#266 - Change validation information (#271)

* #266 - Change validation information - add mutable criterion and structured query classes that can be easily annotated during validation. Provide converters to convert immutable to mutable and vice versa - remove validatedstructuredquery - add validation issues - remove invalidCriteria from entities - rename TermCodeValidation to StructuredQueryValidation - rename getinvalidcriteria - modify tests - add skipValidation parameter to get query and get template - modify swagger file
medizininformatik-initiative · Mar 22, 2024 · e592f79 · e592f79
1 parent ca4b4e2
commit e592f79
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Showing 28 changed files with 889 additions and 359 deletions.
diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/common/api/Criterion.java b/src/main/java/de/numcodex/feasibility_gui_backend/common/api/Criterion.java
@@ -6,6 +6,7 @@
 import de.numcodex.feasibility_gui_backend.query.api.AttributeFilter;
 import de.numcodex.feasibility_gui_backend.query.api.TimeRestriction;
 import de.numcodex.feasibility_gui_backend.query.api.ValueFilter;
+import de.numcodex.feasibility_gui_backend.query.api.status.ValidationIssue;
 import lombok.Builder;
 
 import java.util.List;
@@ -17,7 +18,17 @@ public record Criterion (
     @JsonProperty("termCodes") List<TermCode> termCodes,
     @JsonProperty("attributeFilters") List<AttributeFilter> attributeFilters,
     @JsonProperty("valueFilter") ValueFilter valueFilter,
-    @JsonProperty("timeRestriction") TimeRestriction timeRestriction
+    @JsonProperty("timeRestriction") TimeRestriction timeRestriction,
+    @JsonProperty("issues") List<ValidationIssue> validationIssues
 ) {
-
+  public static Criterion createImmutableCriterion(MutableCriterion mutableCriterion) {
+    return Criterion.builder()
+        .termCodes(mutableCriterion.termCodes)
+        .context(mutableCriterion.context)
+        .attributeFilters(mutableCriterion.attributeFilters)
+        .valueFilter(mutableCriterion.valueFilter)
+        .timeRestriction(mutableCriterion.timeRestriction)
+        .validationIssues(mutableCriterion.validationIssues)
+        .build();
+  }
 }
diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/common/api/MutableCriterion.java b/src/main/java/de/numcodex/feasibility_gui_backend/common/api/MutableCriterion.java
@@ -0,0 +1,36 @@
+package de.numcodex.feasibility_gui_backend.common.api;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonInclude.Include;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import de.numcodex.feasibility_gui_backend.query.api.AttributeFilter;
+import de.numcodex.feasibility_gui_backend.query.api.TimeRestriction;
+import de.numcodex.feasibility_gui_backend.query.api.ValueFilter;
+import de.numcodex.feasibility_gui_backend.query.api.status.ValidationIssue;
+import lombok.Builder;
+import lombok.Data;
+
+import java.util.List;
+
+@JsonInclude(Include.NON_NULL)
+@Builder
+@Data
+public class MutableCriterion {
+    @JsonProperty("context") TermCode context;
+    @JsonProperty("termCodes") List<TermCode> termCodes;
+    @JsonProperty("attributeFilters") List<AttributeFilter> attributeFilters;
+    @JsonProperty("valueFilter") ValueFilter valueFilter;
+    @JsonProperty("timeRestriction") TimeRestriction timeRestriction;
+    @JsonProperty("issues") List<ValidationIssue> validationIssues;
+
+    public static MutableCriterion createMutableCriterion (Criterion criterion) {
+      return MutableCriterion.builder()
+          .termCodes(criterion.termCodes())
+          .context(criterion.context())
+          .attributeFilters(criterion.attributeFilters())
+          .valueFilter(criterion.valueFilter())
+          .timeRestriction(criterion.timeRestriction())
+          .validationIssues(criterion.validationIssues())
+          .build();
+    }
+}
diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/query/QueryHandlerService.java b/src/main/java/de/numcodex/feasibility_gui_backend/query/QueryHandlerService.java
@@ -2,7 +2,6 @@
 
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import de.numcodex.feasibility_gui_backend.common.api.Criterion;
 import de.numcodex.feasibility_gui_backend.query.api.Query;
 import de.numcodex.feasibility_gui_backend.query.api.QueryTemplate;
 import de.numcodex.feasibility_gui_backend.query.api.SavedQuery;
@@ -15,7 +14,7 @@
 import de.numcodex.feasibility_gui_backend.query.result.ResultService;
 import de.numcodex.feasibility_gui_backend.query.templates.QueryTemplateException;
 import de.numcodex.feasibility_gui_backend.query.templates.QueryTemplateHandler;
-import de.numcodex.feasibility_gui_backend.terminology.validation.TermCodeValidation;
+import de.numcodex.feasibility_gui_backend.terminology.validation.StructuredQueryValidation;
 import lombok.NonNull;
 import lombok.RequiredArgsConstructor;
 import org.springframework.dao.DataIntegrityViolationException;
@@ -61,7 +60,7 @@ public enum ResultDetail {
     private final SavedQueryRepository savedQueryRepository;
 
     @NonNull
-    private final TermCodeValidation termCodeValidation;
+    private final StructuredQueryValidation structuredQueryValidation;
 
     @NonNull
     private ObjectMapper jsonUtil;
@@ -242,35 +241,52 @@ public String getAuthorId(Long queryId) throws QueryNotFoundException {
 
     public QueryListEntry convertQueryToQueryListEntry(de.numcodex.feasibility_gui_backend.query.persistence.Query query,
                                                        boolean skipValidation) {
-        List<Criterion> invalidCriteria;
-        if (skipValidation) {
-            invalidCriteria = List.of();
-        } else {
-          try {
-            var sq = jsonUtil.readValue(query.getQueryContent().getQueryContent(), StructuredQuery.class);
-              invalidCriteria = termCodeValidation.getInvalidCriteria(sq);
-          } catch (JsonProcessingException e) {
-              invalidCriteria = List.of();
-          }
+        boolean isValid = true;
+        if (!skipValidation) {
+            try {
+                var sq = jsonUtil.readValue(query.getQueryContent().getQueryContent(), StructuredQuery.class);
+                isValid = structuredQueryValidation.isValid(sq);
+            } catch (JsonProcessingException e) {
+                isValid = false;
+            }
         }
 
         if (query.getSavedQuery() != null) {
-            return
-                QueryListEntry.builder()
-                    .id(query.getId())
-                    .label(query.getSavedQuery().getLabel())
-                    .comment(query.getSavedQuery().getComment())
-                    .totalNumberOfPatients(query.getSavedQuery().getResultSize())
-                    .createdAt(query.getCreatedAt())
-                    .invalidCriteria(invalidCriteria)
-                    .build();
+            if (skipValidation) {
+                return
+                    QueryListEntry.builder()
+                        .id(query.getId())
+                        .label(query.getSavedQuery().getLabel())
+                        .comment(query.getSavedQuery().getComment())
+                        .totalNumberOfPatients(query.getSavedQuery().getResultSize())
+                        .createdAt(query.getCreatedAt())
+                        .build();
+            } else {
+                return
+                    QueryListEntry.builder()
+                        .id(query.getId())
+                        .label(query.getSavedQuery().getLabel())
+                        .comment(query.getSavedQuery().getComment())
+                        .totalNumberOfPatients(query.getSavedQuery().getResultSize())
+                        .createdAt(query.getCreatedAt())
+                        .isValid(isValid)
+                        .build();
+            }
         } else {
-            return
-                QueryListEntry.builder()
-                    .id(query.getId())
-                    .createdAt(query.getCreatedAt())
-                    .invalidCriteria(invalidCriteria)
-                    .build();
+            if (skipValidation) {
+                return
+                    QueryListEntry.builder()
+                        .id(query.getId())
+                        .createdAt(query.getCreatedAt())
+                        .build();
+            } else {
+                return
+                    QueryListEntry.builder()
+                        .id(query.getId())
+                        .createdAt(query.getCreatedAt())
+                        .isValid(isValid)
+                        .build();
+            }
         }
     }
 

diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/query/api/MutableStructuredQuery.java b/src/main/java/de/numcodex/feasibility_gui_backend/query/api/MutableStructuredQuery.java
@@ -0,0 +1,54 @@
+package de.numcodex.feasibility_gui_backend.query.api;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonInclude.Include;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import de.numcodex.feasibility_gui_backend.common.api.Criterion;
+import de.numcodex.feasibility_gui_backend.common.api.MutableCriterion;
+import de.numcodex.feasibility_gui_backend.query.api.validation.StructuredQueryValidation;
+import lombok.Builder;
+import lombok.Data;
+
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.List;
+
+@JsonInclude(Include.NON_EMPTY)
+@Builder
+@Data
+public class MutableStructuredQuery {
+    @JsonProperty URI version;
+    @JsonProperty("inclusionCriteria") List<List<MutableCriterion>> inclusionCriteria;
+    @JsonProperty("exclusionCriteria") List<List<MutableCriterion>> exclusionCriteria;
+    @JsonProperty("display") String display;
+
+    public static MutableStructuredQuery createMutableStructuredQuery(StructuredQuery structuredQuery) {
+        List<List<MutableCriterion>> mutableInclusionCriteria = new ArrayList<>();
+        if (structuredQuery.inclusionCriteria() != null) {
+            for (List<Criterion> outerList : structuredQuery.inclusionCriteria()) {
+                List<MutableCriterion> innerList = new ArrayList<>();
+                for (Criterion criterion : outerList) {
+                    innerList.add(MutableCriterion.createMutableCriterion(criterion));
+                }
+                mutableInclusionCriteria.add(innerList);
+            }
+        }
+
+        List<List<MutableCriterion>> mutableExclusionCriteria = new ArrayList<>();
+        if (structuredQuery.exclusionCriteria() != null) {
+            for (List<Criterion> outerList : structuredQuery.exclusionCriteria()) {
+                List<MutableCriterion> innerList = new ArrayList<>();
+                for (Criterion criterion : outerList) {
+                    innerList.add(MutableCriterion.createMutableCriterion(criterion));
+                }
+                mutableExclusionCriteria.add(innerList);
+            }
+        }
+        return MutableStructuredQuery.builder()
+            .version(structuredQuery.version())
+            .inclusionCriteria(mutableInclusionCriteria)
+            .exclusionCriteria(mutableExclusionCriteria)
+            .display(structuredQuery.display())
+            .build();
+    }
+}
diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/query/api/Query.java b/src/main/java/de/numcodex/feasibility_gui_backend/query/api/Query.java
@@ -3,19 +3,15 @@
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonInclude.Include;
 import com.fasterxml.jackson.annotation.JsonProperty;
-import de.numcodex.feasibility_gui_backend.common.api.Criterion;
 import lombok.Builder;
 
-import java.util.List;
-
 @JsonInclude(Include.NON_NULL)
 @Builder
 public record Query(
     @JsonProperty long id,
     @JsonProperty StructuredQuery content,
     @JsonProperty String label,
-    @JsonProperty String comment,
-    @JsonProperty List<Criterion> invalidCriteria
+    @JsonProperty String comment
 ) {
 
 }
diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/query/api/QueryListEntry.java b/src/main/java/de/numcodex/feasibility_gui_backend/query/api/QueryListEntry.java
@@ -3,11 +3,9 @@
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonInclude.Include;
 import com.fasterxml.jackson.annotation.JsonProperty;
-import de.numcodex.feasibility_gui_backend.common.api.Criterion;
 import lombok.Builder;
 
 import java.sql.Timestamp;
-import java.util.List;
 
 @JsonInclude(Include.NON_NULL)
 @Builder
@@ -17,7 +15,7 @@ public record QueryListEntry(
     @JsonProperty String comment,
     @JsonProperty Timestamp createdAt,
     @JsonProperty Long totalNumberOfPatients,
-    @JsonProperty List<Criterion> invalidCriteria
+    @JsonProperty Boolean isValid
 )  {
 
 }
diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/query/api/QueryTemplate.java b/src/main/java/de/numcodex/feasibility_gui_backend/query/api/QueryTemplate.java
@@ -3,12 +3,9 @@
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonInclude.Include;
 import com.fasterxml.jackson.annotation.JsonProperty;
-import de.numcodex.feasibility_gui_backend.common.api.Criterion;
 import de.numcodex.feasibility_gui_backend.query.api.validation.QueryTemplateValidation;
 import lombok.Builder;
 
-import java.util.List;
-
 @JsonInclude(Include.NON_NULL)
 @QueryTemplateValidation
 @Builder
@@ -19,7 +16,6 @@ public record QueryTemplate(
     @JsonProperty String comment,
     @JsonProperty String lastModified,
     @JsonProperty String createdBy,
-    @JsonProperty List<Criterion> invalidCriteria,
     @JsonProperty Boolean isValid
 ) {
 

diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/query/api/StructuredQuery.java b/src/main/java/de/numcodex/feasibility_gui_backend/query/api/StructuredQuery.java
@@ -4,11 +4,12 @@
 import com.fasterxml.jackson.annotation.JsonInclude.Include;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import de.numcodex.feasibility_gui_backend.common.api.Criterion;
-import de.numcodex.feasibility_gui_backend.common.api.TermCode;
+import de.numcodex.feasibility_gui_backend.common.api.MutableCriterion;
 import de.numcodex.feasibility_gui_backend.query.api.validation.StructuredQueryValidation;
 import lombok.Builder;
 
 import java.net.URI;
+import java.util.ArrayList;
 import java.util.List;
 
 @JsonInclude(Include.NON_EMPTY)
@@ -20,5 +21,30 @@ public record StructuredQuery(
     @JsonProperty("exclusionCriteria") List<List<Criterion>> exclusionCriteria,
     @JsonProperty("display") String display
 ) {
+  public static StructuredQuery createImmutableStructuredQuery(MutableStructuredQuery mutableStructuredQuery) {
+    List<List<Criterion>> inclusionCriteria = new ArrayList<>();
+    for (List<MutableCriterion> outerList : mutableStructuredQuery.getInclusionCriteria()) {
+      List<Criterion> innerList = new ArrayList<>();
+      for (MutableCriterion criterion : outerList) {
+        innerList.add(Criterion.createImmutableCriterion(criterion));
+      }
+      inclusionCriteria.add(innerList);
+    }
 
+    List<List<Criterion>> exclusionCriteria = new ArrayList<>();
+    for (List<MutableCriterion> outerList : mutableStructuredQuery.getExclusionCriteria()) {
+      List<Criterion> innerList = new ArrayList<>();
+      for (MutableCriterion criterion : outerList) {
+        innerList.add(Criterion.createImmutableCriterion(criterion));
+      }
+      exclusionCriteria.add(innerList);
+    }
+
+    return StructuredQuery.builder()
+        .version(mutableStructuredQuery.getVersion())
+        .display(mutableStructuredQuery.getDisplay())
+        .inclusionCriteria(inclusionCriteria)
+        .exclusionCriteria(exclusionCriteria)
+        .build();
+  }
 }
diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/query/api/ValidatedStructuredQuery.java b/src/main/java/de/numcodex/feasibility_gui_backend/query/api/ValidatedStructuredQuery.java