Importing from Mendeley to Zotero with large PDF database.

Bourde

I have been a Mendeley user for... ever. I have decided however to move to Zotero. As you suppose, my library is immense (over 7K entries) and I have at least 50% of PDFs in my local database (not synced online). If I wanted to migrate to Zotero, would I keep all my PDFs attached to each entry? Reassigning them is out of question, given that there are too many. Hopefully this is possible. Thanks in advance!

dstillman

See our importing documentation for the process.

As explained there, you'd need to sync all data and files to Mendeley servers in order to import into Zotero. We feel strongly that you shouldn't have to, but that's the situation Mendeley has created. No information on local file paths is ever uploaded, so even a clean Mendeley installation on your computer would lose links to your local files, and the database encryption they added means that Zotero can't read your current database directly to get the current paths. The best you can do is upload all the files, and then Zotero can redownload them.

As long as all your files are uploaded, when you import into Zotero, all your files will be copied into Zotero's data directory, and you can then remove them from elsewhere on your computer. (There are ways to recreate an external linked-file structure in Zotero afterward, if you want, though we recommend using stored files.)

Bourde

Thanks.
I followed the steps but got stuck when logging into my Mendeley account.
I get a pop-up window asking me to sign into my Mendeley account.
After I enter my credentials, a window shows the message "Check your inbox - An email to XX is on its way that will letyou sign in to your account.

However, when I get the the email and click on the link to log in, it does nothing else. I am still stuck at the "Check your inbox" window in Zotero.

I am wondering if there is an easier way to have my library moved to Zotero:
1. Exporting each folder (category) in Mendeley to a .bib file and importing to Zotero by folder.
2. After this step, is Zotero somehow able to find the respective PDFs if I point to the PDF folder? All my PDF have the format [AUTHOR - YEAR - TITLE].PDF. Is Zotero smart enough to do the "pairing"?

Thanks in advance for all your help

dstillman

After I enter my credentials, a window shows the message "Check your inbox - An email to XX is on its way that will letyou sign in to your account.

We haven't seen this. Do you have some sort of two-factor authentication turned on for your Elsevier account? If so, you'll need to turn it off.

If you log in to your library on the Mendeley website, does that send an email?

Do you have some sort of institutional login to Mendeley?

I am wondering if there is an easier way to have my library moved to Zotero:
1. Exporting each folder (category) in Mendeley to a .bib file and importing to Zotero by folder.

No, absolutely not. You'll lose data and end up with duplicates. Don't do this.

Bourde

I have had this issue with other apps and never found a workaround.
You mentioned that I shouldn't copy the bibtex entries and paste them because I would lose data. What do you mean? I just tested this and it worked perfectly.
Even if I end up with duplicates, I can remove them a posteriori, is this correct?

dstillman

I have had this issue with other apps and never found a workaround.

What issue? Are you referring to your Mendeley account specifically? This isn't some sort of general issue.

You mentioned that I shouldn't copy the bibtex entries and paste them because I would lose data.

It's explained on the linked page. As it says, the official importer is the only way to import all of your data.

And you'll end up with duplicates if you have items in more than one folder in Mendeley.

Bourde

Yes, I was referring to Mendeley account.
As for the copy&paste solution I was proposing, is the duplication of files the only resulting problems? I copied several collections and they are functioning correctly now.

dstillman

As I've said a couple times, and as it explains on the linked page, you will lose data if you transfer via anything but the official importer:

The export formats supported by Mendeley don’t contain folders, various metadata fields (date added, favorite, and others), or PDF annotations.

Whether the exported/imported data is complete enough is entirely up to you. If you're happy with what you have, you can just stick with that.

dstillman

You also didn't answer my questions as to whether you get the email prompt when you try to log in to Mendeley from a browser, whether you've checked to see if there's some sort of two-factor authentication set up on your Elsevier account, and whether this is an institutional login.

Bourde

I have thoroughly checked my Mendeley account settings, but couldn't find any two-factor authentication setting. I deleted all cookies from my browser and tried again, unsuccessfully. I am not using my institutional login (although I have one), I use my persona gmail account with Mendeley.

dstillman

You still haven’t answered my question as to whether you get this just logging in to Mendeley normally in a browser.

If you do, you should contact Mendeley and ask them how to fix that on your account, without mentioning Zotero.

We’re using standard Mendeley API authentication for the importer, and if it requires an email step for you that’s not going to work.

Bourde

If I log into my library on the Mendeley website, I have no issues at all.

dstillman

OK, I'm afraid this seems to be some sort of problem with your Mendeley account or its treatment of your IP address. We haven't received any other reports of this, and there's not really much we can do differently — we're following the standard process for third-party authentication, which isn't compatible with email verification.

If you do want to perform a direct import in lieu of the BibTeX transfers, you can follow the alternative import instructions, which involve importing from an old, pre-encryption version of Mendeley Desktop. (These were our main instructions until we rolled out the online importer a couple weeks ago.)

Bourde

I agree this is some intricate problem with my account.
I think I will this method a try, probably is the only thing I can do and it seems easy enough and without any cons (?). Thanks again for all your time!