Notebook won't open (ein:content-query-contents--error REQUEST-STATUS timeout DATA interrupt)

[dickmao]

I read the docs regarding trust. It's there to prevent random javascript embedded in cell outputs from executing upon notebook-open (another browser-related thing that doesn't apply to EIN). That's why removing outputs cures the problem. One no-going-back way of doing this is:

jupyter nbconvert --clear-output --inplace foo.ipynb

I've found jupyter trust foo.ipynb can be hit or miss on remote servers since the signature file you just re-permissioned is very likely not the one squirreled away in /opt/conda, or whatever arcane directory the remote server is running out of.

This issue remains open insofar as we need to produce a less cryptic error.

Was #773 #361

[sam-s]

jupyter trust does not help

[impaktor]

I had the same problem, the notebook had 2-3 figures (file is 2 MB). jupyter trust seems to fix it.

[sam-s]

I get

[error] request--callback: peculiar error [4 times]
ein: [error] ein:content-query-contents--error http://dev-dsk-sdsg-1e-cfbb346a.us-east-1.amazon.com:8080/aps-split.ipynb REQUEST-STATUS timeout DATA interrupt: 2

even after

$ jupyter trust aps-split.ipynb 
Signing notebook: aps-split.ipynb

the notebook is 1,740,383 bytes.

[sam-s]

Moreover, file size does not determine success or failure. I just opened a 2.2MB notebook (the one mentioned above, i.e., it failed before!), but failed to open a 722kB one (neither is trusted - the server was rebooted, apparently, jupyter trust does not persist).

[sam-s]

The abovementioned notebook works, but cannot be saved:

Debugger entered--Lisp error: (error "process request curl no longer connected to pipe; ...")
  process-send-region(#<process request curl> 1 2917121)
  request--curl("http://dev-dsk-sdsg-1e-cfbb346a.us-east-1.amazon.c..." :type "PUT" :headers (("Content-Type" . "application/json") ("User-Agent" . "Mozilla/5.0") ("X-XSRFTOKEN" . "2|c1fc5c61|6d0dd2baa4654b678afe8333c038e3cb|162448...")) :data "{\"type\":\"notebook\",\"name\":\"aps-split.ipynb\",\"path\"..." :success #f(compiled-function (&rest args2) #<bytecode -0x2e42f5c1ea266bc>) :error #f(compiled-function (&rest args2) #<bytecode 0xfb274d250702ed7>) :timeout 1.0 :sync nil :encoding binary :url "http://dev-dsk-sdsg-1e-cfbb346a.us-east-1.amazon.c..." :response #s(request-response :status-code nil :history nil :data nil :error-thrown (error "Timeout") :symbol-status timeout :url "http://dev-dsk-sdsg-1e-cfbb346a.us-east-1.amazon.c..." :done-p nil :settings (:type "PUT" :headers (("Content-Type" . "application/json") ("User-Agent" . "Mozilla/5.0") ("X-XSRFTOKEN" . "2|c1fc5c61|6d0dd2baa4654b678afe8333c038e3cb|162448...")) :data "{\"type\":\"notebook\",\"name\":\"aps-split.ipynb\",\"path\"..." :success #f(compiled-function (&rest args2) #<bytecode -0x2e42f5c1ea266bc>) :error #f(compiled-function (&rest args2) #<bytecode 0xfb274d250702ed7>) :timeout 1.0 :sync nil :encoding binary :url "http://dev-dsk-sdsg-1e-cfbb346a.us-east-1.amazon.c..." :response #21) :-buffer #<buffer  *request curl*-809205> :-raw-header nil :-timer [t 24805 63341 922829 nil request-response--timeout-callback (#21) nil 0] :-backend curl))
  apply(request--curl "http://dev-dsk-sdsg-1e-cfbb346a.us-east-1.amazon.c..." (:type "PUT" :headers (("Content-Type" . "application/json") ("User-Agent" . "Mozilla/5.0") ("X-XSRFTOKEN" . "2|c1fc5c61|6d0dd2baa4654b678afe8333c038e3cb|162448...")) :data "{\"type\":\"notebook\",\"name\":\"aps-split.ipynb\",\"path\"..." :success #f(compiled-function (&rest args2) #<bytecode -0x2e42f5c1ea266bc>) :error #f(compiled-function (&rest args2) #<bytecode 0xfb274d250702ed7>) :timeout 1.0 :sync nil :encoding binary :url "http://dev-dsk-sdsg-1e-cfbb346a.us-east-1.amazon.c..." :response #s(request-response :status-code nil :history nil :data nil :error-thrown (error "Timeout") :symbol-status timeout :url "http://dev-dsk-sdsg-1e-cfbb346a.us-east-1.amazon.c..." :done-p nil :settings #3 :-buffer #<buffer  *request curl*-809205> :-raw-header nil :-timer [t 24805 63341 922829 nil request-response--timeout-callback (#23) nil 0] :-backend curl)))
  request("http://dev-dsk-sdsg-1e-cfbb346a.us-east-1.amazon.c..." :type "PUT" :headers (("Content-Type" . "application/json") ("User-Agent" . "Mozilla/5.0") ("X-XSRFTOKEN" . "2|c1fc5c61|6d0dd2baa4654b678afe8333c038e3cb|162448...")) :data "{\"type\":\"notebook\",\"name\":\"aps-split.ipynb\",\"path\"..." :success #f(compiled-function (&rest args2) #<bytecode -0x2e42f5c1ea266bc>) :error #f(compiled-function (&rest args2) #<bytecode 0xfb274d250702ed7>) :timeout 1.0 :sync nil :encoding binary)
  apply(request "http://dev-dsk-sdsg-1e-cfbb346a.us-east-1.amazon.c..." (:type "PUT" :headers (("Content-Type" . "application/json") ("User-Agent" . "Mozilla/5.0") ("X-XSRFTOKEN" . "2|c1fc5c61|6d0dd2baa4654b678afe8333c038e3cb|162448...")) :data "{\"type\":\"notebook\",\"name\":\"aps-split.ipynb\",\"path\"..." :success #f(compiled-function (&rest args2) #<bytecode -0x2e42f5c1ea266bc>) :error #f(compiled-function (&rest args2) #<bytecode 0xfb274d250702ed7>) :timeout 1.0 :sync nil :encoding binary))
  ein:query-singleton-ajax("http://dev-dsk-sdsg-1e-cfbb346a.us-east-1.amazon.c..." :type "PUT" :headers (("Content-Type" . "application/json")) :data "{\"type\":\"notebook\",\"name\":\"aps-split.ipynb\",\"path\"..." :success #f(compiled-function (&rest args2) #<bytecode -0x2e42f5c1ea266bc>) :error #f(compiled-function (&rest args2) #<bytecode 0xfb274d250702ed7>))
  ein:content-save(#s(ein:$content :url-or-port "http://dev-dsk-sdsg-1e-cfb..." :notebook-version 6 :name "aps-split.ipynb" :path "aps-split.ipynb" :type "notebook" :writable nil :created nil :last-modified nil :mimetype nil :raw-content ((nbformat . 4) (nbformat_minor . 5) (metadata :kernelspec ... :language_info ... :name "aps-split.ipynb") (cells . ...)) :format nil :session-p nil) ein:notebook-save-notebook-success (#s(ein:$notebook :url-or-port "http://dev-dsk-sdsg-1e-cfb..." :notebook-id nil :notebook-path "aps-split.ipynb" :kernel #s(ein:$kernel :url-or-port "http://dev-dsk-sdsg-1e-cfb..." :path "aps-split.ipynb" :kernelspec ... :events #<ein:events ein:events-1ffcafeafe78> :api-version 6 :session-id "dd17ee1a-e952-49ec-abdc-73..." :kernel-id "7244d874-6449-4a0e-88c4-65..." :shell-channel nil :iopub-channel nil :websocket ... :base-url "/api/kernels" :kernel-url "/api/kernels/7244d874-6449..." :ws-url "ws://dev-dsk-sdsg-1e-cfbb3..." :username "username" :msg-callbacks #<hash-table equal 33/65 0x1ffcb1e67737> :oinfo-cache #<hash-table equal 0/65 0x1ffcb1e6e36d> :after-start-hook nil :after-execute-hook nil) :kernelinfo #<ein:kernelinfo ein:kernelinfo-1ffcb02211b8> :kernelspec #s(ein:$kernelspec :name "python3" :display-name "Python 3" :resources ... :spec ... :language "python") :pager "*ein:pager http://dev-dsk-..." :dirty nil :metadata (:kernelspec ... :language_info ... :name "aps-split.ipynb") :notebook-name "aps-split.ipynb" :nbformat 4 :nbformat-minor 5 :events #<ein:events ein:events-1ffcafeafe78> :worksheets (#<ein:worksheet ein:worksheet-1ffcb099dbec>) :scratchsheets nil :api-version 6) nil nil) ein:notebook-save-notebook-error (#s(ein:$notebook :url-or-port "http://dev-dsk-sdsg-1e-cfb..." :notebook-id nil :notebook-path "aps-split.ipynb" :kernel #s(ein:$kernel :url-or-port "http://dev-dsk-sdsg-1e-cfb..." :path "aps-split.ipynb" :kernelspec ... :events #<ein:events ein:events-1ffcafeafe78> :api-version 6 :session-id "dd17ee1a-e952-49ec-abdc-73..." :kernel-id "7244d874-6449-4a0e-88c4-65..." :shell-channel nil :iopub-channel nil :websocket ... :base-url "/api/kernels" :kernel-url "/api/kernels/7244d874-6449..." :ws-url "ws://dev-dsk-sdsg-1e-cfbb3..." :username "username" :msg-callbacks #<hash-table equal 33/65 0x1ffcb1e67737> :oinfo-cache #<hash-table equal 0/65 0x1ffcb1e6e36d> :after-start-hook nil :after-execute-hook nil) :kernelinfo #<ein:kernelinfo ein:kernelinfo-1ffcb02211b8> :kernelspec #s(ein:$kernelspec :name "python3" :display-name "Python 3" :resources ... :spec ... :language "python") :pager "*ein:pager http://dev-dsk-..." :dirty nil :metadata (:kernelspec ... :language_info ... :name "aps-split.ipynb") :notebook-name "aps-split.ipynb" :nbformat 4 :nbformat-minor 5 :events #<ein:events ein:events-1ffcafeafe78> :worksheets (#<ein:worksheet ein:worksheet-1ffcb099dbec>) :scratchsheets nil :api-version 6) nil))
  ein:notebook-save-notebook(#s(ein:$notebook :url-or-port "http://dev-dsk-sdsg-1e-cfbb346a.us-east-1.amazon.c..." :notebook-id nil :notebook-path "aps-split.ipynb" :kernel #s(ein:$kernel :url-or-port "http://dev-dsk-sdsg-1e-cfbb346a.us-east-1.amazon.c..." :path "aps-split.ipynb" :kernelspec #s(ein:$kernelspec :name "python3" :display-name "Python 3" :resources (:logo-32x32 "/kernelspecs/python3/logo-32x32.png" :logo-64x64 "/kernelspecs/python3/logo-64x64.png") :spec (:argv ["/usr/bin/python3" "-m" "ipykernel_launcher" "-f" "{connection_file}"] :env nil :display_name "Python 3" :language "python" :interrupt_mode "signal" :metadata nil :name "python3") :language "python") :events #<ein:events ein:events-1ffcafeafe78> :api-version 6 :session-id "dd17ee1a-e952-49ec-abdc-7344dd7ae4f0" :kernel-id "7244d874-6449-4a0e-88c4-656e6f7571d9" :shell-channel nil :iopub-channel nil :websocket #s(ein:$websocket :ws #s(websocket :ready-state open :client-data #3 :on-open #f(compiled-function (&rest args2) #<bytecode -0x196ea8a8587b0861>) :on-message #f(compiled-function (&rest args2) #<bytecode 0x154504bff2cc9863>) :on-close #f(compiled-function (ws) #<bytecode -0x184dd7910c00d38e>) :on-error #f(compiled-function (ws action err) #<bytecode 0x45924031f5b73af>) :negotiated-protocols nil :negotiated-extensions nil :server-p nil :url "ws://dev-dsk-sdsg-1e-cfbb346a.us-east-1.amazon.com..." :protocols nil :extensions nil :conn #<process websocket to ws://dev-dsk-sdsg-1e-cfbb346a.us-east-1.amazon.com:8080/api/kernels/7244d874-6449-4a0e-88c4-656e6f7571d9/channels?session_id=dd17ee1a-e952-49ec-abdc-7344dd7ae4f0> :server-conn nil :accept-string "zR33+3VybAEj0DZFm92ifFgcfO0=" :inflight-input nil) :kernel #2 :closed-by-client nil) :base-url "/api/kernels" :kernel-url "/api/kernels/7244d874-6449-4a0e-88c4-656e6f7571d9" :ws-url "ws://dev-dsk-sdsg-1e-cfbb346a.us-east-1.amazon.com..." :username "username" :msg-callbacks #<hash-table equal 33/65 0x1ffcb1e67737> :oinfo-cache #<hash-table equal 0/65 0x1ffcb1e6e36d> :after-start-hook nil :after-execute-hook nil) :kernelinfo #<ein:kernelinfo ein:kernelinfo-1ffcb02211b8> :kernelspec #s(ein:$kernelspec :name "python3" :display-name "Python 3" :resources (:logo-32x32 "/kernelspecs/python3/logo-32x32.png" :logo-64x64 "/kernelspecs/python3/logo-64x64.png") :spec (:argv ["/usr/bin/python3" "-m" "ipykernel_launcher" "-f" "{connection_file}"] :env nil :display_name "Python 3" :language "python" :interrupt_mode "signal" :metadata nil :name "python3") :language "python") :pager "*ein:pager http://dev-dsk-sdsg-1e-cfbb346a.us-east..." :dirty nil :metadata (:kernelspec (:argv ["/usr/bin/python3" "-m" "ipykernel_launcher" "-f" "{connection_file}"] :env nil :display_name "Python 3" :language "python" :interrupt_mode "signal" :metadata nil :name "python3") :language_info (:codemirror_mode (:name "ipython" :version 3) :file_extension ".py" :mimetype "text/x-python" :name "python" :nbconvert_exporter "python" :pygments_lexer "ipython3" :version "3.7.9") :name "aps-split.ipynb") :notebook-name "aps-split.ipynb" :nbformat 4 :nbformat-minor 5 :events #<ein:events ein:events-1ffcafeafe78> :worksheets (#<ein:worksheet ein:worksheet-1ffcb099dbec>) :scratchsheets nil :api-version 6))

[natsirtguy]

I've noticed that if I quickly try to open a notebook again when experiencing this issue (by hitting enter twice or clicking repeatedly on the Open link) and trigger a <Notebook name> pending open! Retry? message and then say y, the notebook will open. Seems like there might be some timeout that is ignored if you say you want to retry?

[slackline]

Still experiencing this too.

[grantjenks]

For me the trick was clearing all outputs in the notebook 🤷

[nyambol]

Clearing outputs allows me to get into the notebook - but I can't save it after re-running the cells. That's not useful. I really was hoping to get away from that clunky web interface. :-\

[error] request--callback: peculiar error
ein: [error] ein:content-save-error: http://127.0.0.1:8888/api/contents/Case_Study1_Notebook.ipynb peculiar error.
ein: [warn] Failed saving notebook!
ein: [warn] ein:cell-append-mime-type: no viewer method found in mailcap

• Windows 10 Pro
• GNU Emacs 29.0.50 (build 1, x86_64-w64-mingw32) of 2021-10-12

[acegallagher]

I can report that I have the same issue on linux using emacs28. Clearing the notebook also solves the problem, I have the following jupyter packages:

Selected Jupyter core packages... IPython : 7.26.0 ipykernel : 6.4.1 ipywidgets : 7.6.5 jupyter_client : 6.1.12 jupyter_core : 4.8.1 jupyter_server : 1.10.2 jupyterlab : 3.1.9 nbclient : 0.5.4 nbconvert : 6.1.0 nbformat : 5.1.3 notebook : 6.4.4 qtconsole : 5.1.1 traitlets : 5.1.0

[matheusvcorrea]

Still a problem. After manually start a jupyter notebook on a remote server and trying to open a notebook with emacs26 get this from *ein:log-all* buffer. This notebook seems to be a bit heavy and take few seconds till be available from browser. It is also a trusted notebook.

18:43:43:261: [info] Login to http://10.41.128.71:8835 complete. @#<buffer *GNU Emacs*>
18:43:44:369: [verbose] Opening notebooklist at http://10.41.128.71:8835 @#<buffer *GNU Emacs*>
18:43:49:938: [verbose] Opening notebooklist at http://10.41.128.71:8835/models @#<buffer *ein:notebooklist http://10.41.128.71:8835*>
18:44:06:913: [verbose] Retry content-query-contents #0 in response to nil @#<buffer *ein:notebooklist http://10.41.128.71:8835*>
18:44:08:422: [verbose] Retry content-query-contents #1 in response to nil @#<buffer *ein:notebooklist http://10.41.128.71:8835*>
18:44:10:432: [verbose] Retry content-query-contents #2 in response to nil @#<buffer *ein:notebooklist http://10.41.128.71:8835*>
18:44:12:941: [error] ein:content-query-contents--error http://10.41.128.71:8835/models/XGBoost_V1.ipynb REQUEST-STATUS timeout DATA interrupt
 @#<buffer *ein:notebooklist http://10.41.128.71:8835*>

[matheusvcorrea]

This works for me: M-x customize-variable RET ein:query-timeout and modify the de default value to something like 100000 ms and apply this.

[psaris]

increasing the value of ein:query-timeout solved this issue for me as well. thank you @matheusvcorrea

[sam-s]

I set ein:query-timeout to nil and I still get

[error] request--callback: peculiar error: 403
ein: [error] ein:content-save-error: http://127.0.0.1:8888/api/contents/eeg.ipynb peculiar error: 403.
ein: [warn] Failed saving notebook!

in *Messages* and

[W 11:11:20.920 NotebookApp] 403 POST /api/sessions (127.0.0.1): XSRF cookie does not match POST argument
[W 11:11:20.920 NotebookApp] XSRF cookie does not match POST argument
[W 11:11:20.921 NotebookApp] 403 POST /api/sessions (127.0.0.1) 0.910000ms referer=None

in terminal and

11:11:20:913: [verbose] ein:kernel-session-p--success: session-id=6f0fe42c-9b4c-43df-b74a-1ad2546ae531 session-p=t @#<buffer  *ein: http://127.0.0.1:8888/eeg.ipynb*[python]>
11:11:20:925: [verbose] ein:kernel-retrieve-session--error [error], 2 tries left @#<buffer  *ein: http://127.0.0.1:8888/eeg.ipynb*[python]>
11:11:21:455: [verbose] ein:kernel-retrieve-session--error [error], 1 tries left @#<buffer  *ein: http://127.0.0.1:8888/eeg.ipynb*[python]>
11:11:22:477: [verbose] ein:kernel-retrieve-session--error [error], 0 tries left @#<buffer  *ein: http://127.0.0.1:8888/eeg.ipynb*[python]>

in *ein:log-all*