Use behind proxy

[BenoitTS]

I'm trying to use ontobio behind a proxy but when importing package with

from ontobio.ontol_factory import OntologyFactory

I get the following error (note that I do no get that when no proxy is used):

Traceback (most recent call last):
  File "<path_to_project>/venv/lib/python3.8/site-packages/urllib3/connection.py", line 169, in _new_conn
    conn = connection.create_connection(
  File "<path_to_project>/venv/lib/python3.8/site-packages/urllib3/util/connection.py", line 96, in create_connection
    raise err
  File "<path_to_project>/venv/lib/python3.8/site-packages/urllib3/util/connection.py", line 86, in create_connection
    sock.connect(sa)
TimeoutError: [Errno 110] Connection timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "<path_to_project>/venv/lib/python3.8/site-packages/urllib3/connectionpool.py", line 699, in urlopen
    httplib_response = self._make_request(
  File "<path_to_project>/venv/lib/python3.8/site-packages/urllib3/connectionpool.py", line 382, in _make_request
    self._validate_conn(conn)
  File "<path_to_project>/venv/lib/python3.8/site-packages/urllib3/connectionpool.py", line 1010, in _validate_conn
    conn.connect()
  File "<path_to_project>/venv/lib/python3.8/site-packages/urllib3/connection.py", line 353, in connect
    conn = self._new_conn()
  File "<path_to_project>/venv/lib/python3.8/site-packages/urllib3/connection.py", line 181, in _new_conn
    raise NewConnectionError(
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7fe09119df70>: Failed to establish a new connection: [Errno 110] Connection timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "<path_to_project>/venv/lib/python3.8/site-packages/requests/adapters.py", line 439, in send
    resp = conn.urlopen(
  File "<path_to_project>/venv/lib/python3.8/site-packages/urllib3/connectionpool.py", line 755, in urlopen
    retries = retries.increment(
  File "<path_to_project>/venv/lib/python3.8/site-packages/urllib3/util/retry.py", line 573, in increment
    raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='raw.githubusercontent.com', port=443): Max retries exceeded with url: /prefixcommons/biocontext/master/registry/monarch_context.jsonld (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7fe09119df70>: Failed to establish a new connection: [Errno 110] Connection timed out'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "<input>", line 1, in <module>
  File "/snap/pycharm-community/226/plugins/python-ce/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "<path_to_project>/venv/lib/python3.8/site-packages/ontobio/__init__.py", line 6, in <module>
    from .ontol_factory import OntologyFactory
  File "/snap/pycharm-community/226/plugins/python-ce/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "<path_to_project>/venv/lib/python3.8/site-packages/ontobio/ontol_factory.py", line 7, in <module>
    import ontobio.obograph_util as obograph_util
  File "/snap/pycharm-community/226/plugins/python-ce/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "<path_to_project>/venv/lib/python3.8/site-packages/ontobio/obograph_util.py", line 8, in <module>
    from ontobio.golr.golr_associations import search_associations
  File "/snap/pycharm-community/226/plugins/python-ce/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "<path_to_project>/venv/lib/python3.8/site-packages/ontobio/golr/golr_associations.py", line 13, in <module>
    from ontobio.golr.golr_query import *
  File "/snap/pycharm-community/226/plugins/python-ce/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "<path_to_project>/venv/lib/python3.8/site-packages/ontobio/golr/golr_query.py", line 49, in <module>
    from prefixcommons.curie_util import expand_uri
  File "/snap/pycharm-community/226/plugins/python-ce/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "<path_to_project>/venv/lib/python3.8/site-packages/prefixcommons/__init__.py", line 4, in <module>
    from .curie_util import expand_uri, contract_uri, NoPrefix
  File "/snap/pycharm-community/226/plugins/python-ce/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "<path_to_project>/venv/lib/python3.8/site-packages/prefixcommons/curie_util.py", line 79, in <module>
    default_curie_maps = [read_biocontext('monarch_context'),read_biocontext('obo_context')]
  File "<path_to_project>/venv/lib/python3.8/site-packages/prefixcommons/curie_util.py", line 75, in read_biocontext
    return read_remote_jsonld_context("https://raw.githubusercontent.com/prefixcommons/biocontext/master/registry/"+name+".jsonld")
  File "<path_to_project>/venv/lib/python3.8/site-packages/prefixcommons/curie_util.py", line 56, in read_remote_jsonld_context
    with closing(requests.get(url, stream=False)) as resp:
  File "<path_to_project>/venv/lib/python3.8/site-packages/requests/api.py", line 76, in get
    return request('get', url, params=params, **kwargs)
  File "<path_to_project>/venv/lib/python3.8/site-packages/requests/api.py", line 61, in request
    return session.request(method=method, url=url, **kwargs)
  File "<path_to_project>/venv/lib/python3.8/site-packages/requests/sessions.py", line 542, in request
    resp = self.send(prep, **send_kwargs)
  File "<path_to_project>/venv/lib/python3.8/site-packages/requests/sessions.py", line 655, in send
    r = adapter.send(request, **kwargs)
  File "<path_to_project>/venv/lib/python3.8/site-packages/requests/adapters.py", line 516, in send
    raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPSConnectionPool(host='raw.githubusercontent.com', port=443): Max retries exceeded with url: /prefixcommons/biocontext/master/registry/monarch_context.jsonld (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7fe09119df70>: Failed to establish a new connection: [Errno 110] Connection timed out'))

[GarrettJenkinson]

Bumping this issue as it currently also prevents use of this package on compute cluster nodes that lack internet access. Ideally, this package should be able to get imported without the need for downloading external data (e.g., if we plan to use local ".obo" files).

[remerjohnson]

I'll echo this issue. I am using two local obojson ontology files in order to do lexical mapping, so getting connection errors is not making much sense when I just need to make some ofactory/afactory objects.