Add proxy support
Mitmischer opened this issue · 0 comments
Mitmischer commented
Hello,
I am behind a university proxy and trying to download the human genome using genomepy. This yields the following error:
$ genomepy install hg38
13:04:17 | WARNING | GENCODE appears to be offline.
13:05:07 | INFO | Downloading assembly summaries from UCSC
Traceback (most recent call last):
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/mysql/connector/connection_cext.py", line 268, in _open_connection
self._cmysql.connect(**cnx_kwargs)
_mysql_connector.MySQLInterfaceError: Can't connect to MySQL server on 'genome-mysql.soe.ucsc.edu:3306' (110)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/mabe/.conda/envs/mabe/bin/genomepy", line 10, in <module>
sys.exit(cli())
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/cli.py", line 262, in install
genomepy.install_genome(
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/functions.py", line 208, in install_genome
provider = _provider_selection(name, localname, genomes_dir, provider)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/functions.py", line 371, in _provider_selection
return _lazy_provider_selection(name, provider)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/functions.py", line 342, in _lazy_provider_selection
for p in online_providers(provider):
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/providers/__init__.py", line 104, in online_providers
yield create(provider)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/providers/__init__.py", line 60, in create
return p()
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/providers/ucsc.py", line 72, in __init__
self.genomes = get_genomes(ADRESSES["api"])
File "/home/mabe/.conda/envs/mabe/lib/python3.10/contextlib.py", line 79, in inner
return func(*args, **kwds)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/diskcache/core.py", line 1875, in wrapper
result = func(*args, **kwargs)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/providers/ucsc.py", line 430, in get_genomes
genomes = add_accessions1(genomes)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/providers/ucsc.py", line 457, in add_accessions1
df = pd.DataFrame.from_records(ret)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/pandas/core/frame.py", line 2297, in from_records
first_row = next(data)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/genomepy/providers/ucsc.py", line 526, in query_ucsc
cnx = mysql.connector.connect(
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/mysql/connector/pooling.py", line 286, in connect
return CMySQLConnection(*args, **kwargs)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/mysql/connector/connection_cext.py", line 101, in __init__
self.connect(**kwargs)
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/mysql/connector/abstracts.py", line 1108, in connect
self._open_connection()
File "/home/mabe/.conda/envs/mabe/lib/python3.10/site-packages/mysql/connector/connection_cext.py", line 273, in _open_connection
raise get_mysql_exception(
mysql.connector.errors.DatabaseError: 2003 (HY000): Can't connect to MySQL server on 'genome-mysql.soe.ucsc.edu:3306' (110)
I found that there is no mention of proxy support in README or when googling.
Is there any plan to add proxy support in the near future?