Package: credbl
Credbl: database settings and credentials simplifiedThere are many moving parts when setting up programmatic access to a database. Credbl divides (and conquers) those bits and pieces the following way:[connect-where] database server specific settings are read from a YAML configuration file provided by the database admin[connect-who] user's credentials are requested and stored inkeyringor winreg (on Windows).The first time the user connects to the database withconnect_*functions, the credentials will be requested and stored. Subsequent times, they will be silently retrieved and used to authenticate. If authentication fails due to wrong credentials, the user will be asked to enter credentials again.[connect-how] database drivers are chosen based on user's Operation system.Currently credbl focuses on MS SQL Server and MongoDB connections. You are welcome to submit issues and pull requests for other database types.InstallationPython packagefrom terminal shell (standard):latest release:pip install credblbleeding edge:pip install git+git://github.com/BCHSI/credbl.git#egg=credbldevelopment modegit clone https://github.com/BCHSI/credbl
  cd credbl
  pip install -e .R packagefrom R:install.packages('devtools')library(devtools)install_github('https://github.com/BCHSI/credbl')or terminal + R:git clone https://github.com/BCHSI/credbl
cd credbl
R
> install.packages('devtools')
> library(devtools)
> install('.')get help:?credblUsage examples:connecting to a MS SQL Serverfrom credbl import connect_mssql
conn = connect_mssql("tp-mssql-settings.yaml")Contents of database configuration fileIn a previous example,"tp-mssql-settings.yaml"must contain:server:    12.34.56.78 (OR) mydatabase.mybusiness.com
port:      1234
database:  tp-inventory
driver:    FreeTDS (optional)Low-level interface:You might need to understand it if you would like to use SQL drivers
or driver wrappers other than pyodbc, such as SQLAlchemy.with pyodbcimport pyodbc
from credbl import get_mssql_connection_string 

# if called for the first time, will request credentials
# second time may ask for your _system_ credentials; mark "always allow"

connection_str = get_mssql_connection_string("tp-mssql-settings.yaml")
# you'll be requested to enter your credentials when running it for the first time
conn = pyodbc.connect(connection_str)if you believe you've entered wrong credentials first time, call withreset=Trueconnection_str = get_mssql_connection_string("tp-mssql-settings.yaml", reset=True)

conn = pyodbc.connect(connection_str)with SqlAlchemyimport sqlalchemy
from credbl import get_mssql_connection_string 

connection_str_encoded = get_mssql_connection_string('covid19_omop.yaml',
                                                 urlencode=True)
connection_uri = 'mssql+pyodbc:///?odbc_connect={}'.format(connection_str_encoded)
conn = sqlalchemy.create_engine(connection_uri)connecting to mongodbfrom credbl import connect_mongodb

# if called for the first time, will request database credentials
mdb = connect_mongodb("mongo-settings.yaml")

mdb.list_collection_names()The"mongo-settings.yaml"file must contain following:url: mongodb://10.20.30.40:27017
db: 'databasename'Alternatively / optionally to URL, server or IP address and port can be provided:server: xyz.company.org
ip: 10.20.30.40
port: 27017storing credentials inkeyring(Mac, Unix) or Windows key storage:In [1]: import credbl

In [2]: credbl.get_credentials('something')
enter user name for 'something': []: myname
enter password for 'myname':
Out[2]: ('myname', 'xyz')

In [3]: credbl.get_credentials('something')
Out[3]: ('myname', 'xyz')Filesdbfunctions.Rauthentication (keyring and Windows ODBC) and dbplyr-based shortcutscredentials.pyauthenticationmongodb_utils.pywrapper for db connection and authentication for MongoDB