merge main

service/src/main/java/bio/terra/tanagra/app/controller/CohortsApiController.java

@@ -20,9 +20,12 @@
 import bio.terra.tanagra.generated.model.ApiCohortCloneInfo;
 import bio.terra.tanagra.generated.model.ApiCohortCountQuery;
 import bio.terra.tanagra.generated.model.ApiCohortCreateInfo;
+import bio.terra.tanagra.generated.model.ApiCohortIdVisualizationsBody;
 import bio.terra.tanagra.generated.model.ApiCohortList;
 import bio.terra.tanagra.generated.model.ApiCohortUpdateInfo;
 import bio.terra.tanagra.generated.model.ApiInstanceCountList;
+import bio.terra.tanagra.generated.model.ApiVisualization;
+import bio.terra.tanagra.generated.model.ApiVisualizationList;
 import bio.terra.tanagra.service.UnderlayService;
 import bio.terra.tanagra.service.accesscontrol.AccessControlService;
 import bio.terra.tanagra.service.accesscontrol.Permissions;
@@ -37,6 +40,7 @@
 import bio.terra.tanagra.underlay.entitymodel.Entity;
 import java.util.List;
 import java.util.stream.Collectors;
+import org.apache.commons.lang3.NotImplementedException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
@@ -220,4 +224,34 @@ public ResponseEntity<ApiInstanceCountList> queryCohortCounts(
             body.getPageSize());
     return ResponseEntity.ok(ToApiUtils.toApiObject(countQueryResult));
   }
+
+  @Override
+  public ResponseEntity<ApiVisualizationList> visualizeCohortCounts(
+      String studyId, String cohortId, ApiCohortIdVisualizationsBody body) {
+    accessControlService.checkReadAccess(studyId, List.of(cohortId), List.of());
+    Cohort cohort = cohortService.getCohort(studyId, cohortId);
+
+    accessControlService.throwIfUnauthorized(
+        SpringAuthentication.getCurrentUser(),
+        Permissions.forActions(UNDERLAY, READ),
+        ResourceId.forUnderlay(cohort.getUnderlay()));
+
+    EntityFilter cohortFilter =
+        filterBuilderService.buildFilterForCohortRevision(
+            cohort.getUnderlay(), cohort.getMostRecentRevision());
+
+    if (cohortFilter != null) {
+      // TODO(BENCH-4945): add support for charts
+      throw new NotImplementedException(
+          "visualizeCohortCounts not implemented yet for cohorts with filters");
+    }
+
+    Underlay underlay = underlayService.getUnderlay(cohort.getUnderlay());
+    List<ApiVisualization> vizList =
+        body.getVisualizationNames().parallelStream()
+            .map(id -> ToApiUtils.toApiObject(underlay.getPrecomputedVisualization(id)))
+            .toList();
+
+    return ResponseEntity.ok(new ApiVisualizationList().visualizations(vizList));
+  }
 }

service/src/main/java/bio/terra/tanagra/app/controller/objmapping/ToApiUtils.java

@@ -35,13 +35,19 @@
 import bio.terra.tanagra.generated.model.ApiStudy;
 import bio.terra.tanagra.generated.model.ApiUnderlaySummary;
 import bio.terra.tanagra.generated.model.ApiValueDisplay;
+import bio.terra.tanagra.generated.model.ApiVisualization;
+import bio.terra.tanagra.generated.model.ApiVisualizationData;
+import bio.terra.tanagra.generated.model.ApiVisualizationDataKey;
+import bio.terra.tanagra.generated.model.ApiVisualizationDataValue;
 import bio.terra.tanagra.service.artifact.model.AnnotationValue;
 import bio.terra.tanagra.service.artifact.model.Cohort;
 import bio.terra.tanagra.service.artifact.model.CohortRevision;
 import bio.terra.tanagra.service.artifact.model.Criteria;
 import bio.terra.tanagra.service.artifact.model.Study;
 import bio.terra.tanagra.underlay.Underlay;
 import bio.terra.tanagra.underlay.entitymodel.Attribute;
+import bio.terra.tanagra.underlay.visualization.Visualization;
+import bio.terra.tanagra.underlay.visualization.VisualizationData;
 import bio.terra.tanagra.utils.SqlFormatter;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -322,4 +328,31 @@ public static ApiUnderlaySummary toApiObject(Underlay underlay) {
         .description(underlay.getDescription())
         .primaryEntity(underlay.getPrimaryEntity().getName());
   }
+
+  private static ApiVisualizationData toApiObject(VisualizationData vizData) {
+    return new ApiVisualizationData()
+        .keys(
+            vizData.getKeys().stream()
+                .map(
+                    k ->
+                        new ApiVisualizationDataKey()
+                            .name(k.name())
+                            .numericId(k.numericId())
+                            .stringId(k.stringId()))
+                .toList())
+        .values(
+            vizData.getValues().stream()
+                .map(
+                    v ->
+                        new ApiVisualizationDataValue()
+                            .numeric(v.numeric())
+                            .quartiles(v.quartiles()))
+                .toList());
+  }
+
+  public static ApiVisualization toApiObject(Visualization visualization) {
+    return new ApiVisualization()
+        .name(visualization.getName())
+        .vizDataList(visualization.getVizDataList().stream().map(ToApiUtils::toApiObject).toList());
+  }
 }

service/src/main/resources/api/service_openapi.yaml

@@ -556,6 +556,40 @@ paths:
         500:
           $ref: "#/components/responses/ServerError"
 
+  "/v2/studies/{studyId}/cohorts/{cohortId}/visualizations":
+    parameters:
+    - $ref: "#/components/parameters/ParamStudyId"
+    - $ref: "#/components/parameters/ParamCohortId"
+    post:
+      summary: Return visualizations for a cohort
+      operationId: visualizeCohortCounts
+      tags: [Cohorts]
+      requestBody:
+        required: true
+        content:
+          application/json:
+            schema:
+              type: object
+              properties:
+                visualizationNames:
+                  type: array
+                  description: Names (IDs) of requested visualizations
+                  items:
+                    $ref: "#/components/schemas/VisualizationName"
+              required:
+              - visualizationNames
+      responses:
+        200:
+          description: OK
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/VisualizationList"
+        404:
+          $ref: "#/components/responses/NotFound"
+        500:
+          $ref: "#/components/responses/ServerError"
+
   # --------------- Studies: Reviews ---------------
 
   "/v2/studies/{studyId}/cohorts/{cohortId}/reviews":
@@ -2122,6 +2156,16 @@ components:
         numRowsAcrossAllPages:
           $ref: "#/components/schemas/NumRowsAcrossAllPages"
 
+
+    VisualizationList:
+      type: object
+      description: List of cohort visualizations
+      properties:
+        visualizations:
+          type: array
+          items:
+            $ref: "#/components/schemas/Visualization"
+
     DisplayHint:
       type: object
       description: Display hint for entity attribute
@@ -2364,6 +2408,68 @@ components:
       type: string
       description: Description of the cohort
 
+    Visualization:
+      type: object
+      description: Description of the Visualization
+      properties:
+        name:
+          $ref: "#/components/schemas/VisualizationName"
+        title:
+          type: string
+          description: Visualization title
+        vizDataList:
+          type: array
+          items:
+            $ref: "#/components/schemas/VisualizationData"
+      required:
+      - name
+      - title
+      - vizDataList
+
+    VisualizationName:
+      type: string
+      description: Name (ID) of the visualization, immutable
+
+    VisualizationData:
+      type: object
+      description: Visualization data for a cohort
+      properties:
+        keys:
+          type: array
+          items:
+            $ref: "#/components/schemas/VisualizationDataKey"
+        values:
+          type: array
+          items:
+            $ref: "#/components/schemas/VisualizationDataValue"
+      required:
+      - keys
+      - values
+
+    VisualizationDataKey:
+      type: object
+      description: Visualization data key
+      properties:
+        name:
+          type: string
+        numericId:
+          type: integer
+        stringId:
+          type: string
+      required:
+      - name
+
+    VisualizationDataValue:
+      type: object
+      description: Visualization data value
+      properties:
+        numeric:
+          type: integer
+        quartiles:
+          type: array
+          items:
+            type: integer
+
     FeatureSet:
       type: object
       properties:

underlay/src/main/java/bio/terra/tanagra/underlay/ConfigReader.java

@@ -18,8 +18,10 @@
 import com.google.common.collect.ImmutableMap;
 import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
 import jakarta.annotation.Nullable;
+import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -455,4 +457,14 @@ private static Pair<String, String> parseTwoPartPath(String path) {
   public static DataType deserializeDataType(@Nullable SZDataType szDataType) {
     return szDataType == null ? null : DataType.valueOf(szDataType.name());
   }
+
+  public static <T> T deserializeStringToObj(String str, Class<T> clazz) {
+    try {
+      return JacksonMapper.readFileIntoJavaObject(
+          new ByteArrayInputStream(str.getBytes(StandardCharsets.UTF_8)), clazz);
+    } catch (IOException e) {
+      throw new InvalidConfigException(
+          "Error deserializing string to class: " + clazz.getSimpleName(), e);
+    }
+  }
 }