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NOTE: This is the old query library (and examples) which is in maintenance mode and will be deprecated in the future. Our new approach is SQL based. At the moment it uses direct SQL statements but will eventually be based on FHIR-views and SQL-on-FHIR v2 spec. Please see the query directory for details of the new approach and examples.

How to query the data warehouse

This directory contains a query library for easy querying of FHIR based data warehouses. The library intend to hide details of the distributed environment in which the underlying data is stored and processed like Apache Spark/Parquet or BigQuery.

For more details see these slides. For a quick start on how to use the library, see this notebook.

The rest of this document describes how the query library can be set up and developed with a focus on the Spark+Parquet use case.

Setting up Apache Spark

Details on how to set up a Spark cluster with all different cluster management options is beyond this doc. Here we only show how to run the sample queries in the local mode.

The sample queries are written using the Python API of Spark (a.k.a. pyspark) so it is a good idea to first create a Python virtualenv:

$ virtualenv -p python3.8 venv
$ . ./venv/bin/activate
(venv) $ pip3 install pyspark
(venv) $ pip3 install pandas

Or you can just do pip3 install -r requirements.txt in the venv.

Tip: The initial step of the validate_indicators.sh script creates a venv_test and sets up all the dependencies.

Once this is done, you can run pyspark to get into an interactive console. This is useful for developing queries step by step, but we won't use it once we have developed the full query plan.

Some test Parquet files are stored in the dwh/test_files directory. These are generated by the batch pipeline from the demo data in the test docker image. In particular, there are Patient and Observation sub-folders with some Parquet files in them. Here is a sample command for the indicator calculation script:

spark-submit indicators.py --src_dir=./test_files --last_date=2020-12-30 \
  --num_days=28 --output_csv=TX_PVLS.csv

To see a list of options with their descriptions, try:

$ python3 indicators.py --help

There is also a sample_indicator.py script to show how the same query with PySpark API can be done with Spark SQL:

spark-submit sample_indicator.py --src_dir=test_files/ \
  --base_patient_url=http://localhost:8099/openmrs/ws/fhir2/R4/Patient/ \
  --num_days=60 --last_date=2020-04-30
  --code_list {SPACE SEPARATED LIST OF CODES}

Using Jupyter Notebooks

While in your virtualenv, run:

(venv) $ pip3 install jupyter

Then from a terminal that can run GUI applications, run:

(venv) $ jupyter notebook

This should start a Jupyter server and bring up its UI in a browser tab.

In case that auto-completion functionality is not working, this might be due to a recent regression; check the solution here to downgrade your jedi.

Also if you like to automatically record the execution time of different cells (and other nice features/extensions) install nbextensions.

A sample notebook is provided at dwh/test_spark.ipynb which uses matplotlib too, so to run this you need to install it too:

(venv) $ pip3 install matplotlib

At the end of this notebook, we wrap up the tests into reusable functions that we can use outside the Jupyter environment e.g., for automated indicator computation.