{"id":366,"date":"2017-01-31T20:07:08","date_gmt":"2017-01-31T20:07:08","guid":{"rendered":"https:\/\/staff.fnwi.uva.nl\/b.terwijn\/?page_id=366"},"modified":"2022-10-10T09:29:23","modified_gmt":"2022-10-10T09:29:23","slug":"pure-publication-lists","status":"publish","type":"page","link":"https:\/\/staff.fnwi.uva.nl\/b.terwijn\/pure-publication-lists\/","title":{"rendered":"Pure publication lists"},"content":{"rendered":"

How to automatically update a list of publications from Pure<\/a> on a research group’s website?<\/p>\n

Official route<\/h2>\n

Ask Pure people for the UUID of the research group and use UvA Dare which looks like:<\/p>\n

http:\/\/dare.uva.nl\/search?org-uuid=1f129de9-e2f4-41a0-a223-94f32e993ac1&smode=iframe<\/a><\/p>\n

but only validated publications will appear which I find unsatisfactory. Fortunately there is an unofficial route.<\/p>\n

Unofficial route<\/h2>\n

Make a report in Pure, schedule it to be emailed, receive it, and process it. This will include not-yet-validated publications, but it gets messy:<\/p>\n

– Make a report<\/h3>\n

See the video and use report type ‘Listing’:
\nhttp:\/\/www.atira.dk\/en\/pure\/screencasts\/how-to-get-familiar-with-reporting-4.12.html<\/a><\/p>\n

– Schedule it to be emailed<\/h3>\n

Schedule the report to be send in HTML format to a gmail account dedicated for this purpose:
\n\"SchedulePureReport\"<\/p>\n

– Receive it<\/h3>\n

Set your gmail-name and gmail-password in the script below and use it to install and configure ‘fetchmail’, ‘procmail’ and ‘mpack’. Only tested on Ubuntu Linux.<\/p>\n

# based on: https:\/\/outhereinthefield.wordpress.com\/2015\/06\/14\/scripting-gmail-download-and-saving-the-attachments-with-fetchmail-pro\ncmail-and-munpack\/\n####################################\nemail=my-gmail-name\npassword=my-gmail-password\n####################################\n\n### install software\nsudo apt-get install fetchmail procmail mpack\n\n### config fetchmail\necho \"poll pop.gmail.com\nprotocol pop3\ntimeout 300\nport 995\nusername \\\"${email}@gmail.com\\\" password \\\"${password}\\\"\nkeep\nmimedecode\nssl\nsslcertck\nsslproto TLS1\nmda \\\"\/usr\/bin\/procmail -m '$HOME\/.procmailrc'\\\"\" > $HOME\/.fetchmailrc\n\nchmod 700 $HOME\/.fetchmailrc\n\n### config procmail\necho \"LOGFILE=\/home\/${USER}\/.procmail.log\nMAILDIR=\/home\/${USER}\/\nVERBOSE=on\n\n:0\nMaildir\/\" > $HOME\/.procmailrc\n\nmkdir -p $HOME\/Maildir\/process\nmkdir -p $HOME\/Maildir\/process\/landing\nmkdir -p $HOME\/Maildir\/process\/extract\nmkdir -p $HOME\/Maildir\/process\/store\nmkdir -p $HOME\/Maildir\/process\/archive\n<\/pre>\n
Then use this script in a cron job to copy the ‘.html’ attachment to the target file (email with report is expected around 1:00 am):<\/p>\n
#!\/bin\/bash\n####################################\ntargetfile=\/var\/www\/publications.html\n####################################\n\nDIR=$HOME\/Maildir\nLOG=$HOME\/Maildir\/getpublications.log\ndate +%r-%-d\/%-m\/%-y >> $LOG\nfetchmail\nmv $DIR\/new\/* $DIR\/process\/landing\/\ncd $DIR\/process\/landing\/\nshopt -s nullglob\nfor i in *\ndo\n  echo \"processing $i\" >> $LOG\n  mkdir $DIR\/process\/extract\/$i\n  cp $i $DIR\/process\/extract\/$i\/\n  echo \"saving backup $i to archive\"  >> $LOG\n  mv $i $DIR\/process\/archive\n  echo \"unpacking $i\" >> $LOG\n  munpack -C $DIR\/process\/extract\/$i -q $DIR\/process\/extract\/$i\/$i\n  find $DIR\/process\/extract\/$i -name '*.html' -exec cp {} ${targetfile} \\;\n\ndone\nshopt -u nullglob\necho \"finishing..\" >> $LOG\nmv $DIR\/process\/extract\/* $DIR\/process\/store\/ \necho \"done!\" >> $LOG\n<\/pre>\n
– Process it<\/h3>\n
Add this to the script above to clean up the report and add links:<\/p>\n
# remove header and footer\nperl -i -0pe 's\/<h1 class=\"ReportTitle\">.*?<br>\/\/igs' ${targetfile}\nperl -i -0pe '$datestring = localtime(); s\/<span class=\"body\">.*?<br>.*?<br>\/<span class=\"body\">updated $datestring<\\\/span>\/igs' ${targetfile} # insert update time\nperl -i -0pe 's\/<h2 class=\"ReportElementTitle\">.*?<\\\/h2>\/\/igs' ${targetfile}\nperl -i -0pe 's\/<p class=\"reportdescription\">.*?<\\\/p>\/\/igs' ${targetfile}\n\n# remove paragraph counts\nperl -i -0pe 's\/(<h3 class=\"ListGroupingTitle1\">).*?\\. \/$1\/igs' ${targetfile}\n\n# add links\nperl  -i -0pe 's\/(?<total><strong>(?<title>.*?)<\\\/strong>)\/<a href=\"https:\\\/\\\/www.google.nl\\\/#q=%22$+{title}%22\">$+{total}<\\\/a>\/igs' ${targetfile}\n<\/pre>\n","protected":false},"excerpt":{"rendered":"
How to automatically update a list of publications from Pure on a research group’s website? Official route Ask Pure people for the UUID of the research group and use UvA Dare which looks like: http:\/\/dare.uva.nl\/search?org-uuid=1f129de9-e2f4-41a0-a223-94f32e993ac1&smode=iframe but only validated publications will appear which I find unsatisfactory. Fortunately there is an unofficial route. Unofficial route Make a […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/staff.fnwi.uva.nl\/b.terwijn\/wp-json\/wp\/v2\/pages\/366"}],"collection":[{"href":"https:\/\/staff.fnwi.uva.nl\/b.terwijn\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/staff.fnwi.uva.nl\/b.terwijn\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/staff.fnwi.uva.nl\/b.terwijn\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/staff.fnwi.uva.nl\/b.terwijn\/wp-json\/wp\/v2\/comments?post=366"}],"version-history":[{"count":26,"href":"https:\/\/staff.fnwi.uva.nl\/b.terwijn\/wp-json\/wp\/v2\/pages\/366\/revisions"}],"predecessor-version":[{"id":811,"href":"https:\/\/staff.fnwi.uva.nl\/b.terwijn\/wp-json\/wp\/v2\/pages\/366\/revisions\/811"}],"wp:attachment":[{"href":"https:\/\/staff.fnwi.uva.nl\/b.terwijn\/wp-json\/wp\/v2\/media?parent=366"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}