rkimoakbioinformatics
commented
2 years ago @Marfantyk Thanks. I'll take a look.
Closed marfantyk closed 1 year ago
rkimoakbioinformatics
commented
2 years ago @Marfantyk Thanks. I'll take a look.
rkimoakbioinformatics
commented
2 years ago @Marfantyk It could have been a glitch in the server hosting the download files. As I test now, the problem module is installed without an error. Can you try ov system setup again?
marfantyk
commented
2 years ago @rkimoakbioinformatics just tried to do it again and got the same error.
rkimoakbioinformatics
commented
2 years ago @Marfantyk Is this file accessible/downloadable on your computer? https://c7i1.va21.idrivee2-1.com/oakvar-modules/reporters/excelreporter/2.2.0/excelreporter__2.2.1__code.zip
antonkulaga
commented
2 years ago I think the problem is that this file is on a server that is blocked in some countries. I remember @winternewt had the same problem. However, I am not totally sure.
wget https://c7i1.va21.idrivee2-1.com/oakvar-modules/reporters/excelreporter/2.2.0/excelreporter__2.2.1__code.zipworks for me
marfantyk
commented
2 years ago @rkimoakbioinformatics yes, I can't download it. So the problem is in blocking in my country. I will try to use vpn tomorrow to setup it. Thank you!
rkimoakbioinformatics
commented
2 years ago @Marfantyk My pleasure. Hope that you'll be able to download with the vpn.
rkimoakbioinformatics
commented
2 years ago @antonkulaga I see. I'll look into it.
rkimoakbioinformatics
commented
2 years ago @Marfantyk I have just published the excelreporter to a different server. Hope this helps and let me know if it still does not work.
marfantyk
commented
2 years ago @rkimoakbioinformatics yes, excelreporter was downloaded, but now there is the same problem for gencode.
Here is log:
[2022:09:30 18:19:40] Downloading code archive of gencode:41.0.2... Traceback (most recent call last): File "/usr/lib/python3.8/urllib/request.py", line 1354, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/usr/lib/python3.8/http/client.py", line 1256, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/lib/python3.8/http/client.py", line 1302, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/lib/python3.8/http/client.py", line 1251, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib/python3.8/http/client.py", line 1011, in _send_output self.send(msg) File "/usr/lib/python3.8/http/client.py", line 951, in send self.connect() File "/usr/lib/python3.8/http/client.py", line 1418, in connect super().connect() File "/usr/lib/python3.8/http/client.py", line 922, in connect self.sock = self._create_connection( File "/usr/lib/python3.8/socket.py", line 808, in create_connection raise err File "/usr/lib/python3.8/socket.py", line 796, in create_connection sock.connect(sa) socket.timeout: timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/marfantyk/.local/lib/python3.8/site-packages/download/download.py", line 208, in _fetch_file
u = urllib.request.urlopen(req, timeout=timeout)
File "/usr/lib/python3.8/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/usr/lib/python3.8/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/usr/lib/python3.8/urllib/request.py", line 542, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
File "/usr/lib/python3.8/urllib/request.py", line 502, in _call_chain
result = func(*args)
File "/usr/lib/python3.8/urllib/request.py", line 1397, in https_open
return self.do_open(http.client.HTTPSConnection, req,
File "/usr/lib/python3.8/urllib/request.py", line 1357, in do_open
raise URLError(err)
urllib.error.URLError:
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/marfantyk/.local/bin/ov", line 8, in
marfantyk
commented
2 years ago @rkimoakbioinformatics I kept installing with vpn and it worked fine. Then I tried to install some modules without vpn. There were problems with some of them too. But, again, vpn fixes this problem. Do you need a list of such modules?
rkimoakbioinformatics
commented
2 years ago @Marfantyk I'm glad that at least using a VPN helped. Yes, such a list would be helpful.
antonkulaga
commented
1 year ago @Marfantyk it looks no longer relevan, please close
System configuration file: /home/marfantyk/.oakvar/conf/system.yml User configuration file: /home/marfantyk/.oakvar/oakvar.yml. No store update to fetch No store update to fetch No store update to fetch cravat-converter==1.1.2 is already installed. Use -f/--force to overwrite casecontrol==1.2.0 is already installed. Use -f/--force to overwrite The following modules will be installed:
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/download/download.py", line 208, in _fetch_file u = urllib.request.urlopen(req, timeout=timeout) File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/urllib/request.py", line 519, in open response = self._open(req, data) File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/urllib/request.py", line 496, in _call_chain result = func(*args) File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/urllib/request.py", line 1391, in https_open return self.do_open(http.client.HTTPSConnection, req, File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError:
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/marfantyk/micromamba/envs/oakvar-longevity/bin/ov", line 8, in
sys.exit(main())
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/main.py", line 169, in main
handle_exception(e)
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/main.py", line 151, in handle_exception
raise e
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/main.py", line 162, in main
ret = args.func(args)
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/decorators.py", line 5, in change_args_for_cli
ret = func(args)
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/cli/system.py", line 7, in cli_system_setup
setup(args)
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/decorators.py", line 32, in run_cli_func
handle_exception(e)
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/main.py", line 151, in handle_exception
raise e
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/decorators.py", line 24, in run_cli_func
ret = func(args)
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/cli/system.py", line 14, in setup
setup_system(args)
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/system/init.py", line 32, in setup_system
ret = installbase(args)
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/decorators.py", line 32, in run_cli_func
handle_exception(e)
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/main.py", line 151, in handle_exception
raise e
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/decorators.py", line 24, in run_cli_func
ret = func(args)
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/cli/module.py", line 374, in installbase
ret = install(m_args)
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/decorators.py", line 32, in run_cli_func
handle_exception(e)
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/main.py", line 151, in handle_exception
raise e
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/decorators.py", line 24, in run_cli_func
ret = func(args)
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/cli/module.py", line 223, in install
ret = install_module(
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/module/init.py", line 577, in install_module
raise e
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/module/init.py", line 542, in install_module
if not download_code_or_data(kind="code", args=args):
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/module/init.py", line 345, in download_code_or_data
download(urls[i], part_path)
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/oakvar/util/download.py", line 10, in download
download_util.download(url, fpath, kind="file", verbose=False, replace=True)
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/download/download.py", line 119, in download
_fetch_file(
File "/home/marfantyk/micromamba/envs/oakvar-longevity/lib/python3.10/site-packages/download/download.py", line 277, in _fetch_file
raise RuntimeError(
RuntimeError: Error while fetching file https://c7i1.va21.idrivee2-1.com/oakvar-modules/reporters/excelreporter/2.2.0/excelreporter__2.2.1__code.zip. Dataset fetching aborted.
Error: