Available in preview: Zotero PDF reader and new note editor

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  • dstillman Zotero Team
    @danieltomasz: New threads are great — just haven't looked into yours yet.
  • danieltomasz
    edited March 6, 2021
    Another problem - earlier zotero beta provided Zotero connector for Safari, I installed both of them alongside and used the stable, but now with this new Beta is not possible to use the same database for stable and beta,

    >This Zotero database requires Zotero 5.0.97-beta.1+586a6f1dd or later.

    >Current version: 5.0.96.1
  • dstillman Zotero Team
    @danieltomasz: Correct. From the beta download page:
    note that beta versions occasionally update the database such that downgrading isn't possible without reverting to a backup copy of zotero.sqlite in the Zotero data directory or waiting for the next release version of Zotero
    This beta includes major changes and the database isn’t backwards-compatible.
  • danieltomasz
    edited March 6, 2021
    Yes, thanks, I noticed that and I could wait for the next stable release.

    I think that description of how to get a safari connector may be updated to state more explicitly about changes in the database, people who will be looking for it may not know about those changes https://www.zotero.org/support/kb/safari_compatibility
  • Kittys
    Hi, I apologise for my extra rookie question but I installed 5.0.97 beta but can't find the PDF reader? My Zotero desktop looks just as it did before.
    Thank you for your help! M Kittys
  • adamsmith
    @Kittys You need to enable the new layout it in the General tab of the Zotero preferences.
  • manonmr
    What good news! The fact that Zotero didn't have a PDF reader was the mean reason why I prefer Mendeley, even if Zotero is a the best reference manager for me.

    I can suggest you some improvements :)

    1) The bookmarks window is not very useful:
    - I prefer when we can see the hierarchy between all bookmarks
    - and when we can grow / reduce the bookmarks. It is written that it's possible with a double clic, but it doesn't work for me...

    2) Maybe a bigger color palette ?

    3) The PDFs are a bit long to open (compared to Mendeley).

    In any case, thank you for this upgrade ! (and sorry for my bad english...)
  • dstillman Zotero Team
    @manonmr:
    I prefer when we can see the hierarchy between all bookmarks
    The outline pane is currently missing styling, and that includes indentation. We'll fix that in an upcoming version.

    Editing bookmarks isn't currently supported. I'm not sure it will be, but we've noted your feature request.
  • bentle
    edited March 6, 2021
    First - the beta looks fantastic. A huge step forward!

    - Regarding editing bookmarks. That would be a major addition for me. I use bookmarks extensively when working with PDFs, and quite differently than annotations. I use bookmarks as a permanent map through papers that cuts across projects, whereas annotations are, for me, more likely to be project-related.
  • mlhodge
    This is SUCH a great development—it saves SO much time from uploading a PDF into my PDF editor, downloading the annotated PDF, attaching the annotated PDF to the parent item, and extracting the annotations!

    One question: when searching within the PDF reader for a bit of text, the search terms aren't highlighted even when "Highlight all" is selected, making it very difficult to locate the desired text on the page. Not sure whether it's just me having this issue.
  • adamsmith
    @mlhodge yes, there's already an open ticket for that https://github.com/zotero/zotero/issues/1982
  • safonso
    edited March 7, 2021
    This is a great improvement! Thanks!

    Some suggestions on the pdf reader. Probably regarding pdf.js viewer features. Most surely already in your pipeline or unfeasible.

    1. Allow us to navigate to the next or the previous page using scrollwheel events over the page number text box, as in other pdf readers (on scrollwheel click down, one next page event). It helps navigating a document *much* faster.

    2. Add next and previous "view" buttons. This would be a great feature and is found in other pdf readers. Say you are in a place in the document and use a hyperlink to a figure appendix many pages below the current one. The back button, similar to the browser's one, takes you to the previous view. It would also work for scrolling with the wheel and page u/d keypresses, discarding those intermediate ones in a rapid succession of events. The best implementation that I know of this is that of the PDF-Xchange Viewer/Editor. It stores internally a list of x, y and zoom coords of all the views.

    3. When closing a PDF, the UI in Zotero should switch to the library - not to the next PDF opened.

    4. Internal PDF hyperlinks don't seem to work.

    5. Add ctrl+z support for PDF highlights.

    6. Add a feature to internet search selected pdf text.

    7. Drawing, arrows and other markup support - especially for systems with styluses. Killer feature.

    8. Middle click button on a PDF tab should close it, as does ctrl+w.

    Thanks again!!
  • bjohas
    edited March 8, 2021
    This is absolutely awesome!!

    The problem of course is that once you put it out there, people are going to come up with a bunch of suggestions and requests :) So, let me contribute! In order of priority: I would love

    (1) Availability of the feature in group libraries. We practically only use group libraries in our research, and it would be great to have this.

    (2) Keyboard shortcuts. It would be amazing to have keyboard shortcuts, e.g. for hiding panels as well as for selecting the annotation tools and colours.

    (Rationale: Here's a thing that most PDF annotation apps do: The 'axis of tools [highlight/note]' is 'orthogonal' to the 'axis of colour': I.e., there's a tool choice, and a colour choice. Now, in Okular, you can set up any number of tools, and e.g. have a separate tool for "highlight in yellow" vs. "highlight in red" (bound to separate shortcuts). Sure, most applications don't have that, but for Okular I have three colours set up, and I find that really really helpful. It's not a thing that people realise is useful, because most PDF annotation apps don't have it. Now, If there was a keyboard shortcut for selecting a specific colour and a specific tool, that would be just as good as this one. Btw. I love the way you can easily change colours on the note - that is super cool, and goes some way towards it, but having different tools in different colours would make it easier...)

    (3)/(4) moved to here https://forums.zotero.org/discussion/88066/pdf-editor-beta-some-notes-on-notes

    (5) Let users customise colours and colour names. (Why colour names? Select intuitive names/colourblindness...)

    (6) The new notes editor is nice - I would really like a preference for setting the overall text size of the notes, to have a larger font-size (for those wearing glasses). This may of course be possible already. (Possible already.)

    Well, those are just a few very simple changes, I'm sure :) Only joking!

    This is an amazing development - very good!

    (Is there a list of other things coming with Zotero 6?)

  • bjohas
    edited March 8, 2021
    Another two considerations:

    (7) One issue with ZotFile has been indicating the correct 'logical page number'. Often the PDF's logical and physical page numbers don't correspond. It would be great if the 'logical' page number could be entered. (I'm aware that PDFs have got the ability to set the logical page number separately from the physical one, but that's not always done by the PDF producers.)

    (8) Sometimes you also need to extract pages - e.g. where the article is part of proceedings, and you were only able to download proceedings. There's of course ways to do that, but would be amazing if it was part of the workflow for the new editor. (This could just mean marking pages as 'deleted' so that they don't show, even if they weren't actually deleted from the PDF.)

    (One can also see how 7 and 8 could work together.)

    Edit:

    (9) Would it be good to have a text-select tool for copy/paste into the sidebar to complete metadata? Moved to https://forums.zotero.org/discussion/88066/pdf-editor-beta-some-notes-on-notes

    (10) Where are the annotations kept?

    how do you export the PDF file with annotations? -> Answer: Use Save-As.

    (11) Keyboard shortcuts would also be good in the new note editor. ctrl-b/i/u works, but it would be good to have some kinda shortcuts for headings (ctrl-alt-0/1/2/3 as in Word/GDocs, or similar). Moved to https://forums.zotero.org/discussion/88066/pdf-editor-beta-some-notes-on-notes

    Also, I would still really like to be able to highlight text in colour, as the old editor permitted. This is planned.

    Björn
  • eporte
    Thank you very much for this great step towards multiple annotation. Thanks to the "drag and drop" of text excerpts into the notes, we will be able to make different notes from the same text very easily. This is excellent for reproducible research.

    Would it be possible to eventually have export options to contemporary scientific writing text formats (markdown, org-mode)?
  • sicahjes
    @dstillman - thanks for the clarification.
    The Notes pane exists for the note editor — that's the point of it, not the notes list. The note editor is where you take general notes on a PDF and where you collect your annotations and start writing around them.
    Ah, I was adding notes in the PDF. This would be useful for overall notes. Although personally, I would still prefer to not have all the notes ever made in this pane when I am focusing on a particular article. My feedback would be perhaps this could be seperate.
    Those aren't "ZotFile annotations" — those are just annotations that you saved to the file in whatever PDF reader you were using before, and now you're viewing the PDF in Zotero.
    I meant that they are the annotations from when I was using the zofile system. The point being that they are locked, and I cannot make any changes/updates to them.
  • bjohas
    @Jes.Mullins - It seems that existing annotations in the PDF file (such as existing highlights) cannot be edited in the new editor. So they appear as a 'locked annotation' (in the left pane). They can be extracted e.g. using the ZotFile system (as you did), but they cannot be edited in the new system it seems.
  • dstillman Zotero Team
    Although personally, I would still prefer to not have all the notes ever made in this pane when I am focusing on a particular article. My feedback would be perhaps this could be seperate.
    @Jes.Mullins: You wouldn't see the notes list except when you're trying to open a note, in which case this lets you choose between item notes and all notes depending on which you want to open — it wouldn't make sense to have to go somewhere else just to open a standalone note in the same editor. And it only shows the 7 most recent other notes by default, though you can search across all of them.

    To be clear, you can just close this pane if you're not using the note editor. It needn't be distracting while you're annotating the PDF, and if you're editing a note you're just in the note editor, not the list.

    See the other thread I linked to for more details on the notes list and note editor, and post there if you have further comments on that.
    They can be extracted e.g. using the ZotFile system (as you did), but they cannot be edited in the new system it seems.
    @bjohas: I discussed this in my initial response to Jes.Mullins. You can now extract them to a note with Zotero itself, but you can't edit them from within Zotero. (ZotFile, of course, never had anything to do with editing annotations, so there's no change there. You can still open all PDFs externally if you prefer, or you can open in an external reader via right-click → Show File if you want to selectively do so.)
  • dstillman Zotero Team
    @bjohas:
    (1) Availability of the feature in group libraries. We practically only use group libraries in our research, and it would be great to have this.
    Group libraries will certainly be supported — the new functionality is just disabled there for now to avoid causing problems for group members not trying the preview.
    (2) Keyboard shortcuts. It would be amazing to have keyboard shortcuts, e.g. for hiding panels as well as for selecting the annotation tools and colours.
    Yes, there'll be much better keyboard support in the PDF reader in later versions, both for accessibility and general usability.
    (It would also be nice if the annotations panel showed who made the annotation.)
    It will, in group libraries. It's not relevant in a user library.
    (7) One issue with ZotFile has been indicating the correct 'logical page number'. Often the PDF's logical and physical page numbers don't correspond. It would be great if the 'logical' page number could be entered.
    It can — click on the page number in the annotation sidebar. A future update will offer the ability to adjust all subsequent page labels by the same amount.
    (9) Would it be good to have a text-select tool for copy/paste into the sidebar to complete metadata?
    Not sure what you mean by that, but you can already copy text from the PDF into the item pane using the keyboard. A context menu with a Copy option will be added in a future version.
    (10) Where are the annotations kept / how do you export the PDF file with annotations?
    Discussed in the announcement.
    (11) Keyboard shortcuts would also be good in the new note editor. ctrl-b/i/u works, but it would be good to have some kinda shortcuts for headings (ctrl-alt-0/1/2/3 as in Word/GDocs, or similar).
    Additional keyboard shortcuts in the note editor are planned.
    Also, I would still really like to be able to highlight text in colour, as the old editor permitted.
    Yes, this will be restored.
  • eporte
    Hello,

    After a few hours of use, a small comment. It would seem useful to me to set the display of the panels by tab. Currently, if I select stacked display it affects the main tab of the library AND the PDF viewer.
    Is this intentional?
  • dstillman Zotero Team
    @eporte: Yes, it's intentional. The View settings in most programs tend to be global, and that's the case here as well. Standard vs. stacked in particular is assumed to be a function of your screen size and/or personal preference, not something you'd want to be different in different tabs.
  • eporte
    @dstillman : Ok, it make sense.
  • bjohas
    Hi @dstillman, thanks!!

    || (It would also be nice if the annotations panel showed who made the annotation.)
    | It will, in group libraries. It's not relevant in a user library.

    I was thinking that the panel would show either the person who made the annotation in the new Zotero PDF editor OR who made the annotation traditionally. So I might import a PDF with existing annotations into my personal library, where I'd want to see who has made the annotation. I.e., it would be good for the annotations panel to show the person in both cases.

    Thanks!!
  • bjohas
    Hi @dstillman,

    Just want to say again: Having the PDF viewer in Zotero, as an 'annotation centric' PDF viewer is amazing, and something I'd wanted for a long time.

    As I said above - having thought and tested it some more - I would love to see this in groups as soon as possible. It will really make our workflows better.

    Thanks again!
    Björn
  • mr.curiosity
    Hi @dstillman, I tried the PDF viewer and editor and it looks indeed nice. However, I would love to have the annotations/highlights also saved in the original PDF file. One thing caused me to leave Mendeley and other literature managers was that I found out all of my highlights were kept in the software, a kind of vendor lock-in effect that I really oppose to.
  • dstillman Zotero Team
    edited March 8, 2021
    @mr.curiosity: There's no even theoretical lock-in here. From the announcement post:
    Annotations are stored in the Zotero database, not in the PDF file, which allows for much more advanced functionality as well as fast syncing. The File menu contains a new option to export PDFs, which will convert any Zotero annotations into standard annotations in the exported file. (An upcoming version will let you omit annotations, but in the meantime you can drag files to your filesystem to copy just the file.) Similarly, when exporting metadata from your library, there's a new “Include Annotations” option under “Export Files”. We plan to support other ways to export annotations in future updates. Your annotations will never be locked in Zotero.
    There's no comparison with Mendeley. Zotero annotations can be batch-exported to files with standard embedded annotations from Day 1, both as standalone files and as part of metadata export. Zotero's database is and always will remain open and unencrypted. And Zotero is open-source software that runs on your own computer, with no login required. There's simply no way you would ever not be able to get your PDFs out of Zotero with standard embedded annotations.
  • mschwarze
    edited March 8, 2021
    I find it very useful that the new version makes it possible to view a newly added pdf while manually adding metadata to the parent item in the right pane. However, when copying text to a field, quotation marks are automatically added. This makes sense when adding text to a note but not in this context. Maybe it can be turned off here.
  • dstillman Zotero Team
    However, when copying text to a field, quotation marks are automatically added.
    Oh, that's a bug. We'll fix — thanks.
  • mschwarze
    Perfect, thanks!
  • eporte
    @dstillman : Could it be considered that these changes could open up the possibility for the ability to annotate PDFs on both the computer and an android phone/tablet? If so, how?

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