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Also added an integration test that failed with the previos mutable increment population
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,93 @@ | ||
| #!/bin/bash -e | ||
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| INPUT_MEASURE=$1 | ||
| BASE_OUTPUT_DIR=$PWD/.github/integration-test/evaluate-multiple-stratifiers | ||
| mkdir "$BASE_OUTPUT_DIR" | ||
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| docker run -v "$INPUT_MEASURE":/app/measure.json -v "$BASE_OUTPUT_DIR":/app/output/ -e FHIR_SERVER=http://fhir-server:8080/fhir \ | ||
| -e TZ="$(cat /etc/timezone)" --network integration-test_testing-network fhir-data-evaluator | ||
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| today=$(date +"%Y-%m-%d") | ||
| OUTPUT_DIR=$(find "$BASE_OUTPUT_DIR" -type d -name "*$today*" | head -n 1) | ||
| REPORT="$OUTPUT_DIR/measure-report.json" | ||
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| find_stratum() { | ||
| local STRATIFIER_INDEX="$1" | ||
| local EXPECTED_VALUE="$2" | ||
| local STRATUM=$(jq -c --arg EXPECTED_VALUE "$EXPECTED_VALUE" --argjson STRATIFIER_INDEX "$STRATIFIER_INDEX" ' | ||
| .group[0].stratifier[$STRATIFIER_INDEX].stratum[] | select(.value.coding[0].code == $EXPECTED_VALUE)' "$REPORT" ) | ||
| echo "$STRATUM" | ||
| } | ||
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| validate_stratum() { | ||
| local STRATUM="$1" | ||
| local STRATUM_VALUE="$2" | ||
| local EXPECTED_INITIAL_POP_COUNT="$3" | ||
| local EXPECTED_MEASURE_POP_COUNT="$4" | ||
| local EXPECTED_OBSERVATION_POP_COUNT="$5" | ||
| local EXPECTED_MEASURE_SCORE="$6" | ||
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| local INITIAL_POP_COUNT=$(jq '.population[] | select(.code.coding[0].code == "initial-population").count' <<< "$STRATUM") | ||
| local MEASURE_POP_COUNT=$(jq '.population[] | select(.code.coding[0].code == "measure-population").count' <<< "$STRATUM") | ||
| local OBSERVATION_POP_COUNT=$(jq '.population[] | select(.code.coding[0].code == "measure-observation").count' <<< "$STRATUM") | ||
| local MEASURE_SCORE=$(jq '.measureScore.value' <<< "$STRATUM") | ||
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| if [ "$INITIAL_POP_COUNT" = "$EXPECTED_INITIAL_POP_COUNT" ]; then | ||
| echo "OK 👍: initial population count ($INITIAL_POP_COUNT) equals the expected count for (value=$STRATUM_VALUE)" | ||
| else | ||
| echo "Fail 😞: stratum count ($INITIAL_POP_COUNT) != $EXPECTED_INITIAL_POP_COUNT for initial population (value=$STRATUM_VALUE)" | ||
| exit 1 | ||
| fi | ||
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| if [ "$MEASURE_POP_COUNT" = "$EXPECTED_MEASURE_POP_COUNT" ]; then | ||
| echo "OK 👍: measure population count ($MEASURE_POP_COUNT) equals the expected count for (value=$STRATUM_VALUE)" | ||
| else | ||
| echo "Fail 😞: stratum count ($MEASURE_POP_COUNT) != $EXPECTED_MEASURE_POP_COUNT for measure population (value=$STRATUM_VALUE)" | ||
| exit 1 | ||
| fi | ||
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| if [ "$OBSERVATION_POP_COUNT" = "$EXPECTED_OBSERVATION_POP_COUNT" ]; then | ||
| echo "OK 👍: observation population count ($OBSERVATION_POP_COUNT) equals the expected count for (value=$STRATUM_VALUE)" | ||
| else | ||
| echo "Fail 😞: stratum count ($OBSERVATION_POP_COUNT) != $EXPECTED_OBSERVATION_POP_COUNT for measure observation (value=$STRATUM_VALUE)" | ||
| exit 1 | ||
| fi | ||
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| if [ "$MEASURE_SCORE" = "$EXPECTED_MEASURE_SCORE" ]; then | ||
| echo "OK 👍: measure score ($MEASURE_SCORE) equals the expected count for (value=$STRATUM_VALUE)" | ||
| else | ||
| echo "Fail 😞: stratum count ($MEASURE_SCORE) != $EXPECTED_MEASURE_SCORE for measure score (value=$STRATUM_VALUE)" | ||
| exit 1 | ||
| fi | ||
| } | ||
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| get_stratum() { | ||
| local STRATIFIER_INDEX="$1" | ||
| local STRATUM_INDEX="$2" | ||
| echo $(jq --argjson STRATIFIER_INDEX "$STRATIFIER_INDEX" --argjson STRATUM_INDEX "STRATUM_INDEX" '.population[] | ||
| | select(.code.coding[0].code == "initial-population").count' "$STRATUM") | ||
| } | ||
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| EXPECTED_STRATUM_VALUE_1="I48.0" | ||
| EXPECTED_STRATUM_INITIAL_POP_1=108 | ||
| EXPECTED_STRATUM_MEASURE_POP_1=108 | ||
| EXPECTED_STRATUM_OBESERVATION_POP_1=108 | ||
| EXPECTED_STRATUM_MEASURE_SCORE_1=108 | ||
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| EXPECTED_STRATUM_VALUE_2="fail-no-value-found" | ||
| EXPECTED_STRATUM_INITIAL_POP_2=12072 | ||
| EXPECTED_STRATUM_MEASURE_POP_2=12072 | ||
| EXPECTED_STRATUM_OBESERVATION_POP_2=12072 | ||
| EXPECTED_STRATUM_MEASURE_SCORE_2=12040 | ||
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| STRATUM=$(find_stratum 0 $EXPECTED_STRATUM_VALUE_1) | ||
| validate_stratum "$STRATUM" $EXPECTED_STRATUM_VALUE_1 $EXPECTED_STRATUM_INITIAL_POP_1 $EXPECTED_STRATUM_MEASURE_POP_1 \ | ||
| $EXPECTED_STRATUM_OBESERVATION_POP_1 $EXPECTED_STRATUM_MEASURE_SCORE_1 | ||
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| STRATUM=$(find_stratum 1 $EXPECTED_STRATUM_VALUE_2) | ||
| validate_stratum "$STRATUM" $EXPECTED_STRATUM_VALUE_2 $EXPECTED_STRATUM_INITIAL_POP_2 $EXPECTED_STRATUM_MEASURE_POP_2 \ | ||
| $EXPECTED_STRATUM_OBESERVATION_POP_2 $EXPECTED_STRATUM_MEASURE_SCORE_2 |
109 changes: 109 additions & 0 deletions
109
.github/integration-test/measures/multiple-stratifiers.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,109 @@ | ||
| { | ||
| "resourceType": "Measure", | ||
| "meta": { | ||
| "profile": [ | ||
| "http://fhir-data-evaluator/StructureDefinition/FhirDataEvaluatorContinuousVariableMeasure" | ||
| ] | ||
| }, | ||
| "version": "1.0", | ||
| "url": "https://medizininformatik-initiative.de/fhir/fdpg/Measure/ExampleCdsCriteria", | ||
| "status": "active", | ||
| "experimental": false, | ||
| "publisher": "FDPG-Plus", | ||
| "name": "ExampleCdsCriteria", | ||
| "title": "Example Measure To Count CDS Criteria", | ||
| "description": "Example measure to count CDS criteria", | ||
| "group": [ | ||
| { | ||
| "population": [ | ||
| { | ||
| "code": { | ||
| "coding": [ | ||
| { | ||
| "system": "http://terminology.hl7.org/CodeSystem/measure-population", | ||
| "code": "initial-population" | ||
| } | ||
| ] | ||
| }, | ||
| "criteria": { | ||
| "language": "text/x-fhir-query", | ||
| "expression": "Condition?_profile=https://www.medizininformatik-initiative.de/fhir/core/modul-diagnose/StructureDefinition/Diagnose" | ||
| }, | ||
| "id": "initial-population-identifier-1" | ||
| }, | ||
| { | ||
| "code": { | ||
| "coding": [ | ||
| { | ||
| "system": "http://terminology.hl7.org/CodeSystem/measure-population", | ||
| "code": "measure-population" | ||
| } | ||
| ] | ||
| }, | ||
| "criteria": { | ||
| "language": "text/fhirpath", | ||
| "expression": "Condition" | ||
| }, | ||
| "id": "measure-population-identifier-1" | ||
| }, | ||
| { | ||
| "code": { | ||
| "coding": [ | ||
| { | ||
| "system": "http://terminology.hl7.org/CodeSystem/measure-population", | ||
| "code": "measure-observation" | ||
| } | ||
| ] | ||
| }, | ||
| "criteria": { | ||
| "language": "text/fhirpath", | ||
| "expression": "Condition.subject.reference" | ||
| }, | ||
| "extension": [ | ||
| { | ||
| "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-aggregateMethod", | ||
| "valueCode": "unique-count" | ||
| }, | ||
| { | ||
| "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-criteriaReference", | ||
| "valueString": "measure-population-identifier-1" | ||
| } | ||
| ], | ||
| "id": "measure-observation-identifier-1" | ||
| } | ||
| ], | ||
| "stratifier": [ | ||
| { | ||
| "criteria": { | ||
| "language": "text/fhirpath", | ||
| "expression": "Condition.code.coding.where(system='http://fhir.de/CodeSystem/bfarm/icd-10-gm')" | ||
| }, | ||
| "code": { | ||
| "coding": [ | ||
| { | ||
| "system": "http://fhir-evaluator/strat/system", | ||
| "code": "condition-icd10-code" | ||
| } | ||
| ] | ||
| }, | ||
| "id": "strat-1" | ||
| }, | ||
| { | ||
| "criteria": { | ||
| "language": "text/fhirpath", | ||
| "expression": "Condition.code.coding.where(system='http://snomed.info/sct')" | ||
| }, | ||
| "code": { | ||
| "coding": [ | ||
| { | ||
| "system": "http://fhir-evaluator/strat/system", | ||
| "code": "condition-sct-code" | ||
| } | ||
| ] | ||
| }, | ||
| "id": "strat-2" | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| #!/usr/bin/env bash | ||
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| MII_TESTDATA_DOWNLOAD_URL="https://health-atlas.de/data_files/594/download?version=1" | ||
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| wget -O testdata.zip "$MII_TESTDATA_DOWNLOAD_URL" | ||
| unzip testdata.zip -d testdata-temp | ||
| cd testdata-temp/Vorhofflimmern || exit | ||
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| for file in *.json.zip | ||
| do | ||
| unzip -o "$file" -d ../../.github/integration-test/Vorhofflimmern | ||
| done | ||
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| cd ../../ | ||
| rm testdata.zip | ||
| rm -rf testdata-temp |
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9 changes: 8 additions & 1 deletion
9
src/main/java/de/medizininformatikinitiative/fhir_data_evaluator/ComponentExpression.java
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