Quality measures¶

Who this is for: someone who knows DHIS2 indicators and has never scored a clinical quality measure. Read CQL first: a measure is a CQL library with four conventions on top, and this page assumes you know what a retrieve and a context are.

Before you start: uv add dhis2w-fhir-engine, or uv sync inside this repository. Everything here runs against inline data; the last section needs a seeded DHIS2 instance.

You will be able to:

name the populations a measure declares and say who is in each
choose between proportion, ratio, and cohort scoring
run MeasureEvaluator over a population and read the typed report
render that report as a FHIR R4 MeasureReport
score a measure over a real DHIS2 cohort, and see where the DHIS2 knowledge starts and stops

A measure is a fraction whose halves are logic¶

A DHIS2 indicator has a numerator expression and a denominator expression. So does a quality measure. The difference is that a measure is precise about who is in each half, and it says so with named populations rather than with a single expression per half.

Five names carry almost every measure:

Population	Who it is
Initial population	Everyone the measure looks at, before any narrowing.
Denominator	Who the measure holds to account.
Denominator exclusion	People removed from the denominator outright - they should never have been counted.
Numerator	The ones who met the measure.
Numerator exclusion	People removed from the numerator, but left in the denominator.

The two exclusions are the reason this vocabulary exists rather than one fraction. A child with a documented contraindication belongs in neither half - that is a denominator exclusion. A dose recorded twice should count once - that is a numerator exclusion, and the child stays in the denominator either way. Written as one expression, those two cases look identical; written as populations, they do not.

Writing one¶

A measure is a CQL library with context Patient and a definition named for each population:

library MeaslesCoverage version '1.0'
using FHIR version '4.0.1'

context Patient

define "Initial Population":
    true

define "Denominator":
    "Initial Population"

define "Denominator Exclusion":
    Patient.gender = 'unknown'

define "Numerator":
    exists [Immunization]

context Patient is what makes this a measure rather than a report: the library is evaluated once per person, and every retrieve inside it sees only that person's records. exists [Immunization] therefore asks "does this child have a dose", not "does anyone".

MeasureEvaluator finds each population by the conventional definition name, so nothing above needs wiring:

from dhis2w_fhir_engine.r4 import BundleDataSource, MeasureEvaluator, MeasureScoring

data_source = BundleDataSource(bundle)
evaluator = MeasureEvaluator(data_source=data_source)
evaluator.set_scoring(MeasureScoring.PROPORTION)
evaluator.load_measure(MEASURE_SOURCE)

When you want the groups declared explicitly rather than by convention - several groups, or names that do not follow it - add_population and add_stratifier state them directly.

Scoring¶

The scoring rule says what the counts mean.

Scoring	What it reports
`PROPORTION`	Numerator divided by denominator, as a fraction. Coverage measures.
`RATIO`	Two counts related to each other, where neither is a subset of the other.
`COHORT`	Who qualified. Membership is the whole answer; there is no fraction.
`CONTINUOUS_VARIABLE`	An observation aggregated over a measure population.

The engine computes a measure_score for proportion measures. For a cohort the score is None, deliberately - the populations are the report:

measure MeaslesCoverage, scored as a proportion
  counts    {"initial-population": 4, "denominator": 4, "denominator-exclusion": 0, "numerator": 3}
  score     0.75

the same library scored as a cohort:
  counts    {"initial-population": 4, "denominator": 4, "denominator-exclusion": 0, "numerator": 3}
  score     None   (a cohort reports membership, not a fraction)

Same library, same memberships, different question asked of them.

Running it¶

evaluate_population takes the people to evaluate and returns a typed report:

report = evaluator.evaluate_population(patients, data_source=data_source)
group = report.groups[0]

The report carries the counts, and for each population the identifiers of the people in it:

measure MeaslesCoverage, scored as a proportion
4 people evaluated, one at a time under `context Patient`

population              n   who
  initial-population      4   child-1, child-2, child-3, child-4
  denominator             4   child-1, child-2, child-3, child-4
  denominator-exclusion   0   -
  numerator               3   child-1, child-2, child-3

measure score = numerator / denominator = 3 / 4 = 0.75

Naming the members, not just counting them, is what makes a measure auditable. A number that says 3 of 4 is a claim; a number that also names the fourth child is a worklist.

The report also holds the per-person decision, which is what you read when a count surprises you:

per person, as the evaluator decided it, within this group:
  child-1    initial-population, denominator, numerator
  child-2    initial-population, denominator, numerator
  child-3    initial-population, denominator, numerator
  child-4    initial-population, denominator

evaluate_patient answers the same question for one person, when you want to explain a single case rather than score a cohort. A measure can declare several groups, and every decision is held per group: populations_for(group_id) and stratifier_values_for(group_id) read one group's membership, and each group is counted, scored, and stratified from its own state alone.

When a definition cannot be evaluated¶

A definition that fails - an unknown function, a value set the library never declares, a stratifier that raises - is never counted as a negative result. The failure lands in report.errors as an EvaluationError naming the patient, the group, the definition, and the message; the group holding it gets no measure_score; and to_fhir() emits status: "error" with a contained OperationOutcome listing every failure. Evaluation still returns a report, so a partly broken measure shows what it could compute and what it could not, instead of reading as a plausible score.

The contained OperationOutcome is pointed at by an extension on the MeasureReport, under this project's own canonical https://winterop-com.github.io/dhis2w/fhir/StructureDefinition/measure-evaluation-errors, and this page is where it is defined.

The FHIR MeasureReport¶

to_fhir() renders the typed report as a FHIR R4 MeasureReport - the resource an aggregator, a registry, or a dashboard expects:

to_fhir() -> a MeasureReport, status complete, type summary
  measure   MeaslesCoverage
  counts    {"initial-population": 4, "denominator": 4, "denominator-exclusion": 0, "numerator": 3}
  score     0.75

That resource is the deliverable. The logic stays in the library, published and versioned; the answer travels as FHIR, and the receiving system needs no CQL engine to read it.

From the command line¶

cql measure scores a measure without Python. A Bundle behind --data supplies both halves of the run: every Patient entry is a person to evaluate, and the whole Bundle is the data source the numerator retrieves from. The measure above is examples/fhir/engine/measles-coverage.cql and the clinic is clinic.json beside it:

$ d2w-fhir-engine cql measure measles-coverage.cql --data clinic.json
Measure: measles-coverage.cql
Evaluating 4 patient(s)...

          Group: default
┏━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━┓
┃ Population            ┃  Count ┃
┡━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━┩
│ initial-population    │      4 │
│ denominator           │      4 │
│ denominator-exclusion │      0 │
│ numerator             │      3 │
│ Score                 │ 75.00% │
└───────────────────────┴────────┘

Four children, three with a dose recorded: the same 3 of 4 the Python run above scores, from the command line and against the same clinic.

--patients reads a directory of Patient JSON files instead. That names who is evaluated but supplies no data source, so a numerator written as a retrieve finds nothing and the measure scores 0.00% - reach for --patients when the people carry their own answer, and for a Bundle when the numerator has to look something up. --output writes the FHIR MeasureReport to disk, and --verbose adds the stratifier results.

Scoring a real DHIS2 cohort¶

The engine has no DHIS2 dependency. It evaluates expressions over FHIR-shaped JSON and knows nothing about programs, stages, or data elements - which is what makes the end-to-end example worth reading: everything DHIS2-specific happens above the engine, and the engine sees only FHIR.

Three steps:

Read. One page of Child Programme (IpHINAT79UW) tracked entities off the instance, with their enrollments and the weight data values recorded on their events.
Map. Each tracked entity becomes a Patient; each weight data value becomes an Observation; both go into one collection Bundle.
Score. A measure whose numerator is "has a weight recorded", evaluated once per child.

Against the seeded Sierra Leone demo database:

$ uv run python examples/fhir/engine/e2e_measure_from_dhis2.py
reading Child Programme (IpHINAT79UW) tracked entities from http://localhost:8080
  12 tracked entities, 22 weight data values
  11 of those children carry at least one weight

mapped to a collection Bundle of 34 FHIR resources
  one Patient per tracked entity, one Observation per weight data value

measure Dhis2ChildProgrammeWeightRecorded, scored as a proportion
  denominator  12   every mapped tracked entity
  numerator    11   those with a weight recorded on a DHIS2 event
  score        0.9167

to_fhir() -> a MeasureReport citing measure Dhis2ChildProgrammeWeightRecorded

The example recomputes the DHIS2-side answer in Python before asking the engine anything, and fails loudly if the two disagree - so it is a check on the mapping, not only a demonstration of it.

One detail in that example is a workaround rather than a design: the tracker read orders by createdAt, not by trackedEntity, because ordering by the identifier answers 409 E7145 with an ambiguous column reference on 2.43.1. See BUGS.md entry 97.

The DHIS2 payoff: indicators as computable measures¶

That example maps a cohort by hand. The destination is that a guide carries the measures itself.

Today a DHIS2 indicator's numerator and denominator exist only as DHIS2 expressions, and a generated Implementation Guide carries no computable measure at all: a consumer receives the forms, the terminology, and the data, and has to reimplement the arithmetic to know what any of it means.

The target shape is a generate measures target beside the existing ones. Each selected indicator becomes a FHIR Measure - percentage indicators scored as proportion, per-thousand as ratio, plain sums as cohort - whose population criteria are real CQL in an attached Library. A consumer could then evaluate the indicator without DHIS2's analytics engine, which is the difference between publishing numbers and publishing a definition.

Everything on this page is the second half of that: the parser, the evaluator, the population vocabulary, and the MeasureReport writer all exist and are what a generated Library would be evaluated by. What does not exist yet is the compiler from a DHIS2 indicator expression to CQL, and that is the actual work.

The design record for it is the Mid-term section of the FHIR roadmap - see Computable measures: DHIS2 indicators as FHIR Measure + CQL, which states the scoring mapping, the doctrine that the parser layer derives from the official HL7 ANTLR grammars, and the decisions still reserved to the owner.

The runnable versions¶

File	Shows
`measure_report.py`	The populations, both scorings, the per-person decisions, and `to_fhir()`
`e2e_measure_from_dhis2.py`	Read a DHIS2 cohort, map it to FHIR, score it, check the counts against DHIS2's own records

The first needs nothing running. The second needs make dhis2-run and reads DHIS2_URL, DHIS2_USERNAME, and DHIS2_PASSWORD.

The Python surface is documented in the dhis2w_fhir_engine API reference.