Integration with Highlights

[martinjp]

Jon, could you tell us more about how version 12.5.6 integrates with the Highlights app? We can now open a PDF in Highlights, but can we then export the text that Highlights extracts and organizes back into Bookends? On the Highlights webpage, it's stated that Papers is currently the only reference manager with which Highlights is integrated. Might this change in the future?

This seems a promising step, and I've downloaded a trial version of Highlights to explore further.

Martin

[Jon]

They may not have released the upgrade that communicates with Bookends yet -- I'll contact them.

If you have imported PDF metadata into Highlights, it will be as underlined text. Click on it and you'll switch to Bookends and go to that reference in Bookends. If the reference does not exist, the online version will open in Bookends Browser, and you can go from there.

Jon
Sonny Software

[Jon]

They haven't released their update yet. It will be their version 1.3.1 when it appears on the Mac App Store.

Jon
Sonny Software

[martinjp]

And is there a way of exporting notes made in Highlights into the Bookends notes fields?

[Jon]

Any notes, annotations, etc. will be visible in the note stream, just like with any marked up PDF (Highlights uses PDFKit). If you want to import them into note cards you'd do it, again, just like with any PDF marked up with PDFKit.

Jon
Sonny Software

[martinjp]

Including images?

[Jon]

Notecards only hold text, no images. You could highlight text in, say, the figure legend. And then if you click the notecard holding that text you'd be taken instantly to the image in the PDF. Again, this is not specific for Highlights, it's how Bookends works with PDFs.

Jon
Sonny Software

[martinjp]

Jon, I'm using the trial version of Highlights, and feeling a bit lost. When I save the marked up pdf and return to Bookends, nothing is visible in either the Notes field or the Note Stream window, until I select Show Highlighted PDF Text as Notecards. At that point, the selections I've made in the PDF show up in the Note Stream, but not in the Notes window. However, they are locked; I can't make any changes (which I'd like to do because words are run together). Moreover, I can't yet figure out how to have Comments made in Highlights appear in the Bookends Notes.

Is this all expected behavior?

To be honest, Highlights - at least the Demo - seems still in beta. For example, if I close the file window and then switch to another application, Highlights Demo quits and needs to be launched again. However, I feel there is potential here for a usefully improved workflow.

Martin

[Jon]

Nothing you're describing about displaying annotations has anything to do with Highlights. Please see the user guide (Help menu), near the beginning, where how PDFs are displayed in Bookends, and the section (later on) about how annotations are displayed in the note stream. The Bookends notes field won't display annotations (or markup of any type -- that's reserved for the note stream.

As far as Highlights, as I wrote they haven't released an updated version yet that will switch to Bookends and display a reference with the same DOI. But all comments and suggestions for that app should go to the developer -- I have absolutely nothing to do with Highlights, except I cooperated with them to enable the feature I described earlier in this thread.

Jon
Sonny Software

[martinjp]

Yes, I've communicated my concerns about Highlights directly to the author.

So Bookends can create comments, notes, and tags in a pdf, and in addition Notecards as notes and Notecards as quotations. It can also create Notecards from highlighted text in the pdf; these will be locked.

Highlights can create comments, notes, tags, and highlights in a pdf, but only the latter will show up in Bookends as (locked) Notecards.

In terms of flexibility, Bookends wins hands down, and I can see no reason to incorporate Highlights into my workflow. The only reason I was considering an alternative is that sometimes the display of the pdf in Bookends becomes flakey (see attachment; note that only one line of the pdf is visible, at the bottom of the window). I think Jon has said that this is due to problems within TextKit. (I wonder, though, whether setting a fixed window width might help, since changing the width sometimes fixes the problem, and sometimes causes it.)

Martin

[Jon]

Bookends will create a *virtual* notecard from highlighted text in a PDF (it can be read by not edited because Bookends doesn't contain the data in its database, it's only highlighted text in the PDF -- you can go to that text by clicking on the notecard). But you CAN import that highlighted text into Bookends as a real, editable, notecard with the corresponding command in the Action popup menu.

As for the display, the problem is with PDFKit. But it only happens if the PDF is zoomed. in Bookends 12.5.6 we've added new features where choosing to display as "Actual Size" will restore the proper display, and this setting will be remembered between PDFs and even between launches (you can change it to Automatically Resize or another setting whenever you want).

Jon
Sonny Software

[martinjp]

Problem is that Actual Size is too small to read!

[Jon]

For me, too, but you do get the note stream, etc. There's a great way to temporarily enlarge your view -- in System Preferences -> Accessibility -> Zoom, check "Use scroll gesture with modifier keys to zoom:" ^ Control. You can zoom in and out of any portion of the screen instantly. I use this all the time, and it would let you read the PDF at actual size.

Note that I'm giving you workarounds for bugs in the OS APIs. The bugs are still there.

Jon
Sonny Software

[martinjp]

Yes, I use scroll to zoom too. The only disadvantage is a loss of resolution when zoomed in, whereas when a pdf is increased in size the text is redrawn with a larger font at the same resolution (so far as I can tell).

But that's an issue between me and Apple! Bookends still rocks.