python-3.xjupyter-notebookanacondapywin32jupyter-lab

Reputation: 341

jupyter notebook on anaconda - "win32security" kernal error

After a lot of fiddling and installing unistalling anconda I have finally got to this dead end trying to run jupyter notebook from "Anaconda3 2019.07 64bit" with "Python 3.7" on "windows 8.1 Enterprise 64bit SP0"

The issue is:

jupyter notebook runs fine with NO kernal errors with the default installation on base env.
when installing the following packages, something causes jupyter notebook to upgrade which causes kernal errors to show up when creating new python3 notebook!

packages installed:

conda install -c conda-forge awscli boto3
conda install shapely tensorflow opencv

This is a dump of the kernel error:

Traceback (most recent call last):
  File "C:\Users\xxx\.conda\envs\logAna\lib\site-packages\tornado\web.py", line 1699, in _execute
    result = await result
  File "C:\Users\xxx\.conda\envs\logAna\lib\site-packages\tornado\gen.py", line 742, in run
    yielded = self.gen.throw(*exc_info)  # type: ignore
  File "C:\Users\xxx\.conda\envs\logAna\lib\site-packages\notebook\services\sessions\handlers.py", line 72, in post
    type=mtype))
  File "C:\Users\sxxx\.conda\envs\logAna\lib\site-packages\tornado\gen.py", line 735, in run
    value = future.result()
  File "C:\Users\xxx\.conda\envs\logAna\lib\site-packages\tornado\gen.py", line 742, in run
    yielded = self.gen.throw(*exc_info)  # type: ignore
  File "C:\Users\xxx\.conda\envs\logAna\lib\site-packages\notebook\services\sessions\sessionmanager.py", line 88, in create_session
    kernel_id = yield self.start_kernel_for_session(session_id, path, name, type, kernel_name)
  File "C:\Users\xxx\.conda\envs\logAna\lib\site-packages\tornado\gen.py", line 735, in run
    value = future.result()
  File "C:\Users\xxx\.conda\envs\logAna\lib\site-packages\tornado\gen.py", line 742, in run
    yielded = self.gen.throw(*exc_info)  # type: ignore
  File "C:\Users\xxx\.conda\envs\logAna\lib\site-packages\notebook\services\sessions\sessionmanager.py", line 101, in start_kernel_for_session
    self.kernel_manager.start_kernel(path=kernel_path, kernel_name=kernel_name)
  File "C:\Users\xxx\.conda\envs\logAna\lib\site-packages\tornado\gen.py", line 735, in run
    value = future.result()
  File "C:\Users\xxx\.conda\envs\logAna\lib\site-packages\tornado\gen.py", line 209, in wrapper
    yielded = next(result)
  File "C:\Users\xxx\.conda\envs\logAna\lib\site-packages\notebook\services\kernels\kernelmanager.py", line 168, in start_kernel
    super(MappingKernelManager, self).start_kernel(**kwargs)
  File "C:\Users\xxx\.conda\envs\logAna\lib\site-packages\jupyter_client\multikernelmanager.py", line 110, in start_kernel
    km.start_kernel(**kwargs)
  File "C:\Users\xxx\.conda\envs\logAna\lib\site-packages\jupyter_client\manager.py", line 240, in start_kernel
    self.write_connection_file()
  File "C:\Users\xxx\.conda\envs\logAna\lib\site-packages\jupyter_client\connect.py", line 547, in write_connection_file
    kernel_name=self.kernel_name
  File "C:\Users\xxx\.conda\envs\logAna\lib\site-packages\jupyter_client\connect.py", line 212, in write_connection_file
    with secure_write(fname) as f:
  File "C:\Users\xxx\.conda\envs\logAna\lib\contextlib.py", line 112, in __enter__
    return next(self.gen)
  File "C:\Users\xxx\.conda\envs\logAna\lib\site-packages\jupyter_client\connect.py", line 100, in secure_write
    win32_restrict_file_to_user(fname)
  File "C:\Users\xxx\.conda\envs\logAna\lib\site-packages\jupyter_client\connect.py", line 61, in win32_restrict_file_to_user
    sd = win32security.GetFileSecurity(fname, win32security.DACL_SECURITY_INFORMATION)
pywintypes.error: (50, 'GetFileSecurity', 'The request is not supported.')

I have created a new environment installing all packages I need but could not find how to install the same version of jupyter notebook in "base" environment assuming that the new version of jupyter notebook has a bug.

I am relatively new to both Python and Anaconda and not getting much joy with them at the moment following three full days of agony trying all sorts of ways round the problem!

This is the dump from the terminal feed when this error occurs!:

(base) C:\WINDOWS\system32>activate test

(test) C:\WINDOWS\system32>jupyter lab
[I 15:50:55.678 LabApp] JupyterLab extension loaded from C:\Users\xxx\
.conda\envs\test\lib\site-packages\jupyterlab
[I 15:50:55.678 LabApp] JupyterLab application directory is C:\Users\xxx\.conda\envs\test\share\jupyter\lab
[I 15:50:55.682 LabApp] Serving notebooks from local directory: C:\WINDOWS\syste
m32
[I 15:50:55.682 LabApp] The Jupyter Notebook is running at:
[I 15:50:55.682 LabApp] http://localhost:8888/?token=e2f1c73d291f7e884d3c618eb43
83196c2d75484a0f88d96
[I 15:50:55.682 LabApp]  or http://127.0.0.1:8888/?token=e2f1c73d291f7e884d3c618
eb4383196c2d75484a0f88d96
[I 15:50:55.682 LabApp] Use Control-C to stop this server and shut down all kern
els (twice to skip confirmation).
[C 15:50:55.914 LabApp]

    To access the notebook, open this file in a browser:
        file://A-FILEDATA-COV-P/Profile/xxx/AppData/Roaming/jupyter/ru
ntime/nbserver-8544-open.html
    Or copy and paste one of these URLs:
        http://localhost:8888/?token=e2f1c73d291f7e884d3c618eb4383196c2d75484a0f
88d96
     or http://127.0.0.1:8888/?token=e2f1c73d291f7e884d3c618eb4383196c2d75484a0f
88d96
[W 15:51:04.157 LabApp] Could not determine jupyterlab build status without node
js
[E 15:51:13.236 LabApp] Uncaught exception POST /api/sessions?1569509473167 (::1
)
    HTTPServerRequest(protocol='http', host='localhost:8888', method='POST', uri
='/api/sessions?1569509473167', version='HTTP/1.1', remote_ip='::1')
    Traceback (most recent call last):
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\tornado\we
b.py", line 1699, in _execute
        result = await result
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\tornado\ge
n.py", line 742, in run
        yielded = self.gen.throw(*exc_info)  # type: ignore
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\notebook\s
ervices\sessions\handlers.py", line 72, in post
        type=mtype))
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\tornado\ge
n.py", line 735, in run
        value = future.result()
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\tornado\ge
n.py", line 742, in run
        yielded = self.gen.throw(*exc_info)  # type: ignore
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\notebook\s
ervices\sessions\sessionmanager.py", line 88, in create_session
        kernel_id = yield self.start_kernel_for_session(session_id, path, name,
type, kernel_name)
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\tornado\ge
n.py", line 735, in run
        value = future.result()
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\tornado\ge
n.py", line 742, in run
        yielded = self.gen.throw(*exc_info)  # type: ignore
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\notebook\s
ervices\sessions\sessionmanager.py", line 101, in start_kernel_for_session
        self.kernel_manager.start_kernel(path=kernel_path, kernel_name=kernel_na
me)
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\tornado\ge
n.py", line 735, in run
        value = future.result()
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\tornado\ge
n.py", line 209, in wrapper
        yielded = next(result)
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\notebook\s
ervices\kernels\kernelmanager.py", line 168, in start_kernel
        super(MappingKernelManager, self).start_kernel(**kwargs)
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\jupyter_cl
ient\multikernelmanager.py", line 110, in start_kernel
        km.start_kernel(**kwargs)
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\jupyter_cl
ient\manager.py", line 240, in start_kernel
        self.write_connection_file()
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\jupyter_cl
ient\connect.py", line 547, in write_connection_file
        kernel_name=self.kernel_name
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\jupyter_cl
ient\connect.py", line 212, in write_connection_file
        with secure_write(fname) as f:
      File "C:\Users\xxx\.conda\envs\test\lib\contextlib.py", line 112
, in __enter__
        return next(self.gen)
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\jupyter_cl
ient\connect.py", line 100, in secure_write
        win32_restrict_file_to_user(fname)
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\jupyter_cl
ient\connect.py", line 61, in win32_restrict_file_to_user
        sd = win32security.GetFileSecurity(fname, win32security.DACL_SECURITY_IN
FORMATION)
    pywintypes.error: (50, 'GetFileSecurity', 'The request is not supported.')
[W 15:51:13.245 LabApp] Unhandled error
[E 15:51:13.247 LabApp] {
      "Host": "localhost:8888",
      "Connection": "keep-alive",
      "Content-Length": "97",
      "Authorization": "token e2f1c73d291f7e884d3c618eb4383196c2d75484a0f88d96",

      "Origin": "http://localhost:8888",
      "X-Xsrftoken": "2|e0797587|bfb0295d2cfd16737a016247e6e4c3bb|1569403253",
      "User-Agent": "Mozilla/5.0 (Windows NT 6.3; Win64; x64) AppleWebKit/537.36
 (KHTML, like Gecko) Chrome/73.0.3683.75 Safari/537.36",
      "Content-Type": "application/json",
      "Accept": "*/*",
      "Referer": "http://localhost:8888/lab",
      "Accept-Encoding": "gzip, deflate, br",
      "Accept-Language": "en-US,en;q=0.9",
      "Cookie": "_xsrf=2|e0797587|bfb0295d2cfd16737a016247e6e4c3bb|1569403253; u
sername-localhost-8889=\"2|1:0|10:1569504770|23:username-localhost-8889|44:NGY0Y
jJmZTI2MDZiNGU1ZDk5MTNjYjY3MTcwYjdlMDM=|caa84e45c938a438e74fe746b2d337a2e50d7882
a22c70ec0f114d22aa337feb\"; username-localhost-8888=\"2|1:0|10:1569509473|23:use
rname-localhost-8888|44:MDFkMmNlYjcwYzgxNGY3M2JlYmFjYTA4OTE2MGMwNDI=|d3bdb147f2b
afff4d6e7528326a74e6b7d13199b6f63400e84e2c00af8337dbf\""
    }
[E 15:51:13.248 LabApp] 500 POST /api/sessions?1569509473167 (::1) 69.19ms refer
er=http://localhost:8888/lab
[E 15:51:38.978 LabApp] Uncaught exception POST /api/sessions?1569509497781 (::1
)
    HTTPServerRequest(protocol='http', host='localhost:8888', method='POST', uri
='/api/sessions?1569509497781', version='HTTP/1.1', remote_ip='::1')
    Traceback (most recent call last):
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\tornado\we
b.py", line 1699, in _execute
        result = await result
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\tornado\ge
n.py", line 742, in run
        yielded = self.gen.throw(*exc_info)  # type: ignore
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\notebook\s
ervices\sessions\handlers.py", line 72, in post
        type=mtype))
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\tornado\ge
n.py", line 735, in run
        value = future.result()
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\tornado\ge
n.py", line 742, in run
        yielded = self.gen.throw(*exc_info)  # type: ignore
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\notebook\s
ervices\sessions\sessionmanager.py", line 88, in create_session
        kernel_id = yield self.start_kernel_for_session(session_id, path, name,
type, kernel_name)
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\tornado\ge
n.py", line 735, in run
        value = future.result()
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\tornado\ge
n.py", line 742, in run
        yielded = self.gen.throw(*exc_info)  # type: ignore
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\notebook\s
ervices\sessions\sessionmanager.py", line 101, in start_kernel_for_session
        self.kernel_manager.start_kernel(path=kernel_path, kernel_name=kernel_na
me)
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\tornado\ge
n.py", line 735, in run
        value = future.result()
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\tornado\ge
n.py", line 209, in wrapper
        yielded = next(result)
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\notebook\s
ervices\kernels\kernelmanager.py", line 168, in start_kernel
        super(MappingKernelManager, self).start_kernel(**kwargs)
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\jupyter_cl
ient\multikernelmanager.py", line 110, in start_kernel
        km.start_kernel(**kwargs)
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\jupyter_cl
ient\manager.py", line 240, in start_kernel
        self.write_connection_file()
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\jupyter_cl
ient\connect.py", line 547, in write_connection_file
        kernel_name=self.kernel_name
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\jupyter_cl
ient\connect.py", line 212, in write_connection_file
        with secure_write(fname) as f:
      File "C:\Users\xxx\.conda\envs\test\lib\contextlib.py", line 112
, in __enter__
        return next(self.gen)
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\jupyter_cl
ient\connect.py", line 100, in secure_write
        win32_restrict_file_to_user(fname)
      File "C:\Users\xxx\.conda\envs\test\lib\site-packages\jupyter_cl
ient\connect.py", line 61, in win32_restrict_file_to_user
        sd = win32security.GetFileSecurity(fname, win32security.DACL_SECURITY_IN
FORMATION)
    pywintypes.error: (50, 'GetFileSecurity', 'The request is not supported.')
[W 15:51:38.984 LabApp] Unhandled error
[E 15:51:38.985 LabApp] {
      "Host": "localhost:8888",
      "Connection": "keep-alive",
      "Content-Length": "97",
      "Pragma": "no-cache",
      "Cache-Control": "no-cache",
      "Authorization": "token e2f1c73d291f7e884d3c618eb4383196c2d75484a0f88d96",

      "Origin": "http://localhost:8888",
      "X-Xsrftoken": "2|e0797587|bfb0295d2cfd16737a016247e6e4c3bb|1569403253",
      "User-Agent": "Mozilla/5.0 (Windows NT 6.3; Win64; x64) AppleWebKit/537.36
 (KHTML, like Gecko) Chrome/73.0.3683.75 Safari/537.36",
      "Content-Type": "application/json",
      "Accept": "*/*",
      "Referer": "http://localhost:8888/lab",
      "Accept-Encoding": "gzip, deflate, br",
      "Accept-Language": "en-US,en;q=0.9",
      "Cookie": "_xsrf=2|e0797587|bfb0295d2cfd16737a016247e6e4c3bb|1569403253; u
sername-localhost-8889=\"2|1:0|10:1569504770|23:username-localhost-8889|44:NGY0Y
jJmZTI2MDZiNGU1ZDk5MTNjYjY3MTcwYjdlMDM=|caa84e45c938a438e74fe746b2d337a2e50d7882
a22c70ec0f114d22aa337feb\"; username-localhost-8888=\"2|1:0|10:1569509486|23:use
rname-localhost-8888|44:OWMzYTU5MjgzZDQ0NDQ5Zjk3ZDZkYzUzNTE5MDYxMjQ=|fc18aa7b12f
dfb162c64a2236e57c93d1088d13b7ae52fd63a37ffd9e815de38\""
    }
[E 15:51:38.986 LabApp] 500 POST /api/sessions?1569509497781 (::1) 25.07ms refer
er=http://localhost:8888/lab

Upvotes: 0

Answers (3)

crisprog

Reputation: 2444

You probably have solved the problem by yourselves in the meantime, but since I just spent a whole Sunday finding a solution I want to share it with you.

My problem was the same as yours and I could NOT downgrade Jupyter client because spyder is requiring me to have the most recent one. The source of the problem was a roaming-drive which seems to have issues with Jupyter. You seem to have the same issue (see file://A-FILEDATA-COV-P/Profile/xxx/...).

The solution was inspired by a Github issue comment(see below) and involves the following:

Open the Start Search, type in “env”, and choose “Edit the system environment variables”:
Click the “Environment Variables…” button.
Then 'New' System Variable.
Variable name = "JUPYTER_RUNTIME_DIR".
Value = %path you want%
I had "D:\Jupyter".

Press 'New' System Variable again.

Variable name = "JUPYTER_DATA_DIR".
Value = %path you want% (I had "D:\Jupyter\data")

This finally solved the issue of Jupyter notebook AND spyder ipython console, without downgrading anything. Hope it helps to whoever reads it and prevents another wasted Sunday.

https://github.com/jupyter/jupyter_client/issues/481#issuecomment-586637730

Upvotes: 1

Anky

Reputation: 13

I tried downgrading the jupyter notebook to 5.3.1 and it worked for me.

pip install jupyter-client==5.3.1

Upvotes: 0

Sal

Reputation: 341

Installing some packages, caused Jupyter to upgrade to the latest version, which has a bug related to file permissions on windows.

a work around for anyone facing this problem is to downgrade Jupyter version again after completing the installation of all packages you need.

The problem is related to Jupyter client but to retain full functionality you will find that you need to downgrade jupyter server too. Here is the command lines to do it in Anaconda:

conda install jupyterlab_server=1.0.0 jupyter_client=5.3.1

here is a link to the ticket I opened on Jupyter client gitHub for more details: https://github.com/jupyter/jupyter_client/issues/481

The comments mentions an update to Jupyter that fixes this issues, but I have not tested that yet.

updated answer:

The problem you have may be due to access rights for the browser as well as for jupyter lab to run as I have painfully just found.

My original answer can be found here: https://github.com/jupyter/jupyter_client/issues/481

But here is my story for others who want to continue to use the latest Jupyter lab/Notebook version:

(I run Anconda which comes pre installed with Jupyter):

1- When checking the environment paths by using this command: jupyter --paths I get two roaming locations one for runtime and one for data! This is because I use a corporate laptop and Windows is setup to store user data files in a roaming location on the network!

(base) C:\>jupyter --paths
config:
    C:\Users\user_x\.jupyter
    C:\ProgramData\Anaconda3\etc\jupyter
    C:\ProgramData\jupyter
data:
    \\A-FILEDATA-P\Profile\use_x\AppData\Roaming\jupyter
    C:\ProgramData\Anaconda3\share\jupyter
    C:\ProgramData\jupyter
runtime:
    \\A-FILEDATA-P\Profile\use_x\AppData\Roaming\jupyter\runtime

(base) C:\>

2- So, I tried modifying C:\Users\user_xxx.jupyter\jupyter_notebook_config.py by adding JUPYTER_RUNTIME_DIR = 'C:\Users\user_x\AppData\Roaming\jupyter\runtime' but it did not work!

2- However, Big note here: I noticed that jupyter lab command fire a "stand alone" Chrome I have on a removable usb harddisk! which under the corporate Windows setup does not have any rights to write to other folder location on the laptop, thus the security error!

3- The solution was to setup two folders on my usb disk, where stand alone Chrome is found and set the environment variables to point to those locations like this:

set JUPYTER_RUNTIME_DIR=D:\jupyter\runtime
set JUPYTER_DATA_DIR=D:\jupyter

4- The only catch is that you have to do these two commands at the start of every new session as they don't persist say when you restart Jupyter lab! and as @Shongololo pointed out you can only run other programs like Spyder from the command line only for it to read the correct settings!

It remains to be found out how this could be resolved permanently.

Upvotes: 0

jupyter notebook on anaconda - &quot;win32security&quot; kernal error

Answers (3)

Related Questions

jupyter notebook on anaconda - "win32security" kernal error