vanheeringen-lab/genomepy

Add proxy support

Mitmischer opened this issue · 0 comments

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?