Update visualizations to count distinct people

DataBiosphere · Dec 5, 2024 · 5ebcd7a · 5ebcd7a
1 parent 7696caf
commit 5ebcd7a
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Showing 9 changed files with 58 additions and 57 deletions.
diff --git a/ui/src/cohortReview/newReviewDialog.tsx b/ui/src/cohortReview/newReviewDialog.tsx
@@ -56,15 +56,7 @@ export function NewReviewDialog(props: NewReviewDialogProps) {
       cohort: props.cohort,
     },
     async () =>
-      (
-        await studySource.cohortCount(
-          studyId,
-          props.cohort.id,
-          undefined,
-          undefined,
-          []
-        )
-      )?.[0]?.count ?? 0
+      (await studySource.cohortCount(studyId, props.cohort.id))?.[0]?.count ?? 0
   );
 
   const cohortCount = countState.data;

diff --git a/ui/src/data/source.tsx b/ui/src/data/source.tsx
@@ -80,6 +80,14 @@ export type FilterCountValue = {
   [x: string]: DataValue;
 };
 
+export type CohortCountOptions = {
+  groupSectionId?: string;
+  groupId?: string;
+  groupByAttributes?: string[];
+  entity?: string;
+  countDistinctAttribute?: string;
+};
+
 export type PropertyMap = {
   [key: string]: string;
 };
@@ -431,10 +439,7 @@ export interface StudySource {
   cohortCount(
     studyId: string,
     cohortId: string,
-    groupSectionId?: string,
-    groupId?: string,
-    groupByAttributes?: string[],
-    entity?: string
+    options?: CohortCountOptions
   ): Promise<FilterCountValue[]>;
 
   getFeatureSetMetadata(
@@ -1344,10 +1349,7 @@ export class BackendStudySource implements StudySource {
   async cohortCount(
     studyId: string,
     cohortId: string,
-    groupSectionId?: string,
-    groupId?: string,
-    groupByAttributes?: string[],
-    entity?: string
+    options?: CohortCountOptions
   ): Promise<FilterCountValue[]> {
     let pageMarker: string | undefined;
     const instanceCounts: tanagra.InstanceCount[] = [];
@@ -1358,13 +1360,15 @@ export class BackendStudySource implements StudySource {
           studyId,
           cohortId,
           cohortCountQuery: {
-            countDistinctAttribute: undefined,
+            countDistinctAttribute: options?.countDistinctAttribute,
             groupByAttributes:
-              groupByAttributes == null ? [] : groupByAttributes,
-            criteriaGroupSectionId: groupSectionId,
-            criteriaGroupId: groupId,
+              options?.groupByAttributes == null
+                ? []
+                : options?.groupByAttributes,
+            criteriaGroupSectionId: options?.groupSectionId,
+            criteriaGroupId: options?.groupId,
             pageMarker,
-            entity,
+            entity: options?.entity,
             limit: 1000000,
           },
         })

diff --git a/ui/src/overview.tsx b/ui/src/overview.tsx
@@ -191,17 +191,7 @@ function GroupList() {
   const studySource = useStudySource();
 
   const fetchCount = useCallback(async () => {
-    return (
-      (
-        await studySource.cohortCount(
-          studyId,
-          cohort.id,
-          undefined,
-          undefined,
-          []
-        )
-      )?.[0]?.count ?? 0
-    );
+    return (await studySource.cohortCount(studyId, cohort.id))?.[0]?.count ?? 0;
   }, [studyId, cohort]);
 
   const countState = useSWRImmutable(
@@ -292,7 +282,9 @@ function ParticipantsGroupSection(props: {
     }
 
     return (
-      await studySource.cohortCount(studyId, cohort.id, backendGroupSection.id)
+      await studySource.cohortCount(studyId, cohort.id, {
+        groupSectionId: backendGroupSection.id,
+      })
     )[0].count;
   }, [studyId, cohort.id, cohort.underlayName, backendGroupSection]);
 
@@ -764,12 +756,10 @@ function ParticipantsGroup(props: {
     }
 
     return (
-      await studySource.cohortCount(
-        studyId,
-        cohort.id,
-        backendGroupSection.id,
-        backendGroup.id
-      )
+      await studySource.cohortCount(studyId, cohort.id, {
+        groupSectionId: backendGroupSection.id,
+        groupId: backendGroup.id,
+      })
     )[0].count;
   }, [
     studyId,

diff --git a/ui/src/viz/vizContainer.tsx b/ui/src/viz/vizContainer.tsx
@@ -152,21 +152,18 @@ async function fetchVizData(
       `Visualizations of ${vizSource.criteriaSelector} are not supported.`
     );
   }
-  if (vizSource.joins?.length) {
-    throw new Error("Joins are unsupported.");
+  if (vizSource.joins?.find((j) => j.entity !== "person" || j.aggregation)) {
+    throw new Error("Only unique joins to person are supported.");
   }
   if (!vizSource.attributes?.length || vizSource.attributes.length > 2) {
     throw new Error("Only 1 or 2 attributes are supported.");
   }
 
-  const fcvs = await studySource.cohortCount(
-    studyId,
-    cohort.id,
-    undefined,
-    undefined,
-    vizSource.attributes.map((a) => a.attribute),
-    entity
-  );
+  const fcvs = await studySource.cohortCount(studyId, cohort.id, {
+    groupByAttributes: vizSource.attributes.map((a) => a.attribute),
+    entity,
+    countDistinctAttribute: vizSource.joins?.length ? "person_id" : undefined,
+  });
 
   return processFilterCountValues(vizConfig, fcvs);
 }
diff --git a/underlay/src/main/proto/viz/viz_config.proto b/underlay/src/main/proto/viz/viz_config.proto
@@ -27,14 +27,14 @@ message VizConfig {
 
       message Aggregation {
         enum AggregationType {
-          UNKNOWN = 0;
+          UNIQUE = 0;
           MIN = 1;
           MAX = 2;
           AVERAGE = 3;
         }
 
         // The type of aggregation being performed.
-        AggregationType type = 1;
+        optional AggregationType type = 1;
 
         // The output is always ids and values but aggregation may occur over
         // another field (e.g. date to find the most recent value).
@@ -45,7 +45,9 @@ message VizConfig {
       // 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.
+      // 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).
       optional Aggregation aggregation = 2;
     }
 

diff --git a/underlay/src/main/resources/config/ui/omop/viz/topConditions/topConditions.json b/underlay/src/main/resources/config/ui/omop/viz/topConditions/topConditions.json
@@ -2,7 +2,11 @@
   "sources": [
     {
       "criteriaSelector": "conditions",
-      "joins": [],
+      "joins": [
+        {
+          "entity": "person"
+        }
+      ],
       "attributes": [
         {
           "attribute": "condition",

diff --git a/underlay/src/main/resources/config/ui/omop/viz/topIngredients/topIngredients.json b/underlay/src/main/resources/config/ui/omop/viz/topIngredients/topIngredients.json
@@ -2,7 +2,11 @@
   "sources": [
     {
       "criteriaSelector": "ingredients",
-      "joins": [],
+      "joins": [
+        {
+          "entity": "person"
+        }
+      ],
       "attributes": [
         {
           "attribute": "ingredient",

diff --git a/underlay/src/main/resources/config/ui/omop/viz/topMeasurements/topMeasurements.json b/underlay/src/main/resources/config/ui/omop/viz/topMeasurements/topMeasurements.json
@@ -2,7 +2,11 @@
   "sources": [
     {
       "criteriaSelector": "measurements",
-      "joins": [],
+      "joins": [
+        {
+          "entity": "person"
+        }
+      ],
       "attributes": [
         {
           "attribute": "measurement",

diff --git a/underlay/src/main/resources/config/ui/omop/viz/topProcedures/topProcedures.json b/underlay/src/main/resources/config/ui/omop/viz/topProcedures/topProcedures.json
@@ -2,7 +2,11 @@
   "sources": [
     {
       "criteriaSelector": "procedures",
-      "joins": [],
+      "joins": [
+        {
+          "entity": "person"
+        }
+      ],
       "attributes": [
         {
           "attribute": "procedure",