Using MongoDB

Introduction/Setup

Learning Objectives

Ensure participants have a running local mongodb, the sample data, and an open notebook
Introduce the Jupyter Notebook environment

Setup for Windows

W.1 MongoDB

Full setup instructions are at https://docs.mongodb.org/manual/tutorial/install-mongodb-on-windows/.

W.1.1 Determine which MongoDB you need, download it, and install it

Go to https://www.mongodb.org/downloads and download the MSI installer. This section of the above installation tutorial walks through how to determine which version of the installer will be best for your system.
Run the installer, accept the license, and choose a “Complete” installation.

W.1.2 Set up the MongoDB environment

Once, installed, open a Command Prompt and type in

md \data\db

to create the default data directory for MongoDB to use on your system. Then, start the server (called the mongo daemon) by typing in

"C:\Program Files\MongoDB\Server\3.2\bin\mongod.exe"

or whatever the path is to where you have MongoDB installed. If you get an error when running mongod.exe, you may have to specify another storage engine:

"C:\Program Files\MongoDB\Server\3.2\bin\mongod.exe" --storageEngine=mmapv1

W.1.3 Connect to MongoDB

Open another Command Prompt window, and this time call mongo.exe (no d at the end) to open a connection to your running server:

"C:\Program Files\MongoDB\Server\3.2\bin\mongo.exe"

Type help and hit enter, and you should see a listing of commands. Type exit and hit enter to exit the MongoDB shell and return to your Windows command prompt.

Congratulations! You have a running MongoDB server that will be sufficient for the lesson.

W.2 Python and Interactive Notebooks

W.2.1 Install Anaconda

Go to https://www.continuum.io/downloads#_windows to download and install Anaconda for Windows, the Python 3.5 version. This will give you an isolated installation that you can use in this lesson and beyond. It’s isolated because all files will be in a single folder – no existing or future Python environments on your system will be affected, and you can delete it all at any time by simply deleting the folder.

W.2.2 Install extra packages used by this lesson

Open Anaconda Prompt (there should be a link in your Start Menu) and

pip install mongomock
pip install pymongo

to install the mongomock and pymongo packages. Now, you can close the Anaconda Prompt window and open Jupyter Notebook. This will start a notebook server and open its interface in your web browser.

W.2.3 Connect to MongoDB through Python

Now, Let’s work on your Desktop and test your local MongoDB connection.

Click the Desktop link in the directory listing
Click on the New dropdown at the upper right and select Python 3.

In the cell, put in the following lines:

from pymongo import MongoClient
client = MongoClient()
db = client.swc_lbl
db.labs.insert_one({"name": "LBL"})
db.labs.count()

and run qthe cell. If the output is 1 (or just not an error; if you run it multiple times, the count will keep going up!), then you should be good to go for the lesson! Congratulations!

Setup for Mac OS X

M.1 MongoDB

Homebrew, “the missing package manager for OS X”, installs binary packages based on published “formulae”. To install, open a Terminal window and enter (one line)

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

and if you already have brew installed, run brew update to update your installation’s package database.

To install the MongoDB binaries, run the following:

M.1.1 Download and install MongoDB

At a Terminal prompt,

brew install mongodb

M.1.2 Launch MongoDB

Use brew services to launch the mongodb daemon (mongod) and ensure it re-launches if your system restarts:

brew tap homebrew/services
brew services restart mongodb

M.1.3 Connect to MongoDB

Run mongo at a terminal prompt to open a connection to your running server. Type help and hit enter, and you should see a listing of commands. Type exit and hit enter to exit the MongoDB shell.

Congratulations! You have a running MongoDB server that will be sufficient for the lesson.

M.2 Python and Interactive Notebooks

M.2.1 Install Anaconda

Go to https://www.continuum.io/downloads#_macosx to download and install Anaconda for OS X, the Python 3.5 version. This will give you an isolated installation that you can use in this lesson and beyond. It’s isolated because all files will be in a single folder – no existing or future Python environments on your system will be affected, and you can delete it all at any time by simply deleting the folder.

M.2.2 Install extra packages used by this lesson

At your terminal prompt, prepend Anaconda’s binaries to your PATH for the current terminal window by entering the following (replacing jdoe with your username):

export PATH="/Users/jdoe/anaconda/bin:$PATH"

This assumes you installed Anaconda to the anaconda folder in your home directory (the default). It’s possible the Anaconda installer already added a line to the end of your ~/.bash_profile file to do this automatically every time you open a terminal prompt.

Ensure that when you type python at the prompt, “Python 3.5” and “Anaconda” appears in the first line of output. Enter exit() to enter the Python session. Next, enter the commands

pip install mongomock
pip install pymongo

to install the mongomock and pymongo packages. Finally, enter jupyter notebook at the prompt. This will start a notebook server and open its interface in your web browser.

M.2.3 Connect to MongoDB through Python

Now, Let’s work on your Desktop and test your local MongoDB connection.

Click the Desktop link in the directory listing
Click on the New dropdown at the upper right and select Python 3.

In the cell, put in the following lines:

from pymongo import MongoClient
client = MongoClient()
db = client.swc_lbl
db.labs.insert_one({"name": "LBL"})
db.labs.count()

and run the cell. If the output is 1 (or just not an error; if you run it multiple times, the count will keep going up!), then you should be good to go for the lesson! Congratulations!

Setup for Linux

The procedure maps more or less to that for Mac OS X above. Consult https://docs.mongodb.org/manual/administration/install-on-linux/ for MongoDB setup intructions particular to your flavor of Linux, use the Linux installer for Anaconda, and ensure everything works as described in the Mac OS X instructions above.

Tour the Jupyter Interface

Go to Help->User Interface Tour in your open Jupyter notebook to learn about the interface.

Learn a few Jupyter Keyboard Shortcuts

Go to Help->Keyboard Shortcuts in an open Jupyter notebook. Practice running cells, inserting cells, and switching between Code and Markdown modes.