Add new API to fetch visualizations

annotationProcessor/src/main/java/bio/terra/tanagra/annotation/UnderlayConfigPath.java

@@ -57,6 +57,23 @@ public class UnderlayConfigPath extends AnnotationPath {
           SZPrepackagedCriteria.class,
           SZRollupCountsSql.class,
           SZVisualization.class,
+          SZVisualization.SZVisualizationDataConfig.class,
+          SZVisualization.SZVisualizationDataConfig.SZVisualizationDCSource.class,
+          SZVisualization.SZVisualizationDataConfig.SZVisualizationDCSource.SZVisualizationDCSJoin
+              .class,
+          SZVisualization.SZVisualizationDataConfig.SZVisualizationDCSource.SZVisualizationDCSJoin
+              .SZVisualizationDCSJAggregation.class,
+          SZVisualization.SZVisualizationDataConfig.SZVisualizationDCSource.SZVisualizationDCSJoin
+              .SZVisualizationDCSJAggregation.SZVisualizationDCSJAType.class,
+          SZVisualization.SZVisualizationDataConfig.SZVisualizationDCSource
+              .SZVisualizationDCSAttribute.class,
+          SZVisualization.SZVisualizationDataConfig.SZVisualizationDCSource
+              .SZVisualizationDCSAttribute.SZVisualizationDCSANumericBucketing.class,
+          SZVisualization.SZVisualizationDataConfig.SZVisualizationDCSource
+              .SZVisualizationDCSAttribute.SZVisualizationDCSANumericBucketing
+              .SZVisualizationDCSANBIntervals.class,
+          SZVisualization.SZVisualizationDataConfig.SZVisualizationDCSource
+              .SZVisualizationDCSAttribute.SZVisualizationDCSASortType.class,
           SZCorePlugin.class);
 
   @Override

docs/generated/UNDERLAY_CONFIG.md

@@ -32,6 +32,15 @@ This documentation is generated from annotations in the configuration classes.
 * [SZTextSearch](#sztextsearch)
 * [SZUnderlay](#szunderlay)
 * [SZVisualization](#szvisualization)
+* [SZVisualizationDCSANBIntervals](#szvisualizationdcsanbintervals)
+* [SZVisualizationDCSANumericBucketing](#szvisualizationdcsanumericbucketing)
+* [SZVisualizationDCSASortType](#szvisualizationdcsasorttype)
+* [SZVisualizationDCSAttribute](#szvisualizationdcsattribute)
+* [SZVisualizationDCSJAType](#szvisualizationdcsjatype)
+* [SZVisualizationDCSJAggregation](#szvisualizationdcsjaggregation)
+* [SZVisualizationDCSJoin](#szvisualizationdcsjoin)
+* [SZVisualizationDCSource](#szvisualizationdcsource)
+* [SZVisualizationDataConfig](#szvisualizationdataconfig)
 
 ## SZAttribute
 Attribute or property of an entity.
@@ -1339,6 +1348,11 @@ This file should be in the same directory as the visualization (e.g. `gender.jso
 
 If this property is specified, the value of the `config` property is ignored.
 
+### SZVisualization.dataConfigObj
+**required** [SZVisualizationDataConfig](#szvisualizationdataconfig)
+
+Deserialized configuration of the visualization. VizDataConfig protocol buffer as Java object.
+
 ### SZVisualization.name
 **required** String
 
@@ -1374,3 +1388,195 @@ Visible title of the visualization.
 
 
 
+## SZVisualizationDCSANBIntervals
+Intervals {min:1, max:5, count: 2}, creates buckets [1, 3) and [3, 5).
+
+### SZVisualizationDCSANBIntervals.count
+**required** int
+
+Count
+
+### SZVisualizationDCSANBIntervals.max
+**required** double
+
+Maximum
+
+### SZVisualizationDCSANBIntervals.min
+**required** double
+
+Minimum
+
+
+
+## SZVisualizationDCSANumericBucketing
+Converts a continuous numeric range into ids with count as the value.
+
+### SZVisualizationDCSANumericBucketing.includeLesser
+**optional** boolean
+
+Whether to create buckets for values lesser than the explicitly specified ones or ignore them
+
+### SZVisualizationDCSANumericBucketing.includeLesser
+**optional** boolean
+
+Whether to create buckets for values greater than the explicitly specified ones or ignore them
+
+### SZVisualizationDCSANumericBucketing.intervals
+**optional** [SZVisualizationDCSANBIntervals](#szvisualizationdcsanbintervals)
+
+Intervals
+
+### SZVisualizationDCSANumericBucketing.thresholds
+**required** List [ Double ]
+
+Buckets can be specified as either a list of thresholds or a range and number of buckets. For thresholds [18, 45, 65], results in two buckets [18, 45), and [45, 65). Lesser and greater buckets can be added if desired.
+
+
+
+## SZVisualizationDCSASortType
+Sort type.
+
+### SZVisualizationDCSASortType.NAME
+**required** [SZVisualizationDCSASortType](#szvisualizationdcsasorttype)
+
+Name.
+
+### SZVisualizationDCSASortType.UNKNOWN
+**required** [SZVisualizationDCSASortType](#szvisualizationdcsasorttype)
+
+Unknown.
+
+### SZVisualizationDCSASortType.VALUE
+**required** [SZVisualizationDCSASortType](#szvisualizationdcsasorttype)
+
+Value.
+
+
+
+## SZVisualizationDCSAttribute
+Attribute configuration.
+
+### SZVisualizationDCSAttribute.attribute
+**required** String
+
+The attribute to read.
+
+### SZVisualizationDCSAttribute.limit
+**optional** int
+
+Whether a limited amount of data should be returned (e.g. 10 most common conditions).
+
+### SZVisualizationDCSAttribute.numericBucketing
+**required** [SZVisualizationDCSANumericBucketing](#szvisualizationdcsanumericbucketing)
+
+Numeric Bucketing.
+
+### SZVisualizationDCSAttribute.sortDescending
+**optional** boolean
+
+Whether to sort in descending order.
+
+### SZVisualizationDCSAttribute.sortType
+**optional** [SZVisualizationDCSASortType](#szvisualizationdcsasorttype)
+
+How to sort this attribute for display. Defaults to NAME.
+
+*Default value:* `NAME`
+
+
+
+## SZVisualizationDCSJAType
+Aggregation type.
+
+### SZVisualizationDCSJAType.AVERAGE
+**required** [SZVisualizationDCSJAType](#szvisualizationdcsjatype)
+
+Average.
+
+### SZVisualizationDCSJAType.MAX
+**required** [SZVisualizationDCSJAType](#szvisualizationdcsjatype)
+
+Maximum.
+
+### SZVisualizationDCSJAType.MIN
+**required** [SZVisualizationDCSJAType](#szvisualizationdcsjatype)
+
+Minimum.
+
+### SZVisualizationDCSJAType.UNIQUE
+**required** [SZVisualizationDCSJAType](#szvisualizationdcsjatype)
+
+Unique.
+
+
+
+## SZVisualizationDCSJAggregation
+Aggregation configuration.
+
+### SZVisualizationDCSJAggregation.attribute
+**optional** String
+
+The output is always ids and values but aggregation may occur over another field (e.g. date to find the most recent value).
+
+### SZVisualizationDCSJAggregation.type
+**optional** [SZVisualizationDCSJAType](#szvisualizationdcsjatype)
+
+The type of aggregation being performed.
+
+
+
+## SZVisualizationDCSJoin
+Join configuration.
+
+### SZVisualizationDCSJoin.aggregation
+**required** [SZVisualizationDCSJAggregation](#szvisualizationdcsjaggregation)
+
+When joining an entity with an N:1 relationship (e.g. multiple weight values to a person), an aggregation is often required to make the data visualizable. For example to visualize weight vs. race, each person needs to have a single weight value associated with them, such as the average or most recent. For simple cases, simply counting unique instances of a related entity  may be sufficient (e.g. to count people with related condition occurrences).
+
+### SZVisualizationDCSJoin.entity
+**required** String
+
+The next entity to join to in order to eventually get to the entity the visualization is displaying (e.g. person when joining condition_occurences to age). 
+
+
+
+## SZVisualizationDCSource
+Configuration for a single visualization data config source.
+
+### SZVisualizationDCSource.attributes
+**required** List [ SZVisualization$SZVisualizationDataConfig$SZVisualizationDCSource$SZVisualizationDCSAttribute ]
+
+Attributes to be returned from the selected data source (e.g. condition_name from condition_occurrence or age from person). 
+
+### SZVisualizationDCSource.criteriaSelector
+**required** String
+
+Name of the criteriaSelector.
+
+### SZVisualizationDCSource.entity
+**optional** String
+
+Name of the entity (for criteria selectors that return more than one entity).
+
+### SZVisualizationDCSource.joins
+**required** List [ SZVisualization$SZVisualizationDataConfig$SZVisualizationDCSource$SZVisualizationDCSJoin ]
+
+To visualize data from different entities, the data must be joined to a common entity. Each source must specify a series of joins that ends up atthe same entity if it does not already come from that entity.
+
+### SZVisualizationDCSource.selectionData
+**optional** String
+
+Specified criteria selection. (e.g. to select conditions under diabetes)
+
+
+
+## SZVisualizationDataConfig
+Configuration for a single visualization data config.
+
+### SZVisualizationDataConfig.sources
+**required** List [ SZVisualization$SZVisualizationDataConfig$SZVisualizationDCSource ]
+
+List of data config sources for a single visualization.
+
+
+

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 +224,35 @@ 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");
+    }
+
+    List<ApiVisualization> vizList =
+        body.getVisualizationNames().stream()
+            .map(
+                vizName ->
+                    ToApiUtils.toApiObject(
+                        underlayService.getVisualization(cohort.getUnderlay(), vizName)))
+            .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());
+  }
 }