Import from Bookends

Two questions about File-Import-References from Bookends:

(1) Is there any way to direct the import to a specific group (such as the currently selected group) rather than the default “Bookends” group?

(2) Is there a template I could use to change the format of the import? In particular, if the Bookends reference includes a URL to the citation, can that citation be depicted in DT3 as a clickable hyperlink?

  1. No.

  2. No. The content is provided by Bookends actually.

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Bookends has a pretty sophisticated formatting editor. For a manual bibliography export from Bookends it is possible to specify a specific Export format. Is this an option when you do it using the DT3 File-Import feature (presumably using Applescript in your code?)

DEVONthink uses currently the Summary format.

Thank you - that is very helpful - now I need to explore if there a way to specify a hyperlink in that format.

@cgrunenberg - The tip about the Summary format was very helpful.

The solution is to edit the Format so instead of z for the PubMed URL you replace it with

<<z><z>>

image

Then the active hyperlink works well in DT3 after import

Where did you find this solution?

It is in the fairly densely written (but extremely informative) Bookends User Guide:

As a solution which extends to other academic disciplines that go beyond the PubMed database, you can also extend the concept and easily import into DT3 active hyperlinks to the original paper using the DOI like this:

image

@cgrunenberg

Question - Do you use a regular Applescript for the Import References from Bookends feature in DT3 and then somehow compile that into the overall DT3 app? If so, could that be customizable somehow by users? Or even easier, could you just keep the code as it is now but share with us the Applescript that you used?

The reason I ask is that there are a variety of other metadata fields available in Bookends including 20 custom user fields; it would be really nice to be able to use those fields in Bookends and also import them into custom metadata in DT3. Even if you kept the code as it is, if we had the Applescript then we could create our own external script without having to re-invent the wheel for the part that you have already done well for the regular metadata.

It’s a mixture of Cocoa and AppleScript and can’t be customized.

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Thanks - turns out all of those fields can be included in the “Summary Format” if desired so they can be imported to Devonthink that way. And then if desired by smart rule it is possible to act on that data in whatever way is desired.

Hello, I am using the “Import from Bookends” feature regularly; but is there a way to delete in DT’s Bookends group the references that I have deleted in Bookends? They don’t seem to be removed when I use the import feature. I don’t want to re-import the whole library because I’ve been extensively labeling and organizing the Bookends references within DT, but I am ending up with duplicates that I don’t know how to find. Thank you.

DEVONthink and Bookends aren’t syncing with each other. It’s a unidirectional import so yes, you’d end up with duplicates if you ran the command more than once.

You can find duplicates in a database via the Duplicates smart group in the database.
However, you may want to enable Preferences > General > General > Stricter recognition of duplicates.

Thanks very much for the fast reply. I will definitely use that function re the duplicates-- I actually don’t find regular duplication from multiple imports, to be clear; I just have duplicates from my own ‘user error’.

The real issue is the orphaned references-- Would there be any way to edit the script to remove the references in DT that have been deleted in Bookends? Those won’t show up as duplicates, obviously.

It’s a great feature without this ability but over time I can imagine ending up with a lot of orphaned references, so just wondering what the potential is. Thank you.

You’re welcome.

The real issue is the orphaned references-- Would there be any way to edit the script to remove the references in DT that have been deleted in Bookends? Those won’t show up as duplicates, obviously.

This would require much more intimate connection with Bookends and potentially well-defined behavior, e.g., you have to delete in DEVONthink or something similar. Development would have to assess this request.

Thank you. If there was a way to be able to filter the references that are not ‘matched’ with Bookends in an import, that would be great too-- the ‘delete’ step (or any other step) can be up to the user, but I cannot tell on my end which references no longer ‘match’ to Bookends, and that’s really the core of what I’m looking for. Appreciate all the responses.

No problem.
So you are deleting items in Bookends and trying to balance the two apps’ contents?