cumulus-library-data-metrics 4.0.2

Data quality and characterization metrics for Cumulus

Data Metrics

A Cumulus-based implementation of the qualifier metrics.

Implemented Metrics

The following qualifier metrics are implemented (per June 2024 qualifer definitions).

• c_pt_count
• c_pt_deceased_count
• c_resource_count
• c_resources_per_pt
• c_system_use
• c_us_core_v4_count *
• q_date_recent
• q_ref_target_pop
• q_ref_target_valid
• q_system_use
• q_valid_us_core_v4 *

* These are US Core profile-based metrics, and the following profiles are not yet implemented:

• Implantable Device (due to the difficulty in identify implantable records)
• The various Vital Signs sub-profiles like Blood Pressure (just haven't gotten around to them yet)

Installing

pip install cumulus-library-data-metrics

Running the Metrics

These metrics are designed as a Cumulus Library study and are run using the cumulus-library command.

Local Ndjson

First, you'll want to organize your ndjson into the following file tree format:

root/
  condition/
    my-conditions.ndjson
  medicationrequest/
    1.ndjson
    2.ndjson
  patient/
    Patient.ndjson

(This is the same format that Cumulus ETL writes out when using --output-format=ndjson.)

Here's a sample command to run against that pile of ndjson data:

cumulus-library build \
  --db-type duckdb \
  --database output-tables.db \
  --load-ndjson-dir path/to/ndjson/root \
  --target data_metrics

And then you can load output-tables.db in a DuckDB session and see the results. Or read below to export the counts tables.

Athena

Here's a sample command to run against your Cumulus data in Athena:

cumulus-library build \
  --database your-glue-database \
  --workgroup your-athena-workgroup \
  --profile your-aws-credentials-profile \
  --target data_metrics

And then you can see the resulting tables in Athena. Or read below to export the counts tables.

Exporting Counts

For the metrics that have exportable counts (the characterization metrics mostly), you can easily export those using Cumulus Library, by replacing build in the above commands with export ./output-folder. Like so:

cumulus-library export \
  ./output-folder \
  --db-type duckdb \
  --database output-tables.db \
  --target data_metrics

Aggregate counts

This study generates CUBE output by default. If it's easier to work with simple aggregate counts of every value combination (that is, without the partial value combinations that CUBE() generates), run the build step with --option output-mode:aggregate.

That is, run it like:

cumulus-library build --option output-mode:aggregate ...