
+tranquilize
+tranquilized
+tranquilizer
+tranquilizers
+tranquilizes
+tranquilizing
+tranquility
+tranquilize
+tranquilized
+tranquilizer
+tranquilizers
+tranquilizes
+tranquilizing
+tranquility
+transistorized
+traumatize
+traumatized
+traumatizes
+traumatizing
+traveled
+traveler
+travelers
+traveling
+travelog
+travelogs
+trialed
+trialing
+tricolor
+tricolors
+trivialize
+trivialized
+trivializes
+trivializing
+tumor
+tumors
+tunneled
+tunneling
+tyrannize
+tyrannized
+tyrannizes
+tyrannizing
+tire
+tires
+unauthorized
+uncivilized
+underutilized
+unequaled
+unfavorable
+unfavorably
+unionization
+unionize
+unionized
+unionizes
+unionizing
+unorganized
+unraveled
+unraveling
+unrecognizable
+unrecognized
+unrivaled
+unsavory
+untrammeled
+urbanization
+urbanize
+urbanized
+urbanizes
+urbanizing
+utilizable
+utilization
+utilize
+utilized
+utilizes
+utilizing
+valor
+vandalize
+vandalized
+vandalizes
+vandalizing
+vaporization
+vaporize
+vaporized
+vaporizes
+vaporizing
+vapor
+vapors
+verbalize
+verbalized
+verbalizes
+verbalizing
+victimization
+victimize
+victimized
+victimizes
+victimizing
+videodisk
+videodisks
+vigor
+visualization
+visualizations
+visualize
+visualized
+visualizes
+visualizing
+vocalization
+vocalizations
+vocalize
+vocalized
+vocalizes
+vocalizing
+vulcanized
+vulgarization
+vulgarize
+vulgarized
+vulgarizes
+vulgarizing
+wagon
+wagons
+watercolor
+watercolors
+weaseled
+weaseling
+westernization
+westernize
+westernized
+westernizes
+westernizing
+womanize
+womanized
+womanizer
+womanizers
+womanizes
+womanizing
+woolen
+woolens
+woolies
+wooly
+worshiped
+worshiping
+worshiper
+yodeled
+yodeling
+yogurt
+yogurts
+yogurt
+yogurts
+
+
+for $x in $list1//*:uk
+let $count-uk := count($list1/*:uk)
+let $pos := ($count-uk - count($x/following-sibling::*:uk))
+let $us := $list2/*:us[position() = $pos]
+return if ($us/@class) then ()
+else
+
+
+
diff --git a/unlink-refs.xq b/unlink-refs.xq
new file mode 100644
index 0000000..f78440c
--- /dev/null
+++ b/unlink-refs.xq
@@ -0,0 +1,9 @@
+for $x in collection('plos-xml')//*:article
+let $r := count(for $y in $x//*:ref
+ let $id := $y/@id
+ return if ($y/ancestor::*:article//*:xref[@rid = $id]) then ()
+ else $x
+ )
+return
+if ($r = 0) then ()
+else $r
\ No newline at end of file
diff --git a/update-articles-db.xq b/update-articles-db.xq
new file mode 100644
index 0000000..8af2057
--- /dev/null
+++ b/update-articles-db.xq
@@ -0,0 +1,14 @@
+let $db := 'articles'
+let $article-store := '/Users/fredatherden/Documents/GitHub/elife-article-xml/articles'
+let $list := {
+ for $x in collection($db)//*:article
+ return {$x/base-uri()}
+}
+
+for $x in file:list($article-store)
+let $uri := ('/'||$db||'/'||$x)
+let $xml := doc(concat($article-store,'/',$x))
+return
+if (not(matches($x,'\.xml$'))) then ()
+else if ($uri = $list//*:item/text()) then ()
+else db:replace($db,$x,$xml)
\ No newline at end of file
diff --git a/update-biorxiv-db.xq b/update-biorxiv-db.xq
new file mode 100644
index 0000000..7734d45
--- /dev/null
+++ b/update-biorxiv-db.xq
@@ -0,0 +1,6 @@
+let $db := 'biorxiv'
+let $dir := '/Users/fredatherden/Documents/biorxiv-xml/xml/'
+
+for $file in file:list($dir)
+let $xml := doc($dir||$file)
+return db:replace($db,$file,$xml)
\ No newline at end of file
diff --git a/update-jats-support-tests.xq b/update-jats-support-tests.xq
new file mode 100644
index 0000000..27eb46b
--- /dev/null
+++ b/update-jats-support-tests.xq
@@ -0,0 +1,13 @@
+let $path := '/Users/fredatherden/Documents/GitHub/jats-support-2/tests/cases/contrib-group'
+
+for $x in file:list($path)
+let $doc := doc($path||'/'||$x)
+let $new-doc := copy $copy := $doc
+modify(
+ for $root in $copy/*[1]
+ return
+ insert node (processing-instruction {'expected-error'}{('message="'||' in <> is ignored."'||' node="'||'/contrib-group"')},'
','
') before $root
+)
+return $copy
+
+return file:write(($path||'/'||$x),$new-doc)
\ No newline at end of file
diff --git a/validate.xq b/validate.xq
new file mode 100644
index 0000000..8db4031
--- /dev/null
+++ b/validate.xq
@@ -0,0 +1,28 @@
+(: In order for this query to functino you have to installed the schematron module:
+'repo:install('https://github.com/Schematron/schematron-basex/raw/master/dist/schematron-basex-1.2.xar')'
+:)
+
+import module namespace schematron = "http://github.com/Schematron/schematron-basex";
+
+let $xml := doc('/Users/fredatherden/desktop/elife51101.xml')
+
+let $sch := schematron:compile(doc('/Users/fredatherden/Documents/GitHub/eLife-JATS-schematron/src/pre-JATS-schematron.sch'))
+
+let $svrl := schematron:validate($xml, $sch)
+
+let $report-1 := {$svrl//(*:failed-assert|*:successful-report)}
+
+let $report-2 := copy $copy := $report-1
+modify(
+ for $x in $copy//*:failed-assert[@id="gen-country-test"]
+ return delete node $x,
+
+ for $y in $copy//(*:failed-assert|*:successful-report)
+ return delete node $y/@test
+)
+return $copy
+
+return $report-2
+
+
+
diff --git a/validate2-example.xq b/validate2-example.xq
new file mode 100644
index 0000000..85bf845
--- /dev/null
+++ b/validate2-example.xq
@@ -0,0 +1,15 @@
+(: In order for this query to functino you have to installed the schematron module:
+'repo:install('https://github.com/Schematron/schematron-basex/raw/master/dist/schematron-basex-1.2.xar')'
+:)
+
+import module namespace schematron = "http://github.com/Schematron/schematron-basex";
+
+let $xsl := schematron:compile(doc('/Users/fredatherden/Desktop/test2.sch'))
+let $dir := '/Users/fredatherden/Desktop/test2/'
+
+for $x in collection('articles')//*:article[*:body]
+let $output := xslt:transform($x,$xsl)
+let $name := substring-after($x/base-uri(),'articles/')
+return
+if ($output//*:failed-assert[not(contains(@location,'object-id'))]) then file:write(($dir||$name),$output)
+else ()
\ No newline at end of file
,'build/main/'),'\.mml','.png'),'StrictContent','Content')})
+