Moving from Mendeley to Zotero - importing bib files with document attachments

madhusudansingh

Hello,

I use the Chrome zotero plugin to import journal articles and PDF documents directly from webpages. I absolutely love this feature.

Another feature I love is the ability to save Zotero attachments to a WebDAV server of my choosing. My University runs an ownCloud implementation and this is a perfect match for this case.

Previously, I have used Mendeley extensively but am now in the process of switching to Zoteo because I believe that the non-open source nature of Mendeley coupled with its recent acquisition makes things rather uncertain for academicians. I do not want to wake up one day and find that years' worth of bibliographic data I have accumulated is suddenly behind a paywall or a non-open format that I cannot get at without Mendeley. I know - they promise that they won't do anything of the kind, but commercial promises of that nature run the risk of being worthless because of the profit motive.

Now, the only reliable way of moving my data from Mendeley to Zotero is to export a bib file from Mendeley and then import this in Zotero. I have done it for a few collections, and it appears to work wonderfully. Now, I could not help but wonder but is it possible for this bib import to trigger Zotero into looking up each article and download PDFs if I have access to them through my University? It does not seem this exists as this automatic PDF download is a feature of the Chrome Zotero plugin. Could this be improvised somewhow?

Or is this a feature request that could make future transitions to Zotero a lot simpler? Can this be done on the web when I am logged into my Zotero account in some fashion. It would save me so much work if this were to be possible somehow.

One thing I do not like so far (or at least have not been able to figure out with Zotfile) is the missing watched folder feature (that Mendeley has). But I guess I have now moved beyond that with the WebDAV feature.

M

adamsmith

It does not seem this exists as this automatic PDF download is a feature of the Chrome Zotero plugin. Could this be improvised somewhow?

no. You can import existing attachments that you have in Mendeley, but Zotero can't look for and attach PDFs. We're thinking about that and it might happen in the feature, but it's very much not-trivial to implement and won't happen very soon.
I don't quite understand what that has to do with transitioning from Mendeley, though? If you have the PDFs attached to Mendeley items it should be pretty easy to get the bib or RIS import working in a way that includes them in Zotero.

madhusudansingh

Thanks for your response.

Can you please suggest a working example? I have PDFs attached to about 60 articles in a collection in Mendeley. I selected all, and then exported them to a bib file. When I import that bib file in Zotero, I get the articles but not the PDF attachments.

If that had worked, I wouldn't have posted my question :)

adamsmith

Mendeley's file export in bibtex is broken, and especially on Windows it requires a fair amount of tweaking the .bib file before it will import PDFs and is basically impossible if you have PDFs in different locations. You can export to RIS from Mendeley (you can select the file type when you select the location to save the export to) and that should just work.

Sunnysky

I had a share dropbox with all my folders of files to be indexed by Zotero and was horrified to find them all moved to the firefox hidden folders in separate folders for each file.

I didn't want all the source files moved. How do I prevent this if I move them back.

adamsmith

unfortunately it's not currently possible to import with file links intact but without importing the files into Zotero.
See e.g.
https://forums.zotero.org/discussion/32504/linking-attachments-by-ris-import/
and
https://forums.zotero.org/discussion/29033/bibtex-and-other-bibliographic-import-adding-pdfs-as-links-instead-of-attachments/

It is possible to set up ZotFile (http://zotfile.com/)to move imported attachments out of the Firefox folder, so you're not tied to having them there, but they'll get copied either way.

Sunnysky

argh

dstillman

(I understand it's not what you want, but nothing is moved, by the way. They're copied.)

Sunnysky

1) I found my dropbox empty of all my files and found them all under the firefox folders one per file + indexes

2) Not only that but I had duplicates of most. (PITA)
3) None of the files were indexed but I could selected them one by one or in groups of PDFs and get metafile info ( ok but tedious)
4) half of the files (like IEEE documents) failed to be found in Search Metafiles, but could be found on Google Scholar) _PITA)_

It took me all afternoon to recover my files from Dropbox server one by one and now I am wishing I had my old OSX box so I could use SENTE which was intuitive and easy

adamsmith

1) not sure what you did, but as Dan says, that's most definitely not Zotero's doing. Zotero doesn't move/delete files, so if they disappeared from Dropbox something else did that (and you probably want to look into what did to prevent it from re-occurring).

I can't really speak to the rest, but from 2-4 it seems your issues were unrelated to this thread since it doesn't sound like you used a bib file or transferred from Mendeley, so if you do want more help, please start a new thread and describe what you actually did.

Sunnysky

HMmm I was trying to migrate from Mendeley when this mess started.. I guess the drag and drop did it, which worked well in other Citation apps


now I deleted the duplicate folders with APp shutoff as I read...
Now it says
[Exception... "Component returned failure code: 0x80630001 (NS_ERROR_STORAGE_BUSY) [mozIStorageConnection.executeSimpleSQL]" nsresult: "0x80630001 (NS_ERROR_STORAGE_BUSY)" location: "JS frame :: chrome://zotero/content/xpcom/db.js :: <TOP_LEVEL> :: line 149" data: no] [QUERY: DELETE FROM itemTypesCombined] [ERROR: database is locked]

adamsmith

Please start a new thread and provide more details starting at the beginning of how and what you imported. It's unfortunately entirely unclear to me what you're doing so there's no way to help.