Zotfile no option to extract annotations

  • Thank you for your input, @tre2017. If I understand your workaround correctly, it will not work for me, unfortunately. That's because I need a link after every annotation/highlight to keep track of them after splitting them up throughout my thesis.

    So in the end, I decided to switch back to Zotero 5.0 for the time being. This has led to a further problem, however: Clicking on the zotero://open-pdf/ links is still opening the beta version of Zotero. Is there a way to change which version the links refer to? Thank you all for your help!
  • Just to note here, we've added note templates for annotations, which should replace some of the hidden options in ZotFile for customizing the format of annotations added to notes.
  • edited March 8, 2022
    I absolutely love the way the new editor works, and we'll use this for light-weight literature reviews. Esp. the collab nature is amazing.

    We've also wrapped our extracted notes using zotfile. Currently, the exported note has this:

    TEXT ([Author, year, p. 1](zotero://select/groups/123/items/AAA)) ([pdf](zotero://open-pdf/groups/123/items/BBB?page=1&annotation=CCC)) COMMENT

    That's really very cool - we do use the item keys for all sorts of things, and this is really great.

    We would love to:

    (1) Get out all information we put in, i.e., we would love to have the color and tags for the annotation.

    (2) We love to have the user name (either created or edited, whatever you have), potentially the date/time as well (created or edited, whatever you have).

    (3) Both the physical and logical page number would be good.

    We're not concerned about how this is stored in the note, but some kind of machine-readable way would be good. Also, it would be really cool if this could work not only when exporting, but if it was possible to copy/paste, either from within the note, or even from within the left panel of the reader.

    For example, it would be amazing to have a right-click option 'copy as html with data' or 'copy as json' on a note in the left panel of the reader, which places the html/json on the clipboard. We can then easily post-process this before pasting it into a document.

    We of course appreciate that not all users want this, but if there was an option to do this, we'd appreciate it.

    EDIT. Ah - seems that the formatting is possible already with https://www.zotero.org/support/note_templates. So the request would be template-based export straight from the right panel in the reader (and/or from the exported note).
  • I just discoverd this and panicked, but I have now found the zotero extraction menu item. However the notes extrated do not seem to have a link to the highlight or notation in the pdf file.
    Is there a way to get that back ? Alternatively can I downgrade to the zotero and zotfile I had a monthe ago?
  • edited March 20, 2022
    However the notes extrated do not seem to have a link to the highlight or notation in the pdf file.
    @Mprehn: Click on the highlight and click "Show on Page" from the popup. And those are turned into zotero://open-pdf links on Markdown export.
  • sorry - this is not clear to me.
    In zotero I open the annotation, and with each there is a citation, If I move the mouse over it, it highlighs. clicking on this highlight gives me the options: 'show item' 'edit citation' and 'hide citation' ..
    I have been playing with it and I DID see the 'show on page' that linked to the highlight, but I dont understand when that link will appear and when it does not,
    I am not using Zotero to view and comment PDFs - will that make a difference ?
  • - Now I see it. when I left-click on the tect of the highlight a popup appears with the 'show on page option' - when the highlighted text is long, it can be far away and I did not see it..
  • edited March 21, 2022
    Edit update: NEVERMIND, I figured out how to revert

    @droitalaville how did you revert to Zotero 5.0? I have been trying all morning to remove Zotero 6.0 to regain the functionality of my workflow for extracting annotations > Zotfile/MDnotes > Obsidian. I am dying without the block ID splits and my custom configs for my note extractions in Obsidian. I am in the middle of my comprehensive exam so maybe my panic is missing the obvious reversion ? :(.

    I know how to avoid the Zotero editor for pdf editing but can't seem to avoid the destruction of my plugins by Zotero 6.0.

  • edited March 24, 2022
    Ok so I looked into this, I am not familiar with HTML coding so perhaps stupid to try out. I understand that the variables for extracting notes can be configured. Does this mean that I click and modify one of the existing templates and add some strings of code to it from the example. How would that code look if I add it to an existing template?
    Something like:

    {{citation}} {{comment}}

    {{if tag}} for the standardtemplate extensions.zotero.annotations.noteTemplates.note. (It seems like the code examples disappear in the post).
    I also notice that the "Add note from annotations" function merges all the different citations into one. I presume that this can also be modified with the templates as well as getting the item reference with the note in Libre office.
    I fully understand that you don't want to teach me HTML and maybe it is better for me to just wait for the update.
  • Hi,
    I've recently installed Zotero on a new laptop and can't find an extract annotation functionality. I also can't see a built-in PDF reader.
  • edited March 25, 2022
    The extracted notes used to have links back to the location in the PDF - very convenient to rapidly jump to the location in the document and see the broader context. I can't get that to work anymore. Am I missing something or has this not yet been implemented? If not, is there a hack that can be implemented in the advanced options to make this work?

    ... OK, I see this problem has been solved: "To view the annotation in context, click the annotation [must be the actual text] and click “Show on Page” in the popup that appears." from: https://www.zotero.org/support/pdf_reader
  • @grovesteyn yes, the notes include backlinks to both the item in the library and the PDF page.

    If you give more details, we could help you. If you are exporting to Obsidian, you will need to disable the Setup > Editor > "Auto convert HTML" option in Obsidian setup
  • edited March 25, 2022
    I have just discovered that zotfile no longer works and Zotero has a new in-house feature for extracting annotations. However Zotfile had one cool thing it did when it extracted annotations, which is that it automatically deleted the soft line breaks (i.e., not between paragraphs but at the end of each line) that were in the pdf, while Zotero seems to be keeping them, which is annoying. Is there a way to fix this problem within Zotero?

    There also seems to be a bug with some of the extracted text where it gives me repeated letters, e.g.: “LLaa ccaarrrriièèrree ddeess iinnssttiittuutteeuurrss”.

    Please let me know if I need to start a new thread for these questions. Thanks.
  • As a follow-up: I just tried the feature "Show Annotation Colors" and the text in color did have those soft line breaks removed. So I'm wondering why that can't be done with the extractions that don't show the colors. Thanks.
  • @isabelleheadrick: See Doubled Highlights. The text without the colors was put into comments by an external PDF reader. Zotero strips newlines properly in the highlight text it extracts. As noted there, we're going to see if we can ignore doubled text automatically (which I believe ZotFile did) in a future version, but the real fix would be to turn this off in your external PDF reader.
    There also seems to be a bug with some of the extracted text where it gives me repeated letters, e.g.: “LLaa ccaarrrriièèrree ddeess iinnssttiittuutteeuurrss”.
    If you're seeing this in the highlight text (which Zotero creates) rather than the comment text (which it doesn't), let us know in a new thread and provide a link to the PDF in question.
  • The text did seem to work better once highlighted, thanks.
  • @isabelleheadrick: No, that's not the issue — see the linked page, which explains this. The doubled text is from your external PDF reader, not from Zotero.
  • So, is there any timeline that Zotfile's full extraction functions will be implemented, not just those so-called main functions as claimed here?
  • @astroHao: No idea what you're referring to here. This thread is over two months old, from before the release of Zotero 6 and before we added note templates, which was the main bit of advanced ZotFile functionality that wasn't initially implemented. Zotero 6 now supports the vast majority of both basic and advanced ZotFile functionality, while allowing for far more advanced functionality and customizability by both Zotero and by plugins, now and going forward.

    If there's a particular workflow that you feel isn't currently supported, start a new thread and say more.

    Closing this now.
This discussion has been closed.