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Lucas0TLucas0T
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Support Nested Lists
closes #499
1 parent 9ad7a69 commit 7465d04

34 files changed

+1151
-846
lines changed

‎src/main/java/de/medizininformatikinitiative/torch/model/crtdl/FieldCondition.java‎

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package de.medizininformatikinitiative.torch.model.crtdl;
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import de.medizininformatikinitiative.torch.model.crtdl.annotated.AnnotatedAttribute;
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import java.util.ArrayList;
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import java.util.List;
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import static java.util.Objects.requireNonNull;
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public record FieldCondition(String fieldName, String condition) {
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public FieldCondition {
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requireNonNull(fieldName, "fieldName must not be null");
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requireNonNull(condition, "condition must not be null");
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}
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public String fhirPath() {
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return fieldName + condition;
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}
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/**
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* Splits a FHIR path segment into a field and a condition (e.g., `.where(...)`, `.ofType(...)` or `.type(...)`).
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* <p>
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* If the segment contains a function call, the field will be everything before the first function,
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* and the condition will include the function call itself (including parentheses and nested content).
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*
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* @param segment the FHIR path segment to parse
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* @return a {@link FieldCondition} object with field and condition separated
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*/
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private static FieldCondition parseSegment(String segment) {
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String[] functions = {"where(", "ofType(", "type("};
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int firstFuncIndex = -1;
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for (String func : functions) {
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int idx = segment.indexOf("." + func);
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if (idx >= 0 && (firstFuncIndex == -1 || idx < firstFuncIndex)) {
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firstFuncIndex = idx;
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}
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}
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if (firstFuncIndex >= 0) {
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// Field is everything before the first function
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String field = segment.substring(0, firstFuncIndex).trim();
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// Condition is everything from the first function onwards
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String cond = segment.substring(firstFuncIndex).trim();
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return new FieldCondition(field, cond);
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} else {
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return new FieldCondition(segment.trim(), "");
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}
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}
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/**
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* Splits a FHIRPath expression into sequential segments as {@link FieldCondition} objects.
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* <p>
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* Rules for splitting:
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* <ul>
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* <li>Splits after each {@code where} clause, keeping the clause as part of the condition.</li>
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* <li>Splits at each {@code .} (dot) when not inside parentheses and not immediately followed by a function call like {@code where()} or {@code ofType()}.</li>
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* <li>Keeps nested function calls intact.</li>
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* </ul>
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* Example:
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* <pre>
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* Input: "Observation.value.ofType(Quantity).where(value &gt; 5).unit"
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* Output: [
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* FieldCondition(field="Observation", condition=""),
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* FieldCondition(field="value", condition=".ofType(Quantity)"),
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* FieldCondition(field="", condition=".where(value &gt; 5)"),
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* FieldCondition(field="unit", condition="")
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* ]
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* </pre>
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*
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* @return a non-null {@link List} of {@link FieldCondition} objects representing each segment of the FHIRPath
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*/
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public static List<FieldCondition> splitFhirPath(AnnotatedAttribute attr) {
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String fhirPath = attr.fhirPath();
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List<FieldCondition> result = new ArrayList<>();
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int start = 0;
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int parenDepth = 0;
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for (int i = 0; i < fhirPath.length(); i++) {
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char c = fhirPath.charAt(i);
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if (c == '(') parenDepth++;
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else if (c == ')') parenDepth--;
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else if (c == '.' && parenDepth == 0) {
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// Look ahead to check for function calls: where(), ofType(), type()
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String remaining = fhirPath.substring(i + 1);
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if (remaining.startsWith("where(") || remaining.startsWith("ofType(") || remaining.startsWith("type(")) {
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continue; // skip splitting for this dot
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}
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result.add(parseSegment(fhirPath.substring(start, i)));
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start = i + 1;
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}
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}
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if (start < fhirPath.length()) {
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result.add(parseSegment(fhirPath.substring(start)));
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}
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return result;
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}
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}

‎src/main/java/de/medizininformatikinitiative/torch/model/crtdl/annotated/AnnotatedAttribute.java‎

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@@ -8,14 +8,12 @@
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@JsonIgnoreProperties(ignoreUnknown = true)
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public record AnnotatedAttribute(String attributeRef, String fhirPath,
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String terserPath,
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boolean mustHave,
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List<String> linkedGroups) {
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public AnnotatedAttribute {
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requireNonNull(attributeRef);
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requireNonNull(fhirPath);
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requireNonNull(terserPath);
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linkedGroups = linkedGroups == null ? List.of() : List.copyOf(linkedGroups);
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}
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@@ -24,9 +22,10 @@ public record AnnotatedAttribute(String attributeRef, String fhirPath,
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*/
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public AnnotatedAttribute(String attributeRef,
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String fhirPath,
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String terserPath,
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boolean mustHave
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) {
30-
this(attributeRef, fhirPath, terserPath, mustHave, List.of()); // Default value for includeReferenceOnly
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this(attributeRef, fhirPath, mustHave, List.of()); // Default value for includeReferenceOnly
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}
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}
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‎src/main/java/de/medizininformatikinitiative/torch/model/crtdl/annotated/AnnotatedAttributeGroup.java‎

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@@ -1,9 +1,11 @@
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package de.medizininformatikinitiative.torch.model.crtdl.annotated;
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import de.medizininformatikinitiative.torch.model.crtdl.FieldCondition;
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import de.medizininformatikinitiative.torch.model.crtdl.Filter;
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import de.medizininformatikinitiative.torch.model.fhir.Query;
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import de.medizininformatikinitiative.torch.model.fhir.QueryParams;
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import de.medizininformatikinitiative.torch.model.management.CopyTreeNode;
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import de.medizininformatikinitiative.torch.model.mapping.DseMappingTreeBase;
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import org.hl7.fhir.r4.model.Resource;
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@@ -105,4 +107,17 @@ public List<AnnotatedAttribute> refAttributes() {
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return attributes.stream().filter(annotatedAttribute -> !annotatedAttribute.linkedGroups().isEmpty()).toList();
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}
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public CopyTreeNode buildTree() {
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CopyTreeNode root = new CopyTreeNode(resourceType());
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for (AnnotatedAttribute attr : attributes) {
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List<FieldCondition> parts = FieldCondition.splitFhirPath(attr);
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CopyTreeNode current = root;
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for (int i = 1; i < parts.size(); i++) {
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current = current.getOrCreateChild(parts.get(i));
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}
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}
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return root;
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}
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}

‎src/main/java/de/medizininformatikinitiative/torch/model/management/CopyTreeNode.java‎

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package de.medizininformatikinitiative.torch.model.management;
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import de.medizininformatikinitiative.torch.model.crtdl.FieldCondition;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.stream.Stream;
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public record CopyTreeNode(FieldCondition fieldCondition,
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List<CopyTreeNode> children) {
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public CopyTreeNode(String fieldName) {
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this(new FieldCondition(fieldName, ""), new ArrayList<>());
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}
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public CopyTreeNode(String fieldName, String condition, List<CopyTreeNode> children) {
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this(new FieldCondition(fieldName, condition), children);
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}
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public CopyTreeNode(FieldCondition fieldCondition) {
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this(fieldCondition, new ArrayList<>());
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}
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public CopyTreeNode {
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Objects.requireNonNull(fieldCondition);
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children = new ArrayList<>(children); // mutable copy
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}
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public boolean isConditional() {
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return !fieldCondition.condition().isEmpty();
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}
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public String fhirPath() {
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return fieldCondition.fhirPath();
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}
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public String condition() {
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return fieldCondition.condition();
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}
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public String fieldName() {
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return fieldCondition.fieldName();
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}
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public CopyTreeNode getOrCreateChild(FieldCondition fieldCondition) {
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return getChild(fieldCondition).orElseGet(() -> {
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CopyTreeNode child = new CopyTreeNode(fieldCondition);
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children.add(child);
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return child;
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});
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}
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public Optional<CopyTreeNode> getChild(FieldCondition fieldCondition) {
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return children.stream()
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.filter(c -> c.fieldCondition.equals(fieldCondition))
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.findFirst();
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}
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/**
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* Merges this {@code CopyTreeNode} with another node, combining children while respecting
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* unconditional and conditional branches.
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* <p>
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* Merge rules:
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* <ul>
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* <li>Unconditional children (condition == "") are merged recursively.</li>
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* <li>Conditional children (condition != "") are kept unless fully covered by an
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* unconditional child with empty children.</li>
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* <li>Conditional children that are partially covered by an unconditional child
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* will keep only the remaining, uncovered children.</li>
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* <li>This merge is applied recursively for all child nodes.</li>
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* </ul>
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*
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* <p>Example:</p>
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* <pre>
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* Node a: identifier -> [] (unconditional, empty children)
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* Node b: identifier.where(type='official') -> [value]
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* Merged result: identifier -> [] (conditional branch removed)
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* </pre>
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*
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* @param other the other {@code CopyTreeNode} to merge with
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* @return a new {@code CopyTreeNode} containing the merged structure
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*/
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public CopyTreeNode merged(CopyTreeNode other) {
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// Step 0: combine unconditional children first
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List<CopyTreeNode> allChildren = new ArrayList<>();
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// Collect all unconditional children from both trees
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List<CopyTreeNode> uncondThis = this.children().stream()
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.filter(c -> c.fieldCondition.condition().isEmpty())
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.toList();
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List<CopyTreeNode> uncondOther = other.children().stream()
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.filter(c -> c.fieldCondition.condition().isEmpty())
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.toList();
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// Merge unconditional children by fieldName recursively
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List<CopyTreeNode> mergedUncond = new ArrayList<>();
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for (CopyTreeNode c : uncondThis) {
101+
CopyTreeNode match = uncondOther.stream()
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.filter(o -> o.fieldCondition.fieldName().equals(c.fieldCondition.fieldName()))
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.findFirst()
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.orElse(null);
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106+
if (match != null) {
107+
mergedUncond.add(c.merged(match));
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} else {
109+
mergedUncond.add(c);
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}
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}
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// Add unconditional children from other that were not in this
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uncondOther.stream()
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.filter(o -> mergedUncond.stream().noneMatch(m -> m.fieldCondition.fieldName().equals(o.fieldCondition.fieldName())))
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.forEach(mergedUncond::add);
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118+
allChildren.addAll(mergedUncond);
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// Step 1: handle conditional children
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List<CopyTreeNode> condChildren = Stream.concat(
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this.children().stream().filter(c -> !c.fieldCondition.condition().isEmpty()),
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other.children().stream().filter(c -> !c.fieldCondition.condition().isEmpty())
124+
).toList();
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126+
for (CopyTreeNode c : condChildren) {
127+
// Find corresponding unconditional child with same fieldName
128+
CopyTreeNode uncondMatch = mergedUncond.stream()
129+
.filter(u -> u.fieldCondition.fieldName().equals(c.fieldCondition.fieldName()))
130+
.findFirst().orElse(null);
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132+
List<CopyTreeNode> remainingChildren;
133+
if (uncondMatch != null) {
134+
// Remove any children that are already in the unconditional branch
135+
remainingChildren = c.children().stream()
136+
.filter(ch -> uncondMatch.children().stream().noneMatch(uCh -> uCh.equals(ch)))
137+
.toList();
138+
} else {
139+
remainingChildren = new ArrayList<>(c.children());
140+
}
141+
142+
if (!remainingChildren.isEmpty()) {
143+
allChildren.add(new CopyTreeNode(c.fieldCondition, remainingChildren));
144+
}
145+
}
146+
147+
return new CopyTreeNode(this.fieldCondition, allChildren);
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}
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}

‎src/main/java/de/medizininformatikinitiative/torch/model/management/ExtractionRedactionWrapper.java‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -12,21 +12,21 @@
1212
* @param resource Resource to be processed
1313
* @param profiles profiles of structure definitions of the applied groups
1414
* @param references map from elementid to reference string
15-
* @param attributes merged attributes for the extraction
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* @param copyTree merged attributes for the extraction
1616
*/
1717
public record ExtractionRedactionWrapper(DomainResource resource, Set<String> profiles,
1818
Map<String, Set<String>> references,
19-
Set<de.medizininformatikinitiative.torch.model.crtdl.annotated.AnnotatedAttribute> attributes) {
19+
CopyTreeNode copyTree) {
2020

2121
public ExtractionRedactionWrapper {
2222
Objects.requireNonNull(resource);
23+
Objects.requireNonNull(copyTree);
2324
profiles = Set.copyOf(profiles);
24-
attributes = Set.copyOf(attributes);
2525
references = Map.copyOf(references);
2626
}
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2828
public ExtractionRedactionWrapper updateWithResource(DomainResource resource) {
29-
return new ExtractionRedactionWrapper(resource, profiles, references, attributes);
29+
return new ExtractionRedactionWrapper(resource, profiles, references, copyTree);
3030
}
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3232
}

‎src/main/java/de/medizininformatikinitiative/torch/model/management/ProfileAttributeCollection.java‎

Lines changed: 0 additions & 14 deletions
This file was deleted.

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