Abbreviated Journal Names with Mendeley - Replace Long Journal Names Automatically
I created a small bash script that replaces the full journal names with the abbreviated ones (MEDLINE-standard).
You need to download the list of journals from pubmed and place it within the same folder of the script.
Additionally you need sqlite3 (sudo apt-get install sqlite3) under Ubuntu Linux. On Windows systems you need to install cygwin or something similar first i think… but it easier to make the conversion on a linux box on the campus.
Then you should adjust the path to your database file according to your operating system:
- Windows XP: C:\Documents and Settings\<Your Name>\Local Settings\Application Data\Mendeley Ltd\Mendeley Desktop\
- Windows Vista / Windows 7: %LOCALAPPDATA%\Mendeley Ltd.\Mendeley Desktop\
- Mac OS X: /Users/<Your username>/Library/Application Support/Mendeley Desktop/
- Linux: ~/.local/share/data/Mendeley Ltd./Mendeley Desktop/
After you have done so, I recommend running the script once in echo only mode. If the result looks okay, change the last echo to sqlite3 $db.
Please feel free to leave comments…
Good luck 
#!/bin/bash
db=test.sqlite # set the db-file here. The location depends on the OS you use.
limit="WHERE confirmed='true' AND type='JournalArticle'"
sqlite3 $db "SELECT id FROM Documents $limit" > temp_ids.txt
cat temp_ids.txt | while read line
do
long=$(sqlite3 $db "SELECT publication FROM Documents WHERE id=$line")
echo "long = $long"
#echo "The id is $line"
line_pubm=$(grep -i -n -m 1 "$long" J_Medline.txt | cut -f1 -d:)
#echo "linenumber in pubm= $line_pubm"
abbr_linen=$(( $line_pubm + 1 ))
short=$(sed -n ${abbr_linen}p J_Medline.txt | sed 's/MedAbbr: //' | tr -cd '[:alnum:]‘)
echo “short= $short”
LEN=$(echo ${#short})
echo $LEN
if [ "$short" ]; then
echo “UPDATE Documents SET publication=’$short’ WHERE id=$line”
# sqlite3 $db
# make a security update of your sqlite-file and replace the echo from above with sqlite3 $db
else
echo “no or short shortname (<3 chars) - not changed”
fi
done
Tags: abbrev, abbreviate, citation, mendeley, sqlite, styles, ubuntu, zotero
April 19th, 2010 at 01:55
Running this script in my ubuntu 9.10, i constantly get:
MendeleyScript.sh: 2: Ltd./Mendeley: not found
However, when I paste the location from your description, i pop right into the Mendeley folder. What am I doing wrong?
January 6th, 2012 at 19:53
Thanks for the script, it is very useful!
On a Mac I had a couple of problems: the quotes have been changed in the HTML to opening and closing quotes, which are different characters that bash doesn\’t recognize. Second, I needed to add \"\" around \"$db\" due to the spaces in the filename on a Mac. The final version that did the job is:
#!/bin/bash
db=\"/Users/rcusack/Library/Application Support/Mendeley Desktop/rhodricusack@gmail.com@www.mendeley.com.sqlite\" # set the db-file here. The location depends on the OS you use.
limit=\"WHERE confirmed=\’true\’ AND type=\’JournalArticle\’\"
sqlite3 \"$db\" \"SELECT id FROM Documents $limit\" > temp_ids.txt
cat temp_ids.txt | while read line
do
long=$(sqlite3 \"$db\" \"SELECT publication FROM Documents WHERE id=$line\")
echo \"long = $long\"
echo \"The id is $line\"
line_pubm=$(grep -i -n -m 1 \"$long\" J_Medline.txt | cut -f1 -d:)
echo \"linenumber in pubm= $line_pubm\"
abbr_linen=$(( $line_pubm + 1 ))
short=$(sed -n ${abbr_linen}p J_Medline.txt | sed \’s/MedAbbr: //\’ | tr -cd \’[:alnum:]\’)
echo “short= $short”
LEN=$(echo ${#short})
echo $LEN
if [ \"$short\" ]; then
echo $short
echo $line
sqlite3 \"$db\" \"UPDATE Documents SET publication=\’${short}\’ WHERE id=${line}\"
# sqlite3 $db
# make a security update of your sqlite-file and replace the echo from above with sqlite3 $db
else
echo \"no or short shortname (<3 chars) - not changed\"
fi
done
January 6th, 2012 at 20:26
The quotes in the comment above have been escaped. A better version is here:
http://www.cusacklab.org/?page_id=559