Closed falematte closed 5 years ago
dickmao
commented
5 years ago So you are running a notebook server locally on 8888 from the parent directory of ownCloudShared, then M-x notebooklist-open or M-x notebooklist-login to 8888, and trying to enter ownCloudShared from the buffer *ein:notebooklist http://127.0.0.1:8888*?
Would be helpful to see the contents of the buffer *ein:log-all*
falematte
commented
5 years ago yep! Here is the log:
09:00:22:725: [info] Starting notebook server in directory: ~/ @#<buffer *scratch*> 09:00:35:431: [info] Login to http://127.0.0.1:8888 complete. Now you can open notebook list byein:notebooklist-open @#<buffer scratch>
09:00:35:506: [verbose] Opened notebooklist at http://127.0.0.1:8888/ @#<buffer ein:notebooklist http://127.0.0.1:8888>
11:51:47:877: [info] Notebook session is already running, check the contents of ein:jupyter-server @#<buffer .emacs>
11:51:47:877: [info] Starting notebook server in directory: ~/ @#<buffer .emacs>
11:51:47:917: [info] Login to http://127.0.0.1:8888 complete. Now you can open notebook list by ein:notebooklist-open @#<buffer .emacs> 11:51:47:940: [verbose] Opened notebooklist at http://127.0.0.1:8888/ @#<buffer *ein:notebooklist http://127.0.0.1:8888*> 12:59:35:962: [verbose] Opened notebooklist at http://127.0.0.1:8888/ownCloud @#<buffer *ein:notebooklist http://127.0.0.1:8888*> 12:59:39:206: [error] ein:content-query-contents--error http://127.0.0.1:8888/ownCloudShared REQUEST-STATUS error DATA (http 404) @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
millejoh
commented
5 years ago @falematte, thanks for sharing the log. Have you confirmed that you can get to the directory using the browser interface? Also, can you share the contents of the *ein:jupyter-server* buffer? Looks like ein was able to log in; the 404 says that for some reason the jupyter server doesn't think that particular directory exists. Is it a symlink?
dickmao
commented
5 years ago Thank you. It looks like ein:jupyter-server-start was run at least twice. My experience has been that EIN doesn't handle two running servers so well. Recent changes prevent that.
I will assume you already have (add-to-list 'package-archives '("melpa" . "http://melpa.org/packages/")) in your .emacs.
Then it should be M-x package-refresh-contents, then M-x package-reinstall RET ein
Edit: I didn't see millejoh's preceding remarks. Yes, you should try what he asks too.
millejoh
commented
5 years ago Maybe all is good now? Reopen if not!
EvanMath
commented
3 years ago Hello and sorry I am writing in a closed thread but my issue is almost the same here. Here is the error: ein: [error] ein:content-query-contents--error http://127.0.0.1:8888/revisions_eda_first_approach.ipynb REQUEST-STATUS timeout DATA interrupt
Some notebooks open correctly but some of them throw the above error.
I have run ein:dev-bug-report-template and the last rows are the same like this: [W 21:36:52.072 NotebookApp] Notebook revisions_eda_first_approach.ipynb is not trusted.
I have already tried the above, to reinstall the package but the problem remains.
dickmao
commented
3 years ago Add to .emacs
(with-eval-after-load 'ein-contents-api
(ein:dev-start-debug))Then when the error reoccurs, M-x ein:dev-bug-report-template and copy output here.
EvanMath
commented
3 years ago Hello and thank you for your reply.
Just to clarify it, should I add this to my init.el or inside the ein configuration block?
dickmao
commented
3 years ago Is an "ein configuration block" a use-package clause? Does the "ein configuration block" live outside init.el? Maybe just put the with-eval-after-load in the init.el right after package-initialize. I am assuming you don't use doom or spacemacs.
EvanMath
commented
3 years ago Is an "ein configuration block" a use-package clause? Does the "ein configuration block" live outside init.el? Maybe just put the with-eval-after-load in the init.el right after package-initialize. I am assuming you don't use doom or spacemacs.
Yes, it is a use-package clause, correct. No, I am not using doom or spacemacs. Ok, the first try gave me a too long report. But I will add this snippet as you said.
dickmao
commented
3 years ago Then something like
(use-package ein
:config
(with-eval-after-load 'ein-contents-api
(ein:dev-start-debug))
;; other :config clauses
)would also work. If by "first try" you mean the error triggered, and ein:dev-bug-report-template produced too much output, then I don't see how a future trigger would produce a shorter report.
EvanMath
commented
3 years ago Correct. Should I put all this output here?
EvanMath
commented
3 years ago ("EIN system info"
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Distributor ID: Ubuntu
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[debug] request--curl-callback: event finished
[debug] request--callback: UNPARSED
HTTP/1.1 200 OK
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[debug] request--callback: executing success
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[debug] request--callback: executing complete
[debug] request--curl-callback: event finished
[debug] request--callback: UNPARSED
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[debug] request--curl-callback: event finished
[debug] request--callback: UNPARSED
HTTP/1.1 200 OK
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[debug] request--callback: PARSED
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[debug] request--callback: executing success
[debug] request--curl: curl --silent --location --cookie /home/emath/.cache/emacs/var/request/storage/curl-cookie-jar --cookie-jar /home/emath/.cache/emacs/var/request/storage/curl-cookie-jar --include --write-out \n(:num-redirects %{num_redirects} :url-effective "%{url_effective}") --trace-ascii /tmp/curl-trace --compressed --request GET --header User-Agent: Mozilla/5.0 --header X-XSRFTOKEN: 2|705cdbca|805d7a3552166f5f00b13fc2f2178050|1611669679 http://127.0.0.1:8888/api/contents
[debug] request--callback: executing complete
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[debug] request--curl-callback: event finished
[debug] request--callback: UNPARSED
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[debug] request--curl-callback: event finished
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[debug] request--callback: executing success
[debug] request--curl: curl --silent --location --cookie /home/emath/.cache/emacs/var/request/storage/curl-cookie-jar --cookie-jar /home/emath/.cache/emacs/var/request/storage/curl-cookie-jar --include --write-out \n(:num-redirects %{num_redirects} :url-effective "%{url_effective}") --trace-ascii /tmp/curl-trace --compressed --request GET --header User-Agent: Mozilla/5.0 --header X-XSRFTOKEN: 2|705cdbca|805d7a3552166f5f00b13fc2f2178050|1611669679 http://127.0.0.1:8888/api/sessions
[debug] request--callback: executing complete
[debug] request--curl-callback: event finished
[debug] request--callback: UNPARSED
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Server: TornadoServer/6.1
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Date: Wed, 27 Jan 2021 14:31:52 GMT
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[debug] request--curl-callback: event finished
[debug] request--callback: UNPARSED
HTTP/1.1 200 OK
Server: TornadoServer/6.1
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Date: Wed, 27 Jan 2021 14:31:52 GMT
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[debug] request--callback: executing success
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[debug] request--curl-callback: event finished
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[debug] request--callback: PARSED
(:name Data :path Data :last_modified 2020-12-16T19:46:53Z :created 2020-12-16T19:46:53Z :content [(:name biographies_rev_histroy.json :path Data/biographies_rev_histroy.json :last_modified 2021-01-16T10:13:41Z :created 2021-01-16T10:13:41Z :content nil :format nil :mimetype application/json :size 727123459 :writable t :type file) (:name pos_domain_words.txt :path Data/pos_domain_words.txt :last_modified 2021-01-21T18:16:09Z :created 2021-01-21T18:16:09Z :content nil :format nil :mimetype text/plain :size 40080 :writable t :type file) (:name biographies_rev_histroy_new.json :path Data/biographies_rev_histroy_new.json :last_modified 2021-01-20T14:05:59Z :created 2021-01-20T14:05:59Z :content nil :format nil :mimetype application/json :size 732627082 :writable t :type file) (:name neg_domain_words.txt :path Data/neg_domain_words.txt :last_modified 2021-01-21T18:16:02Z :created 2021-01-21T18:16:02Z :content nil :format nil :mimetype text/plain :size 38171 :writable t :type file) (:name Angela_Merkel.json :path Data/Angela_Merkel.json :last_modified 2020-12-16T19:50:05Z :created 2020-12-16T19:50:05Z :content nil :format nil :mimetype application/json :size 195478664 :writable t :type file)] :format json :mimetype nil :size nil :writable t :type directory)
[debug] request--callback: executing success
[debug] request--callback: executing complete
[debug] request--curl-callback: event finished
[debug] request--callback: UNPARSED
HTTP/1.1 200 OK
Server: TornadoServer/6.1
Content-Type: application/json
Date: Wed, 27 Jan 2021 14:31:52 GMT
X-Content-Type-Options: nosniff
Content-Security-Policy: frame-ancestors 'self'; report-uri /api/security/csp-report; default-src 'none'
Last-Modified: Wed, 16 Dec 2020 19:46:13 GMT
Etag: "5312d475841c50a91cf0b66719478a0342a15bb8"
Content-Length: 4173
{"name": "Images", "path": "Images", "last_modified": "2020-12-16T19:46:13Z", "created": "2020-12-16T19:46:13Z", "content": [{"name": "mitsotakis_polarity_and_length.jpg", "path": "Images/mitsotakis_polarity_and_length.jpg", "last_modified": "2021-01-05T09:54:42Z", "created": "2021-01-05T09:54:42Z", "content": null, "format": null, "mimetype": "image/jpeg", "size": 59763, "writable": true, "type": "file"}, {"name": "merkel_polarity_and_length.jpg", "path": "Images/merkel_polarity_and_length.jpg", "last_modified": "2021-01-05T10:43:27Z", "created": "2021-01-05T10:43:27Z", "content": null, "format": null, "mimetype": "image/jpeg", "size": 63752, "writable": true, "type": "file"}, {"name": "Sentiment-Length on Angela Merkel's Revisions.png", "path": "Images/Sentiment-Length on Angela Merkel's Revisions.png", "last_modified": "2021-01-08T12:06:29Z", "created": "2021-01-08T12:06:29Z", "content": null, "format": null, "mimetype": "image/png", "size": 41120, "writable": true, "type": "file"}, {"name": "pos_words_dens.png", "path": "Images/pos_words_dens.png", "last_modified": "2021-01-21T20:01:26Z", "created": "2021-01-21T20:01:26Z", "content": null, "format": null, "mimetype": "image/png", "size": 94215, "writable": true, "type": "file"}, {"name": "weekly_polarity.png", "path": "Images/weekly_polarity.png", "last_modified": "2021-01-07T17:17:30Z", "created": "2021-01-07T17:17:30Z", "content": null, "format": null, "mimetype": "image/png", "size": 68164, "writable": true, "type": "file"}, {"name": "Revision's Length of Recep Tayyip Erdo\u011fan's Biography.jpg", "path": "Images/Revision's Length of Recep Tayyip Erdo\u011fan's Biography.jpg", "last_modified": "2020-12-14T08:31:43Z", "created": "2020-12-14T08:31:43Z", "content": null, "format": null, "mimetype": "image/jpeg", "size": 81851, "writable": true, "type": "file"}, {"name": "neg_words_conc_weekly.png", "path": "Images/neg_words_conc_weekly.png", "last_modified": "2021-01-22T16:36:41Z", "created": "2021-01-22T16:36:41Z", "content": null, "format": null, "mimetype": "image/png", "size": 79304, "writable": true, "type": "file"}, {"name": "polarity_monthly.png", "path": "Images/polarity_monthly.png", "last_modified": "2021-01-07T17:17:30Z", "created": "2021-01-07T17:17:30Z", "content": null, "format": null, "mimetype": "image/png", "size": 66198, "writable": true, "type": "file"}, {"name": "subjectivity_on_Angela_Merkel's_Revisions.png", "path": "Images/subjectivity_on_Angela_Merkel's_Revisions.png", "last_modified": "2021-01-10T07:59:58Z", "created": "2021-01-10T07:59:58Z", "content": null, "format": null, "mimetype": "image/png", "size": 28169, "writable": true, "type": "file"}, {"name": "polarity_monthly_more.png", "path": "Images/polarity_monthly_more.png", "last_modified": "2021-01-07T16:59:04Z", "created": "2021-01-07T16:59:04Z", "content": null, "format": null, "mimetype": "image/png", "size": 100371, "writable": true, "type": "file"}, {"name": "polarity_on_Angela_Merkel's_Revisions.png", "path": "Images/polarity_on_Angela_Merkel's_Revisions.png", "last_modified": "2021-01-10T07:58:50Z", "created": "2021-01-10T07:58:50Z", "content": null, "format": null, "mimetype": "image/png", "size": 25383, "writable": true, "type": "file"}, {"name": "Sentiment on Recep Tayyip Erdo\u011fan's Revisions.jpg", "path": "Images/Sentiment on Recep Tayyip Erdo\u011fan's Revisions.jpg", "last_modified": "2020-12-14T08:31:42Z", "created": "2020-12-14T08:31:42Z", "content": null, "format": null, "mimetype": "image/jpeg", "size": 55738, "writable": true, "type": "file"}, {"name": "pos_words_conc_weekly.png", "path": "Images/pos_words_conc_weekly.png", "last_modified": "2021-01-22T16:34:52Z", "created": "2021-01-22T16:34:52Z", "content": null, "format": null, "mimetype": "image/png", "size": 74419, "writable": true, "type": "file"}, {"name": "neg_words_dens.png", "path": "Images/neg_words_dens.png", "last_modified": "2021-01-21T20:07:38Z", "created": "2021-01-21T20:07:38Z", "content": null, "format": null, "mimetype": "image/png", "size": 94763, "writable": true, "type": "file"}], "format": "json", "mimetype": null, "size": null, "writable": true, "type": "directory"}
[debug] request--callback: PARSED
(:name Images :path Images :last_modified 2020-12-16T19:46:13Z :created 2020-12-16T19:46:13Z :content [(:name mitsotakis_polarity_and_length.jpg :path Images/mitsotakis_polarity_and_length.jpg :last_modified 2021-01-05T09:54:42Z :created 2021-01-05T09:54:42Z :content nil :format nil :mimetype image/jpeg :size 59763 :writable t :type file) (:name merkel_polarity_and_length.jpg :path Images/merkel_polarity_and_length.jpg :last_modified 2021-01-05T10:43:27Z :created 2021-01-05T10:43:27Z :content nil :format nil :mimetype image/jpeg :size 63752 :writable t :type file) (:name Sentiment-Length on Angela Merkel's Revisions.png :path Images/Sentiment-Length on Angela Merkel's Revisions.png :last_modified 2021-01-08T12:06:29Z :created 2021-01-08T12:06:29Z :content nil :format nil :mimetype image/png :size 41120 :writable t :type file) (:name pos_words_dens.png :path Images/pos_words_dens.png :last_modified 2021-01-21T20:01:26Z :created 2021-01-21T20:01:26Z :content nil :format nil :mimetype image/png :size 94215 :writable t :type file) (:name weekly_polarity.png :path Images/weekly_polarity.png :last_modified 2021-01-07T17:17:30Z :created 2021-01-07T17:17:30Z :content nil :format nil :mimetype image/png :size 68164 :writable t :type file) (:name Revision's Length of Recep Tayyip Erdoğan's Biography.jpg :path Images/Revision's Length of Recep Tayyip Erdoğan's Biography.jpg :last_modified 2020-12-14T08:31:43Z :created 2020-12-14T08:31:43Z :content nil :format nil :mimetype image/jpeg :size 81851 :writable t :type file) (:name neg_words_conc_weekly.png :path Images/neg_words_conc_weekly.png :last_modified 2021-01-22T16:36:41Z :created 2021-01-22T16:36:41Z :content nil :format nil :mimetype image/png :size 79304 :writable t :type file) (:name polarity_monthly.png :path Images/polarity_monthly.png :last_modified 2021-01-07T17:17:30Z :created 2021-01-07T17:17:30Z :content nil :format nil :mimetype image/png :size 66198 :writable t :type file) (:name subjectivity_on_Angela_Merkel's_Revisions.png :path Images/subjectivity_on_Angela_Merkel's_Revisions.png :last_modified 2021-01-10T07:59:58Z :created 2021-01-10T07:59:58Z :content nil :format nil :mimetype image/png :size 28169 :writable t :type file) (:name polarity_monthly_more.png :path Images/polarity_monthly_more.png :last_modified 2021-01-07T16:59:04Z :created 2021-01-07T16:59:04Z :content nil :format nil :mimetype image/png :size 100371 :writable t :type file) (:name polarity_on_Angela_Merkel's_Revisions.png :path Images/polarity_on_Angela_Merkel's_Revisions.png :last_modified 2021-01-10T07:58:50Z :created 2021-01-10T07:58:50Z :content nil :format nil :mimetype image/png :size 25383 :writable t :type file) (:name Sentiment on Recep Tayyip Erdoğan's Revisions.jpg :path Images/Sentiment on Recep Tayyip Erdoğan's Revisions.jpg :last_modified 2020-12-14T08:31:42Z :created 2020-12-14T08:31:42Z :content nil :format nil :mimetype image/jpeg :size 55738 :writable t :type file) (:name pos_words_conc_weekly.png :path Images/pos_words_conc_weekly.png :last_modified 2021-01-22T16:34:52Z :created 2021-01-22T16:34:52Z :content nil :format nil :mimetype image/png :size 74419 :writable t :type file) (:name neg_words_dens.png :path Images/neg_words_dens.png :last_modified 2021-01-21T20:07:38Z :created 2021-01-21T20:07:38Z :content nil :format nil :mimetype image/png :size 94763 :writable t :type file)] :format json :mimetype nil :size nil :writable t :type directory)
[debug] request--callback: executing success
[debug] request--callback: executing complete
[debug] request--curl: curl --silent --location --cookie /home/emath/.cache/emacs/var/request/storage/curl-cookie-jar --cookie-jar /home/emath/.cache/emacs/var/request/storage/curl-cookie-jar --include --write-out \n(:num-redirects %{num_redirects} :url-effective "%{url_effective}") --trace-ascii /tmp/curl-trace --compressed --request GET --header User-Agent: Mozilla/5.0 --header X-XSRFTOKEN: 2|705cdbca|805d7a3552166f5f00b13fc2f2178050|1611669679 http://127.0.0.1:8888/api/contents/revisions_eda_first_approach.ipynb
[debug] request--curl-callback: event interrupt
[debug] request--callback: UNPARSED
HTTP/1.1 200 OK
Server: TornadoServer/6.1
Content-Type: application/json
Date: Wed, 27 Jan 2021 14:31:56 GMT
X-Content-Type-Options: nosniff
Content-Security-Policy: frame-ancestors 'self'; report-uri /api/security/csp-report; default-src 'none'
Last-Modified: Wed, 20 Jan 2021 14:00:36 GMT
Etag: "e0ddc7a2a578b9b6ca1fcc5023607c83bfc621ea"
Content-Length: 57816516:31:50:738: [info] ein:jupyter-server--run: /home/emath/anaconda3/bin/jupyter notebook --notebook-dir=/home/emath/google-drive/MSc Data Science/AI Lab-Research/Wikipedia API/ --debug --no-browser @#<buffer *scratch*>
16:31:52:198: [debug] Login attempt #0 in response to nil from http://127.0.0.1:8888. @#<buffer *scratch*>
16:31:52:199: [debug] EIN:QUERY-PREPARE-HEADER: Found xsrf: 2|705cdbca|805d7a3552166f5f00b13fc2f2178050|1611669679 @#<buffer *scratch*>
16:31:52:283: [info] Login to http://127.0.0.1:8888 complete. @#<buffer *scratch*>
16:31:52:285: [debug] EIN:QUERY-PREPARE-HEADER: Found xsrf: 2|705cdbca|805d7a3552166f5f00b13fc2f2178050|1611669679 @#<buffer *scratch*>
16:31:52:287: [debug] ein:notebooklist-login--complete STATUS: 200 DATA: (:bad-page nil) @#<buffer *scratch*>
16:31:52:317: [debug] ein:query-notebook-version--complete STATUS: 200 DATA: (:version 6.2.0) @#<buffer *scratch*>
16:31:52:318: [debug] EIN:QUERY-PREPARE-HEADER: Found xsrf: 2|705cdbca|805d7a3552166f5f00b13fc2f2178050|1611669679 @#<buffer *scratch*>
16:31:52:351: [debug] EIN:QUERY-PREPARE-HEADER: Found xsrf: 2|705cdbca|805d7a3552166f5f00b13fc2f2178050|1611669679 @#<buffer *scratch*>
16:31:52:352: [debug] ein:query-kernelspecs--complete STATUS: 200 DATA: (:default python3 :kernelspecs (:python3 (:name python3 :spec (:argv [python -m ipykernel_launcher -f {connection_file}] :env nil :display_name Python 3 :language python :interrupt_mode signal :metadata nil) :resources (:logo-32x32 /kernelspecs/python3/logo-32x32.png :logo-64x64 /kernelspecs/python3/logo-64x64.png)))) @#<buffer *scratch*>
16:31:52:359: [debug] EIN:QUERY-PREPARE-HEADER: Found xsrf: 2|705cdbca|805d7a3552166f5f00b13fc2f2178050|1611669679 @#<buffer *scratch*>
16:31:52:390: [debug] EIN:QUERY-PREPARE-HEADER: Found xsrf: 2|705cdbca|805d7a3552166f5f00b13fc2f2178050|1611669679 @#<buffer *scratch*>
16:31:52:392: [debug] ein:query-sessions--complete STATUS: 200 DATA: [] @#<buffer *scratch*>
16:31:52:393: [verbose] Opening notebooklist at http://127.0.0.1:8888 @#<buffer *scratch*>
16:31:52:403: [debug] EIN:QUERY-PREPARE-HEADER: Found xsrf: 2|705cdbca|805d7a3552166f5f00b13fc2f2178050|1611669679 @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:31:52:404: [debug] ein:query-contents--complete STATUS: 200 DATA: (:name :path :last_modified 2020-11-06T09:10:04Z :created 2020-11-06T09:10:04Z :content [(:name Sentiment_Analysis.ipynb :path Sentiment_Analysis.ipynb :last_modified 2020-11-25T19:50:33Z :created 2020-11-25T19:50:33Z :content nil :format nil :mimetype nil :size 41747 :writable t :type notebook) (:name download_revisions.ipynb :path download_revisions.ipynb :last_modified 2021-01-20T14:06:10Z :created 2021-01-20T14:06:10Z :content nil :format nil :mimetype nil :size 30298 :writable t :type notebook) (:name Images :path Images :last_modified 2020-12-16T19:46:13Z :created 2020-12-16T19:46:13Z :content nil :format nil :mimetype nil :size nil :writable t :type directory) (:name LingBiasWiki.pdf :path LingBiasWiki.pdf :last_modified 2021-01-23T14:53:33Z :created 2021-01-23T14:53:33Z :content nil :format nil :mimetype application/pdf :size 512193 :writable t :type file) (:name eda_timeseries_analysis.ipynb :path eda_times @#<buffer *scratch*>
16:31:52:547: [debug] ein:query-sessions--complete STATUS: 200 DATA: [] @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:31:52:548: [debug] EIN:QUERY-PREPARE-HEADER: Found xsrf: 2|705cdbca|805d7a3552166f5f00b13fc2f2178050|1611669679 @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:31:52:549: [debug] EIN:QUERY-PREPARE-HEADER: Found xsrf: 2|705cdbca|805d7a3552166f5f00b13fc2f2178050|1611669679 @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:31:52:550: [debug] ein:query-contents--complete STATUS: 200 DATA: (:name :path :last_modified 2020-11-06T09:10:04Z :created 2020-11-06T09:10:04Z :content [(:name Sentiment_Analysis.ipynb :path Sentiment_Analysis.ipynb :last_modified 2020-11-25T19:50:33Z :created 2020-11-25T19:50:33Z :content nil :format nil :mimetype nil :size 41747 :writable t :type notebook) (:name download_revisions.ipynb :path download_revisions.ipynb :last_modified 2021-01-20T14:06:10Z :created 2021-01-20T14:06:10Z :content nil :format nil :mimetype nil :size 30298 :writable t :type notebook) (:name Images :path Images :last_modified 2020-12-16T19:46:13Z :created 2020-12-16T19:46:13Z :content nil :format nil :mimetype nil :size nil :writable t :type directory) (:name LingBiasWiki.pdf :path LingBiasWiki.pdf :last_modified 2021-01-23T14:53:33Z :created 2021-01-23T14:53:33Z :content nil :format nil :mimetype application/pdf :size 512193 :writable t :type file) (:name eda_timeseries_analysis.ipynb :path eda_times @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:31:52:593: [debug] ein:query-contents--complete STATUS: 200 DATA: (:name Data :path Data :last_modified 2020-12-16T19:46:53Z :created 2020-12-16T19:46:53Z :content [(:name biographies_rev_histroy.json :path Data/biographies_rev_histroy.json :last_modified 2021-01-16T10:13:41Z :created 2021-01-16T10:13:41Z :content nil :format nil :mimetype application/json :size 727123459 :writable t :type file) (:name pos_domain_words.txt :path Data/pos_domain_words.txt :last_modified 2021-01-21T18:16:09Z :created 2021-01-21T18:16:09Z :content nil :format nil :mimetype text/plain :size 40080 :writable t :type file) (:name biographies_rev_histroy_new.json :path Data/biographies_rev_histroy_new.json :last_modified 2021-01-20T14:05:59Z :created 2021-01-20T14:05:59Z :content nil :format nil :mimetype application/json :size 732627082 :writable t :type file) (:name neg_domain_words.txt :path Data/neg_domain_words.txt :last_modified 2021-01-21T18:16:02Z :created 2021-01-21T18:16:02Z :content nil :format n @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:31:52:595: [debug] ein:query-contents--complete STATUS: 200 DATA: (:name Images :path Images :last_modified 2020-12-16T19:46:13Z :created 2020-12-16T19:46:13Z :content [(:name mitsotakis_polarity_and_length.jpg :path Images/mitsotakis_polarity_and_length.jpg :last_modified 2021-01-05T09:54:42Z :created 2021-01-05T09:54:42Z :content nil :format nil :mimetype image/jpeg :size 59763 :writable t :type file) (:name merkel_polarity_and_length.jpg :path Images/merkel_polarity_and_length.jpg :last_modified 2021-01-05T10:43:27Z :created 2021-01-05T10:43:27Z :content nil :format nil :mimetype image/jpeg :size 63752 :writable t :type file) (:name Sentiment-Length on Angela Merkel's Revisions.png :path Images/Sentiment-Length on Angela Merkel's Revisions.png :last_modified 2021-01-08T12:06:29Z :created 2021-01-08T12:06:29Z :content nil :format nil :mimetype image/png :size 41120 :writable t :type file) (:name pos_words_dens.png :path Images/pos_words_dens.png :last_modified 2021-01-21T20:01:26Z @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:31:56:903: [debug] EIN:QUERY-PREPARE-HEADER: Found xsrf: 2|705cdbca|805d7a3552166f5f00b13fc2f2178050|1611669679 @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:31:57:994: [verbose] Retry content-query-contents #0 in response to nil @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:31:58:499: [debug] EIN:QUERY-PREPARE-HEADER: Found xsrf: 2|705cdbca|805d7a3552166f5f00b13fc2f2178050|1611669679 @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:31:58:502: [debug] ein:query-contents--complete STATUS: nil DATA: nil @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:31:59:531: [verbose] Retry content-query-contents #1 in response to nil @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:32:00:534: [debug] EIN:QUERY-PREPARE-HEADER: Found xsrf: 2|705cdbca|805d7a3552166f5f00b13fc2f2178050|1611669679 @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:32:00:538: [debug] ein:query-contents--complete STATUS: nil DATA: nil @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:32:01:618: [verbose] Retry content-query-contents #2 in response to nil @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:32:03:123: [debug] EIN:QUERY-PREPARE-HEADER: Found xsrf: 2|705cdbca|805d7a3552166f5f00b13fc2f2178050|1611669679 @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:32:03:126: [debug] ein:query-contents--complete STATUS: nil DATA: nil @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:32:04:153: [error] ein:content-query-contents--error http://127.0.0.1:8888/revisions_eda_first_approach.ipynb REQUEST-STATUS timeout DATA interrupt
@#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:32:04:163: [debug] ein:query-contents--complete STATUS: nil DATA: nil @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
16:32:10:320: [warn] ein:dev-packages: Don’t call me! @#<buffer *temp*>[D 16:31:51.026 NotebookApp] Searching ['/home/emath', '/home/emath/.jupyter', '/home/emath/anaconda3/etc/jupyter', '/usr/local/etc/jupyter', '/etc/jupyter'] for config files
[D 16:31:51.027 NotebookApp] Looking for jupyter_config in /etc/jupyter
[D 16:31:51.027 NotebookApp] Looking for jupyter_config in /usr/local/etc/jupyter
[D 16:31:51.027 NotebookApp] Looking for jupyter_config in /home/emath/anaconda3/etc/jupyter
[D 16:31:51.027 NotebookApp] Looking for jupyter_config in /home/emath/.jupyter
[D 16:31:51.027 NotebookApp] Looking for jupyter_config in /home/emath
[D 16:31:51.028 NotebookApp] Looking for jupyter_notebook_config in /etc/jupyter
[D 16:31:51.028 NotebookApp] Looking for jupyter_notebook_config in /usr/local/etc/jupyter
[D 16:31:51.028 NotebookApp] Looking for jupyter_notebook_config in /home/emath/anaconda3/etc/jupyter
[D 16:31:51.028 NotebookApp] Loaded config file: /home/emath/anaconda3/etc/jupyter/jupyter_notebook_config.json
[D 16:31:51.028 NotebookApp] Looking for jupyter_notebook_config in /home/emath/.jupyter
[D 16:31:51.029 NotebookApp] Looking for jupyter_notebook_config in /home/emath
[D 16:31:51.029 NotebookApp] Raising open file limit: soft 1024->4096; hard 1048576->1048576
[D 16:31:51.032 NotebookApp] Paths used for configuration of jupyter_notebook_config:
/etc/jupyter/jupyter_notebook_config.json
[D 16:31:51.033 NotebookApp] Paths used for configuration of jupyter_notebook_config:
/usr/local/etc/jupyter/jupyter_notebook_config.json
[D 16:31:51.033 NotebookApp] Paths used for configuration of jupyter_notebook_config:
/home/emath/anaconda3/etc/jupyter/jupyter_notebook_config.d/jupyterlab.json
/home/emath/anaconda3/etc/jupyter/jupyter_notebook_config.json
[D 16:31:51.034 NotebookApp] Paths used for configuration of jupyter_notebook_config:
/home/emath/.jupyter/jupyter_notebook_config.json
[I 16:31:51.308 NotebookApp] JupyterLab extension loaded from /home/emath/anaconda3/lib/python3.8/site-packages/jupyterlab
[I 16:31:51.308 NotebookApp] JupyterLab application directory is /home/emath/anaconda3/share/jupyter/lab
[I 16:31:51.310 NotebookApp] Serving notebooks from local directory: /home/emath/google-drive/MSc Data Science/AI Lab-Research/Wikipedia API
[I 16:31:51.310 NotebookApp] Jupyter Notebook 6.2.0 is running at:
[I 16:31:51.310 NotebookApp] http://localhost:8888/?
[I 16:31:51.310 NotebookApp] or http://127.0.0.1:8888/?
[I 16:31:51.310 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 16:31:51.313 NotebookApp]
To access the notebook, open this file in a browser:
file:///home/emath/.local/share/jupyter/runtime/nbserver-4410-open.html
Or copy and paste one of these URLs:
http://localhost:8888/?
[I 16:31:52.220 NotebookApp] 302 POST /login (127.0.0.1) 1.540000ms
[I 16:31:52.221 NotebookApp] 302 GET / (127.0.0.1) 0.410000ms
[D 16:31:52.223 NotebookApp] Using contents: services/contents
[D 16:31:52.262 NotebookApp] Path base/images/favicon.ico served from /home/emath/.local/lib/python3.8/site-packages/notebook/static/base/images/favicon.ico
[D 16:31:52.262 NotebookApp] Path components/jquery-ui/themes/smoothness/jquery-ui.min.css served from /home/emath/.local/lib/python3.8/site-packages/notebook/static/components/jquery-ui/themes/smoothness/jquery-ui.min.css
[D 16:31:52.263 NotebookApp] Path components/jquery-typeahead/dist/jquery.typeahead.min.css served from /home/emath/.local/lib/python3.8/site-packages/notebook/static/components/jquery-typeahead/dist/jquery.typeahead.min.css
[D 16:31:52.263 NotebookApp] Path style/style.min.css served from /home/emath/.local/lib/python3.8/site-packages/notebook/static/style/style.min.css
[D 16:31:52.263 NotebookApp] Path components/es6-promise/promise.min.js served from /home/emath/.local/lib/python3.8/site-packages/notebook/static/components/es6-promise/promise.min.js
[D 16:31:52.264 NotebookApp] Path components/react/react.production.min.js served from /home/emath/.local/lib/python3.8/site-packages/notebook/static/components/react/react.production.min.js
[D 16:31:52.264 NotebookApp] Path components/react/react-dom.production.min.js served from /home/emath/.local/lib/python3.8/site-packages/notebook/static/components/react/react-dom.production.min.js
[D 16:31:52.264 NotebookApp] Path components/create-react-class/index.js served from /home/emath/.local/lib/python3.8/site-packages/notebook/static/components/create-react-class/index.js
[D 16:31:52.264 NotebookApp] Path components/requirejs/require.js served from /home/emath/.local/lib/python3.8/site-packages/notebook/static/components/requirejs/require.js
[D 16:31:52.265 NotebookApp] Path base/images/logo.png served from /home/emath/.local/lib/python3.8/site-packages/notebook/static/base/images/logo.png
[D 16:31:52.265 NotebookApp] Path tree/js/main.min.js served from /home/emath/.local/lib/python3.8/site-packages/notebook/static/tree/js/main.min.js
[D 16:31:52.268 NotebookApp] 200 GET /tree (127.0.0.1) 46.590000ms
[D 16:31:52.298 NotebookApp] 200 GET /api (127.0.0.1) 1.460000ms
[D 16:31:52.337 NotebookApp] Found kernel python3 in /home/emath/.local/share/jupyter/kernels
[D 16:31:52.341 NotebookApp] 200 GET /api/kernelspecs (127.0.0.1) 4.790000ms
[D 16:31:52.375 NotebookApp] 200 GET /api/contents (127.0.0.1) 9.040000ms
[D 16:31:52.380 NotebookApp] 200 GET /api/sessions (127.0.0.1) 2.300000ms
[D 16:31:52.409 NotebookApp] 200 GET /api/contents (127.0.0.1) 4.930000ms
[D 16:31:52.416 NotebookApp] 200 GET /api/sessions (127.0.0.1) 0.900000ms
[D 16:31:52.563 NotebookApp] 200 GET /api/contents/Images (127.0.0.1) 6.950000ms
[D 16:31:52.567 NotebookApp] 200 GET /api/contents/Data (127.0.0.1) 3.580000ms
[W 16:31:56.952 NotebookApp] Notebook revisions_eda_first_approach.ipynb is not trusted
[D 16:31:56.975 NotebookApp] 200 GET /api/contents/revisions_eda_first_approach.ipynb (127.0.0.1) 60.630000ms
[W 16:31:58.575 NotebookApp] Notebook revisions_eda_first_approach.ipynb is not trusted
[D 16:31:58.597 NotebookApp] 200 GET /api/contents/revisions_eda_first_approach.ipynb (127.0.0.1) 73.720000ms
[W 16:32:00.603 NotebookApp] Notebook revisions_eda_first_approach.ipynb is not trusted
[D 16:32:00.624 NotebookApp] 200 GET /api/contents/revisions_eda_first_approach.ipynb (127.0.0.1) 61.040000ms
[W 16:32:03.204 NotebookApp] Notebook revisions_eda_first_approach.ipynb is not trusted
[D 16:32:03.227 NotebookApp] 200 GET /api/contents/revisions_eda_first_approach.ipynb (127.0.0.1) 73.560000msIt has a lot more stuff.
dickmao
commented
3 years ago Maybe this is not going to work, in which case I apologize and thank you for your interest.
I saw no mention of ein:content-query-contents--error http://127.0.0.1:8888/revisions_eda_first_approach.ipynb REQUEST-STATUS timeout DATA interrupt, and I saw no commentary for "the steps to reproduce the problem." Here is how I'd like to report to look:
No problem found.
emacs -Q -f package-initialize C-x C-f foo.ipynb C-c C-o
("EIN system info"
:emacs-version
"GNU Emacs 27.1.90 (build 3, x86_64-pc-linux-gnu, GTK+ Version 3.22.30)
of 2021-01-15"
:window-system x
:emacs-variant nil
:build
"--prefix=/home/dick/.local --with-rsvg=yes --with-xml2=yes PKG_CONFIG_PATH=/home/dick/.local/lib/pkgconfig"
:os
(:uname
"Linux dick 4.15.0-99-generic #100-Ubuntu SMP Wed Apr 22 20:32:56 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
"
:lsb-release
"No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 18.04.4 LTS
Release: 18.04
Codename: bionic
")
:jupyter
"jupyter core : 4.6.3
jupyter-notebook : 6.1.5
qtconsole : 4.7.3
ipython : 7.14.0
ipykernel : 5.2.1
jupyter client : 6.1.3
jupyter lab : not installed
nbconvert : 5.6.1
ipywidgets : 7.5.1
nbformat : 5.0.6
traitlets : 4.3.3
"
:image-types
(svg png gif tiff jpeg xpm xbm pbm postscript)
:image-types-available
(svg png gif tiff jpeg xpm xbm pbm postscript)
:request-backend curl
:ein
(:version "0.17.0"
:source-dir "/home/dick/.emacs.d/elpa/ein-0.17.0/")
:lib
((:name "websocket"
:path "~/.emacs.d/elpa/websocket-20200102.637/websocket.elc"
:featurep t
:version-var websocket-version
:version "1.12")
(:name "anaphora"
:path "~/.emacs.d/elpa/anaphora-20180618.1800/anaphora.elc"
:featurep t
:version-var nil
:version nil)
(:name "request"
:path "~/.emacs.d/elpa/request-20200517.1305/request.elc"
:featurep t
:version-var request-version
:version "0.3.0")
(:name "deferred"
:path "~/.emacs.d/elpa/deferred-20170901.630/deferred.elc"
:featurep t
:version-var deferred:version
:version "0.5.0")
(:name "polymode"
:path "~/.emacs.d/elpa/polymode-20200606.1106/polymode.elc"
:featurep t
:version-var nil
:version nil)
(:name "dash"
:path "~/.emacs.d/elpa/dash-20200524.1947/dash.elc"
:featurep t
:version-var nil
:version nil)
(:name "with-editor"
:path "~/.emacs.d/elpa/with-editor-20200522.1112/with-editor.elc"
:featurep t
:version-var nil
:version nil)))http://127.0.0.1:8888/pytorch-fcn-resnet50-in-20-minute.ipynb:[WS] Sending handshake, key: znU9WVoRJPrPWn3iu1m/PQ==, acceptance: lzqveT9jxLsN0CmiPbTjeY76M44=
[WS] Received: HTTP/1.1 101 Switching Protocols
Server: TornadoServer/6.0.4
Date: Wed, 27 Jan 2021 13:54:46 GMT
Upgrade: websocket
Connection: Upgrade
Sec-Websocket-Accept: lzqveT9jxLsN0CmiPbTjeY76M44=
[WS] Checking for accept header regexp: Sec-Web[Ss]ocket-Accept: lzqveT9jxLsN0CmiPbTjeY76M44=
[WS] Checking for upgrade header
[WS] Checking for connection header[debug] request--curl: curl --silent --location --cookie /home/dick/.emacs.d/request/curl-cookie-jar --cookie-jar /home/dick/.emacs.d/request/curl-cookie-jar --include --write-out \n(:num-redirects %{num_redirects} :url-effective "%{url_effective}") --trace-ascii /tmp/curl-trace --compressed --header User-Agent: Mozilla/5.0 --header X-XSRFTOKEN: 2|44521dd7|26335ed7314979bf657d29ae512830c0|1605672558 http://127.0.0.1:8888/api
[debug] request--curl-callback: event finished
[debug] request--callback: UNPARSED
HTTP/1.1 200 OK
Server: TornadoServer/6.0.4
Content-Type: application/json
Date: Wed, 27 Jan 2021 13:54:45 GMT
X-Content-Type-Options: nosniff
Content-Security-Policy: frame-ancestors 'self'; report-uri /api/security/csp-report; default-src 'none'
Etag: "7cfb06929dd1058529bc973b5170ef0bee204d78"
Content-Length: 20
{"version": "6.1.5"}
[debug] request--callback: PARSED
(:version 6.1.5)
[debug] request--callback: executing complete
[debug] request--curl: curl --silent --location --cookie /home/dick/.emacs.d/request/curl-cookie-jar --cookie-jar /home/dick/.emacs.d/request/curl-cookie-jar --include --write-out \n(:num-redirects %{num_redirects} :url-effective "%{url_effective}") --trace-ascii /tmp/curl-trace --compressed --request GET --header User-Agent: Mozilla/5.0 --header X-XSRFTOKEN: 2|44521dd7|26335ed7314979bf657d29ae512830c0|1605672558 http://127.0.0.1:8888/api/kernelspecs
[debug] request--curl-callback: event finished
[debug] request--callback: UNPARSED
HTTP/1.1 200 OK
Server: TornadoServer/6.0.4
Content-Type: application/json
Date: Wed, 27 Jan 2021 13:54:45 GMT
X-Content-Type-Options: nosniff
Content-Security-Policy: frame-ancestors 'self'; report-uri /api/security/csp-report; default-src 'none'
Etag: "82302e34cb2b4dca8cdb88d818af443c8822eb93"
Content-Length: 2772
{"default": "python3", "kernelspecs": {"haskell": {"name": "haskell", "spec": {"argv": ["/home/dick/.local/bin/ihaskell", "kernel", "{connection_file}", "--ghclib", "/home/dick/.stack/programs/x86_64-linux/ghc-8.6.5/lib/ghc-8.6.5", "+RTS", "-M3g", "-N2", "-RTS", "--stack"], "env": {}, "display_name": "Haskell", "language": "haskell", "interrupt_mode": "signal", "metadata": {}}, "resources": {"kernel.js": "/kernelspecs/haskell/kernel.js", "logo-64x64": "/kernelspecs/haskell/logo-64x64.svg"}}, "xcpp17": {"name": "xcpp17", "spec": {"argv": ["/home/dick/miniconda3/envs/cling/bin/xcpp", "-f", "{connection_file}", "-std=c++17"], "env": {}, "display_name": "C++17", "language": "C++17", "interrupt_mode": "signal", "metadata": {}}, "resources": {"logo-32x32": "/kernelspecs/xcpp17/logo-32x32.png", "logo-64x64": "/kernelspecs/xcpp17/logo-64x64.png"}}, "ir": {"name": "ir", "spec": {"argv": ["/usr/lib/R/bin/R", "--slave", "-e", "IRkernel::main()", "--args", "{connection_file}"], "env": {}, "display_name": "R", "language": "R", "interrupt_mode": "signal", "metadata": {}}, "resources": {"kernel.js": "/kernelspecs/ir/kernel.js", "logo-64x64": "/kernelspecs/ir/logo-64x64.png"}}, "julia-1.4": {"name": "julia-1.4", "spec": {"argv": ["/home/dick/.local/share/julia-1.4.1/bin/julia", "-i", "--startup-file=yes", "--color=yes", "--project=@.", "/home/dick/.julia/packages/IJulia/DrVMH/src/kernel.jl", "{connection_file}"], "env": {}, "display_name": "Julia 1.4.1", "language": "julia", "interrupt_mode": "signal", "metadata": {}}, "resources": {"logo-32x32": "/kernelspecs/julia-1.4/logo-32x32.png", "logo-64x64": "/kernelspecs/julia-1.4/logo-64x64.png"}}, "python3": {"name": "python3", "spec": {"argv": ["python3", "-m", "ipykernel_launcher", "-f", "{connection_file}"], "env": {}, "display_name": "Python 3", "language": "python", "interrupt_mode": "signal", "metadata": {}}, "resources": {"logo-32x32": "/kernelspecs/python3/logo-32x32.png", "logo-64x64": "/kernelspecs/python3/logo-64x64.png"}}, "wolframlanguage12.1": {"name": "wolframlanguage12.1", "spec": {"argv": ["/usr/local/Wolfram/WolframEngine/12.1/Executables/WolframKernel", "-script", "/home/dick/WolframLanguageForJupyter/WolframLanguageForJupyter/Resources/KernelForWolframLanguageForJupyter.wl", "{connection_file}", "ScriptInstall"], "env": {}, "display_name": "Wolfram Language 12.1", "language": "Wolfram Language", "interrupt_mode": "signal", "metadata": {}}, "resources": {}}, "lisp": {"name": "lisp", "spec": {"argv": ["sbcl", "--non-interactive", "--load", "/home/dick/cl-jupyter/cl-jupyter.lisp", "/home/dick/cl-jupyter/src", "/home/dick/cl-jupyter", "{connection_file}"], "env": {}, "display_name": "SBCL Lisp", "language": "lisp", "interrupt_mode": "signal", "metadata": {}}, "resources": {}}}}
[debug] request--callback: PARSED
(:default python3 :kernelspecs (:haskell (:name haskell :spec (:argv [/home/dick/.local/bin/ihaskell kernel {connection_file} --ghclib /home/dick/.stack/programs/x86_64-linux/ghc-8.6.5/lib/ghc-8.6.5 +RTS -M3g -N2 -RTS --stack] :env nil :display_name Haskell :language haskell :interrupt_mode signal :metadata nil) :resources (:kernel.js /kernelspecs/haskell/kernel.js :logo-64x64 /kernelspecs/haskell/logo-64x64.svg)) :xcpp17 (:name xcpp17 :spec (:argv [/home/dick/miniconda3/envs/cling/bin/xcpp -f {connection_file} -std=c++17] :env nil :display_name C++17 :language C++17 :interrupt_mode signal :metadata nil) :resources (:logo-32x32 /kernelspecs/xcpp17/logo-32x32.png :logo-64x64 /kernelspecs/xcpp17/logo-64x64.png)) :ir (:name ir :spec (:argv [/usr/lib/R/bin/R --slave -e IRkernel::main() --args {connection_file}] :env nil :display_name R :language R :interrupt_mode signal :metadata nil) :resources (:kernel.js /kernelspecs/ir/kernel.js :logo-64x64 /kernelspecs/ir/logo-64x64.png)) :julia-1.4 (:name julia-1.4 :spec (:argv [/home/dick/.local/share/julia-1.4.1/bin/julia -i --startup-file=yes --color=yes --project=@. /home/dick/.julia/packages/IJulia/DrVMH/src/kernel.jl {connection_file}] :env nil :display_name Julia 1.4.1 :language julia :interrupt_mode signal :metadata nil) :resources (:logo-32x32 /kernelspecs/julia-1.4/logo-32x32.png :logo-64x64 /kernelspecs/julia-1.4/logo-64x64.png)) :python3 (:name python3 :spec (:argv [python3 -m ipykernel_launcher -f {connection_file}] :env nil :display_name Python 3 :language python :interrupt_mode signal :metadata nil) :resources (:logo-32x32 /kernelspecs/python3/logo-32x32.png :logo-64x64 /kernelspecs/python3/logo-64x64.png)) :wolframlanguage12.1 (:name wolframlanguage12.1 :spec (:argv [/usr/local/Wolfram/WolframEngine/12.1/Executables/WolframKernel -script /home/dick/WolframLanguageForJupyter/WolframLanguageForJupyter/Resources/KernelForWolframLanguageForJupyter.wl {connection_file} ScriptInstall] :env nil :display_name Wolfram Language 12.1 :language Wolfram Language :interrupt_mode signal :metadata nil) :resources nil) :lisp (:name lisp :spec (:argv [sbcl --non-interactive --load /home/dick/cl-jupyter/cl-jupyter.lisp /home/dick/cl-jupyter/src /home/dick/cl-jupyter {connection_file}] :env nil :display_name SBCL Lisp :language lisp :interrupt_mode signal :metadata nil) :resources nil)))
[debug] request--callback: executing success
[debug] request--curl: curl --silent --location --cookie /home/dick/.emacs.d/request/curl-cookie-jar --cookie-jar /home/dick/.emacs.d/request/curl-cookie-jar --include --write-out \n(:num-redirects %{num_redirects} :url-effective "%{url_effective}") --trace-ascii /tmp/curl-trace --compressed --request GET --header User-Agent: Mozilla/5.0 --header X-XSRFTOKEN: 2|44521dd7|26335ed7314979bf657d29ae512830c0|1605672558 http://127.0.0.1:8888/api/contents
[debug] request--callback: executing complete
[debug] request--curl: curl --silent --location --cookie /home/dick/.emacs.d/request/curl-cookie-jar --cookie-jar /home/dick/.emacs.d/request/curl-cookie-jar --include --write-out \n(:num-redirects %{num_redirects} :url-effective "%{url_effective}") --trace-ascii /tmp/curl-trace --compressed --request GET --header User-Agent: Mozilla/5.0 --header X-XSRFTOKEN: 2|44521dd7|26335ed7314979bf657d29ae512830c0|1605672558 http://127.0.0.1:8888/api/sessions
[debug] request--curl-callback: event finished
[debug] request--callback: UNPARSED
HTTP/1.1 200 OK
Server: TornadoServer/6.0.4
Content-Type: application/json
Date: Wed, 27 Jan 2021 13:54:45 GMT
X-Content-Type-Options: nosniff
Content-Security-Policy: frame-ancestors 'self'; report-uri /api/security/csp-report; default-src 'none'
Etag: "97d170e1550eee4afc0af065b78cda302a97674c"
Content-Length: 2
[]
[debug] request--callback: PARSED
[]
[debug] request--callback: executing success
[debug] request--curl: curl --silent --location --cookie /home/dick/.emacs.d/request/curl-cookie-jar --cookie-jar /home/dick/.emacs.d/request/curl-cookie-jar --include --write-out \n(:num-redirects %{num_redirects} :url-effective "%{url_effective}") --trace-ascii /tmp/curl-trace --compressed --request GET --header User-Agent: Mozilla/5.0 --header X-XSRFTOKEN: 2|44521dd7|26335ed7314979bf657d29ae512830c0|1605672558 http://127.0.0.1:8888/api/contents
[debug] request--callback: executing complete
[debug] request--curl-callback: event finished
[debug] request--callback: UNPARSED
HTTP/1.1 200 OK
Server: TornadoServer/6.0.4
Content-Type: application/json
Date: Wed, 27 Jan 2021 13:54:45 GMT
X-Content-Type-Options: nosniff
Content-Security-Policy: frame-ancestors 'self'; report-uri /api/security/csp-report; default-src 'none'
Last-Modified: Tue, 26 Jan 2021 23:19:09 GMT
Etag: "666de50f8ce9471571d102d155af9ff129325d36"
Content-Length: 1042
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[debug] request--callback: PARSED
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(:name pytorch-fcn-resnet50-in-20-minute.ipynb :path pytorch-fcn-resnet50-in-20-minute.ipynb :last_modified 2021-01-26T23:19:09.600415Z :created 2021-01-26T23:19:09.600415Z :content (:cells [(:metadata (:_uuid 8f2839f25d086af736a60e9eeb907d3b93b6e0e5 :_cell_guid b1076dfc-b9ad-4769-8c92-a6c4dae69d19 :trusted :json-false) :cell_type code :source import numpy as np
import pandas as pd
import pathlib, sys, os, random, time
import numba, cv2, gc
import matplotlib.pyplot as plt
%matplotlib inline
import warnings
warnings.filterwarnings('ignore')
from tqdm.notebook import tqdm
import albumentations as A :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source import rasterio
from rasterio.windows import Window :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.utils.data as D
import torchvision
from torchvision import transforms as T :execution_count nil :outputs []) (:metadata (:_uuid d629ff2d2480ee46fbb7e2d37f6b5fab8052498a :_cell_guid 79c7e3d0-c299-4dcb-8224-4455121ee9b0 :trusted :json-false) :cell_type code :source def set_seeds(seed=42):
random.seed(seed)
os.environ['PYTHONHASHSEED'] = str(seed)
np.random.seed(seed)
torch.manual_seed(seed)
torch.cuda.manual_seed(seed)
torch.cuda.manual_seed_all(seed)
torch.backends.cudnn.deterministic = True
set_seeds(); :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source DATA_PATH = '../input/hubmap-kidney-segmentation'
EPOCHES = 5
BATCH_SIZE = 32
DEVICE = 'cuda' if torch.cuda.is_available() else 'cpu' :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source # used for converting the decoded image to rle mask
def rle_encode(im):
'''
im: numpy array, 1 - mask, 0 - background
Returns run length as string formated
'''
pixels = im.flatten(order = 'F')
pixels = np.concatenate([[0], pixels, [0]])
runs = np.where(pixels[1:] != pixels[:-1])[0] + 1
runs[1::2] -= runs[::2]
return ' '.join(str(x) for x in runs)
def rle_decode(mask_rle, shape=(256, 256)):
'''
mask_rle: run-length as string formated (start length)
shape: (height,width) of array to return
Returns numpy array, 1 - mask, 0 - background
'''
s = mask_rle.split()
starts, lengths = [np.asarray(x, dtype=int) for x in (s[0:][::2], s[1:][::2])]
starts -= 1
ends = starts + lengths
img = np.zeros(shape[0]*shape[1], dtype=np.uint8)
for lo, hi in zip(starts, ends):
img[lo:hi] = 1
return img.reshape(shape, order='F')
@numba.njit()
def rle_numba(pixels):
size = len(pixels)
points = []
if pixels[0] == 1: points.append(0)
flag = True
for i in range(1, size):
if pixels[i] != pixels[i-1]:
if flag:
points.append(i+1)
flag = False
else:
points.append(i+1 - points[-1])
flag = True
if pixels[-1] == 1: points.append(size-points[-1]+1)
return points
def rle_numba_encode(image):
pixels = image.flatten(order = 'F')
points = rle_numba(pixels)
return ' '.join(str(x) for x in points)
def make_grid(shape, window=256, min_overlap=32):
"""
Return Array of size (N,4), where N - number of tiles,
2nd axis represente slices: x1,x2,y1,y2
"""
x, y = shape
nx = x // (window - min_overlap) + 1
x1 = np.linspace(0, x, num=nx, endpoint=False, dtype=np.int64)
x1[-1] = x - window
x2 = (x1 + window).clip(0, x)
ny = y // (window - min_overlap) + 1
y1 = np.linspace(0, y, num=ny, endpoint=False, dtype=np.int64)
y1[-1] = y - window
y2 = (y1 + window).clip(0, y)
slices = np.zeros((nx,ny, 4), dtype=np.int64)
for i in range(nx):
for j in range(ny):
slices[i,j] = x1[i], x2[i], y1[j], y2[j]
return slices.reshape(nx*ny,4) :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source identity = rasterio.Affine(1, 0, 0, 0, 1, 0)
class HubDataset(D.Dataset):
def __init__(self, root_dir, transform,
window=256, overlap=32, threshold = 100):
self.path = pathlib.Path(root_dir)
self.overlap = overlap
self.window = window
self.transform = transform
self.csv = pd.read_csv((self.path / 'train.csv').as_posix(),
index_col=[0])
self.threshold = threshold
self.x, self.y = [], []
self.build_slices()
self.len = len(self.x)
self.as_tensor = T.Compose([
T.ToTensor(),
T.Normalize([0.625, 0.448, 0.688],
[0.131, 0.177, 0.101]),
])
def build_slices(self):
self.masks = []
self.files = []
self.slices = []
for i, filename in enumerate(self.csv.index.values):
filepath = (self.path /'train'/(filename+'.tiff')).as_posix()
self.files.append(filepath)
print('Transform', filename)
with rasterio.open(filepath, transform = identity) as dataset:
self.masks.append(rle_decode(self.csv.loc[filename, 'encoding'], dataset.shape))
slices = make_grid(dataset.shape, window=self.window, min_overlap=self.overlap)
for slc in tqdm(slices):
x1,x2,y1,y2 = slc
if self.masks[-1][x1:x2,y1:y2].sum() > self.threshold or np.random.randint(100) > 120:
self.slices.append([i,x1,x2,y1,y2])
image = dataset.read([1,2,3],
window=Window.from_slices((x1,x2),(y1,y2)))
# if image.std().mean() < 10:
# continue
# print(image.std().mean(), self.masks[-1][x1:x2,y1:y2].sum())
image = np.moveaxis(image, 0, -1)
self.x.append(image)
self.y.append(self.masks[-1][x1:x2,y1:y2])
# get data operation
def __getitem__(self, index):
image, mask = self.x[index], self.y[index]
augments = self.transform(image=image, mask=mask)
return self.as_tensor(augments['image']), augments['mask'][None]
def __len__(self):
"""
Total number of samples in the dataset
"""
return self.len
:execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source WINDOW=1024
MIN_OVERLAP=32
NEW_SIZE=256
trfm = A.Compose([
A.Resize(NEW_SIZE,NEW_SIZE),
A.HorizontalFlip(p=0.5),
A.VerticalFlip(p=0.5),
A.OneOf([
A.RandomContrast(),
A.RandomGamma(),
A.RandomBrightness(),
A.ColorJitter(brightness=0.07, contrast=0.07,
saturation=0.1, hue=0.1, always_apply=False, p=0.3),
], p=0.3),
A.OneOf([
A.ElasticTransform(alpha=120, sigma=120 * 0.05, alpha_affine=120 * 0.03),
A.GridDistortion(),
A.OpticalDistortion(distort_limit=2, shift_limit=0.5),
], p=0.0),
A.ShiftScaleRotate(),
])
ds = HubDataset(DATA_PATH, window=WINDOW, overlap=MIN_OVERLAP, transform=trfm) :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source image, mask = ds[2]
plt.figure(figsize=(16,8))
plt.subplot(121)
plt.imshow(mask[0], cmap='gray')
plt.subplot(122)
plt.imshow(image[0]);
_ = rle_numba_encode(mask[0]) # compile function with numba :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source valid_idx, train_idx = [], []
for i in range(len(ds)):
if ds.slices[i][0] == 7:
valid_idx.append(i)
else:
train_idx.append(i) :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source train_ds = D.Subset(ds, train_idx)
valid_ds = D.Subset(ds, valid_idx)
# define training and validation data loaders
loader = D.DataLoader(
train_ds, batch_size=BATCH_SIZE, shuffle=True, num_workers=0)
vloader = D.DataLoader(
valid_ds, batch_size=BATCH_SIZE, shuffle=False, num_workers=0) :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source def get_model():
model = torchvision.models.segmentation.fcn_resnet50(False)
pth = torch.load("../input/pretrain-coco-weights-pytorch/fcn_resnet50_coco-1167a1af.pth")
for key in ["aux_classifier.0.weight", "aux_classifier.1.weight", "aux_classifier.1.bias", "aux_classifier.1.running_mean", "aux_classifier.1.running_var", "aux_classifier.1.num_batches_tracked", "aux_classifier.4.weight", "aux_classifier.4.bias"]:
del pth[key]
model.classifier[4] = nn.Conv2d(512, 1, kernel_size=(1, 1), stride=(1, 1))
return model :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source @torch.no_grad()
def validation(model, loader, loss_fn):
losses = []
model.eval()
for image, target in loader:
image, target = image.to(DEVICE), target.float().to(DEVICE)
output = model(image)['out']
loss = loss_fn(output, target)
losses.append(loss.item())
return np.array(losses).mean() :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source # deeplabv3_resnet101_coco-586e9e4e.pth fcn_resnet50_coco-1167a1af.pth
# deeplabv3_resnet50_coco-cd0a2569.pth resnet101-5d3b4d8f.pth
# fcn_resnet101_coco-7ecb50ca.pth resnet50-19c8e357.pth
# Copy pretrain weight for model to cache dir
!mkdir -p /root/.cache/torch/hub/checkpoints/
!cp ../input/pytorch-pretrained-models/resnet50-19c8e357.pth /root/.cache/torch/hub/checkpoints/
!cp ../input/pretrain-coco-weights-pytorch/fcn_resnet50_coco-1167a1af.pth /root/.cache/torch/hub/checkpoints/ :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source model = get_model()
model.to(DEVICE);
optimizer = torch.optim.AdamW(model.parameters(),
lr=1e-4, weight_decay=1e-3) :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source ### Table for results
header = r'''
Train | Valid
Epoch | Loss | Loss | Time, m
'''
# Epoch metrics time
raw_line = '{:6d}' + '\u2502{:7.3f}'*2 + '\u2502{:6.2f}' :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source class SoftDiceLoss(nn.Module):
def __init__(self, smooth=1., dims=(-2,-1)):
super(SoftDiceLoss, self).__init__()
self.smooth = smooth
self.dims = dims
def forward(self, x, y):
tp = (x * y).sum(self.dims)
fp = (x * (1 - y)).sum(self.dims)
fn = ((1 - x) * y).sum(self.dims)
dc = (2 * tp + self.smooth) / (2 * tp + fp + fn + self.smooth)
dc = dc.mean()
return 1 - dc :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source bce_fn = nn.BCEWithLogitsLoss()
dice_fn = SoftDiceLoss()
def loss_fn(y_pred, y_true):
bce = bce_fn(y_pred, y_true)
dice = dice_fn(y_pred.sigmoid(), y_true)
return 0.8*bce+ 0.2*dice
print(header)
best_loss = 10
EPOCHES = 25
for epoch in range(1, EPOCHES+1):
losses = []
start_time = time.time()
model.train()
for image, target in loader:
image, target = image.to(DEVICE), target.float().to(DEVICE)
optimizer.zero_grad()
output = model(image)['out']
loss = loss_fn(output, target)
loss.backward()
optimizer.step()
losses.append(loss.item())
vloss = validation(model, vloader, loss_fn)
print(raw_line.format(epoch, np.array(losses).mean(), vloss,
(time.time()-start_time)/60**1))
losses = []
if vloss < best_loss:
best_loss = vloss
torch.save(model.state_dict(), 'model_best.pth') :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source # del train set
del loader, vloader, train_ds, valid_ds, ds
gc.collect(); :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source trfm = T.Compose([
T.ToPILImage(),
T.Resize(NEW_SIZE),
T.ToTensor(),
T.Normalize([0.625, 0.448, 0.688],
[0.131, 0.177, 0.101]),
])
p = pathlib.Path(DATA_PATH)
subm = {}
model.load_state_dict(torch.load("./model_best.pth"))
model.eval()
for i, filename in enumerate(p.glob('test/*.tiff')):
dataset = rasterio.open(filename.as_posix(), transform = identity)
slices = make_grid(dataset.shape, window=WINDOW, min_overlap=MIN_OVERLAP)
preds = np.zeros(dataset.shape, dtype=np.uint8)
for (x1,x2,y1,y2) in slices:
image = dataset.read([1,2,3],
window=Window.from_slices((x1,x2),(y1,y2)))
image = np.moveaxis(image, 0, -1)
image = trfm(image)
with torch.no_grad():
image = image.to(DEVICE)[None]
score = model(image)['out'][0][0]
score2 = model(torch.flip(image, [0, 3]))['out']
score2 = torch.flip(score2, [3, 0])[0][0]
score3 = model(torch.flip(image, [1, 2]))['out']
score3 = torch.flip(score3, [2, 1])[0][0]
score_mean = (score + score2 + score3) / 3.0
score_sigmoid = score_mean.sigmoid().cpu().numpy()
score_sigmoid = cv2.resize(score_sigmoid, (WINDOW, WINDOW))
preds[x1:x2,y1:y2] = (score_sigmoid > 0.5).astype(np.uint8)
subm[i] = {'id':filename.stem, 'predicted': rle_numba_encode(preds)}
del preds
gc.collect(); :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source submission = pd.DataFrame.from_dict(subm, orient='index')
submission.to_csv('submission.csv', index=False) :execution_count nil :outputs []) (:metadata (:trusted :json-false) :cell_type code :source :execution_count nil :outputs [])] :metadata (:kernelspec (:language python :display_name Python 3 :name python3) :language_info (:pygments_lexer ipython3 :nbconvert_exporter python :version 3.6.4 :file_extension .py :codemirror_mode (:name ipython :version 3) :name python :mimetype text/x-python)) :nbformat 4 :nbformat_minor 4) :format json :mimetype nil :size 14836 :writable t :type notebook)
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08:54:46:783: [debug] ein:query-contents--complete STATUS: 200 DATA: (:name run-remote :path run-remote :last_modified 1970-01-01T00:00:00Z :created 1970-01-01T00:00:00Z :content [(:name gat.1611170609 :path run-remote/gat.1611170609 :last_modified 2021-01-20T19:23:31Z :created 2021-01-20T19:23:31Z :content nil :format nil :mimetype nil :size 3920 :writable t :type file) (:name gat.1611173836 :path run-remote/gat.1611173836 :last_modified 2021-01-20T20:17:18Z :created 2021-01-20T20:17:18Z :content nil :format nil :mimetype nil :size 3582 :writable t :type file) (:name gat.1611180787 :path run-remote/gat.1611180787 :last_modified 2021-01-20T22:13:08Z :created 2021-01-20T22:13:08Z :content nil :format nil :mimetype nil :size 3421 :writable t :type file) (:name gat.1611194573 :path run-remote/gat.1611194573 :last_modified 2021-01-21T02:02:55Z :created 2021-01-21T02:02:55Z :content nil :format nil :mimetype nil :size 4348 :writable t :type file) (:name gat.1611194848 :path run-remote/gat.1 @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
08:54:46:783: [verbose] ein:kernel-retrieve-session--success: kernel-id=3547d2c7-00b5-41a8-876b-9477fd403861 session-id=7fe33e05-ff84-4f56-a8ff-ac0002491795 @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
08:54:46:810: [verbose] WS start: ws://127.0.0.1:8888/api/kernels/3547d2c7-00b5-41a8-876b-9477fd403861/channels?session_id=7fe33e05-ff84-4f56-a8ff-ac0002491795 @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
08:54:46:852: [debug] ein:kernel-retrieve-session--complete STATUS: 201 DATA: (:id 7fe33e05-ff84-4f56-a8ff-ac0002491795 :path pytorch-fcn-resnet50-in-20-minute.ipynb :name nil :type notebook :kernel (:id 3547d2c7-00b5-41a8-876b-9477fd403861 :name python3 :last_activity 2021-01-27T13:54:46.686284Z :execution_state starting :connections 0) :notebook (:path pytorch-fcn-resnet50-in-20-minute.ipynb :name nil)) @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
08:54:47:235: [debug] EIN:QUERY-PREPARE-HEADER: Found xsrf: 2|44521dd7|26335ed7314979bf657d29ae512830c0|1605672558 @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
08:54:47:236: [info] Notebook pytorch-fcn-resnet50-in-20-minute.ipynb is ready @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
08:54:47:236: [verbose] WS opened: ws://127.0.0.1:8888/api/kernels/3547d2c7-00b5-41a8-876b-9477fd403861/channels?session_id=7fe33e05-ff84-4f56-a8ff-ac0002491795 @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
08:54:47:256: [verbose] Opening notebooklist at http://127.0.0.1:8888 @#<buffer *ein: http://127.0.0.1:8888/pytorch-fcn-resnet50-in-20-minute.ipynb*[python]>
08:54:47:257: [debug] EIN:QUERY-PREPARE-HEADER: Found xsrf: 2|44521dd7|26335ed7314979bf657d29ae512830c0|1605672558 @#<buffer *ein:notebooklist http://127.0.0.1:8888*>
08:54:47:257: [debug] ein:query-contents--complete STATUS: 200 DATA: (:name :path :last_modified 2021-01-26T23:19:09.600415Z :created 2021-01-26T23:19:09.600415Z :content [(:name pytorch-fcn-resnet50-in-20-minute.ipynb :path pytorch-fcn-resnet50-in-20-minute.ipynb :last_modified 2021-01-26T23:19:09.600415Z :created 2021-01-26T23:19:09.600415Z :content nil :format nil :mimetype nil :size 14836 :writable t :type notebook) (:name Dockerfile.pytorch-fcn-resnet50-in-20-minute :path Dockerfile.pytorch-fcn-resnet50-in-20-minute :last_modified 2021-01-26T23:18:48.888165Z :created 2021-01-26T23:18:48.888165Z :content nil :format nil :mimetype nil :size 149 :writable t :type file) (:name run-remote :path run-remote :last_modified 1970-01-01T00:00:00Z :created 1970-01-01T00:00:00Z :content nil :format nil :mimetype nil :size nil :writable t :type directory)] :format json :mimetype nil :size nil :writable t :type directory) @#<buffer *ein: http://127.0.0.1:8888/pytorch-fcn-resnet50-in-20-minute.ipynb*[python]>
08:54:47:888: [debug] ein:query-sessions--complete STATUS: 200 DATA: [(:id 7fe33e05-ff84-4f56-a8ff-ac0002491795 :path pytorch-fcn-resnet50-in-20-minute.ipynb :name nil :type notebook :kernel (:id 3547d2c7-00b5-41a8-876b-9477fd403861 :name python3 :last_activity 2021-01-27T13:54:46.686284Z :execution_state starting :connections 1) :notebook (:path pytorch-fcn-resnet50-in-20-minute.ipynb :name nil))] @#<buffer *ein: http://127.0.0.1:8888/pytorch-fcn-resnet50-in-20-minute.ipynb*[python]>
08:54:54:011: [warn] ein:dev-packages: Invalid function: "jupyter" @#<buffer *temp*>[D 08:54:44.378 NotebookApp] Searching ['/home/dick/hubmap', '/home/dick/.jupyter', '/usr/etc/jupyter', '/usr/local/etc/jupyter', '/etc/jupyter'] for config files
[D 08:54:44.378 NotebookApp] Looking for jupyter_config in /etc/jupyter
[D 08:54:44.379 NotebookApp] Looking for jupyter_config in /usr/local/etc/jupyter
[D 08:54:44.379 NotebookApp] Looking for jupyter_config in /usr/etc/jupyter
[D 08:54:44.379 NotebookApp] Looking for jupyter_config in /home/dick/.jupyter
[D 08:54:44.379 NotebookApp] Looking for jupyter_config in /home/dick/hubmap
[D 08:54:44.380 NotebookApp] Looking for jupyter_notebook_config in /etc/jupyter
[D 08:54:44.380 NotebookApp] Looking for jupyter_notebook_config in /usr/local/etc/jupyter
[D 08:54:44.380 NotebookApp] Looking for jupyter_notebook_config in /usr/etc/jupyter
[D 08:54:44.380 NotebookApp] Loaded config file: /usr/etc/jupyter/jupyter_notebook_config.json
[D 08:54:44.380 NotebookApp] Looking for jupyter_notebook_config in /home/dick/.jupyter
[D 08:54:44.380 NotebookApp] Loaded config file: /home/dick/.jupyter/jupyter_notebook_config.py
[D 08:54:44.381 NotebookApp] Looking for jupyter_notebook_config in /home/dick/hubmap
[D 08:54:44.382 NotebookApp] Raising open file limit: soft 1024->4096; hard 1048576->1048576
[D 08:54:44.385 NotebookApp] Paths used for configuration of jupyter_notebook_config:
/etc/jupyter/jupyter_notebook_config.json
[D 08:54:44.386 NotebookApp] Paths used for configuration of jupyter_notebook_config:
/usr/local/etc/jupyter/jupyter_notebook_config.json
[D 08:54:44.386 NotebookApp] Paths used for configuration of jupyter_notebook_config:
/usr/etc/jupyter/jupyter_notebook_config.json
[D 08:54:44.386 NotebookApp] Paths used for configuration of jupyter_notebook_config:
/home/dick/.jupyter/jupyter_notebook_config.json
[W 08:54:44.573 NotebookApp] All authentication is disabled. Anyone who can connect to this server will be able to run code.
[I 08:54:44.575 NotebookApp] Serving notebooks from local directory: /home/dick/hubmap
[I 08:54:44.575 NotebookApp] Jupyter Notebook 6.1.5 is running at:
[I 08:54:44.575 NotebookApp] http://localhost:8888/
[I 08:54:44.575 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[D 08:54:45.607 NotebookApp] 200 GET /api (127.0.0.1) 2.71ms
[D 08:54:45.669 NotebookApp] Found kernel haskell in /home/dick/.local/share/jupyter/kernels
[D 08:54:45.669 NotebookApp] Found kernel xcpp17 in /home/dick/.local/share/jupyter/kernels
[D 08:54:45.669 NotebookApp] Found kernel ir in /home/dick/.local/share/jupyter/kernels
[D 08:54:45.669 NotebookApp] Found kernel julia-1.4 in /home/dick/.local/share/jupyter/kernels
[D 08:54:45.669 NotebookApp] Found kernel python3 in /home/dick/.local/share/jupyter/kernels
[D 08:54:45.669 NotebookApp] Found kernel wolframlanguage12.1 in /home/dick/.local/share/jupyter/kernels
[D 08:54:45.669 NotebookApp] Found kernel lisp in /home/dick/.ipython/kernels
[D 08:54:45.673 NotebookApp] 200 GET /api/kernelspecs (127.0.0.1) 5.72ms
[D 08:54:45.732 NotebookApp] 200 GET /api/contents (127.0.0.1) 2.96ms
[D 08:54:45.762 NotebookApp] 200 GET /api/sessions (127.0.0.1) 1.33ms
[D 08:54:45.852 NotebookApp] 200 GET /api/contents (127.0.0.1) 1.93ms
[W 08:54:45.867 NotebookApp] Notebook pytorch-fcn-resnet50-in-20-minute.ipynb is not trusted
[D 08:54:45.876 NotebookApp] 200 GET /api/contents/pytorch-fcn-resnet50-in-20-minute.ipynb (127.0.0.1) 21.25ms
[D 08:54:45.877 NotebookApp] 200 GET /api/sessions (127.0.0.1) 0.96ms
[D 08:54:46.679 NotebookApp] Starting kernel: ['/usr/bin/python3', '-m', 'ipykernel_launcher', '-f', '/home/dick/.local/share/jupyter/runtime/kernel-3547d2c7-00b5-41a8-876b-9477fd403861.json']
[D 08:54:46.684 NotebookApp] Connecting to: tcp://127.0.0.1:50037
[D 08:54:46.686 NotebookApp] Connecting to: tcp://127.0.0.1:41455
[I 08:54:46.688 NotebookApp] Kernel started: 3547d2c7-00b5-41a8-876b-9477fd403861, name: python3
[D 08:54:46.688 NotebookApp] Kernel args: {'kernel_name': 'python3', 'cwd': '/home/dick/hubmap'}
[D 08:54:46.691 NotebookApp] 201 POST /api/sessions (127.0.0.1) 29.95ms
[D 08:54:46.732 NotebookApp] 200 GET /api/contents/run-remote (127.0.0.1) 42.46ms
[D 08:54:46.853 NotebookApp] Initializing websocket connection /api/kernels/3547d2c7-00b5-41a8-876b-9477fd403861/channels
[D 08:54:46.855 NotebookApp] Requesting kernel info from 3547d2c7-00b5-41a8-876b-9477fd403861
[D 08:54:46.855 NotebookApp] Connecting to: tcp://127.0.0.1:49785
[D 08:54:47.189 NotebookApp] Received kernel info: {'status': 'ok', 'protocol_version': '5.3', 'implementation': 'ipython', 'implementation_version': '7.14.0', 'language_info': {'name': 'python', 'version': '3.6.9', 'mimetype': 'text/x-python', 'codemirror_mode': {'name': 'ipython', 'version': 3}, 'pygments_lexer': 'ipython3', 'nbconvert_exporter': 'python', 'file_extension': '.py'}, 'banner': "Python 3.6.9 (default, Apr 18 2020, 01:56:04) \nType 'copyright', 'credits' or 'license' for more information\nIPython 7.14.0 -- An enhanced Interactive Python. Type '?' for help.\n", 'help_links': [{'text': 'Python Reference', 'url': 'https://docs.python.org/3.6'}, {'text': 'IPython Reference', 'url': 'https://ipython.org/documentation.html'}, {'text': 'NumPy Reference', 'url': 'https://docs.scipy.org/doc/numpy/reference/'}, {'text': 'SciPy Reference', 'url': 'https://docs.scipy.org/doc/scipy/reference/'}, {'text': 'Matplotlib Reference', 'url': 'https://matplotlib.org/contents.html'}, {'text': 'SymPy Reference', 'url': 'http://docs.sympy.org/latest/index.html'}, {'text': 'pandas Reference', 'url': 'https://pandas.pydata.org/pandas-docs/stable/'}]}
[D 08:54:47.190 NotebookApp] 101 GET /api/kernels/3547d2c7-00b5-41a8-876b-9477fd403861/channels?session_id=7fe33e05-ff84-4f56-a8ff-ac0002491795 (127.0.0.1) 337.58ms
[D 08:54:47.190 NotebookApp] Opening websocket /api/kernels/3547d2c7-00b5-41a8-876b-9477fd403861/channels
[D 08:54:47.190 NotebookApp] Getting buffer for 3547d2c7-00b5-41a8-876b-9477fd403861
[D 08:54:47.191 NotebookApp] Connecting to: tcp://127.0.0.1:49785
[D 08:54:47.191 NotebookApp] Connecting to: tcp://127.0.0.1:50037
[D 08:54:47.191 NotebookApp] Connecting to: tcp://127.0.0.1:41455
[D 08:54:47.192 NotebookApp] Connecting to: tcp://127.0.0.1:47391
[D 08:54:47.250 NotebookApp] 200 GET /api/contents (127.0.0.1) 2.89ms
[D 08:54:47.268 NotebookApp] 200 GET /api/sessions (127.0.0.1) 1.68msI have updated the above comment.
dickmao
commented
3 years ago Have you tried:
jupyter trust '/home/emath/google-drive/MSc Data Science/AI Lab-Research/Wikipedia API/revisions_eda_first_approach.ipynb'I don't know precisely what property of a notebook elicits the need for "explicit trusting." I know my notebooks never require this, but I don't know why.
EvanMath
commented
3 years ago Where should I use this? The thing is that other notebooks run fine. And in browser run all fine.
dickmao
commented
3 years ago Where should I use this?
At a shell prompt.
dickmao
commented
3 years ago Content-Length: 578165
Ah wait, it's getting data for revisions_eda_first_approach.ipynb but there is a control character triggering an interrupt signal to the curl process. Try editing the notebook first in the browser to remove all the outputs or suspect inputs that might cause this.
EvanMath
commented
3 years ago Thanks a ton! I use the jupyter trust part and worked fine. Any ideas why is this happening?
dickmao
commented
3 years ago Any ideas why is this happening?
No, I personally think the jupyter ecosystem with all its hanging chads is more trouble than it's worth.
EvanMath
commented
3 years ago Thank you for your help!
Since yesterday I am not able to navigate to my shared folder in Owncloud with ein interface. I got this weird error when I try to open the folder:
ein: [error] ein:content-query-contents--error http://127.0.0.1:8888/ownCloudShared REQUEST-STATUS error DATA (http 404)