Fail to write file to disk

[Groberen]

Related forum thread: https://www.giuspen.com/topic/ctb-write-failed-writing-to-disk/

Sometimes when saving the database an error message appears ".ctb write failed – writing to disk".

My issue is with Windows 10 x64 and Cherrytree 0.38.1 and earlier, and up to version 0.38.3 (as far as i have tested) - so the bug have obviously being lurking around for some time. Earlier on - the issue was present only when the database file was located on a network drive (not administating by me nor have I any control over that file server). What helped my out was to simply relocate the database to a local drive.

On the link provided above, I expain how I found it to be possible to replicate the bug.

The steps to reproduce the bug:

1. Open Cherrytree and load a file
2. Use another program to copy/backup the database file while it is open by Cherrytree. On Windows, I have a Autohotkey script that make backups of the database file.
3. Do some changes (I don't thing it matters if 2 and 3 swaps).
4. Save.

At point 4, Cherrytree will give this error saying it cannot save the file. The only workaround is to save the database as a file with different name, and then save as again using original file name.

[giuspen]

Are you using password protection? Your script is accessing read only? Is it only doing copy/paste or also parsing the sqlite3 database?

[Groberen]

Are you using password protection?

No, I'm not using password protection.

Your script is accessing read only?

No I assume it doesn't. However, the backup job is done without any error.

Is it only doing copy/paste or also parsing the sqlite3 database?

It's a simple file copy.

[k3rne]

I have similar problem. I can't save file, but I also not able to save as. It is possible to somehow save my data without manually moving it?

already running '/root/notes' - 'notes.ctb'
4 run ''
utf-8
pending_new_db_node 1
utf-8
pending_new_db_node 2
sel node id=33, seq=8
sel node id=251, seq=7
sel node id=1, seq=2
sel node id=343, seq=10
sel node id=406, seq=14
sel node id=689, seq=15
sel node id=406, seq=14
sel node id=179, seq=13
sel node id=718, seq=12
sel node id=719, seq=1
sel node id=731, seq=2
sel node id=732, seq=3
sel node id=734, seq=2
sel node id=732, seq=3
sel node id=731, seq=2
win destroy: runn_win found with id 1
sel node id=385, seq=4
sel node id=384, seq=5
sel node id=385, seq=4
Traceback (most recent call last):
  File "/usr/share/cherrytree/modules/core.py", line 1585, in file_save
    if not self.file_write(os.path.join(self.file_dir, self.file_name), first_write=False):
  File "/usr/share/cherrytree/modules/core.py", line 1708, in file_write
    try: xml_string = self.xml_handler.treestore_to_dom()
  File "/usr/share/cherrytree/modules/machines.py", line 321, in treestore_to_dom
    self.append_dom_node(tree_iter, cherrytree, to_disk=True)
  File "/usr/share/cherrytree/modules/machines.py", line 393, in append_dom_node
    self.append_dom_node(tree_iter, dom_iter, to_disk)
  File "/usr/share/cherrytree/modules/machines.py", line 393, in append_dom_node
    self.append_dom_node(tree_iter, dom_iter, to_disk)
  File "/usr/share/cherrytree/modules/machines.py", line 393, in append_dom_node
    self.append_dom_node(tree_iter, dom_iter, to_disk)
  File "/usr/share/cherrytree/modules/machines.py", line 393, in append_dom_node
    self.append_dom_node(tree_iter, dom_iter, to_disk)
  File "/usr/share/cherrytree/modules/machines.py", line 393, in append_dom_node
    self.append_dom_node(tree_iter, dom_iter, to_disk)
  File "/usr/share/cherrytree/modules/machines.py", line 352, in append_dom_node
    curr_buffer = self.dad.get_textbuffer_from_tree_iter(tree_iter)
  File "/usr/share/cherrytree/modules/core.py", line 3125, in get_textbuffer_from_tree_iter
    self.ctdb_handler.read_db_node_content(tree_iter, self.db)
  File "/usr/share/cherrytree/modules/ctdb.py", line 496, in read_db_node_content
    node_row = db.execute('SELECT txt, has_codebox, has_table, has_image FROM node WHERE node_id=?', (node_id,)).fetchone()
sqlite3.OperationalError: disk I/O error
Traceback (most recent call last):
  File "/usr/share/cherrytree/modules/core.py", line 1548, in file_save_as
    if not self.file_write(filepath, first_write=True):
  File "/usr/share/cherrytree/modules/core.py", line 1708, in file_write
    try: xml_string = self.xml_handler.treestore_to_dom()
  File "/usr/share/cherrytree/modules/machines.py", line 321, in treestore_to_dom
    self.append_dom_node(tree_iter, cherrytree, to_disk=True)
  File "/usr/share/cherrytree/modules/machines.py", line 393, in append_dom_node
    self.append_dom_node(tree_iter, dom_iter, to_disk)
  File "/usr/share/cherrytree/modules/machines.py", line 393, in append_dom_node
    self.append_dom_node(tree_iter, dom_iter, to_disk)
  File "/usr/share/cherrytree/modules/machines.py", line 393, in append_dom_node
    self.append_dom_node(tree_iter, dom_iter, to_disk)
  File "/usr/share/cherrytree/modules/machines.py", line 393, in append_dom_node
    self.append_dom_node(tree_iter, dom_iter, to_disk)
  File "/usr/share/cherrytree/modules/machines.py", line 352, in append_dom_node
    curr_buffer = self.dad.get_textbuffer_from_tree_iter(tree_iter)
  File "/usr/share/cherrytree/modules/core.py", line 3125, in get_textbuffer_from_tree_iter
    self.ctdb_handler.read_db_node_content(tree_iter, self.db)
  File "/usr/share/cherrytree/modules/ctdb.py", line 496, in read_db_node_content
    node_row = db.execute('SELECT txt, has_codebox, has_table, has_image FROM node WHERE node_id=?', (node_id,)).fetchone()
sqlite3.OperationalError: disk I/O error

[k3rne]

I am also not able to export ;/

sel node id=382, seq=2
sel node id=388, seq=2
sel node id=385, seq=4
sel node id=1, seq=2
Traceback (most recent call last):
  File "/usr/share/cherrytree/modules/core.py", line 2097, in export_to_ctd
    ctd_handler.nodes_all_export_to_ctd(ctd_filepath)
  File "/usr/share/cherrytree/modules/exports.py", line 162, in nodes_all_export_to_ctd
    try: xml_string = self.dad.xml_handler.treestore_to_dom()
  File "/usr/share/cherrytree/modules/machines.py", line 321, in treestore_to_dom
    self.append_dom_node(tree_iter, cherrytree, to_disk=True)
  File "/usr/share/cherrytree/modules/machines.py", line 393, in append_dom_node
    self.append_dom_node(tree_iter, dom_iter, to_disk)
  File "/usr/share/cherrytree/modules/machines.py", line 393, in append_dom_node
    self.append_dom_node(tree_iter, dom_iter, to_disk)
  File "/usr/share/cherrytree/modules/machines.py", line 393, in append_dom_node
    self.append_dom_node(tree_iter, dom_iter, to_disk)
  File "/usr/share/cherrytree/modules/machines.py", line 393, in append_dom_node
    self.append_dom_node(tree_iter, dom_iter, to_disk)
  File "/usr/share/cherrytree/modules/machines.py", line 352, in append_dom_node
    curr_buffer = self.dad.get_textbuffer_from_tree_iter(tree_iter)
  File "/usr/share/cherrytree/modules/core.py", line 3125, in get_textbuffer_from_tree_iter
    self.ctdb_handler.read_db_node_content(tree_iter, self.db)
  File "/usr/share/cherrytree/modules/ctdb.py", line 496, in read_db_node_content
    node_row = db.execute('SELECT txt, has_codebox, has_table, has_image FROM node WHERE node_id=?', (node_id,)).fetchone()
sqlite3.OperationalError: disk I/O error

[giuspen]

@k3rne are you running latest 0.38.5?

[k3rne]

yes, CherryTree 0.38.5

[k3rne]

If I try to 'save as' it's saves only 40K.

m$ file note.ctb
note.ctb: SQLite 3.x database, last written using SQLite version 3024000
m$ cat note.ctb
SQLite format 3@
�$�
U       {��
 �

�
 {
  ��tablebookmarkbookmark	CREATE TABLE bookmark (
node_id INTEGER UNIQUE,
sequence INTEGER
)/	Cindexsqlite_autoindex_bookmark_1bookmark
r�7tablechildrenchildrenCREATE TABLE children (
node_id INTEGER UNIQUE,
father_id INTEGER,
sequence INTEGER
)/Cindexsqlite_autoindex_children_1childre� �tableimageimageCREATE TABLE image (
node_id INTEGER,
offset INTEGER,
justification TEXT,
anchor TEXT,
png BLOB,
filename TEXT,
link TEXT,
time INTEGER
)�
�wtablegridgridCREATE TABLE grid (
node_id INTEGER,
offset INTEGER,
justification TEXT,
txt TEXT,
col_min INTEGER,
col_max INTEGER
)�b�ablecodeboxcodeboxCREATE TABLE codebox (
node_id INTEGER,
offset INTEGER,
justification TEXT,
txt TEXT,
syntax TEXT,
width INTEGER,
height INTEGER,
is_width_pix INTEGER,
do_highl_bra INTEGER,
do_show_linenum INTEGER
)��mtablenodenodeCREATE TABLE node (
node_id INTEGER UNIQUE,
name TEXT,
txt TEXT,
syntax TEXT,
tags TEXT,
is_ro INTEGER,
is_richtxt INTEGER,
has_codebox INTEGER,
has_table INTEGER,
has_image INTEGER,
level INTEGER,
ts_creation INTEGER,
ts_lastsave INTEGER
)';indexsqlite_autoindex_node_1node

[k3rne]

Any chances to save this notes?

[k3rne]

Never mind I moved those data, if I use ctd am I safe?

[giuspen]

Hi, I'm sorry I could not help with that, if you find what actions caused cherrytree to be unable to save successfully please let me know. CTD is pure XML rather than a DB, the drawback is that the whole document is re-saved every time so it's slower, and same for the read when you open the document

[DancingCritter]

I had a similar issue. Unfortunately, I lost tons of work. If the error ends in '-writing to disk' is there some way to recover the file? Where was it written?

[giuspen]

@DancingCritter no but be patient in future C++ gtk3 version the problem will go

[DancingCritter]

That is depressing. So I was using it for a month without restarting my computer thinking autosave was working. When I restarted my computer only the most recently created nodes were saved on the file, everything else was deleted. Not sure if that detail is useful to you or not. :/

[Groberen]

On a windows computer - I hav taken the following measurements in order to prevent data loss:

• Using a script to make a backup of the file before opening cs.
• Store the database on a local disk. Any attempt to store the file on the external file server will cause data loss.

[golimarrrr]

I also get the "write failed - writing to disk" error: I'm curious about another smaller file that appeared next to the ctb file:

notas.ctb
notas.ctb-journal

Is this created by CherryTree or is something related to the filesystem?

[giuspen]

@golimarrrr the -journal is surely not generated by cherrytree

[casainho]

I was also getting this issue and I was saving cherrytree database file over a samba share on Linux. I found a solution that seems to work well and that is to use a specific option on samba mount about lock/unlock, as explained here: https://support.shotgunsoftware.com/hc/en-us/community/posts/209491808-Getting-database-is-locked-on-NFS-and-CIFS-setup

Here is my config on /etc/fstab (NOTE the nolock option):

//192.167.2.30/home_gpd_2_pocket_pc /media/HOME_GPD2_POCKET_PC cifs vers=3.0,username=xxx,password=xxx,nolock,iocharset=utf8,uid=1000 0 0

[firepainting]

Hi Giuspen and everyone,

Ended up here after finding a thread on your site.

I’m having similar issues (if not the same) as others: "[DIRECTORY]/[FILE NAME].ctb write failed - writing to disk"

This happens after:

1. I import a whole tree (multiple nodes, CherryTree to CherryTree)
2. I create a new node

This does not happen when I simply edit the contents (or notes) in existing nodes.

My CT databases/files are mainly on Dropbox, with which I use Cryptomator.

Right now I'm on my Linux Mint 19.1 Cinnamon laptop (for about a week now) and it's where I'm getting the error. I have a Windows 8.1 desktop but haven't gotten errors yet.

It was on Windows that I copied all my notes (from MS OneNote and Zhorn Stickies). (Linux laptop is brand new.)

Anyway, I uploaded files on Dropbox+Cryptomator on Windows, and then downloaded on Linux.

Before today I got the occassional errors—maybe once or twice a day. The workaround was:

1. Lock Vault on Cryptomator
2. Remove the Vault
3. Add it back again...and then open.
4. (The point of all that is to open a “fresh” (sort of) mounted drive.)

But today I can not save anymore. “Save As” doesn’t help.

I tried replicating the error by copying the database out from Dropbox, saving it on my local PC—the error's indeed the same.

The “blank” CT also happens: a database is suddenly reduced to 40kb—with nothing. Good thing I’ve set 2 backups for every save.

Some info that might help (on Linux Mint):

• CT version 0.38.8, installed from the Software Manager
• CT notes' directory when opened via Dropbox+Cryptomator: /home/[PC NAME]/.local/share/Cryptomator/mnt/bUAwzbT6S4pP_0/[CT FOLDER]/[.CTB FILE]

Thank you, and thanks heaps for CherryTree. I like its simplicity (even though I don’t do coding, with which CT was created with that in mind I think?) And more important, it being cross-platform.

[chamalis]

Personally I didn't move, copy, etc, it just happened write failed - writing to disk, but with a different debug message sqlite3.OperationalError: attempt to write a readonly database.

• It happends only with sqlite (.ctb)
• Several backup files are left behind
• Permissions are (it runs as root here, but also did that with regular user / perms in debian):

drwxr-xr-x 1 root root     4096 Jun 14  2019 .
drwxr-xr-x 1 root root     4096 Jun 10 18:11 ..
-rw-r--r-- 1 root root 24268800 Jun 14  2019 myfile.ctb
-rw-r--r-- 1 root root 24268800 Jun 14  2019 myfile.ctb~
-rw-r--r-- 1 root root 24268800 Jun 14  2019 myfile.ctb~~
-rw-r--r-- 1 root root 24268800 Jun 14  2019 myfile.ctb~~~
-rw-r--r-- 1 root root 31991195 Jun 14  2019 myfile.ctd
-rw-r--r-- 1 root root 31991123 Jun 14  2019 myfile.ctd~

versions:

linux kali 4.19.0-kali5-amd64
cherrrytree 0.38.8

Stdout:

sel node id=131, seq=2
pending_edit_db_node_buff 131
sel node id=131, seq=2
write node content, node_id 42 , write_dict {'upd': True, 'buff': True, 'hier': False, 'child': False, 'prop': False}
Traceback (most recent call last):
  File "/usr/share/cherrytree/modules/core.py", line 1585, in file_save
    if not self.file_write(os.path.join(self.file_dir, self.file_name), first_write=False):
  File "/usr/share/cherrytree/modules/core.py", line 1721, in file_write
    self.file_write_low_level(filepath, xml_string, first_write)
  File "/usr/share/cherrytree/modules/core.py", line 1622, in file_write_low_level
    else: self.ctdb_handler.pending_data_write(self.db)
  File "/usr/share/cherrytree/modules/ctdb.py", line 61, in pending_data_write
    self.write_db_node(db, tree_iter, node_sequence, node_father_id, write_dict)
  File "/usr/share/cherrytree/modules/ctdb.py", line 375, in write_db_node
    db.execute('UPDATE node SET txt=?, syntax=?, is_richtxt=?, has_codebox=?, has_table=?, has_image=?, ts_lastsave=? WHERE node_id=?', (txt, syntax, is_richtxt, has_codebox, has_table, has_image, ts_lastsave, node_id))
sqlite3.OperationalError: attempt to write a readonly database

• Workaround: Saving to xml (.ctd) and then again to sqlite, works.

• SOLVED: In my case the folder where the file was saved was a shared VirtualBox folder between host:Debian <-> guest:Kali (Debian). Moving the file into guest's filesystem, solved the issue.

[cmessias]

I've got the same problem after moving and deleting some nodes around. Everything works fine when I am only saving text on existing nodes. Running on Linux 4.20.17-1-MANJARO and cherrytree 0.38.8.

[nmroque]

Hello,

I’m having similar issue with CherryTree 0.38.8 on Windows.

cherrytree.exe.log: Traceback (most recent call last): File "core.pyc", line 1548, in file_save_as File "core.pyc", line 1721, in file_write File "main.pyc", line 238, in main File "dbus\bus.pyc", line 241, in get_object File "dbus\proxies.pyc", line 248, in __init__ File "dbus\bus.pyc", line 180, in activate_name_owner File "dbus\bus.pyc", line 278, in start_service_by_name File "dbus\connection.pyc", line 651, in call_blocking dbus.exceptions.DBusException: org.freedesktop.DBus.Error.ServiceUnknown: The name com.giuspen.CherryTreeService was not provided by any .service files

[gahisee]

Same write error in my setup as follows:

• cherrytree 0.38.9 running on kubuntu 19.04
• sql.ctb resides on a remote kubuntu machine mounted as cifs
• using xml has always worked
• using sql fails with this write error ONLY when my local machine comes up (for whatever reason) with the remote NOT mounted. if the remote is manually mounted, it does not help cherrytree. the machine has to come up with it mounted.

here's my fstab entry: //192.168.1.150/music /mnt/NUCi cifs username=xxx,password=xxx,noauto,x-systemd.automount,x-systemd.device-timeout=10,nolock,uid=xxx,gid=xxx,file_mode=0777,dir_mode=0777 0 0

[bitboy85]

Same issue if ctb is located in a mounted network drive. If the connection is lost its not possible to save changes to the DB even after network connection is restored.

OS: win10 x64 Recent cherrytree version

[StellerJay]

I had the write error only when adding a new node, not data. I saved-as under the same name and overwrote the existing data file. Problem solved, I have been able to save nodes and sub-nodes. My first guess is that the years-old data file had code incompatible with the current CT version. Second guess is that the old data file was corrupted.

Linux Mint 19.2, local computer ( ie no network involved ), cherrytree 0.35.10 Mike

[donjps]

Same problem on Linux (currently Lubuntu 19.10). I can write text and save to an existing node but I can't save a new node or save images I have copied to an existing node. No problems on my Windows 10 machine.

[donjps]

"Same problem on Linux (currently Lubuntu 19.10). I can write text and save to an existing node but I can't save a new node or save images I have copied to an existing node. No problems on my Windows 10 machine." - I should say that directory structure and content of my documents including the location of the Cherrytree DB is mirrored on my Windows 10 machine via a cloud service.

[LSchueler]

I get the same problem when creating a new node with Ubuntu 18.10 and the ctb file format with CherryTree version 0.37.6

[donjps]

A work around that worked for me - saved cherrytree file to another name as in saving "orginal_file.ctb" to "original_file_copy.ctb" which worked. I then resaved it back to my original_file.ctb.

I also had a similar problem with Wikidpad which also used sqlite. As with Cherrytree I used it on Windows and Linux but had the problem only with Linux.

[dan-osul]

Same problem as noted in the above comments. I was running 0.37.6 on Ubuntu 19.10 with my ctb on Dropbox. Issue was resolved for me by updating to 0.38.9 via https://www.giuspen.com/cherrytree/#downl

Hope it helps.

[r0bag]

same issue as the folks above, for me it helped to rename one of the autosaves, then open the renamed file, and save it in sqlite, which then continued to work again. saving it as xml failed. the autosave option should be turned on by default. i had version 0.38.5.