Export to Endnote EASY

studentofscience

Well those of you who need help, I found a solution; perhaps zotero folks can now emulate this method:

If you are in OSX, and want to move to endnote from zotero, download Mendeley, use it to import zotero, then export to a .ris, then have endnote import that.

Rintze

You're doing a great job getting yourself banned: https://www.zotero.org/support/forum_guidelines#etiquette

noksagt

The account's been open for a few years; I'm going to assume good faith on their part and chalk up the vitriol to frustration.

In the RIS it exports, Mendeley uses file URIs to point to PDFs:L1 - file:///tmp/Mendeley/file.pdfPRO: should be importable by most tools, including (apparently) EndNote.
CON: Not portable. Cannot be used easily to provide another researcher with your exported files.

Zotero uses relative paths:L1 - files/1497/file.pdfPRO: Portable. You can copy the Exported folder elsewhere, zip it up, email it to a colleague, whatever.
CON: Doesn't work with some tools. I thought this works on Endnote on Windows, but haven't tested in a while. It didn't import to Mendeley for me and apparently does not import to EndNote for Mac.

noksagt

It is hard to make everyone happy. Would it be too perverse to include a shell script/batch file in the exported directory to change these local links to full file URIs?

adamsmith

Personally, I wouldn't do this with a shell script -- I think running that is a fairly high hurdle for many people, especially on windows.
Options I see:

- We can add the absolute link in the export with files unchecked. We used to do this in bibtex -- are we still?

- We could implement an option in the RIS export to use absolute paths. Should be pretty quick&easy, but lots of options here.

- We could just add a kb article with search&replace instructions (i.e. L1 - files/ ---> L1 - file:///<path>/files/

Obviously pros and cons for each of these.

noksagt

W.R.T. Endnote XML, Mendeley copies the pdf to [ExportFileName].Data/PDF/file.pdf and exports: <pdf-urls>
<url>internal-pdf://file.pdf</url>
</pdf-urls>Zotero copies the pdf to PDF/1497/file.pdf (note the absence of the [ExportFileName].Data subdirectory) and exports <pdf-urls>
<url>internal-pdf://1497/test.pdf</url>
</pdf-urls>I'm less familiar with Endnote XML, but is this directory structure an issue?

EDIT: add emphasis to note that it is the file directory that I think is wrong, not necessarily the links int he Endnote XML file.

adamsmith

I don't have a working version of EN for testing anymore, so not sure about that one, but looking at the import code https://github.com/zotero/translators/blob/master/Endnote%20XML.js#L630 (that I'm certain worked), Endnote actually starts the relative link from inside the .Data folder, so what we do would seem to be correct.

I'd be curious if this works for EN import if someone can test.

noksagt

- We can add the absolute link in the export with files unchecked. We used to do this in bibtex -- are we still?

We are doing this still, yes. This solution would, at least, be consistent.

The particular setting checkbox is not particularly intuitive, though....

noksagt

Endnote actually starts the relative link from inside the .Data folder, so what we do would seem to be correct.

But we don't even make the .Data folder.

adamsmith

But we don't even make the .Data folder.

I may be missing something, but how could that be relevant? If Endnote expects internal-pdf:// to start inside Endnote.Data, why would the name of that folder matter (I really am just asking here).

As for what we do in bibtex -- I agree, this is not at all intuitive.

noksagt

If Endnote expects internal-pdf:// to start inside Endnote.Data, why would the name of that folder matter

Yes, Endnote expects the files in, e.g. Export.Data. But Zotero doesn't actually copy files to Export.Data.

I suspect this is correct:$ find Mendeley/
Mendeley/
Mendeley/ExportFromMendeley.Data
Mendeley/ExportFromMendeley.Data/PDF
Mendeley/ExportFromMendeley.Data/PDF/file.pdf
Mendeley/ExportFromMendeley.xmlI suspect what we do is incorrect due to the lack of a Zotero.Data directory:$ find Zotero/
Zotero/
Zotero/PDF
Zotero/PDF/1497
Zotero/PDF/1497/test.pdf
Zotero/Zotero.xml

adamsmith

Ah OK.
The thing is that Endnote by default saves Endnote.xml into Endnote.Data, not into its parent folder. Changing the behavior to Mendeley's is trivially easy, but I'd want to see that tested before.

I.e. the way I understand how this works in Endnote, Endnote.Data is what you have as "Mendeley" and "Zotero" respectively.

noksagt

Here's what the present version of EndNote on Windows exports (it seems to do what Mendeley does, but what we do not do):EndNote/
EndNote/EndNote Library.Data
EndNote/EndNote Library.Data/PDF
EndNote/EndNote Library.Data/PDF/file.pdf
EndNote/EndNote Library.xml

adamsmith

OK -- is that
EndNote/EndNote Library.Data/PDF/file.pdf
for the file or is that actually not in the PDF folder?

noksagt

Yes. It is in the PDF folder. Sorry for the typo.

studentofscience

My job is part software design and my fraustration is when someone says it cannot be done. That is counter intuitive to me. Nothing is not possible. Especially for Zotero which does not have a board of trustees and a CEO to pay millions, adding an export to endnote that actually works, seems trivial yet super critical.

According to yourself, you care about portability? well what if your fellow researchers have endnote?

simple few lines of code for zotero software people, .... after all in this community of academics, are we not producing tools to address problems?

noksagt

Since you've been involved in software design, then perhaps you'll also appreciate specifications that are poorly specified and that change.

The RIS spec is still completely silent on how to format locators to attachments.

And we can't even use EndNote as a reference implementation, because it is a moving target their too. Older versions of EndNote did not support true file:// URIs (as it seems to now). Instead, they used relative file locators (somewhat similar to what we use now).

We do our best to support Postel's robustness principle on import/export, but that can be very difficult with legacy formats like this. Supporting the current version of EndNote by default means losing functionality for other clients by default (possibly including older versions of EndNote)!

As adamsmith notes, we have an interest in and ideas to improve RIS export. But we need to balance the needs of many use cases, not just import into EndNote. Hopefully, you can appreciate that.

studentofscience

What you call balance, I call lack of wanting to be compatible.

For your sake here is a pseudocode:
1- If endote is install, get PDF dir
2- export pdf/notes to this dir
3- export a RIS (xml or whatever; just with correct syntax & link dir)

in endnote, one imports the RIS, the files are already there ... and you get the job done.

No need for mendeley either.

DWL-SDCA

I began using Niles EndNote in the very early 1990s (or was it the late 1980s) when it was exclusively a Mac program. Earlier I had used Reference Manager under CP/M. Even after EndNote was aquired by the ISI, there was little interest in the portability of data between the two. At first EndNote didn't recognize RIS tagged format at all. Even after several updates, EndNote couldn't perfectly import even basic RIS. That attitude and behavior has continued. The Zotero experts here have discussed the difficulties of exporting Zotero libraries in a format that is suitable for import into the most recent versions of EndNote and the greater difficulty with earlier EndNote versions.

Zotero has export capabilities in multiple standard formats. It is EndNote that lacks the ability to import these formats.

edit
Others of the many personal bibliography management programs can import Zotero library data because the developers of those programs made them compatible with standards.

adamsmith

I think following up on noksagt's and my conversation on how to improve export to Endnote is useful, in particular if anyone is willing to spend some time testing out possible solutions or has thoughts on preferences among the RIS options I describe.

I'd strongly suggest to ignore the rest of the conversation. It's going nowhere.

cb102

I was pointed to that thread out of this Issue
https://github.com/zotero/zotero/issues/1193#issuecomment-284178851

My case is when export external files is unchecked. This means no file folder is created beside the ris-file.
In that case it would be nice to have correct L2 (or L1) value pointing to the correct file inside the zotero profile folder.