unable to launch specviz from command line

[skendrew]

I have an extracted JWST pipeline output spectrum from MIRI LRS. In python, I can read it into a Spectrum1D object directly -so the file should be readable by specviz. However when I do

jdaviz --layout specviz miri_lrs_slit_pt_nod2_v2_x1d.fits

on the command line, the browser window launches but shows only the following:

[pllim]

On my machine (Linux), I sometimes have to minimize it and then show it again for it to finish loading. Not sure if that will also fix your problem. Which browser is this? Try a different browser too by providing --browser option.

[skendrew]

I'm using Safari. Minimizing did nothing. Tried Firefox and was the same.

[pllim]

What about Chrome? Didn't work on Firefox for me either and I don't use Safari but worked on Chrome on Linux.

[skendrew]

Tried Chrome and still the same! I'm on a Mac, 10.15.7 (Catalina)

The screen output on the command line is as follows:
(miricle) sarahkloaner:b77-e2e skendrew$ jdaviz --layout specviz --browser chrome miri_lrs_slit_pt_nod2_v2_x1d.fits
[Voila] Using /var/folders/9l/lthyqbnd6md29c4bpkgdp_980001p3/T to store connection files
[Voila] Storing connection files in /var/folders/9l/lthyqbnd6md29c4bpkgdp_980001p3/T/voila_jfyeq94u.
[Voila] Serving static files from /Users/skendrew/anaconda3/envs/miricle/lib/python3.8/site-packages/voila/static.
[Voila] Voilà is running at:
http://localhost:8866/
[Voila] WARNING | Notebook notebook.ipynb is not trusted
[Voila] Kernel started: 1212ae83-7f24-4ca0-b3eb-c0a5ffcf0582
WARNING:tornado.general:403 GET /voila/files/favicon.ico (::1): File not whitelisted
WARNING:tornado.access:403 GET /voila/files/favicon.ico (::1) 1.01ms

[pllim]

Thanks for checking! 😿

[duytnguyendtn]

Out of curiosity, if you try to load Specviz without data, does it come up at all?

[skendrew]

it does not load, it complains about the lack of a file:

(miricle) sarahkloaner:b77-e2e skendrew$ jdaviz --layout specviz --browser chrome
Usage: jdaviz [OPTIONS] FILENAME
Try 'jdaviz --help' for help.

Error: Missing argument 'FILENAME'.
(miricle) sarahkloaner:b77-e2e skendrew$

[skendrew]

(it does work in a notebook, fwiw. but somewhat buggy.)

[havok2063]

I've also experienced the same thing. Loading jdaviz in desktop mode results in perpetually executing notebook display. I think I've tried Cubeviz and Specviz in Chrome.

[pllim]

jdaviz --layout=specviz --browser=/path/to/your/chrome-executable-name filename

Example on Linux:

jdaviz --layout=specviz --browser=/usr/bin/chromium-browser myfits.fits

[havok2063]

I just tested it again with jdaviz --layout=specviz filename and it works for me.

[skendrew]

no, sorry, none of them working. it does open the correct browser and a new tab, but always shows the same screen as I put in my original message.

[havok2063]

If you open up the browser console (right click, go to Inspect or Developer Tools, click Console tab) and reload the page, do you see any errors or output?

[skendrew]

this is from the developer console in Chrome:

Executing cell 1 of 1
:8866/voila/files/favicon.ico:1 Failed to load resource: the server responded with a status of 403 (Forbidden)
voila.js:455 Uncaught (in promise) TypeError: Cannot read property 'kernelChanged' of undefined
at new so (voila.js:455)
at new Ys (voila.js:469)
at getWidgetManager ((index):376)
at window.init ((index):409)
DevTools failed to load SourceMap: Could not load content for http://localhost:8866/voila/static/voila.js.map: HTTP error: status code 403, net::ERR_HTTP_RESPONSE_CODE_FAILURE

[havok2063]

what version of Voila do you have installed? check if it's voila==0.2.8. If so, try downgrading to 0.2.7 with pip install voila==0.2.7. I've had some issues with the recent release of Voila, and this error looks similar to those.

[skendrew]

had 0.2.9, downgraded to 0.2.7 and still same.

there's a couple of warning messages in the terminal:

**http://localhost:8866/
[Voila] WARNING | Notebook notebook.ipynb is not trusted
[Voila] Kernel started: 6ef68ab6-3b22-4ea7-a0f0-815a4622a1d5
WARNING:tornado.general:403 GET /voila/files/favicon.ico (::1): File not whitelisted
WARNING:tornado.access:403 GET /voila/files/favicon.ico (::1) 0.96ms
[Voila] WARNING | Notebook notebook.ipynb is not trusted
[Voila] Kernel started: 3cff2c57-8f5f-4307-9d8d-b69453d5abe9
WARNING:tornado.general:403 GET /voila/files/favicon.ico (::1): File not whitelisted
WARNING:tornado.access:403 GET /voila/files/favicon.ico (::1) 0.47ms
WARNING:tornado.general:404 GET /api/kernels/1315e026-1150-4016-982c-3e89e803be05/channels?session_id=71ea2c04-ec20-445b-b4f7-87739a595c78 (::1): Kernel does not exist: 1315e026-1150-4016-982c-3e89e803be05
WARNING:tornado.access:404 GET /api/kernels/1315e026-1150-4016-982c-3e89e803be05/channels?session_id=71ea2c04-ec20-445b-b4f7-87739a595c78 (::1) 20.25ms
WARNING:tornado.general:403 GET /voila/static/voila.js.map (::1): voila.js.map is not in root static directory
WARNING:tornado.access:403 GET /voila/static/voila.js.map (::1) 1.11ms
^C[Voila] Stopping...
[Voila] Kernel shutdown: 6ef68ab6-3b22-4ea7-a0f0-815a4622a1d5
**

[havok2063]

hmm. And do you see the same error as before in the developer console?

[skendrew]

yes same error

[havok2063]

Hi @skendrew we've merged a potential fix for this. It's not in a release yet, so you'll need to use the latest main branch of jdaviz. Can you pull the latest changes, and upgrade voila to the latest 0.2.10, and try again? If you still get an error, can you paste the content from the Voila terminal window as well as the browser developer console?

[skendrew]

Hi @havok2063 I pip uninstalled jdaviz and then pulled the code from GitHub & installed from there. With Safari I now get a blank screen with 500: Internal Server Error.

The terminal output looks like this:

(miricle) sarahkloaner:b77-e2e skendrew$ jdaviz --layout specviz miri_lrs_slit_pt_nod1_v2_x1d.fits
[Voila] Using /var/folders/9l/lthyqbnd6md29c4bpkgdp_980001p3/T to store connection files
[Voila] Storing connection files in /var/folders/9l/lthyqbnd6md29c4bpkgdp_980001p3/T/voila_feheztf0.
[Voila] Serving static files from /Users/skendrew/anaconda3/envs/miricle/lib/python3.8/site-packages/voila/static.
[Voila] Voilà is running at:
http://localhost:8866/
[Voila] WARNING | Notebook notebook.ipynb is not trusted
ERROR:tornado.application:Uncaught exception GET / (::1)
HTTPServerRequest(protocol='http', host='localhost:8866', method='GET', uri='/', version='HTTP/1.1', remote_ip='::1')
Traceback (most recent call last):
File "/Users/skendrew/anaconda3/envs/miricle/lib/python3.8/site-packages/tornado/web.py", line 1704, in _execute
result = await result
File "/Users/skendrew/anaconda3/envs/miricle/lib/python3.8/site-packages/voila/handler.py", line 154, in get
async for html_snippet, resources in self.exporter.generate_from_notebook_node(notebook, resources=resources, extra_context=extra_context):
File "/Users/skendrew/anaconda3/envs/miricle/lib/python3.8/site-packages/voila/exporter.py", line 100, in generate_from_notebook_node
async for output in self.template.generate_async(nb=nb_copy, resources=resources, **extra_context, static_url=self.static_url):
File "/Users/skendrew/anaconda3/envs/miricle/lib/python3.8/site-packages/nbconvert/exporters/templateexporter.py", line 148, in template
self._template_cached = self._load_template()
File "/Users/skendrew/anaconda3/envs/miricle/lib/python3.8/site-packages/nbconvert/exporters/templateexporter.py", line 355, in _load_template
return self.environment.get_template(template_file)
File "/Users/skendrew/anaconda3/envs/miricle/lib/python3.8/site-packages/jinja2/environment.py", line 883, in get_template
return self._load_template(name, self.make_globals(globals))
File "/Users/skendrew/anaconda3/envs/miricle/lib/python3.8/site-packages/jinja2/environment.py", line 857, in _load_template
template = self.loader.load(self, name, globals)
File "/Users/skendrew/anaconda3/envs/miricle/lib/python3.8/site-packages/jinja2/loaders.py", line 429, in load
raise TemplateNotFound(name)
jinja2.exceptions.TemplateNotFound: index.html.j2
ERROR:tornado.access:500 GET / (::1) 64.59ms
WARNING:tornado.general:403 GET /voila/static/theme-light.css (::1): theme-light.css is not in root static directory
WARNING:tornado.access:403 GET /voila/static/theme-light.css (::1) 2.69ms
WARNING:tornado.general:403 GET /voila/static/index.css (::1): index.css is not in root static directory
WARNING:tornado.access:403 GET /voila/static/index.css (::1) 3.15ms
WARNING:tornado.access:404 GET /voila/files/apple-touch-icon-precomposed.png (::1) 1.16ms
WARNING:tornado.general:403 GET /voila/files/favicon.ico (::1): File not whitelisted
WARNING:tornado.access:403 GET /voila/files/favicon.ico (::1) 0.66ms
WARNING:tornado.access:404 GET /voila/files/apple-touch-icon.png (::1) 0.76ms

[skendrew]

I am trying to use a different browser but this doesn't work anymore in the same way that I did before. If I put --browser=chrome (the exact same command as I mention in the comments above), the terminal tells me 69:77: execution error: Can’t get application "chrome". (-1728) and no browser opens. I've tried with the full path to the application (/Applications/Google Chrome.app) with same result.

[pllim]

I think you need to call the binary executable: https://stackoverflow.com/questions/31083901/how-to-find-the-executable-file-for-open-command-in-mac

[havok2063]

@skendrew Hmm.. it looks like it could be an issue where Voila cannot find the correct template to use when rendering the notebook as html. Are you working in a clean conda environment? I've had similar issues with this index.html.j2 for Voila in my conda envs where it was looking in the wrong place. To resolve it I reinstalled voila in that environment, then deactivated and reactivated the conda env, to clear the conda cache. Can you try the following :

• run which voila and verify that it is pointing to your correct conda environment
• check that you're using nbconvert > 6 and traitlets > 5
• run hash -r in the terminal shell to clear your PATH cache
• or deactivate and reactivate the conda environment

Could there be a conflicting voila configuration? You can also try running in the terminal, in the conda env, voila --Voila.show_config=True to see if that returns anything odd. It would return a printout of any custom config parameters. If it returns nothing, that means the default Voila configuration is being used.

I just tried creating a clean python 3.8 environment, installing the latest jdaviz git repo, and it worked for me. It took a moment to start up but the spectrum loaded.

conda create -n jtest python=3.8 ipython
conda activate jtest

cd ~/path/to/git/checkout/jdaviz
git pull
pip install -e .

jdaviz --layout specviz ~/Work/jwst/1.1/jw00212-o035_t007_miri_ch2-medium_x1d.fits

[Voila] Using /var/folders/js/s2zfzbv16019vjh0dft_l_w0000263/T to store connection files
[Voila] Storing connection files in /var/folders/js/s2zfzbv16019vjh0dft_l_w0000263/T/voila_5qtawz1c.
[Voila] Serving static files from /Users/bcherinka/anaconda3/envs/jtest/lib/python3.8/site-packages/voila/static.
[Voila] Voilà is running at:
http://localhost:8866/
[Voila] WARNING | Notebook notebook.ipynb is not trusted
[Voila] Kernel started: 8a320fd6-2966-4ce1-a084-3effee9c9e5c
WARNING:tornado.general:403 GET /voila/files/favicon.ico (::1): File not whitelisted
WARNING:tornado.access:403 GET /voila/files/favicon.ico (::1) 1.47ms

I also tried jdaviz --layout specviz --browser=chrome ~/Work/jwst/1.1/jw00212-o035_t007_miri_ch2-medium_x1d.fits and that worked as well.

[skendrew]

I didn't try all of that but I created the clean conda environment and then it did work with safari. I haven't got time to sort out the different browser options right now, but it looks like the basic issue of not launching is fixed!

[havok2063]

Ok, great! I'm glad it's working now. When in doubt burn it down and start again!