2011
01.25

Introduction:

For some years I have used the Bibus python script as my reference manager software. The software works fine but the import of new references was always a bit cumbersome. Then Zotero and later on Mendeley appeared as viable alternatives to Bibus. Both featuring much better import and synchronization features. I have used Zotero for some time to collect scientific references and webpages. However I couldn't figure out a transparent way to import my old collection from Bibus. My trials in importing via a RIS file failed badly and I couldn't find a way to import my old collection of pdf files which were referenced in the bibus database. When I first tried the RIS import in Mendeley it worked immediately which means it did import all the records without giving up somewhere in the middle. However there were some minor problems related to file paths, conference proceedings and keywords. In the end I was able to fix all this by editing the RIS file before importing it. The details are given below.

 

Export/Import via a RIS file

 

1) Export all references from within Bibus (~200009 as a RIS file using UTF-8 character encoding

2) Editing the RIS text file (I have  used the Scite editor for this)

2a) Set encoding of file to UTF-8

2b) Conference Proceedings titles were tagged by ‘BT  - ‘ which turned out not to work with Mendeley. I replaced all ‘BT  - ‘ tags with ‘JF  - ‘.

2c) I replaced all local url file path to reflect the new location ( z:\bibus\files\ was replaced by c:/pdflib/) . Note the use of forward slashes in the file path!

2d) Bibus exported the hierarchical keywords using a ‘U5  -‘ tag. Different keys were separated by hyphens. Unfortunately replacing U5 by KW is not sufficient to import the keywords separately. For this I wrote a little python script to format the keywords in the correct way:

Bibus output: KW  - physics;semiconductor;LED

required formatting:

KW  - physics

KW – semiconductor

KW – LED

More on the script below!

3) Copy over all the pdf’s referenced in the bibus database to the new location

4) In Mendeley go to ‘Add documents’ – Add Files and select the edited ris file. The file must have the ‘.ris’ extension!

5) Now wait for the import to finish. It took a few minutes on my notebook to import the 20000 references. Be aware that once the import seems to be finished, Mendeley continues to grind in the background for a couple of minutes more! I think it is creating the search index…

6) Done! Mendeley is clever enough to see that the pdf’s imported via the url field are local files and so the same file is also appearing in Mendeleys file field! Great!

7) Set the file management options in Mendeley:

image

 

 

Here’s the crude python script I used to reformat the keyword field (path of input and output files directly coded into the script code….).

# -*- coding: utf-8 -*-

# input and out files:
inp = 'c:/Users/klaus/Downloads/~~allrefs.ris'
outp = 'c:/Users/klaus/Downloads/~~allrefs-new.ris'
f = open(inp,'r')
f2 = open(outp,'w')

for line in f:
    if 'KW  - ' in line :
         tmp = line.split('KW  - ')
         tmp2 = tmp[1].split(';')
         s = ''
        for x in tmp2:
        s = s + 'KW  - ' + x + '\n'
       f2.write(s[:-1])

  else :
       f2.write(line)

f.close()
f2.close()

 

 

Managing pdf files

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