#260 - Endpoint Modification for Template and savedQueries Retrieval …

…with activated Validation

- change query and template endpoints to include getting invalid terms by default
- this will most likely change when validation is extended to also include missing contexts or invalid filters

src/main/java/de/numcodex/feasibility_gui_backend/query/QueryHandlerService.java

@@ -2,6 +2,7 @@
 
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import de.numcodex.feasibility_gui_backend.common.api.TermCode;
 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;
@@ -14,6 +15,7 @@
 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 lombok.NonNull;
 import lombok.RequiredArgsConstructor;
 import org.springframework.dao.DataIntegrityViolationException;
@@ -58,6 +60,9 @@ public enum ResultDetail {
     @NonNull
     private final SavedQueryRepository savedQueryRepository;
 
+    @NonNull
+    private final TermCodeValidation termCodeValidation;
+
     @NonNull
     private ObjectMapper jsonUtil;
 
@@ -235,28 +240,44 @@ public String getAuthorId(Long queryId) throws QueryNotFoundException {
         return queryRepository.getAuthor(queryId).orElseThrow(QueryNotFoundException::new);
     }
 
-    public List<QueryListEntry> convertQueriesToQueryListEntries(List<de.numcodex.feasibility_gui_backend.query.persistence.Query> queryList) {
-        var ret = new ArrayList<QueryListEntry>();
+    public QueryListEntry convertQueryToQueryListEntry(de.numcodex.feasibility_gui_backend.query.persistence.Query query,
+                                                       boolean skipValidation) {
+        List<TermCode> invalidTermCodes;
+        if (skipValidation) {
+            invalidTermCodes = List.of();
+        } else {
+          try {
+            var sq = jsonUtil.readValue(query.getQueryContent().getQueryContent(), StructuredQuery.class);
+            invalidTermCodes = termCodeValidation.getInvalidTermCodes(sq);
+          } catch (JsonProcessingException e) {
+              invalidTermCodes = List.of();
+          }
+        }
 
-        queryList.forEach(q -> {
-            if (q.getSavedQuery() != null) {
-                ret.add(
-                        QueryListEntry.builder()
-                                .id(q.getId())
-                                .label(q.getSavedQuery().getLabel())
-                                .comment(q.getSavedQuery().getComment())
-                                .totalNumberOfPatients(q.getSavedQuery().getResultSize())
-                                .createdAt(q.getCreatedAt())
-                                .build());
-            } else {
-                ret.add(
-                        QueryListEntry.builder()
-                                .id(q.getId())
-                                .createdAt(q.getCreatedAt())
-                                .build());
-            }
-        });
+        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())
+                    .invalidTerms(invalidTermCodes)
+                    .build();
+        } else {
+            return
+                QueryListEntry.builder()
+                    .id(query.getId())
+                    .createdAt(query.getCreatedAt())
+                    .invalidTerms(invalidTermCodes)
+                    .build();
+        }
+    }
 
+    public List<QueryListEntry> convertQueriesToQueryListEntries(List<de.numcodex.feasibility_gui_backend.query.persistence.Query> queryList,
+                                                                 boolean skipValidation) {
+        var ret = new ArrayList<QueryListEntry>();
+        queryList.forEach(q -> ret.add(convertQueryToQueryListEntry(q, skipValidation)));
         return ret;
     }
 

src/main/java/de/numcodex/feasibility_gui_backend/query/api/QueryListEntry.java

@@ -3,9 +3,11 @@
 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.TermCode;
 import lombok.Builder;
 
 import java.sql.Timestamp;
+import java.util.List;
 
 @JsonInclude(Include.NON_NULL)
 @Builder
@@ -14,7 +16,8 @@ public record QueryListEntry(
     @JsonProperty String label,
     @JsonProperty String comment,
     @JsonProperty Timestamp createdAt,
-    @JsonProperty Long totalNumberOfPatients
+    @JsonProperty Long totalNumberOfPatients,
+    @JsonProperty List<TermCode> invalidTerms
 )  {
 
 }

src/main/java/de/numcodex/feasibility_gui_backend/query/v3/QueryHandlerRestController.java

@@ -185,11 +185,12 @@ private URI buildResultLocationUri(HttpServletRequest httpServletRequest,
   @GetMapping("")
   public List<QueryListEntry> getQueryList(
       @RequestParam(name = "filter", required = false) String filter,
+      @RequestParam(value = "skipValidation", required = false, defaultValue = "false") boolean skipValidation,
       Principal principal) {
     var userId = principal.getName();
     var savedOnly = (filter != null && filter.equalsIgnoreCase("saved"));
     var queryList = queryHandlerService.getQueryListForAuthor(userId, savedOnly);
-    return queryHandlerService.convertQueriesToQueryListEntries(queryList);
+    return queryHandlerService.convertQueriesToQueryListEntries(queryList, skipValidation);
   }
 
   @PostMapping("/{id}/saved")
@@ -296,7 +297,7 @@ public List<QueryListEntry> getQueryListForUser(
       @RequestParam(name = "filter", required = false) String filter) {
     var savedOnly = (filter != null && filter.equalsIgnoreCase("saved"));
     var queryList =  queryHandlerService.getQueryListForAuthor(userId, savedOnly);
-    return queryHandlerService.convertQueriesToQueryListEntries(queryList);
+    return queryHandlerService.convertQueriesToQueryListEntries(queryList, true);
   }
 
   @GetMapping("/{id}")

src/main/java/de/numcodex/feasibility_gui_backend/query/v3/QueryTemplateHandlerRestController.java

@@ -97,22 +97,31 @@ public ResponseEntity<Object> getQueryTemplate(@PathVariable(value = "queryId")
   }
 
   @GetMapping(path = "")
-  public ResponseEntity<Object> getQueryTemplates(Principal principal) {
+  public ResponseEntity<Object> getQueryTemplates(
+      @RequestParam(value = "skipValidation", required = false, defaultValue = "false") boolean skipValidation,
+      Principal principal) {
 
     var queries = queryHandlerService.getQueryTemplatesForAuthor(principal.getName());
     var ret = new ArrayList<QueryTemplate>();
     queries.forEach(q -> {
       try {
         QueryTemplate convertedQuery = queryHandlerService.convertTemplatePersistenceToApi(q);
+        List<TermCode> invalidTermCodes;
+        if (skipValidation) {
+          invalidTermCodes = List.of();
+        } else {
+          invalidTermCodes = termCodeValidation.getInvalidTermCodes(
+              convertedQuery.content());
+        }
         var convertedQueryWithoutContent = QueryTemplate.builder()
-                .id(convertedQuery.id())
-                .label(convertedQuery.label())
-                .comment(convertedQuery.comment())
-                .lastModified(convertedQuery.lastModified())
-                .createdBy(convertedQuery.createdBy())
-                .invalidTerms(convertedQuery.invalidTerms())
-                .isValid(convertedQuery.isValid())
-                .build();
+            .id(convertedQuery.id())
+            .label(convertedQuery.label())
+            .comment(convertedQuery.comment())
+            .lastModified(convertedQuery.lastModified())
+            .createdBy(convertedQuery.createdBy())
+            .invalidTerms(invalidTermCodes)
+            .isValid(convertedQuery.isValid())
+            .build();
         ret.add(convertedQueryWithoutContent);
       } catch (JsonProcessingException e) {
         log.error("Error converting query");
@@ -143,32 +152,4 @@ public ResponseEntity<Object> deleteQueryTemplate(@PathVariable(value = "queryTe
       return new ResponseEntity<>(HttpStatus.NOT_FOUND);
     }
   }
-
-  @GetMapping(path = "/validate")
-  public ResponseEntity<Object> validateTemplates(Principal principal) {
-
-    var queries = queryHandlerService.getQueryTemplatesForAuthor(principal.getName());
-    var ret = new ArrayList<QueryTemplate>();
-    queries.forEach(q -> {
-      try {
-        QueryTemplate convertedQuery = queryHandlerService.convertTemplatePersistenceToApi(q);
-        List<TermCode> invalidTermCodes = termCodeValidation.getInvalidTermCodes(
-            convertedQuery.content());
-        var convertedQueryWithoutContent = QueryTemplate.builder()
-                .id(convertedQuery.id())
-                .label(convertedQuery.label())
-                .comment(convertedQuery.comment())
-                .lastModified(convertedQuery.lastModified())
-                .createdBy(convertedQuery.createdBy())
-                .invalidTerms(invalidTermCodes)
-                .isValid(convertedQuery.isValid())
-                .build();
-        ret.add(convertedQueryWithoutContent);
-      } catch (JsonProcessingException e) {
-        log.error("Error converting query");
-      }
-    });
-    return new ResponseEntity<>(ret, HttpStatus.OK);
-  }
-
 }

src/main/resources/static/v3/api-docs/swagger.yaml

@@ -87,6 +87,13 @@ paths:
             type: string
             enum:
               - saved
+        - name: skipValidation
+          in: query
+          description: If true, do not validate the query and do not include a list of invalid terms
+          required: false
+          schema:
+            type: boolean
+            default: false
       responses:
         200:
           description: successful operation
@@ -505,6 +512,14 @@ paths:
       summary: Read list of query templates
       description: Returns the list of all query templates of the current user
       operationId: getQueryTemplateList
+      parameters:
+        - name: skipValidation
+          in: query
+          description: If true, do not validate the query and do not include a list of invalid terms
+          required: false
+          schema:
+            type: boolean
+            default: false
       responses:
         200:
           description: OK
@@ -612,27 +627,6 @@ paths:
       security:
         - feasibility_auth:
             - user
-  /query/template/validate:
-    get:
-      tags:
-        - templates
-      summary: Check all own query templates for invalid or outdated termcodes
-      description: Returns a list of query templates with the additional info if a query is valid
-      operationId: validateQueryTemplateList
-      responses:
-        200:
-          description: OK
-          content:
-            application/json:
-              schema:
-                items:
-                  $ref: '#/components/schemas/QueryTemplate'
-        401:
-          description: Unauthorized - please login first
-          content: { }
-      security:
-        - feasibility_auth:
-            - read:query
   /terminology/categories:
     get:
       tags:
@@ -817,6 +811,7 @@ components:
       required:
         - id
         - label
+        - invalidTerms
       properties:
         id:
           type: integer
@@ -830,6 +825,10 @@ components:
           format: 'date-time'
         totalNumberOfPatients:
           type: integer
+        invalidTerms:
+          type: array
+          items:
+            $ref: "#/components/schemas/TermCode"
     Query:
       type: object
       required:
@@ -912,6 +911,7 @@ components:
       type: object
       required:
         - label
+        - invalidTerms
       properties:
         id:
           type: integer
@@ -930,6 +930,13 @@ components:
         createdBy:
           type: string
           description: Keycloak id of the user who created the query
+        invalidTerms:
+          type: array
+          items:
+            $ref: "#/components/schemas/TermCode"
+        isValid:
+          type: boolean
+          description: is the query valid?
     QueryTemplate:
       type: object
       required:

src/test/java/de/numcodex/feasibility_gui_backend/query/QueryHandlerServiceIT.java

@@ -24,16 +24,17 @@
 import java.net.URI;
 import java.util.List;
 
+import de.numcodex.feasibility_gui_backend.terminology.validation.TermCodeValidation;
 import org.junit.jupiter.api.DisplayName;
 import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.EnumSource;
-import org.mockito.Spy;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase;
 import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest;
+import org.springframework.boot.test.mock.mockito.MockBean;
 import org.springframework.context.annotation.Import;
 import org.springframework.dao.DataIntegrityViolationException;
 import org.testcontainers.junit.jupiter.Testcontainers;
@@ -100,6 +101,9 @@ public class QueryHandlerServiceIT {
     @Autowired
     private QueryHashCalculator queryHashCalculator;
 
+    @MockBean
+    private TermCodeValidation termCodeValidation;
+
     @Autowired
     @Qualifier("translation")
     private ObjectMapper jsonUtil;