Upgrade StorageZotFile - Advanced PDF management for Zotero
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Can you submit a Debug log for saving an item with a PDF? Also, if you right-click the attachment -> Manage Attachments -> Rename Attachments, does ZotFile move/rename the item?
In addition to the questions aurimas has, testing in Zotero Standalone would be quite interesting.
1. Versions
Iceweasel 32.0.3
Zotero 4.0.22
Zotfile 3.1
2. I recorded the log corresponding to the action of saving a item with a pdf (exactly the same action I did on the screencast). The Debug ID is D1782313090. The big message in French is about encoding (utf8).
3. I did try Zotero standalone with the same zotfile settings: I was unable to register the pdf at all. The debug ID of this action with zotero standalone is D1501544986.
P-S: I use Debug ID but I have no idea where the code is send. How can I see my own log with the Debug ID?
[JavaScript Error: "[Exception... "Component not initialized"nsresult: "0xc1f30001 (NS_ERROR_NOT_INITIALIZED)"
location: "JS frame :: chrome://zotfile/content/zotfile.js ::
Zotero.ZotFile.autoRename.notify :: line 467" data: no]"
{file: "chrome://zotero/content/xpcom/notifier.js" line: 165}]
Update about extraction of annotations in zotfile
Annotation extraction has made great progress over the last versions. I am now using a testing framework to ensure that changes do not break other files (which happened in the past). Here is an overview of the improvements for different zotfile versions. Most of my own files just work. These are some of the problematic files I collected over time.The difference between 90% and 100% is big(!). A lot of wrong word segmentation with misplaced or missing spaces. Below is an example. The main improvements are coming from more recent pdf.js versions that support more pdf standards (e.g. test-1.pdf and many other files) and improvements in the extraction algorithms mainly for word segmentation (e.g. Imbens-2004.pdf). Zotfile is still not working well with pdfs that screw up the order of characters (Connell-2005.pdf, Sanders-2002.pdf). They are generally older and I don't encounter them very often.
Comparison of Zotfile versions
Here is an example:
Copy & paste from Preview on Mac (88.25% correct):
"Recentlytherehasbeenasurgeineconometricworkfocusing onestimatingaveragetreatmenetffectsundervarioussetsofassumptions. Onestrandof thisliteraturheasdevelopedmethodsforestimatingaverage treatmenteffects for a binarytreatmentunderassumptionsvariously describedas exogeneity,unconfoundednesso,r selectionon observables"
Zotfile 3.1 (95.55% correct):
"Recently there has been a surge n econometricwork focusing on estimatingaveragetreatmenteffects undervarioussets of assumptions. One strandof this literaturehas developedmethodsfor estimatingaverage treatmenteffects for a binary treatmentunder assumptionsvariously describedas exogeneity,unconfoundedness,r selection on observable"
Zotfile 4.1b (98.78% correct):
"Recently there has been a surge n econometric work focusing on estimating average treatment effects under various sets of assumptions. One strand of this literature has developed methods for estimating average treatment effects for a binary treatment under assumptions variously described as exogeneity, unconfoundedness, or selection on observable"
How you can help
More test cases are always good. If you have a file that is not working properly, upload it somewhere and share the link here on the forum. Or join the zotfile zotero group and upload files to the group. Please include the correct text for annotations in json format. "markup" is the highlighted text and "content" are notes. Here is an example for a pdf with three annotations (2x highlighted text and one note):
[
{
"markup": "Recently there has been a surge in econometric work...",
"content": ""
},
{
"markup": "The implication of these assumptions is that...",
"content": ""
},
{
"markup": "",
"content": "This is a note."
}
]
Remind: On my Debian computer with iceweasel, Zotfile isn't moving and renaming attachments (pdfs) even if the settings say to do so. Instead, the attachments are send to zotero cloud and not renamed.
I tried with another computer with the exact same zotfile settings and with the same zotero account. This computer is using ubuntu (so firefox and not iceweasel) and zotfile is working as expected (attachments are moved and renamed).
So there are two possibilities:
1. There is a bug with zotfile and Iceweasel. Maybe zotfile calls firefox instead of iceweasel when moving and renaming file. Here is the debug log when I add an entry with pdf from the url bar icon with iceweasel : http://pastebin.de/142984
2. Javascript is not working properly on Debian unstable or I have so package needed not installed.
I've encountered a problem that seems to be related to Zotfile.
I've got two machines with Zotero 4.0.23.1:
- Laptop with Ubuntu 14.04 and Firefox 33.0
- Laptop with OSX Yosemite and Firefox 32.0.3
On both machines, I've tried installing Zotile 3.1 and 4.0 (at different times). On both machines, I've taken these steps to make use of Zotfiles "send to tablet" function:
1. Installing Zotfile
2. Zotfile Preferences --> Tablet Settings --> Use Zotfile to send and get files from tablet --> (setting directory to .../Dropbox/Zotfile)
3. Selecting an arbitrary Zotero entry with a PDF
4. Right-click (CTRL-click) Manage Attachments --> Send to tablet
As intended, this results in a PDF copied to the .../Dropbox/Zotfile location. But upon next Zotero sync, I get a brief error that looks like this:
Component returned failure code: 0x80520008 (NS_ERROR_FILE_ALREADY_EXISTS) [nsIFile.create]
And the file syncing error appears to affect Zotero sync on the other laptop, even if Zotfile has not been installed. I've submitted the complete error report as issue 563331324.
Since I've encountered this error several times, I've decided to remove Zotfile from both machines, delete all local Zotero data, and start from scracth by reinstalling Zotero. The errors are no longer being reported at this point.
I would like some help identifying the source of the problem as Zotfile really seems like a viable solution to a problem I have: syncing PDFs to my Android tablet. What steps could I take after installing Zotfile to eliminate this problem? Are there conditions in my own Zotero database that might contribute to this? Any guidance in troubleshooting this would be welcome.
Thanks,
Will
Make sure that syncing works before you send a file to the tablet.
I'll trying reinstalling 4.0 as you suggest and then confirm that syncing to Zotero data storage works before sending any files to tablet.
I just installed 4.0 from Github. Immediately after installing and enabling, I restarted FF and synced Zotero without any trouble. Then I went to Zotfile preferences and chose the option for "send to tablet". I tried syncing again without any trouble. Next, I chose an arbitrary PDF file and tried to send it. I was able to do this successfully.
However, when I tried syncing again, I got this error:
[JavaScript Error: "[Exception... "Component returned failure code: 0x80520008 (NS_ERROR_FILE_ALREADY_EXISTS) [nsIFile.create]" nsresult: "0x80520008 (NS_ERROR_FILE_ALREADY_EXISTS)" location: "JS frame :: chrome://zotero/content/xpcom/file.js :: Zotero.File</this.createShortened :: line 326" data: no]" {file: "chrome://zotero/content/xpcom/file.js" line: 657}]
[JavaScript Error: "[Exception... "Component returned failure code: 0x80520008 (NS_ERROR_FILE_ALREADY_EXISTS) [nsIFile.create]" nsresult: "0x80520008 (NS_ERROR_FILE_ALREADY_EXISTS)" location: "JS frame :: chrome://zotero/content/xpcom/file.js :: Zotero.File</this.createShortened :: line 326" data: no]" {file: "chrome://zotero/content/xpcom/sync.js" line: 586}]
version => 4.0.23.1, platform => MacIntel, oscpu => Intel Mac OS X 10.10, locale => en-US, appName => Firefox, appVersion => 33.0.2, extensions => LastPass (3.1.1, extension), 1Password (4.2.4, extension), LibX (2.0.15861.0, extension), ZotFile (4.0, extension), OpenH264 Video Codec provided by Cisco Systems, Inc. (1.1, plugin), Shockwave Flash (15.0.0.152, plugin), AdobeAAMDetect (AdobeAAMDetect 2.0.0.0, plugin, disabled), QuickTime Plug-in 7.7.3 (7.7.3, plugin, disabled), Default Browser Helper (600, plugin, disabled)
Any advice on what I can try next?
Dan, are there any additional information in the error report (563331324)?
Yes, I can open the attachment by double-clicking it.
And yes, I have no idea how to tell whether I'm running in "background mode" or not. It sounds like that's something I would need to manually change somehow; I haven't done so.
Also, if it helps, I obtained the debug output logging for the last manual Zotero sync I invoked. The complete output is posted at the link below.
http://pastebin.com/Grw9TshJ
Thanks for your help!
Will
1) Create a new FF profile and start FF with that profile
https://support.mozilla.org/en-US/kb/profile-manager-create-and-remove-firefox-profiles
2) Install Zotero
3) Install Zotfile 4
4) Enable Zotfile's tablet feature
5) Capture this article with Zotero (download pdf manually if it doesn't get added automatically)
http://www.sociologicalscience.com/pathways-science-engineering-bachelors-degrees-men-women/
6) Set up a new Zotero account for testing
7) Sync
8) Send pdf to tablet
9) Sync again
I followed your steps precisely. The one exception was that I when I took step #8 (Send PDF to tablet) for the first time, no PDF was actually written to the location. I went on to step #9 anyway--it was successful. Then I repeated steps #8 and #9 again. No problems.
It's encouraging that this works with a very simple example.
What steps would you recommend for me to troubleshoot my issue?
Thanks so much for your continued assistance.
Will
I say 'almost' because ZotFile takes all of my annotations and lumps them into a single note, while I prefer each one to be separate since each annotation is an atomic part of the paper. I don't want/need to annotate in multiple colors, so I can't use the colorNotes option. It would be great if there was an option to just make a new note for every new annotation.
If you have a moderately sized library with 1000 items, each with 100-200 notes, Zotero will become all but unusable.
Even if one-note-per-annotation is a hidden option that's off by default, I would be very grateful to have it because I would be able to work with ZotFile using the workflow I'm accustomed to.
It would be great if some people can download this version and report any problems (or lack of problems)!
Basically, I'm looking for a way to keep my annotations in sync as searchable notes in Zotero without having to remember which PDFs I've annotated and select each one individually for extraction with Zotfile.