era-check-ejp.xq

(: 
1. visit https://submit.elifesciences.org/cgi-bin/main.plex?form_type=rpt_qt_run_query&j_id=415&ms_id_key=81ftdoA0VUgcfQ3sK4l8CZPOxMw&ft_key=1AcgvYJ7m7hz790tlav2ww&rq_id=2529 and donwload excel file 

2. Save as csv

3. Run this query

4. Run era-ejp-update.xq with output of $xml-update or edit in oXygen using WebDav connection
:)

let $eras := distinct-values(for $x in collection('era')//*:article return $x/@id)
let $csv := csv:parse(file:read-text('/Users/fredatherden/Desktop/eLife_query_tool_executable_research_article_answers.csv'))

let $records-of-interest := 
      for $x in $csv//*:record[contains(*:entry[1],'eLife')]
      let $id-string := substring-after($x/*:entry[1],'eLife-')
      let $id := if (contains($id-string,'R')) 
                  then if (matches(substring-before($id-string,'R'),'\d{5}')) then substring-before($id-string,'R')
                  else ('unknown - '||$x/*:entry[3])
             else if (matches($id-string,'\d{5}')) then $id-string
             else ('unknown - '||$x/*:entry[3])
      where (not($id=$eras) and contains(lower-case($x/*:entry[5]),'accept'))
      return 
      copy $copy := $x
      modify(
        insert node attribute id {$id} into $copy
      )
      return $copy

let $xml-update := <update>{
  for $x in $records-of-interest
  return <article id="{$x/@id}" status="contacted/ignored"/>
}</update>

return (
  for $x in $records-of-interest 
  return ($x/entry[1]||' '||$x/*:entry[5])
  ,
  $xml-update
)