Rename viz_config to viz_data_config (#1146)

docs/generated/PROTOCOL_BUFFERS.md

@@ -101,17 +101,17 @@
 - [value.proto](#value-proto)
     - [Value](#tanagra-Value)
 
-- [viz/viz_config.proto](#viz_viz_config-proto)
-    - [VizConfig](#tanagra-viz-VizConfig)
-    - [VizConfig.Source](#tanagra-viz-VizConfig-Source)
-    - [VizConfig.Source.Attribute](#tanagra-viz-VizConfig-Source-Attribute)
-    - [VizConfig.Source.Attribute.NumericBucketing](#tanagra-viz-VizConfig-Source-Attribute-NumericBucketing)
-    - [VizConfig.Source.Attribute.NumericBucketing.Intervals](#tanagra-viz-VizConfig-Source-Attribute-NumericBucketing-Intervals)
-    - [VizConfig.Source.Join](#tanagra-viz-VizConfig-Source-Join)
-    - [VizConfig.Source.Join.Aggregation](#tanagra-viz-VizConfig-Source-Join-Aggregation)
+- [viz/viz_data_config.proto](#viz_viz_data_config-proto)
+    - [VizDataConfig](#tanagra-viz-VizDataConfig)
+    - [VizDataConfig.Source](#tanagra-viz-VizDataConfig-Source)
+    - [VizDataConfig.Source.Attribute](#tanagra-viz-VizDataConfig-Source-Attribute)
+    - [VizDataConfig.Source.Attribute.NumericBucketing](#tanagra-viz-VizDataConfig-Source-Attribute-NumericBucketing)
+    - [VizDataConfig.Source.Attribute.NumericBucketing.Intervals](#tanagra-viz-VizDataConfig-Source-Attribute-NumericBucketing-Intervals)
+    - [VizDataConfig.Source.Join](#tanagra-viz-VizDataConfig-Source-Join)
+    - [VizDataConfig.Source.Join.Aggregation](#tanagra-viz-VizDataConfig-Source-Join-Aggregation)
 
-    - [VizConfig.Source.Attribute.SortType](#tanagra-viz-VizConfig-Source-Attribute-SortType)
-    - [VizConfig.Source.Join.Aggregation.AggregationType](#tanagra-viz-VizConfig-Source-Join-Aggregation-AggregationType)
+    - [VizDataConfig.Source.Attribute.SortType](#tanagra-viz-VizDataConfig-Source-Attribute-SortType)
+    - [VizDataConfig.Source.Join.Aggregation.AggregationType](#tanagra-viz-VizDataConfig-Source-Join-Aggregation-AggregationType)
 
 - [Scalar Value Types](#scalar-value-types)
 
@@ -1270,31 +1270,31 @@ A single selected categorical value (e.g. {value: 1234, name: "Diabetes"
 
 
 
-<a name="viz_viz_config-proto"></a>
+<a name="viz_viz_data_config-proto"></a>
 <p align="right"><a href="#top">Top</a></p>
 
-## viz/viz_config.proto
+## viz/viz_data_config.proto
 
 
 
-<a name="tanagra-viz-VizConfig"></a>
+<a name="tanagra-viz-VizDataConfig"></a>
 
-### VizConfig
+### VizDataConfig
 The configuration of a underlay or cohort level visualization.
 
 
 | Field | Type | Label | Description |
 | ----- | ---- | ----- | ----------- |
-| sources | [VizConfig.Source](#tanagra-viz-VizConfig-Source) | repeated | The visualization must have one or two sources of data to display. |
+| sources | [VizDataConfig.Source](#tanagra-viz-VizDataConfig-Source) | repeated | The visualization must have one or two sources of data to display. |
 
 
 
 
 
 
-<a name="tanagra-viz-VizConfig-Source"></a>
+<a name="tanagra-viz-VizDataConfig-Source"></a>
 
-### VizConfig.Source
+### VizDataConfig.Source
 
 
 
@@ -1303,25 +1303,25 @@ The configuration of a underlay or cohort level visualization.
 | criteriaSelector | [string](#string) |  | The criteria selector (e.g. condition) determines which entities the data is being pulled from. |
 | selectionData | [string](#string) | optional | Configuration of the specified criteria selection (e.g. to select conditions under diabetes). |
 | entity | [string](#string) | optional | For criteria selectors that return more than one entity. |
-| joins | [VizConfig.Source.Join](#tanagra-viz-VizConfig-Source-Join) | repeated | 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 at the same entity if it does not already come from that entity. |
-| attributes | [VizConfig.Source.Attribute](#tanagra-viz-VizConfig-Source-Attribute) | repeated | Which attributes should be returned from the selected data source (e.g. condition_name from condition_occurrence or age from person). |
+| joins | [VizDataConfig.Source.Join](#tanagra-viz-VizDataConfig-Source-Join) | repeated | 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 at the same entity if it does not already come from that entity. |
+| attributes | [VizDataConfig.Source.Attribute](#tanagra-viz-VizDataConfig-Source-Attribute) | repeated | Which attributes should be returned from the selected data source (e.g. condition_name from condition_occurrence or age from person). |
 
 
 
 
 
 
-<a name="tanagra-viz-VizConfig-Source-Attribute"></a>
+<a name="tanagra-viz-VizDataConfig-Source-Attribute"></a>
 
-### VizConfig.Source.Attribute
+### VizDataConfig.Source.Attribute
 
 
 
 | Field | Type | Label | Description |
 | ----- | ---- | ----- | ----------- |
 | attribute | [string](#string) |  | The attribute to read. |
-| numeric_bucketing | [VizConfig.Source.Attribute.NumericBucketing](#tanagra-viz-VizConfig-Source-Attribute-NumericBucketing) |  |  |
-| sort_type | [VizConfig.Source.Attribute.SortType](#tanagra-viz-VizConfig-Source-Attribute-SortType) | optional | How to sort this attribute for display. Defaults to NAME. |
+| numeric_bucketing | [VizDataConfig.Source.Attribute.NumericBucketing](#tanagra-viz-VizDataConfig-Source-Attribute-NumericBucketing) |  |  |
+| sort_type | [VizDataConfig.Source.Attribute.SortType](#tanagra-viz-VizDataConfig-Source-Attribute-SortType) | optional | How to sort this attribute for display. Defaults to NAME. |
 | sort_descending | [bool](#bool) | optional | Whether to sort in descending order. |
 | limit | [int64](#int64) | optional | Whether a limited amount of data should be returned (e.g. 10 most common conditions). |
 
@@ -1330,16 +1330,16 @@ The configuration of a underlay or cohort level visualization.
 
 
 
-<a name="tanagra-viz-VizConfig-Source-Attribute-NumericBucketing"></a>
+<a name="tanagra-viz-VizDataConfig-Source-Attribute-NumericBucketing"></a>
 
-### VizConfig.Source.Attribute.NumericBucketing
+### VizDataConfig.Source.Attribute.NumericBucketing
 Converts a continuous numeric range into ids with count as the value.
 
 
 | Field | Type | Label | Description |
 | ----- | ---- | ----- | ----------- |
 | thresholds | [double](#double) | repeated | 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. |
-| intervals | [VizConfig.Source.Attribute.NumericBucketing.Intervals](#tanagra-viz-VizConfig-Source-Attribute-NumericBucketing-Intervals) | optional |  |
+| intervals | [VizDataConfig.Source.Attribute.NumericBucketing.Intervals](#tanagra-viz-VizDataConfig-Source-Attribute-NumericBucketing-Intervals) | optional |  |
 | includeLesser | [bool](#bool) | optional | Whether to create buckets for values outside of the explicitly specified ones or ignore them. |
 | includeGreater | [bool](#bool) | optional |  |
 
@@ -1348,9 +1348,9 @@ Converts a continuous numeric range into ids with count as the value.
 
 
 
-<a name="tanagra-viz-VizConfig-Source-Attribute-NumericBucketing-Intervals"></a>
+<a name="tanagra-viz-VizDataConfig-Source-Attribute-NumericBucketing-Intervals"></a>
 
-### VizConfig.Source.Attribute.NumericBucketing.Intervals
+### VizDataConfig.Source.Attribute.NumericBucketing.Intervals
 For intervals {min:1, max:5, count: 2}, creates two buckets [1, 3)
 and [3, 5).
 
@@ -1366,31 +1366,31 @@ and [3, 5).
 
 
 
-<a name="tanagra-viz-VizConfig-Source-Join"></a>
+<a name="tanagra-viz-VizDataConfig-Source-Join"></a>
 
-### VizConfig.Source.Join
+### VizDataConfig.Source.Join
 
 
 
 | Field | Type | Label | Description |
 | ----- | ---- | ----- | ----------- |
 | entity | [string](#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). |
-| aggregation | [VizConfig.Source.Join.Aggregation](#tanagra-viz-VizConfig-Source-Join-Aggregation) | optional | 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). |
+| aggregation | [VizDataConfig.Source.Join.Aggregation](#tanagra-viz-VizDataConfig-Source-Join-Aggregation) | optional | 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). |
 
 
 
 
 
 
-<a name="tanagra-viz-VizConfig-Source-Join-Aggregation"></a>
+<a name="tanagra-viz-VizDataConfig-Source-Join-Aggregation"></a>
 
-### VizConfig.Source.Join.Aggregation
+### VizDataConfig.Source.Join.Aggregation
 
 
 
 | Field | Type | Label | Description |
 | ----- | ---- | ----- | ----------- |
-| type | [VizConfig.Source.Join.Aggregation.AggregationType](#tanagra-viz-VizConfig-Source-Join-Aggregation-AggregationType) | optional | The type of aggregation being performed. |
+| type | [VizDataConfig.Source.Join.Aggregation.AggregationType](#tanagra-viz-VizDataConfig-Source-Join-Aggregation-AggregationType) | optional | The type of aggregation being performed. |
 | attribute | [string](#string) | optional | The output is always ids and values but aggregation may occur over another field (e.g. date to find the most recent value). |
 
 
@@ -1400,9 +1400,9 @@ and [3, 5).
 
 
 
-<a name="tanagra-viz-VizConfig-Source-Attribute-SortType"></a>
+<a name="tanagra-viz-VizDataConfig-Source-Attribute-SortType"></a>
 
-### VizConfig.Source.Attribute.SortType
+### VizDataConfig.Source.Attribute.SortType
 
 
 | Name | Number | Description |
@@ -1413,9 +1413,9 @@ and [3, 5).
 
 
 
-<a name="tanagra-viz-VizConfig-Source-Join-Aggregation-AggregationType"></a>
+<a name="tanagra-viz-VizDataConfig-Source-Join-Aggregation-AggregationType"></a>
 
-### VizConfig.Source.Join.Aggregation.AggregationType
+### VizDataConfig.Source.Join.Aggregation.AggregationType
 
 
 | Name | Number | Description |

docs/generated/UNDERLAY_CONFIG.md

@@ -1328,7 +1328,7 @@ Configuration for a single visualization.
 ### SZVisualization.dataConfig
 **required** String
 
-Serialized configuration of the visualization. VizConfig protocol buffer as JSON.
+Serialized configuration of the visualization. VizDataConfig protocol buffer as JSON.
 
 ### SZVisualization.dataConfigFile
 **required** String

ui/src/tanagra-underlay/underlayConfig.ts

@@ -37,7 +37,7 @@ export enum SZCorePlugin {
   SURVEY = "SURVEY",
   TEXT_SEARCH = "TEXT_SEARCH",
   UNHINTED_VALUE = "UNHINTED_VALUE",
-};
+}
 
 export type SZCriteriaOccurrence = {
   criteriaEntity: string;
@@ -88,7 +88,7 @@ export enum SZDataType {
   INT64 = "INT64",
   STRING = "STRING",
   TIMESTAMP = "TIMESTAMP",
-};
+}
 
 export type SZDataflow = {
   dataflowLocation: string;

ui/src/viz/viz.ts

@@ -1,7 +1,7 @@
 import { VALUE_SUFFIX } from "data/configuration";
 import { FilterCountValue } from "data/source";
 import { compareDataValues } from "data/types";
-import * as vizProto from "proto/viz/viz_config";
+import * as vizProto from "proto/viz/viz_data_config";
 import { useMemo } from "react";
 import { isValid } from "util/valid";
 
@@ -48,10 +48,10 @@ export type VizDataFormat = {
 };
 
 export function processFilterCountValues(
-  vizConfig: vizProto.VizConfig,
+  vizDataConfig: vizProto.VizDataConfig,
   fcvs: FilterCountValue[]
 ): VizData[] {
-  const vizSource = vizConfig.sources[0];
+  const vizSource = vizDataConfig.sources[0];
 
   const dataMap = new Map<string, VizData>();
   fcvs.forEach((d) => {
@@ -149,11 +149,13 @@ export function processFilterCountValues(
       if (!attrib.numericBucketing) {
         if (
           !attrib.sortType ||
-          attrib.sortType === vizProto.VizConfig_Source_Attribute_SortType.NAME
+          attrib.sortType ===
+            vizProto.VizDataConfig_Source_Attribute_SortType.NAME
         ) {
           sortValue = compareDataValues(a.keys[i].name, b.keys[i].name);
         } else if (
-          attrib.sortType === vizProto.VizConfig_Source_Attribute_SortType.VALUE
+          attrib.sortType ===
+          vizProto.VizDataConfig_Source_Attribute_SortType.VALUE
         ) {
           sortValue = compareDataValues(
             a.values[i].numeric,

ui/src/viz/vizContainer.tsx

@@ -11,7 +11,7 @@ import { useCohort, useStudyId } from "hooks";
 import emptyImage from "images/empty.svg";
 import { GridBox, GridBoxPaper } from "layout/gridBox";
 import GridLayout from "layout/gridLayout";
-import * as configProto from "proto/viz/viz_config";
+import * as configProto from "proto/viz/viz_data_config";
 import { useMemo, useState } from "react";
 import useSWRImmutable from "swr/immutable";
 import { getVizPlugin, processFilterCountValues, VizData } from "viz/viz";
@@ -24,7 +24,7 @@ type UnparsedConfig = {
 };
 
 type ParsedConfig = {
-  dataConfig: configProto.VizConfig;
+  dataConfig: configProto.VizDataConfig;
   plugin: string;
   pluginConfig: object;
   title: string;
@@ -45,7 +45,7 @@ export function VizContainer(props: VizContainerProps) {
   const config = useMemo(
     (): ParsedConfig => ({
       ...props.config,
-      dataConfig: configProto.VizConfig.fromJSON(
+      dataConfig: configProto.VizDataConfig.fromJSON(
         JSON.parse(props.config.dataConfig)
       ),
       pluginConfig: JSON.parse(props.config.pluginConfig ?? "{}"),
@@ -134,16 +134,16 @@ const selectorToEntity: { [key: string]: string } = {
   measurements: "measurementOccurrence",
 };
 async function fetchVizData(
-  vizConfig: configProto.VizConfig,
+  vizDataConfig: configProto.VizDataConfig,
   studySource: StudySource,
   studyId: string,
   cohort: Cohort
 ): Promise<VizData[]> {
-  const vizSource = vizConfig.sources[0];
+  const vizSource = vizDataConfig.sources[0];
 
   // TODO(tjennison): Remove these limitations once the backend sufficiently
   // supports the query generation.
-  if (!vizSource || vizConfig.sources.length > 1) {
+  if (!vizSource || vizDataConfig.sources.length > 1) {
     throw new Error("Only 1 visualization source is supported.");
   }
   const entity = selectorToEntity[vizSource.criteriaSelector];
@@ -165,5 +165,5 @@ async function fetchVizData(
     countDistinctAttribute: vizSource.joins?.length ? "person_id" : undefined,
   });
 
-  return processFilterCountValues(vizConfig, fcvs);
+  return processFilterCountValues(vizDataConfig, fcvs);
 }

underlay/src/main/java/bio/terra/tanagra/underlay/serialization/SZVisualization.java

@@ -20,7 +20,7 @@ public class SZVisualization {
   @AnnotatedField(
       name = "SZVisualization.dataConfig",
       markdown =
-          "Serialized configuration of the visualization. VizConfig protocol buffer as JSON.")
+          "Serialized configuration of the visualization. VizDataConfig protocol buffer as JSON.")
   public String dataConfig;
 
   @AnnotatedField(

underlay/src/main/proto/viz/viz_config.proto → underlay/src/main/proto/viz/viz_data_config.proto

@@ -6,7 +6,7 @@ option java_package = "bio.terra.tanagra.proto.viz";
 option java_outer_classname = "Viz";
 
 // The configuration of a underlay or cohort level visualization.
-message VizConfig {
+message VizDataConfig {
   message Source {
     // The criteria selector (e.g. condition) determines which entities the data
     // is being pulled from.