annotate attached PDFs

normadize
Hi,

Is there a way I could annotate the attached PDF of an entry? Even if I chose to "Open in External Viewer" (full Adobe Acrobat, with edit capabilities), I cannot save it as apparently Zotero keeps the PDF open / read-only.

Am I missing something trivial here?

Regards.

p.s. This is one feature I really like about Mendeley as it can do this from within the Mendeley client directly, but it does other things worse than Zotero, so I'd like to stick to Zotero.
  • adamsmith
    Zotero just passes the PDF on to the file system - it doesn't open them in read-only - windows likes to mess with read only tags, though - you'd need to check that in the file system. I annotate all my PDFs in an external viewer (pdfXchange).
    I actually think having dedicated software to annotate pdfs is preferable to using mediocre annotation software like the one included with Mendeley.
  • normadize
    > windows likes to mess with read only tags, though

    No, it doesn't. However, I apparently do ... it was my fault as the same pdf was open inside the browser by Zotero (maybe zotero could make FireFox release the file handle in that case when "open in external viewer" is selected so that the external viewer can edit and save it; took me a while to realise the error).

    > I actually think having dedicated software
    > to annotate pdfs is preferable to using
    > mediocre annotation software like the
    > one included with Mendeley.

    Maybe. Currently double-clicking on an entry opens the PDF inside the browser using the "zotero://" handler. Even though I have Adobe Acrobat installed and configured for PDF vieweing in FireFox, it doesn't allow editing. I don't think this is Zotero's fault becasue the same holds when opening PDFs from other websites inside the browser. Can the double-click in Zotero be configured to open the PDF in an external viewer rather than inside the browser?

    Regards.
  • adamsmith
    Can the double-click in Zotero be configured to open the PDF in an external viewer rather than inside the browser?
    yes. Set the lauchNonNativeFiles hidden preference to true:
    http://www.zotero.org/support/preferences/hidden_preferences#general_preferences
  • normadize
    edited June 16, 2012
    Brilliant!! Thanks very much.

    p.s. are you always this active on these forums? I'm impressed.
  • TTLP
    I have tried resetting the above hidden preferences for both Firebox and standalone - but neither works for me.

    I have also restarted both programs and still the I can only read pdfs as external to firebox and standalone.

    I have also in firefox changed the pdf setting to read within Firebox. But still the pdf only comes as external.

    My pdf program is Acrobat 11 from Adobe Creative Cloud.
  • adamsmith
    Could you say what behavior exactly you're expecting? And are other PDFs opening for you in Firefox?
  • TTLP
    I now realised that I have to change in Firefox's options - with Acrobat in Firefox rather than just Acrobat.

    But thought I might include the following link for others with similar issues:

    https://forums.zotero.org/discussion/29559/cannot-view-pdf-attachment-in-firefox/#Item_0
  • TTLP
    edited October 15, 2013
    I wrote too soon...

    Whilst synching, my Firefox crashed. So I restarted, and now clicking the file, nothing fires up. Only works if one right-click mouse to view externally via Acrobat.
  • adamsmith
    what exactly happens when you double-click a pdf (or select "view pdf")? Actually nothing at all? That would be odd.
  • TTLP
    In the browser navigation ribbon, it seems to be trying to process something, then it generates for example:

    "zotero://attachment/16/"

    Namely there is no change from original address.
  • adamsmith
    that looks right. And do you see an empty grey page as described in the thread you link to above? In that case, have you made sure you've installed the dev version of pdf.js?
  • TTLP
    edited October 15, 2013
    Funny I just discovered if I toggle to tag mode for Zotero in Firefox, it works...

    Is that what one needs? Or it is it related to dev version of pdf.js?

    Do I need to change anything?
  • adamsmith
    this shouldn't require tab mode. Have you installed the dev version of pdf.js? If so this should work in regular mode as well.
  • TTLP
    How do I know if I have the dev version?

    Sorry I have lost track.
  • adamsmith
    The dev version would be listed as PDF Viewer under tools -->add-ons --> extensions in Firefox. The regular version wouldn't appear there. (also, you'd have to have specifically installed the dev version)
  • TTLP
    No I don't have that in my Firefox's extensions.
  • adamsmith
    then follow the instructions in the
    https://forums.zotero.org/discussion/29559/cannot-view-pdf-attachment-in-firefox/#Item_0 thread to get the dev version of pdf.js. I believe this will be in regular Firefox with version 25, so this won't be necessary soon (and just to be clear, this is a Firefox bug, not a Zotero bug).
  • dstillman
    edited October 16, 2013
    I think this was fixed in Firefox 24. It seems to work fine for me without installing the dev extension.

    TTLP, make sure you're running Firefox 24.
  • TTLP
    Yes I have Firefox 24.

    I have added pdf viewer from Firefox add-ons. But then my Acrobat wouldnt work. Disenabling that would at least allow Acrobat to open in tab (provided I toggle the tab).

    I went through pretty much everything Adobe suggested I should do but still I cant read Acrobat pdf within Firefox (unless I use the toggle tab). I could live with this.

    But strange thing is I can no longer import RIS & Bibtex files - either from Firefox or Standalone.

    I have experimented with just 10k RIS and Bibtex files, the import bar goes 3 quarters of the way, then the tags in the background disappear, and the whole thing seem to freeze.

    I've tried to disable non-essential add-ons to Zotero, I still have the problems.

    Here are my Debug ID: D573407524 and Report ID: 141199654
  • adamsmith
    start a new thread on ris/bibtex import please.
  • TTLP
    Here is the new thread, but would also be curious if the debugging notes can still address the Acrobat pdf open in browser (without tag toggle) issue.

    https://forums.zotero.org/discussion/32526/importing-bibtex-ris-problems/
  • adamsmith
    can you open regular PDFs - not opened from Zotero - in acrobat for Firefox?
  • TTLP
    Yes I can open them in Firefox.
  • dstillman
    http://www.zotero.org/support/kb/file_handling_issues
  • TTLP
    edited October 17, 2013
    From the file handling link:

    Unexpected behavior (wrong action, gibberish ("%PDF..."), etc.) when opening files from Zotero


    Deleting mimeTypes.rdf from your profile directory and restarting Firefox or Zotero Standalone is generally what's needed to fix file handling issues. mimeTypes.rdf stores file handling associations and will be recreated automatically the next time you restart Firefox or Zotero Standalone.

    For Zotero for Firefox, Zotero itself doesn't tell Firefox how to handle a file—it simply checks if a file can be handled within Firefox (natively or via a plugin) and then either sends it to Firefox if so or otherwise launches it via the OS. Problems in mimeTypes.rdf can prevent this from working properly, however.


    ________________



    I've got Windows 7 - Do I go into Zotero or Firefox profile folder?

    It is a problem to have Firefox Zotero's Data folder to be linked to Zotero's profile standalone folder?

    In terms of changing files - I take it that's for Linux. How do you do it for Windows?

    Also suppose I have inadvertently installed the pdfjs developer's version, how could I uninstall it?
  • adamsmith

    I've got Windows 7 - Do I go into Zotero or Firefox profile folder?
    Firefox.
    It is a problem to have Firefox Zotero's Data folder to be linked to Zotero's profile standalone folder?
    if by "linked" you mean that one points to the other than no, that's not a problem, that's recommended.
    Also suppose I have inadvertently installed the pdfjs developer's version, how could I uninstall it?
    it would be listed under tools-->add-ons-->extensions, where you can uninstall it.
    n terms of changing files - I take it that's for Linux. How do you do it for Windows?
    that's typically not necessary, that's why it's not listed. Within Firefox, you can set default programs for different content under preferences -->applications
  • TTLP
    Think this helped:

    Deleting mimeTypes.rdf from your profile directory and restarting Firefox or Zotero Standalone is generally what's needed to fix file handling issues. mimeTypes.rdf stores file handling associations and will be recreated automatically the next time you restart Firefox or Zotero Standalone.


    Now can access acrobat from Zotero Firefox within browser!!! Thanks.

    Don't have the pdfjs in extension.
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