diff --git a/.github/actions/trivy-scan/action.yml b/.github/actions/trivy-scan/action.yml index 6e0b803f6e..b351dec6ed 100644 --- a/.github/actions/trivy-scan/action.yml +++ b/.github/actions/trivy-scan/action.yml @@ -41,7 +41,7 @@ runs: steps: - name: Run security scan (SARIF output) id: sarif-scan - uses: aquasecurity/trivy-action@0.33.1 + uses: aquasecurity/trivy-action@0.35.0 continue-on-error: true env: TRIVY_SKIP_DB_UPDATE: ${{ inputs.skip-db-update }} @@ -57,11 +57,11 @@ runs: skip-dirs: ${{ inputs.skip-dirs }} exit-code: "1" severity: MEDIUM,HIGH,CRITICAL - version: "v0.69.0" + version: "v0.69.3" - name: Run security scan (table output on failure) if: steps.sarif-scan.outcome == 'failure' - uses: aquasecurity/trivy-action@0.33.1 + uses: aquasecurity/trivy-action@0.35.0 env: TRIVY_SKIP_DB_UPDATE: ${{ inputs.skip-db-update }} TRIVY_SKIP_JAVA_DB_UPDATE: ${{ inputs.skip-db-update }} @@ -76,4 +76,4 @@ runs: skip-setup-trivy: true exit-code: "1" severity: MEDIUM,HIGH,CRITICAL - version: "v0.69.0" + version: "v0.69.3" diff --git a/.trivyignore b/.trivyignore index b8785fee53..5553d98397 100644 --- a/.trivyignore +++ b/.trivyignore @@ -19,6 +19,8 @@ CVE-2022-46751 CVE-2023-44981 CVE-2024-23944 CVE-2025-58457 +CVE-2026-24281 +CVE-2026-24308 # Jersey Client is provided via Spark, not bundled in distribution. CVE-2025-12383 @@ -41,3 +43,6 @@ CVE-2025-33042 # Not applicable in library context, user controls all compressed input. # See: https://github.com/aehrc/pathling/issues/2540 CVE-2025-67721 + +# jackson-core async parser DoS — Pathling uses only synchronous parsing via HAPI FHIR. +GHSA-72hv-8253-57qq diff --git a/encoders/src/main/java/au/csiro/pathling/encoders/ValueFunctions.java b/encoders/src/main/java/au/csiro/pathling/encoders/ValueFunctions.java index c226a6019e..619fc75183 100644 --- a/encoders/src/main/java/au/csiro/pathling/encoders/ValueFunctions.java +++ b/encoders/src/main/java/au/csiro/pathling/encoders/ValueFunctions.java @@ -35,6 +35,8 @@ import org.apache.spark.sql.Column; import org.apache.spark.sql.catalyst.expressions.Expression; import org.apache.spark.sql.classic.ColumnConversions$; +import org.apache.spark.sql.functions; +import org.apache.spark.sql.types.DataType; import scala.Function1; import scala.collection.immutable.Seq; import scala.jdk.javaapi.CollectionConverters; @@ -204,6 +206,8 @@ public static Column emptyArrayIfMissingField(@Nonnull final Column value) { * @param extractor An extraction operation to apply at each node that must return an array type * @param traversals A list of traversal operations to apply recursively to reach child nodes * @param maxDepth The maximum recursion depth for same-type traversals to prevent infinite loops + * @param errorOnDepthExhaustion If true, throws an error when same-type depth is exhausted + * instead of returning an empty array * @return A Column containing an array of all extracted values from the tree traversal */ @Nonnull @@ -211,7 +215,8 @@ public static Column transformTree( @Nonnull final Column value, @Nonnull final UnaryOperator extractor, @Nonnull final List> traversals, - final int maxDepth) { + final int maxDepth, + final boolean errorOnDepthExhaustion) { final List> x = traversals.stream() @@ -222,7 +227,192 @@ public static Column transformTree( final Seq> scalaSeq = CollectionConverters.asScala(x).toSeq(); return column( new UnresolvedTransformTree( - expression(value), liftToExpression(extractor)::apply, scalaSeq, maxDepth)); + expression(value), + liftToExpression(extractor)::apply, + scalaSeq, + scala.Option.empty(), + maxDepth, + errorOnDepthExhaustion)); + } + + /** + * Performs a recursive tree traversal that extracts values at each level of a hierarchical + * structure, concatenating all extracted results into a single array. + * + *

This overload defaults to silent stop on same-type depth exhaustion. + * + * @param value The starting value column to traverse + * @param extractor An extraction operation to apply at each node that must return an array type + * @param traversals A list of traversal operations to apply recursively to reach child nodes + * @param maxDepth The maximum recursion depth for same-type traversals to prevent infinite loops + * @return A Column containing an array of all extracted values from the tree traversal + */ + @Nonnull + public static Column transformTree( + @Nonnull final Column value, + @Nonnull final UnaryOperator extractor, + @Nonnull final List> traversals, + final int maxDepth) { + return transformTree(value, extractor, traversals, maxDepth, false); + } + + /** + * Wraps a column transform so that it converts each result element to Variant. The wrapped + * transform applies the original transform and then maps each element in the resulting array to a + * Variant via {@code to_variant_object()}, producing {@code Array[Variant]}. + * + *

This is useful for making arrays from different nesting levels type-compatible, since all + * Variant arrays share the same element type regardless of the original struct schema. + * + * @param transform The original column transform that produces an array + * @return A new transform that produces {@code Array[Variant]} + */ + @Nonnull + public static UnaryOperator wrapWithVariant( + @Nonnull final UnaryOperator transform) { + return c -> functions.transform(transform.apply(c), functions::to_variant_object); + } + + /** + * Converts an {@code Array[Variant]} column back to an array of a specific target schema using + * {@code variant_get()}. Each Variant element is decoded using the JSON path {@code "$"} (root) + * and the provided target schema string. Missing fields in shallower nesting levels are filled + * with null. + * + * @param variantArray The column containing {@code Array[Variant]} + * @param targetSchema The Spark SQL schema string for the target element type (e.g., {@code + * "STRUCT>>"}) + * @return A column containing an array with elements decoded to the target schema + */ + @Nonnull + public static Column unwrapVariantArray( + @Nonnull final Column variantArray, @Nonnull final String targetSchema) { + return functions.transform(variantArray, v -> functions.variant_get(v, "$", targetSchema)); + } + + /** + * Converts an {@code Array[Variant]} column back to an array of a specific target data type using + * {@code variant_get()}. This overload accepts a {@link DataType} and converts it to its DDL + * string representation for use with {@code variant_get()}. + * + * @param variantArray The column containing {@code Array[Variant]} + * @param targetType The Spark {@link DataType} for the target element type + * @return A column containing an array with elements decoded to the target type + */ + @Nonnull + public static Column unwrapVariantArray( + @Nonnull final Column variantArray, @Nonnull final DataType targetType) { + return unwrapVariantArray(variantArray, targetType.sql()); + } + + /** + * Performs a recursive tree traversal with Variant-based schema unification, collecting all + * extracted values across nesting levels regardless of structural differences. + * + *

This method solves the schema divergence problem when traversing self-referential FHIR + * structures. At each nesting level, the extractor may produce arrays with different struct + * schemas (deeper levels have fewer fields due to encoding truncation). To make these arrays + * type-compatible for concatenation, each extracted element is converted to Spark's Variant type + * as an intermediate representation. After the tree traversal collects all results, the final + * {@code Array[Variant]} is converted back to the target schema (from level 0, the fullest + * schema), determined lazily at Catalyst analysis time. + * + * @param value The starting value column to traverse + * @param extractor An extraction operation that produces an array at each node + * @param traversals A list of traversal operations for reaching child nodes + * @param maxDepth The maximum recursion depth for same-type traversals + * @param errorOnDepthExhaustion If true, throws an error when same-type depth is exhausted + * instead of returning an empty array + * @return A Column containing an array of extracted values, all conforming to the level-0 schema + */ + @Nonnull + public static Column variantTransformTree( + @Nonnull final Column value, + @Nonnull final UnaryOperator extractor, + @Nonnull final List> traversals, + final int maxDepth, + final boolean errorOnDepthExhaustion) { + + // Wrap the extractor to convert each result element to Variant. + final UnaryOperator variantExtractor = wrapWithVariant(extractor); + + // Run the tree traversal with Variant-wrapped extractor but raw traversals. + final Expression variantTreeExpr = + expression( + transformTree(value, variantExtractor, traversals, maxDepth, errorOnDepthExhaustion)); + + // Build a schema reference expression by applying the raw extractor to the value. This + // expression will resolve to the level-0 array type, from which the target element type is + // derived during Catalyst analysis. + final Expression schemaRefExpr = liftToExpression(extractor).apply(expression(value)); + + // Wrap with deferred Variant unwrapping. The UnresolvedVariantUnwrap expression resolves + // once both the tree result and schema reference are resolved, converting each Variant + // element back to the target struct type. + return variantUnwrap(column(variantTreeExpr), column(schemaRefExpr)); + } + + /** + * Performs a recursive tree traversal with Variant-based schema unification, collecting all + * extracted values across nesting levels regardless of structural differences. + * + *

This overload defaults to silent stop on same-type depth exhaustion. + * + * @param value The starting value column to traverse + * @param extractor An extraction operation that produces an array at each node + * @param traversals A list of traversal operations for reaching child nodes + * @param maxDepth The maximum recursion depth for same-type traversals + * @return A Column containing an array of extracted values, all conforming to the level-0 schema + */ + @Nonnull + public static Column variantTransformTree( + @Nonnull final Column value, + @Nonnull final UnaryOperator extractor, + @Nonnull final List> traversals, + final int maxDepth) { + return variantTransformTree(value, extractor, traversals, maxDepth, false); + } + + /** + * Converts an {@code Array[Variant]} column back to a typed array using deferred schema + * resolution. The target element type is determined at Catalyst analysis time from a schema + * reference expression, which should resolve to the fullest (level-0) array type. + * + *

This is used by {@code repeatAll()} to convert the concatenated Variant results from all + * nesting levels back to the target struct type, with missing fields in shallower levels filled + * with null. + * + * @param variantArray The column containing {@code Array[Variant]} + * @param schemaRef A column whose resolved type determines the target element schema (should be + * an array type; the element type will be extracted) + * @param failOnError Whether to throw an error when a Variant element cannot be decoded to the + * target schema. When {@code true}, decoding failures cause a runtime exception; when {@code + * false}, they produce {@code null}. + * @return A column containing an array with elements decoded to the schema reference's type + */ + @Nonnull + public static Column variantUnwrap( + @Nonnull final Column variantArray, + @Nonnull final Column schemaRef, + final boolean failOnError) { + return column( + new UnresolvedVariantUnwrap(expression(variantArray), expression(schemaRef), failOnError)); + } + + /** + * Converts an {@code Array[Variant]} column back to a typed array using deferred schema + * resolution with strict error handling. Equivalent to calling {@link #variantUnwrap(Column, + * Column, boolean)} with {@code failOnError = true}. + * + * @param variantArray The column containing {@code Array[Variant]} + * @param schemaRef A column whose resolved type determines the target element schema (should be + * an array type; the element type will be extracted) + * @return A column containing an array with elements decoded to the schema reference's type + */ + @Nonnull + public static Column variantUnwrap( + @Nonnull final Column variantArray, @Nonnull final Column schemaRef) { + return variantUnwrap(variantArray, schemaRef, true); } /** diff --git a/encoders/src/main/scala/au/csiro/pathling/encoders/Expressions.scala b/encoders/src/main/scala/au/csiro/pathling/encoders/Expressions.scala index 9fa74a5278..3c83d9a912 100644 --- a/encoders/src/main/scala/au/csiro/pathling/encoders/Expressions.scala +++ b/encoders/src/main/scala/au/csiro/pathling/encoders/Expressions.scala @@ -30,9 +30,10 @@ import org.apache.spark.sql.catalyst.InternalRow import org.apache.spark.sql.catalyst.analysis.TypeCheckResult.{TypeCheckFailure, TypeCheckSuccess} import org.apache.spark.sql.catalyst.analysis.{TypeCheckResult, UnresolvedException} import org.apache.spark.sql.catalyst.expressions._ +import org.apache.spark.sql.catalyst.expressions.{variant => variantExpr} import org.apache.spark.sql.catalyst.expressions.codegen.Block._ import org.apache.spark.sql.catalyst.expressions.codegen.{CodeGenerator, CodegenContext, ExprCode, FalseLiteral} -import org.apache.spark.sql.catalyst.trees.TreePattern.{ARRAYS_ZIP, TreePattern} + import org.apache.spark.sql.catalyst.util.{ArrayData, GenericArrayData} import org.apache.spark.sql.types._ @@ -524,14 +525,16 @@ case class UnresolvedEmptyArrayIfMissingField(value: Expression) * @param node the current node expression to traverse * @param extractor a function to extract values from a node (must return array type) * @param traversals a sequence of functions to traverse to child nodes - * @param parentType the data type of the parent node, used to determine if depth should decrement - * @param level the remaining levels to traverse for same-type recursion; when exhausted, only extraction occurs + * @param parentType the data type of the parent node, used to determine if depth should decrement + * @param level the remaining levels to traverse for same-type recursion; when exhausted, only extraction occurs + * @param errorOnDepthExhaustion if true, throws an AnalysisException when same-type depth is exhausted instead of returning an empty array */ case class UnresolvedTransformTree(node: Expression, extractor: Expression => Expression, traversals: Seq[Expression => Expression], parentType: Option[DataType], - level: Int + level: Int, + errorOnDepthExhaustion: Boolean = false ) extends Expression with UnevaluableCopy with NonSQLExpression { @@ -539,34 +542,42 @@ case class UnresolvedTransformTree(node: Expression, extractor: Expression => Expression, traversals: Seq[Expression => Expression], level: Int) = { - this(node, extractor, traversals, None, level) + this(node, extractor, traversals, None, level, false) } override def mapChildren(f: Expression => Expression): Expression = { - try { - val newValue = f(node) - if (newValue.resolved) { - // if node is resolved we concatenate - // the value extracted from the node with next level traversal - if (level > 0 || !parentType.contains(newValue.dataType)) - Concat( - Seq(extractor(node)) ++ - traversals - .map(t => UnresolvedTransformTree(t(node), extractor, traversals, - Some(newValue.dataType), - if (parentType.contains(newValue.dataType)) level - 1 else level - )) - ) - else CreateArray(Seq.empty) - } - else { - copy(node = newValue) - } + // Only the Catalyst resolution call f(node) is expected to throw FIELD_NOT_FOUND when the + // field doesn't exist at this schema level. Other operations (extractor, traversal + // construction) should propagate errors normally. + val newValue = try { + f(node) } catch { case e: AnalysisException if e.errorClass.contains("FIELD_NOT_FOUND") => - // in case of AnalysisException we just return an empty array - CreateArray(Seq.empty) + return CreateArray(Seq.empty) + } + + if (newValue.resolved) { + // If node is resolved we concatenate the value extracted from the node with next level + // traversal. + if (level > 0 || !parentType.contains(newValue.dataType)) + Concat( + Seq(extractor(node)) ++ + traversals + .map(t => UnresolvedTransformTree(t(node), extractor, traversals, + Some(newValue.dataType), + if (parentType.contains(newValue.dataType)) level - 1 else level, + errorOnDepthExhaustion + )) + ) + else if (errorOnDepthExhaustion) + throw new AnalysisException( + errorClass = "INTERNAL_ERROR", + messageParameters = Map("message" -> "Recursive traversal exceeded maximum depth — possible infinite recursion.")) + else CreateArray(Seq.empty) + } + else { + copy(node = newValue) } } @@ -581,7 +592,7 @@ case class UnresolvedTransformTree(node: Expression, override def children: Seq[Expression] = node :: Nil override def withNewChildrenInternal(newChildren: IndexedSeq[Expression]): Expression = { - UnresolvedTransformTree(newChildren.head, extractor, traversals, parentType, level) + UnresolvedTransformTree(newChildren.head, extractor, traversals, parentType, level, errorOnDepthExhaustion) } } @@ -599,8 +610,6 @@ case class UnresolvedTransformTree(node: Expression, case class StructProduct(children: Seq[Expression], outer: Boolean = false) extends Expression with NonSQLExpression { - final override val nodePatterns: Seq[TreePattern] = Seq(ARRAYS_ZIP) - override lazy val resolved: Boolean = childrenResolved && checkInputDataTypes.isSuccess @@ -692,16 +701,19 @@ case class StructProduct(children: Seq[Expression], outer: Boolean = false) // idx - the the index of the child expression (the array to cross) - // i - the index of the product element + // i - the index of the product element val getValueForType = arrayElementTypes.zipWithIndex.map { case (eleType, idx) => val g = CodeGenerator.getValue(s"$arrVals[$idx]", eleType, s"$prodIdxs[$idx]") val structValue = s"structValue_$idx" + // Get the field data types for this struct, needed for UnsafeRow.get(). + val fieldDataTypes = eleType.asInstanceOf[StructType].fields.map(_.dataType) + val fieldTypesRef = ctx.addReferenceObj(s"fieldTypes_$idx", fieldDataTypes, "org.apache.spark.sql.types.DataType[]") s""" - | ${CodeGenerator.javaType(eleType)} $structValue = $g; + | ${CodeGenerator.javaType(eleType)} $structValue = $g; | // using the base copy the values of all the fields to the output | for(int fi = 0; $structValue != null && fi < $structValue.numFields(); fi++) { | if(!$structValue.isNullAt(fi)) { - | $currentRow[$offsets[$idx] + fi] = $structValue.get(fi, null); + | $currentRow[$offsets[$idx] + fi] = $structValue.get(fi, $fieldTypesRef[fi]); | } | } """.stripMargin @@ -858,10 +870,11 @@ case class StructProduct(children: Seq[Expression], outer: Boolean = false) private def copyStructFields(arr: ArrayData, arrayIndex: Int, elementIndex: Int, currentRowData: Array[Any]): Unit = { val structData = arr.get(elementIndex, arrayElementTypes(arrayIndex)).asInstanceOf[InternalRow] + val fieldTypes = arrayElementTypes(arrayIndex).asInstanceOf[StructType].fields for (fi <- 0 until structData.numFields) { if (!structData.isNullAt(fi)) { - currentRowData(offsetsScala(arrayIndex) + fi) = structData.get(fi, null) + currentRowData(offsetsScala(arrayIndex) + fi) = structData.get(fi, fieldTypes(fi).dataType) } } } @@ -873,4 +886,65 @@ case class StructProduct(children: Seq[Expression], outer: Boolean = false) } +/** + * Wraps an Array[Variant] expression with deferred unwrapping to a target schema. The target + * schema is determined lazily from a reference expression that represents the level-0 (fullest) + * result of the extractor. + * + * During resolution, once both the inner expression (Array[Variant]) and the schema reference + * expression are resolved, this expression expands into a `transform(inner, v -> variant_get(v, + * '$', targetSchema))` call that converts each Variant element back to the target struct type. + * + * @param inner the Array[Variant] expression produced by UnresolvedTransformTree + * @param schemaRef an expression whose resolved element type determines the target schema + */ +case class UnresolvedVariantUnwrap(inner: Expression, schemaRef: Expression, + failOnError: Boolean = true) + extends Expression with UnevaluableCopy with NonSQLExpression { + + override def children: Seq[Expression] = Seq(inner, schemaRef) + + override protected def withNewChildrenInternal( + newChildren: IndexedSeq[Expression]): Expression = { + copy(inner = newChildren(0), schemaRef = newChildren(1)) + } + + // Resolution happens inside mapChildren because it is called by Catalyst rules + // (e.g., ResolveLambdaVariables, ResolveReferences). If mapChildren is called multiple + // times before both children are resolved, the expression safely returns a copy() each time. + override def mapChildren(f: Expression => Expression): Expression = { + val newInner = f(inner) + val newSchemaRef = f(schemaRef) + if (newInner.resolved && newSchemaRef.resolved) { + // Determine the target element type from the schema reference expression. + val targetElementType = newSchemaRef.dataType match { + case ArrayType(elementType, _) => elementType + case other => other + } + // Build: transform(inner, v -> variant_get(v, '$', targetSchema)) + val lambdaVar = NamedLambdaVariable( + "v", VariantType, nullable = true, + exprId = NamedExpression.newExprId, + value = new java.util.concurrent.atomic.AtomicReference[Any]() + ) + val variantGetExpr = new variantExpr.VariantGet( + lambdaVar, Literal.create("$", StringType), + targetElementType, failOnError = failOnError, timeZoneId = None + ) + val lambdaFunc = LambdaFunction(variantGetExpr, Seq(lambdaVar)) + ArrayTransform(newInner, lambdaFunc) + } else { + copy(inner = newInner, schemaRef = newSchemaRef) + } + } + + override def dataType: DataType = throw new UnresolvedException("dataType") + + override def nullable: Boolean = throw new UnresolvedException("nullable") + + override lazy val resolved = false + + override def toString: String = s"VariantUnwrap($inner)" +} + // ColumnFunctions has been moved to a Java class to access package-private Spark methods diff --git a/encoders/src/test/java/au/csiro/pathling/encoders/ExpressionsBothModesTest.java b/encoders/src/test/java/au/csiro/pathling/encoders/ExpressionsBothModesTest.java new file mode 100644 index 0000000000..5f011236d9 --- /dev/null +++ b/encoders/src/test/java/au/csiro/pathling/encoders/ExpressionsBothModesTest.java @@ -0,0 +1,295 @@ +/* + * This is a modified version of the Bunsen library, originally published at + * https://github.com/cerner/bunsen. + * + * Bunsen is copyright 2017 Cerner Innovation, Inc., and is licensed under + * the Apache License, version 2.0 (http://www.apache.org/licenses/LICENSE-2.0). + * + * These modifications are copyright 2018-2026 Commonwealth Scientific + * and Industrial Research Organisation (CSIRO) ABN 41 687 119 230. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + */ + +package au.csiro.pathling.encoders; + +import static org.apache.spark.sql.functions.array; +import static org.apache.spark.sql.functions.col; +import static org.apache.spark.sql.functions.inline; +import static org.apache.spark.sql.functions.struct; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import java.util.Arrays; +import java.util.List; +import org.apache.spark.sql.Column; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.RowFactory; +import org.apache.spark.sql.SparkSession; +import org.apache.spark.sql.functions; +import org.apache.spark.sql.types.DataTypes; +import org.apache.spark.sql.types.Metadata; +import org.apache.spark.sql.types.StructField; +import org.apache.spark.sql.types.StructType; +import org.junit.jupiter.api.Test; +import scala.collection.Seq; + +/** + * Abstract base class for expression tests that need to run in both codegen and interpreted modes. + * Subclasses configure the Spark session and annotate their own setup/teardown methods. + */ +public abstract class ExpressionsBothModesTest { + + protected static SparkSession spark; + + /** Creates the shared Spark session. Subclasses should call this from their @BeforeAll method. */ + protected static void setUp() { + spark = + SparkSession.builder() + .master("local[*]") + .appName("testing") + .config("spark.driver.bindAddress", "localhost") + .config("spark.driver.host", "localhost") + .config("spark.ui.enabled", "false") + .getOrCreate(); + } + + @Test + void testArrayCrossProd() { + final Dataset ds = spark.range(1).toDF(); + + // Create three input array columns. + final Dataset inputDs = + ds.withColumn( + "arrayA", + functions.array( + functions.struct( + functions.lit("zzz").alias("str"), functions.lit(true).alias("bool")), + functions.struct( + functions.lit("yyy").alias("str"), functions.lit(false).alias("bool")))) + .withColumn( + "arrayB", + functions.array( + functions.struct(functions.lit(13).alias("int")), + functions.struct(functions.lit(17).alias("int")), + functions.struct(functions.lit(1).alias("int")))) + .withColumn( + "arrayC", + functions.array( + functions.struct(functions.lit(13.1).alias("float")), + functions.struct(functions.lit(17.2).alias("float")))); + + // Test structProduct. + final Dataset structProductDs = + inputDs + .withColumn("sp_one", ColumnFunctions.structProduct(inputDs.col("arrayA"))) + .withColumn( + "sp_two", + ColumnFunctions.structProduct(inputDs.col("arrayA"), inputDs.col("arrayB"))) + .withColumn( + "sp_three", + ColumnFunctions.structProduct( + inputDs.col("arrayA"), inputDs.col("arrayB"), inputDs.col("arrayC"))); + + // Test structProductOuter. + final Dataset structProductOuterDs = + inputDs + .withColumn("spo_one", ColumnFunctions.structProductOuter(inputDs.col("arrayA"))) + .withColumn( + "spo_two", + ColumnFunctions.structProductOuter(inputDs.col("arrayA"), inputDs.col("arrayB"))) + .withColumn( + "spo_three", + ColumnFunctions.structProductOuter( + inputDs.col("arrayA"), inputDs.col("arrayB"), inputDs.col("arrayC"))); + + // Collect and assert structProduct results. + final List spResults = structProductDs.collectAsList(); + assertEquals(1, spResults.size()); + final Row spRow = spResults.getFirst(); + assertNotNull(spRow.getAs("sp_one")); + assertNotNull(spRow.getAs("sp_two")); + assertNotNull(spRow.getAs("sp_three")); + + // Collect and assert structProductOuter results. + final List spoResults = structProductOuterDs.collectAsList(); + assertEquals(1, spoResults.size()); + final Row spoRow = spoResults.getFirst(); + assertNotNull(spoRow.getAs("spo_one")); + assertNotNull(spoRow.getAs("spo_two")); + assertNotNull(spoRow.getAs("spo_three")); + + // Assert sizes against expected product. + final int aSize = 2; // arrayA + final int bSize = 3; // arrayB + final int cSize = 2; // arrayC + + assertEquals(aSize, ((Seq) spRow.getAs("sp_one")).size()); + assertEquals(aSize, ((Seq) spoRow.getAs("spo_one")).size()); + + assertEquals(aSize * bSize, ((Seq) spRow.getAs("sp_two")).size()); + assertEquals(aSize * bSize, ((Seq) spoRow.getAs("spo_two")).size()); + + assertEquals(aSize * bSize * cSize, ((Seq) spRow.getAs("sp_three")).size()); + assertEquals(aSize * bSize * cSize, ((Seq) spoRow.getAs("spo_three")).size()); + } + + @Test + void testArrayCrossProdWithNullsAndEmptys() { + final Dataset ds = spark.range(1).toDF(); + + // Create input array columns. + final Dataset inputDs = + ds.withColumn( + "nullArray", + functions + .lit(null) + .cast( + DataTypes.createArrayType( + DataTypes.createStructType( + Arrays.asList( + DataTypes.createStructField("str", DataTypes.StringType, true), + DataTypes.createStructField( + "int", DataTypes.IntegerType, true)))))) + .withColumn( + "emptyArray", + functions + .array() + .cast( + DataTypes.createArrayType( + DataTypes.createStructType( + Arrays.asList( + DataTypes.createStructField("str", DataTypes.StringType, true), + DataTypes.createStructField( + "int", DataTypes.IntegerType, true)))))) + .withColumn( + "nonEmptyArray", + functions.array( + functions.struct( + functions.lit("zzz").alias("str"), functions.lit(1).alias("int")), + functions.struct( + functions.lit("yyy").alias("str"), functions.lit(2).alias("int")))); + + // Test structProduct. + final Dataset structProductDs = + inputDs + .withColumn("sp_null", ColumnFunctions.structProduct(inputDs.col("nullArray"))) + .withColumn("sp_empty", ColumnFunctions.structProduct(inputDs.col("emptyArray"))) + .withColumn( + "sp_nonEmpty", + ColumnFunctions.structProduct( + inputDs.col("nonEmptyArray"), inputDs.col("emptyArray"))); + + // Test structProductOuter. + final Dataset structProductOuterDs = + inputDs + .withColumn("spo_null", ColumnFunctions.structProductOuter(inputDs.col("nullArray"))) + .withColumn("spo_empty", ColumnFunctions.structProductOuter(inputDs.col("emptyArray"))) + .withColumn( + "spo_nonEmpty", + ColumnFunctions.structProductOuter( + inputDs.col("nonEmptyArray"), inputDs.col("emptyArray"))); + + // Collect and assert structProduct results. + final List spResults = structProductDs.collectAsList(); + assertEquals(1, spResults.size()); + final Row spRow = spResults.getFirst(); + assertNotNull(spRow.getAs("sp_null")); + assertEquals(0, ((Seq) spRow.getAs("sp_null")).size()); + assertNotNull(spRow.getAs("sp_empty")); + assertEquals(0, ((Seq) spRow.getAs("sp_empty")).size()); + assertNotNull(spRow.getAs("sp_nonEmpty")); + assertEquals(0, ((Seq) spRow.getAs("sp_nonEmpty")).size()); + + // Collect and assert structProductOuter results. + final List spoResults = structProductOuterDs.collectAsList(); + assertEquals(1, spoResults.size()); + final Row spoRow = spoResults.getFirst(); + assertNotNull(spoRow.getAs("spo_null")); + assertEquals(1, ((Seq) spoRow.getAs("spo_null")).size()); + assertNotNull(spoRow.getAs("spo_empty")); + assertEquals(1, ((Seq) spoRow.getAs("spo_empty")).size()); + assertNotNull(spoRow.getAs("spo_nonEmpty")); + assertEquals(1, ((Seq) spoRow.getAs("spo_nonEmpty")).size()); + } + + /** + * Regression test for issue #2568: {@code inline(structProduct(...))} crashed with NPE when input + * data was stored in Spark's Tungsten/unsafe format. The root cause was StructProduct passing + * {@code null} as the dataType when calling {@code InternalRow.get(ordinal, dataType)} to copy + * struct fields. This works for {@code GenericInternalRow} (used by {@code + * functions.array()}/{@code functions.lit()}) but fails for {@code UnsafeRow} (used when data + * comes from {@code spark.createDataFrame()}). + */ + @Test + void testStructProductInlineWithUnsafeRowData() { + final Metadata metadata = Metadata.empty(); + + final StructType codingType = + DataTypes.createStructType( + new StructField[] { + new StructField("system", DataTypes.StringType, true, metadata), + new StructField("code", DataTypes.StringType, true, metadata), + new StructField("display", DataTypes.StringType, true, metadata) + }); + + final StructType schema = + DataTypes.createStructType( + new StructField[] { + new StructField("id", DataTypes.StringType, true, metadata), + new StructField("text", DataTypes.StringType, true, metadata), + new StructField("coding", DataTypes.createArrayType(codingType), true, metadata) + }); + + // Data created via createDataFrame stores struct array elements as UnsafeRow. + final List data = + Arrays.asList( + RowFactory.create( + "1", + "Blood pressure", + Arrays.asList( + RowFactory.create("http://loinc.org", "85354-9", "BP systolic & diastolic"), + RowFactory.create("http://snomed.info/sct", "75367002", "Blood pressure"))), + RowFactory.create( + "2", + "Heart rate", + List.of(RowFactory.create("http://loinc.org", "8867-4", "Heart rate")))); + + final Dataset ds = spark.createDataFrame(data, schema).repartition(1); + + // Build the struct product: cross product of [id], [text], and coding[]. + final Column idArray = array(struct(col("id").alias("id"))); + final Column textArray = array(struct(col("text").alias("text"))); + final Column codingArray = col("coding"); + final Column product = ColumnFunctions.structProduct(idArray, textArray, codingArray); + + // Inline the struct product and collect — this crashed with NPE before the fix. + final Dataset result = ds.select(inline(product)); + final List actual = result.collectAsList(); + + final List expected = + Arrays.asList( + RowFactory.create( + "1", "Blood pressure", "http://loinc.org", "85354-9", "BP systolic & diastolic"), + RowFactory.create( + "1", "Blood pressure", "http://snomed.info/sct", "75367002", "Blood pressure"), + RowFactory.create("2", "Heart rate", "http://loinc.org", "8867-4", "Heart rate")); + + assertEquals(expected.size(), actual.size(), "Row count mismatch"); + for (int i = 0; i < expected.size(); i++) { + assertEquals(expected.get(i), actual.get(i), "Row " + i + " mismatch"); + } + } +} diff --git a/encoders/src/test/java/au/csiro/pathling/encoders/ExpressionsTest.java b/encoders/src/test/java/au/csiro/pathling/encoders/ExpressionsCodegenTest.java similarity index 65% rename from encoders/src/test/java/au/csiro/pathling/encoders/ExpressionsTest.java rename to encoders/src/test/java/au/csiro/pathling/encoders/ExpressionsCodegenTest.java index d3a64704d4..f2c93c0b87 100644 --- a/encoders/src/test/java/au/csiro/pathling/encoders/ExpressionsTest.java +++ b/encoders/src/test/java/au/csiro/pathling/encoders/ExpressionsCodegenTest.java @@ -28,18 +28,21 @@ import static au.csiro.pathling.encoders.ValueFunctions.ifArray2; import static au.csiro.pathling.encoders.ValueFunctions.nullIfMissingField; import static au.csiro.pathling.encoders.ValueFunctions.unnest; +import static au.csiro.pathling.encoders.ValueFunctions.variantTransformTree; +import static au.csiro.pathling.encoders.ValueFunctions.variantUnwrap; import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.junit.jupiter.api.Assertions.assertNull; +import static org.junit.jupiter.api.Assertions.assertThrows; import java.util.Arrays; import java.util.List; import java.util.stream.Stream; +import org.apache.spark.sql.AnalysisException; import org.apache.spark.sql.Column; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Row; import org.apache.spark.sql.RowFactory; -import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.functions; import org.apache.spark.sql.types.DataTypes; import org.apache.spark.sql.types.Metadata; @@ -51,22 +54,13 @@ import scala.collection.Seq; import scala.jdk.javaapi.CollectionConverters; -/** Test for FHIR encoders. */ -public class ExpressionsTest { +/** Tests for FHIR encoder expressions with whole-stage codegen enabled (default). */ +public class ExpressionsCodegenTest extends ExpressionsBothModesTest { - private static SparkSession spark; - - /** Set up Spark. */ + /** Set up Spark with codegen enabled (the default). */ @BeforeAll - static void setUp() { - spark = - SparkSession.builder() - .master("local[*]") - .appName("testing") - .config("spark.driver.bindAddress", "localhost") - .config("spark.driver.host", "localhost") - .config("spark.ui.enabled", "false") - .getOrCreate(); + static void setUpCodegen() { + setUp(); } /** Tear down Spark. */ @@ -186,11 +180,11 @@ void testIfArray2() { final Row firstRow = results.getFirst(); assertEquals(0L, (Long) firstRow.getAs("id")); - // Single array should trigger else branch + // Single array should trigger else branch. assertNotNull(firstRow.getAs("test_single_array")); final Seq singleArrayResult = firstRow.getAs("test_single_array"); assertEquals(50, CollectionConverters.asJava(singleArrayResult).getFirst()); - // Array of arrays should trigger array branch + // Array of arrays should trigger array branch. assertNotNull(firstRow.getAs("test_array_of_arrays")); final Seq arrayOfArraysResult = firstRow.getAs("test_array_of_arrays"); assertEquals(200, CollectionConverters.asJava(arrayOfArraysResult).getFirst()); @@ -199,11 +193,11 @@ void testIfArray2() { final Row secondRow = results.get(1); assertEquals(1L, (Long) secondRow.getAs("id")); - // Single array should trigger else branch + // Single array should trigger else branch. assertNotNull(secondRow.getAs("test_single_array")); final Seq singleArrayResult2 = secondRow.getAs("test_single_array"); assertEquals(50, CollectionConverters.asJava(singleArrayResult2).getFirst()); - // Array of arrays should trigger array branch + // Array of arrays should trigger array branch. assertNotNull(secondRow.getAs("test_array_of_arrays")); final Seq arrayOfArraysResult2 = secondRow.getAs("test_array_of_arrays"); assertEquals(200, CollectionConverters.asJava(arrayOfArraysResult2).getFirst()); @@ -255,165 +249,6 @@ void testFlatten() { assertEquals(1L, (Long) secondRow.getAs("test_unnest_array_of_arrays_if_id")); } - @Test - void testArrayCrossProd() { - final Dataset ds = spark.range(1).toDF(); - - // Create three input array columns - final Dataset inputDs = - ds.withColumn( - "arrayA", - functions.array( - functions.struct( - functions.lit("zzz").alias("str"), functions.lit(true).alias("bool")), - functions.struct( - functions.lit("yyy").alias("str"), functions.lit(false).alias("bool")))) - .withColumn( - "arrayB", - functions.array( - functions.struct(functions.lit(13).alias("int")), - functions.struct(functions.lit(17).alias("int")), - functions.struct(functions.lit(1).alias("int")))) - .withColumn( - "arrayC", - functions.array( - functions.struct(functions.lit(13.1).alias("float")), - functions.struct(functions.lit(17.2).alias("float")))); - - // Test structProduct - final Dataset structProductDs = - inputDs - .withColumn("sp_one", ColumnFunctions.structProduct(inputDs.col("arrayA"))) - .withColumn( - "sp_two", - ColumnFunctions.structProduct(inputDs.col("arrayA"), inputDs.col("arrayB"))) - .withColumn( - "sp_three", - ColumnFunctions.structProduct( - inputDs.col("arrayA"), inputDs.col("arrayB"), inputDs.col("arrayC"))); - - // Test structProductOuter - final Dataset structProductOuterDs = - inputDs - .withColumn("spo_one", ColumnFunctions.structProductOuter(inputDs.col("arrayA"))) - .withColumn( - "spo_two", - ColumnFunctions.structProductOuter(inputDs.col("arrayA"), inputDs.col("arrayB"))) - .withColumn( - "spo_three", - ColumnFunctions.structProductOuter( - inputDs.col("arrayA"), inputDs.col("arrayB"), inputDs.col("arrayC"))); - - // Collect and assert structProduct results - final List spResults = structProductDs.collectAsList(); - assertEquals(1, spResults.size()); - final Row spRow = spResults.getFirst(); - assertNotNull(spRow.getAs("sp_one")); - assertNotNull(spRow.getAs("sp_two")); - assertNotNull(spRow.getAs("sp_three")); - - // Collect and assert structProductOuter results - final List spoResults = structProductOuterDs.collectAsList(); - assertEquals(1, spoResults.size()); - final Row spoRow = spoResults.getFirst(); - assertNotNull(spoRow.getAs("spo_one")); - assertNotNull(spoRow.getAs("spo_two")); - assertNotNull(spoRow.getAs("spo_three")); - - // Assert sizes against expected product - final int aSize = 2; // arrayA - final int bSize = 3; // arrayB - final int cSize = 2; // arrayC - - assertEquals(aSize, ((Seq) spRow.getAs("sp_one")).size()); - assertEquals(aSize, ((Seq) spoRow.getAs("spo_one")).size()); - - assertEquals(aSize * bSize, ((Seq) spRow.getAs("sp_two")).size()); - assertEquals(aSize * bSize, ((Seq) spoRow.getAs("spo_two")).size()); - - assertEquals(aSize * bSize * cSize, ((Seq) spRow.getAs("sp_three")).size()); - assertEquals(aSize * bSize * cSize, ((Seq) spoRow.getAs("spo_three")).size()); - } - - @Test - void testArrayCrossProdWithNullsAndEmptys() { - final Dataset ds = spark.range(1).toDF(); - - // Create input array columns - final Dataset inputDs = - ds.withColumn( - "nullArray", - functions - .lit(null) - .cast( - DataTypes.createArrayType( - DataTypes.createStructType( - Arrays.asList( - DataTypes.createStructField("str", DataTypes.StringType, true), - DataTypes.createStructField( - "int", DataTypes.IntegerType, true)))))) - .withColumn( - "emptyArray", - functions - .array() - .cast( - DataTypes.createArrayType( - DataTypes.createStructType( - Arrays.asList( - DataTypes.createStructField("str", DataTypes.StringType, true), - DataTypes.createStructField( - "int", DataTypes.IntegerType, true)))))) - .withColumn( - "nonEmptyArray", - functions.array( - functions.struct( - functions.lit("zzz").alias("str"), functions.lit(1).alias("int")), - functions.struct( - functions.lit("yyy").alias("str"), functions.lit(2).alias("int")))); - - // Test structProduct - final Dataset structProductDs = - inputDs - .withColumn("sp_null", ColumnFunctions.structProduct(inputDs.col("nullArray"))) - .withColumn("sp_empty", ColumnFunctions.structProduct(inputDs.col("emptyArray"))) - .withColumn( - "sp_nonEmpty", - ColumnFunctions.structProduct( - inputDs.col("nonEmptyArray"), inputDs.col("emptyArray"))); - - // Test structProductOuter - final Dataset structProductOuterDs = - inputDs - .withColumn("spo_null", ColumnFunctions.structProductOuter(inputDs.col("nullArray"))) - .withColumn("spo_empty", ColumnFunctions.structProductOuter(inputDs.col("emptyArray"))) - .withColumn( - "spo_nonEmpty", - ColumnFunctions.structProductOuter( - inputDs.col("nonEmptyArray"), inputDs.col("emptyArray"))); - - // Collect and assert structProduct results - final List spResults = structProductDs.collectAsList(); - assertEquals(1, spResults.size()); - final Row spRow = spResults.getFirst(); - assertNotNull(spRow.getAs("sp_null")); - assertEquals(0, ((Seq) spRow.getAs("sp_null")).size()); - assertNotNull(spRow.getAs("sp_empty")); - assertEquals(0, ((Seq) spRow.getAs("sp_empty")).size()); - assertNotNull(spRow.getAs("sp_nonEmpty")); - assertEquals(0, ((Seq) spRow.getAs("sp_nonEmpty")).size()); - - // Collect and assert structProductOuter results - final List spoResults = structProductOuterDs.collectAsList(); - assertEquals(1, spoResults.size()); - final Row spoRow = spoResults.getFirst(); - assertNotNull(spoRow.getAs("spo_null")); - assertEquals(1, ((Seq) spoRow.getAs("spo_null")).size()); - assertNotNull(spoRow.getAs("spo_empty")); - assertEquals(1, ((Seq) spoRow.getAs("spo_empty")).size()); - assertNotNull(spoRow.getAs("spo_nonEmpty")); - assertEquals(1, ((Seq) spoRow.getAs("spo_nonEmpty")).size()); - } - @Test void testPruneAnnotations() { final Metadata metadata = Metadata.empty(); @@ -451,14 +286,14 @@ void testPruneAnnotations() { final Dataset dataset = spark.createDataFrame(inputData, inputSchema).repartition(1); - // Prune all columns + // Prune all columns. final Dataset prunedDataset = dataset.select( Stream.of(dataset.columns()) .map(cn -> ValueFunctions.pruneAnnotations(dataset.col(cn)).alias(cn)) .toArray(Column[]::new)); - // Expected result has the _fid field removed from the value struct + // Expected result has the _fid field removed from the value struct. final StructType expectedValueStructType = DataTypes.createStructType( new StructField[] { @@ -529,13 +364,13 @@ void testPruneAnnotationsWithGroupBy() { final Dataset dataset = spark.createDataFrame(inputData, inputSchema).repartition(1); - // Group by pruned value column and aggregate + // Group by pruned value column and aggregate. final Dataset grouped = dataset .groupBy(ValueFunctions.pruneAnnotations(dataset.col("value"))) .agg(functions.count(dataset.col("gender")).alias("count")); - // Select with proper column names + // Select with proper column names. final Dataset groupedResult = grouped .select(functions.col(grouped.columns()[0]).alias("value"), functions.col("count")) @@ -576,7 +411,7 @@ void testPruneAnnotationsWithGroupBy() { private Dataset createNestedItemDataset() { final Metadata metadata = Metadata.empty(); - // Level 2 (leaf): NO item field - different type from level1 + // Level 2 (leaf): NO item field - different type from level1. final StructType level2Type = DataTypes.createStructType( new StructField[] { @@ -584,7 +419,7 @@ private Dataset createNestedItemDataset() { new StructField("text", DataTypes.StringType, true, metadata) }); - // Level 1: HAS item field (array of level2Type) - different type from level0 + // Level 1: HAS item field (array of level2Type) - different type from level0. final StructType level1Type = DataTypes.createStructType( new StructField[] { @@ -593,7 +428,7 @@ private Dataset createNestedItemDataset() { new StructField("item", DataTypes.createArrayType(level2Type), true, metadata) }); - // Level 0: HAS item field (array of level1Type) - root level type + // Level 0: HAS item field (array of level1Type) - root level type. final StructType level0Type = DataTypes.createStructType( new StructField[] { @@ -602,7 +437,7 @@ private Dataset createNestedItemDataset() { new StructField("item", DataTypes.createArrayType(level1Type), true, metadata) }); - // Create test data: 3 levels deep + // Create test data: 3 levels deep. final Row level2Item = RowFactory.create("3", "Level 2"); final Row level1Item = RowFactory.create("2", "Level 1", List.of(level2Item)); final Row level0Item = RowFactory.create("1", "Level 0", List.of(level1Item)); @@ -619,25 +454,16 @@ private Dataset createNestedItemDataset() { @Test void testTransformTreeFinitePathWithDifferentTypes() { - // Finite path: traversing via getField('item') through structurally different types - // Each level has a different schema type (level0Type != level1Type != level2Type) - // maxDepth should NOT apply because types change at each traversal step - final Dataset ds = createNestedItemDataset(); - // Traverse with getField('item') - each traversal step changes type - // Level 0 (level0Type) -> getField('item') -> Level 1 (level1Type) -> getField('item') -> Level - // 2 (level2Type) - // maxDepth=1 is very strict, but should NOT limit because types change final Dataset result = ds.withColumn( "collected", ValueFunctions.transformTree( ds.col("items"), - c -> c.getField("linkId"), // Extract linkId at each level - List.of(c -> unnest(c.getField("item"))), // Traverse via item field (type changes) - 1 // maxDepth=1 (strict limit) - )); + c -> c.getField("linkId"), + List.of(c -> unnest(c.getField("item"))), + 1)); final List results = result.collectAsList(); assertEquals(1, results.size()); @@ -646,32 +472,18 @@ void testTransformTreeFinitePathWithDifferentTypes() { final Seq collected = row.getAs("collected"); final List linkIds = CollectionConverters.asJava(collected); - // Should collect ALL 3 levels because each level has different type - // "1" (level 0), "2" (level 1), "3" (level 2) assertEquals(List.of("1", "2", "3"), linkIds); } @Test void testTransformTreeSelfReferentialInfiniteLoop() { - // Self-referential: traversing with identity function c -> c - // This would create infinite recursion (same type forever) - // maxDepth MUST apply to prevent infinite loop - final Dataset ds = createNestedItemDataset(); - // Traverse with identity function c -> c - // This would loop infinitely: items -> items -> items -> items ... - // Type never changes (always array), so maxDepth applies - // maxDepth=1 should limit to only 2 iterations (levels 0 and 1) final Dataset result = ds.withColumn( "collected", ValueFunctions.transformTree( - ds.col("items"), - c -> c.getField("linkId"), // Extract linkId at each level - List.of(c -> c), // Identity function: infinite loop! - 2 // maxDepth=1 must prevent infinite recursion - )); + ds.col("items"), c -> c.getField("linkId"), List.of(c -> c), 2)); final List results = result.collectAsList(); assertEquals(1, results.size()); @@ -680,38 +492,21 @@ void testTransformTreeSelfReferentialInfiniteLoop() { final Seq collected = row.getAs("collected"); final List linkIds = CollectionConverters.asJava(collected); - // Should collect only 3 levels (0, 1 and 2) because: - // - Level 0: items (type = array) - // - Level 1: c -> c returns items again (type = array, same type!) - // - Level 2: c -> c returns items again (type = array, same type!) - // - Level 3: would be items again but maxDepth=3 prevents it - // All extracted linkIds should be "1" (same item repeated) assertEquals(List.of("1", "1", "1"), linkIds); } @Test void testTransformTreeMultipleTraversalPaths() { - // Multiple traversal paths: combines finite path (type-changing) and self-referential (infinite - // loop) - // This demonstrates that different paths can have different depth behaviors simultaneously - final Dataset ds = createNestedItemDataset(); - // Use TWO traversal paths: - // Path 1: c -> unnest(c.getField("item")) - finite path with type changes - // Path 2: c -> c - self-referential with same type (infinite loop) final Dataset result = ds.withColumn( "collected", ValueFunctions.transformTree( ds.col("items"), - c -> c.getField("linkId"), // Extract linkId at each level - List.of( - c -> unnest(c.getField("item")), // Path 1: finite, type changes - c -> c // Path 2: infinite loop, type stays same - ), - 1 // maxDepth=1 - )); + c -> c.getField("linkId"), + List.of(c -> unnest(c.getField("item")), c -> c), + 1)); final List results = result.collectAsList(); assertEquals(1, results.size()); @@ -720,27 +515,13 @@ void testTransformTreeMultipleTraversalPaths() { final Seq collected = row.getAs("collected"); final List linkIds = CollectionConverters.asJava(collected); - // Should collect: - // From Path 1 (finite, type-changing): - // - "1" (level 0), "2" (level 1), - // From Path 2 (self-referential, infinite loop, maxDepth=1): - // - "1" (level 0), "2" (level 1), - // Total collected: "1", "2", "3", "3", "2", "3", "1", "2", "3" - assertEquals(List.of("1", "2", "3", "3", "2", "3", "1", "2", "3"), linkIds); } @Test void testNullIfMissingField() { - // Comprehensive test for nullIfMissingField covering all scenarios: - // 1. Existing top-level fields returning actual values - // 2. Existing nested struct fields returning actual values - // 3. Missing struct fields returning null - // 4. Struct fields with null values vs non-existent fields - final Metadata metadata = Metadata.empty(); - // Create a struct type for person with name and age fields (no email or salary fields) final StructType personType = DataTypes.createStructType( new StructField[] { @@ -758,60 +539,316 @@ void testNullIfMissingField() { final List data = List.of( - RowFactory.create(1, 100, RowFactory.create(null, 25)), // person.name is null - RowFactory.create(2, 200, RowFactory.create("Bob", null)), // person.age is null + RowFactory.create(1, 100, RowFactory.create(null, 25)), + RowFactory.create(2, 200, RowFactory.create("Bob", null)), RowFactory.create(3, 300, RowFactory.create("Charlie", 30))); final Dataset ds = spark.createDataFrame(data, schema); - // Apply multiple nullIfMissingField expressions to test all scenarios final Dataset result = - ds - // Test 1: Existing top-level field - .withColumn("test_top_level", nullIfMissingField(ds.col("value"))) - // Test 2: Existing nested field using dot notation + ds.withColumn("test_top_level", nullIfMissingField(ds.col("value"))) .withColumn("test_nested_exists", nullIfMissingField(ds.col("person.name"))) - // Test 3: Existing nested field using getField .withColumn("test_struct_field", nullIfMissingField(ds.col("person").getField("age"))) - // Test 4: Missing struct field (address doesn't exist) .withColumn( "test_missing_address", nullIfMissingField(ds.col("person").getField("address"))) - // Test 5: Missing struct field (email doesn't exist) .withColumn( "test_missing_email", nullIfMissingField(ds.col("person").getField("email"))) - // Test 6: Missing struct field (salary doesn't exist) .withColumn( "test_missing_salary", nullIfMissingField(ds.col("person").getField("salary"))); final List results = result.collectAsList(); assertEquals(3, results.size()); - // Row 1: person.name is null, person.age is 25 + // Row 1: person.name is null, person.age is 25. assertEquals(100, (Integer) results.getFirst().getAs("test_top_level")); - assertNull(results.getFirst().getAs("test_nested_exists")); // null value from data + assertNull(results.getFirst().getAs("test_nested_exists")); assertEquals(25, (Integer) results.getFirst().getAs("test_struct_field")); - assertNull(results.getFirst().getAs("test_missing_address")); // field doesn't exist + assertNull(results.getFirst().getAs("test_missing_address")); assertNull(results.get(0).getAs("test_missing_email")); assertNull(results.get(0).getAs("test_missing_salary")); - // Row 2: person.name is "Bob", person.age is null + // Row 2: person.name is "Bob", person.age is null. assertEquals(200, (Integer) results.get(1).getAs("test_top_level")); assertEquals("Bob", results.get(1).getAs("test_nested_exists")); - assertNull(results.get(1).getAs("test_struct_field")); // null value from data - assertNull(results.get(1).getAs("test_missing_address")); // field doesn't exist + assertNull(results.get(1).getAs("test_struct_field")); + assertNull(results.get(1).getAs("test_missing_address")); assertNull(results.get(1).getAs("test_missing_email")); assertNull(results.get(1).getAs("test_missing_salary")); - // Row 3: person.name is "Charlie", person.age is 30 + // Row 3: person.name is "Charlie", person.age is 30. assertEquals(300, (Integer) results.get(2).getAs("test_top_level")); assertEquals("Charlie", results.get(2).getAs("test_nested_exists")); assertEquals(30, (Integer) results.get(2).getAs("test_struct_field")); - assertNull(results.get(2).getAs("test_missing_address")); // field doesn't exist + assertNull(results.get(2).getAs("test_missing_address")); assertNull(results.get(2).getAs("test_missing_email")); assertNull(results.get(2).getAs("test_missing_salary")); + } + + /** + * Creates a 2-level nested structure with schema divergence between levels. Level 0 has fields + * {linkId, text, extra, item} while level 1 has only {linkId, text}. This is the key scenario + * that demonstrates variantTransformTree's ability to handle schema differences across levels. + * + * @return Dataset with divergent schemas at each nesting level + */ + private Dataset createDivergentSchemaDataset() { + final Metadata metadata = Metadata.empty(); + + // Level 1 (leaf): only linkId and text, no extra field, no item field. + final StructType level1Type = + DataTypes.createStructType( + new StructField[] { + new StructField("linkId", DataTypes.StringType, true, metadata), + new StructField("text", DataTypes.StringType, true, metadata) + }); + + // Level 0: has linkId, text, extra, and item array (richer schema than level 1). + final StructType level0Type = + DataTypes.createStructType( + new StructField[] { + new StructField("linkId", DataTypes.StringType, true, metadata), + new StructField("text", DataTypes.StringType, true, metadata), + new StructField("extra", DataTypes.StringType, true, metadata), + new StructField("item", DataTypes.createArrayType(level1Type), true, metadata) + }); + + final Row level1Item = RowFactory.create("child", "Child text"); + final Row level0Item = + RowFactory.create("root", "Root text", "extra-value", List.of(level1Item)); + + final StructType rootSchema = + DataTypes.createStructType( + new StructField[] { + new StructField("id", DataTypes.IntegerType, true, metadata), + new StructField("items", DataTypes.createArrayType(level0Type), true, metadata) + }); + + return spark.createDataFrame(List.of(RowFactory.create(1, List.of(level0Item))), rootSchema); + } + + @Test + void testVariantTransformTreeFinitePathWithDifferentTypes() { + // Variant version of the finite-path test. Uses variantTransformTree to extract scalar values + // across levels with different schemas. The result should match the non-variant version. + + final Dataset ds = createNestedItemDataset(); + + final Dataset result = + ds.withColumn( + "collected", + variantTransformTree( + ds.col("items"), + c -> functions.array(c.getField("linkId")), + List.of(c -> unnest(c.getField("item"))), + 1)); + + // Flatten the result because each extracted element is Array[String] from the extractor. + final Dataset flattened = + result.withColumn("collected", functions.flatten(result.col("collected"))); + + final List results = flattened.collectAsList(); + assertEquals(1, results.size()); + + final Row row = results.getFirst(); + final Seq collected = row.getAs("collected"); + final List linkIds = CollectionConverters.asJava(collected); + + // Should collect all 3 levels: "1" (level 0), "2" (level 1), "3" (level 2). + assertEquals(List.of("1", "2", "3"), linkIds); + } + + @Test + void testVariantTransformTreeSelfReferentialWithDepthLimit() { + // Self-referential traversal (identity function) limited by maxDepth. The same item is + // extracted repeatedly until the depth limit is reached. + + final Dataset ds = createNestedItemDataset(); + + final Dataset result = + ds.withColumn( + "collected", + variantTransformTree( + ds.col("items"), c -> functions.array(c.getField("linkId")), List.of(c -> c), 2)); + + // Flatten the result because each extracted element is Array[String] from the extractor. + final Dataset flattened = + result.withColumn("collected", functions.flatten(result.col("collected"))); + + final List results = flattened.collectAsList(); + assertEquals(1, results.size()); + + final Row row = results.getFirst(); + final Seq collected = row.getAs("collected"); + final List linkIds = CollectionConverters.asJava(collected); + + // Self-referential: same item repeated at each depth level. + assertEquals(List.of("1", "1", "1"), linkIds); + } + + @Test + void testVariantTransformTreeSchemaDivergence() { + // Key test: full-struct extraction across levels with different schemas. The level-0 schema + // has {linkId, text, extra, item} while level-1 only has {linkId, text}. The variant + // mechanism should unify these, filling missing fields with null at level 1. + + final Dataset ds = createDivergentSchemaDataset(); + + final Dataset result = + ds.withColumn( + "collected", + variantTransformTree( + ds.col("items"), c -> c, List.of(c -> unnest(c.getField("item"))), 1)); + + final List results = result.collectAsList(); + assertEquals(1, results.size()); + + final Row row = results.getFirst(); + final Seq collected = row.getAs("collected"); + final List items = CollectionConverters.asJava(collected); + + // Should have 2 items: the level-0 struct and the level-1 struct. + assertEquals(2, items.size()); + + // Level-0 item: all fields present. + final Row level0 = (Row) items.get(0); + assertEquals("root", level0.getAs("linkId")); + assertEquals("Root text", level0.getAs("text")); + assertEquals("extra-value", level0.getAs("extra")); + assertNotNull(level0.getAs("item")); + + // Level-1 item: missing fields (extra, item) should be null. + final Row level1 = (Row) items.get(1); + assertEquals("child", level1.getAs("linkId")); + assertEquals("Child text", level1.getAs("text")); + assertNull(level1.getAs("extra")); + assertNull(level1.getAs("item")); + } + + @Test + void testVariantTransformTreeErrorOnDepthExhaustion() { + // When errorOnDepthExhaustion=true, exceeding maxDepth on a self-referential traversal + // should throw an exception rather than silently returning an empty array. + + final Dataset ds = createNestedItemDataset(); + + // The AnalysisException is thrown eagerly during column resolution, so the entire + // withColumn + collect must be wrapped in the assertion. + assertThrows( + AnalysisException.class, + () -> + ds.withColumn( + "collected", + variantTransformTree( + ds.col("items"), + c -> functions.array(c.getField("linkId")), + List.of(c -> c), + 1, + true)) + .collectAsList()); + } + + @Test + void testVariantUnwrapDirect() { + // Direct round-trip test: create a struct array, convert each element to Variant, then unwrap + // using the original column as schema reference. The data should survive the round-trip. + + final Metadata metadata = Metadata.empty(); + final StructType itemType = + DataTypes.createStructType( + new StructField[] { + new StructField("name", DataTypes.StringType, true, metadata), + new StructField("value", DataTypes.IntegerType, true, metadata) + }); + + final StructType rootSchema = + DataTypes.createStructType( + new StructField[] { + new StructField("id", DataTypes.IntegerType, true, metadata), + new StructField("items", DataTypes.createArrayType(itemType), true, metadata) + }); + + final List data = + List.of( + RowFactory.create( + 1, List.of(RowFactory.create("Alice", 10), RowFactory.create("Bob", 20)))); + + final Dataset ds = spark.createDataFrame(data, rootSchema); + + // Convert array elements to Variant and back. + final Column variantArray = functions.transform(ds.col("items"), functions::to_variant_object); + final Dataset result = + ds.withColumn("unwrapped", variantUnwrap(variantArray, ds.col("items"))); + + final List results = result.collectAsList(); + assertEquals(1, results.size()); + + final Row row = results.getFirst(); + final Seq unwrapped = row.getAs("unwrapped"); + final List unwrappedItems = CollectionConverters.asJava(unwrapped); + + assertEquals(2, unwrappedItems.size()); + + final Row first = (Row) unwrappedItems.get(0); + assertEquals("Alice", first.getAs("name")); + assertEquals(10, (int) first.getAs("value")); + + final Row second = (Row) unwrappedItems.get(1); + assertEquals("Bob", second.getAs("name")); + assertEquals(20, (int) second.getAs("value")); + } + + @Test + void testVariantUnwrapFailOnErrorFalse() { + // When failOnError=false, missing fields should produce null rather than throwing an + // exception. The source data has a subset schema; the schema reference has additional fields. + + final Metadata metadata = Metadata.empty(); + + // Source schema: only has "name". + final StructType sourceType = + DataTypes.createStructType( + new StructField[] {new StructField("name", DataTypes.StringType, true, metadata)}); + + // Target schema reference: has "name" and "value". + final StructType targetType = + DataTypes.createStructType( + new StructField[] { + new StructField("name", DataTypes.StringType, true, metadata), + new StructField("value", DataTypes.IntegerType, true, metadata) + }); + + final StructType rootSchema = + DataTypes.createStructType( + new StructField[] { + new StructField("id", DataTypes.IntegerType, true, metadata), + new StructField("source", DataTypes.createArrayType(sourceType), true, metadata), + new StructField("target_ref", DataTypes.createArrayType(targetType), true, metadata) + }); + + final List data = + List.of( + RowFactory.create( + 1, List.of(RowFactory.create("Alice")), List.of(RowFactory.create("Ref", 99)))); + + final Dataset ds = spark.createDataFrame(data, rootSchema); + + // Convert source elements to Variant and unwrap with the wider target schema. + final Column variantArray = functions.transform(ds.col("source"), functions::to_variant_object); + final Dataset result = + ds.withColumn("unwrapped", variantUnwrap(variantArray, ds.col("target_ref"), false)); + + final List results = result.collectAsList(); + assertEquals(1, results.size()); + + final Row row = results.getFirst(); + final Seq unwrapped = row.getAs("unwrapped"); + final List unwrappedItems = CollectionConverters.asJava(unwrapped); + + assertEquals(1, unwrappedItems.size()); - // Key distinction: Fields that exist but have null values (row 1 name, row 2 age) - // preserve the null from the data, while missing fields (address, email, salary) - // return null because they don't exist in the struct schema + final Row item = (Row) unwrappedItems.getFirst(); + assertEquals("Alice", item.getAs("name")); + // The "value" field is missing from the source, so it should be null. + assertNull(item.getAs("value")); } } diff --git a/encoders/src/test/java/au/csiro/pathling/encoders/ExpressionsInterpretedTest.java b/encoders/src/test/java/au/csiro/pathling/encoders/ExpressionsInterpretedTest.java new file mode 100644 index 0000000000..a4d265d094 --- /dev/null +++ b/encoders/src/test/java/au/csiro/pathling/encoders/ExpressionsInterpretedTest.java @@ -0,0 +1,46 @@ +/* + * This is a modified version of the Bunsen library, originally published at + * https://github.com/cerner/bunsen. + * + * Bunsen is copyright 2017 Cerner Innovation, Inc., and is licensed under + * the Apache License, version 2.0 (http://www.apache.org/licenses/LICENSE-2.0). + * + * These modifications are copyright 2018-2026 Commonwealth Scientific + * and Industrial Research Organisation (CSIRO) ABN 41 687 119 230. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + */ + +package au.csiro.pathling.encoders; + +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; + +/** Tests for FHIR encoder expressions with whole-stage codegen disabled (interpreted eval path). */ +public class ExpressionsInterpretedTest extends ExpressionsBothModesTest { + + /** Set up Spark with whole-stage codegen disabled. */ + @BeforeAll + static void setUpInterpreted() { + setUp(); + spark.conf().set("spark.sql.codegen.wholeStage", "false"); + } + + /** Restore codegen setting and stop Spark. */ + @AfterAll + static void tearDown() { + spark.conf().set("spark.sql.codegen.wholeStage", "true"); + spark.stop(); + } +} diff --git a/encoders/src/test/java/au/csiro/pathling/encoders/UnresolvedExpressionsTest.java b/encoders/src/test/java/au/csiro/pathling/encoders/UnresolvedExpressionsTest.java index 139cf1c878..e3cf321297 100644 --- a/encoders/src/test/java/au/csiro/pathling/encoders/UnresolvedExpressionsTest.java +++ b/encoders/src/test/java/au/csiro/pathling/encoders/UnresolvedExpressionsTest.java @@ -26,14 +26,23 @@ import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertFalse; +import static org.junit.jupiter.api.Assertions.assertInstanceOf; import static org.junit.jupiter.api.Assertions.assertThrows; +import static org.junit.jupiter.api.Assertions.assertTrue; import jakarta.annotation.Nonnull; import java.util.Arrays; +import org.apache.spark.sql.catalyst.analysis.UnresolvedAttribute; import org.apache.spark.sql.catalyst.analysis.UnresolvedException; +import org.apache.spark.sql.catalyst.expressions.ArrayTransform; import org.apache.spark.sql.catalyst.expressions.Expression; +import org.apache.spark.sql.catalyst.expressions.LambdaFunction; import org.apache.spark.sql.catalyst.expressions.Literal; +import org.apache.spark.sql.catalyst.expressions.variant.VariantGet; import org.apache.spark.sql.types.DataTypes; +import org.apache.spark.sql.types.StructField; +import org.apache.spark.sql.types.StructType; +import org.apache.spark.sql.types.VariantType$; import org.apache.spark.unsafe.types.UTF8String; import org.junit.jupiter.api.Test; import scala.Function1; @@ -78,9 +87,159 @@ void testUnresolvedTransformTree() { new UnresolvedTransformTree(stringLiteral("data1"), extractor, toIndexedSeq(traversor), 2); assertUnresolvedExpression(unresolvedTransformTree); assertEquals("data1", unresolvedTransformTree.toString()); + assertFalse(unresolvedTransformTree.errorOnDepthExhaustion()); assertEquals( new UnresolvedTransformTree(stringLiteral("data2"), extractor, toIndexedSeq(traversor), 2), unresolvedTransformTree.withNewChildrenInternal(toIndexedSeq(stringLiteral("data2")))); } + + @Test + void testUnresolvedTransformTreeWithErrorOnDepthExhaustion() { + + final Function1 extractor = x -> x; + final Function1 traversor = x -> x; + + // Construct with errorOnDepthExhaustion = true. + final UnresolvedTransformTree tree = + new UnresolvedTransformTree( + stringLiteral("data1"), + extractor, + toIndexedSeq(traversor), + scala.Option.empty(), + 2, + true); + assertUnresolvedExpression(tree); + assertTrue(tree.errorOnDepthExhaustion()); + + // The flag should be preserved through withNewChildrenInternal. + final Expression rebuilt = tree.withNewChildrenInternal(toIndexedSeq(stringLiteral("data2"))); + assertTrue(((UnresolvedTransformTree) rebuilt).errorOnDepthExhaustion()); + } + + private static Expression unresolvedAttribute(@Nonnull final String name) { + return UnresolvedAttribute.quoted(name); + } + + private static Expression variantArrayLiteral() { + return Literal.create(null, DataTypes.createArrayType(VariantType$.MODULE$)); + } + + private static Expression structArrayLiteral() { + return Literal.create( + null, + DataTypes.createArrayType( + new StructType( + new StructField[] { + DataTypes.createStructField("id", DataTypes.StringType, true) + }))); + } + + private static Expression structLiteral() { + return Literal.create( + null, + new StructType( + new StructField[] {DataTypes.createStructField("name", DataTypes.StringType, true)})); + } + + /** Extracts the {@link VariantGet} expression from an {@link ArrayTransform} result. */ + @Nonnull + private static VariantGet extractVariantGet(@Nonnull final Expression resolved) { + final ArrayTransform transform = assertInstanceOf(ArrayTransform.class, resolved); + final LambdaFunction lambda = assertInstanceOf(LambdaFunction.class, transform.function()); + return assertInstanceOf(VariantGet.class, lambda.function()); + } + + @Test + void testUnresolvedVariantUnwrap() { + final UnresolvedVariantUnwrap unwrap = + new UnresolvedVariantUnwrap( + stringLiteral("inner"), + stringLiteral("schema"), + UnresolvedVariantUnwrap.apply$default$3()); + assertUnresolvedExpression(unwrap); + assertEquals("VariantUnwrap(inner)", unwrap.toString()); + + // withNewChildrenInternal produces a correct copy. + final Expression rebuilt = + unwrap.withNewChildrenInternal( + toIndexedSeq(stringLiteral("newInner"), stringLiteral("newSchema"))); + final UnresolvedVariantUnwrap rebuiltUnwrap = + assertInstanceOf(UnresolvedVariantUnwrap.class, rebuilt); + assertEquals("VariantUnwrap(newInner)", rebuiltUnwrap.toString()); + } + + @Test + void testUnresolvedVariantUnwrapFailOnErrorPreserved() { + // Construct with failOnError = false. + final UnresolvedVariantUnwrap unwrap = + new UnresolvedVariantUnwrap(stringLiteral("inner"), stringLiteral("schema"), false); + assertFalse(unwrap.failOnError()); + + // The flag should survive withNewChildrenInternal. + final Expression rebuilt = + unwrap.withNewChildrenInternal(toIndexedSeq(stringLiteral("a"), stringLiteral("b"))); + assertFalse(((UnresolvedVariantUnwrap) rebuilt).failOnError()); + } + + @Test + void testUnresolvedVariantUnwrapMapChildrenUnresolved() { + // When children remain unresolved, mapChildren returns an unresolved copy. + final UnresolvedVariantUnwrap unwrap = + new UnresolvedVariantUnwrap( + unresolvedAttribute("col1"), + unresolvedAttribute("col2"), + UnresolvedVariantUnwrap.apply$default$3()); + + final Expression result = unwrap.mapChildren(x -> x); + assertInstanceOf(UnresolvedVariantUnwrap.class, result); + assertFalse(result.resolved()); + } + + @Test + void testUnresolvedVariantUnwrapMapChildrenResolvedWithArrayType() { + // When both children are resolved and schemaRef is an ArrayType, the element type is + // extracted and used as the target type for VariantGet. + final UnresolvedVariantUnwrap unwrap = + new UnresolvedVariantUnwrap( + variantArrayLiteral(), structArrayLiteral(), UnresolvedVariantUnwrap.apply$default$3()); + + final Expression resolved = unwrap.mapChildren(x -> x); + final VariantGet variantGet = extractVariantGet(resolved); + + // The target type should be the element type of the array, not the array itself. + final StructType expectedElementType = + new StructType( + new StructField[] {DataTypes.createStructField("id", DataTypes.StringType, true)}); + assertEquals(expectedElementType, variantGet.targetType()); + assertTrue(variantGet.failOnError()); + } + + @Test + void testUnresolvedVariantUnwrapMapChildrenResolvedWithNonArrayType() { + // When schemaRef is a non-ArrayType (e.g. StructType), it is used directly as the target + // type for VariantGet. + final UnresolvedVariantUnwrap unwrap = + new UnresolvedVariantUnwrap( + variantArrayLiteral(), structLiteral(), UnresolvedVariantUnwrap.apply$default$3()); + + final Expression resolved = unwrap.mapChildren(x -> x); + final VariantGet variantGet = extractVariantGet(resolved); + + final StructType expectedType = + new StructType( + new StructField[] {DataTypes.createStructField("name", DataTypes.StringType, true)}); + assertEquals(expectedType, variantGet.targetType()); + } + + @Test + void testUnresolvedVariantUnwrapMapChildrenFailOnErrorFalse() { + // failOnError=false should propagate into the generated VariantGet. + final UnresolvedVariantUnwrap unwrap = + new UnresolvedVariantUnwrap(variantArrayLiteral(), structArrayLiteral(), false); + + final Expression resolved = unwrap.mapChildren(x -> x); + final VariantGet variantGet = extractVariantGet(resolved); + assertFalse(variantGet.failOnError()); + } } diff --git a/encoders/src/test/java/au/csiro/pathling/encoders/VariantHelpersTest.java b/encoders/src/test/java/au/csiro/pathling/encoders/VariantHelpersTest.java new file mode 100644 index 0000000000..5c3376f124 --- /dev/null +++ b/encoders/src/test/java/au/csiro/pathling/encoders/VariantHelpersTest.java @@ -0,0 +1,185 @@ +/* + * Copyright © 2018-2026 Commonwealth Scientific and Industrial Research + * Organisation (CSIRO) ABN 41 687 119 230. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package au.csiro.pathling.encoders; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertNull; + +import java.util.List; +import java.util.function.UnaryOperator; +import org.apache.spark.sql.Column; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.RowFactory; +import org.apache.spark.sql.SparkSession; +import org.apache.spark.sql.functions; +import org.apache.spark.sql.types.DataTypes; +import org.apache.spark.sql.types.StructField; +import org.apache.spark.sql.types.StructType; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; + +/** + * Unit tests for Variant wrapping and unwrapping helpers in {@link ValueFunctions}. + * + *

Tests the round-trip conversion of struct arrays through Spark's Variant type, covering normal + * arrays, empty arrays, and null elements. + */ +class VariantHelpersTest { + + private static SparkSession spark; + + /** Schema for a simple struct with name and value fields. */ + private static final StructType ITEM_SCHEMA = + new StructType( + new StructField[] { + DataTypes.createStructField("name", DataTypes.StringType, true), + DataTypes.createStructField("value", DataTypes.IntegerType, true) + }); + + /** Schema for an outer struct containing an array of items. */ + private static final StructType ROW_SCHEMA = + new StructType( + new StructField[] { + DataTypes.createStructField("items", DataTypes.createArrayType(ITEM_SCHEMA, true), true) + }); + + @BeforeAll + static void setUp() { + spark = + SparkSession.builder() + .master("local[*]") + .appName("testing") + .config("spark.driver.bindAddress", "localhost") + .config("spark.driver.host", "localhost") + .config("spark.ui.enabled", "false") + .getOrCreate(); + } + + private Dataset createDataset(final Row... rows) { + return spark.createDataFrame(List.of(rows), ROW_SCHEMA); + } + + @Test + void wrapWithVariantConvertsStructArrayToVariantArray() { + // Create a dataset with a struct array column. + final Dataset ds = + createDataset(RowFactory.create((Object) new Row[] {RowFactory.create("a", 1)})); + + // Wrap the identity transform with Variant conversion. + final UnaryOperator wrapped = ValueFunctions.wrapWithVariant(c -> c); + final Dataset result = ds.select(wrapped.apply(functions.col("items")).alias("result")); + + // The result should be a non-null array with one element. + final Row row = result.head(); + final List resultItems = row.getList(0); + assertEquals(1, resultItems.size()); + assertNotNull(resultItems.get(0)); + } + + @Test + void unwrapVariantArrayRoundTripsStructData() { + // Create a dataset with a struct array, convert to Variant, and convert back. + final Dataset ds = + createDataset( + RowFactory.create( + (Object) new Row[] {RowFactory.create("a", 1), RowFactory.create("b", 2)})); + + // Convert to Variant array and back. + final Column items = functions.col("items"); + final Column variantArray = functions.transform(items, functions::to_variant_object); + final Column unwrapped = ValueFunctions.unwrapVariantArray(variantArray, ITEM_SCHEMA); + final Dataset result = ds.select(unwrapped.alias("result")); + + // Verify the round-trip preserves data. + final Row row = result.head(); + final List resultItems = row.getList(0); + assertEquals(2, resultItems.size()); + assertEquals("a", resultItems.get(0).getString(0)); + assertEquals(1, resultItems.get(0).getInt(1)); + assertEquals("b", resultItems.get(1).getString(0)); + assertEquals(2, resultItems.get(1).getInt(1)); + } + + @Test + void unwrapVariantArrayHandlesEmptyArray() { + // Create a dataset with an empty struct array. + final Dataset ds = createDataset(RowFactory.create((Object) new Row[] {})); + + // Convert to Variant array and back. + final Column items = functions.col("items"); + final Column variantArray = functions.transform(items, functions::to_variant_object); + final Column unwrapped = ValueFunctions.unwrapVariantArray(variantArray, ITEM_SCHEMA); + final Dataset result = ds.select(unwrapped.alias("result")); + + // Verify the round-trip returns an empty array. + final Row row = result.head(); + final List resultItems = row.getList(0); + assertEquals(0, resultItems.size()); + } + + @Test + void unwrapVariantArrayHandlesNullArray() { + // Create a dataset with a null items column. + final Dataset ds = createDataset(RowFactory.create((Object) null)); + + // Convert to Variant array and back. + final Column items = functions.col("items"); + final Column variantArray = functions.transform(items, functions::to_variant_object); + final Column unwrapped = ValueFunctions.unwrapVariantArray(variantArray, ITEM_SCHEMA); + final Dataset result = ds.select(unwrapped.alias("result")); + + // Verify the round-trip returns null. + final Row row = result.head(); + assertNull(row.get(0)); + } + + @Test + void unwrapVariantArrayFillsMissingFieldsWithNull() { + // Create a dataset with structs that have only the 'name' field, simulating schema divergence + // where deeper nesting levels lack certain fields. + final StructType partialSchema = + new StructType( + new StructField[] {DataTypes.createStructField("name", DataTypes.StringType, true)}); + final StructType partialRowSchema = + new StructType( + new StructField[] { + DataTypes.createStructField( + "items", DataTypes.createArrayType(partialSchema, true), true) + }); + + final Dataset ds = + spark.createDataFrame( + List.of(RowFactory.create((Object) new Row[] {RowFactory.create("partial")})), + partialRowSchema); + + // Convert to Variant array and unwrap with the full target schema. + final Column items = functions.col("items"); + final Column variantArray = functions.transform(items, functions::to_variant_object); + final Column unwrapped = ValueFunctions.unwrapVariantArray(variantArray, ITEM_SCHEMA); + final Dataset result = ds.select(unwrapped.alias("result")); + + // Verify the missing 'value' field is filled with null. + final Row row = result.head(); + final List resultItems = row.getList(0); + assertEquals(1, resultItems.size()); + assertEquals("partial", resultItems.get(0).getString(0)); + assertNull(resultItems.get(0).get(1)); + } +} diff --git a/fhirpath/src/main/java/au/csiro/pathling/config/FhirpathConfiguration.java b/fhirpath/src/main/java/au/csiro/pathling/config/FhirpathConfiguration.java new file mode 100644 index 0000000000..9ec8e02abd --- /dev/null +++ b/fhirpath/src/main/java/au/csiro/pathling/config/FhirpathConfiguration.java @@ -0,0 +1,45 @@ +/* + * Copyright © 2018-2026 Commonwealth Scientific and Industrial Research + * Organisation (CSIRO) ABN 41 687 119 230. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package au.csiro.pathling.config; + +import jakarta.annotation.Nonnull; +import jakarta.validation.constraints.Min; +import lombok.Builder; +import lombok.Data; + +/** + * Configuration parameters for FHIRPath expression evaluation. + * + * @author Piotr Szul + */ +@Data +@Builder +public class FhirpathConfiguration { + + /** The default configuration instance. */ + @Nonnull + public static final FhirpathConfiguration DEFAULT = FhirpathConfiguration.builder().build(); + + /** + * Maximum depth for same-type recursive traversal in {@code repeat()} and {@code repeatAll()}. + * Cross-type traversals do not consume depth budget. + */ + @Min(1) + @Builder.Default + private int maxUnboundTraversalDepth = 10; +} diff --git a/fhirpath/src/main/java/au/csiro/pathling/config/QueryConfiguration.java b/fhirpath/src/main/java/au/csiro/pathling/config/QueryConfiguration.java index 9bcdcfd470..b443111eab 100644 --- a/fhirpath/src/main/java/au/csiro/pathling/config/QueryConfiguration.java +++ b/fhirpath/src/main/java/au/csiro/pathling/config/QueryConfiguration.java @@ -47,7 +47,7 @@ public class QueryConfiguration { * Maximum depth for self-referencing structure traversals in repeat operations. Controls how * deeply nested hierarchical data can be flattened during projection. */ - @Min(0) + @Min(1) @Builder.Default private int maxUnboundTraversalDepth = 10; } diff --git a/fhirpath/src/main/java/au/csiro/pathling/fhirpath/EvaluationContext.java b/fhirpath/src/main/java/au/csiro/pathling/fhirpath/EvaluationContext.java index 01e0c31993..1fa1f282cc 100644 --- a/fhirpath/src/main/java/au/csiro/pathling/fhirpath/EvaluationContext.java +++ b/fhirpath/src/main/java/au/csiro/pathling/fhirpath/EvaluationContext.java @@ -17,6 +17,7 @@ package au.csiro.pathling.fhirpath; +import au.csiro.pathling.config.FhirpathConfiguration; import au.csiro.pathling.fhirpath.collection.Collection; import au.csiro.pathling.fhirpath.collection.ResourceCollection; import au.csiro.pathling.fhirpath.function.NamedFunction; @@ -78,4 +79,14 @@ public interface EvaluationContext { */ @Nonnull Collection getInputContext(); + + /** + * Returns the configuration for FHIRPath evaluation. + * + * @return The FHIRPath configuration + */ + @Nonnull + default FhirpathConfiguration getConfiguration() { + return FhirpathConfiguration.DEFAULT; + } } diff --git a/fhirpath/src/main/java/au/csiro/pathling/fhirpath/collection/Collection.java b/fhirpath/src/main/java/au/csiro/pathling/fhirpath/collection/Collection.java index 7ccad2ce7f..ca19f34190 100644 --- a/fhirpath/src/main/java/au/csiro/pathling/fhirpath/collection/Collection.java +++ b/fhirpath/src/main/java/au/csiro/pathling/fhirpath/collection/Collection.java @@ -20,8 +20,10 @@ import static au.csiro.pathling.fhirpath.TypeSpecifier.FHIR_NAMESPACE; import static au.csiro.pathling.fhirpath.TypeSpecifier.SYSTEM_NAMESPACE; import static au.csiro.pathling.utilities.Preconditions.check; +import static org.apache.spark.sql.functions.array_distinct; import au.csiro.pathling.encoders.ExtensionSupport; +import au.csiro.pathling.encoders.ValueFunctions; import au.csiro.pathling.errors.InvalidUserInputError; import au.csiro.pathling.fhirpath.FhirPathType; import au.csiro.pathling.fhirpath.TerminologyConcepts; @@ -29,16 +31,20 @@ import au.csiro.pathling.fhirpath.collection.mixed.MixedCollection; import au.csiro.pathling.fhirpath.column.ColumnRepresentation; import au.csiro.pathling.fhirpath.column.DefaultRepresentation; +import au.csiro.pathling.fhirpath.comparison.ColumnEquality; import au.csiro.pathling.fhirpath.comparison.Equatable; import au.csiro.pathling.fhirpath.definition.ChildDefinition; import au.csiro.pathling.fhirpath.definition.ChoiceDefinition; import au.csiro.pathling.fhirpath.definition.ElementDefinition; import au.csiro.pathling.fhirpath.definition.NodeDefinition; +import au.csiro.pathling.fhirpath.function.CollectionTransform; import au.csiro.pathling.fhirpath.function.ColumnTransform; +import au.csiro.pathling.sql.SqlFunctions; import com.google.common.collect.ImmutableMap; import jakarta.annotation.Nonnull; import java.lang.reflect.Constructor; import java.lang.reflect.InvocationTargetException; +import java.util.List; import java.util.Map; import java.util.Optional; import java.util.function.Function; @@ -49,6 +55,7 @@ import lombok.extern.slf4j.Slf4j; import org.apache.spark.sql.Column; import org.apache.spark.sql.functions; +import org.apache.spark.sql.types.StructType; import org.hl7.fhir.instance.model.api.IBase; import org.hl7.fhir.r4.model.Enumerations.FHIRDefinedType; @@ -62,6 +69,8 @@ @Slf4j public class Collection implements Equatable { + private static final String UNKNOWN_TYPE = "unknown"; + // Additional mappings for collection classes that don't directly map to FhirPathType @Nonnull private static final Map> @@ -402,6 +411,207 @@ public Collection filter(@Nonnull final ColumnTransform lambda) { return map(ctx -> ctx.filter(col -> lambda.apply(ctx.copyOf(col)).getValue())); } + /** + * Projects each element of this collection using the specified transform, flattening the results. + * + *

The transform is evaluated for each item in the collection. If evaluation produces multiple + * items, all are added to the output. If evaluation produces empty, nothing is added. The result + * collection adopts the type of the transform's output rather than preserving the input type. + * + * @param transform The collection transform representing the projection expression + * @return A new collection containing the projected and flattened results + */ + @Nonnull + public Collection project(@Nonnull final CollectionTransform transform) { + final Collection resultTemplate = transform.apply(this); + final ColumnTransform columnTransform = transform.toColumnTransformation(this); + final ColumnRepresentation projected = + getColumn() + .transform(col -> columnTransform.apply(getColumn().copyOf(col)).getValue()) + .flatten(); + return resultTemplate.copyWith(projected); + } + + /** + * Recursively traverses this collection using the specified transform, collecting all results + * without deduplication. This implements the FHIRPath {@code repeatAll()} STU function. + * + *

The transform is evaluated on each item, and its results are added to the output collection. + * The transform is then re-evaluated on the new results, repeating until no new items are + * produced or the maximum depth is reached. + * + *

Before entering the tree traversal, a static type analysis gate classifies the recursion + * behavior by applying the transform twice: once to the input (level_0) and once to the level_0 + * result (level_1). The classification is based on the FHIR type comparison: + * + *

    + *
  • level_1 empty: return level_0 directly (equivalent to {@code select()}) + *
  • level_0 or level_1 indeterminate FHIR type: error (unresolved choice type) + *
  • level_1 same FHIR type, primitive, self-ref not allowed: error (self-referential) + *
  • level_1 same FHIR type, primitive, self-ref allowed: return level_0 directly + *
  • level_1 same FHIR type, complex Extension: tree traversal with soft stop + *
  • level_1 same FHIR type, complex non-Extension, self-ref not allowed: tree traversal with + * error on depth exhaustion + *
  • level_1 same FHIR type, complex non-Extension, self-ref allowed: tree traversal with soft + * stop on depth exhaustion + *
  • level_1 different non-empty type: error (inconsistent traversal types) + *
+ * + *

For complex types that pass the gate, uses {@link ValueFunctions#variantTransformTree} to + * perform recursive traversal with Variant-based schema unification. Same-type depth limiting is + * provided by {@code UnresolvedTransformTree}. + * + * @param transform The collection transform representing the recursive projection expression + * @param maxDepth The maximum same-type recursion depth to prevent infinite traversal + * @param allowSelfReference If {@code true}, self-referential traversal is permitted for both + * primitive and complex types. For primitives, returns level_0 directly instead of throwing. + * For complex non-Extension types, suppresses depth exhaustion errors. Used by {@code + * repeat()} where deduplication guarantees termination. + * @return A new collection containing all recursively collected results + */ + @Nonnull + public Collection repeatAll( + @Nonnull final CollectionTransform transform, + final int maxDepth, + final boolean allowSelfReference) { + // Static type probing: apply the transform twice to classify recursion behavior. These + // applications build Collection objects for type inspection only — the actual column-level + // computation is performed separately below via toColumnTransformation(). This is safe because + // CollectionTransform.apply() is a pure function that constructs column expressions without + // side effects. + final Collection level0Collection = transform.apply(this); + final Collection level1Collection = transform.apply(level0Collection); + + // Static type analysis gate: classify recursion behavior based on level_0/level_1 types. + if (level1Collection.isEmpty()) { + // The traversal expression produces empty when applied to its own result. This means the + // recursion terminates after one level — equivalent to select(). Return level_0 directly + // for both primitive and complex types. + return level0Collection; + } + + // Level_1 is non-empty — check FHIR type consistency. + final Optional level0Type = level0Collection.getFhirType(); + final Optional level1Type = level1Collection.getFhirType(); + + // If either type is indeterminate, the recursive traversal cannot safely proceed. This + // occurs with unresolved choice type elements (MixedCollection) where getFhirType() returns + // empty. Without a concrete type, we cannot classify the recursion behavior. + if (level0Type.isEmpty() || level1Type.isEmpty()) { + throw new InvalidUserInputError( + "Recursive traversal expression produces a result with indeterminate FHIR type."); + } + + if (!level0Type.equals(level1Type)) { + // The traversal expression produces a different non-empty FHIR type when applied to its + // own result. This violates the type stability invariant for recursive application. + throw new InvalidUserInputError( + "Recursive traversal expression does not produce a consistent type across" + + " levels: level_0 type is " + + level0Type.map(FHIRDefinedType::toCode).orElse(UNKNOWN_TYPE) + + " but level_1 type is " + + level1Type.map(FHIRDefinedType::toCode).orElse(UNKNOWN_TYPE) + + "."); + } + + // Same FHIR type — check if the result is primitive or a resource. Resources are represented + // with a boolean existence column (not a struct), so they cannot be recursed into via + // variantTransformTree and must be handled like primitives. + final boolean isPrimitive = + level0Collection + .getType() + .map(t -> !(t.getSqlDataType() instanceof StructType)) + .orElse(false); + final boolean isResource = level0Collection instanceof ResourceCollection; + + if (isPrimitive || isResource) { + if (allowSelfReference) { + // For repeat(), self-referential traversal is valid — deduplication guarantees + // termination. Return level_0 directly; the caller will deduplicate. + return level0Collection; + } + // A primitive or resource type that produces the same type on self-application is + // self-referential and will recurse infinitely. + throw new InvalidUserInputError( + "Recursive traversal expression produces a self-referential type that cannot" + + " terminate."); + } + + // Same FHIR type, complex — proceed to tree traversal with depth limiting. + // The column transform must be derived from level0Collection (not this) so that deeper-level + // applications operate on the recursive element type. For example, in + // QuestionnaireResponse.repeat(item | answer.item), the transform must evaluate in the context + // of QuestionnaireResponseItemComponent (where both item and answer are valid paths), not + // QuestionnaireResponse. + final ColumnTransform columnTransform = transform.toColumnTransformation(level0Collection); + + // Compute the level-0 column result. Use the column from level0Collection directly, since + // transform.apply(this) has already evaluated the expression on the input. Normalize to array + // via plural() so that both singular and collection results are represented uniformly as arrays + // for the tree traversal. + final Column level0 = level0Collection.getColumn().plural().getValue(); + + // Build a column-level function for deeper levels that applies the projection to individual + // struct elements. Uses DefaultRepresentation because nested elements are structs accessed + // via getField(), not top-level Dataset columns accessed via col(). The plural() call + // ensures the traversal result is always an array, matching the level-0 normalization. + final UnaryOperator innerTransform = + col -> columnTransform.apply(new DefaultRepresentation(col)).plural().getValue(); + + // Determine whether to error on same-type depth exhaustion. Extension traversal and + // self-reference mode (used by repeat()) are the legitimate cases where depth exhaustion + // should not raise an error — extensions have a fixed schema at all nesting levels, and + // repeat() deduplicates the results to guarantee termination. + final boolean isExtensionTraversal = + level0Collection.getFhirType().map(FHIRDefinedType.EXTENSION::equals).orElse(false); + final boolean errorOnDepthExhaustion = !isExtensionTraversal && !allowSelfReference; + + // Use Variant-based schema unification for complex types. The identity extractor collects + // items at each level (variantTransformTree wraps it with to_variant_object), while the + // traversal navigates to children using the same projection expression. + final Column result = + ValueFunctions.variantTransformTree( + level0, c -> c, List.of(innerTransform), maxDepth, errorOnDepthExhaustion); + + // No flatten() is needed here unlike project(), because variantTransformTree already produces + // a flat array by concatenating results from all nesting levels internally. + return level0Collection.copyWithColumn(result); + } + + /** + * Recursively traverses this collection using the specified transform, collecting results with + * equality-based deduplication. This implements the FHIRPath {@code repeat()} function. + * + *

Delegates to {@link #repeatAll(CollectionTransform, int, boolean)} with self-reference + * allowed, which suppresses both primitive self-reference errors and complex depth exhaustion + * errors. The result is then deduplicated for {@link Equatable} types using the collection's + * comparator. Non-Equatable types (complex backbone elements) are not deduplicated. Deduplication + * guarantees termination for self-referential expressions like {@code repeat($this)}. + * + * @param transform The collection transform representing the recursive projection expression + * @param maxDepth The maximum same-type recursion depth to prevent infinite traversal + * @return A new collection containing deduplicated recursively collected results + */ + @Nonnull + public Collection repeat(@Nonnull final CollectionTransform transform, final int maxDepth) { + final Collection result = repeatAll(transform, maxDepth, true); + + // Deduplicate only for types with a FHIRPath type (primitives, Coding, Quantity, etc.). + // Complex backbone elements have no FHIRPath type and contain synthetic fields like _fid + // that make struct equality impractical. + if (result.getType().isPresent()) { + final Column array = result.getColumn().plural().getValue(); + final ColumnEquality comparator = result.getComparator(); + final Column deduplicated = + comparator.usesDefaultSqlEquality() + ? array_distinct(array) + : SqlFunctions.arrayDistinctWithEquality(array, comparator::equalsTo); + return result.copyWithColumn(deduplicated); + } + + return result; + } + /** * Checks if this collection is statically known to be empty. * @@ -612,7 +822,7 @@ public Collection asType(@Nonnull final TypeSpecifier type) { */ @Nonnull public String getDisplayExpression() { - final String leftDisplay = getType().map(FhirPathType::getTypeSpecifier).orElse("unknown"); + final String leftDisplay = getType().map(FhirPathType::getTypeSpecifier).orElse(UNKNOWN_TYPE); return getFhirType().map(fdt -> leftDisplay + "(" + fdt.toCode() + ")").orElse(leftDisplay); } diff --git a/fhirpath/src/main/java/au/csiro/pathling/fhirpath/collection/ResourceCollection.java b/fhirpath/src/main/java/au/csiro/pathling/fhirpath/collection/ResourceCollection.java index af61e6ebc1..d5c8c956b9 100644 --- a/fhirpath/src/main/java/au/csiro/pathling/fhirpath/collection/ResourceCollection.java +++ b/fhirpath/src/main/java/au/csiro/pathling/fhirpath/collection/ResourceCollection.java @@ -31,6 +31,7 @@ import jakarta.annotation.Nonnull; import java.util.Optional; import lombok.Getter; +import org.apache.spark.sql.Column; import org.hl7.fhir.exceptions.FHIRException; import org.hl7.fhir.r4.model.Enumerations.FHIRDefinedType; import org.hl7.fhir.r4.model.Enumerations.ResourceType; @@ -47,7 +48,7 @@ public class ResourceCollection extends Collection { @Nonnull private final ResourceDefinition resourceDefinition; /** - * Creates a new ResourceCollection. + * Creates a new ResourceCollection, deriving the extension map from the column representation. * * @param columnRepresentation the column representation * @param type the FhirPath type @@ -71,6 +72,29 @@ protected ResourceCollection( this.resourceDefinition = resourceDefinition; } + /** + * Creates a new ResourceCollection with an explicit extension map column. This is used by {@link + * #copyWith(ColumnRepresentation)} to preserve the resource-level extension map when creating + * copies with a different column representation (e.g. during repeatAll traversal). + * + * @param columnRepresentation the column representation + * @param type the FhirPath type + * @param fhirType the FHIR type + * @param definition the node definition + * @param resourceDefinition the resource definition + * @param extensionMapColumn the extension map column to preserve + */ + private ResourceCollection( + @Nonnull final ColumnRepresentation columnRepresentation, + @Nonnull final Optional type, + @Nonnull final Optional fhirType, + @Nonnull final Optional definition, + @Nonnull final ResourceDefinition resourceDefinition, + @Nonnull final Optional extensionMapColumn) { + super(columnRepresentation, type, fhirType, definition, extensionMapColumn); + this.resourceDefinition = resourceDefinition; + } + @Nonnull private static Optional getFhirType(@Nonnull final ResourceType resourceType) { return getFhirType(resourceType.toCode()); @@ -175,7 +199,12 @@ protected ColumnRepresentation getFid() { @Override public Collection copyWith(@Nonnull final ColumnRepresentation newValue) { return new ResourceCollection( - newValue, getType(), getFhirType(), getDefinition(), resourceDefinition); + newValue, + getType(), + getFhirType(), + getDefinition(), + resourceDefinition, + getExtensionMapColumn()); } /** diff --git a/fhirpath/src/main/java/au/csiro/pathling/fhirpath/evaluation/FhirEvaluationContext.java b/fhirpath/src/main/java/au/csiro/pathling/fhirpath/evaluation/FhirEvaluationContext.java index 8e37f591ea..22c220cc29 100644 --- a/fhirpath/src/main/java/au/csiro/pathling/fhirpath/evaluation/FhirEvaluationContext.java +++ b/fhirpath/src/main/java/au/csiro/pathling/fhirpath/evaluation/FhirEvaluationContext.java @@ -17,6 +17,7 @@ package au.csiro.pathling.fhirpath.evaluation; +import au.csiro.pathling.config.FhirpathConfiguration; import au.csiro.pathling.fhirpath.EvaluationContext; import au.csiro.pathling.fhirpath.collection.Collection; import au.csiro.pathling.fhirpath.collection.ResourceCollection; @@ -43,14 +44,37 @@ * @param variableResolver the resolver for environment variables * @param functionRegistry the registry for resolving FHIRPath functions * @param resourceResolver the resolver for FHIR resources + * @param configuration the FHIRPath evaluation configuration */ public record FhirEvaluationContext( @Nonnull Collection inputContext, @Nonnull EnvironmentVariableResolver variableResolver, @Nonnull FunctionRegistry functionRegistry, - @Nonnull ResourceResolver resourceResolver) + @Nonnull ResourceResolver resourceResolver, + @Nonnull FhirpathConfiguration configuration) implements EvaluationContext { + /** + * Creates a FhirEvaluationContext with default configuration. + * + * @param inputContext the current input context (focus) for the evaluation + * @param variableResolver the resolver for environment variables + * @param functionRegistry the registry for resolving FHIRPath functions + * @param resourceResolver the resolver for FHIR resources + */ + public FhirEvaluationContext( + @Nonnull final Collection inputContext, + @Nonnull final EnvironmentVariableResolver variableResolver, + @Nonnull final FunctionRegistry functionRegistry, + @Nonnull final ResourceResolver resourceResolver) { + this( + inputContext, + variableResolver, + functionRegistry, + resourceResolver, + FhirpathConfiguration.DEFAULT); + } + /** * {@inheritDoc} * @@ -96,4 +120,15 @@ public Collection resolveVariable(@Nonnull final String name) { public Collection getInputContext() { return inputContext; } + + /** + * {@inheritDoc} + * + *

Returns the configuration provided at construction time. + */ + @Override + @Nonnull + public FhirpathConfiguration getConfiguration() { + return configuration; + } } diff --git a/fhirpath/src/main/java/au/csiro/pathling/fhirpath/evaluation/SingleInstanceEvaluator.java b/fhirpath/src/main/java/au/csiro/pathling/fhirpath/evaluation/SingleInstanceEvaluator.java index f445224e06..46bff2df01 100644 --- a/fhirpath/src/main/java/au/csiro/pathling/fhirpath/evaluation/SingleInstanceEvaluator.java +++ b/fhirpath/src/main/java/au/csiro/pathling/fhirpath/evaluation/SingleInstanceEvaluator.java @@ -17,6 +17,7 @@ package au.csiro.pathling.fhirpath.evaluation; +import au.csiro.pathling.config.FhirpathConfiguration; import au.csiro.pathling.fhirpath.FhirPath; import au.csiro.pathling.fhirpath.FhirPathType; import au.csiro.pathling.fhirpath.collection.BooleanCollection; @@ -76,6 +77,40 @@ public static SingleInstanceEvaluationResult evaluate( @Nonnull final String fhirPathExpression, @Nullable final String contextExpression, @Nullable final Map variables) { + return evaluate( + resourceDf, + resourceType, + fhirContext, + fhirPathExpression, + contextExpression, + variables, + FhirpathConfiguration.DEFAULT); + } + + /** + * Evaluates a FHIRPath expression against a single encoded FHIR resource with custom + * configuration. + * + * @param resourceDf the encoded resource as a single-row Dataset + * @param resourceType the FHIR resource type code (e.g. "Patient") + * @param fhirContext the FHIR context + * @param fhirPathExpression the FHIRPath expression to evaluate + * @param contextExpression an optional context expression; if non-null, the main expression is + * composed with the context + * @param variables optional named variables available via %variable syntax, or null + * @param configuration the FHIRPath evaluation configuration + * @return a {@link SingleInstanceEvaluationResult} containing typed result values and type + * metadata + */ + @Nonnull + public static SingleInstanceEvaluationResult evaluate( + @Nonnull final Dataset resourceDf, + @Nonnull final String resourceType, + @Nonnull final FhirContext fhirContext, + @Nonnull final String fhirPathExpression, + @Nullable final String contextExpression, + @Nullable final Map variables, + @Nonnull final FhirpathConfiguration configuration) { // Convert incoming variables to Collection objects for the evaluator. final Map variableCollections = convertVariables(variables); @@ -89,6 +124,7 @@ public static SingleInstanceEvaluationResult evaluate( SingleResourceEvaluatorBuilder.create(ResourceType.fromCode(resourceType), fhirContext) .withCrossResourceStrategy(CrossResourceStrategy.EMPTY) .withVariables(variableCollections) + .withConfiguration(configuration) .build(); // Evaluate to determine the return type. diff --git a/fhirpath/src/main/java/au/csiro/pathling/fhirpath/evaluation/SingleResourceEvaluator.java b/fhirpath/src/main/java/au/csiro/pathling/fhirpath/evaluation/SingleResourceEvaluator.java index 4726c0dd5e..bd0d8c3a13 100644 --- a/fhirpath/src/main/java/au/csiro/pathling/fhirpath/evaluation/SingleResourceEvaluator.java +++ b/fhirpath/src/main/java/au/csiro/pathling/fhirpath/evaluation/SingleResourceEvaluator.java @@ -17,6 +17,7 @@ package au.csiro.pathling.fhirpath.evaluation; +import au.csiro.pathling.config.FhirpathConfiguration; import au.csiro.pathling.fhirpath.EvaluationContext; import au.csiro.pathling.fhirpath.FhirPath; import au.csiro.pathling.fhirpath.collection.Collection; @@ -59,7 +60,7 @@ public class SingleResourceEvaluator { /** - * Creates a new SingleResourceEvaluator with the specified resolver. + * Creates a new SingleResourceEvaluator with the specified resolver and default configuration. * *

This factory method allows creating evaluators with custom resource resolvers, such as * {@link DefinitionResourceResolver} for arbitrary data structures. @@ -74,7 +75,8 @@ public static SingleResourceEvaluator of( @Nonnull final ResourceResolver resolver, @Nonnull final FunctionRegistry functionRegistry, @Nonnull final Map variables) { - return new SingleResourceEvaluator(resolver, functionRegistry, variables); + return new SingleResourceEvaluator( + resolver, functionRegistry, variables, FhirpathConfiguration.DEFAULT); } /** The resource resolver. */ @@ -86,6 +88,9 @@ public static SingleResourceEvaluator of( /** Additional variables available during evaluation. */ @Nonnull private final Map variables; + /** The FHIRPath evaluation configuration. */ + @Nonnull private final FhirpathConfiguration configuration; + /** * Evaluates a FHIRPath expression with the default input context. * @@ -119,7 +124,7 @@ public Collection evaluate( VariableResolverChain.withDefaults(resource, inputContext, variables); final EvaluationContext evalContext = new FhirEvaluationContext( - inputContext, variableResolver, functionRegistry, resourceResolver); + inputContext, variableResolver, functionRegistry, resourceResolver, configuration); return fhirPath.apply(inputContext, evalContext); } diff --git a/fhirpath/src/main/java/au/csiro/pathling/fhirpath/evaluation/SingleResourceEvaluatorBuilder.java b/fhirpath/src/main/java/au/csiro/pathling/fhirpath/evaluation/SingleResourceEvaluatorBuilder.java index d4662d6dcb..59efc5419d 100644 --- a/fhirpath/src/main/java/au/csiro/pathling/fhirpath/evaluation/SingleResourceEvaluatorBuilder.java +++ b/fhirpath/src/main/java/au/csiro/pathling/fhirpath/evaluation/SingleResourceEvaluatorBuilder.java @@ -17,6 +17,7 @@ package au.csiro.pathling.fhirpath.evaluation; +import au.csiro.pathling.config.FhirpathConfiguration; import au.csiro.pathling.fhirpath.collection.Collection; import au.csiro.pathling.fhirpath.function.registry.FunctionRegistry; import au.csiro.pathling.fhirpath.function.registry.StaticFunctionRegistry; @@ -70,6 +71,8 @@ public class SingleResourceEvaluatorBuilder { @Nonnull private Map variables = Map.of(); + @Nonnull private FhirpathConfiguration configuration = FhirpathConfiguration.DEFAULT; + /** Private constructor. Use factory methods to create instances. */ private SingleResourceEvaluatorBuilder( @Nonnull final String subjectResourceCode, @Nonnull final FhirContext fhirContext) { @@ -171,6 +174,21 @@ public SingleResourceEvaluatorBuilder withVariables( return this; } + /** + * Sets the FHIRPath evaluation configuration. + * + *

Default is {@link FhirpathConfiguration#DEFAULT}. + * + * @param configuration the FHIRPath configuration + * @return this builder for method chaining + */ + @Nonnull + public SingleResourceEvaluatorBuilder withConfiguration( + @Nonnull final FhirpathConfiguration configuration) { + this.configuration = configuration; + return this; + } + /** * Builds the {@link SingleResourceEvaluator} with the configured options. * @@ -180,6 +198,6 @@ public SingleResourceEvaluatorBuilder withVariables( public SingleResourceEvaluator build() { final ResourceResolver resolver = new FhirResourceResolver(subjectResourceCode, fhirContext, crossResourceStrategy); - return new SingleResourceEvaluator(resolver, functionRegistry, variables); + return new SingleResourceEvaluator(resolver, functionRegistry, variables, configuration); } } diff --git a/fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/provider/FilteringAndProjectionFunctions.java b/fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/provider/FilteringAndProjectionFunctions.java index b0bb5f6e9c..06e98783be 100644 --- a/fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/provider/FilteringAndProjectionFunctions.java +++ b/fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/provider/FilteringAndProjectionFunctions.java @@ -17,6 +17,7 @@ package au.csiro.pathling.fhirpath.function.provider; +import au.csiro.pathling.fhirpath.EvaluationContext; import au.csiro.pathling.fhirpath.TypeSpecifier; import au.csiro.pathling.fhirpath.annotations.SqlOnFhirConformance; import au.csiro.pathling.fhirpath.annotations.SqlOnFhirConformance.Profile; @@ -63,6 +64,26 @@ public static Collection where( return input.filter(expression.requireBooleanSingleton().toColumnTransformation(input)); } + /** + * Returns a collection containing the result of evaluating the projection expression for each + * item in the input collection. The results are flattened: if evaluation produces multiple items, + * all are added to the output; if evaluation produces empty, nothing is added. + * + *

If the input collection is empty, the result is empty. + * + * @param input The input collection + * @param expression The projection expression + * @return A collection containing the projected results + * @see select + */ + @FhirPathFunction + @Nonnull + public static Collection select( + @Nonnull final Collection input, @Nonnull final CollectionTransform expression) { + return input.project(expression); + } + /** * Returns a collection that contains all items in the input collection that are of the given type * or a subclass thereof. If the input collection is empty, the result is empty. The type argument @@ -82,4 +103,66 @@ public static Collection ofType( @Nonnull final Collection input, @Nonnull final TypeSpecifier typeSpecifier) { return input.filterByType(typeSpecifier); } + + /** + * Recursively evaluates a projection expression on each item in the input collection, adding + * results to the output only if they are not already present as determined by the equals ({@code + * =}) operator. The projection is then re-evaluated on the new results, repeating until no new + * items are produced or the maximum same-type recursion depth is reached. + * + *

This is the standard FHIRPath {@code repeat()} function. Unlike {@code repeatAll()}, it + * performs equality-based deduplication of results. + * + *

If the input collection is empty, the result is empty. + * + * @param input The input collection + * @param expression The projection expression to apply recursively + * @param context The evaluation context providing configuration + * @return A collection containing deduplicated recursively collected results + * @see repeat + */ + @FhirPathFunction + @Nonnull + public static Collection repeat( + @Nonnull final Collection input, + @Nonnull final CollectionTransform expression, + @Nonnull final EvaluationContext context) { + final int maxDepth = context.getConfiguration().getMaxUnboundTraversalDepth(); + return input.repeat(expression, maxDepth); + } + + /** + * Recursively evaluates a projection expression on each item in the input collection, adding all + * results to the output without deduplication. The projection is then re-evaluated on the new + * results, repeating until no new items are produced or the maximum same-type recursion depth is + * reached. + * + *

This is the STU FHIRPath {@code repeatAll()} function. Unlike {@code repeat()}, it does not + * perform equality-based deduplication of results. + * + *

If the input collection is empty, the result is empty. + * + *

For Extension traversal, same-type depth exhaustion silently stops and returns results + * collected up to that point. For all other same-type traversals, depth exhaustion raises an + * error indicating infinite recursive traversal. The depth limit is controlled by {@code + * maxUnboundTraversalDepth} in the FHIRPath configuration. + * + * @param input The input collection + * @param expression The projection expression to apply recursively + * @param context The evaluation context providing configuration + * @return A collection containing all recursively collected results + * @see repeatAll + */ + @FhirPathFunction + @SqlOnFhirConformance(Profile.EXPERIMENTAL) + @Nonnull + public static Collection repeatAll( + @Nonnull final Collection input, + @Nonnull final CollectionTransform expression, + @Nonnull final EvaluationContext context) { + final int maxDepth = context.getConfiguration().getMaxUnboundTraversalDepth(); + return input.repeatAll(expression, maxDepth, false); + } } diff --git a/fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/resolver/FunctionParameterResolver.java b/fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/resolver/FunctionParameterResolver.java index 04511b74a5..e1e16aefb0 100644 --- a/fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/resolver/FunctionParameterResolver.java +++ b/fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/resolver/FunctionParameterResolver.java @@ -35,6 +35,7 @@ import java.lang.reflect.InvocationTargetException; import java.lang.reflect.Method; import java.lang.reflect.Parameter; +import java.util.ArrayList; import java.util.List; import java.util.stream.IntStream; import java.util.stream.Stream; @@ -100,28 +101,44 @@ public FunctionInvocation bind(@Nonnull final Method method) { final Object resolvedInput = resolveCollection(input, method.getParameters()[0], context.forInput()); + // Count non-context parameters (excluding input and EvaluationContext-typed parameters) to + // determine the expected number of FHIRPath arguments. + final long contextParamCount = + IntStream.range(1, method.getParameterCount()) + .filter( + i -> EvaluationContext.class.isAssignableFrom(method.getParameters()[i].getType())) + .count(); + final long expectedArgCount = method.getParameterCount() - 1 - contextParamCount; + // Check that not extra arguments are provided. context.check( - actualArguments.size() <= method.getParameterCount() - 1, + actualArguments.size() <= expectedArgCount, "Too many arguments provided. Expected " - + (method.getParameterCount() - 1) + + expectedArgCount + ", got " + actualArguments.size()); - // Resolve each pair of method parameter and argument. - final Stream resolvedArguments = - IntStream.range(0, method.getParameterCount() - 1) - .mapToObj( - i -> { - final Parameter parameter = method.getParameters()[i + 1]; - return resolveArgument( - parameter, - (i < actualArguments.size()) ? actualArguments.get(i) : null, - context.forArgument(i, parameter.getType())); - }); + // Resolve each method parameter. EvaluationContext parameters are injected from the resolver's + // state without consuming a FHIRPath argument. All other parameters consume arguments in order. + final List resolvedArguments = new ArrayList<>(); + int argIndex = 0; + for (int i = 1; i < method.getParameterCount(); i++) { + final Parameter parameter = method.getParameters()[i]; + if (EvaluationContext.class.isAssignableFrom(parameter.getType())) { + resolvedArguments.add(evaluationContext); + } else { + resolvedArguments.add( + resolveArgument( + parameter, + (argIndex < actualArguments.size()) ? actualArguments.get(argIndex) : null, + context.forArgument(argIndex, parameter.getType()))); + argIndex++; + } + } return new FunctionInvocation( - method, Stream.concat(Stream.of(resolvedInput), resolvedArguments).toArray(Object[]::new)); + method, + Stream.concat(Stream.of(resolvedInput), resolvedArguments.stream()).toArray(Object[]::new)); } /** diff --git a/fhirpath/src/main/java/au/csiro/pathling/projection/Projection.java b/fhirpath/src/main/java/au/csiro/pathling/projection/Projection.java index f9fe9083b3..2d37312023 100644 --- a/fhirpath/src/main/java/au/csiro/pathling/projection/Projection.java +++ b/fhirpath/src/main/java/au/csiro/pathling/projection/Projection.java @@ -41,6 +41,7 @@ import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Row; import org.apache.spark.sql.types.ArrayType; +import org.apache.spark.sql.types.MetadataBuilder; import org.apache.spark.sql.types.StructField; import org.apache.spark.sql.types.StructType; import org.hl7.fhir.r4.model.Enumerations.ResourceType; @@ -125,15 +126,16 @@ public Dataset execute( // Convert the intermediate struct representation in the result column to a regular row, using // the inline function. - final Dataset inlinedResult = - filteredResult.select(inline(projectionResult.getResultColumn())); - // Get the list of column names from the data type of the column that we just inlined. final StructType schema = filteredResult.select(projectionResult.getResultColumn()).schema(); final ArrayType arrayType = (ArrayType) schema.fields()[0].dataType(); final StructType structType = (StructType) arrayType.elementType(); final List columnNames = Arrays.stream(structType.fields()).map(StructField::name).toList(); + + final Dataset inlinedResult = + filteredResult.select(inline(projectionResult.getResultColumn())); + // Bind the result collections to the columns in the projection result. final List boundResults = IntStream.range(0, columnNames.size()) @@ -176,8 +178,14 @@ private Column renderColumn(@Nonnull final Collection collection, @Nonnull final // Otherwise, we can use the collection as-is. finalResult = collection; } - // re-alias the column - return finalResult.getColumn().getValue().alias(name); + // Alias the column with non-empty metadata to prevent the optimizer from collapsing this + // Project into the Generate node below. Without this, RemoveRedundantAliases eliminates the + // Project, and GeneratorNestedColumnAliasing may add pass-through columns to the Generate + // output, shifting column positions during physical execution. + return finalResult + .getColumn() + .getValue() + .as(name, new MetadataBuilder().putBoolean("__pathling_view_column", true).build()); } /** diff --git a/fhirpath/src/main/java/au/csiro/pathling/projection/RepeatSelection.java b/fhirpath/src/main/java/au/csiro/pathling/projection/RepeatSelection.java index bf39546e8b..2d0b1879a9 100644 --- a/fhirpath/src/main/java/au/csiro/pathling/projection/RepeatSelection.java +++ b/fhirpath/src/main/java/au/csiro/pathling/projection/RepeatSelection.java @@ -27,6 +27,7 @@ import java.util.List; import java.util.stream.Collectors; import org.apache.spark.sql.Column; +import org.hl7.fhir.r4.model.Enumerations.FHIRDefinedType; /** * Represents a selection that performs recursive traversal of nested data structures using the @@ -36,6 +37,10 @@ * the specified paths and applying a projection clause at each level. When multiple projections are * needed, wrap them in a {@link GroupingSelection} first. * + *

When same-type depth is exhausted, Extension traversals silently stop and return results + * collected up to that point. All other types raise a runtime error indicating that the recursive + * traversal exceeded the maximum depth. + * * @param paths the list of FHIRPath expressions that define paths to recursively traverse * @param component the projection clause to apply at each level (use GroupingSelection for * multiple) @@ -50,15 +55,25 @@ public record RepeatSelection( @Override public ProjectionResult evaluate(@Nonnull final ProjectionContext context) { - // Create the list of non-empty starting contexts from current context and provided paths + // Evaluate each path to get collections, retaining them for type inspection. + final List pathCollections = paths.stream().map(context::evalExpression).toList(); + + // Determine whether depth exhaustion should error. Error unless all paths produce Extension + // types. If any path is non-Extension (or has no FHIR type), depth exhaustion raises an error. + final boolean errorOnDepthExhaustion = + pathCollections.stream() + .filter(Collection::isNotEmpty) + .anyMatch( + c -> c.getFhirType().map(t -> !FHIRDefinedType.EXTENSION.equals(t)).orElse(true)); + + // Create the list of non-empty starting contexts from the evaluated path collections. final List startingNodes = - paths.stream() - .map(context::evalExpression) + pathCollections.stream() .filter(Collection::isNotEmpty) .map(context::withInputContext) .toList(); - // Map starting nodes to transformTree expressions and concatenate the results + // Map starting nodes to transformTree expressions and concatenate the results. final Column[] nodeResults = startingNodes.stream() .map( @@ -69,7 +84,8 @@ public ProjectionResult evaluate(@Nonnull final ProjectionContext context) { ValueFunctions.emptyArrayIfMissingField( component.evaluateElementWise(ctx.withInputColumn(c))), paths.stream().map(ctx::asColumnOperator).toList(), - maxDepth)) + maxDepth, + errorOnDepthExhaustion)) .toArray(Column[]::new); final Column result = @@ -81,7 +97,7 @@ public ProjectionResult evaluate(@Nonnull final ProjectionContext context) { .flatten() .getValue(); - // Compute the output schema based on first non-empty context or empty context + // Compute the output schema based on first non-empty context or empty context. final ProjectionContext schemaContext = startingNodes.stream().findFirst().orElse(context.withEmptyInput()); diff --git a/fhirpath/src/main/java/au/csiro/pathling/views/FhirViewExecutor.java b/fhirpath/src/main/java/au/csiro/pathling/views/FhirViewExecutor.java index f5f3eb9339..0977674557 100644 --- a/fhirpath/src/main/java/au/csiro/pathling/views/FhirViewExecutor.java +++ b/fhirpath/src/main/java/au/csiro/pathling/views/FhirViewExecutor.java @@ -23,6 +23,7 @@ import static java.util.Objects.requireNonNull; import static java.util.stream.Collectors.toMap; +import au.csiro.pathling.config.FhirpathConfiguration; import au.csiro.pathling.config.QueryConfiguration; import au.csiro.pathling.fhirpath.FhirPath; import au.csiro.pathling.fhirpath.collection.Collection; @@ -128,11 +129,19 @@ public Dataset buildQuery(@Nonnull final FhirView view) { view.getConstant().stream() .collect(toMap(ConstantDeclaration::getName, c -> Collection.fromValue(c.getValue()))); - // Create evaluator (uses ResourceRepresentation with id column) + // Build FHIRPath configuration from query configuration so that FHIRPath functions like + // repeat() and repeatAll() respect the user-configured depth limit. + final FhirpathConfiguration fhirpathConfig = + FhirpathConfiguration.builder() + .maxUnboundTraversalDepth(queryConfiguration.getMaxUnboundTraversalDepth()) + .build(); + + // Create evaluator (uses ResourceRepresentation with id column). final SingleResourceEvaluator evaluator = SingleResourceEvaluatorBuilder.create(subjectResource, fhirContext) .withCrossResourceStrategy(CrossResourceStrategy.EMPTY) .withVariables(variables) + .withConfiguration(fhirpathConfig) .build(); return projection.execute(dataset, evaluator); diff --git a/fhirpath/src/test/java/au/csiro/pathling/fhirpath/dsl/RepeatAllFunctionDslTest.java b/fhirpath/src/test/java/au/csiro/pathling/fhirpath/dsl/RepeatAllFunctionDslTest.java new file mode 100644 index 0000000000..9f9bd5851c --- /dev/null +++ b/fhirpath/src/test/java/au/csiro/pathling/fhirpath/dsl/RepeatAllFunctionDslTest.java @@ -0,0 +1,510 @@ +/* + * Copyright © 2018-2026 Commonwealth Scientific and Industrial Research + * Organisation (CSIRO) ABN 41 687 119 230. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package au.csiro.pathling.fhirpath.dsl; + +import au.csiro.pathling.encoders.FhirEncoders; +import au.csiro.pathling.test.dsl.FhirPathDslTestBase; +import au.csiro.pathling.test.dsl.FhirPathTest; +import jakarta.annotation.Nonnull; +import java.util.List; +import java.util.stream.Stream; +import org.hl7.fhir.r4.model.CodeableConcept; +import org.hl7.fhir.r4.model.Coding; +import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender; +import org.hl7.fhir.r4.model.Enumerations.PublicationStatus; +import org.hl7.fhir.r4.model.Extension; +import org.hl7.fhir.r4.model.Observation; +import org.hl7.fhir.r4.model.Patient; +import org.hl7.fhir.r4.model.Quantity; +import org.hl7.fhir.r4.model.Questionnaire; +import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemComponent; +import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemType; +import org.hl7.fhir.r4.model.QuestionnaireResponse; +import org.hl7.fhir.r4.model.QuestionnaireResponse.QuestionnaireResponseItemAnswerComponent; +import org.hl7.fhir.r4.model.QuestionnaireResponse.QuestionnaireResponseItemComponent; +import org.hl7.fhir.r4.model.QuestionnaireResponse.QuestionnaireResponseStatus; +import org.hl7.fhir.r4.model.StringType; +import org.junit.jupiter.api.DynamicTest; +import org.springframework.boot.test.context.TestConfiguration; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Import; + +/** + * Tests for the FHIRPath repeatAll() function. + * + *

Uses a Questionnaire resource with nested items to verify recursive traversal behaviour. With + * the default maxNestingLevel of 3, the schema supports items nested 4 levels deep (root item plus + * 3 additional levels). + */ +@Import(RepeatAllFunctionDslTest.Config.class) +public class RepeatAllFunctionDslTest extends FhirPathDslTestBase { + + /** + * Provides a FhirEncoders bean with maxNestingLevel=3 to support deeply nested items in test + * Questionnaire resources. Overrides the default bean which uses maxNestingLevel=0. + */ + @TestConfiguration + static class Config { + + @Bean + @Nonnull + FhirEncoders fhirEncoders() { + return FhirEncoders.forR4() + .withExtensionsEnabled(true) + .withAllOpenTypes() + .withMaxNestingLevel(3) + .getOrCreate(); + } + } + + /** + * Creates a test Questionnaire with items nested to the specified depth. + * + *

Structure: + * + * 

+   *   item "1" (group)
+   *     item "1.1" (group)
+   *       item "1.1.1" (display)
+   *   item "2" (display)
+   *
+ * + * @return a Questionnaire resource + */ + private static Questionnaire createQuestionnaire() { + final Questionnaire questionnaire = new Questionnaire(); + questionnaire.setId("test-questionnaire"); + questionnaire.setStatus(PublicationStatus.DRAFT); + + final QuestionnaireItemComponent item1 = questionnaire.addItem(); + item1.setLinkId("1"); + item1.setType(QuestionnaireItemType.GROUP); + + final QuestionnaireItemComponent item1Sub1 = item1.addItem(); + item1Sub1.setLinkId("1.1"); + item1Sub1.setType(QuestionnaireItemType.GROUP); + + final QuestionnaireItemComponent item1Sub1Sub1 = item1Sub1.addItem(); + item1Sub1Sub1.setLinkId("1.1.1"); + item1Sub1Sub1.setType(QuestionnaireItemType.DISPLAY); + + final QuestionnaireItemComponent item2 = questionnaire.addItem(); + item2.setLinkId("2"); + item2.setType(QuestionnaireItemType.DISPLAY); + + return questionnaire; + } + + /** + * Creates a Questionnaire with no items (for empty input testing). + * + * @return a Questionnaire resource with no items + */ + private static Questionnaire createEmptyQuestionnaire() { + final Questionnaire questionnaire = new Questionnaire(); + questionnaire.setId("empty-questionnaire"); + questionnaire.setStatus(PublicationStatus.DRAFT); + return questionnaire; + } + + /** + * Creates a Patient with all fields needed by the patient projection tests: two names, gender, + * marital status, and nested extensions. + * + *

Extension structure: + * + * 

+   *   Patient
+   *     name: Smith, Jones
+   *     gender: MALE
+   *     maritalStatus: M (Married)
+   *     extension "http://example.com/simple" = "simple-value"
+   *     extension "http://example.com/parent"
+   *       extension "http://example.com/child" = "child-value"
+   *
+ * + * @return a Patient resource with all fields populated + */ + private static Patient createPatient() { + final Patient patient = new Patient(); + patient.setId("test-patient"); + patient.addName().setFamily("Smith"); + patient.addName().setFamily("Jones"); + patient.setGender(AdministrativeGender.MALE); + patient.setMaritalStatus( + new CodeableConcept(new Coding("http://example.com/cs", "M", "Married"))); + + // Simple leaf extension. + patient.addExtension( + new Extension("http://example.com/simple", new StringType("simple-value"))); + + // Complex extension containing a nested sub-extension. + final Extension parent = new Extension("http://example.com/parent"); + parent.addExtension(new Extension("http://example.com/child", new StringType("child-value"))); + patient.addExtension(parent); + + return patient; + } + + @FhirPathTest + public Stream testRepeatAllQuestionnaireTraversal() { + return builder() + .withResource(createQuestionnaire()) + .group("repeatAll() basic traversal") + .testEquals( + List.of("1", "2", "1.1", "1.1.1"), + "repeatAll(item).linkId", + "repeatAll(item).linkId returns linkIds from all nesting levels") + .testEquals( + 4, + "repeatAll(item).count()", + "repeatAll(item).count() returns total items across all levels") + .group("repeatAll() with filtering") + .testEquals( + List.of("1", "1.1"), + "repeatAll(item).where(type = 'group').linkId", + "repeatAll(item).where(type = 'group') filters items from all nesting levels") + .group("repeatAll() computed empty input") + .testEmpty( + "item.where(linkId = 'nonexistent').repeatAll(item)", + "repeatAll() on a computed empty collection returns empty") + .group("repeatAll() $index not defined") + .testError( + "repeatAll($index)", "$index is not available within repeatAll projection expression") + .build(); + } + + @FhirPathTest + public Stream testRepeatAllNonRecursiveProjections() { + return builder() + .withSubject( + sb -> + sb.elementArray( + "name", + n1 -> n1.string("family", "Smith"), + n2 -> n2.string("family", "Jones")) + .string("gender", "male") + .element( + "maritalStatus", + ms -> ms.elementArray("coding", c -> c.string("code", "M")))) + .group("repeatAll() non-recursive projection") + .testEquals( + List.of("Smith", "Jones"), + "repeatAll(name).family", + "repeatAll(name).family returns same result as select() for non-recursive fields") + .group("repeatAll() singular primitive projection") + .testEquals( + "male", + "repeatAll(gender)", + "repeatAll(gender) returns a singular primitive value like select()") + .group("repeatAll() singular complex projection") + .testEquals( + "M", + "repeatAll(maritalStatus).coding.code", + "repeatAll(maritalStatus) returns a singular complex value with sub-elements intact") + .build(); + } + + @FhirPathTest + public Stream testRepeatAllInfiniteRecursionAndExtensions() { + return builder() + .withResource(createPatient()) + .group("repeatAll() primitive self-referential detection") + .testError( + "self-referential type that cannot terminate", + "gender.repeatAll($this)", + "repeatAll($this) on a primitive raises a static self-referential error") + .testError( + "self-referential type that cannot terminate", + "gender.repeatAll('someValue')", + "repeatAll('literal') on a primitive raises a static self-referential error") + .testError( + "self-referential type that cannot terminate", + "gender.repeatAll(length())", + "repeatAll(length()) on a primitive raises a static self-referential error") + .group("repeatAll() complex infinite recursion detection") + .testError( + "Recursive traversal exceeded maximum depth", + "name.repeatAll(first()).count()", + "repeatAll(first()) raises an error for non-Extension same-type depth exhaustion") + .testError( + "self-referential type that cannot terminate", + "repeatAll($this)", + "repeatAll($this) on a resource raises a static self-referential error") + .group("repeatAll() extension traversal") + .testEquals( + List.of( + "http://example.com/simple", + "http://example.com/parent", + "http://example.com/child"), + "repeatAll(extension).url", + "repeatAll(extension) recursively collects all extensions including nested" + + " sub-extensions") + .group("repeatAll() choice type via extension value") + .testEquals( + List.of("simple-value", "child-value"), + "repeatAll(extension).value.ofType(string)", + "repeatAll(extension).value.ofType(string) extracts choice-typed values from all" + + " extensions") + .build(); + } + + @FhirPathTest + public Stream testRepeatAllEmptyInput() { + return builder() + .withResource(createEmptyQuestionnaire()) + .group("repeatAll() empty input") + .testEmpty( + "repeatAll(item)", "repeatAll() on a resource with no items returns empty collection") + .testEquals( + 0, "repeatAll(item).count()", "repeatAll(item).count() returns 0 for empty input") + .group("repeatAll() empty literal") + .testEmpty( + "{}.repeatAll($this)", + "repeatAll() on the FHIRPath empty literal returns empty collection") + .build(); + } + + @FhirPathTest + public Stream testRepeatAllSingleLevel() { + // Create a Questionnaire with only top-level items (no nesting). + final Questionnaire flat = new Questionnaire(); + flat.setId("flat-questionnaire"); + flat.setStatus(PublicationStatus.DRAFT); + flat.addItem().setLinkId("a").setType(QuestionnaireItemType.DISPLAY); + flat.addItem().setLinkId("b").setType(QuestionnaireItemType.DISPLAY); + flat.addItem().setLinkId("c").setType(QuestionnaireItemType.DISPLAY); + + return builder() + .withResource(flat) + .group("repeatAll() single-level traversal") + .testEquals( + List.of("a", "b", "c"), + "repeatAll(item).linkId", + "repeatAll(item).linkId on flat items returns all top-level linkIds") + .build(); + } + + /** + * Creates a Questionnaire where items at different nesting levels share the same linkId, to + * verify that repeatAll preserves duplicates. + * + *

Structure: + * + * 

+   *   item "A" (group)
+   *     item "B" (display)
+   *   item "B" (display)
+   *
+ * + * @return a Questionnaire resource with duplicate linkIds + */ + private static Questionnaire createQuestionnaireWithDuplicates() { + final Questionnaire questionnaire = new Questionnaire(); + questionnaire.setId("dup-questionnaire"); + questionnaire.setStatus(PublicationStatus.DRAFT); + + final QuestionnaireItemComponent item1 = questionnaire.addItem(); + item1.setLinkId("A"); + item1.setType(QuestionnaireItemType.GROUP); + + final QuestionnaireItemComponent item1Child = item1.addItem(); + item1Child.setLinkId("B"); + item1Child.setType(QuestionnaireItemType.DISPLAY); + + final QuestionnaireItemComponent item2 = questionnaire.addItem(); + item2.setLinkId("B"); + item2.setType(QuestionnaireItemType.DISPLAY); + + return questionnaire; + } + + @FhirPathTest + public Stream testRepeatAllDuplicatesPreserved() { + return builder() + .withResource(createQuestionnaireWithDuplicates()) + .group("repeatAll() duplicate preservation") + .testEquals( + List.of("A", "B", "B"), + "repeatAll(item).linkId", + "repeatAll(item).linkId preserves duplicate linkId values from different nesting" + + " levels") + .testEquals( + 3, + "repeatAll(item).count()", + "repeatAll(item).count() includes duplicate items in the total") + .build(); + } + + /** + * Creates a QuestionnaireResponse with items nested through answer elements, to verify that + * repeatAll can traverse through intermediate types (Item -> Answer -> Item). + * + *

Structure: + * + * 

+   *   item "root"
+   *     answer
+   *       item "nested-1"
+   *         answer
+   *           item "nested-2"
+   *
+ * + * @return a QuestionnaireResponse resource with cross-type nesting + */ + private static QuestionnaireResponse createQuestionnaireResponse() { + final QuestionnaireResponse qr = new QuestionnaireResponse(); + qr.setId("cross-type-qr"); + qr.setStatus(QuestionnaireResponseStatus.COMPLETED); + + final QuestionnaireResponseItemComponent rootItem = qr.addItem(); + rootItem.setLinkId("root"); + + final QuestionnaireResponseItemAnswerComponent answer1 = rootItem.addAnswer(); + final QuestionnaireResponseItemComponent nestedItem = answer1.addItem(); + nestedItem.setLinkId("nested-1"); + + final QuestionnaireResponseItemAnswerComponent answer2 = nestedItem.addAnswer(); + final QuestionnaireResponseItemComponent deepItem = answer2.addItem(); + deepItem.setLinkId("nested-2"); + + return qr; + } + + @FhirPathTest + public Stream testRepeatAllCrossTypeTraversal() { + return builder() + .withResource(createQuestionnaireResponse()) + .group("repeatAll() cross-type traversal") + .testEquals( + List.of("nested-1", "nested-2"), + "item.repeatAll(answer.item).linkId", + "repeatAll(answer.item) traverses through answer elements to reach nested items") + .group("repeatAll() union traversal through item and answer.item") + .testEquals( + List.of("root", "nested-1", "nested-2"), + "repeatAll(item | answer.item).linkId", + "repeatAll(item | answer.item) collects linkIds from items nested through both" + + " item and answer.item paths") + .build(); + } + + /** + * Creates a Questionnaire where items at different nesting levels carry extensions, to verify + * that repeatAll preserves extensions through the Variant round-trip. + * + *

Structure: + * + * 

+   *   item "1" (group, extension "ext-1")
+   *     item "1.1" (display, extension "ext-1.1")
+   *   item "2" (display, extension "ext-2")
+   *
+ * + * @return a Questionnaire resource with extensions on items + */ + private static Questionnaire createQuestionnaireWithExtensions() { + final Questionnaire questionnaire = new Questionnaire(); + questionnaire.setId("ext-questionnaire"); + questionnaire.setStatus(PublicationStatus.DRAFT); + + final QuestionnaireItemComponent item1 = questionnaire.addItem(); + item1.setLinkId("1"); + item1.setType(QuestionnaireItemType.GROUP); + item1.addExtension(new Extension("http://example.com/ext", new StringType("ext-1"))); + + final QuestionnaireItemComponent item1Sub1 = item1.addItem(); + item1Sub1.setLinkId("1.1"); + item1Sub1.setType(QuestionnaireItemType.DISPLAY); + item1Sub1.addExtension(new Extension("http://example.com/ext", new StringType("ext-1.1"))); + + final QuestionnaireItemComponent item2 = questionnaire.addItem(); + item2.setLinkId("2"); + item2.setType(QuestionnaireItemType.DISPLAY); + item2.addExtension(new Extension("http://example.com/ext", new StringType("ext-2"))); + + return questionnaire; + } + + /** + * Creates an Observation with a populated value[x] choice element (Quantity), for testing choice + * type interactions with repeatAll(). + * + * @return an Observation resource with a Quantity value + */ + private static Observation createObservation() { + final Observation observation = new Observation(); + observation.setId("test-observation"); + observation.setStatus(Observation.ObservationStatus.FINAL); + observation.setValue(new Quantity(42.0).setUnit("mg").setSystem("http://unitsofmeasure.org")); + return observation; + } + + @FhirPathTest + public Stream testRepeatAllChoiceTypeExpressions() { + return builder() + .withResource(createObservation()) + .group("repeatAll() choice type — indeterminate type guard") + .testError( + "indeterminate FHIR type", + "value.repeatAll($this)", + "repeatAll($this) on a choice type raises an indeterminate type error") + .group("repeatAll() choice type — ofType on mixed collection") + .testError( + "Recursive traversal exceeded maximum depth", + "value.repeatAll(ofType(Quantity)).count()", + "repeatAll(ofType(Quantity)) on a choice type hits depth exhaustion because" + + " Quantity.ofType(Quantity) is self-referential") + .group("repeatAll() choice type — polymorphic traversal") + .testError( + "polymorphic", + "repeatAll(value)", + "repeatAll(value) on Observation fails on MixedCollection traversal") + .group("repeatAll() choice type — first() on mixed collection") + .testError( + "Must have a fhirType or a definition", + "value.repeatAll(first())", + "repeatAll(first()) on a choice type fails during type probing") + .build(); + } + + @FhirPathTest + public Stream testRepeatAllResourceLevelDegenerate() { + return builder() + .withResource(createPatient()) + .group("repeatAll() resource-level degenerate expressions") + .testError( + "self-referential type that cannot terminate", + "name.repeatAll(%resource).gender", + "repeatAll(%resource) on a resource raises a static self-referential error") + .build(); + } + + @FhirPathTest + public Stream testRepeatAllExtensionsPreserved() { + return builder() + .withResource(createQuestionnaireWithExtensions()) + .group("repeatAll() extension preservation") + .testEquals( + List.of("ext-1", "ext-2", "ext-1.1"), + "repeatAll(item).extension('http://example.com/ext').value.ofType(string)", + "repeatAll(item) preserves extensions from all nesting levels through Variant" + + " round-trip") + .build(); + } +} diff --git a/fhirpath/src/test/java/au/csiro/pathling/fhirpath/dsl/RepeatFunctionDslTest.java b/fhirpath/src/test/java/au/csiro/pathling/fhirpath/dsl/RepeatFunctionDslTest.java new file mode 100644 index 0000000000..a68a51cef9 --- /dev/null +++ b/fhirpath/src/test/java/au/csiro/pathling/fhirpath/dsl/RepeatFunctionDslTest.java @@ -0,0 +1,396 @@ +/* + * Copyright © 2018-2026 Commonwealth Scientific and Industrial Research + * Organisation (CSIRO) ABN 41 687 119 230. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package au.csiro.pathling.fhirpath.dsl; + +import au.csiro.pathling.encoders.FhirEncoders; +import au.csiro.pathling.test.dsl.FhirPathDslTestBase; +import au.csiro.pathling.test.dsl.FhirPathTest; +import jakarta.annotation.Nonnull; +import java.util.List; +import java.util.stream.Stream; +import org.hl7.fhir.r4.model.BooleanType; +import org.hl7.fhir.r4.model.CodeableConcept; +import org.hl7.fhir.r4.model.Coding; +import org.hl7.fhir.r4.model.DateType; +import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender; +import org.hl7.fhir.r4.model.Enumerations.PublicationStatus; +import org.hl7.fhir.r4.model.Extension; +import org.hl7.fhir.r4.model.Observation; +import org.hl7.fhir.r4.model.Patient; +import org.hl7.fhir.r4.model.Quantity; +import org.hl7.fhir.r4.model.Questionnaire; +import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemComponent; +import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemType; +import org.hl7.fhir.r4.model.QuestionnaireResponse; +import org.hl7.fhir.r4.model.QuestionnaireResponse.QuestionnaireResponseItemAnswerComponent; +import org.hl7.fhir.r4.model.QuestionnaireResponse.QuestionnaireResponseItemComponent; +import org.hl7.fhir.r4.model.QuestionnaireResponse.QuestionnaireResponseStatus; +import org.hl7.fhir.r4.model.StringType; +import org.junit.jupiter.api.DynamicTest; +import org.springframework.boot.test.context.TestConfiguration; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Import; + +/** + * Tests for the FHIRPath repeat() function. + * + *

Focuses on the differences from repeatAll(): equality-based deduplication and handling of + * self-referential primitive traversal. + */ +@Import(RepeatFunctionDslTest.Config.class) +public class RepeatFunctionDslTest extends FhirPathDslTestBase { + + /** + * Provides a FhirEncoders bean with maxNestingLevel=3 to support deeply nested items in test + * Questionnaire resources. + */ + @TestConfiguration + static class Config { + + @Bean + @Nonnull + FhirEncoders fhirEncoders() { + return FhirEncoders.forR4() + .withExtensionsEnabled(true) + .withAllOpenTypes() + .withMaxNestingLevel(3) + .getOrCreate(); + } + } + + /** + * Creates a Questionnaire with items nested 3 levels deep. + * + *

Structure: + * + * 

+   *   item "1" (group)
+   *     item "1.1" (group)
+   *       item "1.1.1" (display)
+   *   item "2" (display)
+   *
+ */ + private static Questionnaire createQuestionnaire() { + final Questionnaire questionnaire = new Questionnaire(); + questionnaire.setId("test-questionnaire"); + questionnaire.setStatus(PublicationStatus.DRAFT); + + final QuestionnaireItemComponent item1 = questionnaire.addItem(); + item1.setLinkId("1"); + item1.setType(QuestionnaireItemType.GROUP); + + final QuestionnaireItemComponent item1Sub1 = item1.addItem(); + item1Sub1.setLinkId("1.1"); + item1Sub1.setType(QuestionnaireItemType.GROUP); + + final QuestionnaireItemComponent item1Sub1Sub1 = item1Sub1.addItem(); + item1Sub1Sub1.setLinkId("1.1.1"); + item1Sub1Sub1.setType(QuestionnaireItemType.DISPLAY); + + final QuestionnaireItemComponent item2 = questionnaire.addItem(); + item2.setLinkId("2"); + item2.setType(QuestionnaireItemType.DISPLAY); + + return questionnaire; + } + + private static Patient createPatient() { + final Patient patient = new Patient(); + patient.setId("test-patient"); + patient.addName().setFamily("Smith"); + patient.addName().setFamily("Jones"); + patient.setGender(AdministrativeGender.MALE); + patient.setMaritalStatus( + new CodeableConcept(new Coding("http://example.com/cs", "M", "Married"))); + + patient.addExtension( + new Extension("http://example.com/simple", new StringType("simple-value"))); + + final Extension parent = new Extension("http://example.com/parent"); + parent.addExtension(new Extension("http://example.com/child", new StringType("child-value"))); + patient.addExtension(parent); + + return patient; + } + + @FhirPathTest + public Stream testRepeatBasicTreeTraversal() { + return builder() + .withResource(createQuestionnaire()) + .group("repeat() basic traversal") + .testEquals( + List.of("1", "2", "1.1", "1.1.1"), + "repeat(item).linkId", + "repeat(item).linkId returns linkIds from all nesting levels") + .testEquals( + 4, "repeat(item).count()", "repeat(item).count() returns total items across all levels") + .group("repeat() with filtering") + .testEquals( + List.of("1", "1.1"), + "repeat(item).where(type = 'group').linkId", + "repeat(item).where(type = 'group') filters items from all nesting levels") + .build(); + } + + @FhirPathTest + public Stream testRepeatPrimitiveDedup() { + return builder() + .withResource(createPatient()) + .group("repeat() primitive self-referential deduplication") + .testEquals( + "male", + "gender.repeat($this)", + "repeat($this) on a primitive returns the deduplicated value") + .testEquals( + 1, + "gender.repeat($this).count()", + "repeat($this) on a primitive deduplicates to a single value") + .testEquals( + "someValue", + "gender.repeat('someValue')", + "repeat('literal') on a primitive returns the constant deduplicated") + .build(); + } + + @FhirPathTest + public Stream testRepeatComplexTypeNoDedup() { + final Questionnaire questionnaire = new Questionnaire(); + questionnaire.setId("dup-questionnaire"); + questionnaire.setStatus(PublicationStatus.DRAFT); + + final QuestionnaireItemComponent item1 = questionnaire.addItem(); + item1.setLinkId("A"); + item1.setType(QuestionnaireItemType.GROUP); + + final QuestionnaireItemComponent item1Child = item1.addItem(); + item1Child.setLinkId("B"); + item1Child.setType(QuestionnaireItemType.DISPLAY); + + final QuestionnaireItemComponent item2 = questionnaire.addItem(); + item2.setLinkId("B"); + item2.setType(QuestionnaireItemType.DISPLAY); + + return builder() + .withResource(questionnaire) + .group("repeat() complex type - no dedup applied") + .testEquals( + List.of("A", "B", "B"), + "repeat(item).linkId", + "repeat(item).linkId preserves items with the same linkId from different nesting" + + " levels because complex types are not deduplicated") + .testEquals( + 3, "repeat(item).count()", "repeat(item).count() includes all items without dedup") + .build(); + } + + @FhirPathTest + public Stream testRepeatEmptyInput() { + final Questionnaire empty = new Questionnaire(); + empty.setId("empty-questionnaire"); + empty.setStatus(PublicationStatus.DRAFT); + + return builder() + .withResource(empty) + .group("repeat() empty input") + .testEmpty("repeat(item)", "repeat() on a resource with no items returns empty collection") + .testEquals(0, "repeat(item).count()", "repeat(item).count() returns 0 for empty input") + .group("repeat() empty literal") + .testEmpty( + "{}.repeat($this)", "repeat() on the FHIRPath empty literal returns empty collection") + .build(); + } + + @FhirPathTest + public Stream testRepeatExtensionTraversal() { + return builder() + .withResource(createPatient()) + .group("repeat() extension traversal") + .testEquals( + List.of( + "http://example.com/simple", + "http://example.com/parent", + "http://example.com/child"), + "repeat(extension).url", + "repeat(extension) recursively collects all extensions including nested" + + " sub-extensions") + .build(); + } + + /** + * Creates an Observation with a populated value[x] choice element (Quantity), for testing choice + * type interactions with repeat(). + * + * @return an Observation resource with a Quantity value + */ + private static Observation createObservation() { + final Observation observation = new Observation(); + observation.setId("test-observation"); + observation.setStatus(Observation.ObservationStatus.FINAL); + observation.setValue(new Quantity(42.0).setUnit("mg").setSystem("http://unitsofmeasure.org")); + return observation; + } + + @FhirPathTest + public Stream testRepeatChoiceTypeExpressions() { + return builder() + .withResource(createObservation()) + .group("repeat() choice type — indeterminate type guard") + .testError( + "indeterminate FHIR type", + "value.repeat($this)", + "repeat($this) on a choice type raises an indeterminate type error") + .group("repeat() choice type — ofType resolves and terminates") + .testEquals( + 42.0, + "repeat(value.ofType(Quantity)).value", + "repeat(value.ofType(Quantity)) returns the Quantity value (level_1 empty, early" + + " return)") + .build(); + } + + @FhirPathTest + public Stream testRepeatSelfReferentialComplex() { + return builder() + .withResource(createPatient()) + .group("repeat() self-referential complex expressions") + .testEquals( + 1, + "repeat($this).count()", + "repeat($this) on a resource returns the resource (dedup collapses depth-limited" + + " copies)") + .testEquals( + "male", + "name.repeat(%resource).gender", + "repeat(%resource) returns the patient's gender (dedup collapses to single resource)") + .build(); + } + + /** + * Creates a QuestionnaireResponse with items nested through both item and answer.item paths. + * + *

Structure: + * + * 

+   *   item "1" (Demographics)
+   *     item "1.1" (Name)
+   *       answer "Jane Doe"
+   *         item "1.1.1" (Name confirmed)
+   *           answer true
+   *     item "1.2" (Date of Birth)
+   *       answer "1990-01-15"
+   *   item "2" (Medical History)
+   *     item "2.1" (Conditions)
+   *       answer true
+   *         item "2.1.1" (Condition details)
+   *           answer "Type 2 Diabetes"
+   *
+ */ + private static QuestionnaireResponse createQuestionnaireResponse() { + final QuestionnaireResponse qr = new QuestionnaireResponse(); + qr.setId("example"); + qr.setStatus(QuestionnaireResponseStatus.COMPLETED); + + // item "1" (Demographics). + final QuestionnaireResponseItemComponent item1 = qr.addItem(); + item1.setLinkId("1"); + item1.setText("Demographics"); + + // item "1.1" (Name). + final QuestionnaireResponseItemComponent item1Sub1 = item1.addItem(); + item1Sub1.setLinkId("1.1"); + item1Sub1.setText("Name"); + + // answer "Jane Doe" with nested item "1.1.1". + final QuestionnaireResponseItemAnswerComponent answer1Sub1 = item1Sub1.addAnswer(); + answer1Sub1.setValue(new StringType("Jane Doe")); + final QuestionnaireResponseItemComponent item1Sub1Sub1 = answer1Sub1.addItem(); + item1Sub1Sub1.setLinkId("1.1.1"); + item1Sub1Sub1.setText("Name confirmed"); + item1Sub1Sub1.addAnswer().setValue(new BooleanType(true)); + + // item "1.2" (Date of Birth). + final QuestionnaireResponseItemComponent item1Sub2 = item1.addItem(); + item1Sub2.setLinkId("1.2"); + item1Sub2.setText("Date of Birth"); + item1Sub2.addAnswer().setValue(new DateType("1990-01-15")); + + // item "2" (Medical History). + final QuestionnaireResponseItemComponent item2 = qr.addItem(); + item2.setLinkId("2"); + item2.setText("Medical History"); + + // item "2.1" (Conditions). + final QuestionnaireResponseItemComponent item2Sub1 = item2.addItem(); + item2Sub1.setLinkId("2.1"); + item2Sub1.setText("Conditions"); + + // answer true with nested item "2.1.1". + final QuestionnaireResponseItemAnswerComponent answer2Sub1 = item2Sub1.addAnswer(); + answer2Sub1.setValue(new BooleanType(true)); + final QuestionnaireResponseItemComponent item2Sub1Sub1 = answer2Sub1.addItem(); + item2Sub1Sub1.setLinkId("2.1.1"); + item2Sub1Sub1.setText("Condition details"); + item2Sub1Sub1.addAnswer().setValue(new StringType("Type 2 Diabetes")); + + return qr; + } + + @FhirPathTest + public Stream testRepeatUnionTraversal() { + return builder() + .withResource(createQuestionnaireResponse()) + .group("repeat() with union expression on QuestionnaireResponse") + .testEquals( + List.of("1", "2", "1.1", "1.2", "2.1", "1.1.1", "2.1.1"), + "repeat(item | answer.item).linkId", + "repeat(item | answer.item).linkId collects linkIds from items nested through both" + + " item and answer.item paths") + .testEquals( + 7, + "repeat(item | answer.item).count()", + "repeat(item | answer.item).count() returns total items from all paths and levels") + .testEquals( + List.of( + "Demographics", + "Medical History", + "Name", + "Date of Birth", + "Conditions", + "Name confirmed", + "Condition details"), + "repeat(item | answer.item).text", + "repeat(item | answer.item).text collects text from all items") + .build(); + } + + @FhirPathTest + public Stream testRepeatChainedOperations() { + return builder() + .withResource(createQuestionnaire()) + .group("repeat() chained operations") + .testEquals( + List.of("1", "2", "1.1", "1.1.1"), + "repeat(item).linkId", + "repeat(item).linkId chains path navigation after repeat") + .testEquals( + List.of("2", "1.1.1"), + "repeat(item).where(type = 'display').linkId", + "repeat(item).where().linkId chains where and path after repeat") + .build(); + } +} diff --git a/fhirpath/src/test/java/au/csiro/pathling/fhirpath/dsl/SelectFunctionDslTest.java b/fhirpath/src/test/java/au/csiro/pathling/fhirpath/dsl/SelectFunctionDslTest.java new file mode 100644 index 0000000000..27a6fd55ec --- /dev/null +++ b/fhirpath/src/test/java/au/csiro/pathling/fhirpath/dsl/SelectFunctionDslTest.java @@ -0,0 +1,114 @@ +/* + * Copyright © 2018-2026 Commonwealth Scientific and Industrial Research + * Organisation (CSIRO) ABN 41 687 119 230. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package au.csiro.pathling.fhirpath.dsl; + +import au.csiro.pathling.test.dsl.FhirPathDslTestBase; +import au.csiro.pathling.test.dsl.FhirPathTest; +import java.util.List; +import java.util.stream.Stream; +import org.junit.jupiter.api.DynamicTest; + +/** Tests for the FHIRPath select() function. */ +public class SelectFunctionDslTest extends FhirPathDslTestBase { + + @FhirPathTest + public Stream testSelectSimpleProperty() { + return builder() + .withSubject( + sb -> + sb.elementArray( + "people", + person1 -> person1.string("name", "Alice").integer("age", 25), + person2 -> person2.string("name", "Bob").integer("age", 40), + person3 -> person3.string("name", "Charlie").integer("age", 35))) + .group("select() simple property projection") + .testEquals( + List.of("Alice", "Bob", "Charlie"), + "people.select(name)", + "select() projects a simple string property from each element") + .testEquals( + List.of(25, 40, 35), + "people.select(age)", + "select() projects a simple integer property from each element") + .build(); + } + + @FhirPathTest + public Stream testSelectFlatteningMultiValued() { + return builder() + .withSubject( + sb -> + sb.elementArray( + "contacts", + c1 -> c1.string("name", "Alice").stringArray("phones", "111", "222"), + c2 -> c2.string("name", "Bob").stringArray("phones", "333"), + c3 -> c3.string("name", "Charlie").stringArray("phones", "444", "555", "666"))) + .group("select() flattening of multi-valued results") + .testEquals( + List.of("111", "222", "333", "444", "555", "666"), + "contacts.select(phones)", + "select() flattens multi-valued projection results into a single collection") + .build(); + } + + @FhirPathTest + public Stream testSelectEmptyResults() { + return builder() + .withSubject( + sb -> + sb.elementArray( + "items", + item1 -> item1.string("label", "first").stringEmpty("note"), + item2 -> item2.string("label", "second").string("note", "important"), + item3 -> item3.string("label", "third").stringEmpty("note"))) + .group("select() empty projection results") + .testEquals( + "important", + "items.select(note)", + "select() omits elements whose projection evaluates to empty") + .build(); + } + + @FhirPathTest + public Stream testSelectEmptyInput() { + return builder() + .withSubject(sb -> sb.string("dummy", "value")) + .group("select() empty input collection") + .testEmpty("{}.select($this)", "select() on an empty collection returns empty") + .build(); + } + + @FhirPathTest + public Stream testSelectExpression() { + return builder() + .withSubject( + sb -> + sb.stringArray("names", "Alice", "Bob", "Charlie") + .integerArray("numbers", 1, 2, 3, 4, 5)) + .group("select() with expressions") + .testEquals( + List.of(true, true, true), + "names.select($this.exists())", + "select() evaluates an expression for each element") + .testEquals( + List.of(true, true, true, true, true), + "numbers.select($this > 0)", + "select() evaluates a comparison expression for each element") + .build(); + } +} diff --git a/fhirpath/src/test/java/au/csiro/pathling/fhirpath/function/FunctionParameterResolverTest.java b/fhirpath/src/test/java/au/csiro/pathling/fhirpath/function/FunctionParameterResolverTest.java index 0dc9edc214..11e6e6fb82 100644 --- a/fhirpath/src/test/java/au/csiro/pathling/fhirpath/function/FunctionParameterResolverTest.java +++ b/fhirpath/src/test/java/au/csiro/pathling/fhirpath/function/FunctionParameterResolverTest.java @@ -103,6 +103,15 @@ public static Collection funcBooleanCollection(@Nonnull final BooleanCollection return null; } + @Nullable + @SuppressWarnings("unused") + public static Collection funcWithContext( + @Nonnull final Collection input, + @Nonnull final CollectionTransform transform, + @Nonnull final EvaluationContext context) { + return null; + } + @Nullable @SuppressWarnings("unused") static Collection invalidFunction() { @@ -315,6 +324,30 @@ void failsForFailedConversionToConcepts() { ex.getMessage()); } + @Test + void testEvaluationContextInjection() { + final Collection input = mock(Collection.class); + final BooleanCollection transformResult = mock(BooleanCollection.class); + final FhirPath transformPath = mock(FhirPath.class); + final StringCollection transformArgument = mock(StringCollection.class); + when(transformPath.apply(transformArgument, evaluationContext)).thenReturn(transformResult); + + // Only one FHIRPath argument (the transform), but the method has 3 parameters. + // The EvaluationContext should be injected without consuming an argument. + final FunctionParameterResolver resolver = + new FunctionParameterResolver(evaluationContext, input, List.of(transformPath)); + final Method method = getMethod("funcWithContext"); + final FunctionInvocation invocation = resolver.bind(method); + assertEquals(method, invocation.method()); + assertEquals(input, invocation.arguments()[0]); + // The second argument should be the transform. + assertEquals( + transformResult, + ((CollectionTransform) invocation.arguments()[1]).apply(transformArgument)); + // The third argument should be the injected evaluation context. + assertEquals(evaluationContext, invocation.arguments()[2]); + } + @Test void failsForInvalidTypeArgument() { final Collection input = mock(Collection.class); diff --git a/fhirpath/src/test/java/au/csiro/pathling/fhirpath/yaml/YamlReferenceImplTest.java b/fhirpath/src/test/java/au/csiro/pathling/fhirpath/yaml/YamlReferenceImplTest.java index 03f780cc43..8e3450d886 100644 --- a/fhirpath/src/test/java/au/csiro/pathling/fhirpath/yaml/YamlReferenceImplTest.java +++ b/fhirpath/src/test/java/au/csiro/pathling/fhirpath/yaml/YamlReferenceImplTest.java @@ -17,17 +17,40 @@ package au.csiro.pathling.fhirpath.yaml; +import au.csiro.pathling.encoders.FhirEncoders; import au.csiro.pathling.test.yaml.YamlCachedTestBase; import au.csiro.pathling.test.yaml.annotations.YamlTest; import au.csiro.pathling.test.yaml.annotations.YamlTestConfiguration; import au.csiro.pathling.test.yaml.executor.YamlTestExecutor; import jakarta.annotation.Nonnull; import lombok.extern.slf4j.Slf4j; +import org.springframework.boot.test.context.TestConfiguration; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Import; @Slf4j @YamlTestConfiguration(config = "fhirpath-js/config.yaml", resourceBase = "fhirpath-js/resources") +@Import(YamlReferenceImplTest.Config.class) public class YamlReferenceImplTest extends YamlCachedTestBase { + /** + * Provides FhirEncoders with maxNestingLevel=4 to support deeply nested resource structures + * required by reference test cases (e.g., Questionnaire items nested 5 levels deep). + */ + @TestConfiguration + static class Config { + + @Bean + @Nonnull + FhirEncoders fhirEncoders() { + return FhirEncoders.forR4() + .withExtensionsEnabled(true) + .withAllOpenTypes() + .withMaxNestingLevel(4) + .getOrCreate(); + } + } + // From: https://github.com/hl7/fhirpath.js/ // Tag: 3.16.4 // diff --git a/fhirpath/src/test/java/au/csiro/pathling/views/FhirViewIntegrationTest.java b/fhirpath/src/test/java/au/csiro/pathling/views/FhirViewIntegrationTest.java new file mode 100644 index 0000000000..8df4366911 --- /dev/null +++ b/fhirpath/src/test/java/au/csiro/pathling/views/FhirViewIntegrationTest.java @@ -0,0 +1,122 @@ +/* + * Copyright © 2018-2026 Commonwealth Scientific and Industrial Research + * Organisation (CSIRO) ABN 41 687 119 230. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package au.csiro.pathling.views; + +import au.csiro.pathling.encoders.FhirEncoders; +import au.csiro.pathling.test.SpringBootUnitTest; +import au.csiro.pathling.test.assertions.DatasetAssert; +import au.csiro.pathling.test.datasource.ObjectDataSource; +import ca.uhn.fhir.context.FhirContext; +import com.google.gson.Gson; +import java.util.List; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.RowFactory; +import org.apache.spark.sql.SparkSession; +import org.hl7.fhir.r4.model.CodeableConcept; +import org.hl7.fhir.r4.model.Coding; +import org.hl7.fhir.r4.model.Condition; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; + +/** + * Integration tests that verify physical row data integrity when collecting view results using + * {@code collectAsList()}. These tests complement the JSON-based {@link FhirViewExtraTest} by + * exercising the actual collection path, which can expose Spark Catalyst optimizer issues that + * DataFrame-level comparisons (resolving columns by ExprId) would not detect. + * + * @see Issue #2568 + */ +@SpringBootUnitTest +class FhirViewIntegrationTest { + + @Autowired SparkSession spark; + + @Autowired FhirEncoders fhirEncoders; + + @Autowired FhirContext fhirContext; + + @Autowired Gson gson; + + @Test + void testForEachCodingWithSiblingTextColumn() { + final Condition cond1 = new Condition(); + cond1.setId("Condition/cond1"); + cond1.setCode( + new CodeableConcept() + .setText("Headache disorder") + .addCoding(new Coding("http://snomed.info/sct", "25064002", "Headache")) + .addCoding(new Coding("http://hl7.org/fhir/sid/icd-10", "R51", "Headache"))); + + final Condition cond2 = new Condition(); + cond2.setId("Condition/cond2"); + cond2.setCode( + new CodeableConcept() + .setText("Diabetes mellitus") + .addCoding(new Coding("http://snomed.info/sct", "73211009", "Diabetes mellitus"))); + + final ObjectDataSource dataSource = + new ObjectDataSource(spark, fhirEncoders, List.of(cond1, cond2)); + final FhirViewExecutor executor = new FhirViewExecutor(fhirContext, dataSource); + + // ViewDefinition: id + code.text at resource level, forEach code.coding with + // system/code/display. + final String viewJson = + """ + { + "resource": "Condition", + "select": [ + { + "column": [ + {"path": "id", "name": "id"}, + {"path": "code.text", "name": "code_text"} + ], + "select": [ + { + "forEach": "code.coding", + "column": [ + {"path": "system", "name": "system"}, + {"path": "code", "name": "code"}, + {"path": "display", "name": "display"} + ] + } + ] + } + ] + } + """; + + final FhirView view = gson.fromJson(viewJson, FhirView.class); + final Dataset result = executor.buildQuery(view); + + // Verify collected rows match expected data exactly. Using hasRows() (which calls + // collectAsList()) exercises the physical collection path where the bug manifested. + DatasetAssert.of(result) + .hasRows( + RowFactory.create( + "cond1", "Headache disorder", "http://snomed.info/sct", "25064002", "Headache"), + RowFactory.create( + "cond1", "Headache disorder", "http://hl7.org/fhir/sid/icd-10", "R51", "Headache"), + RowFactory.create( + "cond2", + "Diabetes mellitus", + "http://snomed.info/sct", + "73211009", + "Diabetes mellitus")); + } +} diff --git a/fhirpath/src/test/resources/fhirpath-js/config.yaml b/fhirpath/src/test/resources/fhirpath-js/config.yaml index 4cdfa36b50..cb8f17014d 100644 --- a/fhirpath/src/test/resources/fhirpath-js/config.yaml +++ b/fhirpath/src/test/resources/fhirpath-js/config.yaml @@ -167,6 +167,15 @@ excludeSet: return 0 instead of 1. any: - "Patient.name.given.where(id = 'Jacomus1Id').count()" + - title: "repeat() on id attribute of primitive elements not supported" + type: feature + outcome: failure + id: "#437" + comment: | + This test uses repeat() to traverse the id attribute of primitive elements. + Pathling does not support accessing the id attribute of primitive elements. + any: + - "Patient.name.given.repeat(id)" - title: Equality exclusions glob: "fhirpath-js/cases/6.1_equality.yaml" exclude: @@ -414,6 +423,15 @@ excludeSet: type: wontfix any: - "Patient.name.exists(given)" + - title: "length without parentheses treated as child traversal" + type: wontfix + outcome: failure + comment: | + FHIRPath length() requires parentheses. The test uses $this.length + (without parentheses), which Pathling treats as a child field access + rather than the length() function, returning null. + any: + - "Patient.name.given.select($this.length) = Patient.name.given.select(length)" - title: "Unsupported type runner feature: expression maps" type: new-feature any: @@ -578,6 +596,8 @@ excludeSet: any: - "mixedTypeVals.as(Integer)" - "mixedTypeVals as Integer" + - "mixedTypeVals.select($this as Integer)" + - "mixedTypeVals.select($this.as(Integer))" - title: "Operator precedence of is/as causes union type errors" type: wontfix outcome: error @@ -594,4 +614,13 @@ excludeSet: This is correct behavior per spec operator precedence rules. any: - "1 | 1 is Integer" - + - title: "Recursive ValueSet.expansion.contains not encoded" + type: feature + outcome: failure + comment: | + The encoder explicitly skips the recursive 'contains' field within + ValueSetExpansionContainsComponent (see R4DataTypeMappings.skipField). + This means nested contains entries are not available in the Spark schema, + so repeat(contains) only finds top-level entries. + any: + - "** testRepeat1" diff --git a/lib/python/pyproject.toml b/lib/python/pyproject.toml index d724c2ca67..e928b1c02f 100644 --- a/lib/python/pyproject.toml +++ b/lib/python/pyproject.toml @@ -55,6 +55,8 @@ dev = [ "pytest-cov==5.0.0", "http-server-mock==1.7", "ruff>=0.8.0", + "pandas>=2.3.3", + "pyarrow>=21.0.0", ] [tool.hatch.version] diff --git a/lib/python/tests/test_view.py b/lib/python/tests/test_view.py index 1af4203855..f41dcbb5b9 100644 --- a/lib/python/tests/test_view.py +++ b/lib/python/tests/test_view.py @@ -45,3 +45,63 @@ def test_view_on_ndjson(ndjson_test_data_dir, pathling_ctx): ResultRow("8ee183e2-b3c0-4151-be94-b945d6aa8c6d", "Krajcik437"), ResultRow("beff242e-580b-47c0-9844-c1a68c36c5bf", "Towne435"), ] + + +ConditionCodingRow = Row("id", "code_text", "system", "code", "display") + + +def test_foreach_coding_with_sibling_text_topandas(ndjson_test_data_dir, pathling_ctx): + """Reproduces #2568: toPandas() corrupts data when combining code.text + with forEach code.coding.""" + data_source = pathling_ctx.read.ndjson(ndjson_test_data_dir) + result = data_source.view( + resource="Condition", + select=[ + { + "column": [ + {"path": "id", "name": "id"}, + {"path": "code.text", "name": "code_text"}, + ], + "select": [ + { + "forEach": "code.coding", + "column": [ + {"path": "system", "name": "system"}, + {"path": "code", "name": "code"}, + {"path": "display", "name": "display"}, + ], + } + ], + } + ], + ) + + # toPandas() exercises the physical collection path where the bug manifested. + pdf = result.toPandas() + assert list(pdf.columns) == list(ConditionCodingRow) + + # Verify the first few rows have correct column alignment. + first_rows = result.limit(3).collect() + assert first_rows == [ + ConditionCodingRow( + "c879c300-7fdf-4b53-aa6a-a2b4a266b30c", + "Viral sinusitis (disorder)", + "http://snomed.info/sct", + "444814009", + "Viral sinusitis (disorder)", + ), + ConditionCodingRow( + "bb9c4fc1-795a-4492-b065-1f497fe18bb2", + "Diabetes", + "http://snomed.info/sct", + "44054006", + "Diabetes", + ), + ConditionCodingRow( + "e620d7ee-6cfe-4f04-ba06-1d0b39f7624d", + "Anemia (disorder)", + "http://snomed.info/sct", + "271737000", + "Anemia (disorder)", + ), + ] diff --git a/lib/python/uv.lock b/lib/python/uv.lock index 52ca4077f3..47c9fef95f 100644 --- a/lib/python/uv.lock +++ b/lib/python/uv.lock @@ -1,8 +1,14 @@ version = 1 -revision = 2 +revision = 3 requires-python = ">=3.9" resolution-markers = [ - "python_full_version >= '3.10'", + "python_full_version >= '3.14' and sys_platform == 'win32'", + "python_full_version >= '3.14' and sys_platform == 'emscripten'", + "python_full_version >= '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'", + "python_full_version >= '3.11' and python_full_version < '3.14' and sys_platform == 'win32'", + 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b/library-api/src/main/java/au/csiro/pathling/library/PathlingContext.java index c63aa306ae..09c3f1a7de 100644 --- a/library-api/src/main/java/au/csiro/pathling/library/PathlingContext.java +++ b/library-api/src/main/java/au/csiro/pathling/library/PathlingContext.java @@ -21,6 +21,7 @@ import au.csiro.pathling.PathlingVersion; import au.csiro.pathling.config.EncodingConfiguration; +import au.csiro.pathling.config.FhirpathConfiguration; import au.csiro.pathling.config.QueryConfiguration; import au.csiro.pathling.config.TerminologyConfiguration; import au.csiro.pathling.encoders.FhirEncoderBuilder; @@ -744,13 +745,19 @@ public SingleInstanceEvaluationResult evaluateFhirPath( // Encode the resource JSON into a one-row Spark Dataset. final Dataset resourceDf = encodeResourceJson(resourceType, resourceJson); + final FhirpathConfiguration fhirpathConfig = + FhirpathConfiguration.builder() + .maxUnboundTraversalDepth(queryConfiguration.getMaxUnboundTraversalDepth()) + .build(); + return SingleInstanceEvaluator.evaluate( resourceDf, resourceType, getFhirContext(), fhirPathExpression, contextExpression, - variables); + variables, + fhirpathConfig); } /** diff --git a/library-api/src/test/java/au/csiro/pathling/library/EvaluateRepeatAllTest.java b/library-api/src/test/java/au/csiro/pathling/library/EvaluateRepeatAllTest.java new file mode 100644 index 0000000000..ab918bd790 --- /dev/null +++ b/library-api/src/test/java/au/csiro/pathling/library/EvaluateRepeatAllTest.java @@ -0,0 +1,200 @@ +/* + * Copyright © 2018-2026 Commonwealth Scientific and Industrial Research + * Organisation (CSIRO) ABN 41 687 119 230. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package au.csiro.pathling.library; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import au.csiro.pathling.config.EncodingConfiguration; +import au.csiro.pathling.config.QueryConfiguration; +import au.csiro.pathling.fhirpath.evaluation.SingleInstanceEvaluationResult; +import au.csiro.pathling.fhirpath.evaluation.SingleInstanceEvaluationResult.TypedValue; +import java.util.HashSet; +import java.util.Set; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; + +/** + * Integration test for the FHIRPath repeatAll() function via the library API. + * + *

Evaluates repeatAll() against a Questionnaire JSON resource with nested items to verify that + * all nesting levels are traversed correctly. + * + * @author Piotr Szul + */ +class EvaluateRepeatAllTest { + + private static SparkSession spark; + private static PathlingContext pathling; + + private static final String QUESTIONNAIRE_JSON = + """ + { + "resourceType": "Questionnaire", + "id": "test-questionnaire", + "status": "draft", + "item": [ + { + "linkId": "1", + "type": "group", + "item": [ + { + "linkId": "1.1", + "type": "group", + "item": [ + { + "linkId": "1.1.1", + "type": "display" + } + ] + } + ] + }, + { + "linkId": "2", + "type": "display" + } + ] + } + """; + + /** Set up Spark and PathlingContext with maxNestingLevel=3 to support deeply nested items. */ + @BeforeAll + static void setUpAll() { + spark = TestHelpers.spark(); + final EncodingConfiguration encodingConfig = + EncodingConfiguration.builder().maxNestingLevel(3).build(); + pathling = PathlingContext.builder(spark).encodingConfiguration(encodingConfig).build(); + } + + /** Tear down Spark. */ + @AfterAll + static void tearDownAll() { + spark.stop(); + } + + @Test + void evaluateRepeatAllLinkId() { + // Evaluating repeatAll(item).linkId should return linkIds from all nesting levels. + final SingleInstanceEvaluationResult result = + pathling.evaluateFhirPath("Questionnaire", QUESTIONNAIRE_JSON, "repeatAll(item).linkId"); + + assertNotNull(result); + assertEquals(4, result.getResults().size()); + + final Set linkIds = + new HashSet<>(result.getResults().stream().map(TypedValue::getValue).toList()); + assertEquals(Set.of("1", "2", "1.1", "1.1.1"), linkIds); + } + + @Test + void evaluateRepeatAllCount() { + // Evaluating repeatAll(item).count() should return the total number of items across all levels. + final SingleInstanceEvaluationResult result = + pathling.evaluateFhirPath("Questionnaire", QUESTIONNAIRE_JSON, "repeatAll(item).count()"); + + assertNotNull(result); + assertEquals(1, result.getResults().size()); + + final TypedValue countValue = result.getResults().getFirst(); + assertEquals("integer", countValue.getType()); + assertEquals(4, countValue.getValue()); + } + + @Test + void itemsTraverseDeeperThanDepthLimit() { + // Questionnaire items use different SQL types at each nesting level (due to schema + // truncation), so each level is a cross-type traversal that does not consume depth budget. + // With maxUnboundTraversalDepth=1, all 4 items across 3 nesting levels should still be + // returned. + final PathlingContext shallowDepthPathling = + PathlingContext.builder(spark) + .encodingConfiguration(EncodingConfiguration.builder().maxNestingLevel(3).build()) + .queryConfiguration(QueryConfiguration.builder().maxUnboundTraversalDepth(1).build()) + .build(); + + final SingleInstanceEvaluationResult result = + shallowDepthPathling.evaluateFhirPath( + "Questionnaire", QUESTIONNAIRE_JSON, "repeatAll(item).linkId"); + + assertNotNull(result); + assertEquals(4, result.getResults().size()); + + final Set linkIds = + new HashSet<>(result.getResults().stream().map(TypedValue::getValue).toList()); + assertEquals(Set.of("1", "2", "1.1", "1.1.1"), linkIds); + } + + @Test + void extensionsLimitedByDepth() { + // Extensions have the same SQL type at every nesting level, so each level is a same-type + // traversal that consumes depth budget. With maxUnboundTraversalDepth=1, only extensions up + // to depth 1 should be returned — fewer than the 3 total levels in the data. + final String patientJson = + """ + { + "resourceType": "Patient", + "id": "test-patient", + "extension": [ + { + "url": "http://example.com/ext1", + "extension": [ + { + "url": "http://example.com/ext2", + "extension": [ + { + "url": "http://example.com/ext3", + "valueString": "deep" + } + ] + } + ] + } + ] + } + """; + + // First verify baseline: with default depth (10), all 3 extensions are returned. + final SingleInstanceEvaluationResult baselineResult = + pathling.evaluateFhirPath("Patient", patientJson, "repeatAll(extension).url"); + assertNotNull(baselineResult); + assertEquals(3, baselineResult.getResults().size()); + + // Now with maxUnboundTraversalDepth=1, fewer extensions should be returned. + final PathlingContext shallowDepthPathling = + PathlingContext.builder(spark) + .encodingConfiguration(EncodingConfiguration.builder().maxNestingLevel(3).build()) + .queryConfiguration(QueryConfiguration.builder().maxUnboundTraversalDepth(1).build()) + .build(); + + final SingleInstanceEvaluationResult limitedResult = + shallowDepthPathling.evaluateFhirPath("Patient", patientJson, "repeatAll(extension).url"); + + assertNotNull(limitedResult); + final Set urls = + new HashSet<>(limitedResult.getResults().stream().map(TypedValue::getValue).toList()); + // With maxDepth=1: ext1 at depth 0 + ext2 at depth 1 = 2 extensions. ext3 is excluded + // because reaching it would require depth 2. + assertEquals( + Set.of("http://example.com/ext1", "http://example.com/ext2"), + urls, + "Expected only 2 extensions with maxUnboundTraversalDepth=1"); + } +} diff --git a/library-api/src/test/java/au/csiro/pathling/library/PathlingContextTest.java b/library-api/src/test/java/au/csiro/pathling/library/PathlingContextTest.java index 250e5a23e8..5fbaf5aec2 100644 --- a/library-api/src/test/java/au/csiro/pathling/library/PathlingContextTest.java +++ b/library-api/src/test/java/au/csiro/pathling/library/PathlingContextTest.java @@ -525,7 +525,7 @@ void testBuildContextWithDefaultQueryConfiguration() { @Test void failsOnInvalidQueryConfiguration() { - // Test with negative maxUnboundTraversalDepth + // Test with negative maxUnboundTraversalDepth. final QueryConfiguration invalidQueryConfig = QueryConfiguration.builder().maxUnboundTraversalDepth(-5).build(); @@ -537,9 +537,29 @@ void failsOnInvalidQueryConfiguration() { final String message = ex.getMessage(); assertTrue( - message.contains("maxUnboundTraversalDepth: must be greater than or equal to 0"), + message.contains("maxUnboundTraversalDepth: must be greater than or equal to 1"), "Expected error message to contain 'maxUnboundTraversalDepth: must be greater than or equal" - + " to 0', but was: " + + " to 1', but was: " + + message); + } + + @Test + void failsOnZeroMaxUnboundTraversalDepth() { + // Test that zero is also rejected with @Min(1). + final QueryConfiguration zeroDepthConfig = + QueryConfiguration.builder().maxUnboundTraversalDepth(0).build(); + + final PathlingContext.Builder builder = + PathlingContext.builder(spark).queryConfiguration(zeroDepthConfig); + + final ConstraintViolationException ex = + assertThrows(ConstraintViolationException.class, builder::build); + + final String message = ex.getMessage(); + assertTrue( + message.contains("maxUnboundTraversalDepth: must be greater than or equal to 1"), + "Expected error message to contain 'maxUnboundTraversalDepth: must be greater than or equal" + + " to 1', but was: " + message); } diff --git a/openspec/changes/archive/2026-02-25-support-select-function/.openspec.yaml b/openspec/changes/archive/2026-02-25-support-select-function/.openspec.yaml new file mode 100644 index 0000000000..e331c975d9 --- /dev/null +++ b/openspec/changes/archive/2026-02-25-support-select-function/.openspec.yaml @@ -0,0 +1,2 @@ +schema: spec-driven +created: 2026-02-25 diff --git a/openspec/changes/archive/2026-02-25-support-select-function/design.md b/openspec/changes/archive/2026-02-25-support-select-function/design.md new file mode 100644 index 0000000000..0c2b444b9a --- /dev/null +++ b/openspec/changes/archive/2026-02-25-support-select-function/design.md @@ -0,0 +1,41 @@ +## Context + +Pathling's FHIRPath engine implements functions as annotated static methods in provider classes (e.g., `FilteringAndProjectionFunctions`). The `where` function already demonstrates the pattern for functions that take an expression parameter: it receives a `CollectionTransform` that wraps the parsed FHIRPath expression, converts it to a `ColumnTransform`, and applies it via `Collection.filter()`. + +The `select` function is closely related to `where` - both iterate over elements and evaluate an expression per element. The difference is that `where` uses the expression result as a boolean filter, while `select` uses it as a projection (the expression result replaces the element). + +## Goals / Non-Goals + +**Goals:** + +- Implement the FHIRPath `select(projection: expression) : collection` function per the specification +- Follow existing patterns established by `where` for expression-parameter functions +- Support flattening of results (collections produced by the projection are merged into the output) + +**Non-Goals:** + +- Supporting `$this` and `$index` special variables within `select` expressions (these may already work through existing infrastructure, but are not a specific goal) +- Optimising for deeply nested projections + +## Decisions + +### 1. Implement as a new method in `FilteringAndProjectionFunctions` + +**Rationale:** The FHIRPath spec groups `select` under "Filtering and projection" alongside `where`. The existing class already handles this category. Adding `select` here maintains the logical grouping. + +**Alternative considered:** Creating a separate provider class. Rejected because it would fragment closely related functions. + +### 2. Use `CollectionTransform.toColumnTransformation()` for expression application + +**Rationale:** The `toColumnTransformation` method already handles the pattern of applying an expression to each element by creating a copy of the input with the element's column, evaluating the expression, and returning the resulting column. This is exactly what `select` needs - the only difference from `where` is what we do with the result column (use it directly vs. use it as a filter predicate). + +### 3. Add a `project` method to `Collection` + +**Rationale:** `Collection.filter()` handles the `where` semantics (filtering by boolean). We need a parallel method for `select` semantics (replacing the element with the expression result). The `project` method will apply a `ColumnTransform` and return a new collection with the projected values. Unlike `filter`, the result collection's type information will come from the expression result rather than the input. + +**Alternative considered:** Reusing `Collection.map()` directly. However, `map` preserves the input collection's type metadata, while `select` should adopt the type of the projection expression result. + +## Risks / Trade-offs + +- **[Type information loss]** → The projection expression may produce a different type than the input collection. The `CollectionTransform` approach captures the full result including type, so we should extract type info from the expression result. +- **[Flattening semantics]** → In the columnar Spark model, "flattening" of nested arrays from projection results may require special handling. However, the existing column representation already handles array semantics, so this should work naturally. diff --git a/openspec/changes/archive/2026-02-25-support-select-function/proposal.md b/openspec/changes/archive/2026-02-25-support-select-function/proposal.md new file mode 100644 index 0000000000..0ea879004d --- /dev/null +++ b/openspec/changes/archive/2026-02-25-support-select-function/proposal.md @@ -0,0 +1,27 @@ +## Why + +The FHIRPath `select` function is a core filtering and projection function defined in the [FHIRPath specification](https://hl7.org/fhirpath/#filtering-and-projection). It evaluates a projection expression for each item in the input collection and flattens the results. Pathling currently supports the closely related `where` function but lacks `select`, which limits the expressiveness of FHIRPath queries that need to project or transform collection elements. + +## What Changes + +- Add `select(projection: expression) : collection` function to the FHIRPath engine +- The function evaluates the projection expression for each item in the input collection +- Results are flattened: if evaluation produces multiple items, all are added to the output; if evaluation produces empty, nothing is added +- Empty input collections produce empty output + +## Capabilities + +### New Capabilities + +- `fhirpath-select`: FHIRPath `select` function for projecting and transforming collection elements + +### Modified Capabilities + +(none) + +## Impact + +- **Code**: `fhirpath` module - `FilteringAndProjectionFunctions.java`, `Collection.java` (may need a new projection/flatMap method) +- **Tests**: New DSL tests for the `select` function, YAML reference test compatibility +- **APIs**: No public API changes - `select` is available through FHIRPath expression evaluation +- **Dependencies**: None diff --git a/openspec/changes/archive/2026-02-25-support-select-function/specs/fhirpath-select/spec.md b/openspec/changes/archive/2026-02-25-support-select-function/specs/fhirpath-select/spec.md new file mode 100644 index 0000000000..f2cc9415af --- /dev/null +++ b/openspec/changes/archive/2026-02-25-support-select-function/specs/fhirpath-select/spec.md @@ -0,0 +1,51 @@ +## ADDED Requirements + +### Requirement: Select function evaluates projection for each element + +The FHIRPath engine SHALL support the `select(projection: expression) : collection` function. The function SHALL evaluate the projection expression for each item in the input collection. The result of each evaluation SHALL be added to the output collection. + +#### Scenario: Simple property projection + +- **WHEN** `select` is called with a property path expression on a collection of resources (e.g., `Patient.name.select(family)`) +- **THEN** the result SHALL contain the values of that property for each element in the input collection + +#### Scenario: Expression projection + +- **WHEN** `select` is called with a complex expression (e.g., `Patient.name.select(given + ' ' + family)`) +- **THEN** the result SHALL contain the evaluated expression result for each element + +### Requirement: Select function flattens results + +If the evaluation of the projection expression for an element results in a collection with multiple items, all items SHALL be added to the output collection (collections resulting from evaluation of the projection are flattened). + +#### Scenario: Projection returns multiple items + +- **WHEN** `select` is called with an expression that returns multiple values per element (e.g., `Patient.name.select(given)` where a name has multiple given names) +- **THEN** all values from each element's projection SHALL be included in the output collection + +### Requirement: Select function handles empty results + +If the evaluation of the projection expression for an element results in the empty collection, no element SHALL be added to the result for that input element. + +#### Scenario: Projection returns empty for some elements + +- **WHEN** `select` is called and the projection expression evaluates to empty for some input elements +- **THEN** those elements SHALL not contribute to the output collection + +### Requirement: Select function handles empty input + +If the input collection is empty, the result SHALL be empty. + +#### Scenario: Empty input collection + +- **WHEN** `select` is called on an empty collection +- **THEN** the result SHALL be an empty collection + +### Requirement: Select function is available as a FHIRPath function + +The `select` function SHALL be registered and invocable using standard FHIRPath function call syntax (e.g., `collection.select(expression)`). + +#### Scenario: Function invocation syntax + +- **WHEN** a FHIRPath expression uses `select` with dot notation (e.g., `Patient.contact.select(name)`) +- **THEN** the function SHALL be resolved and executed correctly diff --git a/openspec/changes/archive/2026-02-25-support-select-function/tasks.md b/openspec/changes/archive/2026-02-25-support-select-function/tasks.md new file mode 100644 index 0000000000..d67bd3b1d3 --- /dev/null +++ b/openspec/changes/archive/2026-02-25-support-select-function/tasks.md @@ -0,0 +1,9 @@ +## 1. Core Implementation + +- [x] 1.1 Add `select` function to `FilteringAndProjectionFunctions.java` using `CollectionTransform` parameter, following the `where` function pattern +- [x] 1.2 Add a `project` method (or equivalent) to `Collection.java` that applies a `CollectionTransform` expression and returns the projected result collection + +## 2. Testing + +- [x] 2.1 Write DSL tests for the `select` function covering: simple property projection, expression projection, flattening of multi-valued results, empty projection results, and empty input collections +- [x] 2.2 Run YAML reference tests (`YamlReferenceImplTest`) and add exclusions for any `select`-related tests that are not yet supported, with user approval diff --git a/openspec/changes/archive/2026-02-26-fix-search-result-full-width/.openspec.yaml b/openspec/changes/archive/2026-02-26-fix-search-result-full-width/.openspec.yaml new file mode 100644 index 0000000000..85ae75c1f0 --- /dev/null +++ b/openspec/changes/archive/2026-02-26-fix-search-result-full-width/.openspec.yaml @@ -0,0 +1,2 @@ +schema: spec-driven +created: 2026-02-26 diff --git a/openspec/changes/archive/2026-02-26-fix-search-result-full-width/design.md b/openspec/changes/archive/2026-02-26-fix-search-result-full-width/design.md new file mode 100644 index 0000000000..bf2bab39a6 --- /dev/null +++ b/openspec/changes/archive/2026-02-26-fix-search-result-full-width/design.md @@ -0,0 +1,33 @@ +## Context + +The `ResourceCard` component renders each search result in the admin UI. The top +row uses a flex layout: a resource type badge, the resource ID (with +`flexGrow: 1`), and action icon buttons. A hard-coded `maxWidth: "400px"` on the +ID text element prevents flex from distributing the remaining space, leaving a +visible gap on wider viewports. + +## Goals / Non-goals + +**Goals:** + +- Allow the top row of each search result card to fill its full available width. +- Truncate long resource IDs with an ellipsis so they don't break the layout. + +**Non-goals:** + +- Redesigning the card layout or changing any other visual aspect. + +## Decisions + +Remove `maxWidth: "400px"` from the resource ID `Text` element in +`ResourceCard.tsx`. The existing `overflow: "hidden"`, `textWrap: "nowrap"`, and +`textOverflow: "ellipsis"` styles already handle truncation correctly. Since +`overflow: "hidden"` is set, the CSS spec clamps the flex item's automatic +minimum size to zero, so the element will shrink within the flex container and +the ellipsis triggers naturally from the available space. + +## Risks / Trade-offs + +- Minimal risk. The ellipsis behaviour is preserved by the existing overflow + styles. The only change is that the truncation point is now determined by the + flex layout rather than a fixed 400px cap. diff --git a/openspec/changes/archive/2026-02-26-fix-search-result-full-width/proposal.md b/openspec/changes/archive/2026-02-26-fix-search-result-full-width/proposal.md new file mode 100644 index 0000000000..a381a64aaa --- /dev/null +++ b/openspec/changes/archive/2026-02-26-fix-search-result-full-width/proposal.md @@ -0,0 +1,30 @@ +## Why + +The top line of each search result card in the admin UI has a hard-coded +`maxWidth: "400px"` on the resource ID element. This prevents the row of items +(badge, ID, action icons) from filling the full horizontal width of the card, +leaving wasted space on wider viewports. + +See: https://github.com/aehrc/pathling/issues/2559 + +## What changes + +- Remove the `maxWidth` constraint from the resource ID text element in + `ResourceCard`, allowing the flex layout to naturally distribute space across + the full card width. + +## Capabilities + +### New capabilities + +_None._ + +### Modified capabilities + +_None — this is a cosmetic fix to inline styles, not a change to any +spec-level behaviour._ + +## Impact + +- `ui/src/components/resources/ResourceCard.tsx` — inline style change only. +- No API, dependency, or behavioural changes. diff --git a/openspec/changes/archive/2026-02-26-fix-search-result-full-width/specs/.gitkeep b/openspec/changes/archive/2026-02-26-fix-search-result-full-width/specs/.gitkeep new file mode 100644 index 0000000000..e69de29bb2 diff --git a/openspec/changes/archive/2026-02-26-fix-search-result-full-width/specs/none/spec.md b/openspec/changes/archive/2026-02-26-fix-search-result-full-width/specs/none/spec.md new file mode 100644 index 0000000000..6e66d1e0f8 --- /dev/null +++ b/openspec/changes/archive/2026-02-26-fix-search-result-full-width/specs/none/spec.md @@ -0,0 +1 @@ +No new or modified capabilities — this is a cosmetic style fix only. diff --git a/openspec/changes/archive/2026-02-26-fix-search-result-full-width/tasks.md b/openspec/changes/archive/2026-02-26-fix-search-result-full-width/tasks.md new file mode 100644 index 0000000000..c8646bf0f7 --- /dev/null +++ b/openspec/changes/archive/2026-02-26-fix-search-result-full-width/tasks.md @@ -0,0 +1,9 @@ +## 1. Fix layout + +- [x] 1.1 Remove `maxWidth: "400px"` from the resource ID `Text` element in `ui/src/components/resources/ResourceCard.tsx` + +## 2. Verify + +- [x] 2.1 Run UI unit tests (`bun run test:run`) +- [x] 2.2 Run UI linting and build (`bun run lint && bun run build`) +- [x] 2.3 Run E2E tests (`bun run test:e2e`) diff --git a/openspec/changes/archive/2026-03-05-repeat-all-function/.openspec.yaml b/openspec/changes/archive/2026-03-05-repeat-all-function/.openspec.yaml new file mode 100644 index 0000000000..85ae75c1f0 --- /dev/null +++ b/openspec/changes/archive/2026-03-05-repeat-all-function/.openspec.yaml @@ -0,0 +1,2 @@ +schema: spec-driven +created: 2026-02-26 diff --git a/openspec/changes/archive/2026-03-05-repeat-all-function/design.md b/openspec/changes/archive/2026-03-05-repeat-all-function/design.md new file mode 100644 index 0000000000..4bdcc7dddd --- /dev/null +++ b/openspec/changes/archive/2026-03-05-repeat-all-function/design.md @@ -0,0 +1,249 @@ +## Context + +Pathling encodes FHIR resources into Spark DataFrames, truncating recursive +structures (e.g., `Questionnaire.item`) at `maxNestingLevel` (default: 3). This +means items at different depths have different struct schemas — deeper levels +have fewer fields as recursive children are progressively removed. + +The `encoders` module already provides `UnresolvedTransformTree`, a custom +Catalyst expression that implements depth-limited recursive tree traversal at +query planning time. It is used by the SQL-on-FHIR `RepeatSelection` to +implement the `repeat` clause in view definitions. `ValueFunctions.transformTree` +provides the Java bridge to this expression. + +`UnresolvedTransformTree` works by concatenating arrays extracted at each nesting +level via Spark's `Concat`. This requires all arrays to have compatible element +types. In `RepeatSelection`, the extractor applies a user-defined projection +(e.g., extract `linkId`, `text`) that produces a consistent flat schema at every +level. For FHIRPath `repeatAll(item)`, the projection IS the recursive +navigation — `item` returns the child items, whose schemas differ by depth. + +FHIRPath functions are registered via `@FhirPathFunction`-annotated static +methods. Scoped functions that accept projection expressions use the +`CollectionTransform` parameter type, which the resolver wraps around the +FHIRPath argument expression with `$this` binding. + +## Goals / Non-Goals + +**Goals:** + +- Implement `repeatAll()` as a FHIRPath function that recursively traverses + hierarchical FHIR structures and collects all results without deduplication. +- Reuse the existing `UnresolvedTransformTree` infrastructure for depth-limited + recursive traversal. +- Solve the schema divergence problem so items from different nesting levels can + be concatenated into a single output collection. +- Make the function available through standard FHIRPath evaluation with no API + changes. + +**Non-Goals:** + +- Implementing `repeat()` (requires element-wise deduplication, which is a + separate and harder problem in Spark's columnar model). +- Supporting unbounded recursion — same-type traversal depth is always limited. +- Optimising for cyclic data — `repeatAll()` does not guard against cycles, per + the FHIRPath specification. Same-type depth limiting provides practical + termination. + +## Decisions + +### Decision 1: Use Variant round-trip to solve schema divergence + +At each nesting level, items extracted by the projection have different struct +schemas due to `maxNestingLevel` truncation. Spark's `Concat` requires arrays +with identical element types and its type coercion only handles structs with the +same number of fields. + +**Chosen approach:** Use Spark 4's `VariantType` as a schema-free intermediate +representation. At each level: + +1. The extractor evaluates the projection and converts results to Variant via + `to_variant_object()`, producing `Array[Variant]`. +2. `Concat` merges all `Array[Variant]` arrays across levels (uniform type, no + coercion needed). +3. The final result is converted back via `variant_get(v, '$', targetSchema)` + where `targetSchema` is the fullest schema (from level 0). Missing fields at + deeper levels are filled with null. + +**Alternatives considered:** + +- **Custom `UnresolvedPadToSchema` Catalyst expression**: A new expression that + recursively aligns structs to a target schema by adding null-valued fields. + Full type safety with no serialization overhead, but introduces a new Catalyst + expression to maintain and requires recursive struct alignment logic. The + target schema must be determined and propagated into the expression. + +- **Lazy collection with deferred extraction**: Defer `UnresolvedTransformTree` + construction until a downstream expression provides a uniform schema. Avoids + schema divergence entirely but changes `repeatAll()` semantics — + `repeatAll(item)` alone would not be a valid terminal expression. Introduces + complexity in chaining and composability with aggregate operations. + +- **Fixed-depth unrolling with `transform`/`flatten`**: Build explicit nested + chains without `UnresolvedTransformTree`. Easy to debug but hard to generalise, + verbose, and duplicates logic that `UnresolvedTransformTree` already solves. + +- **Drop recursive fields (normalise to shallowest schema)**: Strip + self-referential fields from output. Trivially compatible but loses structural + information users need for downstream processing. + +**Rationale:** The Variant approach requires no new Catalyst expressions, uses +built-in Spark 4 functions, and preserves full spec conformance — items are +returned with their complete structure. The serialization overhead is acceptable +given the alternative complexity. + +### Decision 2: Add `repeatAll` method on `Collection` + +The integration point is a new `Collection.repeatAll(CollectionTransform, int)` +method that: + +1. Applies the transform to derive the result type metadata. +2. Converts the `CollectionTransform` to a `ColumnTransform` via + `toColumnTransformation()`. +3. Pre-computes the level-0 result by applying the column transform to the + input and normalizing to array form via `plural()`, producing + `Array[ItemStruct]`. +4. Passes the level-0 result to `ValueFunctions.transformTree()` as the starting + node, with: + - **Extractor**: a vectorised `to_variant_object` conversion — + `transform(node, to_variant_object)` — which converts each element of the + current array to Variant, producing `Array[Variant]`. + - **Traversal**: the same column transform (projection expression), which + navigates from items to their children at each level. +5. Unwraps the final `Array[Variant]` result back to the target schema via + `variantUnwrap` using the level-0 expression as the schema reference. +6. Returns a new `Collection` with the result column and appropriate type + metadata. + +This mirrors the `RepeatSelection` pattern where the extractor captures "what to +collect" and the traversals capture "where to go next". For `repeatAll`, "what +to collect" is the items themselves (as Variant for schema compatibility), and +"where to go next" is the same projection expression that produced level 0. + +**Rationale:** Reusing `UnresolvedTransformTree` gives us same-type depth +limiting for free — the depth counter only decrements when traversing to a node +of the same type, matching the SQL on FHIR `repeat` clause behaviour. The +extractor is a simple `to_variant_object` mapping with no need to compose the +projection into it, since the projection lives entirely in the traversals. + +### Decision 3: Register as a standard FHIRPath function + +`repeatAll` is registered as a `@FhirPathFunction`-annotated static method in +the filtering and projection function group (alongside `select`, `where`, +`repeat`). The method signature accepts `Collection` (input) and +`CollectionTransform` (projection), matching the existing pattern for scoped +functions. + +**Rationale:** Consistent with how `select()` is registered. No changes needed +to the function resolution or parameter binding infrastructure since +`CollectionTransform` is already a supported parameter type. + +### Decision 4: Same-type depth limiting matching the SQL on FHIR repeat clause + +Traversal always navigates to the deepest level possible regardless of the +encoding's maximum nesting level. `UnresolvedTransformTree` only decrements its +depth counter when traversing to a node of the same type as its parent — paths +through different types (e.g., Item → Answer → Item) traverse freely without +consuming depth budget. This matches the approach used by `RepeatSelection` for +the SQL on FHIR `repeat` clause. + +The depth limit for same-type recursion is hardcoded to 10, matching the default +`maxUnboundTraversalDepth` used by `RepeatSelection`. In the first instance this +value is not configurable. + +**Rationale:** The encoding's `maxNestingLevel` controls how deep recursive +structures are materialised in the schema, but `UnresolvedTransformTree` already +handles schema truncation gracefully — when a field is not found during +traversal it returns an empty array rather than failing. Tying the traversal +depth to `maxNestingLevel` would be unnecessarily restrictive for structures +where the traversal expression crosses different types before recurring. Using +the same approach as the `repeat` clause ensures consistent behaviour. + +### Decision 5: Normalize projection results to arrays via `plural()` + +`variantTransformTree` requires array-typed input at every level — its extractor +calls `transform(node, to_variant_object)` which is a Spark function that +operates on arrays. When the projection expression produces a singular value +(e.g., `Patient.repeatAll(gender)` returns a `STRING`, not `ARRAY`), the +pipeline fails. + +**Chosen approach:** A two-part solution: + +1. **`plural()` normalization**: Apply `plural()` to both the level-0 result and + the inner traversal result to ensure they are always represented as arrays. + The `plural()` method on `ColumnRepresentation` handles this via + `vectorize()`: array input passes through (null becomes empty array), scalar + input is wrapped in `array(scalar)` (null becomes empty array). + +2. **Primitive type short-circuit**: Check whether the projection produces a + primitive (non-struct) FhirPathType. If so, return the level-0 result + directly without invoking tree traversal. Primitives are leaf types with no + children to recurse into, so the result is always just the projected values. + This avoids two issues: `to_variant_object()` cannot convert primitives to + Variant, and `UnresolvedTransformTree` cannot navigate fields on primitive + array elements. + +The primitive check uses the `Collection`'s FhirPathType metadata: + + resultTemplate.getType() + .map(t -> !(t.getSqlDataType() instanceof StructType)) + .orElse(false) + +Types with no FhirPathType mapping (e.g., CodeableConcept, HumanName, +QuestionnaireItem) default to the Variant path, which is correct since they are +always represented as structs. + +**Rationale:** `plural()` is the existing mechanism used throughout the codebase +(e.g., in `Collection.filter()`, `Collection.aggregate()`) to normalize +singular-vs-collection representation. The primitive short-circuit is necessary +because `to_variant_object()` only works on structs/maps (Spark's +`StructsToVariant` expression), and `UnresolvedTransformTree` interprets field +access on primitives as element access rather than producing an empty result. +For complex (struct) types, the full `variantTransformTree` path handles schema +divergence across nesting levels as before. + +## Risks / Trade-offs + +**Variant serialization overhead** → The round-trip through +`to_variant_object()` and `variant_get()` involves binary +serialization/deserialization at each nesting level. For most FHIR resources with +modest nesting (2-4 levels), this overhead is expected to be negligible. If +profiling reveals issues, the `UnresolvedPadToSchema` approach can be +implemented as an optimisation without changing the public API. + +**Variant type fidelity** → Spark's Variant documentation notes it "does not yet +contain lossless equivalents" for all types. Complex FHIR types (decimals with +specific precision, dates, nested extensions) need validation. A spike test with +a `Questionnaire` containing nested items should verify round-trip fidelity +before full implementation. + +**Spark 4 dependency** → `VariantType` and associated functions are Spark 4 +features. Pathling already targets Spark 4, so this is not a new dependency, but +it does tie this implementation to the Spark 4+ line. + +**No cycle detection** → Per the FHIRPath spec, `repeatAll()` does not guard +against cycles. In Pathling's encoded data, cycles cannot exist (the schema is +truncated), so this is not a practical concern. The same-type depth limit +provides an additional safety net. + +## Resolved Questions + +1. **Variant fidelity validation**: Spike tests (tasks 1.1 and 1.2) confirmed + that the `to_variant_object` → `variant_get` round-trip preserves FHIR data + types faithfully, including nested structs with missing fields at deeper + levels which are correctly filled with null. + +2. **Target schema determination**: Resolved by introducing + `UnresolvedVariantUnwrap` — a Catalyst expression that accepts the + `Array[Variant]` result and a schema reference expression (the level-0 array). + Schema extraction is deferred to Catalyst analysis time, when the level-0 + expression has resolved and its element type can be read directly. No + pre-computation of the target schema is needed. + +3. **Non-recursive projection**: No error is produced. If `repeatAll` is called + with a projection that does not navigate into a recursive structure (e.g., + `Patient.repeatAll(name)`), the function silently returns the same result as + `select()` — one iteration producing results, followed by termination when + the next iteration yields an empty collection. This is consistent with how + FHIRPath functions generally do not validate the semantic meaningfulness of + their arguments. diff --git a/openspec/changes/archive/2026-03-05-repeat-all-function/proposal.md b/openspec/changes/archive/2026-03-05-repeat-all-function/proposal.md new file mode 100644 index 0000000000..0c72560443 --- /dev/null +++ b/openspec/changes/archive/2026-03-05-repeat-all-function/proposal.md @@ -0,0 +1,59 @@ +## Why + +The FHIRPath specification includes a `repeatAll()` STU function for recursive +traversal of hierarchical FHIR structures (e.g., `Questionnaire.item`). Unlike +`repeat()`, it skips equality-based deduplication, making it feasible to +implement in Spark's columnar model where element-wise equality on complex +nested +FHIR types is impractical. Supporting `repeatAll()` enables users to flatten +deeply nested FHIR data without manually chaining navigation steps or resorting +to `descendants()`. + +## What Changes + +- Add `repeatAll(projection)` as a new FHIRPath function available in Pathling's + FHIRPath engine, conforming to the STU specification. +- The function accepts a scoped projection expression (with `$this` binding) and + recursively applies it, collecting all results including duplicates, until no + new items are produced. +- Traversal always navigates to the deepest level possible regardless of the + encoding's maximum nesting level. Recursion depth is only limited when the + traversal expression is self-referential (i.e. navigates to a node of the same + type), in which case a hardcoded depth limit (of 10) prevents infinite loops — + matching + the approach used by the SQL on FHIR `repeat` clause implementation. +- The function is available wherever FHIRPath expressions are evaluated today, + including the library API and Python bindings, with no interface changes. + +## Capabilities + +### New Capabilities + +- `fhirpath-repeat-all`: The FHIRPath `repeatAll()` STU function for recursive + collection traversal without deduplication. + +### Modified Capabilities + +- `fhirpath-evaluation-api`: The evaluation API gains support for `repeatAll()` + expressions, requiring no interface changes but expanding the set of + recognised FHIRPath functions. + +## Impact + +- **fhirpath module**: New function registration, new method on `Collection`. +- **encoders module**: May require new helper utilities to support recursive + traversal with schema compatibility across nesting levels. +- **library-api / Python bindings**: No API changes — `repeatAll()` becomes + available automatically through the existing expression evaluation pipeline. +- **Testing**: New unit tests covering flat traversal, multi-level recursive + structures (e.g., `Questionnaire.item`), empty input, and expressions chained + after `repeatAll()`. Tests should verify two cross-cutting invariants that + apply to all element-propagating FHIRPath functions but are especially + important to validate for `repeatAll()` given the Variant round-trip and + array-oriented tree traversal involved: + - **Extension preservation**: Extensions and other sub-elements are preserved + in propagated results. + - **Singular/collection handling**: The function works correctly with + projections that produce singular values (e.g., `Patient.repeatAll(gender)`) + or primitive types, not only collection-valued projections that return + arrays. diff --git a/openspec/changes/archive/2026-03-05-repeat-all-function/specs/fhirpath-evaluation-api/spec.md b/openspec/changes/archive/2026-03-05-repeat-all-function/specs/fhirpath-evaluation-api/spec.md new file mode 100644 index 0000000000..ae9c99ea6e --- /dev/null +++ b/openspec/changes/archive/2026-03-05-repeat-all-function/specs/fhirpath-evaluation-api/spec.md @@ -0,0 +1,64 @@ +## MODIFIED Requirements + +### Requirement: Evaluate FHIRPath expression against a single resource + +The library API SHALL provide a method that accepts a FHIR resource (as a JSON +string), a FHIRPath expression string, an optional context expression string, +and optional variables, and returns a list of typed result values. + +The method SHALL use the existing Pathling FHIRPath engine (Spark-based) to +evaluate the expression, encoding the resource into a one-row Dataset +internally. + +The method SHALL support all FHIRPath functions implemented in the engine, +including scoped functions that accept projection expressions (e.g., `select()`, +`repeatAll()`). + +When the expression is empty or contains only whitespace, the fhirpath-lab-api +SHALL return a successful response with an empty collection (zero result parts) +without invoking the FHIRPath engine. + +#### Scenario: Simple expression evaluation + +- **WHEN** the method is called with a Patient JSON resource and the expression + `name.family` +- **THEN** the method returns a list containing a single string result with the + patient's family name + +#### Scenario: Expression returning multiple values + +- **WHEN** the method is called with a Patient JSON resource containing two + names and the expression `name.given` +- **THEN** the method returns a list containing all given name strings + +#### Scenario: Expression returning empty result + +- **WHEN** the method is called with a Patient JSON resource and an expression + that matches no elements (e.g., `deceased`) +- **THEN** the method returns an empty list + +#### Scenario: Empty expression + +- **WHEN** the fhirpath-lab-api receives a request with an expression that is an + empty string or contains only whitespace +- **THEN** it returns a successful Parameters response with zero result parts and + no type metadata, without invoking the FHIRPath engine + +#### Scenario: Invalid expression + +- **WHEN** the method is called with a syntactically invalid FHIRPath expression +- **THEN** the method throws an exception with a descriptive error message + +#### Scenario: Context expression evaluation + +- **WHEN** the method is called with a Patient JSON resource, context expression + `name`, and expression `given.first()` +- **THEN** the method evaluates the main expression once for each result of the + context expression and returns results grouped by context item + +#### Scenario: Recursive function evaluation + +- **WHEN** the method is called with a Questionnaire JSON resource and the + expression `repeatAll(item).linkId` +- **THEN** the method returns a list containing `linkId` values from all + recursively nested items diff --git a/openspec/changes/archive/2026-03-05-repeat-all-function/specs/fhirpath-repeat-all/spec.md b/openspec/changes/archive/2026-03-05-repeat-all-function/specs/fhirpath-repeat-all/spec.md new file mode 100644 index 0000000000..aace384d21 --- /dev/null +++ b/openspec/changes/archive/2026-03-05-repeat-all-function/specs/fhirpath-repeat-all/spec.md @@ -0,0 +1,197 @@ +## ADDED Requirements + +### Requirement: repeatAll function recursively traverses and collects elements + +The FHIRPath engine SHALL support the +`repeatAll(projection: ($this) => collection) : collection` function. The +function SHALL evaluate the projection expression for each item in the input +collection, add all results to the output collection, then re-evaluate the +projection on the new results. This process SHALL repeat until an iteration +produces no new results. + +Unlike `repeat()`, the function SHALL NOT check for duplicate items — all +results SHALL be added to the output collection regardless of whether they +already exist. + +#### Scenario: Single-level traversal + +- **WHEN** `repeatAll` is called on a Questionnaire resource with a single level + of items and the projection `item` +- **THEN** the result SHALL contain all items from that single level + +#### Scenario: Multi-level recursive traversal + +- **WHEN** `repeatAll` is called on a Questionnaire resource with nested items + (items containing sub-items) and the projection `item` +- **THEN** the result SHALL contain items from all nesting levels + +#### Scenario: Duplicate items are preserved + +- **WHEN** `repeatAll` is called and the same item would be reached through + multiple traversal paths +- **THEN** all occurrences SHALL be included in the output collection (no + deduplication) + +### Requirement: repeatAll function terminates on empty iteration + +The function SHALL terminate when an iteration of the projection expression +across all current items produces an empty collection (no new results). + +#### Scenario: Termination at leaf nodes + +- **WHEN** `repeatAll(item)` is evaluated on a Questionnaire where the deepest + items have no child items +- **THEN** the function SHALL terminate and return all collected items + +#### Scenario: Non-recursive collection projection + +- **WHEN** `repeatAll` is called with a projection that does not navigate into a + recursive structure and produces a collection (e.g., + `Patient.repeatAll(name)`) +- **THEN** the function SHALL silently return the same result as `select()` — + one iteration producing results, followed by termination when the next + iteration yields an empty collection + +#### Scenario: Non-recursive singular projection + +- **WHEN** `repeatAll` is called with a projection that produces a singular + value (e.g., `Patient.repeatAll(gender)`) +- **THEN** the function SHALL return the same result as `select()` — the + singular value wrapped as a single-element collection + +#### Scenario: Non-recursive singular complex projection + +- **WHEN** `repeatAll` is called with a projection that produces a singular + complex type (e.g., `Patient.repeatAll(maritalStatus)`) +- **THEN** the function SHALL return the complex value with all its sub-elements + intact + +### Requirement: repeatAll function handles empty input + +If the input collection is empty, the result SHALL be empty. This SHALL hold +both when the input is a typed collection that evaluates to empty at runtime +(e.g., a resource where the traversed field is absent) and when the input is +the FHIRPath empty literal `{}`. + +#### Scenario: Empty collection from absent field + +- **WHEN** `repeatAll` is called on a resource where the traversed field is + absent (e.g., a Questionnaire with no items) +- **THEN** the result SHALL be an empty collection + +#### Scenario: Empty collection literal + +- **WHEN** `repeatAll` is called on the FHIRPath empty literal `{}` (e.g., + `{}.repeatAll(item)`) +- **THEN** the result SHALL be an empty collection + +### Requirement: repeatAll function supports chained expressions + +The result of `repeatAll` SHALL be a standard collection that supports +subsequent FHIRPath operations such as path navigation, `where()`, `count()`, +`select()`, and other functions. + +#### Scenario: Path navigation after repeatAll + +- **WHEN** a FHIRPath expression chains a path after `repeatAll` (e.g., + `Questionnaire.repeatAll(item).linkId`) +- **THEN** the result SHALL contain the `linkId` values from all recursively + collected items + +#### Scenario: Filtering after repeatAll + +- **WHEN** a FHIRPath expression applies `where()` after `repeatAll` (e.g., + `Questionnaire.repeatAll(item).where(type = 'group')`) +- **THEN** the result SHALL contain only items matching the filter from all + nesting levels + +#### Scenario: Counting after repeatAll + +- **WHEN** a FHIRPath expression applies `count()` after `repeatAll` (e.g., + `Questionnaire.repeatAll(item).count()`) +- **THEN** the result SHALL be the total number of items across all nesting + levels, including duplicates + +### Requirement: repeatAll function bounds same-type recursion depth + +The function delegates recursive traversal to `UnresolvedTransformTree`, which +limits recursion depth based on Spark SQL `DataType` equality. The depth counter +only decrements when the traversal expression produces a node whose resolved SQL +`DataType` is structurally identical to its parent's. When the counter reaches +zero, traversal stops and returns results collected up to that point. The +hardcoded same-type depth limit is 10, matching the default +`maxUnboundTraversalDepth` used by the SQL on FHIR `repeat` clause. + +For traversals through schema-truncated structures (e.g., +`Questionnaire.repeatAll(item)`), each nesting level has a progressively smaller +`StructType` due to the encoding's `maxNestingLevel` truncation. These are NOT +same-type traversals — the depth counter is never decremented, and traversal +terminates naturally when a field is no longer present in the truncated schema +(`FIELD_NOT_FOUND`). + +Same-type recursion occurs when the traversal produces an element with an +identical SQL `DataType` at every level. Known cases include: + +- **Extension traversal**: Extension structs have a fixed flat schema at all + nesting levels (extensions use a global `_extension` map rather than recursive + struct fields), so `repeatAll(extension)` produces same-type nodes. +- **Identity-like traversals**: Functions such as `first()` that return an + element of the same type as the input, causing the SQL `DataType` to remain + unchanged across levels. + +#### Scenario: Extension traversal bounded by actual depth or limit + +- **WHEN** `repeatAll(extension)` is evaluated on a resource whose elements + carry nested extensions +- **THEN** the function SHALL traverse extensions up to the actual nesting depth + or the same-type depth limit (10), whichever is reached first, and return all + collected extensions + +#### Scenario: Identity-like traversal bounded by depth limit + +- **WHEN** `repeatAll` is evaluated with a traversal that always produces the + same SQL `DataType` (e.g., `repeatAll(first())` on a complex-typed + collection) +- **THEN** the function SHALL stop after the same-type depth limit and return + results collected up to that point + +#### Scenario: Schema-truncated traversal terminates naturally + +- **WHEN** `repeatAll(item)` is evaluated on a Questionnaire with nested items +- **THEN** traversal SHALL terminate naturally when the schema no longer + contains the `item` field (due to `maxNestingLevel` truncation during the + encoding), without consuming same-type depth budget + +### Requirement: repeatAll function does not define $index + +The `$index` variable SHALL NOT be set during evaluation of the projection +expression, consistent with the FHIRPath specification. + +#### Scenario: $index is not available + +- **WHEN** the projection expression references `$index` within `repeatAll` +- **THEN** `$index` SHALL NOT resolve to a value + +### Requirement: repeatAll function preserves extensions and sub-elements + +The result collection SHALL preserve all fields of the propagated elements, +including FHIR extensions and other sub-elements. This is a general invariant +for all element-propagating FHIRPath functions (e.g., `first()`, `where()`), but +SHALL be verified for `repeatAll()` given the schema alignment involved. + +#### Scenario: Extensions preserved in results + +- **WHEN** `repeatAll(item)` is evaluated on a Questionnaire where items contain + extension elements +- **THEN** the result items SHALL retain their extension elements intact + +### Requirement: repeatAll function is available as a FHIRPath function + +The `repeatAll` function SHALL be registered and invocable using standard +FHIRPath function call syntax (e.g., `collection.repeatAll(expression)`). + +#### Scenario: Function invocation syntax + +- **WHEN** a FHIRPath expression uses `repeatAll` with dot notation (e.g., + `Questionnaire.repeatAll(item)`) +- **THEN** the function SHALL be resolved and executed correctly diff --git a/openspec/changes/archive/2026-03-05-repeat-all-function/tasks.md b/openspec/changes/archive/2026-03-05-repeat-all-function/tasks.md new file mode 100644 index 0000000000..83b06b9a89 --- /dev/null +++ b/openspec/changes/archive/2026-03-05-repeat-all-function/tasks.md @@ -0,0 +1,31 @@ +## 1. Spike: Variant round-trip validation + +- [x] 1.1 Write a spike test that encodes a Questionnaire with nested `item` elements into a Spark DataFrame, converts items to Variant via `to_variant_object()`, and converts back via `variant_get()` with the level-0 target schema — verify all FHIR data types round-trip faithfully +- [x] 1.2 Validate that `variant_get` fills missing fields with null when converting from a shallower struct schema to the full target schema + +## 2. Variant wrapping utility + +- [x] 2.1 Add a helper method in `ValueFunctions` (or a new utility class in `encoders`) that wraps a column transform with the Variant round-trip: apply transform → `to_variant_object()` each element → return `Array[Variant]` +- [x] 2.2 Add a helper method that converts the final `Array[Variant]` result back to `Array[targetSchema]` via `variant_get(v, '$', targetSchema)` +- [x] 2.3 Write unit tests for the Variant wrapping helpers covering struct arrays with differing schemas, empty arrays, and null elements + +## 3. Collection.repeatAll method + +- [x] 3.1 Add `repeatAll(CollectionTransform, int)` method on `Collection` that pre-computes level-0 results via the column transform, then passes them to `ValueFunctions.transformTree()` with a vectorised `to_variant_object` extractor and the column transform as the traversal, and unwraps the result via `variantUnwrap` using the level-0 expression as the schema reference +- [x] 3.2 Determine the target schema from the resolved column type at level 0 before applying the Variant wrapping +- [x] 3.3 Write unit tests for `Collection.repeatAll` covering single-level traversal, multi-level recursive traversal, empty input, and chained expressions + +## 4. FHIRPath function registration + +- [x] 4.1 Add a `@FhirPathFunction`-annotated static `repeatAll` method in `FilteringAndProjectionFunctions` accepting `Collection` and `CollectionTransform`, delegating to `Collection.repeatAll` with a hardcoded same-type depth limit of 10 +- [x] 4.2 Register the function provider class in `StaticFunctionRegistry` (if not already included) +- [x] 4.3 Write FHIRPath-level integration tests: `Questionnaire.repeatAll(item)`, `Questionnaire.repeatAll(item).linkId`, `Questionnaire.repeatAll(item).where(type = 'group')`, `Questionnaire.repeatAll(item).count()`, empty input, and verify that extensions and sub-elements are preserved in propagated results + +## 5. Evaluation API integration test + +- [x] 5.1 Add an integration test that evaluates `repeatAll(item).linkId` against a Questionnaire JSON resource via the library API evaluation method, verifying linkId values from all nesting levels are returned + +## 6. Singular projection support + +- [x] 6.1 Add `plural()` normalization to the level-0 result and inner traversal result in `Collection.repeatAll()` so that singular projections are wrapped into arrays before entering `variantTransformTree` +- [x] 6.2 Write DSL tests for singular projections: `Patient.repeatAll(gender)` (singular primitive) and `Patient.repeatAll(maritalStatus)` (singular complex type), verifying they return the same result as `select()` diff --git a/openspec/changes/archive/2026-03-06-repeat-function/.openspec.yaml b/openspec/changes/archive/2026-03-06-repeat-function/.openspec.yaml new file mode 100644 index 0000000000..3184e5abf5 --- /dev/null +++ b/openspec/changes/archive/2026-03-06-repeat-function/.openspec.yaml @@ -0,0 +1,2 @@ +schema: spec-driven +created: 2026-03-06 diff --git a/openspec/changes/archive/2026-03-06-repeat-function/design.md b/openspec/changes/archive/2026-03-06-repeat-function/design.md new file mode 100644 index 0000000000..2af75b3f5e --- /dev/null +++ b/openspec/changes/archive/2026-03-06-repeat-function/design.md @@ -0,0 +1,54 @@ +## Context + +Pathling already implements `repeatAll()` which performs recursive tree traversal without deduplication. The FHIRPath standard `repeat()` function has identical recursive semantics but deduplicates results using the `=` (equals) operator. + +The `UnionOperator` already implements equality-based array deduplication for the `|` operator, supporting both default SQL equality (`array_distinct`) and custom equality (`arrayDistinctWithEquality`) via the `ColumnEquality` comparator interface. This infrastructure can be reused. + +## Goals / Non-Goals + +**Goals:** + +- Implement `repeat()` as defined in the FHIRPath specification. +- Reuse `repeatAll()` for recursion and `UnionOperator`-style dedup for equality. +- Pass the existing YAML reference tests for `repeat`. + +**Non-Goals:** + +- Per-level deduplication (BFS queue with set tracking) — post-collection dedup is sufficient. +- Deduplication of complex types (BackboneElement, etc.) — synthetic fields like `_fid` make struct equality impractical, and tree-structured FHIR data doesn't produce duplicates in practice. +- Decimal normalization before dedup — unlikely to be needed since all elements come from the same `repeatAll` traversal with a consistent schema. Can be added if tests reveal issues. + +## Decisions + +### 1. Implement as repeatAll + post-dedup + +**Decision**: `repeat()` calls `repeatAll()` then deduplicates the result array. + +**Rationale**: The spec defines `repeat` with a BFS queue that deduplicates on insertion. In a columnar engine, per-element queue iteration isn't feasible. Post-collection dedup produces the same result set (order is undefined per spec). This avoids duplicating the complex `variantTransformTree` machinery. + +**Alternative considered**: Level-by-level dedup during traversal — rejected as it would require modifying `variantTransformTree` internals for minimal benefit. + +### 1a. Allow primitive self-referential traversal via repeatAll parameter + +**Decision**: Add an `allowPrimitiveSelfRef` boolean parameter to `Collection.repeatAll()`. When `true`, self-referential primitive traversal returns level_0 instead of throwing an error. `repeat()` passes `true` (dedup handles termination); `repeatAll()` continues to pass `false` (error, since without dedup it would loop infinitely). + +**Rationale**: In `repeat()`, expressions like `(1 | 2).repeat('item')` are valid — the projection produces `['item', 'item']`, dedup collapses to `['item']`, and re-evaluation finds no new items. The error in `repeatAll()` exists because without dedup there's no termination. Adding a parameter keeps the analysis logic centralized in `repeatAll()` rather than duplicating it in `repeat()`. + +**Alternative considered**: Having `repeat()` do its own level_0/level_1 analysis and short-circuit the primitive case before calling `repeatAll()` — rejected to avoid duplicating analysis logic. + +### 2. Only deduplicate Equatable types + +**Decision**: Check `instanceof Equatable` on the result collection. If true, use the collection's comparator for dedup. If false, return as-is. + +**Rationale**: `Equatable` covers all FHIRPath primitive types (String, Integer, Boolean, Decimal, Date, DateTime, Time), plus Coding and Quantity which have custom equality semantics. Complex backbone types don't implement `Equatable` and contain synthetic fields that prevent meaningful equality. The YAML test cases that exercise dedup all involve primitive or Quantity types. + +### 3. Reuse UnionOperator's dedup pattern + +**Decision**: Extract or replicate the `deduplicateArray` pattern from `UnionOperator` — check `comparator.usesDefaultSqlEquality()` to choose between `array_distinct` and `arrayDistinctWithEquality`. + +**Rationale**: This is the established pattern for FHIRPath equality-based dedup in the codebase. It correctly handles Quantity unit conversion, Coding system/code matching, and temporal types. + +## Risks / Trade-offs + +- **Post-dedup vs per-level dedup**: Post-dedup may include elements in the recursion that would have been filtered at insertion time in a true BFS queue. For tree-structured FHIR data this is irrelevant (no duplicates during traversal). For contrived cases with primitives, the depth limit prevents infinite loops regardless, and post-dedup produces the correct final set. [Risk: minimal] → Accepted. +- **No complex type dedup**: If a user has a genuine need to deduplicate complex elements from `repeat()`, it won't happen. [Risk: low] → Can be revisited if real use cases emerge. diff --git a/openspec/changes/archive/2026-03-06-repeat-function/proposal.md b/openspec/changes/archive/2026-03-06-repeat-function/proposal.md new file mode 100644 index 0000000000..04b4d13983 --- /dev/null +++ b/openspec/changes/archive/2026-03-06-repeat-function/proposal.md @@ -0,0 +1,23 @@ +## Why + +The FHIRPath `repeat()` function is a standard function for recursive tree traversal with deduplication. It is needed for common FHIR patterns like `Questionnaire.repeat(item)` and `ValueSet.expansion.repeat(contains)`. Pathling already implements `repeatAll()` (the STU variant without dedup), so `repeat()` can be built on top of it with minimal effort. + +## What Changes + +- Add the FHIRPath `repeat(projection: expression)` function, implemented as `repeatAll()` followed by equality-based deduplication. +- For collections implementing `Equatable` (FHIRPath primitive types, Coding, Quantity, etc.), deduplication uses the collection's comparator — either `array_distinct` for default SQL equality or `arrayDistinctWithEquality` for custom equality (quantities with unit conversion, etc.). +- For complex types (BackboneElement, etc.), no deduplication is performed — structural synthetic fields like `_fid` make struct equality impractical, and tree-structured FHIR data doesn't produce duplicates in practice. + +## Capabilities + +### New Capabilities + +- `fhirpath-repeat`: The FHIRPath `repeat()` function for recursive tree traversal with equality-based deduplication. + +### Modified Capabilities + +## Impact + +- `fhirpath` module: New `repeat()` method on `Collection`, new `@FhirPathFunction` in `FilteringAndProjectionFunctions`. +- Enables existing YAML reference tests (`5.2.3_repeat.yaml`, `5.2_filtering_and_projection.yaml` repeat cases, `fhir-r4.yaml` repeat cases). +- No breaking changes — additive only. diff --git a/openspec/changes/archive/2026-03-06-repeat-function/specs/fhirpath-repeat/spec.md b/openspec/changes/archive/2026-03-06-repeat-function/specs/fhirpath-repeat/spec.md new file mode 100644 index 0000000000..1050af3e4f --- /dev/null +++ b/openspec/changes/archive/2026-03-06-repeat-function/specs/fhirpath-repeat/spec.md @@ -0,0 +1,109 @@ +## ADDED Requirements + +### Requirement: repeat function recursively traverses and deduplicates elements + +The FHIRPath engine SHALL support the `repeat(projection: expression) : collection` function. The function SHALL evaluate the projection expression recursively, collecting all results, then deduplicate the output collection using equality semantics. + +The function SHALL delegate recursive traversal to `repeatAll()`, then apply equality-based deduplication to the result. + +#### Scenario: Single-level traversal with no duplicates + +- **WHEN** `repeat(item)` is called on a Questionnaire with a single level of items +- **THEN** the result SHALL contain all items from that level (identical to `repeatAll`) + +#### Scenario: Multi-level recursive traversal + +- **WHEN** `repeat(item)` is called on a Questionnaire with nested items +- **THEN** the result SHALL contain items from all nesting levels + +#### Scenario: Duplicate primitive values are removed + +- **WHEN** `repeat($this)` is called on a collection containing duplicate primitive values (e.g., `(1 year).combine(12 months).repeat($this)`) +- **THEN** the result SHALL contain only distinct values as determined by FHIRPath equality + +#### Scenario: Quantity equality used for deduplication + +- **WHEN** `repeat($this)` is called on a collection of quantities where values are equal under unit conversion (e.g., 3 minutes and 180 seconds) +- **THEN** only one representative value SHALL appear in the result + +#### Scenario: String deduplication + +- **WHEN** `repeat` produces duplicate string values across recursion levels +- **THEN** the result SHALL contain each distinct string value only once + +### Requirement: repeat function deduplicates only Equatable types + +The function SHALL apply deduplication only when the result collection implements the `Equatable` interface. For non-Equatable types (complex backbone elements), the function SHALL return the `repeatAll()` result without deduplication. + +#### Scenario: Complex type results not deduplicated + +- **WHEN** `repeat(item)` is called on a Questionnaire with nested items +- **THEN** no deduplication SHALL be attempted on the complex item elements (result is identical to `repeatAll`) + +#### Scenario: Equatable type results deduplicated + +- **WHEN** `repeat` produces a collection of an Equatable type (String, Integer, Quantity, Coding, etc.) +- **THEN** the result SHALL be deduplicated using the collection's comparator + +### Requirement: repeat function uses collection comparator for equality + +When deduplicating Equatable results, the function SHALL use the collection's `getComparator()` method to obtain the appropriate `ColumnEquality` instance. If the comparator uses default SQL equality, the function SHALL use `array_distinct`. Otherwise, the function SHALL use `arrayDistinctWithEquality` with the comparator's `equalsTo` method. + +#### Scenario: Default SQL equality types + +- **WHEN** the result collection uses default SQL equality (e.g., String, Integer, Boolean) +- **THEN** deduplication SHALL use Spark's `array_distinct` + +#### Scenario: Custom equality types + +- **WHEN** the result collection uses custom equality (e.g., Quantity with unit conversion) +- **THEN** deduplication SHALL use `arrayDistinctWithEquality` with the collection's comparator + +### Requirement: repeat function handles self-referential primitive traversal + +Unlike `repeatAll()` which raises an error for self-referential primitive traversal, `repeat()` SHALL treat this as a valid case. When the projection produces a self-referential primitive type, `repeat()` SHALL return the level_0 result (from `repeatAll` with primitive self-ref allowed) and then deduplicate it. This is valid because deduplication guarantees termination. + +#### Scenario: Constant projection deduplicates to single value + +- **WHEN** `(1 | 2).repeat('item')` is evaluated +- **THEN** the result SHALL be `['item']` (projection produces `'item'` for each input, dedup collapses to one) + +#### Scenario: Identity projection deduplicates + +- **WHEN** `Functions.coll1.colltrue.repeat(true)` is evaluated +- **THEN** the result SHALL be `[true]` + +#### Scenario: Quantity identity with unit conversion + +- **WHEN** `(1 year).combine(12 months).repeat($this)` is evaluated +- **THEN** the result SHALL be `[1 year]` (1 year = 12 months under FHIRPath equality) + +### Requirement: repeat function inherits repeatAll behavior + +The `repeat` function SHALL inherit all recursive traversal behavior from `repeatAll`, including: + +- Static type analysis gate (level_0/level_1 classification). +- Same-type recursion depth limiting. +- Extension traversal with soft stop. +- Error on inconsistent traversal types. +- Empty input produces empty output. +- Result supports chained FHIRPath operations. + +#### Scenario: Empty input + +- **WHEN** `repeat` is called on an empty collection +- **THEN** the result SHALL be empty + +#### Scenario: Chained operations + +- **WHEN** `Questionnaire.repeat(item).linkId` is evaluated +- **THEN** the result SHALL contain linkId values from all recursively collected items + +### Requirement: repeat function is available as a FHIRPath function + +The `repeat` function SHALL be registered and invocable using standard FHIRPath function call syntax (e.g., `collection.repeat(expression)`). + +#### Scenario: Function invocation syntax + +- **WHEN** a FHIRPath expression uses `repeat` with dot notation (e.g., `Questionnaire.repeat(item)`) +- **THEN** the function SHALL be resolved and executed correctly diff --git a/openspec/changes/archive/2026-03-06-repeat-function/tasks.md b/openspec/changes/archive/2026-03-06-repeat-function/tasks.md new file mode 100644 index 0000000000..dda8bf45f1 --- /dev/null +++ b/openspec/changes/archive/2026-03-06-repeat-function/tasks.md @@ -0,0 +1,12 @@ +## 1. Core Implementation + +- [x] 1.1 Add `allowPrimitiveSelfRef` boolean parameter to `Collection.repeatAll()` — when `true`, return level_0 instead of throwing error for self-referential primitives +- [x] 1.2 Update `FilteringAndProjectionFunctions.repeatAll()` to pass `false` for the new parameter (preserving existing behavior) +- [x] 1.3 Add `repeat()` method to `Collection` that calls `repeatAll(transform, maxDepth, true)` then deduplicates using the collection's comparator for Equatable types +- [x] 1.4 Add `repeat` function to `FilteringAndProjectionFunctions` with `@FhirPathFunction` annotation + +## 2. Testing + +- [x] 2.1 Verify YAML reference tests pass (`5.2.3_repeat.yaml`, repeat cases in `5.2_filtering_and_projection.yaml`, repeat cases in `fhir-r4.yaml`) +- [x] 2.2 Add exclusions for any YAML tests that require unsupported features (e.g., primitive element `id` attribute) +- [x] 2.3 Write DSL tests for `repeat()` covering: basic tree traversal, primitive dedup, quantity dedup, complex type no-dedup, empty input, chained operations diff --git a/openspec/changes/archive/2026-03-06-repeatall-depth-config/.openspec.yaml b/openspec/changes/archive/2026-03-06-repeatall-depth-config/.openspec.yaml new file mode 100644 index 0000000000..8f0b86992e --- /dev/null +++ b/openspec/changes/archive/2026-03-06-repeatall-depth-config/.openspec.yaml @@ -0,0 +1,2 @@ +schema: spec-driven +created: 2026-03-05 diff --git a/openspec/changes/archive/2026-03-06-repeatall-depth-config/design.md b/openspec/changes/archive/2026-03-06-repeatall-depth-config/design.md new file mode 100644 index 0000000000..67c251ea24 --- /dev/null +++ b/openspec/changes/archive/2026-03-06-repeatall-depth-config/design.md @@ -0,0 +1,172 @@ +## Context + +Pathling's `repeatAll()` function uses `UnresolvedTransformTree`, a Catalyst +expression that performs depth-limited recursive tree traversal. The depth +counter only decrements for same-type traversals (where the Spark SQL +`DataType` is identical across levels). Currently, when the depth limit is +exhausted, `UnresolvedTransformTree` silently returns an empty array. + +Same-type traversal only occurs when the projection produces an element with an +identical SQL `DataType` at every level. In practice, this means: + +- **Extension traversal** (`repeatAll(extension)`): Extension structs have a + fixed schema at all nesting levels. This is the only legitimate same-type + recursion — extensions are genuinely recursive in FHIR. +- **Identity-like traversals** (`repeatAll($this)`, `repeatAll(first())`, + `repeatAll('const')`): These always produce the same type and are effectively + infinite loops. + +The depth limit is currently hardcoded to 10 in +`FilteringAndProjectionFunctions`. The SQL on FHIR `RepeatSelection` has its +own configurable `maxUnboundTraversalDepth` in `QueryConfiguration`, but +`repeatAll()` does not participate in this configuration. + +`@FhirPathFunction`-annotated static methods currently receive parameters via +`FunctionParameterResolver`, which supports `Collection`, +`CollectionTransform`, `TypeSpecifier`, and `TerminologyConcepts`. There is no +mechanism to inject the `EvaluationContext` or configuration values into +function methods. + +## Goals / Non-Goals + +**Goals:** + +- Make the same-type recursion depth configurable through a new + `FhirpathConfiguration` object. +- Rename the depth concept to `maxExtensionDepth` to reflect its primary + legitimate use case. +- Detect infinite recursive traversal (non-Extension same-type depth + exhaustion) and raise an evaluation error instead of silently stopping. +- Preserve current silent-stop behavior for Extension traversal. +- Enable `@FhirPathFunction` methods to access the `EvaluationContext`. + +**Non-Goals:** + +- Changing the SQL on FHIR `RepeatSelection` behavior — it continues to use + `QueryConfiguration.maxUnboundTraversalDepth` with silent stop semantics. +- Making `UnresolvedTransformTree`'s error message include FHIRPath-level + context (function name, expression text). A generic error message is + sufficient. + +## Decisions + +### Decision 1: Add `errorOnDepthExhaustion` flag to `UnresolvedTransformTree` + +Add a boolean `errorOnDepthExhaustion` parameter to `UnresolvedTransformTree`. +When `true` and the same-type depth limit is exhausted, the expression throws +an `AnalysisException` with the message "Infinite recursive traversal +detected." When `false`, the current behavior (returning an empty array) is +preserved. + +The flag is propagated through recursive construction in `mapChildren` so all +child nodes inherit the same error mode. + +**Alternatives considered:** + +- **Detect at FHIRPath level before tree construction**: Cannot know at + evaluation time whether depth will be exhausted — that depends on schema + structure resolved during Catalyst analysis. +- **Always error on depth exhaustion**: Would break Extension traversal, which + legitimately reaches the depth limit. + +**Rationale:** The detection naturally lives where the depth is tracked — inside +the Catalyst expression. A simple flag keeps the two modes cleanly separated. + +### Decision 2: Thread `errorOnDepthExhaustion` through `ValueFunctions` + +`ValueFunctions.transformTree()` and `variantTransformTree()` gain an +`errorOnDepthExhaustion` boolean parameter that is forwarded to +`UnresolvedTransformTree`. Existing callers (`RepeatSelection`) pass `false` to +preserve current behavior. + +**Rationale:** Minimal API change — one additional parameter on existing +methods. + +### Decision 3: Create `FhirpathConfiguration` record + +A new `FhirpathConfiguration` record in the `fhirpath.config` package (or +`fhirpath` package) holds: + +```java +public record FhirpathConfiguration(int maxExtensionDepth) { + public static final int DEFAULT_MAX_EXTENSION_DEPTH = 10; + public static final FhirpathConfiguration DEFAULT = + new FhirpathConfiguration(DEFAULT_MAX_EXTENSION_DEPTH); +} +``` + +**Rationale:** A dedicated configuration object is extensible for future +FHIRPath evaluation settings without changing the `EvaluationContext` interface +each time. + +### Decision 4: Add `getConfiguration()` to `EvaluationContext` + +The `EvaluationContext` interface gains a default method: + +```java +default FhirpathConfiguration getConfiguration() { + return FhirpathConfiguration.DEFAULT; +} +``` + +`FhirEvaluationContext` overrides this with the actual configuration. + +**Alternatives considered:** + +- **Putting configuration on `Collection`**: Would require threading config + through every collection operation. Too invasive. +- **Static/global configuration**: Not thread-safe, not testable. + +**Rationale:** Default method ensures backward compatibility — existing +`EvaluationContext` implementations get sensible defaults without modification. + +### Decision 5: Support `EvaluationContext` as a parameter type in `FunctionParameterResolver` + +Add a new case in `FunctionParameterResolver.resolveArgument()` that checks for +`EvaluationContext.class.isAssignableFrom(parameter.getType())`. When matched, +the resolver injects the `evaluationContext` directly without consuming an +argument from the argument list. + +The `EvaluationContext` parameter is not a FHIRPath argument — it is injected by +the resolver from its own state. This means `bind()` must distinguish between +argument-consuming parameters and context-injected parameters when iterating +method parameters. + +**Rationale:** General-purpose mechanism — other functions may need context +access in the future. Consistent with how the resolver already handles different +parameter types. + +### Decision 6: Extension detection in `Collection.repeatAll()` + +After applying the transform to get `resultTemplate`, check: + +```java +boolean isExtensionTraversal = resultTemplate.getFhirType() + .map(FHIRDefinedType.EXTENSION::equals) + .orElse(false); +``` + +Pass `errorOnDepthExhaustion = !isExtensionTraversal` to +`variantTransformTree()`. + +**Rationale:** The `fhirType` metadata is already available on the result +collection. Extension is the only FHIR type with a fixed, non-truncating schema +that produces legitimate same-type recursion. + +## Risks / Trade-offs + +**Error during Catalyst analysis** → The error is thrown during query planning, +not data execution. This means `repeatAll($this)` always errors regardless of +data content. This is correct — infinite recursion is a static property of the +expression, not a runtime condition. + +**Unknown fhirType defaults to error mode** → When `getFhirType()` returns +empty, the traversal defaults to error mode (`!false = true`). Types with no +FHIR type mapping (e.g., custom structures) that happen to have same-type +recursion will error. This is conservative and correct — unknown types that hit +the depth limit are more likely bugs than intentional recursion. + +**`RepeatSelection` unaffected** → The SQL on FHIR `RepeatSelection` passes +`false` for `errorOnDepthExhaustion`, preserving its current silent-stop +behavior. This is intentional — `RepeatSelection` serves a different use case +where depth limiting is a normal operating mode, not an error condition. diff --git a/openspec/changes/archive/2026-03-06-repeatall-depth-config/proposal.md b/openspec/changes/archive/2026-03-06-repeatall-depth-config/proposal.md new file mode 100644 index 0000000000..e07eab6fd5 --- /dev/null +++ b/openspec/changes/archive/2026-03-06-repeatall-depth-config/proposal.md @@ -0,0 +1,55 @@ +## Why + +The `repeatAll()` function uses a hardcoded same-type recursion depth limit of 10. This value needs to be configurable, and its semantics need refinement: +same-type depth exhaustion currently silently stops traversal, but for +non-Extension types this indicates infinite recursion (e.g., +`repeatAll($this)`, `repeatAll(first())`) and should produce an evaluation +error. Only Extension traversal is a legitimate same-type recursion that should +silently stop at the depth limit. + +## What Changes + +- Introduce a `FhirpathConfiguration` object that holds configurable FHIRPath + evaluation parameters, starting with `maxExtensionDepth` (renamed from + `DEFAULT_SAME_TYPE_RECURSION_DEPTH`). +- Pass `FhirpathConfiguration` through the `EvaluationContext` so it is + accessible to FHIRPath functions at evaluation time. +- Add `EvaluationContext` as a supported parameter type in + `FunctionParameterResolver`, allowing `@FhirPathFunction`-annotated methods to + receive the evaluation context. +- Add an `errorOnDepthExhaustion` flag to `UnresolvedTransformTree` (Scala + Catalyst expression) so that same-type depth exhaustion can either silently + stop (for Extension traversal) or raise an error (for all other same-type + traversal). +- `repeatAll()` detects whether the projection targets the Extension FHIR type + and selects the appropriate mode: silent stop for Extension, error for + everything else. + +## Capabilities + +### New Capabilities + +- `fhirpath-configuration`: A configuration object for FHIRPath evaluation + parameters, initially containing `maxExtensionDepth`, passed through the + evaluation context. + +### Modified Capabilities + +- `fhirpath-repeat-all`: Same-type depth exhaustion now raises an error for + non-Extension traversals (indicating infinite recursion), while Extension + traversal continues to silently stop at the configured `maxExtensionDepth`. + +## Impact + +- **fhirpath module**: New `FhirpathConfiguration` class, `EvaluationContext` + interface gains `getConfiguration()`, `FunctionParameterResolver` supports + `EvaluationContext` injection, `FilteringAndProjectionFunctions.repeatAll()` + gains `EvaluationContext` parameter. +- **encoders module**: `UnresolvedTransformTree` gains + `errorOnDepthExhaustion` flag, `ValueFunctions.transformTree()` and + `variantTransformTree()` gain corresponding parameter. +- **library-api**: `FhirEvaluationContext` updated to carry + `FhirpathConfiguration`. +- **Testing**: Existing `repeatAll(first())` test updated to expect an error + instead of bounded results. New tests for infinite recursion detection and + configurable depth. diff --git a/openspec/changes/archive/2026-03-06-repeatall-depth-config/specs/fhirpath-configuration/spec.md b/openspec/changes/archive/2026-03-06-repeatall-depth-config/specs/fhirpath-configuration/spec.md new file mode 100644 index 0000000000..a8cc81cae0 --- /dev/null +++ b/openspec/changes/archive/2026-03-06-repeatall-depth-config/specs/fhirpath-configuration/spec.md @@ -0,0 +1,54 @@ +## ADDED Requirements + +### Requirement: FHIRPath evaluation configuration object + +The FHIRPath engine SHALL support a `FhirpathConfiguration` object that holds +configurable parameters for FHIRPath expression evaluation. The configuration +SHALL be accessible to FHIRPath functions through the `EvaluationContext`. + +The configuration SHALL include `maxExtensionDepth` (integer), which controls +the maximum depth for same-type recursive traversal of Extension elements. The +default value SHALL be 10. + +When no explicit configuration is provided, the evaluation context SHALL use a +default configuration with `maxExtensionDepth` set to 10. + +#### Scenario: Default configuration + +- **WHEN** no `FhirpathConfiguration` is explicitly provided to the evaluation + context +- **THEN** the evaluation context SHALL use a default configuration with + `maxExtensionDepth` equal to 10 + +#### Scenario: Custom configuration + +- **WHEN** a `FhirpathConfiguration` with `maxExtensionDepth` set to 5 is + provided to the evaluation context +- **THEN** the evaluation context SHALL use that configuration and Extension + traversal in `repeatAll(extension)` SHALL be limited to depth 5 + +### Requirement: EvaluationContext provides configuration access + +The `EvaluationContext` interface SHALL provide a method to retrieve the +`FhirpathConfiguration`. Implementations that do not explicitly set a +configuration SHALL return the default configuration. + +#### Scenario: Configuration accessible from evaluation context + +- **WHEN** a FHIRPath function accesses the evaluation context during evaluation +- **THEN** the `FhirpathConfiguration` SHALL be available with the configured + `maxExtensionDepth` value + +### Requirement: FHIRPath functions can receive EvaluationContext + +The `FunctionParameterResolver` SHALL support injecting the `EvaluationContext` +into `@FhirPathFunction`-annotated static methods. When a method parameter is +typed as `EvaluationContext`, the resolver SHALL inject the current evaluation +context without consuming an argument from the FHIRPath argument list. + +#### Scenario: EvaluationContext injection + +- **WHEN** a `@FhirPathFunction` method declares an `EvaluationContext` + parameter +- **THEN** the resolver SHALL inject the current evaluation context and the + function SHALL receive it alongside the normal input and arguments diff --git a/openspec/changes/archive/2026-03-06-repeatall-depth-config/specs/fhirpath-repeat-all/spec.md b/openspec/changes/archive/2026-03-06-repeatall-depth-config/specs/fhirpath-repeat-all/spec.md new file mode 100644 index 0000000000..b3de685b51 --- /dev/null +++ b/openspec/changes/archive/2026-03-06-repeatall-depth-config/specs/fhirpath-repeat-all/spec.md @@ -0,0 +1,73 @@ +## MODIFIED Requirements + +### Requirement: repeatAll function bounds same-type recursion depth + +The function delegates recursive traversal to `UnresolvedTransformTree`, which +limits recursion depth based on Spark SQL `DataType` equality. The depth counter +only decrements when the traversal expression produces a node whose resolved SQL +`DataType` is structurally identical to its parent's. + +For traversals through schema-truncated structures (e.g., +`Questionnaire.repeatAll(item)`), each nesting level has a progressively smaller +`StructType` due to the encoding's `maxNestingLevel` truncation. These are NOT +same-type traversals — the depth counter is never decremented, and traversal +terminates naturally when a field is no longer present in the truncated schema +(`FIELD_NOT_FOUND`). + +Same-type recursion occurs when the traversal produces an element with an +identical SQL `DataType` at every level. The function SHALL distinguish two +cases: + +- **Extension traversal**: When the projection produces a result with FHIR type + `Extension`, the function SHALL silently stop traversal when the configured + `maxExtensionDepth` is reached, returning all results collected up to that + point. This supports legitimate recursive navigation of Extension hierarchies. +- **Non-Extension same-type traversal**: When the projection produces a + non-Extension type and same-type depth is exhausted, the function SHALL raise + an evaluation error with a message indicating that infinite recursive + traversal was detected. This covers identity-like traversals such as + `repeatAll($this)`, `repeatAll(first())`, and `repeatAll('const')` that would + otherwise loop indefinitely. + +The same-type recursion depth is controlled by the `maxExtensionDepth` setting +in `FhirpathConfiguration`, with a default value of 10. + +#### Scenario: Extension traversal bounded by configured depth + +- **WHEN** `repeatAll(extension)` is evaluated on a resource whose elements + carry nested extensions and `maxExtensionDepth` is set to 5 +- **THEN** the function SHALL traverse extensions up to depth 5, returning all + collected extensions, and SHALL NOT raise an error + +#### Scenario: Extension traversal with default depth + +- **WHEN** `repeatAll(extension)` is evaluated with default configuration +- **THEN** the function SHALL traverse extensions up to depth 10 + +#### Scenario: Infinite recursion detected for identity traversal + +- **WHEN** `repeatAll($this)` is evaluated on any collection +- **THEN** the function SHALL raise an evaluation error indicating infinite + recursive traversal was detected + +#### Scenario: Infinite recursion detected for first() traversal + +- **WHEN** `name.repeatAll(first())` is evaluated on a resource with name + elements +- **THEN** the function SHALL raise an evaluation error indicating infinite + recursive traversal was detected + +#### Scenario: Schema-truncated traversal terminates naturally + +- **WHEN** `repeatAll(item)` is evaluated on a Questionnaire with nested items +- **THEN** traversal SHALL terminate naturally when the schema no longer + contains the `item` field (due to `maxNestingLevel` truncation during the + encoding), without consuming same-type depth budget and without raising an + error + +#### Scenario: Unknown FHIR type defaults to error mode + +- **WHEN** `repeatAll` is evaluated with a projection whose FHIR type is + unknown and same-type depth is exhausted +- **THEN** the function SHALL raise an evaluation error, as unknown types that + hit the depth limit are more likely bugs than intentional recursion diff --git a/openspec/changes/archive/2026-03-06-repeatall-depth-config/tasks.md b/openspec/changes/archive/2026-03-06-repeatall-depth-config/tasks.md new file mode 100644 index 0000000000..1a5c0169f0 --- /dev/null +++ b/openspec/changes/archive/2026-03-06-repeatall-depth-config/tasks.md @@ -0,0 +1,36 @@ +## 1. UnresolvedTransformTree error mode + +- [x] 1.1 Add `errorOnDepthExhaustion: Boolean = false` parameter to `UnresolvedTransformTree` case class in `Expressions.scala`, propagating it through recursive construction in `mapChildren` and `withNewChildrenInternal` +- [x] 1.2 When `errorOnDepthExhaustion` is `true` and same-type depth is exhausted (`level <= 0 && parentType.contains(newValue.dataType)`), throw an `AnalysisException` with message "Infinite recursive traversal detected." instead of returning an empty array +- [x] 1.3 Add `errorOnDepthExhaustion` boolean parameter to `ValueFunctions.transformTree()` and forward it to `UnresolvedTransformTree` +- [x] 1.4 Add `errorOnDepthExhaustion` boolean parameter to `ValueFunctions.variantTransformTree()` and forward it to `transformTree()` +- [x] 1.5 Update `RepeatSelection` to pass `false` for `errorOnDepthExhaustion` to `ValueFunctions.transformTree()`, preserving current silent-stop behavior +- [x] 1.6 Write unit tests for `UnresolvedTransformTree` verifying: (a) silent stop when `errorOnDepthExhaustion = false`, (b) error thrown when `errorOnDepthExhaustion = true` and same-type depth exhausted + +## 2. FhirpathConfiguration + +- [x] 2.1 Create `FhirpathConfiguration` record in the `fhirpath` module with `maxExtensionDepth` field (int), `DEFAULT_MAX_EXTENSION_DEPTH` constant (10), and `DEFAULT` static instance +- [x] 2.2 Add `getConfiguration()` default method to `EvaluationContext` interface returning `FhirpathConfiguration.DEFAULT` +- [x] 2.3 Add `FhirpathConfiguration` field to `FhirEvaluationContext` record and override `getConfiguration()` +- [x] 2.4 Update all construction sites of `FhirEvaluationContext` to pass `FhirpathConfiguration.DEFAULT` (or a configured value where applicable) + +## 3. EvaluationContext parameter injection + +- [x] 3.1 Add support for `EvaluationContext` as a parameter type in `FunctionParameterResolver.resolveArgument()` — inject the evaluation context without consuming a FHIRPath argument +- [x] 3.2 Update the argument count validation in `FunctionParameterResolver.bind()` to exclude context-injected parameters from the expected argument count +- [x] 3.3 Write unit tests for `FunctionParameterResolver` verifying that `EvaluationContext` parameters are injected correctly alongside normal Collection and CollectionTransform parameters + +## 4. repeatAll() integration + +- [x] 4.1 Update `FilteringAndProjectionFunctions.repeatAll()` to accept an `EvaluationContext` parameter and read `maxExtensionDepth` from the configuration +- [x] 4.2 Remove the `DEFAULT_SAME_TYPE_RECURSION_DEPTH` constant from `FilteringAndProjectionFunctions` +- [x] 4.3 Update `Collection.repeatAll()` to accept an `errorOnDepthExhaustion` boolean parameter and pass it through to `ValueFunctions.variantTransformTree()` +- [x] 4.4 Add Extension detection in `FilteringAndProjectionFunctions.repeatAll()` or `Collection.repeatAll()`: check `resultTemplate.getFhirType()` for `FHIRDefinedType.EXTENSION` and set `errorOnDepthExhaustion = !isExtensionTraversal` + +## 5. Tests + +- [x] 5.1 Update the existing `repeatAll(first())` DSL test to expect an evaluation error instead of bounded results (count of 11) +- [x] 5.2 Add DSL test for `repeatAll($this)` expecting an evaluation error +- [x] 5.3 Verify existing `repeatAll(extension)` test still passes with silent-stop behavior +- [ ] 5.4 ~~Add DSL test with a custom `FhirpathConfiguration` setting `maxExtensionDepth` to a lower value and verify Extension traversal respects it~~ — Deferred: requires adding configuration support to DSL test infrastructure +- [x] 5.5 Verify existing `repeatAll(item)` tests still pass (schema-truncated traversal unaffected) diff --git a/openspec/changes/archive/2026-03-06-repeatall-static-recursion-detection/.openspec.yaml b/openspec/changes/archive/2026-03-06-repeatall-static-recursion-detection/.openspec.yaml new file mode 100644 index 0000000000..3184e5abf5 --- /dev/null +++ b/openspec/changes/archive/2026-03-06-repeatall-static-recursion-detection/.openspec.yaml @@ -0,0 +1,2 @@ +schema: spec-driven +created: 2026-03-06 diff --git a/openspec/changes/archive/2026-03-06-repeatall-static-recursion-detection/design.md b/openspec/changes/archive/2026-03-06-repeatall-static-recursion-detection/design.md new file mode 100644 index 0000000000..f1ba29b422 --- /dev/null +++ b/openspec/changes/archive/2026-03-06-repeatall-static-recursion-detection/design.md @@ -0,0 +1,109 @@ +## Context + +The `repeatAll()` function in `Collection.java` currently uses two mechanisms +for recursion control: + +1. **Primitive shortcut** (`isPrimitive` check): If the traversal expression + produces a primitive type, the function returns `level0` directly without + entering the tree traversal. This bypasses all recursion detection. +2. **Analysis-time detection** (`UnresolvedTransformTree`): For complex types, + Catalyst resolution compares SQL `DataType` at each level. Same-type + depth exhaustion either errors (non-Extension) or silently stops (Extension). + +The primitive shortcut is incorrect: expressions like `gender.repeatAll($this)` +are genuinely infinite but silently return a truncated result. + +## Goals / Non-Goals + +**Goals:** + +- Detect self-referential primitive traversals statically and raise an + immediate error with a descriptive message. +- Unify the "equivalent to select()" shortcut for both primitive and complex + types when the traversal expression produces an empty collection on + self-application. +- Enforce the invariant that recursive application of the traversal expression + must produce either the same FHIR type or empty — anything else is an error. +- Distinguish error messages between static detection and analysis-time + detection. + +**Non-Goals:** + +- Changing the Extension depth-limiting behavior (soft stop at configured + depth). +- Distinguishing `repeatAll(extension)` from `repeatAll($this)` on Extension + collections (accepted limitation — both get soft stop). +- Changing `UnresolvedTransformTree` logic. + +## Decisions + +### Decision 1: Static level_0/level_1 type analysis gate + +**Choice**: Apply the traversal expression twice in `Collection.repeatAll()` +— once to the input (`level_0 = transform.apply(this)`) and once to its own +result (`level_1 = transform.apply(level_0)`) — to classify behavior before +any tree traversal. + +**Rationale**: The `CollectionTransform` already supports self-application. +The FHIR type of the result is statically determined at evaluation time, so +comparing `level_0.getFhirType()` with `level_1.getFhirType()` (or checking +`level_1.isEmpty()`) gives a complete classification without needing Catalyst +resolution. + +**Alternatives**: Could defer all detection to `UnresolvedTransformTree`, but +that requires routing primitives through the tree (adding complexity) and +produces less descriptive error messages. + +### Decision 2: Four-way classification + +The level_0/level_1 comparison produces exactly four outcomes: + +| level_1 state | level_0 type | Action | +| ------------------------ | ------------------ | ---------------------------------------------------- | +| Empty | any | Return level_0 directly (equivalent to select) | +| Same FHIR type | primitive | Error: self-referential primitive | +| Same FHIR type | complex, Extension | `variantTransformTree(errorOnDepthExhaustion=false)` | +| Same FHIR type | complex, other | `variantTransformTree(errorOnDepthExhaustion=true)` | +| Different non-empty type | any | Error: inconsistent traversal types | + +**Rationale**: This is exhaustive and each case has clear, distinct semantics. +The "return level_0" shortcut now applies to ALL types when level_1 is empty, +replacing the previous primitive-only shortcut. + +### Decision 3: Distinct error messages + +Three error contexts warrant different messages: + +1. **Static primitive**: Self-referential primitive type detected at the + `Collection.repeatAll()` level. Fires immediately, no Catalyst involved. +2. **Static inconsistent type**: Traversal expression produces different + non-empty types across recursive application. Fires immediately. +3. **Analysis-time complex**: Same SQL `DataType` depth exhausted in + `UnresolvedTransformTree`. Fires during Catalyst analysis for complex types + where structural convergence can only be determined after schema resolution. + +The existing message in `UnresolvedTransformTree` ("Infinite recursive traversal +detected.") remains unchanged. + +### Decision 4: FHIR type comparison for level_0/level_1 + +**Choice**: Use `FHIRDefinedType` equality to compare level_0 and level_1 +types. `EmptyCollection` is detected via the existing `isEmpty()` static check. + +**Rationale**: FHIR type drives the semantic behavior. SQL type comparison is +appropriate for `UnresolvedTransformTree` (where schema divergence matters) but +not for the static gate (where we need to know if the traversal is +self-referential in FHIR terms). + +## Risks / Trade-offs + +**`Patient.extension.repeatAll($this)` not caught as infinite** → +Accepted limitation. The level_1 check sees Extension→Extension (same FHIR +type, complex, Extension) and routes to soft stop. This is genuinely infinite +but indistinguishable from the legitimate `repeatAll(extension)` case at the +FHIR type level. + +**Double application of transform** → The `transform.apply(level_0)` call +adds one extra static evaluation. This is negligible compared to the Spark +query planning that follows, and avoids entering the tree traversal entirely +for the common non-recursive case. diff --git a/openspec/changes/archive/2026-03-06-repeatall-static-recursion-detection/proposal.md b/openspec/changes/archive/2026-03-06-repeatall-static-recursion-detection/proposal.md new file mode 100644 index 0000000000..1368b32e29 --- /dev/null +++ b/openspec/changes/archive/2026-03-06-repeatall-static-recursion-detection/proposal.md @@ -0,0 +1,51 @@ +## Why + +The current `repeatAll()` implementation uses a primitive type shortcut that +bypasses infinite recursion detection. Expressions like `gender.repeatAll($this)` +or `gender.repeatAll('value')` silently return a truncated result instead of +raising an error. The recursion detection logic should be moved earlier — to a +static analysis phase in `Collection.repeatAll()` — where self-referential +primitive traversals can be caught immediately, and non-recursive traversals +(both primitive and complex) can be shortcut to equivalent `select()` behavior +without entering the tree traversal at all. + +## What Changes + +- Add static type analysis in `Collection.repeatAll()` that applies the + traversal expression twice (level_0 and level_1) to determine recursion + behavior before any tree traversal. +- If level_1 is empty: return level_0 directly (equivalent to `select()`) for + both primitive and complex types. +- If level_1 is same FHIR type as level_0 and primitive: raise an immediate + error with a distinct message for self-referential primitive traversal. +- If level_1 is same FHIR type as level_0 and complex: proceed to + `variantTransformTree()` (with `errorOnDepthExhaustion=false` for Extension, + `true` for all others). +- If level_1 is a different non-empty FHIR type from level_0: raise an error + for inconsistent traversal types. +- Remove the `isPrimitive` shortcut that currently bypasses recursion detection. +- Use distinct error messages to differentiate static detection (primitive + self-reference, inconsistent types) from analysis-time detection (complex + same-SQL-type depth exhaustion). + +## Capabilities + +### New Capabilities + +(none) + +### Modified Capabilities + +- `fhirpath-repeat-all`: Recursion detection moves from purely analysis-time to + a static pre-check. Self-referential primitive traversals now error instead of + silently returning truncated results. Non-recursive traversals shortcut + to level_0 for all types. + +## Impact + +- `fhirpath/src/main/java/.../collection/Collection.java`: Restructure + `repeatAll()` method to add static type analysis gate. +- `fhirpath/src/test/java/.../dsl/RepeatAllFunctionDslTest.java`: Add test + cases for primitive self-referential detection, update existing expectations. +- No public API changes. No configuration changes. The `maxExtensionDepth` + setting continues to control Extension depth limiting. diff --git a/openspec/changes/archive/2026-03-06-repeatall-static-recursion-detection/specs/fhirpath-repeat-all/spec.md b/openspec/changes/archive/2026-03-06-repeatall-static-recursion-detection/specs/fhirpath-repeat-all/spec.md new file mode 100644 index 0000000000..7af4e6f5b8 --- /dev/null +++ b/openspec/changes/archive/2026-03-06-repeatall-static-recursion-detection/specs/fhirpath-repeat-all/spec.md @@ -0,0 +1,159 @@ +## MODIFIED Requirements + +### Requirement: repeatAll function terminates on empty iteration + +The function SHALL terminate when an iteration of the projection expression +across all current items produces an empty collection (no new results). + +When the traversal expression applied to its own result (level_1) produces a +statically empty collection, the function SHALL return the level_0 result +directly for both primitive and complex types. This is equivalent to `select()` +behavior. + +#### Scenario: Termination at leaf nodes + +- **WHEN** `repeatAll(item)` is evaluated on a Questionnaire where the deepest + items have no child items +- **THEN** the function SHALL terminate and return all collected items + +#### Scenario: Non-recursive collection projection + +- **WHEN** `repeatAll` is called with a projection that does not navigate into a + recursive structure and produces a collection (e.g., + `Patient.repeatAll(name)`) +- **THEN** the function SHALL return the level_0 result directly, equivalent to + `select()` + +#### Scenario: Non-recursive singular projection + +- **WHEN** `repeatAll` is called with a projection that produces a singular + value (e.g., `Patient.repeatAll(gender)`) +- **THEN** the function SHALL return the level_0 result directly, equivalent to + `select()` + +#### Scenario: Non-recursive singular complex projection + +- **WHEN** `repeatAll` is called with a projection that produces a singular + complex type (e.g., `Patient.repeatAll(maritalStatus)`) +- **THEN** the function SHALL return the level_0 result directly with all + sub-elements intact, equivalent to `select()` + +### Requirement: repeatAll function bounds same-type recursion depth + +The function SHALL perform a static type analysis before entering tree +traversal. It SHALL apply the traversal expression to the input to produce +level_0, then apply the traversal expression to level_0 to produce level_1. +The function SHALL classify behavior based on the FHIR type comparison between +level_0 and level_1: + +1. **level_1 is empty**: Return level_0 directly (equivalent to `select()`). + This applies to both primitive and complex types. +2. **level_1 is same FHIR type as level_0, primitive**: Raise an immediate + error indicating self-referential primitive traversal. +3. **level_1 is same FHIR type as level_0, complex, Extension**: Proceed to + recursive tree traversal with silent stop on depth exhaustion. +4. **level_1 is same FHIR type as level_0, complex, non-Extension**: Proceed + to recursive tree traversal with error on depth exhaustion. +5. **level_1 is a different non-empty FHIR type from level_0**: Raise an + immediate error indicating inconsistent traversal types. + +For case 3 and 4, the function delegates to `variantTransformTree` with +`UnresolvedTransformTree` providing analysis-time same-SQL-type depth limiting. +The depth limit for Extension traversal is controlled by `maxExtensionDepth` in +`FhirpathConfiguration`. + +#### Scenario: Self-referential primitive identity traversal detected + +- **WHEN** `gender.repeatAll($this)` is evaluated +- **THEN** the function SHALL raise an error indicating self-referential + primitive traversal + +#### Scenario: Self-referential primitive constant traversal detected + +- **WHEN** `gender.repeatAll('someValue')` is evaluated +- **THEN** the function SHALL raise an error indicating self-referential + primitive traversal + +#### Scenario: Self-referential primitive function traversal detected + +- **WHEN** `gender.repeatAll(length())` is evaluated +- **THEN** the function SHALL raise an error indicating self-referential + primitive traversal + +#### Scenario: Infinite recursion detected for identity traversal on complex type + +- **WHEN** `repeatAll($this)` is evaluated on any complex-typed collection +- **THEN** the function SHALL raise an evaluation error indicating infinite + recursive traversal was detected (via analysis-time detection) + +#### Scenario: Infinite recursion detected for first() traversal + +- **WHEN** `name.repeatAll(first())` is evaluated on a resource with name + elements +- **THEN** the function SHALL raise an evaluation error indicating infinite + recursive traversal was detected (via analysis-time detection) + +#### Scenario: Extension traversal bounded by configured depth + +- **WHEN** `repeatAll(extension)` is evaluated on a resource whose elements + carry nested extensions and `maxExtensionDepth` is set to 5 +- **THEN** the function SHALL traverse extensions up to depth 5, returning all + collected extensions, and SHALL NOT raise an error + +#### Scenario: Extension traversal with default depth + +- **WHEN** `repeatAll(extension)` is evaluated with default configuration +- **THEN** the function SHALL traverse extensions up to depth 10 + +#### Scenario: Schema-truncated traversal terminates naturally + +- **WHEN** `repeatAll(item)` is evaluated on a Questionnaire with nested items +- **THEN** traversal SHALL terminate naturally when the schema no longer + contains the `item` field (due to `maxNestingLevel` truncation during the + encoding), without consuming same-type depth budget and without raising an + error + +#### Scenario: Unknown FHIR type defaults to error mode + +- **WHEN** `repeatAll` is evaluated with a projection whose FHIR type is + unknown and same-type depth is exhausted +- **THEN** the function SHALL raise an evaluation error, as unknown types that + hit the depth limit are more likely bugs than intentional recursion + +#### Scenario: Inconsistent traversal types detected + +- **WHEN** `repeatAll` is evaluated with a traversal expression that produces a + different non-empty FHIR type when applied to its own result +- **THEN** the function SHALL raise an error indicating inconsistent traversal + types + +### Requirement: repeatAll function uses distinct error messages + +The function SHALL use distinct error messages to differentiate between +detection contexts: + +1. **Static primitive self-reference**: A message indicating that the traversal + expression produces a self-referential primitive type that cannot terminate. +2. **Static inconsistent types**: A message indicating that the traversal + expression does not produce a consistent type across recursive applications. +3. **Analysis-time complex depth exhaustion**: The existing message "Infinite + recursive traversal detected." from `UnresolvedTransformTree`. + +#### Scenario: Primitive self-reference error message + +- **WHEN** a self-referential primitive traversal is detected statically +- **THEN** the error message SHALL be distinct from the analysis-time + "Infinite recursive traversal detected." message + +#### Scenario: Inconsistent type error message + +- **WHEN** an inconsistent traversal type is detected statically +- **THEN** the error message SHALL indicate that the traversal expression + produces inconsistent types + +#### Scenario: Analysis-time error message preserved + +- **WHEN** a complex non-Extension same-SQL-type depth exhaustion occurs during + Catalyst analysis +- **THEN** the error message SHALL remain "Infinite recursive traversal + detected." diff --git a/openspec/changes/archive/2026-03-06-repeatall-static-recursion-detection/tasks.md b/openspec/changes/archive/2026-03-06-repeatall-static-recursion-detection/tasks.md new file mode 100644 index 0000000000..afc8108e8d --- /dev/null +++ b/openspec/changes/archive/2026-03-06-repeatall-static-recursion-detection/tasks.md @@ -0,0 +1,27 @@ +## 1. Static type analysis gate in Collection.repeatAll() + +- [x] 1.1 Add level_1 computation by applying transform to level_0 (resultTemplate) +- [x] 1.2 Add empty check: if level_1.isEmpty(), return level_0 directly (both primitive and complex) +- [x] 1.3 Add FHIR type comparison between level_0 and level_1 +- [x] 1.4 Add error for self-referential primitive traversal (same FHIR type, primitive level_0) +- [x] 1.5 Add error for inconsistent traversal types (different non-empty FHIR type) +- [x] 1.6 Route same-type complex Extension to variantTransformTree with errorOnDepthExhaustion=false +- [x] 1.7 Route same-type complex non-Extension to variantTransformTree with errorOnDepthExhaustion=true +- [x] 1.8 Remove the isPrimitive shortcut that bypasses recursion detection + +## 2. Error messages + +- [x] 2.1 Define distinct error message for static primitive self-reference detection +- [x] 2.2 Define distinct error message for inconsistent traversal type detection +- [x] 2.3 Verify existing "Infinite recursive traversal detected." message in UnresolvedTransformTree is preserved + +## 3. Tests + +- [x] 3.1 Add test for gender.repeatAll($this) raising primitive self-reference error +- [x] 3.2 Add test for gender.repeatAll('someValue') raising primitive self-reference error +- [x] 3.3 Add test for gender.repeatAll(length()) raising primitive self-reference error +- [x] 3.4 Verify existing test for name.repeatAll(first()) still raises analysis-time error +- [x] 3.5 Verify existing test for repeatAll($this) on complex type still raises analysis-time error +- [x] 3.6 Verify existing tests for Patient.repeatAll(name), Patient.repeatAll(gender), Patient.repeatAll(maritalStatus) still pass (now via level_0 shortcut) +- [x] 3.7 Verify existing Questionnaire.repeatAll(item) tests still pass (variantTransformTree path) +- [x] 3.8 Verify existing extension traversal tests still pass (soft stop path) diff --git a/openspec/changes/archive/2026-03-09-fix-repeatall-empty-type-guard/.openspec.yaml b/openspec/changes/archive/2026-03-09-fix-repeatall-empty-type-guard/.openspec.yaml new file mode 100644 index 0000000000..5cb9e8f6eb --- /dev/null +++ b/openspec/changes/archive/2026-03-09-fix-repeatall-empty-type-guard/.openspec.yaml @@ -0,0 +1,2 @@ +schema: spec-driven +created: 2026-03-09 diff --git a/openspec/changes/archive/2026-03-09-fix-repeatall-empty-type-guard/design.md b/openspec/changes/archive/2026-03-09-fix-repeatall-empty-type-guard/design.md new file mode 100644 index 0000000000..071a840045 --- /dev/null +++ b/openspec/changes/archive/2026-03-09-fix-repeatall-empty-type-guard/design.md @@ -0,0 +1,122 @@ +## Context + +The `repeatAll()` method in `Collection.java` performs a static type analysis +gate before entering recursive tree traversal. It applies the traversal +expression twice — once to produce level_0, once more to produce level_1 — and +classifies behavior based on the FHIR type comparison between them. + +The current classification covers five cases (empty level_1, same-type +primitive, same-type Extension, same-type non-Extension complex, and type +mismatch). However, it assumes `getFhirType()` always returns a populated +`Optional`. When both types are `Optional.empty()`, the equality check +`level0Type.equals(level1Type)` silently passes, treating two unknowns as +"consistent". + +This is reachable through FHIR choice type expressions. A `MixedCollection` +(representing choice elements like `Observation.value[x]`) has +`fhirType = Optional.empty()`. The `$this` transform is pure identity — +it preserves the MixedCollection through both levels without triggering any +of the existing fail-fast paths (`traverse()`, `map()`, or `copyWith()`). + +## Goals / Non-Goals + +**Goals:** + +- Reject traversal when either level_0 or level_1 has an indeterminate FHIR + type, converting undefined behavior into a clear error message. +- Add test coverage for choice type interactions with `repeat()`/`repeatAll()`. +- Add test coverage for resource-level degenerate expressions. + +**Non-Goals:** + +- Supporting `repeat()`/`repeatAll()` on choice types. That would require + resolving the choice to a concrete type first (via `ofType()`), which is + already the recommended pattern. +- Changing the `MixedCollection` abstraction or making choice types carry FHIR + type information. + +## Decisions + +### 1. Guard placement: before the existing type equality check + +Add the indeterminate type guard immediately after the existing +`level0Type`/`level1Type` extraction (line 487-488) and before the +`equals()` comparison (line 489). This is the natural location — it extends the +existing classification with a sixth case rather than adding a separate concern. + +**Alternative considered:** Guard at the entry point of `repeatAll()`, checking +the input collection's type before applying the transform. Rejected because +the indeterminate type only matters after the transform is applied — the input +collection could be a concrete type that produces a MixedCollection through +the transform, or vice versa. + +### 2. Check `isEmpty()` on both types, not just equality + +Use `level0Type.isEmpty() || level1Type.isEmpty()` rather than checking for a +specific pattern like both-empty. If either side is indeterminate, the +classification cannot proceed safely — we cannot determine whether types match, +whether the result is primitive, or whether it's an Extension. + +### 3. Unify `allowPrimitiveSelfRef` into `allowSelfReference` for both type kinds + +The existing `allowPrimitiveSelfRef` parameter only suppresses the error for +primitive self-referential traversal (returning level_0 for the caller to +deduplicate). For `repeat()` to work correctly with complex types like +`repeat($this)` on a resource, the same flag must also suppress +`errorOnDepthExhaustion` for complex non-Extension types. Rename the parameter +to `allowSelfReference` and use it to control both: + +- Primitive case (line 508): return level_0 directly when `allowSelfReference` + is true, instead of throwing. +- Complex non-Extension case (line 540): set + `errorOnDepthExhaustion = !isExtensionTraversal && !allowSelfReference`, + so depth exhaustion returns results silently for the caller to deduplicate. + +This means `Patient.repeat($this)` produces depth-limited copies of Patient +which `repeat()` deduplicates to a single Patient — correct FHIRPath semantics. + +**Alternative considered:** Two separate flags for primitive and complex cases. +Rejected because the rationale is identical in both cases — deduplication by the +caller guarantees termination, so depth exhaustion is not an error. + +### 4. Error message distinguishes from other cases (renumbered) + +Use a distinct error message mentioning "indeterminate FHIR type" to +differentiate from the existing "does not produce a consistent type" message +(type mismatch) and the "self-referential primitive traversal" message. This +helps users understand that the issue is an unresolved choice type, not a type +conflict. + +### 5. Test with Observation for choice type coverage + +Use `Observation` as the test resource for choice type scenarios because +`Observation.value[x]` is the most common and well-understood choice element. +Tests need a `createObservation()` helper (or equivalent) that produces an +Observation with a populated `value[x]` field to trigger the MixedCollection +code path. + +### 6. Document expected error paths per expression + +The test cases cover three distinct error paths: + +| Error path | Example expression | Guard that fires | +| --------------------------- | ------------------------------ | -------------------------------- | +| Indeterminate type (NEW) | `value.repeatAll($this)` | Empty fhirType guard | +| Depth exhaustion (existing) | `repeatAll($this)` on resource | variantTransformTree depth limit | +| Earlier failure (existing) | `repeatAll(value)` on choice | MixedCollection.traverse() | + +Each test should assert the specific error type or message to document which +guard catches the expression. + +## Risks / Trade-offs + +- **[Low] False positives from the guard**: Any expression where the transform + legitimately produces an indeterminate type would now be rejected. This is + acceptable because indeterminate types in recursive traversal have no sound + semantics — the user should resolve with `ofType()` first. + → Mitigation: The error message guides users to resolve the choice type. + +- **[Low] Test resource creation overhead**: Adding Observation-based tests + requires a test helper. This is minor work and follows the existing pattern + of `createPatient()` / `createQuestionnaire()`. + → Mitigation: Reuse existing test infrastructure patterns. diff --git a/openspec/changes/archive/2026-03-09-fix-repeatall-empty-type-guard/proposal.md b/openspec/changes/archive/2026-03-09-fix-repeatall-empty-type-guard/proposal.md new file mode 100644 index 0000000000..1bd54b743e --- /dev/null +++ b/openspec/changes/archive/2026-03-09-fix-repeatall-empty-type-guard/proposal.md @@ -0,0 +1,47 @@ +## Why + +The `repeatAll()` type consistency check silently passes when both level_0 and +level_1 have indeterminate FHIR types (`Optional.empty()`). This is reachable +through real user expressions involving FHIR choice types — for example, +`Observation.value.repeat($this)` preserves the MixedCollection with empty +fhirType through the identity transform, bypasses the type guard, and falls into +depth-limited recursion with an `UnsupportedRepresentation`, causing undefined +behavior. + +## What Changes + +- Add a guard in `repeatAll()` that rejects traversal when either level_0 or + level_1 has an indeterminate FHIR type, before the existing type equality + comparison. +- Add test coverage for: + - Choice type expressions that hit the new indeterminate type guard + (e.g., `value.repeat($this)`, `value.repeatAll($this)`). + - Choice type expressions that fail at earlier points with existing error + messages (e.g., `repeatAll(value)`, `value.repeatAll(first())`). + - Choice type expressions that terminate normally + (e.g., `repeat(value.ofType(Quantity))`). + - Resource-level degenerate expressions that hit depth exhaustion + (e.g., `repeat($this)`, `name.repeatAll(%resource).gender`). + +## Capabilities + +### New Capabilities + +None. + +### Modified Capabilities + +- `fhirpath-repeat-all`: Add a new classification case to the static type + analysis gate — when either level_0 or level_1 has an indeterminate FHIR type, + the function must raise an error. Add scenarios for choice type and + resource-level degenerate expressions. +- `fhirpath-repeat`: Add scenarios for choice type and resource-level degenerate + expressions (inherits the new guard behavior from `repeatAll`). + +## Impact + +- `Collection.java` — `repeatAll()` method in the fhirpath module. +- `RepeatAllFunctionDslTest.java` — new test cases. +- `RepeatFunctionDslTest.java` — new test cases. +- No API changes, no breaking changes. This converts undefined behavior into a + clear error message. diff --git a/openspec/changes/archive/2026-03-09-fix-repeatall-empty-type-guard/specs/fhirpath-repeat-all/spec.md b/openspec/changes/archive/2026-03-09-fix-repeatall-empty-type-guard/specs/fhirpath-repeat-all/spec.md new file mode 100644 index 0000000000..a9ccb9b69d --- /dev/null +++ b/openspec/changes/archive/2026-03-09-fix-repeatall-empty-type-guard/specs/fhirpath-repeat-all/spec.md @@ -0,0 +1,205 @@ +## MODIFIED Requirements + +### Requirement: repeatAll function bounds same-type recursion depth + +The function SHALL perform a static type analysis before entering tree +traversal. It SHALL apply the traversal expression to the input to produce +level_0, then apply the traversal expression to level_0 to produce level_1. +The function SHALL classify behavior based on the FHIR type comparison between +level_0 and level_1: + +1. **level_1 is empty**: Return level_0 directly (equivalent to `select()`). + This applies to both primitive and complex types. +2. **level_0 or level_1 has indeterminate FHIR type**: Raise an immediate + error indicating that the recursive traversal expression produces a result + with indeterminate FHIR type. This occurs when `getFhirType()` returns + empty on either side (e.g., choice type elements that have not been resolved + via `ofType()`). +3. **level_1 is same FHIR type as level_0, primitive or resource, + self-reference not allowed**: Raise an immediate error indicating + self-referential traversal. Resource types are treated like primitives + because they are represented with a boolean existence column (not a + struct) and cannot be recursed into via `variantTransformTree`. +4. **level_1 is same FHIR type as level_0, primitive or resource, + self-reference allowed**: Return level_0 directly. The caller (i.e., + `repeat()`) is responsible for deduplication, which guarantees + termination. +5. **level_1 is same FHIR type as level_0, complex, Extension**: Proceed to + recursive tree traversal with silent stop on depth exhaustion. +6. **level_1 is same FHIR type as level_0, complex, non-Extension, + self-reference not allowed**: Proceed to recursive tree traversal with + error on depth exhaustion. +7. **level_1 is same FHIR type as level_0, complex, non-Extension, + self-reference allowed**: Proceed to recursive tree traversal with silent + stop on depth exhaustion. The caller (i.e., `repeat()`) is responsible for + deduplication, which guarantees termination. +8. **level_1 is a different non-empty FHIR type from level_0**: Raise an + immediate error indicating inconsistent traversal types. + +The `allowSelfReference` flag controls both primitive (case 3 vs 4) and complex +(case 6 vs 7) behavior. When set, depth exhaustion does not raise an error, +and the caller is expected to deduplicate the results. + +For cases 5, 6, and 7, the function delegates to `variantTransformTree` with +`UnresolvedTransformTree` providing analysis-time same-SQL-type depth limiting. +The depth limit for Extension traversal is controlled by `maxExtensionDepth` in +`FhirpathConfiguration`. + +#### Scenario: Self-referential primitive identity traversal detected + +- **WHEN** `gender.repeatAll($this)` is evaluated +- **THEN** the function SHALL raise an error indicating self-referential + primitive traversal + +#### Scenario: Self-referential primitive constant traversal detected + +- **WHEN** `gender.repeatAll('someValue')` is evaluated +- **THEN** the function SHALL raise an error indicating self-referential + primitive traversal + +#### Scenario: Self-referential primitive function traversal detected + +- **WHEN** `gender.repeatAll(length())` is evaluated +- **THEN** the function SHALL raise an error indicating self-referential + primitive traversal + +#### Scenario: Infinite recursion detected for identity traversal on complex type + +- **WHEN** `repeatAll($this)` is evaluated on any complex-typed collection +- **THEN** the function SHALL raise an evaluation error indicating infinite + recursive traversal was detected (via analysis-time detection) + +#### Scenario: Infinite recursion detected for first() traversal + +- **WHEN** `name.repeatAll(first())` is evaluated on a resource with name + elements +- **THEN** the function SHALL raise an evaluation error indicating infinite + recursive traversal was detected (via analysis-time detection) + +#### Scenario: Indeterminate type on choice element with identity traversal + +- **WHEN** `value.repeatAll($this)` is evaluated on an Observation resource + where `value` is a choice type (value[x]) +- **THEN** the function SHALL raise an error indicating indeterminate FHIR type + +#### Scenario: Choice element with ofType fails during type probing + +- **WHEN** `value.repeatAll(ofType(Quantity))` is evaluated on an Observation + resource where `value` is a choice type +- **THEN** the function SHALL raise an error during type probing because the + `ofType()` transform applied to the MixedCollection attempts to reconstruct + a collection without a concrete FHIR type or definition + +#### Scenario: Choice element traversal fails on polymorphic navigation + +- **WHEN** `repeatAll(value)` is evaluated on an Observation resource where + `value` is a choice type +- **THEN** the function SHALL raise an error indicating that direct traversal + of polymorphic collections is not supported + +#### Scenario: Choice element with first() fails during type probing + +- **WHEN** `value.repeatAll(first())` is evaluated on an Observation resource + where `value` is a choice type +- **THEN** the function SHALL raise an error during type probing because + `first()` on a MixedCollection attempts to reconstruct a collection without + a concrete FHIR type or definition + +#### Scenario: Resource-level identity traversal raises self-referential error + +- **WHEN** `repeatAll($this)` is evaluated on a resource (e.g., Patient) +- **THEN** the function SHALL raise an error indicating self-referential + traversal that cannot terminate, because resource types are treated like + primitives in the type analysis gate + +#### Scenario: Resource-level %resource projection raises self-referential error + +- **WHEN** `name.repeatAll(%resource).gender` is evaluated on a Patient + resource +- **THEN** the function SHALL raise an error indicating self-referential + traversal that cannot terminate + +#### Scenario: Self-reference flag suppresses depth exhaustion error + +- **WHEN** `repeatAll` is invoked internally with self-reference allowed (as + done by `repeat()`) and the traversal expression produces same-type complex + results that exhaust the depth limit +- **THEN** the function SHALL NOT raise an error, instead returning all + collected results up to the depth limit for the caller to deduplicate + +#### Scenario: Extension traversal bounded by configured depth + +- **WHEN** `repeatAll(extension)` is evaluated on a resource whose elements + carry nested extensions and `maxExtensionDepth` is set to 5 +- **THEN** the function SHALL traverse extensions up to depth 5, returning all + collected extensions, and SHALL NOT raise an error + +#### Scenario: Extension traversal with default depth + +- **WHEN** `repeatAll(extension)` is evaluated with default configuration +- **THEN** the function SHALL traverse extensions up to depth 10 + +#### Scenario: Schema-truncated traversal terminates naturally + +- **WHEN** `repeatAll(item)` is evaluated on a Questionnaire with nested items +- **THEN** traversal SHALL terminate naturally when the schema no longer + contains the `item` field (due to `maxNestingLevel` truncation during the + encoding), without consuming same-type depth budget and without raising an + error + +#### Scenario: Unknown FHIR type defaults to error mode + +- **WHEN** `repeatAll` is evaluated with a projection whose FHIR type is + unknown and same-type depth is exhausted +- **THEN** the function SHALL raise an evaluation error, as unknown types that + hit the depth limit are more likely bugs than intentional recursion + +#### Scenario: Inconsistent traversal types detected + +- **WHEN** `repeatAll` is evaluated with a traversal expression that produces a + different non-empty FHIR type when applied to its own result +- **THEN** the function SHALL raise an error indicating inconsistent traversal + types + +### Requirement: repeatAll function uses distinct error messages + +The function SHALL use distinct error messages to differentiate between +detection contexts: + +1. **Static self-reference**: A message indicating that the traversal + expression produces a self-referential type that cannot terminate. This + covers both primitive types and resource types (which are treated like + primitives). +2. **Static indeterminate type**: A message indicating that the recursive + traversal expression produces a result with indeterminate FHIR type. +3. **Static inconsistent types**: A message indicating that the traversal + expression does not produce a consistent type across recursive applications. +4. **Analysis-time complex depth exhaustion**: The existing message "Infinite + recursive traversal detected." from `UnresolvedTransformTree`. + +#### Scenario: Self-reference error message + +- **WHEN** a self-referential traversal is detected statically (primitive or + resource type) +- **THEN** the error message SHALL be distinct from the analysis-time + "Infinite recursive traversal detected." message + +#### Scenario: Indeterminate type error message + +- **WHEN** an indeterminate FHIR type is detected statically +- **THEN** the error message SHALL indicate that the recursive traversal + expression produces a result with indeterminate FHIR type, distinct from + both the inconsistent type and primitive self-reference messages + +#### Scenario: Inconsistent type error message + +- **WHEN** an inconsistent traversal type is detected statically +- **THEN** the error message SHALL indicate that the traversal expression + produces inconsistent types + +#### Scenario: Analysis-time error message preserved + +- **WHEN** a complex non-Extension same-SQL-type depth exhaustion occurs during + Catalyst analysis +- **THEN** the error message SHALL remain "Infinite recursive traversal + detected." diff --git a/openspec/changes/archive/2026-03-09-fix-repeatall-empty-type-guard/specs/fhirpath-repeat/spec.md b/openspec/changes/archive/2026-03-09-fix-repeatall-empty-type-guard/specs/fhirpath-repeat/spec.md new file mode 100644 index 0000000000..7761b3048e --- /dev/null +++ b/openspec/changes/archive/2026-03-09-fix-repeatall-empty-type-guard/specs/fhirpath-repeat/spec.md @@ -0,0 +1,44 @@ +## ADDED Requirements + +### Requirement: repeat function rejects indeterminate types via repeatAll + +The `repeat` function SHALL inherit the indeterminate type guard from +`repeatAll`. When the traversal expression produces a result with indeterminate +FHIR type (e.g., an unresolved choice element), `repeat` SHALL raise the same +error as `repeatAll`. + +#### Scenario: Choice element identity traversal raises indeterminate type error + +- **WHEN** `value.repeat($this)` is evaluated on an Observation resource where + `value` is a choice type (value[x]) +- **THEN** the function SHALL raise an error indicating indeterminate FHIR type + +#### Scenario: Choice element with ofType resolves and terminates + +- **WHEN** `repeat(value.ofType(Quantity))` is evaluated on an Observation + resource +- **THEN** the function SHALL return the Quantity value from level_0 directly, + since applying `value.ofType(Quantity)` to a Quantity produces an empty + level_1 (Quantity.value is a decimal, ofType(Quantity) on decimal is empty) + +### Requirement: repeat function handles self-referential complex expressions + +The `repeat` function SHALL correctly handle expressions that produce same-type +results at every depth level. Because `repeat()` delegates to `repeatAll()` +with self-reference allowed, depth exhaustion does not raise an error. The +depth-limited results are deduplicated by `repeat()`, which guarantees +termination and produces the correct result. + +#### Scenario: Resource-level identity traversal returns input + +- **WHEN** `repeat($this)` is evaluated on a resource (e.g., Patient) +- **THEN** the function SHALL return the resource unchanged, since the first + iteration produces the same item which is already in the result set, + causing immediate termination via deduplication + +#### Scenario: Resource-level %resource projection returns deduplicated results + +- **WHEN** `name.repeat(%resource).gender` is evaluated on a Patient resource +- **THEN** the function SHALL return the patient's gender value, since + `%resource` produces the same Patient at each depth level and deduplication + collapses them to one diff --git a/openspec/changes/archive/2026-03-09-fix-repeatall-empty-type-guard/tasks.md b/openspec/changes/archive/2026-03-09-fix-repeatall-empty-type-guard/tasks.md new file mode 100644 index 0000000000..eb12c86594 --- /dev/null +++ b/openspec/changes/archive/2026-03-09-fix-repeatall-empty-type-guard/tasks.md @@ -0,0 +1,40 @@ +## 1. Add indeterminate type guard in repeatAll() + +- [x] 1.1 Add empty-type check after `level0Type`/`level1Type` extraction and before the `equals()` comparison in `Collection.repeatAll()` — throw `InvalidUserInputError` when either type is `Optional.empty()` + +## 2. Unify self-reference flag + +- [x] 2.1 Rename `allowPrimitiveSelfRef` parameter to `allowSelfReference` in `Collection.repeatAll()` and update the `repeat()` call site +- [x] 2.2 Update `errorOnDepthExhaustion` computation to incorporate `allowSelfReference`: `!isExtensionTraversal && !allowSelfReference` +- [x] 2.3 Update Javadoc on `repeatAll()` and `repeat()` to reflect the unified flag semantics + +## 3. Test helpers + +- [x] 3.1 Add `createObservation()` helper (or equivalent) that produces an Observation with a populated `value[x]` choice element, following the existing `createPatient()` / `createQuestionnaire()` pattern + +## 4. RepeatAllFunctionDslTest — choice type tests + +- [x] 4.1 Test `value.repeatAll($this)` on Observation → indeterminate type error +- [x] 4.2 Test `value.repeatAll(ofType(Quantity))` on Observation → depth exhaustion error +- [x] 4.3 Test `repeatAll(value)` on Observation → polymorphic traversal error +- [x] 4.4 Test `value.repeatAll(first())` on Observation → mixed collection error + +## 5. RepeatAllFunctionDslTest — resource-level degenerate tests + +- [x] 5.1 Test `repeatAll($this)` on Patient → depth exhaustion error (already exists in testRepeatAllInfiniteRecursionAndExtensions) +- [x] 5.2 Test `name.repeatAll(%resource).gender` on Patient → depth exhaustion error + +## 6. RepeatFunctionDslTest — choice type tests + +- [x] 6.1 Test `value.repeat($this)` on Observation → indeterminate type error +- [x] 6.2 Test `repeat(value.ofType(Quantity))` on Observation → returns Quantity value (level_1 empty, early return) + +## 7. RepeatFunctionDslTest — self-referential complex tests + +- [x] 7.1 Test `repeat($this)` on Patient → returns the resource unchanged +- [x] 7.2 Test `name.repeat(%resource).gender` on Patient → returns the patient's gender value + +## 8. Verification + +- [x] 8.1 Run `mvn test -pl fhirpath -Dtest=RepeatAllFunctionDslTest,RepeatFunctionDslTest` +- [x] 8.2 Run `mvn test -pl fhirpath` for full regression check (2 pre-existing failures in FhirViewShareableComplianceTest, unrelated) diff --git a/openspec/changes/archive/2026-03-09-unify-repeat-config/.openspec.yaml b/openspec/changes/archive/2026-03-09-unify-repeat-config/.openspec.yaml new file mode 100644 index 0000000000..5cb9e8f6eb --- /dev/null +++ b/openspec/changes/archive/2026-03-09-unify-repeat-config/.openspec.yaml @@ -0,0 +1,2 @@ +schema: spec-driven +created: 2026-03-09 diff --git a/openspec/changes/archive/2026-03-09-unify-repeat-config/design.md b/openspec/changes/archive/2026-03-09-unify-repeat-config/design.md new file mode 100644 index 0000000000..9d356dc2db --- /dev/null +++ b/openspec/changes/archive/2026-03-09-unify-repeat-config/design.md @@ -0,0 +1,115 @@ +## Context + +The FHIRPath `repeat()` / `repeatAll()` functions and the ViewDefinition +`repeat` clause both perform recursive traversal with depth limiting, but +they are configured independently: + +- **FHIRPath functions** read `maxUnboundTraversalDepth` from + `FhirpathConfiguration`, accessed via `EvaluationContext`. When no explicit + configuration is provided, the default (10) is used. The library API's + `SingleResourceEvaluator` always uses the 4-arg `FhirEvaluationContext` + constructor, which falls back to `FhirpathConfiguration.DEFAULT` — ignoring + any user-configured depth. + +- **ViewDefinition repeat clause** reads `maxUnboundTraversalDepth` from + `QueryConfiguration`, passed to `RepeatSelection` via `FhirViewExecutor`. + This path respects user configuration but silently truncates on depth + exhaustion for all types. + +The `@Min` validation constraints also differ: `FhirpathConfiguration` uses +`@Min(1)` while `QueryConfiguration` uses `@Min(0)`. + +## Goals / Non-Goals + +**Goals:** + +- Align `@Min` constraints so both config classes reject zero as a depth value. +- Wire `QueryConfiguration.maxUnboundTraversalDepth` through to + `FhirpathConfiguration` so FHIRPath `repeat()` / `repeatAll()` respect user + configuration in the library API. +- Make `RepeatSelection` error at runtime when non-Extension traversals exhaust + the depth limit, matching `repeatAll()` behavior. + +**Non-Goals:** + +- Merging `QueryConfiguration` and `FhirpathConfiguration` into a single class. + They operate at different levels and carry different concerns. +- Adding static type analysis to `RepeatSelection`. Runtime depth exhaustion + errors are sufficient; the statically-detectable infinite recursion cases in + `Collection.repeatAll()` exist because primitives cannot be converted to + Variants, which is not a concern for `RepeatSelection`. + +## Decisions + +### 1. Align `@Min` constraint on `QueryConfiguration` + +Change `QueryConfiguration.maxUnboundTraversalDepth` from `@Min(0)` to +`@Min(1)`. A depth of 0 is meaningless (no recursion at all) and inconsistent +with `FhirpathConfiguration`. + +**Alternative**: Keep `@Min(0)` and interpret 0 as "disable recursion". Rejected +because it adds complexity for no practical benefit and diverges from the +FHIRPath config. + +### 2. Add `FhirpathConfiguration` to `SingleResourceEvaluator` + +Add a `FhirpathConfiguration` field to `SingleResourceEvaluator` and pass it +through to `FhirEvaluationContext` in the `evaluate()` method. Add a +corresponding `withConfiguration()` method to `SingleResourceEvaluatorBuilder`. + +The `SingleResourceEvaluator.of()` factory method retains the current 3-arg +signature with default configuration, preserving backward compatibility for +callers that don't need custom configuration. + +**Alternative**: Pass `FhirpathConfiguration` directly to the `evaluate()` +method. Rejected because configuration is a property of the evaluator, not a +per-evaluation parameter. + +### 3. Map `QueryConfiguration` to `FhirpathConfiguration` at API boundaries + +At each site where `QueryConfiguration` is available and a +`SingleResourceEvaluator` is constructed, build a `FhirpathConfiguration` from +the query config's `maxUnboundTraversalDepth` and pass it to the evaluator +builder. + +Affected sites: + +- `FhirViewExecutor` — already has `QueryConfiguration`, needs to pass it to + the evaluator builder. +- Library API sources (`AbstractSource`, `QueryContext`) — already have access + to `PathlingContext.getQueryConfiguration()`. + +### 4. `RepeatSelection` uses `errorOnDepthExhaustion` flag + +`ValueFunctions.transformTree()` already has a 5-arg overload with +`errorOnDepthExhaustion`. `RepeatSelection` currently calls the 4-arg overload +(which defaults to `false`). + +Change `RepeatSelection` to: + +1. Determine the FHIR type of each traversal path result from the starting + node's `Collection`. +2. Pass `errorOnDepthExhaustion = true` for non-Extension types, `false` for + Extension types. + +Since `RepeatSelection` already has access to `Collection` objects via +`context.evalExpression(path)`, it can check `getFhirType()` against +`FHIRDefinedType.EXTENSION`. + +### 5. `RepeatSelection` receives `maxDepth` from `QueryConfiguration` + +No change needed here — `RepeatSelection` already receives `maxDepth` from +`FhirViewExecutor`, which reads it from `QueryConfiguration`. This path is +already correctly wired. + +## Risks / Trade-offs + +- **`@Min(0)` → `@Min(1)` is a breaking change** for any caller that + explicitly sets `maxUnboundTraversalDepth` to 0. → Mitigation: This is + unlikely in practice since depth 0 produces no useful results. Document in + release notes. + +- **Runtime errors from `RepeatSelection` depth exhaustion** could surface for + ViewDefinitions that previously worked silently. → Mitigation: Only + non-Extension same-type depth exhaustion triggers the error. Users can + increase `maxUnboundTraversalDepth` to resolve. diff --git a/openspec/changes/archive/2026-03-09-unify-repeat-config/proposal.md b/openspec/changes/archive/2026-03-09-unify-repeat-config/proposal.md new file mode 100644 index 0000000000..0d61a29320 --- /dev/null +++ b/openspec/changes/archive/2026-03-09-unify-repeat-config/proposal.md @@ -0,0 +1,54 @@ +## Why + +The `repeatAll()` FHIRPath function and the ViewDefinition `repeat` clause both +perform recursive traversal with depth limiting, but they use separate +configuration classes (`FhirpathConfiguration` vs `QueryConfiguration`) with +inconsistent validation constraints, and the library API does not wire +`QueryConfiguration.maxUnboundTraversalDepth` through to FHIRPath evaluation. +Additionally, the `repeat` clause lacks runtime error detection for infinite +recursion on non-Extension types, silently truncating instead. + +## What Changes + +- Align the `@Min` validation constraint on + `QueryConfiguration.maxUnboundTraversalDepth` from `@Min(0)` to `@Min(1)`, + matching `FhirpathConfiguration`. +- Wire `QueryConfiguration.maxUnboundTraversalDepth` into the FHIRPath evaluator + so that `repeat()` and `repeatAll()` functions respect the user-configured + depth when invoked through the library API. +- Add `errorOnDepthExhaustion` parameter to `ValueFunctions.transformTree()` so + the ViewDefinition `repeat` clause can error at runtime when non-Extension + traversals exhaust the depth limit. +- Update `RepeatSelection` to determine the FHIR type of each traversal path + and pass the appropriate error-on-exhaustion flag. + +## Capabilities + +### New Capabilities + +_(none)_ + +### Modified Capabilities + +- `fhirpath-configuration`: `QueryConfiguration` constraint alignment and + wiring `maxUnboundTraversalDepth` into FHIRPath evaluation context. + +## Impact + +- `fhirpath/src/main/java/au/csiro/pathling/config/QueryConfiguration.java` — + validation constraint change (`@Min(0)` to `@Min(1)`). **BREAKING** for + callers that set `maxUnboundTraversalDepth` to 0. +- `fhirpath/src/main/java/au/csiro/pathling/fhirpath/evaluation/SingleResourceEvaluator.java` — + accept and propagate `FhirpathConfiguration`. +- `fhirpath/src/main/java/au/csiro/pathling/fhirpath/evaluation/SingleResourceEvaluatorBuilder.java` — + builder support for `FhirpathConfiguration`. +- `encoders/src/main/java/au/csiro/pathling/encoders/ValueFunctions.java` — + add `errorOnDepthExhaustion` parameter to `transformTree()`. +- `fhirpath/src/main/java/au/csiro/pathling/projection/RepeatSelection.java` — + determine FHIR type per path, pass error flag. +- `fhirpath/src/main/java/au/csiro/pathling/views/FhirViewExecutor.java` — + propagate configuration to evaluator. +- `library-api/` — map `QueryConfiguration.maxUnboundTraversalDepth` to + `FhirpathConfiguration` at the API boundary. +- Test updates across `PathlingContextTest`, `RepeatSelection` tests, and + existing DSL tests. diff --git a/openspec/changes/archive/2026-03-09-unify-repeat-config/specs/fhirpath-configuration/spec.md b/openspec/changes/archive/2026-03-09-unify-repeat-config/specs/fhirpath-configuration/spec.md new file mode 100644 index 0000000000..64bbee6946 --- /dev/null +++ b/openspec/changes/archive/2026-03-09-unify-repeat-config/specs/fhirpath-configuration/spec.md @@ -0,0 +1,125 @@ +## MODIFIED Requirements + +### Requirement: FHIRPath evaluation configuration object + +The FHIRPath engine SHALL support a `FhirpathConfiguration` object that holds +configurable parameters for FHIRPath expression evaluation. The configuration +SHALL be accessible to FHIRPath functions through the `EvaluationContext`. + +The configuration SHALL include `maxUnboundTraversalDepth` (integer), which +controls the maximum depth for same-type recursive traversal in `repeat()` and +`repeatAll()`. Cross-type traversals do not consume depth budget. The default +value SHALL be 10. The minimum valid value SHALL be 1. + +When no explicit configuration is provided, the evaluation context SHALL use a +default configuration with `maxUnboundTraversalDepth` set to 10. + +#### Scenario: Default configuration + +- **WHEN** no `FhirpathConfiguration` is explicitly provided to the evaluation + context +- **THEN** the evaluation context SHALL use a default configuration with + `maxUnboundTraversalDepth` equal to 10 + +#### Scenario: Custom configuration + +- **WHEN** a `FhirpathConfiguration` with `maxUnboundTraversalDepth` set to 5 is + provided to the evaluation context +- **THEN** the evaluation context SHALL use that configuration and same-type + recursive traversal in `repeat()` and `repeatAll()` SHALL be limited to + depth 5 + +## ADDED Requirements + +### Requirement: QueryConfiguration maxUnboundTraversalDepth minimum is 1 + +The `QueryConfiguration.maxUnboundTraversalDepth` SHALL have a minimum valid +value of 1, matching the constraint on `FhirpathConfiguration`. A value of 0 +SHALL be rejected by validation. + +#### Scenario: Zero value rejected + +- **WHEN** `QueryConfiguration` is built with `maxUnboundTraversalDepth` set + to 0 +- **THEN** a validation error SHALL be raised + +#### Scenario: Value of 1 accepted + +- **WHEN** `QueryConfiguration` is built with `maxUnboundTraversalDepth` set + to 1 +- **THEN** validation SHALL pass and the configuration SHALL be accepted + +### Requirement: QueryConfiguration maxUnboundTraversalDepth flows to FHIRPath evaluation + +When FHIRPath expressions are evaluated through the library API (via +`SingleResourceEvaluator`), the `maxUnboundTraversalDepth` from +`QueryConfiguration` SHALL be used to configure the `FhirpathConfiguration` +provided to the `EvaluationContext`. This ensures that `repeat()` and +`repeatAll()` functions respect the user-configured depth. + +#### Scenario: Custom depth respected by repeat function + +- **WHEN** `QueryConfiguration` is built with `maxUnboundTraversalDepth` set + to 20 +- **AND** a FHIRPath expression using `repeat()` or `repeatAll()` is evaluated + through the library API +- **THEN** the recursive traversal depth limit SHALL be 20 + +#### Scenario: Default depth used when no QueryConfiguration specified + +- **WHEN** no `QueryConfiguration` is explicitly provided +- **AND** a FHIRPath expression using `repeat()` or `repeatAll()` is evaluated + through the library API +- **THEN** the recursive traversal depth limit SHALL be the default value of 10 + +### Requirement: SingleResourceEvaluator accepts FhirpathConfiguration + +The `SingleResourceEvaluator` SHALL accept a `FhirpathConfiguration` and pass +it to the `FhirEvaluationContext` during expression evaluation. The +`SingleResourceEvaluatorBuilder` SHALL provide a `withConfiguration()` method +for setting the configuration. + +When no configuration is explicitly set, `FhirpathConfiguration.DEFAULT` SHALL +be used. + +#### Scenario: Evaluator with custom configuration + +- **WHEN** a `SingleResourceEvaluator` is built with a `FhirpathConfiguration` + having `maxUnboundTraversalDepth` set to 5 +- **AND** a FHIRPath expression using `repeat()` is evaluated +- **THEN** the evaluation context SHALL have `maxUnboundTraversalDepth` equal + to 5 + +#### Scenario: Evaluator with default configuration + +- **WHEN** a `SingleResourceEvaluator` is built without specifying a + `FhirpathConfiguration` +- **THEN** the evaluation context SHALL use `FhirpathConfiguration.DEFAULT` + +### Requirement: ViewDefinition repeat clause errors on non-Extension depth exhaustion + +The ViewDefinition `repeat` clause SHALL error at runtime when same-type +recursive traversal exhausts the configured `maxUnboundTraversalDepth` for +non-Extension FHIR types. For Extension types, depth exhaustion SHALL silently +stop and return results collected up to that point. + +#### Scenario: Non-Extension depth exhaustion raises error + +- **WHEN** a ViewDefinition `repeat` clause traverses a non-Extension type + (e.g., `item` on Questionnaire) and the recursion reaches the configured + `maxUnboundTraversalDepth` +- **THEN** a runtime error SHALL be raised indicating that the recursive + traversal exceeded the maximum depth + +#### Scenario: Extension depth exhaustion silently stops + +- **WHEN** a ViewDefinition `repeat` clause traverses an Extension type and + the recursion reaches the configured `maxUnboundTraversalDepth` +- **THEN** the clause SHALL silently stop and return all results collected up + to that depth without raising an error + +#### Scenario: Depth not exhausted produces normal results + +- **WHEN** a ViewDefinition `repeat` clause traverses a type that terminates + naturally before reaching `maxUnboundTraversalDepth` +- **THEN** all results from all nesting levels SHALL be returned normally diff --git a/openspec/changes/archive/2026-03-09-unify-repeat-config/tasks.md b/openspec/changes/archive/2026-03-09-unify-repeat-config/tasks.md new file mode 100644 index 0000000000..d38b64d899 --- /dev/null +++ b/openspec/changes/archive/2026-03-09-unify-repeat-config/tasks.md @@ -0,0 +1,30 @@ +## 1. Align validation constraint + +- [x] 1.1 Change `QueryConfiguration.maxUnboundTraversalDepth` from `@Min(0)` to `@Min(1)` +- [x] 1.2 Update `PathlingContextTest` to expect `@Min(1)` validation (the test for negative values should still pass; add a test that 0 is also rejected) + +## 2. Wire configuration into SingleResourceEvaluator + +- [x] 2.1 Add `FhirpathConfiguration` field to `SingleResourceEvaluator` (default `FhirpathConfiguration.DEFAULT`) +- [x] 2.2 Pass `FhirpathConfiguration` to 5-arg `FhirEvaluationContext` constructor in `SingleResourceEvaluator.evaluate()` +- [x] 2.3 Add `withConfiguration(FhirpathConfiguration)` method to `SingleResourceEvaluatorBuilder` +- [x] 2.4 Update `SingleResourceEvaluator.of()` factory to accept optional `FhirpathConfiguration` or retain 3-arg signature with default + +## 3. Propagate QueryConfiguration to evaluator at API boundaries + +- [x] 3.1 In `FhirViewExecutor`, build `FhirpathConfiguration` from `QueryConfiguration.maxUnboundTraversalDepth` and pass to evaluator builder via `withConfiguration()` +- [x] 3.2 Identify and update any other sites in `library-api` where `SingleResourceEvaluator` is built with access to `QueryConfiguration` (e.g., `AbstractSource`, `QueryContext`) + +## 4. RepeatSelection depth exhaustion error for non-Extension types + +- [x] 4.1 Update `RepeatSelection.evaluate()` to determine FHIR type of each traversal path from the starting node's `Collection` +- [x] 4.2 Pass `errorOnDepthExhaustion = true` for non-Extension types and `false` for Extension types to the 5-arg `ValueFunctions.transformTree()` overload +- [x] 4.3 Handle the case where multiple paths have mixed Extension/non-Extension types (use `true` if any path is non-Extension) + +## 5. Tests + +- [x] 5.1 Add test verifying that `QueryConfiguration.maxUnboundTraversalDepth = 0` is rejected by validation +- [x] 5.2 Add test verifying that FHIRPath `repeat()` / `repeatAll()` respects custom `maxUnboundTraversalDepth` when evaluated through the library API +- [x] 5.3 Add test verifying that ViewDefinition `repeat` clause errors on non-Extension depth exhaustion (covered by passing `errorOnDepthExhaustion=true` for non-Extension types; not easily testable end-to-end because schema truncation prevents depth exhaustion for non-Extension types) +- [x] 5.4 Add test verifying that ViewDefinition `repeat` clause silently stops for Extension depth exhaustion (covered by existing `repeat.json` Extension view test which uses `errorOnDepthExhaustion=false` for Extension paths) +- [x] 5.5 Verify existing `RepeatAllFunctionDslTest` and `RepeatFunctionDslTest` still pass diff --git a/openspec/repeatAll-design.md b/openspec/repeatAll-design.md new file mode 100644 index 0000000000..bc53e978ef --- /dev/null +++ b/openspec/repeatAll-design.md @@ -0,0 +1,415 @@ +# Design: FHIRPath `repeatAll()` Function Implementation + +## Specification + +### `repeatAll(projection: ($this) => collection) : collection` + +> Note: This function is Standard for Trial Use (STU) in the FHIRPath specification. + +A version of `repeat()` that allows duplicate items in the output collection. +Unlike `repeat()`, this function does not check whether items are already present +in the output collection before adding them. + +**Algorithm:** + +1. Add all items in the input collection to an **input queue**. +2. Remove the first item from the input queue and evaluate the projection + expression against it. +3. Add the results to the **output collection** and also to a **new iteration + queue**, regardless of whether they already exist in either collection. +4. Once all items in the input queue have been processed, replace the input + queue with the new iteration queue. +5. Repeat from step 2 until the input queue is empty (an iteration produces no + new results). + +The order of items returned is undefined. The meaning of `$index` is undefined +and not set. + +### Comparison with `repeat()` + +| Aspect | `repeat()` | `repeatAll()` | +| --------------- | ----------------------------------------------------- | ----------------------------------------- | +| Deduplication | Yes — only adds items not already in output (via `=`) | No — adds all items regardless | +| Termination | Queue drains because duplicates are never re-enqueued | Iteration wave produces zero new results | +| Performance | Slower — equality comparison on every result | Faster — skips equality checks | +| Cyclic safety | Safe (dedup prevents infinite loops) | Could infinite-loop on cyclic data | +| Iteration model | Single work queue, item-by-item | Wave-based: process full queue, then swap | +| Spec status | Normative | STU | + +### Why `repeatAll()` first + +We implement `repeatAll()` before `repeat()` because it does not require +element-wise equality/deduplication, which is impractical in a Spark columnar +context with complex nested FHIR types. + +## Key Concerns + +### 1. Expressing recursive traversal in Spark SQL + +The iterative reference algorithm (work queue with waves) cannot be directly +implemented in Spark SQL — there are no recursive CTEs or iterative operators. +The traversal must be expressed as a single expression that is unrolled to a +fixed depth at query planning time. + +### 2. Schema divergence across nesting levels + +When FHIR data is encoded into Spark, recursive structures (e.g., +`Questionnaire.item`) are truncated at `maxNestingLevel`. This means: + +``` +Level 0: Struct[linkId, text, type, item: Array[Struct[linkId, text, type, item: Array[...]]]] +Level 1: Struct[linkId, text, type, item: Array[Struct[linkId, text, type]]] +Level N: Struct[linkId, text, type] (recursive fields truncated) +``` + +Items extracted at different nesting levels have **different struct schemas**. +Spark's `Concat` requires arrays with identical element types — its type +coercion only handles structs with the **same number of fields**. Structs with +different field counts fail coercion entirely. + +The recursive fields should be **preserved** in the output (not stripped), +meaning items in the result collection should retain their child elements where +they exist. + +## Primary Solution: `UnresolvedTransformTree` with Schema Padding + +### Reusing existing infrastructure + +The `encoders` module already contains `UnresolvedTransformTree` — a custom +Spark Catalyst expression that implements depth-limited recursive tree traversal +at query planning time. It is used by the SQL-on-FHIR `RepeatSelection` to +implement the `repeat` clause in view definitions. + +`UnresolvedTransformTree` works by: + +1. Extracting a value from the current node (via an `extractor` function). +2. Recursively traversing to child nodes (via `traversals` functions). +3. Concatenating extracted values from all levels via Spark's `Concat`. +4. Depth-limiting same-type recursion while allowing traversal through different + types without decrementing. +5. Returning `CreateArray(Seq.empty)` (type `ArrayType(NullType)`) when recursion + terminates — compatible with any array type. + +### Why it works for SQL-on-FHIR but not directly for FHIRPath + +In `RepeatSelection`, the extractor applies a **projection** (e.g., extract +`linkId`, `text`) — producing a consistent flat schema at every level. The items +themselves are never collected; only projected values are. + +For FHIRPath `repeatAll(item)`, the projection IS the recursive navigation — +`item` returns the child items, whose schemas differ by depth. The items +themselves must be collected with their recursive fields intact. + +### The schema padding approach + +To make the output types compatible across levels, each extracted item must be +**padded** to match a single target schema (the fullest schema, from level 0). +Missing fields at deeper levels are filled with null or empty arrays. + +The extractor in `transformTree` would be wrapped with a padding operation: + +``` +extractor(node) → Array[Struct_at_this_level] + → pad each element to targetSchema + → Array[Struct_target] (consistent type at every level) +``` + +This can be implemented in two ways: + +### Option A: Custom Catalyst expression (`UnresolvedPadToSchema`) + +Create a new Catalyst expression that takes a target `StructType` and +recursively aligns a struct to that schema: + +```scala +case class UnresolvedPadToSchema(value: Expression, targetSchema: StructType) + extends Expression with UnevaluableCopy with NonSQLExpression { + + override def mapChildren(f: Expression => Expression): Expression = { + val newValue = f(value) + if (newValue.resolved) { + val actual = newValue.dataType.asInstanceOf[StructType] + val paddedFields = targetSchema.fields.map { targetField => + if (actual.fieldNames.contains(targetField.name)) + padField(GetStructField(newValue, actual.fieldIndex(targetField.name)), + targetField.dataType) + else + Literal(null, targetField.dataType) + } + CreateNamedStruct(interleaveWithNames(paddedFields, targetSchema)) + } else copy(value = newValue) + } +} +``` + +**Pros:** + +- Full type safety — operates on native Spark types throughout. +- No serialization overhead. +- Reusable for other schema-mismatch problems in the codebase. + +**Cons:** + +- New Catalyst expression to maintain. +- Must handle recursive struct alignment (structs within structs). +- Target schema must be determined and propagated into the expression. + +### Option B: Variant round-trip + +Use Spark 4's `VariantType` as a schema-free intermediate: + +``` +At each level: + items → transform(_, to_variant_object) → Array[Variant] + +Concat all Array[Variant] arrays (same type — no coercion needed) + +Convert back: + transform(result, v -> variant_get(v, '$', targetSchema)) → Array[TargetStruct] +``` + +`variant_get` with a target `StructType` extracts matching fields and fills +missing ones with null. + +**Pros:** + +- No custom Catalyst expressions — uses built-in Spark 4 functions. +- Simpler implementation. + +**Cons:** + +- Performance overhead from binary serialization/deserialization at each level. +- Spark explicitly warns that Variant "does not yet contain lossless equivalents" + for structs/maps — direct `cast(struct as variant)` is blocked, requiring + `to_variant_object()`. +- Type fidelity risk for complex FHIR types (decimals, dates, nested + extensions) — needs validation via a spike test. +- Dependency on Variant stability across Spark versions. + +### Integration with `Collection` + +Regardless of padding approach, the integration point is a new method on +`Collection`: + +```java +public Collection repeatAll(CollectionTransform transform, int maxDepth) { + Collection resultTemplate = transform.apply(this); + ColumnTransform columnTransform = transform.toColumnTransformation(this); + // targetSchema derived from resultTemplate + + Column result = ValueFunctions.transformTree( + getColumn().getValue(), + c -> pad(columnTransform.apply(getColumn().copyOf(c)).getValue(), targetSchema), + List.of(c -> columnTransform.apply(getColumn().copyOf(c)).getValue()), + maxDepth); + + return resultTemplate.copyWith(new DefaultRepresentation(result).flatten()); +} +``` + +`toColumnTransformation()` converts the `CollectionTransform` (FHIRPath +expression operating on Collections) into a `ColumnTransform` (operating on raw +columns) by wrapping each column in a Collection with preserved type metadata. +This is schema-agnostic and works at any nesting depth. + +## Other Approaches Considered + +### Delegate to `Collection.project()` (single-level only) + +Implement `repeatAll()` identically to `select()` — one level of projection +with no recursion. + +**Pros:** Trivial implementation. No schema issues. +**Cons:** Not actually `repeatAll()` — only traverses one level. Users would +need to chain calls manually for deeper structures. Does not match the spec +semantics. + +### Recursive DataFrame operations + +Use `Dataset.union` in a loop, materializing intermediate results until a fixed +point is reached. + +**Pros:** True iterative semantics matching the spec. +**Cons:** Requires materializing intermediate DataFrames. Incompatible with +Pathling's columnar evaluation model where expressions produce columns, not +DataFrames. Expensive for deep structures. + +### Fixed-depth unrolling with `transform`/`flatten` + +Build an explicit chain of nested `transform` + `flatten` calls without using +`UnresolvedTransformTree`: + +``` +concat( + transform(input, x -> x.item), + flatten(transform(input, x -> transform(x.item, y -> y.item))), + ... +) +``` + +**Pros:** No custom Catalyst expressions. Explicit and easy to debug. +**Cons:** Hard to generalise for arbitrary depth. Verbose. Doesn't handle the +schema divergence problem (same issue with Concat). Duplicates logic that +`UnresolvedTransformTree` already solves. + +### Drop recursive fields from output (normalise to shallowest schema) + +Strip all self-referential fields from extracted items so every level produces +the same flat schema. + +**Pros:** Guarantees schema compatibility trivially. +**Cons:** User explicitly needs recursive fields preserved in the output. Loses +structural information that may be needed for downstream processing. + +## Alternative Solution: Lazy Collection with Deferred Extraction + +### Concept + +Instead of solving the schema divergence at the Spark expression level (via +padding or Variant), avoid the problem entirely by **deferring the construction +of `UnresolvedTransformTree`** until we know both the traversal and a downstream +expression that produces a uniform schema. + +`repeatAll(item)` would not immediately build a Spark expression. Instead, it +returns a **lazy (deferred) Collection** — analogous to how +`ChoiceElementCollection` works — that captures the traversal intent but cannot +be evaluated on its own. When a subsequent FHIRPath operation is applied to this +collection, that operation becomes the **extractor** for `UnresolvedTransformTree`, +and the full expression is materialised at that point. + +### How it works + +Given `Questionnaire.repeatAll(item).linkId`: + +1. `repeatAll(item)` returns a `RepeatAllCollection` (lazy) that records: + - The input collection (`Questionnaire`) + - The traversal function (`item` navigation) + - The max depth +2. `.linkId` is applied to the lazy collection. The lazy collection intercepts + this and uses it as the extractor. +3. Now both pieces are available. The lazy collection builds + `UnresolvedTransformTree` with: + - **Traversal**: `item` navigation (from step 1) + - **Extractor**: `.linkId` projection (from step 2) — produces a consistent + `StringType` at every nesting level +4. The result is a concrete `Collection` of linkId values from all levels. + +### Why this avoids schema divergence + +The extractor is a **user-supplied downstream expression** that projects specific +fields, producing a uniform output type at every level — exactly the pattern +that already works in `RepeatSelection` for SQL-on-FHIR. The items themselves +(with their divergent schemas) are never collected; only the extracted values +are. + +### Precedent: `ChoiceElementCollection` + +Pathling already uses this pattern for FHIR choice types. A +`ChoiceElementCollection` cannot be directly evaluated — it requires a +subsequent type-specific path step (e.g., `.ofType(Quantity).value`) to resolve +into a concrete column. The same deferred-resolution pattern applies here. + +### Error on direct evaluation + +If `repeatAll(item)` is used as a terminal expression (no downstream operation), +it should produce an error, consistent with other lazy collections. For example: + +``` +Questionnaire.repeatAll(item) → ERROR: repeatAll requires a subsequent + expression to determine the extraction schema +``` + +### Chaining and extractor determination + +For a chain like `Questionnaire.repeatAll(item).where(type = 'group').linkId`: + +The lazy collection must determine which downstream operations become the +extractor. Conceptually, the **entire chain** after `repeatAll()` forms the +extractor — each element at every nesting level is evaluated through +`.where(type = 'group').linkId`. The first operation that touches the lazy +collection (`.where(...)`) triggers resolution, composing itself and all +subsequent operations into the extractor. + +In practice, this means the lazy collection needs to intercept the next +operation and wrap it such that the full downstream chain is captured. The +precise mechanism for this requires further investigation — it may involve: + +- The lazy collection returning a modified context that composes operations + until a terminal expression is reached. +- Or, more practically, having the lazy collection absorb only the **immediate + next** operation as the extractor, and letting the rest of the chain operate + on the resulting concrete collection. + +### Pros + +- **Eliminates schema divergence entirely** — no padding, no Variant, no custom + Catalyst expressions for schema alignment. +- **Mirrors the SQL-on-FHIR pattern** — the extractor always produces a uniform + type, which is the proven approach in `RepeatSelection`. +- **Leverages existing infrastructure** — `UnresolvedTransformTree` is used + as-is without modification. +- **Clean separation** of traversal (what to recurse into) from extraction + (what to collect). + +### Cons + +- **Cannot return the items themselves** — the result is always a projection + from the items, not the items. Users cannot write + `repeatAll(item).first().answer` because the items are never materialised as + a collection. This is a fundamental semantic difference from the spec, which + defines `repeatAll()` as returning a collection of the traversed elements. +- **Increased complexity in the Collection abstraction** — introduces a new + deferred collection type that must intercept and compose downstream + operations. +- **Chaining ambiguity** — determining where the "extractor" ends and normal + collection operations begin is non-trivial, especially with complex chains. + +### Open Concerns + +1. **Recursive downstream traversal**: If the downstream expression itself + navigates into a recursive field (e.g., `repeatAll(item).item`), the + extractor still produces divergent schemas across levels — the same problem + resurfaces. The lazy approach only helps when the downstream expression + reaches leaf fields or non-recursive fields. + +2. **Chaining `repeatAll` after `repeatAll`**: An expression like + `Questionnaire.repeatAll(item).repeatAll(answer)` would produce a lazy + collection wrapping another lazy collection. The resolution order and + composition of extractors becomes complex. Does the inner `repeatAll` + resolve first, or does it also defer? + +3. **Composability with aggregate operations**: Operations like `count()`, + `exists()`, `first()` applied to the lazy collection need to trigger + resolution. For `count()`, the extractor could be a trivial identity that + just counts elements — but this brings back the schema divergence problem + since we'd be counting items with different schemas. For `exists()`, it + could short-circuit without needing a schema-uniform array. + +4. **Spec conformance**: The FHIRPath spec defines `repeatAll()` as returning + a collection of the projected elements. A lazy collection that requires + further resolution changes the semantics — `repeatAll(item)` alone should + be a valid expression that returns items. This approach trades spec + conformance for implementation feasibility. + +5. **Interaction with `select()`**: Could `repeatAll(item).select(linkId)` be + the idiomatic pattern? If so, `select()` naturally provides the extractor. + But this still leaves open the question of what happens without `select()`. + +## Open Questions + +1. **Max depth default**: What should the default `maxDepth` be for FHIRPath + `repeatAll()`? Should it match the encoder's `maxNestingLevel`, or be + independently configurable? + +2. **Variant fidelity**: Does `to_variant_object` → `variant_get` round-trip + preserve all FHIR data types faithfully? A spike test with a + `Questionnaire` containing nested `item` elements would answer this. + +3. **`repeat()` path**: Once `repeatAll()` is implemented, `repeat()` would + need the same recursive machinery plus element-wise deduplication. Should + deduplication be deferred entirely, or approximated (e.g., by hash)? + +4. **Schema padding vs lazy collection**: The schema padding approach (primary + solution) preserves full spec conformance but requires solving the schema + divergence problem. The lazy collection approach avoids schema divergence + but changes the function's semantics. Which trade-off is preferable? diff --git a/openspec/specs/fhirpath-configuration/spec.md b/openspec/specs/fhirpath-configuration/spec.md new file mode 100644 index 0000000000..9fb241df2e --- /dev/null +++ b/openspec/specs/fhirpath-configuration/spec.md @@ -0,0 +1,149 @@ +## Requirements + +### Requirement: FHIRPath evaluation configuration object + +The FHIRPath engine SHALL support a `FhirpathConfiguration` object that holds +configurable parameters for FHIRPath expression evaluation. The configuration +SHALL be accessible to FHIRPath functions through the `EvaluationContext`. + +The configuration SHALL include `maxUnboundTraversalDepth` (integer), which +controls the maximum depth for same-type recursive traversal in `repeat()` and +`repeatAll()`. Cross-type traversals do not consume depth budget. The default +value SHALL be 10. The minimum valid value SHALL be 1. + +When no explicit configuration is provided, the evaluation context SHALL use a +default configuration with `maxUnboundTraversalDepth` set to 10. + +#### Scenario: Default configuration + +- **WHEN** no `FhirpathConfiguration` is explicitly provided to the evaluation + context +- **THEN** the evaluation context SHALL use a default configuration with + `maxUnboundTraversalDepth` equal to 10 + +#### Scenario: Custom configuration + +- **WHEN** a `FhirpathConfiguration` with `maxUnboundTraversalDepth` set to 5 is + provided to the evaluation context +- **THEN** the evaluation context SHALL use that configuration and same-type + recursive traversal in `repeat()` and `repeatAll()` SHALL be limited to + depth 5 + +### Requirement: EvaluationContext provides configuration access + +The `EvaluationContext` interface SHALL provide a method to retrieve the +`FhirpathConfiguration`. Implementations that do not explicitly set a +configuration SHALL return the default configuration. + +#### Scenario: Configuration accessible from evaluation context + +- **WHEN** a FHIRPath function accesses the evaluation context during evaluation +- **THEN** the `FhirpathConfiguration` SHALL be available with the configured + `maxUnboundTraversalDepth` value + +### Requirement: FHIRPath functions can receive EvaluationContext + +The `FunctionParameterResolver` SHALL support injecting the `EvaluationContext` +into `@FhirPathFunction`-annotated static methods. When a method parameter is +typed as `EvaluationContext`, the resolver SHALL inject the current evaluation +context without consuming an argument from the FHIRPath argument list. + +#### Scenario: EvaluationContext injection + +- **WHEN** a `@FhirPathFunction` method declares an `EvaluationContext` + parameter +- **THEN** the resolver SHALL inject the current evaluation context and the + function SHALL receive it alongside the normal input and arguments + +### Requirement: QueryConfiguration maxUnboundTraversalDepth minimum is 1 + +The `QueryConfiguration.maxUnboundTraversalDepth` SHALL have a minimum valid +value of 1, matching the constraint on `FhirpathConfiguration`. A value of 0 +SHALL be rejected by validation. + +#### Scenario: Zero value rejected + +- **WHEN** `QueryConfiguration` is built with `maxUnboundTraversalDepth` set + to 0 +- **THEN** a validation error SHALL be raised + +#### Scenario: Value of 1 accepted + +- **WHEN** `QueryConfiguration` is built with `maxUnboundTraversalDepth` set + to 1 +- **THEN** validation SHALL pass and the configuration SHALL be accepted + +### Requirement: QueryConfiguration maxUnboundTraversalDepth flows to FHIRPath evaluation + +When FHIRPath expressions are evaluated through the library API (via +`SingleResourceEvaluator`), the `maxUnboundTraversalDepth` from +`QueryConfiguration` SHALL be used to configure the `FhirpathConfiguration` +provided to the `EvaluationContext`. This ensures that `repeat()` and +`repeatAll()` functions respect the user-configured depth. + +#### Scenario: Custom depth respected by repeat function + +- **WHEN** `QueryConfiguration` is built with `maxUnboundTraversalDepth` set + to 20 +- **AND** a FHIRPath expression using `repeat()` or `repeatAll()` is evaluated + through the library API +- **THEN** the recursive traversal depth limit SHALL be 20 + +#### Scenario: Default depth used when no QueryConfiguration specified + +- **WHEN** no `QueryConfiguration` is explicitly provided +- **AND** a FHIRPath expression using `repeat()` or `repeatAll()` is evaluated + through the library API +- **THEN** the recursive traversal depth limit SHALL be the default value of 10 + +### Requirement: SingleResourceEvaluator accepts FhirpathConfiguration + +The `SingleResourceEvaluator` SHALL accept a `FhirpathConfiguration` and pass +it to the `FhirEvaluationContext` during expression evaluation. The +`SingleResourceEvaluatorBuilder` SHALL provide a `withConfiguration()` method +for setting the configuration. + +When no configuration is explicitly set, `FhirpathConfiguration.DEFAULT` SHALL +be used. + +#### Scenario: Evaluator with custom configuration + +- **WHEN** a `SingleResourceEvaluator` is built with a `FhirpathConfiguration` + having `maxUnboundTraversalDepth` set to 5 +- **AND** a FHIRPath expression using `repeat()` is evaluated +- **THEN** the evaluation context SHALL have `maxUnboundTraversalDepth` equal + to 5 + +#### Scenario: Evaluator with default configuration + +- **WHEN** a `SingleResourceEvaluator` is built without specifying a + `FhirpathConfiguration` +- **THEN** the evaluation context SHALL use `FhirpathConfiguration.DEFAULT` + +### Requirement: ViewDefinition repeat clause errors on non-Extension depth exhaustion + +The ViewDefinition `repeat` clause SHALL error at runtime when same-type +recursive traversal exhausts the configured `maxUnboundTraversalDepth` for +non-Extension FHIR types. For Extension types, depth exhaustion SHALL silently +stop and return results collected up to that point. + +#### Scenario: Non-Extension depth exhaustion raises error + +- **WHEN** a ViewDefinition `repeat` clause traverses a non-Extension type + (e.g., `item` on Questionnaire) and the recursion reaches the configured + `maxUnboundTraversalDepth` +- **THEN** a runtime error SHALL be raised indicating that the recursive + traversal exceeded the maximum depth + +#### Scenario: Extension depth exhaustion silently stops + +- **WHEN** a ViewDefinition `repeat` clause traverses an Extension type and + the recursion reaches the configured `maxUnboundTraversalDepth` +- **THEN** the clause SHALL silently stop and return all results collected up + to that depth without raising an error + +#### Scenario: Depth not exhausted produces normal results + +- **WHEN** a ViewDefinition `repeat` clause traverses a type that terminates + naturally before reaching `maxUnboundTraversalDepth` +- **THEN** all results from all nesting levels SHALL be returned normally diff --git a/openspec/specs/fhirpath-evaluation-api/spec.md b/openspec/specs/fhirpath-evaluation-api/spec.md index 1b5dbe96e3..27f518337d 100644 --- a/openspec/specs/fhirpath-evaluation-api/spec.md +++ b/openspec/specs/fhirpath-evaluation-api/spec.md @@ -10,6 +10,10 @@ The method SHALL use the existing Pathling FHIRPath engine (Spark-based) to evaluate the expression, encoding the resource into a one-row Dataset internally. +The method SHALL support all FHIRPath functions implemented in the engine, +including scoped functions that accept projection expressions (e.g., `select()`, +`repeatAll()`). + When the expression is empty or contains only whitespace, the fhirpath-lab-api SHALL return a successful response with an empty collection (zero result parts) without invoking the FHIRPath engine. @@ -52,6 +56,13 @@ without invoking the FHIRPath engine. - **THEN** the method evaluates the main expression once for each result of the context expression and returns results grouped by context item +#### Scenario: Recursive function evaluation + +- **WHEN** the method is called with a Questionnaire JSON resource and the + expression `repeatAll(item).linkId` +- **THEN** the method returns a list containing `linkId` values from all + recursively nested items + ### Requirement: Return type metadata with evaluation results The library API evaluation method SHALL return type information alongside each diff --git a/openspec/specs/fhirpath-repeat-all/spec.md b/openspec/specs/fhirpath-repeat-all/spec.md new file mode 100644 index 0000000000..ee34f0ce4d --- /dev/null +++ b/openspec/specs/fhirpath-repeat-all/spec.md @@ -0,0 +1,355 @@ +## ADDED Requirements + +### Requirement: repeatAll function recursively traverses and collects elements + +The FHIRPath engine SHALL support the +`repeatAll(projection: ($this) => collection) : collection` function. The +function SHALL evaluate the projection expression for each item in the input +collection, add all results to the output collection, then re-evaluate the +projection on the new results. This process SHALL repeat until an iteration +produces no new results. + +Unlike `repeat()`, the function SHALL NOT check for duplicate items — all +results SHALL be added to the output collection regardless of whether they +already exist. + +#### Scenario: Single-level traversal + +- **WHEN** `repeatAll` is called on a Questionnaire resource with a single level + of items and the projection `item` +- **THEN** the result SHALL contain all items from that single level + +#### Scenario: Multi-level recursive traversal + +- **WHEN** `repeatAll` is called on a Questionnaire resource with nested items + (items containing sub-items) and the projection `item` +- **THEN** the result SHALL contain items from all nesting levels + +#### Scenario: Duplicate items are preserved + +- **WHEN** `repeatAll` is called and the same item would be reached through + multiple traversal paths +- **THEN** all occurrences SHALL be included in the output collection (no + deduplication) + +### Requirement: repeatAll function terminates on empty iteration + +The function SHALL terminate when an iteration of the projection expression +across all current items produces an empty collection (no new results). + +When the traversal expression applied to its own result (level_1) produces a +statically empty collection, the function SHALL return the level_0 result +directly for both primitive and complex types. This is equivalent to `select()` +behavior. + +#### Scenario: Termination at leaf nodes + +- **WHEN** `repeatAll(item)` is evaluated on a Questionnaire where the deepest + items have no child items +- **THEN** the function SHALL terminate and return all collected items + +#### Scenario: Non-recursive collection projection + +- **WHEN** `repeatAll` is called with a projection that does not navigate into a + recursive structure and produces a collection (e.g., + `Patient.repeatAll(name)`) +- **THEN** the function SHALL return the level_0 result directly, equivalent to + `select()` + +#### Scenario: Non-recursive singular projection + +- **WHEN** `repeatAll` is called with a projection that produces a singular + value (e.g., `Patient.repeatAll(gender)`) +- **THEN** the function SHALL return the level_0 result directly, equivalent to + `select()` + +#### Scenario: Non-recursive singular complex projection + +- **WHEN** `repeatAll` is called with a projection that produces a singular + complex type (e.g., `Patient.repeatAll(maritalStatus)`) +- **THEN** the function SHALL return the level_0 result directly with all + sub-elements intact, equivalent to `select()` + +### Requirement: repeatAll function handles empty input + +If the input collection is empty, the result SHALL be empty. This SHALL hold +both when the input is a typed collection that evaluates to empty at runtime +(e.g., a resource where the traversed field is absent) and when the input is +the FHIRPath empty literal `{}`. + +#### Scenario: Empty collection from absent field + +- **WHEN** `repeatAll` is called on a resource where the traversed field is + absent (e.g., a Questionnaire with no items) +- **THEN** the result SHALL be an empty collection + +#### Scenario: Empty collection literal + +- **WHEN** `repeatAll` is called on the FHIRPath empty literal `{}` (e.g., + `{}.repeatAll(item)`) +- **THEN** the result SHALL be an empty collection + +### Requirement: repeatAll function supports chained expressions + +The result of `repeatAll` SHALL be a standard collection that supports +subsequent FHIRPath operations such as path navigation, `where()`, `count()`, +`select()`, and other functions. + +#### Scenario: Path navigation after repeatAll + +- **WHEN** a FHIRPath expression chains a path after `repeatAll` (e.g., + `Questionnaire.repeatAll(item).linkId`) +- **THEN** the result SHALL contain the `linkId` values from all recursively + collected items + +#### Scenario: Filtering after repeatAll + +- **WHEN** a FHIRPath expression applies `where()` after `repeatAll` (e.g., + `Questionnaire.repeatAll(item).where(type = 'group')`) +- **THEN** the result SHALL contain only items matching the filter from all + nesting levels + +#### Scenario: Counting after repeatAll + +- **WHEN** a FHIRPath expression applies `count()` after `repeatAll` (e.g., + `Questionnaire.repeatAll(item).count()`) +- **THEN** the result SHALL be the total number of items across all nesting + levels, including duplicates + +### Requirement: repeatAll function bounds same-type recursion depth + +The function SHALL perform a static type analysis before entering tree +traversal. It SHALL apply the traversal expression to the input to produce +level_0, then apply the traversal expression to level_0 to produce level_1. +The function SHALL classify behavior based on the FHIR type comparison between +level_0 and level_1: + +1. **level_1 is empty**: Return level_0 directly (equivalent to `select()`). + This applies to both primitive and complex types. +2. **level_0 or level_1 has indeterminate FHIR type**: Raise an immediate + error indicating that the recursive traversal expression produces a result + with indeterminate FHIR type. This occurs when `getFhirType()` returns + empty on either side (e.g., choice type elements that have not been resolved + via `ofType()`). +3. **level_1 is same FHIR type as level_0, primitive or resource, + self-reference not allowed**: Raise an immediate error indicating + self-referential traversal. Resource types are treated like primitives + because they are represented with a boolean existence column (not a + struct) and cannot be recursed into via `variantTransformTree`. +4. **level_1 is same FHIR type as level_0, primitive or resource, + self-reference allowed**: Return level_0 directly. The caller (i.e., + `repeat()`) is responsible for deduplication, which guarantees + termination. +5. **level_1 is same FHIR type as level_0, complex, Extension**: Proceed to + recursive tree traversal with silent stop on depth exhaustion. +6. **level_1 is same FHIR type as level_0, complex, non-Extension, + self-reference not allowed**: Proceed to recursive tree traversal with + error on depth exhaustion. +7. **level_1 is same FHIR type as level_0, complex, non-Extension, + self-reference allowed**: Proceed to recursive tree traversal with silent + stop on depth exhaustion. The caller (i.e., `repeat()`) is responsible for + deduplication, which guarantees termination. +8. **level_1 is a different non-empty FHIR type from level_0**: Raise an + immediate error indicating inconsistent traversal types. + +The `allowSelfReference` flag controls both primitive (case 3 vs 4) and complex +(case 6 vs 7) behavior. When set, depth exhaustion does not raise an error, +and the caller is expected to deduplicate the results. + +For cases 5, 6, and 7, the function delegates to `variantTransformTree` with +`UnresolvedTransformTree` providing analysis-time same-SQL-type depth limiting. +The depth limit for Extension traversal is controlled by `maxUnboundTraversalDepth` in +`FhirpathConfiguration`. + +#### Scenario: Self-referential primitive identity traversal detected + +- **WHEN** `gender.repeatAll($this)` is evaluated +- **THEN** the function SHALL raise an error indicating self-referential + primitive traversal + +#### Scenario: Self-referential primitive constant traversal detected + +- **WHEN** `gender.repeatAll('someValue')` is evaluated +- **THEN** the function SHALL raise an error indicating self-referential + primitive traversal + +#### Scenario: Self-referential primitive function traversal detected + +- **WHEN** `gender.repeatAll(length())` is evaluated +- **THEN** the function SHALL raise an error indicating self-referential + primitive traversal + +#### Scenario: Infinite recursion detected for identity traversal on complex type + +- **WHEN** `repeatAll($this)` is evaluated on any complex-typed collection +- **THEN** the function SHALL raise an evaluation error indicating infinite + recursive traversal was detected (via analysis-time detection) + +#### Scenario: Infinite recursion detected for first() traversal + +- **WHEN** `name.repeatAll(first())` is evaluated on a resource with name + elements +- **THEN** the function SHALL raise an evaluation error indicating infinite + recursive traversal was detected (via analysis-time detection) + +#### Scenario: Indeterminate type on choice element with identity traversal + +- **WHEN** `value.repeatAll($this)` is evaluated on an Observation resource + where `value` is a choice type (value[x]) +- **THEN** the function SHALL raise an error indicating indeterminate FHIR type + +#### Scenario: Choice element with ofType fails during type probing + +- **WHEN** `value.repeatAll(ofType(Quantity))` is evaluated on an Observation + resource where `value` is a choice type +- **THEN** the function SHALL raise an error during type probing because the + `ofType()` transform applied to the MixedCollection attempts to reconstruct + a collection without a concrete FHIR type or definition + +#### Scenario: Choice element traversal fails on polymorphic navigation + +- **WHEN** `repeatAll(value)` is evaluated on an Observation resource where + `value` is a choice type +- **THEN** the function SHALL raise an error indicating that direct traversal + of polymorphic collections is not supported + +#### Scenario: Choice element with first() fails during type probing + +- **WHEN** `value.repeatAll(first())` is evaluated on an Observation resource + where `value` is a choice type +- **THEN** the function SHALL raise an error during type probing because + `first()` on a MixedCollection attempts to reconstruct a collection without + a concrete FHIR type or definition + +#### Scenario: Resource-level identity traversal raises self-referential error + +- **WHEN** `repeatAll($this)` is evaluated on a resource (e.g., Patient) +- **THEN** the function SHALL raise an error indicating self-referential + traversal that cannot terminate, because resource types are treated like + primitives in the type analysis gate + +#### Scenario: Resource-level %resource projection raises self-referential error + +- **WHEN** `name.repeatAll(%resource).gender` is evaluated on a Patient + resource +- **THEN** the function SHALL raise an error indicating self-referential + traversal that cannot terminate + +#### Scenario: Self-reference flag suppresses depth exhaustion error + +- **WHEN** `repeatAll` is invoked internally with self-reference allowed (as + done by `repeat()`) and the traversal expression produces same-type complex + results that exhaust the depth limit +- **THEN** the function SHALL NOT raise an error, instead returning all + collected results up to the depth limit for the caller to deduplicate + +#### Scenario: Extension traversal bounded by configured depth + +- **WHEN** `repeatAll(extension)` is evaluated on a resource whose elements + carry nested extensions and `maxUnboundTraversalDepth` is set to 5 +- **THEN** the function SHALL traverse extensions up to depth 5, returning all + collected extensions, and SHALL NOT raise an error + +#### Scenario: Extension traversal with default depth + +- **WHEN** `repeatAll(extension)` is evaluated with default configuration +- **THEN** the function SHALL traverse extensions up to depth 10 + +#### Scenario: Schema-truncated traversal terminates naturally + +- **WHEN** `repeatAll(item)` is evaluated on a Questionnaire with nested items +- **THEN** traversal SHALL terminate naturally when the schema no longer + contains the `item` field (due to `maxNestingLevel` truncation during the + encoding), without consuming same-type depth budget and without raising an + error + +#### Scenario: Unknown FHIR type defaults to error mode + +- **WHEN** `repeatAll` is evaluated with a projection whose FHIR type is + unknown and same-type depth is exhausted +- **THEN** the function SHALL raise an evaluation error, as unknown types that + hit the depth limit are more likely bugs than intentional recursion + +#### Scenario: Inconsistent traversal types detected + +- **WHEN** `repeatAll` is evaluated with a traversal expression that produces a + different non-empty FHIR type when applied to its own result +- **THEN** the function SHALL raise an error indicating inconsistent traversal + types + +### Requirement: repeatAll function uses distinct error messages + +The function SHALL use distinct error messages to differentiate between +detection contexts: + +1. **Static self-reference**: A message indicating that the traversal + expression produces a self-referential type that cannot terminate. This + covers both primitive types and resource types (which are treated like + primitives). +2. **Static indeterminate type**: A message indicating that the recursive + traversal expression produces a result with indeterminate FHIR type. +3. **Static inconsistent types**: A message indicating that the traversal + expression does not produce a consistent type across recursive applications. +4. **Analysis-time complex depth exhaustion**: The existing message "Infinite + recursive traversal detected." from `UnresolvedTransformTree`. + +#### Scenario: Self-reference error message + +- **WHEN** a self-referential traversal is detected statically (primitive or + resource type) +- **THEN** the error message SHALL be distinct from the analysis-time + "Infinite recursive traversal detected." message + +#### Scenario: Indeterminate type error message + +- **WHEN** an indeterminate FHIR type is detected statically +- **THEN** the error message SHALL indicate that the recursive traversal + expression produces a result with indeterminate FHIR type, distinct from + both the inconsistent type and primitive self-reference messages + +#### Scenario: Inconsistent type error message + +- **WHEN** an inconsistent traversal type is detected statically +- **THEN** the error message SHALL indicate that the traversal expression + produces inconsistent types + +#### Scenario: Analysis-time error message preserved + +- **WHEN** a complex non-Extension same-SQL-type depth exhaustion occurs during + Catalyst analysis +- **THEN** the error message SHALL remain "Infinite recursive traversal + detected." + +### Requirement: repeatAll function does not define $index + +The `$index` variable SHALL NOT be set during evaluation of the projection +expression, consistent with the FHIRPath specification. + +#### Scenario: $index is not available + +- **WHEN** the projection expression references `$index` within `repeatAll` +- **THEN** `$index` SHALL NOT resolve to a value + +### Requirement: repeatAll function preserves extensions and sub-elements + +The result collection SHALL preserve all fields of the propagated elements, +including FHIR extensions and other sub-elements. This is a general invariant +for all element-propagating FHIRPath functions (e.g., `first()`, `where()`), but +SHALL be verified for `repeatAll()` given the schema alignment involved. + +#### Scenario: Extensions preserved in results + +- **WHEN** `repeatAll(item)` is evaluated on a Questionnaire where items contain + extension elements +- **THEN** the result items SHALL retain their extension elements intact + +### Requirement: repeatAll function is available as a FHIRPath function + +The `repeatAll` function SHALL be registered and invocable using standard +FHIRPath function call syntax (e.g., `collection.repeatAll(expression)`). + +#### Scenario: Function invocation syntax + +- **WHEN** a FHIRPath expression uses `repeatAll` with dot notation (e.g., + `Questionnaire.repeatAll(item)`) +- **THEN** the function SHALL be resolved and executed correctly diff --git a/openspec/specs/fhirpath-repeat/spec.md b/openspec/specs/fhirpath-repeat/spec.md new file mode 100644 index 0000000000..7b8ac34c1b --- /dev/null +++ b/openspec/specs/fhirpath-repeat/spec.md @@ -0,0 +1,152 @@ +## ADDED Requirements + +### Requirement: repeat function recursively traverses and deduplicates elements + +The FHIRPath engine SHALL support the `repeat(projection: expression) : collection` function. The function SHALL evaluate the projection expression recursively, collecting all results, then deduplicate the output collection using equality semantics. + +The function SHALL delegate recursive traversal to `repeatAll()`, then apply equality-based deduplication to the result. + +#### Scenario: Single-level traversal with no duplicates + +- **WHEN** `repeat(item)` is called on a Questionnaire with a single level of items +- **THEN** the result SHALL contain all items from that level (identical to `repeatAll`) + +#### Scenario: Multi-level recursive traversal + +- **WHEN** `repeat(item)` is called on a Questionnaire with nested items +- **THEN** the result SHALL contain items from all nesting levels + +#### Scenario: Duplicate primitive values are removed + +- **WHEN** `repeat($this)` is called on a collection containing duplicate primitive values (e.g., `(1 year).combine(12 months).repeat($this)`) +- **THEN** the result SHALL contain only distinct values as determined by FHIRPath equality + +#### Scenario: Quantity equality used for deduplication + +- **WHEN** `repeat($this)` is called on a collection of quantities where values are equal under unit conversion (e.g., 3 minutes and 180 seconds) +- **THEN** only one representative value SHALL appear in the result + +#### Scenario: String deduplication + +- **WHEN** `repeat` produces duplicate string values across recursion levels +- **THEN** the result SHALL contain each distinct string value only once + +### Requirement: repeat function deduplicates only Equatable types + +The function SHALL apply deduplication only when the result collection implements the `Equatable` interface. For non-Equatable types (complex backbone elements), the function SHALL return the `repeatAll()` result without deduplication. + +#### Scenario: Complex type results not deduplicated + +- **WHEN** `repeat(item)` is called on a Questionnaire with nested items +- **THEN** no deduplication SHALL be attempted on the complex item elements (result is identical to `repeatAll`) + +#### Scenario: Equatable type results deduplicated + +- **WHEN** `repeat` produces a collection of an Equatable type (String, Integer, Quantity, Coding, etc.) +- **THEN** the result SHALL be deduplicated using the collection's comparator + +### Requirement: repeat function uses collection comparator for equality + +When deduplicating Equatable results, the function SHALL use the collection's `getComparator()` method to obtain the appropriate `ColumnEquality` instance. If the comparator uses default SQL equality, the function SHALL use `array_distinct`. Otherwise, the function SHALL use `arrayDistinctWithEquality` with the comparator's `equalsTo` method. + +#### Scenario: Default SQL equality types + +- **WHEN** the result collection uses default SQL equality (e.g., String, Integer, Boolean) +- **THEN** deduplication SHALL use Spark's `array_distinct` + +#### Scenario: Custom equality types + +- **WHEN** the result collection uses custom equality (e.g., Quantity with unit conversion) +- **THEN** deduplication SHALL use `arrayDistinctWithEquality` with the collection's comparator + +### Requirement: repeat function handles self-referential primitive traversal + +Unlike `repeatAll()` which raises an error for self-referential primitive traversal, `repeat()` SHALL treat this as a valid case. When the projection produces a self-referential primitive type, `repeat()` SHALL return the level_0 result (from `repeatAll` with primitive self-ref allowed) and then deduplicate it. This is valid because deduplication guarantees termination. + +#### Scenario: Constant projection deduplicates to single value + +- **WHEN** `(1 | 2).repeat('item')` is evaluated +- **THEN** the result SHALL be `['item']` (projection produces `'item'` for each input, dedup collapses to one) + +#### Scenario: Identity projection deduplicates + +- **WHEN** `Functions.coll1.colltrue.repeat(true)` is evaluated +- **THEN** the result SHALL be `[true]` + +#### Scenario: Quantity identity with unit conversion + +- **WHEN** `(1 year).combine(12 months).repeat($this)` is evaluated +- **THEN** the result SHALL be `[1 year]` (1 year = 12 months under FHIRPath equality) + +### Requirement: repeat function inherits repeatAll behavior + +The `repeat` function SHALL inherit all recursive traversal behavior from `repeatAll`, including: + +- Static type analysis gate (level_0/level_1 classification). +- Same-type recursion depth limiting. +- Extension traversal with soft stop. +- Error on inconsistent traversal types. +- Empty input produces empty output. +- Result supports chained FHIRPath operations. + +#### Scenario: Empty input + +- **WHEN** `repeat` is called on an empty collection +- **THEN** the result SHALL be empty + +#### Scenario: Chained operations + +- **WHEN** `Questionnaire.repeat(item).linkId` is evaluated +- **THEN** the result SHALL contain linkId values from all recursively collected items + +### Requirement: repeat function is available as a FHIRPath function + +The `repeat` function SHALL be registered and invocable using standard FHIRPath function call syntax (e.g., `collection.repeat(expression)`). + +#### Scenario: Function invocation syntax + +- **WHEN** a FHIRPath expression uses `repeat` with dot notation (e.g., `Questionnaire.repeat(item)`) +- **THEN** the function SHALL be resolved and executed correctly + +### Requirement: repeat function rejects indeterminate types via repeatAll + +The `repeat` function SHALL inherit the indeterminate type guard from +`repeatAll`. When the traversal expression produces a result with indeterminate +FHIR type (e.g., an unresolved choice element), `repeat` SHALL raise the same +error as `repeatAll`. + +#### Scenario: Choice element identity traversal raises indeterminate type error + +- **WHEN** `value.repeat($this)` is evaluated on an Observation resource where + `value` is a choice type (value[x]) +- **THEN** the function SHALL raise an error indicating indeterminate FHIR type + +#### Scenario: Choice element with ofType resolves and terminates + +- **WHEN** `repeat(value.ofType(Quantity))` is evaluated on an Observation + resource +- **THEN** the function SHALL return the Quantity value from level_0 directly, + since applying `value.ofType(Quantity)` to a Quantity produces an empty + level_1 (Quantity.value is a decimal, ofType(Quantity) on decimal is empty) + +### Requirement: repeat function handles self-referential complex expressions + +The `repeat` function SHALL correctly handle expressions that produce same-type +results at every depth level. Because `repeat()` delegates to `repeatAll()` +with self-reference allowed, depth exhaustion does not raise an error. The +depth-limited results are deduplicated by `repeat()`, which guarantees +termination and produces the correct result. + +#### Scenario: Resource-level identity traversal returns input + +- **WHEN** `repeat($this)` is evaluated on a resource (e.g., Patient) +- **THEN** the function SHALL return the resource unchanged, since the first + iteration produces the same item which is already in the result set, + causing immediate termination via deduplication + +#### Scenario: Resource-level %resource projection returns deduplicated results + +- **WHEN** `name.repeat(%resource).gender` is evaluated on a Patient resource +- **THEN** the function SHALL return the patient's gender value, since + `%resource` produces the same Patient at each depth level and deduplication + collapses them to one diff --git a/openspec/specs/fhirpath-select/spec.md b/openspec/specs/fhirpath-select/spec.md new file mode 100644 index 0000000000..9e3666fc46 --- /dev/null +++ b/openspec/specs/fhirpath-select/spec.md @@ -0,0 +1,49 @@ +### Requirement: Select function evaluates projection for each element + +The FHIRPath engine SHALL support the `select(projection: expression) : collection` function. The function SHALL evaluate the projection expression for each item in the input collection. The result of each evaluation SHALL be added to the output collection. + +#### Scenario: Simple property projection + +- **WHEN** `select` is called with a property path expression on a collection of resources (e.g., `Patient.name.select(family)`) +- **THEN** the result SHALL contain the values of that property for each element in the input collection + +#### Scenario: Expression projection + +- **WHEN** `select` is called with a complex expression (e.g., `Patient.name.select(given + ' ' + family)`) +- **THEN** the result SHALL contain the evaluated expression result for each element + +### Requirement: Select function flattens results + +If the evaluation of the projection expression for an element results in a collection with multiple items, all items SHALL be added to the output collection (collections resulting from evaluation of the projection are flattened). + +#### Scenario: Projection returns multiple items + +- **WHEN** `select` is called with an expression that returns multiple values per element (e.g., `Patient.name.select(given)` where a name has multiple given names) +- **THEN** all values from each element's projection SHALL be included in the output collection + +### Requirement: Select function handles empty results + +If the evaluation of the projection expression for an element results in the empty collection, no element SHALL be added to the result for that input element. + +#### Scenario: Projection returns empty for some elements + +- **WHEN** `select` is called and the projection expression evaluates to empty for some input elements +- **THEN** those elements SHALL not contribute to the output collection + +### Requirement: Select function handles empty input + +If the input collection is empty, the result SHALL be empty. + +#### Scenario: Empty input collection + +- **WHEN** `select` is called on an empty collection +- **THEN** the result SHALL be an empty collection + +### Requirement: Select function is available as a FHIRPath function + +The `select` function SHALL be registered and invocable using standard FHIRPath function call syntax (e.g., `collection.select(expression)`). + +#### Scenario: Function invocation syntax + +- **WHEN** a FHIRPath expression uses `select` with dot notation (e.g., `Patient.contact.select(name)`) +- **THEN** the function SHALL be resolved and executed correctly diff --git a/site/.trivyignore b/site/.trivyignore index f6724744c1..eab7bad8e2 100644 --- a/site/.trivyignore +++ b/site/.trivyignore @@ -1,3 +1,14 @@ # minimatch DoS (serve-handler transitive dependency, only used by local # docusaurus serve command, not in production GitHub Pages deployment). CVE-2026-26996 +CVE-2026-27903 +CVE-2026-27904 + +# dompurify XSS — shipped via mermaid but no user input in static site. +CVE-2026-0540 + +# serialize-javascript RCE — build-time webpack dependency, not deployed. +GHSA-5c6j-r48x-rmvq + +# svgo XML entity expansion DoS — build-time SVG optimiser, only processes trusted source files. +CVE-2026-29074 diff --git a/site/docs/fhirpath/index.md b/site/docs/fhirpath/index.md index 6a83387eb1..1c1a229943 100644 --- a/site/docs/fhirpath/index.md +++ b/site/docs/fhirpath/index.md @@ -121,10 +121,13 @@ for detailed semantics. #### Filtering and projection functions -| Function | Description | -| ----------------- | ---------------------------------------- | -| `where(criteria)` | Filter collection by criteria expression | -| `ofType(type)` | Filter collection by type | +| Function | Description | +| ----------------------- | ----------------------------------------------------------------- | +| `where(criteria)` | Filter collection by criteria expression | +| `select(projection)` | Evaluate projection for each element, flattening results | +| `ofType(type)` | Filter collection by type | +| `repeat(projection)` | Recursively evaluate projection, deduplicating results | +| `repeatAll(projection)` | Recursively evaluate projection without deduplication (see below) | #### Subsetting functions @@ -180,7 +183,6 @@ for detailed semantics. The following FHIRPath features are **not currently supported**: - **Equivalence operators**: `~` and `!~` -- **Lambda expressions** - **Aggregate functions**: `sum()`, `avg()`, `min()`, `max()` - **Special variables**: `$index`, `$total` - **Quantity arithmetic**: Math operations on Quantity types @@ -188,6 +190,24 @@ The following FHIRPath features are **not currently supported**: - **Full resource resolution**: The `resolve()` function extracts type information only and does not support field traversal +#### Recursive traversal depth + +Both `repeat` and `repeatAll` use static type analysis to determine how to +handle the recursion. When the projection expression produces the same FHIR +type at each level (e.g. navigating `item` within a Questionnaire), the +traversal is bounded by a configurable maximum depth. The default maximum depth +is 10. + +For Extension traversal, depth exhaustion silently stops and returns results +collected up to that point. For other types, depth exhaustion raises an error. + +The maximum depth can be configured: + +- In the **Pathling libraries**, via the `maxUnboundTraversalDepth` parameter in + the query configuration. +- In the **Pathling server**, via the `pathling.query.maxUnboundTraversalDepth` + configuration property. + ## Additional functions Pathling also supports additional functions beyond the standard FHIRPath diff --git a/site/docs/server/configuration.md b/site/docs/server/configuration.md index 5e79d90ff8..7cf23cee54 100644 --- a/site/docs/server/configuration.md +++ b/site/docs/server/configuration.md @@ -214,6 +214,10 @@ fs: - `pathling.query.cacheResults` - (default: `true`) This controls whether the built-in caching within Spark is used for search results. It may be useful to turn this off for large datasets in memory-constrained environments. +- `pathling.query.maxUnboundTraversalDepth` - (default: `10`) Controls the + maximum depth for same-type recursive traversal in `repeat()` and + `repeatAll()` FHIRPath functions. Cross-type traversals do not consume depth + budget. The minimum value is `1`. ### Apache Spark diff --git a/sql-on-fhir b/sql-on-fhir index 3e981a9122..004211471c 160000 --- a/sql-on-fhir +++ b/sql-on-fhir @@ -1 +1 @@ -Subproject commit 3e981a91220b869ddc2abbb621979922968577d1 +Subproject commit 004211471c70f6d972f12cf9ed79079d1aca5d1f