Upgrade StorageZotFile - Advanced PDF management for Zotero
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Please note that while my office computer connects to the NAS drive via WebDAV, my home computer connects via the default protocol Apple uses for local networks. I believe this is SMB2 for a computer running Yosemite.
On both computers, I first tried running Disk Utility to inspect the hard drive and to fix permissions. This didn't seem to have any effect on the problem.
So from this empirical evidence I conclude that there was nothing wrong with the pdf files themselves, the drives, the file systems, or with the network connections. Somehow the interface between the operating system's file access subsystem and Zotero or Zotfile got screwed up.
This may be a hard problem to replicate, but careful inspection of the relevant code may be in order. When I searched for the error messages on the web, most discussions I found dealt with other software and pointed out that the code in question was not using the currently recommended methods to access files. Something similar may be going on here.
Another thought is that on both machines I have Zotero & Zotfile installed as both Standalone and Firefox extension. Maybe the settings on one are affecting the other, although I would think they'd be independent of each other.
Thankfully, if this method of fixing the problem continues to be effective in all cases, the problem is relatively easy to work around.
Is this issue known or has anything been done about it? I justed noticed the same behavior with some extracted annotations.
Same behavior meaning: The Zotero report shows the notes that have been extracted with ZotFile, but some of them are not formatted correctly, they are full of HTML-Tags. Technically they get wrapped up in "plaintext" <p>s I think. If i change something (e.g., press space and delete it again) inside the notes in the Zotero editor they get formatted correctly.
When I do this, the little zotero message box pops up in the right corner of my screen and has a little red 'x' next to the name of the pdf, to indicate that extraction failed, and I have no extracted annotations.
This is in zotero standalone, although my zotero library is in my firefox folder.
Any ideas on how I could fix this?
I found the solution though: I have to force Okular to overwrite the original pdf by clicking 'Save As' and then saving it with the same name. Otherwise I guess it saves the annotation information in some other file somewhere.
When I do that, the notes show up in firefox, but the highlights do not. However, the pdf extraction works, including extracting the highlighted text.
Annoying, but at least it works now.
This may be a question already answered, but on skim through couldn't see it referenced.
Is there a way of getting the extracted PDF highlights text file to automatically import or even better automatically sync into Evernote (or possibly devonthink / tinderbox?).
That way a the highlights / quotes database could be searched / interacted with.
Any similar sync processes?
is there a way to modify the way of extracting annotations in Zotfile. Unfortunately, it extracts the notes and highlights in the order of their creation. But I'd rather have them with respect to their appearance. I.e. sometimes I read a later chapter before an earlier one, but the annotations appear in that order instead of by pages. Do I have to change something in the extract.js?
Thanks,
Michael
So case closed. Thank you!
I am under linux with ZotDile 4.1.6, and using zotero standalone (4.0.27.6) and I am modifying zotfile.pdfExtraction.openPdfLinux via about:config.
What am I doing wrong?
@anthonybrucewilson
I initially had the same problem with "Show File" not working on Windows 10. However, the problem was solved when I removed the leading backslash from the "Use subfolder defined by" option in ZotFile (ie. I used "%w\%y" instead of "\%w\%y"). Hopefully this is the cause of your issue too!
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The attached file could not be found.
It may have been moved or deleted outside of Zotero
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If I select the file in the new zotfile directly it then works.
Is there anyway to update all the file links to the moved folder?
Windows 10, Zotfile 4.16
You can use the Zutilo add-on to batch-change link paths. That should help you here.
Zotfile is truly a dream come true for anyone wanting to annotate PDFs using a tablet, and the annotation extraction is a gift. I am wondering whether it might be possible to extract the logical page number. Currently, it simply extracts the absolute page number of the file. But many PDFs also have logical page numbering (for example, for an article that runs from page 33-56, the first absolute page is page 33).
My apologies if this has already been covered.
Details here:
https://forums.zotero.org/discussion/50545/
patches, I'm assuming, welcome.
Here is what I did.
1. Scanned a chapter from a book with 600 dpi.
2. Used Adobe Acrobat XI Pro to OCR the file with the following settings:
- a. Primary OCR Language: English (USA)
- b. PDF Output Style: ClearScan
- c. Downsample To: 300 dpi
3. I then highlighted and annotated the text Adobe Acrobat XI Pro.
4. When finished, I imported the file into Zotero.
5. I then selected “Manage Attachments >> Extract Annotations”
6. I get a notice “Zotfile: Extracting Annotations…” but no note with extractions is produced.
Information on my system:
• Windows 7 Professional
• Zotfile 4.1.6
• Zotero 4.0.28.3
• Firefox 40.0.3
I can copy text from the PDF. It works fine when I do it manually but it would be a lot of work to extract all my annotations. I have tinkered with Firefox about:config in the past but am not aware of any changes that might temper with Zotfile’s operation.
Please help me troubleshoot this problem. Thanks.
UPDATE: I have been able to extract the annotation with Zotfile on another PC. I therefore think that it might have to do with my about:config configurations. It would be very cumbersome to change everything back to its original state. Do you have any ideas which Firefox configurations have to be in which state for Zotfile extractions to work?