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rkimoakbioinformatics / oakvar

Genomic variant analysis platform
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After setup there is no module webapps #3

Closed Alex-Karmazin closed 2 years ago

Alex-Karmazin commented 2 years ago

After installation and executing command ov system setup, ov gui did not start web server. In log I found thet it could not find webapps folder. Creating manually this folder in modules fix this issue. But when I click "install system modules" button in oakvar web interface it show me other error in terminal. """ OakVar Server is served at 0.0.0.0:8080 (To quit: Press Ctrl-C or Ctrl-Break if run on a Terminal or Windows, or click "Cancel" and then "Quit" if run through OakVar app on Mac OS) [2022:06:13 21:24:10] Starting to install vcfreporter:3.2.1... Collecting pyvcf Using cached PyVCF-0.6.8.tar.gz (34 kB) Preparing metadata (setup.py) ... error error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully. │ exit code: 1 ╰─> [1 lines of output] error in PyVCF setup command: use_2to3 is invalid. [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed

× Encountered error while generating package metadata. ╰─> See above for output.

note: This is an issue with the package mentioned above, not pip. hint: See above for details. """

Last errors in wcravat.log are: """ Traceback (most recent call last): File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/oakvar/cli_gui.py", line 407, in server_done task.result() File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/asyncio/futures.py", line 201, in result raise self._exception File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/asyncio/tasks.py", line 256, in step result = coro.send(None) File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/oakvar/cli_gui.py", line 428, in start self.setup_routes() File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/oakvar/cli_gui.py", line 509, in setup_routes self.app.router.add_static("/webapps", File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/aiohttp/web_urldispatcher.py", line 1124, in add_static resource = StaticResource( File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/aiohttp/web_urldispatcher.py", line 559, in init__ raise ValueError(f"No directory exists at '{directory}'") from error ValueError: No directory exists at '/home/alex/.oakvar/modules/webapps' 2022/06/13 21:19:46: Serving OakVar server at 0.0.0.0:8080 2022/06/13 21:19:46: No directory exists at '/home/alex/.oakvar/modules/webapps' Traceback (most recent call last): File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/aiohttp/web_urldispatcher.py", line 557, in init raise ValueError("Not a directory") ValueError: Not a directory

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/oakvar/cli_gui.py", line 407, in server_done task.result() File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/asyncio/futures.py", line 201, in result raise self._exception File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/asyncio/tasks.py", line 256, in step result = coro.send(None) File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/oakvar/cli_gui.py", line 428, in start self.setup_routes() File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/oakvar/cli_gui.py", line 509, in setup_routes self.app.router.add_static("/webapps", File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/aiohttp/web_urldispatcher.py", line 1124, in add_static resource = StaticResource( File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/aiohttp/web_urldispatcher.py", line 559, in init__ raise ValueError(f"No directory exists at '{directory}'") from error ValueError: No directory exists at '/home/alex/.oakvar/modules/webapps' 2022/06/13 21:23:54: Serving OakVar server at 0.0.0.0:8080 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /submit/nocache/index.html HTTP/1.1" 200 262 "-" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /submit/jquery-3.3.1.min.js HTTP/1.1" 200 251 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /result/js/jquery-ui-1.12.1.custom/jquery-ui.css HTTP/1.1" 200 236 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /result/js/jquery-ui-1.12.1.custom/jquery-ui.min.js HTTP/1.1" 200 252 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /submit/nocache/websubmit.css HTTP/1.1" 200 261 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /result/css/pqselect.min.css HTTP/1.1" 200 234 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /store/nocache/webstore.css HTTP/1.1" 200 261 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /submit/pqselect.dev.customforsubmit.js HTTP/1.1" 200 250 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /submit/nocache/websubmit.js HTTP/1.1" 200 276 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /store/nocache/webstore.js HTTP/1.1" 200 276 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /submit/Chart.bundle.min.js HTTP/1.1" 200 252 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /store/js/showdown-1.9.1.min.js HTTP/1.1" 200 251 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /store/getstoreurl HTTP/1.1" 200 179 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /result/images/question.png HTTP/1.1" 200 235 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /submit/logo.png HTTP/1.1" 200 237 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /result/images/mail.png HTTP/1.1" 200 235 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /submit/nocache/broken_wheel.gif HTTP/1.1" 200 262 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /submit/menu.png HTTP/1.1" 200 233 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /submit/nointernet.png HTTP/1.1" 200 237 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /store/images/left_arrow.png HTTP/1.1" 200 235 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /store/images/x-lg.svg HTTP/1.1" 200 238 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /store/images/right_arrow.png HTTP/1.1" 200 235 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /result/images/back_arrow.png HTTP/1.1" 200 237 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /result/fonts/sourcesanspro-bold-webfont.woff HTTP/1.1" 200 237 "http://0.0.0.0:8080/submit/nocache/websubmit.css" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /result/fonts/roboto-light-webfont.woff HTTP/1.1" 200 237 "http://0.0.0.0:8080/submit/nocache/websubmit.css" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /result/fonts/roboto-bold-webfont.woff HTTP/1.1" 200 237 "http://0.0.0.0:8080/submit/nocache/websubmit.css" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /result/fonts/roboto-medium-webfont.woff HTTP/1.1" 200 237 "http://0.0.0.0:8080/submit/nocache/websubmit.css" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /submit/servermode HTTP/1.1" 200 178 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /submit/reports HTTP/1.1" 200 177 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /store/getbasemodules HTTP/1.1" 200 532 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /submit/getsystemconfinfo HTTP/1.1" 200 1182 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /submit/lastassembly HTTP/1.1" 200 160 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: Exception with /submit/logo_transparent.png 2022/06/13 21:23:55: Not Found Traceback (most recent call last): File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/oakvar/cli_gui.py", line 347, in middleware response = await handler(request) File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/aiohttp/web_urldispatcher.py", line 690, in _handle raise HTTPNotFound aiohttp.web_exceptions.HTTPNotFound: Not Found 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /submit/logo_transparent.png HTTP/1.1" 500 209 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /submit/packageversions HTTP/1.1" 200 213 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:55: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /submit/nocache/index.html HTTP/1.1" 304 202 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:59: 127.0.0.1 [13/Jun/2022:18:23:55 +0000] "GET /store/remote HTTP/1.1" 200 430422 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:59: 127.0.0.1 [13/Jun/2022:18:23:59 +0000] "GET /issystemready HTTP/1.1" 200 198 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:59: 127.0.0.1 [13/Jun/2022:18:23:59 +0000] "GET /submit/jobs HTTP/1.1" 200 158 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:59: 127.0.0.1 [13/Jun/2022:18:23:59 +0000] "GET /store/local HTTP/1.1" 200 69779 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:59: 127.0.0.1 [13/Jun/2022:18:23:59 +0000] "GET /submit/getjobs?ids=%5B%5D HTTP/1.1" 200 158 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:59: 127.0.0.1 [13/Jun/2022:18:23:59 +0000] "GET /submit/annotators HTTP/1.1" 200 711 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:59: 127.0.0.1 [13/Jun/2022:18:23:59 +0000] "GET /store/updates HTTP/1.1" 200 189 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:23:59: 127.0.0.1 [13/Jun/2022:18:23:59 +0000] "GET /submit/help.png HTTP/1.1" 200 235 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" 2022/06/13 21:24:08: Exception with /store/queueinstall?module=vcfreporter 2022/06/13 21:24:08: 'tuple' object has no attribute 'items' Traceback (most recent call last): File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/oakvar/cli_gui.py", line 347, in middleware response = await handler(request) File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/oakvar/webstore/webstore.py", line 256, in queue_install for dep_name, dep_version in deps.items(): AttributeError: 'tuple' object has no attribute 'items' 2022/06/13 21:24:08: 127.0.0.1 [13/Jun/2022:18:24:07 +0000] "GET /store/queueinstall?module=vcfreporter HTTP/1.1" 500 239 "http://0.0.0.0:8080/submit/nocache/index.html" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/98.0.4758.80 Safari/537.36" """

Alex-Karmazin commented 2 years ago

I use Ubuntu 20.04.3 LTS 64 bit

rkimoakbioinformatics commented 2 years ago

@Alex-Karmazin Thanks. I'll look into it.

rkimoakbioinformatics commented 2 years ago

@Alex-Karmazin I have just published OakVar v2.4.8. Can you try this version?

Alex-Karmazin commented 2 years ago

Reinstaled v2.4.8 but still geting errors. """ The following modules will be installed:

× Encountered error while generating package metadata. ╰─> See above for output.

note: This is an issue with the package mentioned above, not pip. hint: See above for details. Following PyPI dependencies could not be installed.

rkimoakbioinformatics commented 2 years ago

@Alex-Karmazin Ah, that is the PyVCF problem which people have been experiencing since a while ago. It should be ported Python 3 somehow eventually by somebody. Until then, here is a solution. Before running ov system setup,

>pip install "setuptools<58" --upgrade
>pip uninstall pyvcf
>pip install pyvcf
>pip install setuptools --upgrade

This will temporarily downgrade setuptools so that Python 2-based PyVCF is installed and then bring it back to the latest version.

After this, ov system setup will work normally.

Alex-Karmazin commented 2 years ago

Thank you it fixed problem.