# Copyright (C) 2018, 2021 Cancer Care Associates
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from typing import Dict, List, Optional, Tuple
from . import connect as _connect
from . import credentials as _credentials
Connection = _connect.Connection
Cursor = _connect.Cursor
[docs]def connect(
hostname: str,
port: int = 1433,
database: str = "MOSAIQ",
alias: Optional[str] = None,
username: Optional[str] = None,
password: Optional[str] = None,
) -> Connection:
"""Connect to a Mosaiq SQL server.
The first time running this function on a system will result in a
prompt to login to the Mosaiq SQL server. The provided credentials
will be stored within the operating system's password storage
facilities. Subsequent calls to this function will pull from that
password storage in order to connect.
Can optionally be called as a context manager. This will close the
database connection once leaving the context manager.
Parameters
----------
hostname : str
The IP address or hostname of the SQL server.
port : int, optional
The port at which the SQL server is hosted, by default ``1433``
database : str, optional
The MSSQL database name, by default ``"MOSAIQ"``
alias : Optional[str], optional
A human readable representation of the server, this is the name
of the server presented to the user should there not be
credentials already on the machine, by default ``"hostname:port/database"``
username : Optional[str], optional
Provide a username to login to the database with, by default the
username is either pulled from the system's credential storage,
or an interactive prompt is used.
password : Optional[str], optional
Provide a password to login to the database with, by default the
password is either pulled from the system's credential storage,
or an interactive prompt is used.
Returns
-------
connection : pymedphys.mosaiq.Connection
A database connection. This connection can be passed to
:func:`pymedphys.mosaiq.execute` to be able to run queries.
The method ``close()`` can be called on this object to close the
database connection.
Examples
--------
See :func:`pymedphys.mosaiq.execute` for examples of usage.
"""
if username is None and password is None:
username, password = _credentials.get_username_password_with_prompt_fallback(
hostname=hostname, port=port, database=database, alias=alias
)
if username is None or password is None:
raise ValueError(
"Must either provide both username and password, or neither of them."
)
connection = _connect.connect_with_credentials(
username, password, hostname=hostname, port=port, database=database
)
return connection
[docs]def execute(
connection: Connection, query: str, parameters: Dict = None
) -> List[Tuple[str, ...]]:
"""Execute SQL queries on a Mosaiq database.
Parameters
----------
connection : pymedphys.mosaiq.Connection
A database connection. This can be retrieved by calling
``pymedphys.mosaiq.connect``
query : str
The SQL query to execute. Do not parse Python variables directly
into this string. Instead create this string as if you
are going to call ``format`` on it
(https://docs.python.org/3/library/stdtypes.html#str.format)
and then utilise the parameters optional argument to this
function. That way, the underlying library ``pymssql`` will
sanitise the parameters to protect against malicious inputs.
parameters : Dict, optional
Parameters to be included within the query. These are sanitised
by the underlying ``pymssql`` library before being included
within the query string, by default None
Returns
-------
results : List[Tuple[str, ...]]
The results from the database query organised so that each row
is an item within the returned list.
Examples
--------
Directly calling the connection object and listing all patients that
have the last name of ``"PHANTOM"``.
>>> import pymedphys.mosaiq
>>> connection = pymedphys.mosaiq.connect('msqsql') # doctest: +SKIP
>>> pymedphys.mosaiq.execute(
... connection,
... '''
... SELECT
... Ident.IDA,
... Patient.Last_Name,
... Patient.First_Name
... FROM Ident, Patient
... WHERE
... Patient.Pat_ID1 = Ident.Pat_ID1 AND
... Patient.Last_Name = %(last_name)s
... ''',
... {"last_name": "PHANTOM"},
... ) # doctest: +SKIP
[('654324', 'PHANTOM', 'CATPHAN'),
('944444', 'PHANTOM', 'DELTA4'),
('654321', 'PHANTOM', 'PELVIS'),
('012534', 'PHANTOM', 'QUASAR4D'),
('987654', 'PHANTOM', 'RESPIRATORY'),
('654325', 'PHANTOM', 'RW3')]
Connecting via a context manager and using pandas to present the
results as a table.
>>> import pandas as pd
>>> import pymedphys.mosaiq
>>> with pymedphys.mosaiq.connect('msqsql') as connection: # doctest: +SKIP
... results = pymedphys.mosaiq.execute(
... connection,
... '''
... SELECT
... Ident.IDA,
... Chklist.Due_DtTm
... FROM Chklist, Staff, Ident
... WHERE
... Chklist.Pat_ID1 = Ident.Pat_ID1 AND
... Staff.Staff_ID = Chklist.Rsp_Staff_ID AND
... Staff.Last_Name = %(qcl_location)s AND
... Chklist.Complete = 0
... ''',
... {"qcl_location": "Physics_Check"},
... )
>>> pd.DataFrame( # doctest: +SKIP
... data=results,
... columns=[
... "patient_id",
... "due",
... ],
... )
patient_id due
0 000000 2021-02-01 23:59:59
1 000001 2021-02-01 23:59:59
2 000002 2021-02-01 23:59:59
3 000003 2021-03-08 23:59:59
"""
with connection.cursor() as cursor:
cursor.execute(query=query, parameters=parameters)
results: List[Tuple[str, ...]] = cursor.fetchall()
return results
