SQL on FHIR view runner #1775
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SQL on FHIR view runner #1775
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…ments to Spark/Catalyst. Initial concept of annotation fhipath based function definition.
Refactoring of ParserTest and related assertion classes, to work with column based approach (WIP).
…Test expectations.
Implementation of 'union' and 'forEach' clauses. Separation of 'v1' FHIRView test from our custom enhanced tests.
Implemented 'getResourceKey()' function.
Implementing `join()` function.
…g deserialization of WhereClause.
Implementing 'collection' and singular value selection semantics for DirectSelection.
…ons. Implementing 'r-keys' functions: getReferenceKey() and getResourceKey(). Cleaning up our extended FhirView tests.
…to allow FHIRView paths like: forEach = 'where(gender='male').name,
…lemented as functions in (StandardFunctions).
This was referenced Jul 4, 2024
# Conflicts: # fhirpath/src/main/java/au/csiro/pathling/sql/boundary/DecimalBoundaryFunction.java
# Conflicts: # deployment/helm/pom.xml # encoders/pom.xml # encoders/src/main/java/au/csiro/pathling/config/EncodingConfiguration.java # fhir-server/pom.xml # fhir-server/src/main/java/au/csiro/pathling/aggregate/AggregateExecutor.java # fhir-server/src/main/java/au/csiro/pathling/async/AsyncAspect.java # fhir-server/src/main/java/au/csiro/pathling/async/JobProvider.java # fhir-server/src/main/java/au/csiro/pathling/caching/EntityTagInterceptor.java # fhir-server/src/main/java/au/csiro/pathling/config/AuthorizationConfiguration.java # fhir-server/src/main/java/au/csiro/pathling/config/ServerConfiguration.java # fhir-server/src/main/java/au/csiro/pathling/errors/DiagnosticContext.java # fhir-server/src/main/java/au/csiro/pathling/errors/ErrorHandlingInterceptor.java # fhir-server/src/main/java/au/csiro/pathling/errors/ErrorReportingInterceptor.java # fhir-server/src/main/java/au/csiro/pathling/extract/ResultProvider.java # fhir-server/src/main/java/au/csiro/pathling/fhir/ConformanceProvider.java # fhir-server/src/main/java/au/csiro/pathling/fhir/FhirServer.java # fhir-server/src/main/java/au/csiro/pathling/fhir/SmartConfigurationInterceptor.java # fhir-server/src/main/java/au/csiro/pathling/search/SearchExecutor.java # fhir-server/src/main/java/au/csiro/pathling/security/SecurityConfiguration.java # fhir-server/src/test/java/au/csiro/pathling/aggregate/DrillDownBuilderTest.java # fhir-server/src/test/java/au/csiro/pathling/extract/ExtractRequestBuilder.java # fhir-server/src/test/java/au/csiro/pathling/fhir/EntityTagInterceptorTest.java # fhir-server/src/test/java/au/csiro/pathling/fhirpath/parser/ParserTest.java # fhir-server/src/test/java/au/csiro/pathling/jmh/SpringBootJmhContext.java # fhir-server/src/test/java/au/csiro/pathling/test/IntegrationTestDependencies.java # fhirpath/pom.xml # fhirpath/src/main/java/au/csiro/pathling/QueryExecutor.java # fhirpath/src/main/java/au/csiro/pathling/QueryHelpers.java # fhirpath/src/main/java/au/csiro/pathling/aggregate/AggregateQueryExecutor.java # fhirpath/src/main/java/au/csiro/pathling/aggregate/AggregateRequest.java # fhirpath/src/main/java/au/csiro/pathling/config/StorageConfiguration.java # fhirpath/src/main/java/au/csiro/pathling/extract/ExtractQueryExecutor.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/FhirPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/Materializable.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/NonLiteralPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/Numeric.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/Referrer.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/ResourcePath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/Temporal.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/TerminologyUtils.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/UntypedResourcePath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/comparison/CodingComparator.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/definition/ResourceDefinition.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/element/BooleanPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/element/CodingPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/element/DatePath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/element/DateTimePath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/element/DecimalPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/element/ElementDefinition.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/element/ElementPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/element/ExtensionPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/element/IntegerPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/element/QuantityPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/element/ReferenceExtensionDefinition.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/element/ReferencePath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/element/StringPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/element/TimePath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/AggregateFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/Arguments.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/BooleansTestFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/CountFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/EmptyFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/ExistsFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/ExtensionFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/FirstFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/IifFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/NamedFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/NamedFunctionInput.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/NotFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/OfTypeFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/ResolveFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/ReverseResolveFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/SumFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/UntilFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/WhereFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/terminology/DesignationFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/terminology/DisplayFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/terminology/MemberOfFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/terminology/PropertyFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/terminology/SubsumesFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/terminology/TranslateFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/literal/BooleanLiteralPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/literal/CodingLiteralPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/literal/DateLiteralPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/literal/DateTimeLiteralPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/literal/DecimalLiteralPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/literal/IntegerLiteralPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/literal/LiteralPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/literal/NullLiteralPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/literal/QuantityLiteralPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/literal/StringLiteralPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/literal/TimeLiteralPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/operator/BinaryOperator.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/operator/BinaryOperatorInput.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/operator/BooleanOperator.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/operator/CombineOperator.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/operator/Comparable.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/operator/ComparisonOperator.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/operator/DateArithmeticOperator.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/operator/MathOperator.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/operator/MembershipOperator.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/operator/Operator.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/operator/PathTraversalInput.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/operator/PathTraversalOperator.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/parser/InvocationVisitor.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/parser/LiteralTermVisitor.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/parser/ParserContext.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/parser/TermVisitor.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/parser/Visitor.java # fhirpath/src/test/java/au/csiro/pathling/UnitTestDependencies.java # fhirpath/src/test/java/au/csiro/pathling/fhirpath/CanBeCombinedWithTest.java # fhirpath/src/test/java/au/csiro/pathling/fhirpath/function/BooleansTestFunctionTest.java # fhirpath/src/test/java/au/csiro/pathling/fhirpath/function/ResolveFunctionTest.java # fhirpath/src/test/java/au/csiro/pathling/fhirpath/function/UntilFunctionTest.java # fhirpath/src/test/java/au/csiro/pathling/fhirpath/function/terminology/DesignationFunctionTest.java # fhirpath/src/test/java/au/csiro/pathling/fhirpath/function/terminology/PropertyFunctionTest.java # fhirpath/src/test/java/au/csiro/pathling/fhirpath/function/terminology/SubsumesFunctionTest.java # fhirpath/src/test/java/au/csiro/pathling/fhirpath/function/terminology/TranslateFunctionTest.java # fhirpath/src/test/java/au/csiro/pathling/fhirpath/operator/ComparisonOperatorTest.java # fhirpath/src/test/java/au/csiro/pathling/fhirpath/operator/DateArithmeticTest.java # fhirpath/src/test/java/au/csiro/pathling/fhirpath/operator/MathOperatorQuantityTest.java # fhirpath/src/test/java/au/csiro/pathling/fhirpath/operator/MathOperatorTest.java # fhirpath/src/test/java/au/csiro/pathling/fhirpath/operator/QuantityOperatorsPrecisionTest.java # fhirpath/src/test/java/au/csiro/pathling/test/assertions/Assertions.java # fhirpath/src/test/java/au/csiro/pathling/test/assertions/BaseFhirPathAssertion.java # fhirpath/src/test/java/au/csiro/pathling/test/assertions/ElementPathAssertion.java # fhirpath/src/test/java/au/csiro/pathling/test/assertions/FhirPathAssertion.java # fhirpath/src/test/java/au/csiro/pathling/test/assertions/LiteralPathAssertion.java # fhirpath/src/test/java/au/csiro/pathling/test/assertions/ResourcePathAssertion.java # fhirpath/src/test/java/au/csiro/pathling/test/builders/ElementPathBuilder.java # fhirpath/src/test/java/au/csiro/pathling/test/builders/ParserContextBuilder.java # fhirpath/src/test/java/au/csiro/pathling/test/builders/ResourcePathBuilder.java # fhirpath/src/test/java/au/csiro/pathling/test/builders/UntypedResourcePathBuilder.java # fhirpath/src/test/java/au/csiro/pathling/test/helpers/SparkHelpers.java # lib/R/pom.xml # lib/import/pom.xml # lib/js/pom.xml # lib/python/Dockerfile # lib/python/pom.xml # library-api/pom.xml # library-api/src/main/java/au/csiro/pathling/library/PathlingContext.java # library-api/src/main/java/au/csiro/pathling/library/io/sink/DataSinkBuilder.java # library-api/src/main/java/au/csiro/pathling/library/io/source/AbstractSource.java # library-api/src/main/java/au/csiro/pathling/library/io/source/QueryableDataSource.java # library-api/src/main/java/au/csiro/pathling/library/query/QueryDispatcher.java # library-api/src/test/java/au/csiro/pathling/library/PathlingContextTest.java # library-runtime/pom.xml # pom.xml # site/pom.xml # terminology/pom.xml # terminology/src/main/java/au/csiro/pathling/config/HttpClientCachingConfiguration.java # terminology/src/main/java/au/csiro/pathling/config/HttpClientConfiguration.java # terminology/src/main/java/au/csiro/pathling/config/TerminologyAuthConfiguration.java # terminology/src/main/java/au/csiro/pathling/config/TerminologyConfiguration.java # terminology/src/main/java/au/csiro/pathling/terminology/DefaultTerminologyService.java # terminology/src/main/java/au/csiro/pathling/terminology/TerminologyServiceFactory.java # terminology/src/main/java/au/csiro/pathling/terminology/caching/CachingTerminologyService.java # terminology/src/test/java/au/csiro/pathling/test/helpers/TerminologyServiceHelpers.java # utilities/pom.xml # utilities/src/main/java/au/csiro/pathling/utilities/Lists.java # utilities/src/main/java/au/csiro/pathling/validation/ValidationUtils.java
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We need to make a corresponding change on this branch for c6b06e7, so that we can properly handle the encoding of arrays of complex elements as null. |
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This pull request adds the ability to execute SQL on FHIR view definitions against data sources within the library API.
It also includes a comprehensive refactoring that integrates this new functionality with the rest of the code base and makes some changes that will improve performance across all of the different FHIRPath query operations.
Resolves #1438 and #1759.