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CQL CLI

A CLI tool for interacting with the CQL engine to run measures against FHIR input data to output structured results to disk.

The CLI is primarily designed for executing single patient or small population workflows. For larger population sets the scalable beam job is a more appropriate solution.

Warning: When using these tools with protected health information (PHI), please be sure to follow your organization's policies with respect to PHI.

Running

To build the program from source run the following from the root of the repository (note you must have Go installed):

go build cmd/cli/cli.go

This will build the cli binary and write it out in your current directory. You can then run the binary:

./cli \
  -cql_dir="path/to/cql/dir/" \
  -fhir_bundle_dir="path/to/bundle/dir/" \
  -fhir_terminology_dir="path/to/terminology/dir/" \
  -json_output_dir="path/to/output/"

Flags

--cql_dir -- Required. The path to a directory containing one or more CQL files. The engine only reads files ending in a .cql suffix. ELM inputs are not currently supported.

--execution_timestamp_override -- Optional. When set overrides the default evaluation timestamp for the engine. This can be used to run CQL at a given point in time. The value should be formatted as a CQL DateTime. If not provided the engine will use the current system DateTime instead.

Example:

--execution_timestamp_override="@2018-02-02T15:02:03.000-04:00"

--fhir_bundle_dir -- Optional. The path containing one or more FHIR bundles. Each of those bundles will cause one evaluation of the input CQL libraries results of which will each directly map to outputs.

Note: Each file in the bundle directory is expected to be one bundle per file.

--fhir_terminology_dir -- Optional. The path to a directory containing json definitions of FHIR ValueSets.

--fhir_parameters_file -- Optional. A file path to a JSON file containing FHIR Parameters which will be used as inputs to the CQL execution environment.

--parameters -- Optional. A comma separated list of parameters which will be used as inputs to the CQL execution environment. These values are passed as raw golang strings to the parsings stage. This provides some limitations for more complicated input value types. For such cases it is recommended to use the flag --fhir_parameters_file instead.

Example:

--parameters=”aString='string value',integerValue=2,a id with spaces='value'”

Note: If both --parameters and --fhir_parameters_file are provided. FHIR Parameters will be loaded first. Any parameters in the --parameters flag will override FHIR Parameters with the same name value.

--json_output_dir -- Optional. A directory for outputting structured json results. Each successful run of an input bundle file will result in one output result file. If no input bundles are supplied the result will be a single result.json file.

Note: The output json structure is currently a custom format and is subject to change.

--return_private_defs -- Optional. When set will have the CQL engine return both private and public definitions in the CQL results. By default only public definitions are emitted.

-V -- Optional. Outputs the engine version as well as the CQL version to the terminal. This flag overrides all other behaviors, so no CQL execution will take place.