Open atthewmay opened 4 years ago
The config.yml for the "glia analyze" looks like:
The docker-compose.yml looks like this
Thanks for creating this issue! I’ll take a closer look tomorrow but in the meantime a couple issues:
epl
If that does not solve the issue, please let me know
Also, in case this is confusing, I had to rename the experiment to be "R1_E3_AMES_540min_ffhq_BnW_6100_9200" rather "than R1_E3_AMES_540min_ffhq_BnW_6100_9201", bc it seemed the lab_notebook.yml had 6100_9200.
From: Tyler Benster notifications@github.com Sent: Wednesday, September 2, 2020 8:40 PM To: tbenst/glia glia@noreply.github.com Cc: Hunt, Matthew huntm@wustl.edu; Author author@noreply.github.com Subject: Re: [tbenst/glia] "glia analyze (filename) integrity" fails with "json.decoder.JSONDecodeError" (#29)
Thanks for creating this issue! I’ll take a closer look tomorrow but in the meantime a couple issues:
If that does not solve the issue, please let me know
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Issue Description
Running "glia analyze --configuration config.yaml R1_E3_AMES_540min_ffhq_BnW_6100_9200 integrity" gives a "json.decoder.JSONDecodeError" in the try-except block of create_epl_gen_v2 in glia/eyecandy.py.
In my eye-candy directory, I ran "docker-compose up" prior to running the above command.
I have performed "git pull" for the eye-candy directory and the glia directory. Tried while on the "master" branch of glia and the 3brain_units branch.
Steps to reproduce.
What's the Actual Result?
Copied below are 1. the error message from glia, and 2. The error message from eyecandy.
From
load_entry_point('glia', 'console_scripts', 'glia')()
File "/Users/matthewhunt/miniconda3/envs/glia/lib/python3.8/site-packages/click/core.py", line 829, in call
return self.main(args, kwargs)
File "/Users/matthewhunt/miniconda3/envs/glia/lib/python3.8/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/Users/matthewhunt/miniconda3/envs/glia/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/matthewhunt/miniconda3/envs/glia/lib/python3.8/site-packages/click/core.py", line 1268, in invoke
Command.invoke(self, ctx)
File "/Users/matthewhunt/miniconda3/envs/glia/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/Users/matthewhunt/miniconda3/envs/glia/lib/python3.8/site-packages/click/core.py", line 610, in invoke
return callback(args, *kwargs)
File "/Users/matthewhunt/miniconda3/envs/glia/lib/python3.8/site-packages/click/decorators.py", line 21, in new_func
return f(get_current_context(), args, kwargs)
File "/Users/matthewhunt/Coding/Seattle_Research/MEA_Project/glia/glia_scripts/command_line.py", line 343, in analyze
metadata, stimulus_list = glia.create_stimuli(
File "/Users/matthewhunt/Coding/Seattle_Research/MEA_Project/glia/glia/eyecandy.py", line 220, in create_stimuli
metadata, stimulus_gen = create_epl_gen_v2(program, epl, window_width,
File "/Users/matthewhunt/Coding/Seattle_Research/MEA_Project/glia/glia/eyecandy.py", line 71, in create_epl_gen_v2
response = r.json()
File "/Users/matthewhunt/miniconda3/envs/glia/lib/python3.8/site-packages/requests/models.py", line 898, in json
return complexjson.loads(self.text, kwargs)
File "/Users/matthewhunt/miniconda3/envs/glia/lib/python3.8/json/init.py", line 357, in loads
return _default_decoder.decode(s)
File "/Users/matthewhunt/miniconda3/envs/glia/lib/python3.8/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/Users/matthewhunt/miniconda3/envs/glia/lib/python3.8/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
Glia
(glia) matthewhunt@Matthews-MacBook-Pro 200818 % glia analyze --configuration config.yaml R1_E3_AMES_540min_ffhq_BnW_6100_9200 integrity version 0.5.1 Analyzing R1_E3_AMES_540min_ffhq_BnW_6100_9200 No .stim file found. Creating from .analog file. couldn't parse json from <Response [500]> Traceback (most recent call last): File "/Users/matthewhunt/miniconda3/envs/glia/bin/glia", line 11, inThe error message from eyecandy: nginx_1 | 172.17.0.1 - - [02/Sep/2020:22:24:17 +0000] "POST /analysis/run-program HTTP/1.1" 500 21 "-" "python-requests/2.24.0" "-" web_1 | <-- POST /analysis/run-program web_1 | analysis/run-program web_1 | compiling EPL. web_1 | xxx POST /analysis/run-program 500 540ms - web_1 | web_1 | ReferenceError: measureIntegrity is not defined web_1 | at vm.js:39:1 web_1 | at Script.runInContext (vm.js:107:20) web_1 | at VM.run (/www/node_modules/vm2/lib/main.js:204:72) web_1 | at compileJSProgram (/www/src/epl/eval.js:43:8) web_1 | at router.post.ctx (/www/src/app.js:268:13) web_1 | at dispatch (/www/node_modules/koa-router/node_modules/koa-compose/index.js:44:32) web_1 | at next (/www/node_modules/koa-router/node_modules/koa-compose/index.js:45:18) web_1 | at /www/node_modules/koa-router/lib/router.js:346:16 web_1 | at dispatch (/www/node_modules/koa-router/node_modules/koa-compose/index.js:44:32) web_1 | at /www/node_modules/koa-router/node_modules/koa-compose/index.js:36:12 web_1 |