Installing DataJoint for Python
Here we will cover installing the DataJoint library for Python and configuring it to connect to a database server. If you don’t have a database server configured yet, be sure to checkout Getting connected to a database!
DataJoint for Python requires Python 3.4 or above to function properly. To check whether you have the right Python version, run the following in the terminal/command prompt:
$ python3 -V
If the above command runs without an error and the version is at least 3.4 (e.g.`3.6.0`), then you are good to go!
Installing the DataJoint Package
The entire source code for DataJoint Python is made available at datajoint/datajoint-python GitHub repository. Although you certainly can install DataJoint directly from the source, it will be much easier to use pip - Python’s package manager. The latest stable DataJoint releases are made available as a package at PyPI. With this you can install DataJoint for Python by just running the following in the terminal:
$ pip3 install datajoint
and that’s it! This should trigger the installation of the latest DataJoint and all of its dependencies. Depending on how your Python environment is configured, you may want to install within a virtual environment, installing for the user. Optionally:
$ pip install virtualenv $ virtualenv venv/ && source venv/bin/activate $ (venv) pip3 install datajoint $ # Later: $ deactivate # to exit from venv
Verify that the package was properly installed by starting a Python 3 console, and try importing the datajoint package:
>>> import datajoint as dj
Make sure you have the DataJoint package installed successfully before moving on.
If you already have an older version of DataJoint package installed on your system and you wish to upgrade to the latest version,
you can run
pip install datajoint again but this time passing in the
--upgrade option. That is:
$ pip3 install --upgrade datajoint
Now you have DataJoint installed, let’s configure the library to connect to the database server. Whichever option you have selected from Getting connected to a database, you will need three pieces of information to connect to the database server: the database address, and your username and password.
If you have signed up for the tutorial database at DataJoint.io you should have received an email with instructions on how to connect to the database, including the host address, username, and your temporary password.
If you have followed the Setting Up a Local Database Server tutorial to setup a local database in Docker, your host address
root and password
If you have a non-local database server setup for your lab/institution that you would like to connect to, simply use the host address, username and password for the target database server. These information are typically provided by your database administrator.
Start an interactive Python 3 console and type in the following commands:
>>> import datajoint as dj >>> dj.config['database.host'] = 'HOST_ADDRESS' >>> dj.config['database.user'] = 'USER_NAME' >>> dj.config['database.password'] = 'PASSWORD'
Here, we are using the
dj.config object to update configurations for DataJoint. Namely, we are specifing
the address of the database (
database.host), and the user name (
database.user) and password
database.password). Be sure to replace
'PASSWORD' with the actual
values for your database connection! Note that these values have to be provided as strings.
Now that we have updated the connection configuration, let’s check the connection status by calling dj.conn():
>>> dj.conn() Connecting root@localhost:3306 DataJoint connection (connected) root@localhost:3306
If you get a message that looks like this, then congratulations! You have just successfully accessed the database server using DataJoint!
The exact message will look different depending on what database server you are connected to.
Once connected, you can easily change your password using
>>> dj.set_password() New Password: (enter your new password) Confirm Password: (enter your new password again) Password updated.
and that’s it!
If you have signed up to and are connected to the tutorial database on Accounts.DataJoint.io, it is strongly recommeded that you change your password from the temporary password that was sent to you in the email!
If everything went well, you now have a fully functional developement environment for DataJoint with Python, connected to a database server. You can now move onto Building your first data pipeline to start learning how to use DataJoint to design and build data pipelines, or explore any other tutorials in this site to learn specific features of DataJoint.