How do I work with Zotfile and Zotero to extract Skim annotations? It won't work for me...
As the title:
I'm a newbie to Zotero, but I've added a few webpages (using the Zotero browser plugin) as well as a few downloaded PDFs to my Zotero library. I use Skim to highlight some passages, then return to Zotero, right click and choose "Manage Attachments->Extract Annotations". Zotero puts up a little dialog saying Zotfile is doing that, then after a moment the dialog disappears. And that's it. Nothing has been extracted. I am using a Mac, 10.12.4, Zotero 5.0.30, Zotfile 5.0.6, Skim 1.4.30 (104).
Another unrelated question: if I add a PDF directly to the Zotero library, I am told Zotfile can't extract annotations because it's a top level item -- so I right-click and do "create parent item". Why is this necessary? Am I doing the right thing? (Even when I do this, I still can't extract annotations, as per above)
I'm a newbie to Zotero, but I've added a few webpages (using the Zotero browser plugin) as well as a few downloaded PDFs to my Zotero library. I use Skim to highlight some passages, then return to Zotero, right click and choose "Manage Attachments->Extract Annotations". Zotero puts up a little dialog saying Zotfile is doing that, then after a moment the dialog disappears. And that's it. Nothing has been extracted. I am using a Mac, 10.12.4, Zotero 5.0.30, Zotfile 5.0.6, Skim 1.4.30 (104).
Another unrelated question: if I add a PDF directly to the Zotero library, I am told Zotfile can't extract annotations because it's a top level item -- so I right-click and do "create parent item". Why is this necessary? Am I doing the right thing? (Even when I do this, I still can't extract annotations, as per above)
See here for more details on getting items into your Zotero library:
http://zotero.org/support/getting_stuff_into_your_library
On an unrelated note: is there a way to export a citation from the Zotfile link? That is, if I want to export a full citation including the page number of annotation (which I realize may not be accurate, since it's counting from the beginning of the document), is there an easy way to do this similar to the "quick copy" of the citation without the page number (in the main Zotero window)?
Qiqqa is closed source and uses its own system to manage notes (it also hasn't seen a lot of uptake, so I'd be very worried about sustainability)
There are several options how you can execute the script. One is by using Alfred Workflows (https://www.alfredapp.com/) as a wrapper: You would select one or more PDFs you want to embed or unembed Skim notes and hit the Alfred shortcut. The script will then process the PDFs. You can embed and unembed the Annotations as you like. I haven't seen any errors during the conversion in my tests.
A second approach would be to wrap the script in an Automator workflow and then attaching the workflow to a folder as a folder action. This would automatically run the script whenever a file is added or changed within the folder.
The script also has a method for batch processing pdf files in a folder with nested subfolders. The performance is quite good: I have used it to embed Skim notes of 568 pdfs scattered in a folder with various subfolders. It took 5 minutes in total.
You can have a look at the script at https://github.com/alexandergogl/SkimPDF