Query by Sets

packages/app/src/App.tsx

@@ -17,6 +17,7 @@ import { configAtom } from './atoms/configAtoms';
 import { queryParamAtom } from './atoms/queryParamAtom';
 import { getMultinetSession } from './api/session';
 
+/** @jsxImportSource @emotion/react */
 // eslint-disable-next-line @typescript-eslint/no-unused-vars
 
 const defaultVisibleSets = 6;

packages/core/src/convertConfig.ts

@@ -3,7 +3,7 @@ import {
   SortByOrder, SortVisibleBy, UpsetConfig,
   AttributePlots,
   ElementSelection,
-  AltText,
+  AltText, SetQuery,
 } from './types';
 import { isUpsetConfig } from './typecheck';
 import { DefaultConfig } from './defaultConfig';
@@ -60,6 +60,79 @@ type Version0_1_0 = {
     userAltText: AltText | null;
 }
 
+type Version0_1_1 = {
+  plotInformation: PlotInformation;
+  horizontal: boolean;
+  firstAggregateBy: AggregateBy;
+  firstOverlapDegree: number;
+  secondAggregateBy: AggregateBy;
+  secondOverlapDegree: number;
+  sortVisibleBy: SortVisibleBy;
+  sortBy: string;
+  sortByOrder: SortByOrder;
+  filters: {
+    maxVisible: number;
+    minVisible: number;
+    hideEmpty: boolean;
+    hideNoSet: boolean;
+  };
+  visibleSets: ColumnName[];
+  visibleAttributes: ColumnName[];
+  attributePlots: AttributePlots;
+  bookmarks: Bookmark[];
+  collapsed: string[];
+  plots: {
+    scatterplots: Scatterplot[];
+    histograms: Histogram[];
+  };
+  allSets: Column[];
+  selected: Row | null;
+  elementSelection: ElementSelection | null;
+  version: '0.1.1';
+  useUserAlt: boolean;
+  userAltText: AltText | null;
+  intersectionSizeLabels: boolean;
+  setSizeLabels: boolean;
+  showHiddenSets: boolean;
+}
+
+type Version0_1_2 = {
+  plotInformation: PlotInformation;
+  horizontal: boolean;
+  firstAggregateBy: AggregateBy;
+  firstOverlapDegree: number;
+  secondAggregateBy: AggregateBy;
+  secondOverlapDegree: number;
+  sortVisibleBy: SortVisibleBy;
+  sortBy: string;
+  sortByOrder: SortByOrder;
+  filters: {
+    maxVisible: number;
+    minVisible: number;
+    hideEmpty: boolean;
+    hideNoSet: boolean;
+  };
+  visibleSets: ColumnName[];
+  visibleAttributes: ColumnName[];
+  attributePlots: AttributePlots;
+  bookmarks: Bookmark[];
+  collapsed: string[];
+  plots: {
+    scatterplots: Scatterplot[];
+    histograms: Histogram[];
+  };
+  allSets: Column[];
+  selected: Row | null;
+  elementSelection: ElementSelection | null;
+  version: '0.1.2';
+  useUserAlt: boolean;
+  userAltText: AltText | null;
+  intersectionSizeLabels: boolean;
+  setSizeLabels: boolean;
+  showHiddenSets: boolean;
+  setQuery: SetQuery | null;
+}
+
 /**
  * Config type before versioning was implemented.
  */
@@ -98,14 +171,27 @@ type PreVersionConfig = {
  * @returns The converted config.
  */
 // eslint-disable-next-line camelcase
-function convert0_1_0(config: Version0_1_0): UpsetConfig {
-  (config as unknown as UpsetConfig).version = '0.1.1';
-  (config as unknown as UpsetConfig).intersectionSizeLabels = DefaultConfig.intersectionSizeLabels;
-  (config as unknown as UpsetConfig).setSizeLabels = DefaultConfig.setSizeLabels;
-  (config as unknown as UpsetConfig).showHiddenSets = DefaultConfig.showHiddenSets;
-  return (config as unknown as UpsetConfig);
+function convert0_1_0(config: Version0_1_0): Version0_1_1 {
+  (config as unknown as Version0_1_1).version = '0.1.1';
+  (config as unknown as Version0_1_1).intersectionSizeLabels = DefaultConfig.intersectionSizeLabels;
+  (config as unknown as Version0_1_1).setSizeLabels = DefaultConfig.setSizeLabels;
+  (config as unknown as Version0_1_1).showHiddenSets = DefaultConfig.showHiddenSets;
+  return (config as unknown as Version0_1_1);
 }
 
+/**
+ * Converts a configuration object from version 0.1.1 to version 0.1.2.
+ *
+ * @param config - The configuration object of version 0.1.1 to be converted.
+ * @returns The updated configuration object with version 0.1.2.
+ */
+function convert0_1_1(config: Version0_1_1): UpsetConfig {
+  (config as unknown as Version0_1_2).version = '0.1.2';
+  (config as unknown as Version0_1_2).setQuery = DefaultConfig.setQuery;
+  return config as unknown as Version0_1_2;
+}
+
+
 /**
  * Converts a pre-versioned config to the current version.
  * @param config The config to convert.
@@ -150,12 +236,11 @@ export function convertConfig(config: unknown): UpsetConfig {
   switch ((config as {version: string}).version) {
     case '0.1.0':
       convert0_1_0(config as Version0_1_0);
-      break;
+    case '0.1.1':
+      convert0_1_1(config as Version0_1_1);
     default:
       void 0;
   }
-  /* eslint-enable no-fallthrough */
-  /* eslint-enable no-void */
 
   if (!isUpsetConfig(config)) {
     // eslint-disable-next-line no-console

packages/core/src/defaultConfig.ts

@@ -10,7 +10,7 @@ export const DefaultConfig: UpsetConfig = {
     title: null,
   },
   horizontal: false,
-  firstAggregateBy: 'None',
+  firstAggregateBy: 'Degree',
   firstOverlapDegree: 2,
   secondAggregateBy: 'None',
   secondOverlapDegree: 2,
@@ -37,8 +37,12 @@ export const DefaultConfig: UpsetConfig = {
   useUserAlt: false,
   userAltText: null,
   elementSelection: null,
-  version: '0.1.1',
+  version: '0.1.2',
   intersectionSizeLabels: true,
   setSizeLabels: true,
   showHiddenSets: true,
+  setQuery: {
+    name: '',
+    query: {},
+  },
 };

packages/core/src/render.ts

@@ -2,16 +2,56 @@ import { firstAggregation, secondAggregation } from './aggregate';
 import { filterRows } from './filter';
 import { getSubsets } from './process';
 import { sortRows } from './sort';
-import { areRowsAggregates, isRowAggregate } from './typeutils';
+import { areRowsAggregates, getBelongingSetsFromSetMembership, isPopulatedSetQuery, isRowAggregate } from './typeutils';
 import {
-  Row, Rows, Sets, UpsetConfig,
+  Row, Rows, SetQueryMembership, Sets, UpsetConfig,
 } from './types';
 
 /**
  * Maps Row IDs to Row objects
  */
 export type RowMap = Record<string, Row>;
 
+/**
+ * Represents a row to be rendered.
+ * 
+ * @typedef {Object} RenderRow
+ * @property {string} id - The unique identifier for the row.
+ * @property {Row} row - The row data to be rendered.
+ */
+export type RenderRow = {
+  id: string;
+  row: Row;
+};
+
+/**
+ * Flattens a hierarchical structure of rows into a flat array of RenderRow objects.
+ *
+ * @param rows - The hierarchical structure of rows to flatten.
+ * @param flattenedRows - The array to store the flattened rows (optional, defaults to an empty array).
+ * @param idPrefix - The prefix to add to the IDs of the flattened rows (optional, defaults to an empty string).
+ * @returns The flattened array of RenderRow objects.
+ */
+const flattenRows = (
+  rows: Rows,
+  flattenedRows: RenderRow[] = [],
+  idPrefix: string = '',
+): RenderRow[] => {
+  rows.order.forEach((rowId) => {
+    const row = rows.values[rowId];
+    const prefix = idPrefix + row.id;
+    flattenedRows.push({
+      id: prefix,
+      row,
+    });
+    if (isRowAggregate(row)) {
+      flattenRows(row.items, flattenedRows, prefix);
+    }
+  });
+
+  return flattenedRows;
+};
+
 /**
  * Calculates the first aggregation for the given data and state.
  * @param data - The data object containing items, sets, and attribute columns.
@@ -58,18 +98,49 @@ const secondAggRR = (data: any, state: UpsetConfig) => {
   return rr;
 };
 
+function getQueryResult(r: Rows, membership: SetQueryMembership): Rows {
+  const queryResults: Rows = { order: [], values: {} };
+  flattenRows(r).forEach((rr) => {
+    let match = true;
+    Object.entries(membership).forEach(([set, status]) => {
+      if (status === 'Yes' && !getBelongingSetsFromSetMembership(rr.row.setMembership).includes(set)) {
+        match = false;
+      }
+      if (status === 'No' && getBelongingSetsFromSetMembership(rr.row.setMembership).includes(set)) {
+        match = false;
+      }
+    });
+
+    if (match) {
+      queryResults.order.push(rr.id);
+      queryResults.values[rr.id] = rr.row;
+    }
+  });
+
+  return queryResults;
+}
+
 /**
  * Sorts the data by RR (Relative Risk) based on the provided state configuration.
  *
  * @param data - The data to be sorted.
  * @param state - The state configuration containing the visible sets and sorting options.
+ * @param ignoreQuery - Whether to ignore the query when sorting the data. Set this to true to get the sorted rows as if there was no query.
  * @returns The sorted rows based on the RR and the provided sorting options.
  */
-const sortByRR = (data: any, state: UpsetConfig) => {
+const sortByRR = (data: any, state: UpsetConfig, ignoreQuery = false) => {
   if (!data || typeof data !== 'object' || !Object.hasOwn(data, 'sets')) return { order: [], values: {} };
 
   const vSets: Sets = Object.fromEntries(Object.entries(data.sets as Sets).filter(([name, _set]) => state.visibleSets.includes(name)));
-  const rr = secondAggRR(data, state);
+
+  let rr: Rows;
+
+  if (!ignoreQuery && state.setQuery !== null && isPopulatedSetQuery(state.setQuery)) {
+    const subsets: Rows = getSubsets(data.items, data.sets, state.visibleSets, data.attributeColumns);
+    rr = getQueryResult(subsets, state.setQuery.query);
+  } else {
+    rr = secondAggRR(data, state);
+  }
 
   return sortRows(rr, state.sortBy, state.sortVisibleBy, vSets, state.sortByOrder);
 };
@@ -79,10 +150,11 @@ const sortByRR = (data: any, state: UpsetConfig) => {
  *
  * @param data - The data to be filtered.
  * @param state - The state object containing the Upset configuration.
+ * @param ignoreQuery - Whether to ignore the query when filtering the data. Set this to true to get the filtered rows as if there was no query.
  * @returns The filtered rows based on the RR algorithm and the provided filters.
  */
-const filterRR = (data: any, state: UpsetConfig) => {
-  const rr = sortByRR(data, state);
+const filterRR = (data: any, state: UpsetConfig, ignoreQuery = false) => {
+  const rr = sortByRR(data, state, ignoreQuery);
 
   return filterRows(rr, state.filters);
 };
@@ -91,42 +163,10 @@ const filterRR = (data: any, state: UpsetConfig) => {
  * Retrieves the rows of data based on the provided data and state.
  * @param data - The data to filter.
  * @param state - The state of the UpsetConfig.
+ * @param ignoreQuery - Whether to ignore the query when filtering the data. Set this to true to get the filtered rows as if there was no query.
  * @returns The filtered rows of data.
  */
-export const getRows = (data: any, state: UpsetConfig) => filterRR(data, state);
-
-export type RenderRow = {
-  id: string;
-  row: Row;
-};
-
-/**
- * Flattens a hierarchical structure of rows into a flat array of RenderRow objects.
- *
- * @param rows - The hierarchical structure of rows to flatten.
- * @param flattenedRows - The array to store the flattened rows (optional, defaults to an empty array).
- * @param idPrefix - The prefix to add to the IDs of the flattened rows (optional, defaults to an empty string).
- * @returns The flattened array of RenderRow objects.
- */
-const flattenRows = (
-  rows: Rows,
-  flattenedRows: RenderRow[] = [],
-  idPrefix: string = '',
-): RenderRow[] => {
-  rows.order.forEach((rowId) => {
-    const row = rows.values[rowId];
-    const prefix = idPrefix + row.id;
-    flattenedRows.push({
-      id: prefix,
-      row,
-    });
-    if (isRowAggregate(row)) {
-      flattenRows(row.items, flattenedRows, prefix);
-    }
-  });
-
-  return flattenedRows;
-};
+export const getRows = (data: any, state: UpsetConfig, ignoreQuery = false) => filterRR(data, state, ignoreQuery);
 
 /**
  * Flattens the rows of data based on the provided state configuration.