Apparently unable to update notebook, Zim 0.55

Looks like the index may be corrupted. You could try "zim --index -V
/path/to/notebook" to fix it.

-- Jaap

Hi, Jaap! Thanks for your quick response.

The command you gave me appeared to succeed. However, the next time I started Zim on the system, I was again presented with the file format update dialog, and it again failed.

Here again is the output when using the --debug switch:

INFO: This is zim 0.55
DEBUG: Python version is sys.version_info(major=2, minor=7, micro=2, releaselevel='final', serial=0)
DEBUG: Platform is posix
DEBUG: Zim revision is:
  branch: pyzim-trunk
  revision: 510 <email address hidden>
  date: 2012-02-28 21:28:58 +0100
DEBUG: Not running from a source dir
DEBUG: Set XDG_DATA_HOME to /home/xxxxxxxx/.local/share
DEBUG: Set XDG_DATA_DIRS to [<Dir: /usr/share>, <Dir: /usr/local/share>]
DEBUG: Set XDG_CONFIG_HOME to /home/xxxxxxxx/.config
DEBUG: Set XDG_CONFIG_DIRS to [<Dir: /etc/xdg>]
DEBUG: Set XDG_CACHE_HOME to /home/xxxxxxxx/.cache
DEBUG: Running command: gui
INFO: Opening default notebook
DEBUG: Wrote /tmp/zim-xxxxxxxx/daemon.pid
INFO: Starting UnixSocketDaemon
DEBUG: Socket address: /tmp/zim-xxxxxxxx/daemon-socket
DEBUG: Sending to daemon: ["ping",[],{}]

DEBUG: Daemon replied: "Ack"
DEBUG: Sending to daemon: ["vivicate",["zim.gui.GtkInterface","file:///home/xxxxxxxx/Data/Zim/Work"],{"usedaemon":true,"notebook":"file:///home/xxxxxxxx/Data/Zim/Work"}]

DEBUG: Child spawned 4899 (u'zim.gui.GtkInterface', u'file:///home/xxxxxxxx/Data/Zim/Work')
DEBUG: No such signal: notebook-list-changed
DEBUG: Daemon replied: true
DEBUG: Sending to daemon: ["relay",[["zim.gui.GtkInterface","file:///home/xxxxxxxx/Data/Zim/Work"],"present",null],{"geometry":null,"fullscreen":null}]

DEBUG: Sending to child 4899: ["present",[null],{"geometry":null,"fullscreen":null}]

DEBUG: Daemon replied: true
DEBUG:
NOTE FOR BUG REPORTS:
        At this point zim has send the command to open a notebook to a
        background process and the current process will no quit.
        If this is the end of your debug output it is probably not useful
        for bug reports. Please close all zim windows, quit the
        zim trayicon (if any), and try again.

[10]+ Done zim
xxxxxxxx@yyyyyyyy:~$ DEBUG: Loading /home/xxxxxxxx/.config/zim/preferences.conf
DEBUG: Gtk version is (2, 24, 10)
DEBUG: Pygtk version is (2, 24, 0)
WARNING: Could not find all icon sizes for the application icon
DEBUG: Loading /home/xxxxxxxx/.config/zim/style.conf
DEBUG: Loaded plugin arithmetic (<ArithmeticPlugin object at 0x9858f04 (zim+plugins+PluginClass at 0x9805a00)>)
DEBUG: Loaded plugin calendar (<CalendarPlugin object at 0x992eeb4 (zim+plugins+PluginClass at 0x9806f70)>)
DEBUG: Registered plugin <InsertDiagramPlugin object at 0x9938c0c (zim+plugins+PluginClass at 0x9806fb0)> for image type "diagram"
DEBUG: Loaded plugin diagrameditor (<InsertDiagramPlugin object at 0x9938c0c (zim+plugins+PluginClass at 0x9806fb0)>)
DEBUG: Registered plugin <InsertEquationPlugin object at 0x9938d74 (zim+plugins+PluginClass at 0x97f7320)> for image type "equation"
DEBUG: Loaded plugin equationeditor (<InsertEquationPlugin object at 0x9938d74 (zim+plugins+PluginClass at 0x97f7320)>)
DEBUG: Registered plugin <InsertGNURPlotPlugin object at 0x993f784 (zim+plugins+PluginClass at 0x9806fd0)> for image type "gnu_r_plot"
DEBUG: Loaded plugin gnu_r_ploteditor (<InsertGNURPlotPlugin object at 0x993f784 (zim+plugins+PluginClass at 0x9806fd0)>)
DEBUG: Loaded plugin inlinecalculator (<InlineCalculatorPlugin object at 0x994739c (zim+plugins+PluginClass at 0x9806f40)>)
DEBUG: Loaded plugin insertsymbol (<InsertSymbolPlugin object at 0x99474b4 (zim+plugins+PluginClass at 0x9807100)>)
DEBUG: Loaded plugin linesorter (<LineSorterPlugin object at 0x9947b94 (zim+plugins+PluginClass at 0x9807270)>)
DEBUG: Loaded plugin linkmap (<LinkMapPlugin object at 0x9947dec (zim+plugins+PluginClass at 0x9808600)>)
DEBUG: Loaded plugin printtobrowser (<PrintToBrowserPlugin object at 0x9954b94 (zim+plugins+PluginClass at 0x98072d0)>)
DEBUG: Loaded plugin quicknote (<QuickNotePlugin object at 0x9987054 (zim+plugins+PluginClass at 0x97f7330)>)
DEBUG: Loaded plugin screenshot (<InsertScreenshotPlugin object at 0x9987be4 (zim+plugins+PluginClass at 0x9807260)>)
DEBUG: Loaded plugin spell (<SpellPlugin object at 0x9987e8c (zim+plugins+PluginClass at 0x9807220)>)
DEBUG: Loaded plugin tasklist (<TaskListPlugin object at 0x99384dc (zim+plugins+tasklist+TaskListPlugin at 0x98086a0)>)
DEBUG: Accelmap: /home/xxxxxxxx/.config/zim/accelmap
DEBUG: Opening notebook: file:///home/xxxxxxxx/Data/Zim/Work
DEBUG: Loading /home/xxxxxxxx/Data/Zim/Work/notebook.zim
DEBUG: Cache dir: /home/xxxxxxxx/Data/Zim/Work/.zim
DEBUG: Index database file: /home/xxxxxxxx/Data/Zim/Work/.zim/index.db
WARNING: This notebook needs to be upgraded to the latest data format
DEBUG: Loading /home/xxxxxxxx/Data/Zim/Work/.zim/state.conf
INFO: Starting async index update
DEBUG: Action: set_pathbar_path
INFO: Open page: <FileStorePage: Calendar:2012:03:15> (<HistoryPath: Calendar:2012:03:15>)
DEBUG: Running QuestionDialog
DEBUG: Q: Upgrade Notebook?
INFO: Accelerator changed for <Actions>/CalendarPlugin/show_calendar
/usr/lib/python2.7/dist-packages/zim/gui/widgets.py:2612: GtkWarning: gdk_window_invalidate_rect_full: assertion `GDK_IS_WINDOW (window)' failed
  gtk.MessageDialog.run(self)
INFO: Index update done
DEBUG: A: True
DEBUG: Opening ProgressBarDialog
INFO: Notebook update started
DEBUG: Wrote /home/xxxxxxxx/Data/Zim/Work/Calendar.txt
DEBUG: Wrote /home/xxxxxxxx/Data/Zim/Work/Calendar/2009/01.txt
DEBUG: Wrote /home/xxxxxxxx/Data/Zim/Work/Calendar/2009/01/16.txt
DEBUG: Wrote /home/xxxxxxxx/Data/Zim/Work/Calendar/2009/01/21.txt
DEBUG: Wrote /home/xxxxxxxx/Data/Zim/Work/Calendar/2009/01/16.txt
DEBUG: Wrote /home/xxxxxxxx/Data/Zim/Work/Calendar/2009/01/21.txt
DEBUG: Wrote /home/xxxxxxxx/Data/Zim/Work/Calendar/2009/01/22.txt
DEBUG: Wrote /home/xxxxxxxx/Data/Zim/Work/Calendar/2009/01/23.txt
DEBUG: Wrote /home/xxxxxxxx/Data/Zim/Work/Calendar/2009/01/29.txt
DEBUG: Wrote /home/xxxxxxxx/Data/Zim/Work/Calendar/2009/01/30.txt
DEBUG: Wrote /home/xxxxxxxx/Data/Zim/Work/Calendar/2009/02.txt
ERROR: Error in child main:
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/zim/daemon.py", line 550, in spawn
    self._main()
  File "/usr/lib/python2.7/dist-packages/zim/daemon.py", line 594, in _main
    obj.main()
  File "/usr/lib/python2.7/dist-packages/zim/gui/__init__.py", line 605, in main
    self.check_notebook_needs_upgrade()
  File "/usr/lib/python2.7/dist-packages/zim/gui/__init__.py", line 1173, in check_notebook_needs_upgrade
    self.notebook.upgrade_notebook(callback=lambda p: dialog.pulse(p.name))
  File "/usr/lib/python2.7/dist-packages/zim/notebook.py", line 1973, in upgrade_notebook
    for page in self.walk():
  File "/usr/lib/python2.7/dist-packages/zim/notebook.py", line 1917, in walk
    for p in self.index.walk(path):
  File "/usr/lib/python2.7/dist-packages/zim/index.py", line 1220, in _walk
    for grandchild in self._walk(child, childpath):
  File "/usr/lib/python2.7/dist-packages/zim/index.py", line 1220, in _walk
    for grandchild in self._walk(child, childpath):
  File "/usr/lib/python2.7/dist-packages/zim/index.py", line 1220, in _walk
    for grandchild in self._walk(child, childpath):
  File "/usr/lib/python2.7/dist-packages/zim/index.py", line 1213, in _walk
    cursor.execute('select * from pages where parent = ? order by sortkey, basename', (path.id,))
InterfaceError: Error binding parameter 0 - probably unsupported type.
DEBUG: Child exited 4899 (u'zim.gui.GtkInterface', u'file:///home/xxxxxxxx/Data/Zim/Work')
INFO: Last instance quit - exiting daemon
INFO: Stopped UnixSocketDaemon

I still haven't figured out what to do about this issue. I have looked at the source files for the notebooks that work properly on the other systems and compared them to the source files for the problem notebook. I see no obvious differences in the headers. When the other notebooks were opened for the first time in Zim 0.55 on the other systems they just opened. I had to re-index them, but then everything worked fine. Zim never offered to update their file formats.

But Zim wants to update the file formats for this notebook, and offers to do so every time I start Zim on the system. The update always just fails, and I have to open the notebook by answer No to the format update dialog.

Is there an efficient way I can just import this data into a new notebook? Would that be a good way to go about solving this issue?

Thanks,
Gilbert

HI, and thanks again for your attention to this.

I did run zim with the "--index" switch on the notebook -- twice now. It appeared to succed both times, but then I still get the file format update dialog when I start the notebook.

I have looked at the files and folders of the notebook at the juncture where the failure appears to occur, and I can't see anything at all unusual about them. This is an old notebook, and it has been maintained over quite a number of new versions of Zim. (If I'm not mistaken I may have created the notebook originally under version 0.23, or something like that.)

Unfortunately, I don't have access to the notebook until Monday because it resides on a machine in a remote location that can't be accessed remotely. I'll check on the "version=0.4" idea Monday morning, but I'm pretty sure that all the files in that notebook already have that parameter specificied.

But thank you for your suggestions -- and for a truly useful piece of software. I'll get back to you with what I learn on Monday.

Regards,
Gilbert

Okay (I say, as I wipe egg off my face) -- not only was there not a "version=0.4" line in the notebook.zim file for the problem notebook, there wasn't even a notebook.zim file at all! Doh!

I'm not quite sure how that happened, but I'm kind of surprised that the notebook would open at all without that file being present.

At any rate, everything now seems to be working perfectly. I'm grateful for your help, and sorry for my noise.

Regards,
Gilbert

Thanks Jaap Karssenberg, that solved my question.

No problem. Still I think problem is in the first place the upgrade
should work and create the notebook.zim file if it doesn't exist. But
no hint on how to troubleshoot any further.

-- Jaap

I will look through the files carefully when I have time. (I made an archive of the entire notebook at the first sign of trouble, so the files within the archive will be in the state they were in when the failure was occurring.) I'll communicate further if I find anything that looks like it may have caused the trouble.

Again, many thanks for your efforts on behalf of the greater community. Zim is one of the most useful software tools I've ever encountered.

Hi!

I have the same problem as Gilbert did, only I run zim on Windows 7. I'm not sure what I am supposed to do to fix this, if you could explain this in very simple terms, step by step, I'd be most grateful!!

Also, I have a notebook, and then tried to create a new one, but the old opened up. I thought that it just made a copy and went on and changed the things I wanted to change, and now the old notebook seems to be gone. Any ideas? Even my backup of the old notebook seem to have changed to the new.

Thank you!

On Tue, Apr 3, 2012 at 12:20 PM, Julia
<email address hidden> wrote:
> I have the same problem as Gilbert did, only I run zim on Windows 7. I'm
> not sure what I am supposed to do to fix this, if you could explain this
> in very simple terms, step by step, I'd be most grateful!!

Could you add the error log, so we can verify the error is exactly the
same, and maybe get a better idea how to fix it? Thanks.

As I understand it Gilbert fixed it by taking the "notebook.zim" file
from a working notebook and copy it. This way the update is no longer
triggered.

If you don't have a working notebook you can create a new one from zim
and use that as a template.

> Also, I have a notebook, and then tried to create a new one, but the old
> opened up. I thought that it just made a copy and went on and changed
> the things I wanted to change, and now the old notebook seems to be
> gone. Any ideas? Even my backup of the old notebook seem to have changed
> to the new.

I'm sorry, but it is not clear to me what you did. Zim works on a
notebook folder. So if you have a backup of that folder there is no
way zim will change both the copy and the original. Although you might
want to double check which of the two you are editing.

Zim typically opens up the default notebook, to change that, you go to
"File", "Open another notebook" and add the new one in the list. Then
you set "default" to the new one.

Also I would advice using the version control plugin, that way you can
at roll back changes and track what happened.

Regards,

Jaap

I managed to restore my notebook, and suddenly everything is working again. It doesn't have to update the notebook when I open zim, and when I choose new notebook, it's a blank one (like I wanted) =)

Thanks!

I had similiar issue.

The notebook in question did not have "notebook.zim" in it's root directory.
I copied one from another notebook, changed the Name value to that of this notebook.

Problem solved.