├── .gitignore ├── .travis.settings.xml ├── .travis.yml ├── README.md ├── config └── config.properties ├── docs ├── DESIGN.md └── img │ ├── circe-uml.png │ └── elm-uml.png ├── phema-elm-to-ohdsi.iml ├── pom.xml ├── repo-badge.svg └── src ├── main ├── java │ └── edu │ │ └── phema │ │ └── elm_to_omop │ │ ├── ElmToOmopConverter.java │ │ ├── api │ │ ├── CohortService.java │ │ ├── CqlToElmTranslator.java │ │ ├── ElmToOmopTranslator.java │ │ └── exception │ │ │ ├── CohortServiceException.java │ │ │ ├── CqlStatementNotFoundException.java │ │ │ └── OmopTranslatorException.java │ │ ├── cql │ │ └── InMemoryLibrarySourceLoader.java │ │ ├── helper │ │ ├── CirceConstants.java │ │ ├── CirceUtil.java │ │ ├── Config.java │ │ ├── MyFormatter.java │ │ └── Terms.java │ │ ├── io │ │ ├── ElmReader.java │ │ ├── FhirReader.java │ │ ├── OmopWriter.java │ │ ├── SpreadsheetReader.java │ │ ├── SpreadsheetWriter.java │ │ └── ValueSetReader.java │ │ ├── phenotype │ │ ├── BundlePhenotype.java │ │ ├── FilePhenotype.java │ │ ├── IPhenotype.java │ │ └── PhenotypeException.java │ │ ├── repository │ │ ├── IOmopRepositoryService.java │ │ ├── ObjectMapperContextResolver.java │ │ ├── OmopRepositoryException.java │ │ └── OmopRepositoryService.java │ │ ├── translate │ │ ├── CorelatedCriteriaTranslator.java │ │ ├── CriteriaGroupTranslator.java │ │ ├── PhemaElmToOmopTranslator.java │ │ ├── PhemaElmToOmopTranslatorContext.java │ │ ├── criteria │ │ │ ├── CriteriaTranslator.java │ │ │ ├── comparison │ │ │ │ └── ComparisonExpressionTranslator.java │ │ │ ├── correlation │ │ │ │ ├── CorrelatedQueryCorelatedCriteriaGenerator.java │ │ │ │ ├── CorrelatedQueryCorelatedCriteriaGeneratorFunction.java │ │ │ │ ├── CorrelatedQueryTranslator.java │ │ │ │ ├── Correlation.java │ │ │ │ ├── CorrelationConstants.java │ │ │ │ ├── CorrelationException.java │ │ │ │ ├── QuickResource.java │ │ │ │ └── QuickResourceAttributePair.java │ │ │ └── demographic │ │ │ │ └── DemographicExpressionTranslator.java │ │ ├── exception │ │ │ ├── PhemaAssumptionException.java │ │ │ ├── PhemaNotImplementedException.java │ │ │ └── PhemaTranslationException.java │ │ └── util │ │ │ ├── TemporalUtil.java │ │ │ └── map │ │ │ ├── FhirResourceCirceCriteriaMap.java │ │ │ ├── NumericRangeOperatorMap.java │ │ │ └── QuickResourceCirceCriteriaMap.java │ │ └── vocabulary │ │ ├── ConceptCodeCsvFileValuesetService.java │ │ ├── ElmCodeResolvingValuesetService.java │ │ ├── EmptyValuesetService.java │ │ ├── FhirBundleConceptSetService.java │ │ ├── IValuesetService.java │ │ ├── MultiModalValuesetService.java │ │ ├── PhemaJsonConceptSetService.java │ │ ├── SpreadsheetValuesetService.java │ │ ├── ValuesetServiceException.java │ │ ├── phema │ │ ├── PhemaCode.java │ │ ├── PhemaConceptSet.java │ │ ├── PhemaConceptSetList.java │ │ └── PhemaValueSet.java │ │ └── translate │ │ ├── PhemaVocabularyTranslationException.java │ │ ├── PhemaVocabularyTranslator.java │ │ └── map │ │ ├── ActCodeToVisitConceptMap.java │ │ └── IVocabularyMap.java └── resources │ ├── atlasWorkingDef.json │ ├── diabetes-ohdsi-definition.json │ ├── diabetes │ ├── Diagnosis-Count-v1.cql │ ├── diabetes.csv │ ├── diabetes_original.csv │ ├── simple-dx-elm.json │ ├── simple-dx-elm.xml │ └── simple-dx.cql │ └── ohdsiCohortDefinition.json └── test ├── java └── edu │ └── phema │ └── elm_to_omop │ ├── CliTest.java │ ├── PhemaTestHelper.java │ ├── api │ ├── CohortServiceTest.java │ └── ElmToOmopTranslatorTest.java │ ├── criteria │ ├── AgeCriteriaTest.java │ ├── CorrelatedQueryTest.java │ └── EncounterCriteriaTest.java │ ├── heart_failure │ └── HeartFailurePhenotypeTest.java │ ├── phenotype │ ├── BundlePhenotypeTest.java │ └── FilePhenotypeTest.java │ ├── repository │ └── OmopRepositoryServiceTest.java │ ├── thrombotic_event │ └── ThromboticEventPhenotypeTest.java │ ├── translate │ └── PhemaElmToOmopTranslatorTest.java │ └── vocabulary │ ├── ConceptCodeCsvFileResponseTransformer.java │ ├── ConceptCodeCsvFileValuesetServiceTest.java │ ├── ElmCodeResolvingValuesetServiceTest.java │ ├── MultiModalValuesetServiceTest.java │ ├── PhemaJsonConceptSetServiceTest.java │ ├── VocabularyTranslationTest.java │ └── VocabularyTranslationTestTransformer.java └── resources ├── BundleValueSet.csv ├── LibraryHelperTests.cql ├── LibraryHelperTests.csv ├── api ├── cohortservice │ └── cohortdefinition.json ├── smoke-test-multiple.cql ├── smoke-test-multiple.omop.json ├── smoke-test-simple-bundle.json ├── smoke-test-simple.cql ├── smoke-test-simple.omop.json └── valuesets │ └── simple.csv ├── cli ├── simple-expected.omop.json ├── simple.cql └── simple.csv ├── criteria ├── age.phenotype.cql ├── correlated-query.cql ├── elm-codes-no-translation.cql ├── encounter-criteria.cql ├── translated │ ├── age.eq.value.omop.json │ ├── age.gt.value.omop.json │ ├── age.gte.value.omop.json │ ├── age.lt.value.omop.json │ ├── age.lte.value.omop.json │ ├── age.neq.value.omop.json │ ├── age.nested.1.omop.json │ ├── age.nested.2.omop.json │ ├── age.nested.3.omop.json │ ├── age.nested.with.diabetes.omop.json │ ├── correlated-query │ │ ├── adult-diabetics.omop.json │ │ ├── composite-encounter-criteria.omop.json │ │ ├── correlated-simple.omop.json │ │ ├── nested-with-multi.omop.json │ │ ├── observation-value-date.omop.json │ │ ├── observation-value.omop.json │ │ ├── simple-with-aggregate.omop.json │ │ ├── workbench-correlation-multiple-nested.omop.json │ │ ├── workbench-correlation-multiple.omop.json │ │ ├── workbench-correlation-simple-expanded-window.omop.json │ │ └── workbench-correlation-simple.omop.json │ ├── encounter │ │ ├── filter-by-code.omop.json │ │ └── simple-case.omop.json │ ├── simple-aggregate.omop.json │ ├── value.eq.age.omop.json │ ├── value.gt.age.omop.json │ ├── value.gte.age.omop.json │ ├── value.lt.age.omop.json │ ├── value.lte.age.omop.json │ └── value.neq.age.omop.json └── valuesets │ ├── correlated-query-valuesets.omop.json │ └── encounter-type-valuesets.omop.json ├── heart-failure ├── cql │ ├── step-0-anyone-with-hf-echo.phenotype.cql │ ├── step-1-adults-only.phenotype.cql │ ├── step-2-adults-with-hf-echo.phenotype.cql │ ├── step-3-adults-with-echo-and-dx.phenotype.cql │ └── step-4-full-heart-failure.phenotype.cql ├── translated │ ├── step-0-anyone-with-hf-echo.omop.json │ ├── step-1-adults-only.omop.json │ ├── step-2-adults-with-hf-echo.omop.json │ ├── step-3-adults-with-echo-and-dx.omop.json │ └── step-4-full-heart-failure.omop.json └── valuesets │ ├── 2.16.840.1.113883.3.526.3.376.heart-failure-icd-and-snomed-diagnosis-codes.valueset.csv │ ├── 2.16.840.1.999999.1.heart-failure-echocardiography-cpt-codes.valueset.csv │ └── omop-json │ ├── 2.16.840.1.999999.1-and-2.16.840.1.113883.3.526.3.376.valueset.omop.json │ ├── 2.16.840.1.999999.1.heart-failure-echocardiography-cpt-codes.valueset.omop.json │ ├── hf-phenotype-valuesets-from-atlas.omop.json │ └── hf-phenotype-valuesets-from-vsac.omop.json ├── phenotype ├── 0.test-phenotype.cql ├── phema-phenotype.0.test-phenotype.bundle.json ├── phenotype-bundle.omop.json ├── phenotype.cql └── phenotype.omop.json ├── repository ├── empty-search-request.omop.json ├── empty-search-results.omop.json ├── multiple-search-request.omop.json ├── multiple-search-results.omop.json ├── single-search-request.omop.json └── single-search-result.omop.json ├── responses ├── cohortdefinition │ ├── cohortdefinition.108.json │ ├── cohortdefinition.87.json │ ├── generate │ │ └── job.171.json │ ├── info │ │ ├── info.108.complete.json │ │ └── info.108.running.json │ ├── report │ │ └── report.108.json │ └── sql │ │ └── sql.87.json ├── cohortservice │ └── getCohortDefinitionSql │ │ └── sql.87.postgresql.json ├── sqlrender │ └── translate │ │ └── sql.87.postgresql.json └── vocabulary │ ├── concept.45917083.json │ └── concepts.45917083.json ├── thrombotic-event ├── bundle │ └── phema-phenotype.1516.thrombotic-event.bundle.json ├── cql │ ├── 1516.thrombotic-event.cql │ └── includes │ │ ├── FHIRHelpers-4.0.0.cql │ │ ├── PhEMAHelpers-1.0.0.cql │ │ └── PhEMATemporal-1.0.0.cql ├── translated │ ├── 1516.thrombotic-event.cohort-definition.omop.json │ ├── 1516.thrombotic-event.cohort-definition.omop.sql │ └── 1516.thrombotic-event.omop.json └── valuesets │ └── 1516.thrombotic-event.valuesets.csv ├── translated ├── BooleanFromExpressions.1.json ├── BooleanFromExpressions.2.json ├── CountDirectCondition.1.json ├── CountDirectCondition.2.json ├── CountDirectCondition.3.json ├── CountDirectCondition.4.json ├── CountDirectCondition.5.json ├── CountExpressionReference.json ├── ExistsDirectCondition.json ├── ExistsFromExpression.json ├── ExistsFromReferencedExpression.json ├── MedicationStatementTest.json ├── NestedBooleanDirectConditions.1.json ├── NestedBooleanDirectConditions.2.json ├── NestedBooleanFromReferencedBooleanExpressions.json ├── OrDirectConditions.json ├── OrFromReferencedExpressions.json ├── OrMixedDirectAndExpression.json ├── ProcedureTest.json ├── ProcedureTest2.json └── old │ ├── BooleanFromExpressions.1.json │ ├── BooleanFromExpressions.2.json │ ├── CountDirectCondition.1.json │ ├── CountDirectCondition.2.json │ ├── CountDirectCondition.3.json │ ├── CountDirectCondition.4.json │ ├── CountDirectCondition.5.json │ ├── CountExpressionReference.json │ ├── ExistsDirectCondition.json │ ├── ExistsFromExpression.json │ ├── ExistsFromReferencedExpression.json │ ├── NestedBooleanDirectConditions.1.json │ ├── NestedBooleanDirectConditions.2.json │ ├── NestedBooleanFromReferencedBooleanExpressions.json │ ├── OrDirectConditions.json │ ├── OrFromReferencedExpressions.json │ └── OrMixedDirectAndExpression.json └── vocabulary ├── all-five-valuesets-combined.omop.json ├── cached ├── icd9-with-cache.csv └── icd9-with-cache.csv.cache ├── cql └── code-and-valueset-vocabularies.cql ├── encounter ├── act-encounter-codes.valueset.csv └── vocabulary-testing-codes.phema-concept-sets.json ├── heart-failure-diagnosis-icd-codes.phema-concept-sets.json ├── 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