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MongoAdapter

MongoAdapter is a Python module containing optimized data adapters for importing data from Mongo databases into NumPy arrays and Pandas DataFrame. It was previously a part of the IOPro project.

Build Requirements

Building MongoAdapter requires a number of dependencies. In addition to a C/C++ dev environment, the following modules are needed, which can be installed via conda:

  • NumPy 1.11
  • Pandas
  • mongo-driver 0.7.1 (C lib)

Building Conda Package

Note: If building under Windows, make sure the following commands are issued within the Visual Studio command prompt for version of Visual Studio that matches the version of Python you're building for. Python 2.6 and 2.7 needs Visual Studio 2008, Python 3.3 and 3.4 needs Visual Studio 2010, and Python 3.5 needs Visual Studio 2015.

  1. Install Docker. Add the current user to the docker group and restart the daemon, so that docker commands can be executed without root privileges

  2. Build MongoAdapter using the following command:

conda build buildscripts/condarecipe --python 3.5
  1. MongoAdapter can now be installed from the built conda package:
conda install mongoadapter --use-local

Building By Hand

Note: If building under Windows, make sure the following commands are issued within the Visual Studio command prompt for version of Visual Studio that matches the version of Python you're building for. Python 2.6 and 2.7 needs Visual Studio 2008, Python 3.3 and 3.4 needs Visual Studio 2010, and Python 3.5 needs Visual Studio 2015.

For building MongoAdapter for local development/testing:

  1. Install most of the above dependencies into environment called 'mongoadapter':
conda env create -f environment.yml

Be sure to activate new mongoadapter environment before proceeding.

  1. Build MongoAdapter using Cython/distutils:
python setup.py build_ext --inplace

Testing

To get a test database running, execute the following command (after installing Docker):

docker run --rm --name mongo-db --publish 27017:27017 mongo:3.0

The Docker image is a ~300MB download. Once downloaded it should take about 5 seconds for the database to start.

The MongoAdapter tests will generate their own test data by creating a collection called 'MongoAdapter_tests' in the Mongo database specified by the above parameters. In another terminal, tests can be run by calling the mongoadapter module's test function:

python -Wignore -c 'import mongoadapter; mongoadapter.test()'

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