Looking through the forum, most of the Bookends and DevonThink threads involve (1) an existing library in Bookends that the user (2) wants to automatically import to DevonThink.
I’m in somewhat the opposite situation. I have a very large database in DevonThink that I want to continue to manage entirely in DevonThink.
But Bookends claims to be able to track down citation information for existing PDFs, which would save me a fair amount of tedium.
So as a test, I right-clicked on an item in my DT database and chose the “Open With Bookends” option. Whereupon Bookends asked if I wanted to “attach” the file.
Okay, fine, but what does “attaching” the file actually do? That is, does a Bookends “attached” file happily stay right where I left it in DT? (Assuming I do not tell Bookends to “Move to Attachment Folder.”) Does Bookends make a copy of it, or just link to the original file? If the item moves in DT, will Bookends still be able to find it? (On the principle that DT Document Links survive document moves.)
(Yes, I know that this is not the Bookends forum, and I will be asking over there, but I found their documentation unhelpful on this point. Plus I figure you all are the experts on “how to avoid mangling your databases.”)
You could try the “Crossref Lookup” script that can be installed via DEVONthink’s script menu (see the “More Scripts…” menu entry). With an article title selected in a PDF, this script attempts to fetch some bibliographic metadata & the article’s formatted citation from CrossRef.
Alternatively, if your PDF contains annotations, you could also try my “DEVONthink Notes from PDF Annotations” script. This script takes a DOI from a PDF record (or extracts it from the PDF’s metadata or its first page) and fetches bibliographic metadata as well as optionally the article’s formatted citation & BibTeX data.
Both options would give you bibliographic metadata for a PDF in DEVONthink. However, this requires that your PDF article has a DOI (digital object identifier).
In the Bookends import dialog, make sure you keep the first two checkboxes (“Move/Copy To Attachment Folder” & “Rename: …”) unchecked and only check the third checkbox (“Attach to a new reference”). Then, Bookends will just link to the original file and won’t move it.
However, there’s one caveat: You should also make sure that a PDF with the same name doesn’t exist already in your Bookends Attachments folder. If there already exists a PDF file with the same name, Bookends will rename the imported PDF and append its own ID to the name. This would render the file inaccessible in DEVONthink.
Something to add to the previous reply – I haven’t used Zotero a lot, but it does seem to do a better job of getting metadata from internet sources than Bookends does. Whether that is worth investigating will depend on many things. Ryan Murphy wrote a post that goes into the question:
There is also the Highlights app, which will get some metadata from the internet.
I’m not sure how this might work together with DEVONthink, but it might be worth a look.
Attachments in BE are external documents, primarily PDFs, that are “linked” to a reference in a BE library database. You may attach to an existing reference or attach while creating a new reference.
When you attach an external document, you have two options. One is to rename the external document at the Finder level. Bookends does not care whether you decide to rename the file or not. It will keep track of its link to the file whether it is called “This report bla 800.pdf” or whether it is called “Jonesetal 2022.pdf”. In the latter case, you might recognize that you have instructed BE to name its attachments by authors and publication year, perhaps because you want to review the external file as such at the Finder level.
The second option when attaching is to Move or Copy the external file into a specific folder location that is managed by BE, the Attachments folder or a sub-folder inside this Attachments folder. This option is useful for example in cases where you may download a PDF from a Website into the Downloads folder and want to put the file instead in the designated BE Attachments folder (or a sub-folder).
With the above information in mind, when you “attach” a PDF that is
imported in a DT database: You should NOT rename the attachment file and you should NOT move/copy the attachment file. Doing so will play havoc with the internal storage mechanisms in DT.
indexed by the DT database: If you are indexing, you probably are set on the organization within the Finder and therefore are also not interested to move or copy the attachment file. You may however decide to rename the attachment file.
Finally, I suspect that, in all cases where you do not move or copy the file, BE will generate an ad hoc attachments folder location for each file that you attach. As their name implies, ad hoc attachment folders are created when necessary. They point to an attachment folder location that is not static / standard to BE, either as the root Attachments or as separate, pre-defined attachment folder for the BE library. I cannot speak to what will happen should you move files about in folder structures within DT and expect that BE still knows where the ad hoc attachments folder is located.
Thank you all, for the suggestions and detailed explanations. I still don’t know if Bookends will do what I want, but I’m confident I can experiment without trashing things in DT.
(And yes, I’m confident in my backup strategy, but I’d still prefer not to need it.)
With your experience and knowledge I surely don’t have to mention, but the thought occurred to me and I’ll say it anyway!. Maybe do you initial tests and setup on a cloned DEVONthink database, inspecting it for any “corruption” that might be caused.
I index the BE’s attachment folder (and subfolder) in Devonthink. To make the corresponding DT groups stand out (so I don’t accidentally mess with them), I copied the BE icon from the application (from Finder info) and changed the DT group icon to the BE icon. Makes it obvious what are BE related groups.