Mendeley -> Zotero via BibTeX: links to attached files are lost
Hi everyone,
I'm trying to migrate from Mendeley to Zotero. On importing the bibtex file exported by Mendeley, many file links are lost. My guess at an explanation: Mendeley renames files using non-ASCII characters. When it exports to bibtex, these characters are escaped. Links containing escaped characters (mostly German umlauts) are not imported by Zotero.
My library contains > 17.000 items, so manual editing is not an option. Jabrefs automatic renaming feature fails.
Any help is appreciated,
Steffen
I'm trying to migrate from Mendeley to Zotero. On importing the bibtex file exported by Mendeley, many file links are lost. My guess at an explanation: Mendeley renames files using non-ASCII characters. When it exports to bibtex, these characters are escaped. Links containing escaped characters (mostly German umlauts) are not imported by Zotero.
My library contains > 17.000 items, so manual editing is not an option. Jabrefs automatic renaming feature fails.
Any help is appreciated,
Steffen
yes, I did, but maybe I got it wrong. As I understood the info on that page, I would have to upload all my pdfs (>35 GB) to Elseviers servers, in order to make any information about attached files available by syncing to an old Mendeley? I'd like to avoid that.
I wouldn't mind loosing any information not in the bibtex export if this is necessary to change to Zotero. So the problem might be solved on the Zotero side rather than on Mendeleys.
Regards,
Steffen
I think we may actually be doing something wrong with the Endnote XML.
IIRC, RIS export in Mendeley doesn't include keywords/tags
TY - JOUR
T1 - General q-exponential model for tree height, volume and stem profile
A1 - Petrauskas, Edmundas
A1 - Rupšys, P
Y1 - 2010///
JF - Latest Trends on System
VL - II
IS - Volume II
SP - 555
EP - 560
SN - 9789604742141
UR - http://www.wseas.us/e-library/conferences/2010/Corfu/SYSTEMS/SYSTEMS2-34.pdf
L1 - file:///D:/Users/Steffen/Documents/Literatur/pdf/Mendeley/Artikel/Petrauskas, Rupšys - 2010 - Latest Trends on System.pdf
ER -
<?xml version="1.0" encoding="UTF-8"?><xml><records><record><database name="Petrauskas.enl" path="Petrauskas.enl">Petrauskas.enl</database><ref-type name="Journal Article">0</ref-type><contributors><authors><author>Petrauskas, Edmundas</author><author>Rupšys, P</author></authors></contributors><titles><title>General q-exponential model for tree height, volume and stem profile</title><secondary-title>Latest Trends on System</secondary-title></titles><periodical><full-title>Latest Trends on System</full-title></periodical><pages>555-560</pages><volume>II</volume><issue>Volume II</issue><keywords/><dates><year>2010</year></dates><isbn>9789604742141</isbn><urls><pdf-urls><url>internal-pdf://Petrauskas, Rupšys - 2010 - Latest Trends on System.pdf</url></pdf-urls><web-urls><url>http://www.wseas.us/e-library/conferences/2010/Corfu/SYSTEMS/SYSTEMS2-34.pdf</url></web-urls></urls><label>Allometrie</label></record></records></xml>
If so, if you place the XML file into that folder and import it from there, does the file import (it should)*
We can then likely tell you how to get label to import as tag (although that is, of course, a Mendeley bug)
*Technically: you'll note the "internal-pdf" in the filepath -- Zotero guesses the filepath for internal-pdf based on the location of the XML file it is importing.
@emilianoeheyns does BBT do better here with importing filenames with non-ascii? Worthwhile for steffen to install that and retry import?
I started importing without BBT, realised the missing file links, found BBT and installed it, made further tests, and then started this discussion.
So my impression is that BBT does not make a difference.
"Oertel, Ruck - 2012 - Bioströmungsmechanik(5).pdf"
is exported by Mendeley as
@article{Oertel2012j,
address = {Wiesbaden},
author = {Oertel, Herbert and Ruck, Sebastian},
doi = {10.1007/978-3-8348-8631-6},
file = {:D$\backslash$:/Users/Steffen/Documents/Literatur/pdf/Mendeley/Artikel/Oertel, Ruck - 2012 - Biostr{\"{o}}mungsmechanik(5).pdf:pdf},
isbn = {978-3-8348-1765-5},
keywords = {DOPPELT},
mendeley-tags = {DOPPELT},
publisher = {Vieweg+Teubner Verlag},
title = {{Biostr{\"{o}}mungsmechanik}},
url = {http://link.springer.com/10.1007/978-3-8348-8631-6},
year = {2012}
}
On import to Zotero, the pdf is lost. Manually replacing "{\"{o}}" with "ö" does not help.
$\backslash$
?file = {D:\\Users\\Steffen\\Documents\\Literatur\\pdf\\Mendeley\\Artikel\\Oertel, Ruck - 2012 - Bioströmungsmechanik(5).pdf},
and imported back into Zotero -> attachment is gone.
I then read the exported item into Jabref, cleaned it, saved it:
file = {D:/Users/Steffen/Documents/Literatur/pdf/Mendeley/Artikel/Oertel, Ruck - 2012 - Bioströmungsmechanik(5).pdf:PDF},
imported into Zotero -> attachment is gone.
The same happens with previously successful imports from the Mendeley export.
Meanwhile I've tried the import via the RIS format on a different machine, but Zotero hasn't finished importing 1/10 of my library in 48 hours (i7 with 16GB RAM). So I cannot report results there.
If you've used JabRef as an intermediary, you should try opening the file from within JabRef. My suspicion is that it will not work. Unlike Zotero, JabRef makes no attend to see if there's a file there until you actually try to open the link.
If you make the attachment in JabRef and then import the created .bib file into Zotero (again, using the stock translator), it should probably work.
Again, my suspicion is that Mendeley really wants to point to the file in some way like this:
file = {:D\:/Users/Steffen/Documents/Literatur/pdf/Mendeley/Artikel/Oertel, Ruck - 2012 - Bioströmungsmechanik(5).pdf:pdf}
Note the initial colon to separate the file name (blank) and location. Note that the second colon (after drive letter) is escaped with a backslash.
Finally: note there are various ways to encode 'ö'. You should make sure that your browser and file explorer are able to find the file using the encoding you are using. If suggest copying and pasting from your file explorer, rather than topping it or pasting from another source.
Exporting from Zotero w/out BBT has the same result: JabRef finds the file, Zotero does not when I reimport.