ZotFile - Advanced PDF management for Zotero

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  • I ran in the same problem as reported by @mtd91429 Zotfile will report an error on not being able to rename a file when added to a publication entry (via drag and drop in my case) and the same when trying to change an existing.

    I found the reason though. The error only occurred when the publication entry didn't have an author field filled in. I guess because it wants to build the file name out of the author name and does not know what to do when that one is empty. What it should do is simply ignore the author or display a warning about this.
    I'm experiencing the same behavior. What's strange is that this has only been happening recently—for as long as I've used zotfile to rename files, it's always ignored empty fields and just started the file name with the first available information. Not sure what to make of this, but for now I'll just have to make sure every entry has an author before I try to rename.
  • edited February 18, 2016
    Thanks for reporting (and particularly figuring out how to reproduce it). Just fixed it. Already on github and version 4.2.1 is under review. I hope it's approved within the next 48 hours.

    Edit: Yes, it was introduced this one of the recent additions.
  • @Joscha Oh so there is a github issue tracker. Good to know for the future ;-) or do you still prefer "bug reports" in this long thread as pointed out by the home page?
  • @dietmarw: Github is good for concrete bug reports (usually reproducible). Any support requests should go here though. And yes, unfortunately this thread is a mess... :(
    But I am not going to maintain a separate forum and usually don't look at other threads in the zotero forum.
  • @Joscha: Understood.
  • Sorry for my English. I'm going to try to make my question.
    I use zotefile and I saved pdf in a Dropbox carpet. The problem is, when I try to open the pdf with zotpad, I can't. Zotpad send to me an error message. I use zotpad to manage pdf in my iPad. Can I do anything to fix it?
  • Beatriz, you'll want to contact ZotPad support for that.
  • When I try to rename an attached PDF from an online group, and move it to a specific local folder, zotfile does not move the file properly. It looks like it’s renaming the local file just fine (placed in ~\AppData\Roaming\Zotero\Zotero\Profiles\skt3imfr.default\zotero\storage\9NVA9I72) but it doesn’t move/copy the file to the folder where I wanted.
    When I tried to rename an attachment PDF in my personal library, it seemed to be working just fine, and moved the file as expected

    I get the following error in the log:

    [JavaScript Error: "1457369944974 Toolkit.Telemetry ERROR TelemetryStorage::loadAbortedSessionPing - error removing ping: PingReadError JS Stack trace: PingReadError@TelemetryStorage.jsm:80:15 < TelemetryStorageImpl.loadPingFile<@TelemetryStorage.jsm:1440:13" {file: "resource://gre/modules/Log.jsm" line: 749}]

    [JavaScript Error: "no element found" {file: "https://khauns13:********@api.zotero.org/groups/494424/items/SM94NBD8/file?auth=1&iskey=1&version=1&info=1" line: 1}]

    version => 4.0.28.7, platform => Win32, oscpu => Windows NT 10.0; WOW64, locale => en-US, appName => Zotero, appVersion => 4.0.28.7

    Is there anything I can do to fix this, or is it a bug?
  • since groups don't allow links to Files in Zotero, ZotFile can't move files in groups (if that's not clear, try doing what you'd like to do manually and you'll see it's not possible).
  • I'm also suddenly having problems renaming attachments w/custom folder after upgrading to 4.2.2 (Zotero Standalone Mac 4.0.29.2):

    1) drag PDF to Zotero
    2) retrieve metadata - Zotero copies to new folder under ~/zotero/storage
    3) Manage attachments > Rename attachment
    4) Zotfile throws "unknown error!" plus "The source folder is not valid".
    5) Clicking to copy "unknown error!" to clipboard gives {} as for mtd91429 and denlinkd
    6) Curiously, it appears Zotfile *has* successfully renamed and moved the file - as per my rules, it is now renamed, in my custom folder in an author-last-name subfolder. However this isn't recognised by Zotero and when I try to open it a "File Not Found" error appears.
    7) Manually fixing the link works, but the PDF filename is not updated from within Zotero itself.

    Zotero also knows about the location of the custom folder; this setup has been working fine for some years until the update(s) (though I can't work out if it was the Zotero update that broke this, or the Zotfile update).
  • What are your exact settings? Renaming rules etc? Can you try whether 4.2.1 works? You can get it here: https://addons.mozilla.org/en-us/firefox/addon/zotfile/versions/
    Do you have some programming experience? Just asking because I would let you run some code to pin down the problem.
  • 4.2.1 works.

    General Settings:

    Location of files: custom location: /path/to/my/Articles
    Use subfolder defined by /%a

    Renaming Rules

    Format for all types except patents: {%a} {%y} {%t}
    Format for Patents: {%a_}{%y_}{%t}
    [odd, actually, as what files get renamed to is author_year_title.pdf, which is what I want]

    Additional settings:
    Delimiter between multiple authors: &
    Change to lower case
    Replace blanks
    Maximum length of title: 80
    Maximum number of authors: 1
    Number of authors to display when authors are omitted: 1

    [things not listed are not checked]

    Happy to run some debugging code if that's useful.
  • edited March 14, 2016
    Hello,

    I've just discovered ZotFile. It's just what i'm looking for. Thanks for all !!

    I've one question (may be already asked, but did not find a topic by searching).

    I want to translocate a pdf by renaming it from one sourcefolder to a targetfolder. If in the targetfolder there's already a pdf with that name, Zotfile still copies the file by adding a suffixnumber at the filename.
    Is it possible to let Zotfile not to take action? This is to avoid duplicates in the target map (in my case: a big shared institutionfolder with 26 subfolders).
  • This to confirm that installing the older version of Zotfile (4.2.1) seems to fix the problem. I have been using Zotfile for a while now without any problems until it stopped working when I tried to back up my Library.
    Here are some of my Zotfile preferences:

    General Settings:
    Location of Files: Custom location: C:\Users\myname\Dropbox\zotero PDFs
    Location of Files on Tablet: C:\Users\myname\Dropbox\Tablet
    Renaming Rules:

    Format for all types except patents: {%a_}{%y_}{%t}
    Format for Patents: {%a_}{%y_}{%t}

    Additional Settings:

    Delimiter between multiple authors: _
    Truncate title after . or : or ?
    Maximum length of title: 80
    Maximum number of authors: 2
    Number of authors to display when authors are omitted: 1
    Add suffix when authors are omitted: et al
  • loubnael, do you also get the "The source folder is not valid" message?

    What are both of your source folder settings?

    Can someone why has this problem try this:

    - Use Zotero for Firefox
    - Check whether the same error occurs with the "The source folder is not valid" warning/error
    - Allow Scratchpad to run in the browser context (see https://developer.mozilla.org/en-US/docs/Tools/Scratchpad under "Running Scratchpad in the browser context")
    - Open Scratchpad under Tools -> Web Developer -> Scratchpad
    - Change Environment to Browser (Environment -> Browser)
    - Run this code (cmd + L to insert results as comment)

    Zotero.ZotFile.getSourceDir(true)

    Are you getting the same error message?
  • @Joscha

    Before the problem was fixed, the message “The source folder is not valid” kept appearing whenever I tried to rename my attachments manually.

    I was trying to download Zotero for Firefox (since I have only been using the standalone for quite some time now) and I was trying to find my way around using Scratchpad when the strangest thing happened: all my Firefox add-ons/extensions suddenly got deleted and now they take for ever to install. I don’t know what exactly happened and I apologize for the inconvenience.
  • What do you mean with "Before the problem was fixed"? In which version? What do you mean with "rename my attachments manually"? What is your source folder?
  • I think I fixed it. Can you try the current version on github?
  • 1. Before the problem was fixed: that is before I replaced the last version of Zotfile with an older one(4.2.1); the replacement fixed the error and Zotfile is working once again.
    2. Rename my attachments manually: when Zotfile wouldn’t rename my uploaded documents automatically, I tried to use one of Zotfile’s listed features to rename them myself: Right Click> Manage Attachments> Rename Attachments.
    3. I am using a custom location (Dropbox) to store my files: C:\Users\myname\Dropbox\zotero PDFs. (Not sure if this answers your question though)
  • Any chance you can try the current version on github?
  • edited March 14, 2016
    @joscha

    If you mean the released version(4.2.2) provided in the following link: https://addons.mozilla.org/en-US/firefox/addon/zotfile/, I have tried it and it didn’t work (the error still appears). But if you mean the development version, I downloaded the zip file, extracted it, but I can’t seem to understand the third step: “recreate .zip file containing all the files at the top level, i.e., install.rdf and the chrome directory need to be at the root of the .zip file and not under Zotfile.”
  • The development version on github. Here is the xpi: http://www.columbia.edu/~jpl2136/zotfile-4.2.3-fx.xpi
  • looks like it's fixed in 4.2.3. thanks!
  • The message about the source folder not being valid doesn't appear anymore, but Zotfile (4.2.3) doesn’t seem to work for me. When I uploaded a PDF as an attachment, Zotfile didn’t rename it and two messages appeared (they did appear before as well) stating that an “unknown error” has occurred and that “attachments skipped because they are top-level items, snapshots or the file does not exist.”
  • loubnael, you will have to be more specific. First, the problem was the same in 4.2.2 and 4.2.1? Or only since 4.2.2? Second, what are the exact steps to reproduce this? What does "uploaded a PDF as an attachment" mean? Drag-and-drop? etc
    Thanks!
  • Hello,
    Sorry for reposting my question. Is it possible to give me some answer? Even a short one is ok for me. Thanks a lot !

    "Hello,

    I've just discovered ZotFile. It's just what i'm looking for. Thanks for all !!

    I've one question (may be already asked, but did not find a topic by searching).

    I want to rename and translocate a pdf it with zotfile from one sourcefolder to a targetfolder. If in the targetfolder there's already a pdf with that name, Zotfile still copies the file by adding a suffixnumber at the filename.
    Is it possible to let Zotfile not to take action? This is to avoid duplicates in the target map (in my case: a big shared institutionfolder with 26 subfolders)."
  • edited March 15, 2016
    @Joscha

    1. Uploading a PDF :
    a. Right Click
    b. Add attachment
    c. Attach Stored Copy of File

    2. Zotfile 4.2.1 is working just fine.

    3. Zotfile 4.2.2 : when I right click on the attached PDF and try
    to rename it (Manage attachments>Rename attachments), 3
    messages appear:
    a. Zotfile Error: Unknown Error!
    b. Zotfile Error: The source folder is not valid. Please
    change the source folder under Zotero-Actions-Zotfile
    preferences.You might have to use a custom folder.
    c. Zotfile: Renamed attachments X author_title.pdf

    4. Zotfile 4.2.3 : when I right click on the attached PDF and
    try to rename it(Manage attachments>Rename attachments), 2
    messages appear:
    a. Zotfile Error: Unknown Error!
    b. Zotfile: Renamed Attachments X author_title.pdf

    5. The “Drag and drop>Right Click>Retrieve Metadata for PDF"
    works in all three versions, but the “right click>Manage
    Attachments>Rename Attachments" is only working in Zotfile
    4.2.1.

    Thank you and I hope this answers your questions.
  • WJan, no, that's currently not possible. Happy to accept a pull request if you want to implement it.

    loubnael, can you try this version and report about the messages that appear? It is a version with specific debug messages. The same error should still occur, just 2-3 additional messages.
    http://www.columbia.edu/~jpl2136/zotfile-4.2.3.99-fx.xpi
  • Joscha,
    many thanks for your comment.
  • Joscha,

    The same two massages that appeared in the case of Zotfile 4.2.3 along with a debug message indicating the location of the PDF file in Zotero's storage folder.
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