def search(self, num_attempts=1, sleep_time=0.5):
"""
Perform a search of the Protein Data Bank using the REST API
Parameters
----------
num_attempts : int
In case of a failed retrieval, the number of attempts to try again
sleep_time : int
The amount of time to wait between requests, in case of
API rate limits
"""
query_text = json.dumps(self.scan_params, indent=4)
response = http_requests.request_limited(self.url,
rtype="POST",
data=query_text)
if response is None or response.status_code != 200:
warnings.warn("Retrieval failed, returning None")
return None
response_val = json.loads(response.text)
if self.return_type == "entry":
idlist = walk_nested_dict(response_val,
"identifier",
maxdepth=25,
outputs=[])
return idlist
else:
return response_val
def get_info(pdb_id, url_root='https://data.rcsb.org/rest/v1/core/entry/'):
'''Look up all information about a given PDB ID
Parameters
----------
pdb_id : string
A 4 character string giving a pdb entry of interest
url_root : string
The string root of the specific url for the request type
Returns
-------
out : dict()
An ordered dictionary object corresponding to entry information
'''
pdb_id = pdb_id.replace(":", "/") # replace old entry identifier
url = url_root + pdb_id
response = http_requests.request_limited(url)
if response is None or response.status_code != 200:
warnings.warn("Retrieval failed, returning None")
return None
result = str(response.text)
out = json.loads(result)
return out
def test_post__first_try_success(self, mock_sleep, mock_post):
mock_response = mock.create_autospec(requests.models.Response)
mock_response.status_code = 200 # A-OK!
mock_post.return_value = mock_response
self.assertEqual(
http_requests.request_limited(url="http://get_your_proteins.com",
rtype="POST"), mock_response)
mock_post.assert_called_once_with("http://get_your_proteins.com")
self.assertEqual(len(mock_sleep.mock_calls), 0)
def test_post__repeatedly_fails_return_nothing(self, mock_sleep, mock_post,
mock_warn):
# Busy response
mock_busy_response = mock.create_autospec(requests.models.Response)
mock_busy_response.status_code = 429
mock_post.return_value = mock_busy_response
self.assertIsNone(
http_requests.request_limited(url="http://protein_data_bank.com",
rtype="POST"))
mock_warn.assert_called_with(
"Too many failures on requests. Exiting...")
self.assertEqual(len(mock_post.mock_calls), 4)
mock_post.assert_called_with("http://protein_data_bank.com")
self.assertEqual(len(mock_sleep.mock_calls), 4)
def test_get__succeeds_third_try(self, mock_sleep, mock_get):
# Busy response
mock_busy_response = mock.create_autospec(requests.models.Response)
mock_busy_response.status_code = 429
# Server Error response
mock_error_response = mock.create_autospec(requests.models.Response)
mock_error_response.status_code = 504
# All good (200)
mock_ok_response = mock.create_autospec(requests.models.Response)
mock_ok_response.status_code = 200
# Mocks `requests.get` to return Busy, then Server Error, then OK
mock_get.side_effect = [
mock_busy_response, mock_error_response, mock_ok_response
]
self.assertEqual(
http_requests.request_limited(url="http://get_your_proteins.com",
rtype="GET"), mock_ok_response)
self.assertEqual(len(mock_get.mock_calls), 3)
mock_get.assert_called_with("http://get_your_proteins.com")
# Should only sleep on being throttled (not server error)
self.assertEqual(len(mock_sleep.mock_calls), 1)
def get_pdb_file(pdb_id: str,
filetype=PDBFileType.PDB,
compression=False) -> Optional[str]:
'''Get the full PDB file associated with a PDB_ID
Parameters
----------
pdb_id : A 4 character string giving a pdb entry of interest
filetype: The file type.
PDB is the older file format,
CIF is the newer replacement.
XML an also be obtained and parsed using the various xml tools included in PyPDB
STRUCTFACT retrieves structure factors (only available for certain PDB entries)
compression : Whether or not to request the data as a compressed (gz) version of the file
(note that the compression is undone by this function)
Returns
-------
result : string
The string representing the full PDB file as an uncompressed string.
(returns None if the request to RCSB failed)
Examples
--------
>>> pdb_file = get_pdb_file('4lza', filetype='cif', compression=True)
>>> print(pdb_file[:200])
data_4LZA
#
_entry.id 4LZA
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 4.032
_audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx
'''
if filetype is PDBFileType.CIF and not compression:
warnings.warn("Consider using `get_pdb_file` with compression=True "
"for CIF files (it makes the file download faster!)")
pdb_url_builder = [PDB_DOWNLOAD_BASE_URL, pdb_id]
if filetype is PDBFileType.STRUCTFACT:
pdb_url_builder.append("-sf.cif")
else:
pdb_url_builder += [".", filetype.value]
if compression:
pdb_url_builder += ".gz"
pdb_url = "".join(pdb_url_builder)
print(
"Sending GET request to {} to fetch {}'s {} file as a string.".format(
pdb_url, pdb_id, filetype.value))
response = http_requests.request_limited(pdb_url)
if response is None or not response.ok:
warnings.warn("Retrieval failed, returning None")
return None
if compression:
return gzip.decompress(response.content)
return response.text
def test_fails_with_invalid_request(self, mock_sleep, mock_warnings):
self.assertIsNone(
http_requests.request_limited(url="http://protein_data_bank.com",
rtype="MAIL"))
mock_warnings.assert_called_once_with("Request type not recognized")
self.assertEqual(len(mock_sleep.mock_calls), 0)
