#401 - Update sq2cql and validate time restrictions (#402)

* #401 - Update sq2cql and validate time restrictions - update sq2cql to 0.6.0 - check if timerestrictions are correct (before date is after afterdate) - add new error code for invalid timerestrictin
medizininformatik-initiative · Nov 28, 2024 · 6233eb8 · 6233eb8
1 parent 5e401f3
commit 6233eb8
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Showing 4 changed files with 74 additions and 2 deletions.
diff --git a/pom.xml b/pom.xml
@@ -213,7 +213,7 @@
     <dependency>
       <groupId>de.medizininformatik-initiative</groupId>
       <artifactId>sq2cql</artifactId>
-      <version>0.5.0</version>
+      <version>0.6.0</version>
     </dependency>
 
     <dependency>

diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/query/api/status/ValidationIssue.java b/src/main/java/de/numcodex/feasibility_gui_backend/query/api/status/ValidationIssue.java
@@ -7,7 +7,8 @@
 @Slf4j
 @JsonSerialize(using = ValidationIssueSerializer.class)
 public enum ValidationIssue {
-  TERMCODE_CONTEXT_COMBINATION_INVALID(20001, "The combination of context and termcode(s) is not found.");
+  TERMCODE_CONTEXT_COMBINATION_INVALID(20001, "The combination of context and termcode(s) is not found."),
+  TIMERESTRICTION_INVALID(20002, "The TimeRestriction is invalid. 'beforeDate' must not be before 'afterDate'");
 
   private static final ValidationIssue[] VALUES;
 

diff --git a/...de/numcodex/feasibility_gui_backend/terminology/validation/StructuredQueryValidation.java b/...de/numcodex/feasibility_gui_backend/terminology/validation/StructuredQueryValidation.java
@@ -5,8 +5,11 @@
 import de.numcodex.feasibility_gui_backend.common.api.TermCode;
 import de.numcodex.feasibility_gui_backend.query.api.MutableStructuredQuery;
 import de.numcodex.feasibility_gui_backend.query.api.StructuredQuery;
+import de.numcodex.feasibility_gui_backend.query.api.TimeRestriction;
 import de.numcodex.feasibility_gui_backend.query.api.status.ValidationIssue;
 import de.numcodex.feasibility_gui_backend.terminology.TerminologyService;
+
+import java.time.LocalDate;
 import java.util.List;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -86,6 +89,10 @@ private void annotateCriteria(List<MutableCriterion> criteria, boolean skipValid
         criterion.setValidationIssues(List.of(ValidationIssue.TERMCODE_CONTEXT_COMBINATION_INVALID));
         continue;
       }
+      if (isTimeRestrictionInvalid(criterion.getTimeRestriction())) {
+        criterion.setValidationIssues(List.of(ValidationIssue.TIMERESTRICTION_INVALID));
+        continue;
+      }
       for (TermCode termCode : criterion.getTermCodes()) {
         if (terminologyService.isExistingTermCode(termCode.system(), termCode.code())) {
           log.trace("termcode ok: {} - {}", termCode.system(), termCode.code());
@@ -103,6 +110,11 @@ private boolean containsInvalidCriteria(List<Criterion> criteria) {
       if (criterion.context() == null) {
         return true;
       }
+      if (isTimeRestrictionInvalid(criterion.timeRestriction())) {
+        log.debug("TimeRestriction invalid. 'beforeDate' ({}) must be after 'afterDate' ({}) but is not",
+            criterion.timeRestriction().beforeDate(), criterion.timeRestriction().afterDate());
+        return true;
+      }
       for (TermCode termCode : criterion.termCodes()) {
         if (terminologyService.isExistingTermCode(termCode.system(), termCode.code())) {
           log.trace("termcode ok: {} - {}", termCode.system(), termCode.code());
@@ -115,4 +127,12 @@ private boolean containsInvalidCriteria(List<Criterion> criteria) {
     }
     return false;
   }
+
+  private boolean isTimeRestrictionInvalid(TimeRestriction timeRestriction) {
+    // If no timeRestriction is set, it is not invalid
+    if (timeRestriction == null) {
+      return false;
+    }
+    return LocalDate.parse(timeRestriction.beforeDate()).isBefore(LocalDate.parse(timeRestriction.afterDate()));
+  }
 }
diff --git a/...umcodex/feasibility_gui_backend/terminology/validation/StructuredQueryValidationTest.java b/...umcodex/feasibility_gui_backend/terminology/validation/StructuredQueryValidationTest.java
@@ -3,6 +3,7 @@
 import de.numcodex.feasibility_gui_backend.common.api.Criterion;
 import de.numcodex.feasibility_gui_backend.common.api.TermCode;
 import de.numcodex.feasibility_gui_backend.query.api.StructuredQuery;
+import de.numcodex.feasibility_gui_backend.query.api.TimeRestriction;
 import de.numcodex.feasibility_gui_backend.terminology.TerminologyService;
 import org.jetbrains.annotations.NotNull;
 import org.junit.jupiter.api.BeforeEach;
@@ -62,6 +63,13 @@ void testIsValid_falseOnMissingContext() {
         assertFalse(isValid);
     }
 
+    @Test
+    void testIsValid_falseOnInvalidTimeRestriction() {
+        var isValid = structuredQueryValidation.isValid(createStructuredQueryWithInvalidTimeRestriction());
+
+        assertFalse(isValid);
+    }
+
     @ParameterizedTest
     @CsvSource({"true,true", "true,false", "false,true", "false,false"})
     void testAnnotateStructuredQuery_emptyIssuesOnValidCriteriaOrSkippedValidation(String withExclusionCriteriaString, String skipValidationString) {
@@ -106,6 +114,18 @@ void testAnnotateStructuredQuery_nonEmptyIssuesOnMissingContext(boolean skipVali
         }
     }
 
+    @ParameterizedTest
+    @ValueSource(booleans = {true, false})
+    void testAnnotateStructuredQuery_nonEmptyIssuesOnInvalidTimeRestriction(boolean skipValidation) {
+        var annotatedStructuredQuery = structuredQueryValidation.annotateStructuredQuery(createStructuredQueryWithInvalidTimeRestriction(), skipValidation);
+
+        if (skipValidation) {
+            assertTrue(annotatedStructuredQuery.inclusionCriteria().get(0).get(0).validationIssues().isEmpty());
+        } else {
+            assertFalse(annotatedStructuredQuery.inclusionCriteria().get(0).get(0).validationIssues().isEmpty());
+        }
+    }
+
     @NotNull
     private static StructuredQuery createValidStructuredQuery(boolean withExclusionCriteria) {
         var context = TermCode.builder()
@@ -150,4 +170,35 @@ private static StructuredQuery createStructuredQueryWithoutContext() {
             .display("foo")
             .build();
     }
+
+    @NotNull
+    private static StructuredQuery createStructuredQueryWithInvalidTimeRestriction() {
+        var context = TermCode.builder()
+            .code("Laboruntersuchung")
+            .system("fdpg.mii.cds")
+            .display("Laboruntersuchung")
+            .version("1.0.0")
+            .build();
+        var termCode = TermCode.builder()
+            .code("19113-0")
+            .system("http://loinc.org")
+            .display("IgE")
+            .build();
+        var timeRestriction = TimeRestriction.builder()
+            .afterDate("1998-05-09")
+            .beforeDate("1991-06-15")
+            .build();
+        var criterion = Criterion.builder()
+            .termCodes(List.of(termCode))
+            .context(context)
+            .attributeFilters(List.of())
+            .timeRestriction(timeRestriction)
+            .build();
+        return StructuredQuery.builder()
+            .version(URI.create("http://to_be_decided.com/draft-2/schema#"))
+            .inclusionCriteria(List.of(List.of(criterion)))
+            .exclusionCriteria(List.of())
+            .display("foo")
+            .build();
+    }
 }