While I am using following parameters:
server = Server(host='http://www.ensembl.org') mart = server['ENSEMBL_MART_SNP'] dataset = mart['hsapiens_snp'] queried = dataset.query(attributes=['chr_name', 'chrom_start', 'chrom_end', 'variation_names', 'phenotype_description', 'refsnp_source'], filters={'chr_name': '15'})
it gives me following error. I checked filters and attributed for that dataset if they are correct. With standard dataset from the docs (hsapiens_gene_ensembl) it works.
How can I solve this problem?
`Traceback (most recent call last):
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/urllib3/connectionpool.py", line 677, in urlopen
chunked=chunked,
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/urllib3/connectionpool.py", line 426, in _make_request
six.raise_from(e, None)
File "", line 3, in raise_from
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/urllib3/connectionpool.py", line 421, in _make_request
httplib_response = conn.getresponse()
File "/usr/lib/python3.7/http/client.py", line 1354, in getresponse
response.begin()
File "/usr/lib/python3.7/http/client.py", line 306, in begin
version, status, reason = self._read_status()
File "/usr/lib/python3.7/http/client.py", line 275, in _read_status
raise RemoteDisconnected("Remote end closed connection without"
http.client.RemoteDisconnected: Remote end closed connection without response
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/requests/adapters.py", line 449, in send
timeout=timeout
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/urllib3/connectionpool.py", line 727, in urlopen
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/urllib3/util/retry.py", line 403, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/urllib3/packages/six.py", line 734, in reraise
raise value.with_traceback(tb)
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/urllib3/connectionpool.py", line 677, in urlopen
chunked=chunked,
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/urllib3/connectionpool.py", line 426, in _make_request
six.raise_from(e, None)
File "", line 3, in raise_from
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/urllib3/connectionpool.py", line 421, in _make_request
httplib_response = conn.getresponse()
File "/usr/lib/python3.7/http/client.py", line 1354, in getresponse
response.begin()
File "/usr/lib/python3.7/http/client.py", line 306, in begin
version, status, reason = self._read_status()
File "/usr/lib/python3.7/http/client.py", line 275, in _read_status
raise RemoteDisconnected("Remote end closed connection without"
urllib3.exceptions.ProtocolError: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/olaf/PycharmProjects/ensembl_cosmic/test.py", line 26, in
filters={'chr_name': ['15']})
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/pybiomart/dataset.py", line 262, in query
response = self.get(query=ElementTree.tostring(root))
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/pybiomart/base.py", line 107, in get
r = requests.get(self.url, params=params)
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/requests/api.py", line 76, in get
return request('get', url, params=params, kwargs)
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/requests/api.py", line 61, in request
return session.request(method=method, url=url, kwargs)
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/requests_cache/core.py", line 136, in request
kwargs
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/requests/sessions.py", line 530, in request
resp = self.send(prep, send_kwargs)
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/requests_cache/core.py", line 109, in send
return send_request_and_cache_response()
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/requests_cache/core.py", line 97, in send_request_and_cache_response
response = super(CachedSession, self).send(request, kwargs)
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/requests/sessions.py", line 643, in send
r = adapter.send(request, kwargs)
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/requests/adapters.py", line 498, in send
raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))
While I am using following parameters:
server = Server(host='http://www.ensembl.org') mart = server['ENSEMBL_MART_SNP'] dataset = mart['hsapiens_snp'] queried = dataset.query(attributes=['chr_name', 'chrom_start', 'chrom_end', 'variation_names', 'phenotype_description', 'refsnp_source'], filters={'chr_name': '15'})
it gives me following error. I checked filters and attributed for that dataset if they are correct. With standard dataset from the docs (hsapiens_gene_ensembl) it works. How can I solve this problem?
`Traceback (most recent call last): File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/urllib3/connectionpool.py", line 677, in urlopen chunked=chunked, File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/urllib3/connectionpool.py", line 426, in _make_request six.raise_from(e, None) File "", line 3, in raise_from
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/urllib3/connectionpool.py", line 421, in _make_request
httplib_response = conn.getresponse()
File "/usr/lib/python3.7/http/client.py", line 1354, in getresponse
response.begin()
File "/usr/lib/python3.7/http/client.py", line 306, in begin
version, status, reason = self._read_status()
File "/usr/lib/python3.7/http/client.py", line 275, in _read_status
raise RemoteDisconnected("Remote end closed connection without"
http.client.RemoteDisconnected: Remote end closed connection without response
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/requests/adapters.py", line 449, in send timeout=timeout File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/urllib3/connectionpool.py", line 727, in urlopen method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2] File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/urllib3/util/retry.py", line 403, in increment raise six.reraise(type(error), error, _stacktrace) File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/urllib3/packages/six.py", line 734, in reraise raise value.with_traceback(tb) File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/urllib3/connectionpool.py", line 677, in urlopen chunked=chunked, File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/urllib3/connectionpool.py", line 426, in _make_request six.raise_from(e, None) File "", line 3, in raise_from
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/urllib3/connectionpool.py", line 421, in _make_request
httplib_response = conn.getresponse()
File "/usr/lib/python3.7/http/client.py", line 1354, in getresponse
response.begin()
File "/usr/lib/python3.7/http/client.py", line 306, in begin
version, status, reason = self._read_status()
File "/usr/lib/python3.7/http/client.py", line 275, in _read_status
raise RemoteDisconnected("Remote end closed connection without"
urllib3.exceptions.ProtocolError: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/olaf/PycharmProjects/ensembl_cosmic/test.py", line 26, in
filters={'chr_name': ['15']})
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/pybiomart/dataset.py", line 262, in query
response = self.get(query=ElementTree.tostring(root))
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/pybiomart/base.py", line 107, in get
r = requests.get(self.url, params=params)
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/requests/api.py", line 76, in get
return request('get', url, params=params, kwargs)
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/requests/api.py", line 61, in request
return session.request(method=method, url=url, kwargs)
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/requests_cache/core.py", line 136, in request
kwargs
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/requests/sessions.py", line 530, in request
resp = self.send(prep, send_kwargs)
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/requests_cache/core.py", line 109, in send
return send_request_and_cache_response()
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/requests_cache/core.py", line 97, in send_request_and_cache_response
response = super(CachedSession, self).send(request, kwargs)
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/requests/sessions.py", line 643, in send
r = adapter.send(request, kwargs)
File "/home/olaf/PycharmProjects/ensembl_cosmic/venv/lib/python3.7/site-packages/requests/adapters.py", line 498, in send
raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))
Process finished with exit code 1 `