Standalone zotero could not read pdf file - Ubuntu - nothing helps

Anadyomene
I am trying to switch to Zotero from Papers (as I work here on a Ubuntu 14.04 comp, Bio linux) and of course I would like to avoid manually creating paper annotations.

I installed Standalone Zotero and the pdftools from within it.

I had a /usr/bin/pdf* installed, so I thought that might be the problem and I deleted them, but that was no help.

Whatever I do, I keep getting a message "zotero could not read the pdf file". On the other hand, on my mac this functions perfectly fine.

I really have no idea what I should try next? Is linux version of zotero looking for the pdfinfo at the wrong places?`How/where can I see that?

Can anybody help me with this? I have been trying to find a solution since 2 weeks, but no success :(

Thanks a lot :)
  • adamsmith
    Is "Zotero could not read the pdf file" actually the message you're getting or are you paraphrasing/translating that?
    Is that happening when you're using retrieve metadata? (In which case I assume it's "Zotero could not read text from pdf")

    You shouldn't have to use retrieve metadata when transferring your database. Export it from papers (e.g. as RIS), then import into Zotero.
  • Anadyomene
    Yes, I'm sorry, I was paraphrasing it, it was late in the day.

    I may have missed something, but I don't find a way to import the library together with pdfs ( I tried copying it and so on), but other then combining them manually with the items, I haven't been successful. And I have thousands of pdfs, so this is not really an option for me.

  • Anadyomene
    OK, so the problem was the location of my pdfs as described here https://forums.zotero.org/discussion/5311/importing-endnote-libaray-including-pdf-attachments

    So, I don't need to worry about that anymore :)

    However that still doesn't solve my first problem. Why can't Zotero on Linux read the text from my pdfs?
    Thanks :)
  • bwiernik
    That is usually an issue with the particular PDF file -- e.g., it may not have been OCRed, so it is just an image, the OCR may be low quality or incomplete.
  • Anadyomene
    No, it is all of them. And they are all OCRed, and the metadata retrieval works fine with ZOtero on Mac.
    So I really have no idea how to fix this...
  • adamsmith
    Could we get a debug ID for an attempt to re-index a PDF (click on the green, round arrow next the "Indexed: No" in the right-hand panel).
    https://www.zotero.org/support/debug_output
    Which location are you running Zotero from? (i.e. the filepath to which you extracted it)
  • Anadyomene
    Sorry for my silence, I was away.

    So, I wanted to have my data directory on a USB stick as I am switching between my laptop and desktop at work. Whereas my laptop (osx el capitan) had no problem with that, it seems that the ubuntu computer does.
    As my library is being imported from papers at the moment on my laptop, I just tried to open and import and retrieve metadata at the linux computer with the default data directory, and in this case everything worked.

    Thanks a lot for your help.
  • Anadyomene
    So I tried to switch again to my custom data folder (now that my whole library is imported from my laptop) and the indexing is not working (D1897880506)

    Zotero is running from /opt/Zotero_linux-x86_64//zotero.
  • dstillman
    It looks like there are '%' characters in the filename of the file you're trying to index. As far as I know that shouldn't cause problems on Linux, but I'd rename/relink that file (or use "Rename File from Parent Metadata") and then try the indexing again.
  • Anadyomene
    That might have been that particular case, but the error ist there regardless of the name of the file. I send one more, filename without any special characters.
    D1385486817
  • dstillman
    You can try running the command in the debug output manually and see if it gives you more info. This also might be due to security software on your system or a noexec flag on that volume.
  • adamsmith
    Yeah, I was thinking that. A noexec flag default on external harddrives would be a quite reasonably security policy -- I wasn't aware Ubuntu did that, but it'd make sense.
  • Anadyomene
    Huh, finally, you pointed me in the right direction.
    My usb stick was formatted as fat32, which was obviusly the reason. I reformatted it as exFAT, and now it works on both osx and ubuntu.
    Thanks for your comments and help!
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