From a0b945b4505452d09774ddc3c0096b12cf1e6e83 Mon Sep 17 00:00:00 2001
From: Steve Reis <stevereis93@gmail.com>
Date: Mon, 4 Apr 2022 10:14:30 +0000
Subject: [PATCH] feat(exareme): Add Anova one way integration
---
.../connectors/datashield/main.connector.ts | 4 +-
.../handlers/algorithms/PCA.handler.spec.ts | 2 +-
.../algorithms/anova-one-way.handler.spec.ts | 159 ++++++++++++++++++
.../algorithms/anova-one-way.handler.ts | 114 +++++++++++++
.../connectors/exareme/handlers/index.ts | 2 +
.../result/common/result-union.model.ts | 8 +-
.../models/result/means-chart-result.model.ts | 33 ++++
.../models/result/table-result.model.ts | 10 +-
api/src/main/app.module.ts | 1 -
api/src/schema.gql | 37 ++--
10 files changed, 349 insertions(+), 21 deletions(-)
create mode 100644 api/src/engine/connectors/exareme/handlers/algorithms/anova-one-way.handler.spec.ts
create mode 100644 api/src/engine/connectors/exareme/handlers/algorithms/anova-one-way.handler.ts
create mode 100644 api/src/engine/models/result/means-chart-result.model.ts
diff --git a/api/src/engine/connectors/datashield/main.connector.ts b/api/src/engine/connectors/datashield/main.connector.ts
index 454654e..2079001 100644
--- a/api/src/engine/connectors/datashield/main.connector.ts
+++ b/api/src/engine/connectors/datashield/main.connector.ts
@@ -27,7 +27,7 @@ import { ListExperiments } from 'src/engine/models/experiment/list-experiments.m
import { RawResult } from 'src/engine/models/result/raw-result.model';
import {
TableResult,
- ThemeType,
+ TableStyle,
} from 'src/engine/models/result/table-result.model';
import { User } from 'src/users/models/user.model';
import {
@@ -141,7 +141,7 @@ export default class DataShieldService implements IEngineService {
const table = transformToTable.evaluate(data);
return {
...table,
- theme: ThemeType.NORMAL,
+ tableStyle: TableStyle.NORMAL,
};
}
diff --git a/api/src/engine/connectors/exareme/handlers/algorithms/PCA.handler.spec.ts b/api/src/engine/connectors/exareme/handlers/algorithms/PCA.handler.spec.ts
index 9aa0115..f390eea 100644
--- a/api/src/engine/connectors/exareme/handlers/algorithms/PCA.handler.spec.ts
+++ b/api/src/engine/connectors/exareme/handlers/algorithms/PCA.handler.spec.ts
@@ -1,7 +1,7 @@
import { Experiment } from '../../../../models/experiment/experiment.model';
import { HeatMapResult } from '../../../../models/result/heat-map-result.model';
import handlers from '..';
-import { BarChartResult } from 'src/engine/models/result/bar-chart-result.model';
+import { BarChartResult } from '../../../../models/result/bar-chart-result.model';
const createExperiment = (): Experiment => ({
id: 'dummy-id',
diff --git a/api/src/engine/connectors/exareme/handlers/algorithms/anova-one-way.handler.spec.ts b/api/src/engine/connectors/exareme/handlers/algorithms/anova-one-way.handler.spec.ts
new file mode 100644
index 0000000..c4cd6dc
--- /dev/null
+++ b/api/src/engine/connectors/exareme/handlers/algorithms/anova-one-way.handler.spec.ts
@@ -0,0 +1,159 @@
+import handlers from '..';
+import { Experiment } from '../../../../models/experiment/experiment.model';
+import AnovaOneWayHandler from './anova-one-way.handler';
+
+const createExperiment = (): Experiment => ({
+ id: 'dummy-id',
+ name: 'Testing purpose',
+ algorithm: {
+ id: 'Anova_OnEway',
+ },
+ datasets: ['desd-synthdata'],
+ domain: 'dementia',
+ variables: ['rightcerebralwhitematter'],
+ coVariables: ['ppmicategory'],
+ results: [],
+});
+
+describe('Anova oneway result handler', () => {
+ const anovaHandler = new AnovaOneWayHandler();
+ const data = {
+ x_label: 'Variable X',
+ y_label: 'Variable Y',
+ df_residual: 1424.0,
+ df_explained: 3.0,
+ ss_residual: 1941.1517872154072,
+ ss_explained: 23.52938815624377,
+ ms_residual: 1.3631683898984601,
+ ms_explained: 7.843129385414589,
+ p_value: 0.0006542139533101455,
+ f_stat: 5.753602741623733,
+ tuckey_test: [
+ {
+ groupA: 'GENPD',
+ groupB: 'HC',
+ meanA: 10.200898765432095,
+ meanB: 10.50253333333334,
+ diff: -0.3016345679012442,
+ se: 0.11017769051976001,
+ t_stat: -2.737710025308137,
+ p_tuckey: 0.03178790563153744,
+ },
+ {
+ groupA: 'GENPD',
+ groupB: 'PD',
+ meanA: 10.200898765432095,
+ meanB: 10.530083456790125,
+ diff: -0.3291846913580301,
+ se: 0.10048653456497285,
+ t_stat: -3.2759084864767125,
+ p_tuckey: 0.005936908999390811,
+ },
+ {
+ groupA: 'GENPD',
+ groupB: 'PRODROMA',
+ meanA: 10.200898765432095,
+ meanB: 10.161453333333334,
+ diff: 0.039445432098760946,
+ se: 0.1534957169892615,
+ t_stat: 0.2569806693793321,
+ p_tuckey: 0.9,
+ },
+ {
+ groupA: 'HC',
+ groupB: 'PD',
+ meanA: 10.50253333333334,
+ meanB: 10.530083456790125,
+ diff: -0.02755012345678587,
+ se: 0.07353521425604895,
+ t_stat: -0.37465211375949203,
+ p_tuckey: 0.9,
+ },
+ {
+ groupA: 'HC',
+ groupB: 'PRODROMA',
+ meanA: 10.50253333333334,
+ meanB: 10.161453333333334,
+ diff: 0.34108000000000516,
+ se: 0.13737110045731235,
+ t_stat: 2.4829094246500176,
+ p_tuckey: 0.0630887851749381,
+ },
+ {
+ groupA: 'PD',
+ groupB: 'PRODROMA',
+ meanA: 10.530083456790125,
+ meanB: 10.161453333333334,
+ diff: 0.368630123456791,
+ se: 0.1297275582960786,
+ t_stat: 2.8415714309172655,
+ p_tuckey: 0.02355122851783331,
+ },
+ ],
+ min_per_group: [
+ {
+ GENPD: 7.2276,
+ HC: 7.2107,
+ PD: 7.0258,
+ PRODROMA: 6.3771,
+ },
+ ],
+ max_per_group: [
+ {
+ GENPD: 13.7312,
+ HC: 14.52,
+ PD: 14.4812,
+ PRODROMA: 12.3572,
+ },
+ ],
+ ci_info: {
+ sample_stds: {
+ GENPD: 1.2338388511229372,
+ HC: 1.1276421260632183,
+ PD: 1.16245855322075,
+ PRODROMA: 1.197046185656396,
+ },
+ means: {
+ GENPD: 10.200898765432095,
+ HC: 10.50253333333334,
+ PD: 10.530083456790125,
+ PRODROMA: 10.161453333333334,
+ },
+ 'm-s': {
+ GENPD: 8.967059914309157,
+ HC: 9.374891207270121,
+ PD: 9.367624903569375,
+ PRODROMA: 8.964407147676939,
+ },
+ 'm+s': {
+ GENPD: 11.434737616555033,
+ HC: 11.630175459396558,
+ PD: 11.692542010010875,
+ PRODROMA: 11.35849951898973,
+ },
+ },
+ };
+
+ it('Test anova 1 way handler', () => {
+ const exp = createExperiment();
+ const table1 = anovaHandler.getSummaryTable(data, exp.coVariables[0]);
+ const table2 = anovaHandler.getTuckeyTable(data);
+ const meanPlot = anovaHandler.getMeanPlot(data);
+
+ handlers(exp, data);
+
+ expect(exp.results.length).toBeGreaterThanOrEqual(3);
+ expect(exp.results).toContainEqual(table1);
+ expect(exp.results).toContainEqual(table2);
+ expect(exp.results).toContainEqual(meanPlot);
+
+ expect(table1.data[0].length).toEqual(6);
+ expect(table2.headers.length).toEqual(8);
+ expect(table2.data).toBeTruthy();
+
+ expect(meanPlot.pointCIs.length).toBeGreaterThan(1);
+ expect(meanPlot.name).toEqual(
+ `Mean Plot: ${data.y_label} ~ ${data.x_label}`,
+ );
+ });
+});
diff --git a/api/src/engine/connectors/exareme/handlers/algorithms/anova-one-way.handler.ts b/api/src/engine/connectors/exareme/handlers/algorithms/anova-one-way.handler.ts
new file mode 100644
index 0000000..c8d9a67
--- /dev/null
+++ b/api/src/engine/connectors/exareme/handlers/algorithms/anova-one-way.handler.ts
@@ -0,0 +1,114 @@
+import * as jsonata from 'jsonata'; // old import style needed due to 'export = jsonata'
+import { MeanChartResult } from 'src/engine/models/result/means-chart-result.model';
+import { Experiment } from '../../../../models/experiment/experiment.model';
+import {
+ TableResult,
+ TableStyle,
+} from '../../../../models/result/table-result.model';
+import BaseHandler from '../base.handler';
+
+export default class AnovaOneWayHandler extends BaseHandler {
+ private static readonly tuckeyTransform = jsonata(`
+ {
+ "name": 'Tuckey Honest Significant Differences',
+ "headers": [
+ {"name": 'A', "type": 'string'},
+ {"name": 'B', "type": 'string'},
+ {"name": 'Mean A', "type": 'string'},
+ {"name": 'Mean B', "type": 'string'},
+ {"name": 'Diff', "type": 'string'},
+ {"name": 'Standard error', "type": 'string'},
+ {"name": 'T value', "type": 'string'},
+ {"name": 'P value', "type": 'string'}
+ ],
+ "data": tuckey_test.[$.groupA, $.groupB, $.meanA, $.meanB, $.diff, $.se, $.t_stat, $.p_tuckey]
+ }
+ `);
+
+ private static readonly meanPlotTransform = jsonata(`
+ (
+ $cats:= $keys(ci_info.means);
+ {
+ "name": "Mean Plot: " & y_label & ' ~ ' & x_label,
+ "xAxis": {
+ "label": x_label,
+ "categories": $cats
+ },
+ "yAxis": {
+ "label": '95% CI: ' & y_label
+ },
+ "pointCIs": $cats.[{
+ "min": $lookup($$.ci_info.'m-s', $),
+ "mean": $lookup($$.ci_info.means, $),
+ "max": $lookup($$.ci_info.'m+s', $)
+ }]
+ })
+ `);
+
+ canHandle(algorithm: string): boolean {
+ return algorithm.toLocaleLowerCase() === 'anova_oneway';
+ }
+
+ getTuckeyTable(data: unknown): TableResult | undefined {
+ const tableData = AnovaOneWayHandler.tuckeyTransform.evaluate(data);
+
+ if (!tableData) return undefined;
+
+ const tableResult: TableResult = {
+ ...tableData,
+ tableStyle: TableStyle.NORMAL,
+ } as unknown as TableResult;
+
+ return tableResult;
+ }
+
+ getSummaryTable(data: unknown, varname: string): TableResult | undefined {
+ const tableSummary: TableResult = {
+ name: 'Annova summary',
+ tableStyle: TableStyle.NORMAL,
+ headers: ['', 'DF', 'SS', 'MS', 'F ratio', 'P value'].map((name) => ({
+ name,
+ type: 'string',
+ })),
+ data: [
+ [
+ varname,
+ data['df_explained'],
+ data['ss_explained'],
+ data['ms_explained'],
+ data['p_value'],
+ data['f_stat'],
+ ],
+ [
+ 'Residual',
+ data['df_residual'],
+ data['ss_residual'],
+ data['ms_residual'],
+ '',
+ '',
+ ],
+ ],
+ };
+
+ return tableSummary;
+ }
+
+ getMeanPlot(data: unknown): MeanChartResult {
+ return AnovaOneWayHandler.meanPlotTransform.evaluate(data);
+ }
+
+ handle(exp: Experiment, data: unknown): void {
+ if (!this.canHandle(exp.algorithm.id)) return super.handle(exp, data);
+
+ const summaryTable = this.getSummaryTable(data, exp.coVariables[0]);
+ if (summaryTable) exp.results.push(summaryTable);
+
+ const tuckeyTable = this.getTuckeyTable(data);
+ if (tuckeyTable) exp.results.push(tuckeyTable);
+
+ const meanPlot = this.getMeanPlot(data);
+ if (meanPlot && meanPlot.pointCIs) exp.results.push(meanPlot);
+
+ super.handle(exp, data); // continue request
+ }
+}
diff --git a/api/src/engine/connectors/exareme/handlers/index.ts b/api/src/engine/connectors/exareme/handlers/index.ts
index f9c6c47..2d7d607 100644
--- a/api/src/engine/connectors/exareme/handlers/index.ts
+++ b/api/src/engine/connectors/exareme/handlers/index.ts
@@ -1,4 +1,5 @@
import { Experiment } from '../../../../engine/models/experiment/experiment.model';
+import AnovaOneWayHandler from './algorithms/anova-one-way.handler';
import AreaHandler from './algorithms/area.handler';
import DescriptiveHandler from './algorithms/descriptive.handler';
import HeatMapHandler from './algorithms/heat-map.handler';
@@ -12,6 +13,7 @@ start
.setNext(new AreaHandler())
.setNext(new DescriptiveHandler())
.setNext(new HeatMapHandler())
+ .setNext(new AnovaOneWayHandler())
.setNext(new PCAHandler())
.setNext(new RawHandler()); // should be last handler as it works as a fallback (if other handlers could not process the results)
diff --git a/api/src/engine/models/result/common/result-union.model.ts b/api/src/engine/models/result/common/result-union.model.ts
index 5c2ffc6..0e38596 100644
--- a/api/src/engine/models/result/common/result-union.model.ts
+++ b/api/src/engine/models/result/common/result-union.model.ts
@@ -1,10 +1,11 @@
import { createUnionType } from '@nestjs/graphql';
-import { BarChartResult } from '../bar-chart-result.model';
import { GroupsResult } from '../groups-result.model';
import { HeatMapResult } from '../heat-map-result.model';
import { LineChartResult } from '../line-chart-result.model';
import { RawResult } from '../raw-result.model';
import { TableResult } from '../table-result.model';
+import { BarChartResult } from '../bar-chart-result.model';
+import { MeanChartResult } from '../means-chart-result.model';
export const ResultUnion = createUnionType({
name: 'ResultUnion',
@@ -15,6 +16,7 @@ export const ResultUnion = createUnionType({
HeatMapResult,
LineChartResult,
BarChartResult,
+ MeanChartResult,
],
resolveType(value) {
if (value.headers) {
@@ -37,6 +39,10 @@ export const ResultUnion = createUnionType({
return BarChartResult;
}
+ if (value.pointCIs) {
+ return MeanChartResult;
+ }
+
return RawResult;
},
});
diff --git a/api/src/engine/models/result/means-chart-result.model.ts b/api/src/engine/models/result/means-chart-result.model.ts
new file mode 100644
index 0000000..12dd974
--- /dev/null
+++ b/api/src/engine/models/result/means-chart-result.model.ts
@@ -0,0 +1,33 @@
+import { Field, ObjectType } from '@nestjs/graphql';
+import { ChartAxis } from './common/chart-axis.model';
+import { Result } from './common/result.model';
+
+@ObjectType()
+export class PointCI {
+ @Field({ nullable: true })
+ min?: number;
+
+ @Field()
+ mean: number;
+
+ @Field({ nullable: true })
+ max?: number;
+}
+
+@ObjectType()
+export class MeanChartResult extends Result {
+ @Field()
+ name: string;
+
+ @Field(() => ChartAxis, { nullable: true })
+ xAxis?: ChartAxis;
+
+ @Field(() => ChartAxis, { nullable: true })
+ yAxis?: ChartAxis;
+
+ @Field(() => [PointCI], {
+ description: 'List of points with confidence information: min, mean, max',
+ defaultValue: [],
+ })
+ pointCIs: PointCI[];
+}
diff --git a/api/src/engine/models/result/table-result.model.ts b/api/src/engine/models/result/table-result.model.ts
index a733683..85fa6ee 100644
--- a/api/src/engine/models/result/table-result.model.ts
+++ b/api/src/engine/models/result/table-result.model.ts
@@ -2,13 +2,13 @@ import { Field, ObjectType, registerEnumType } from '@nestjs/graphql';
import { Header } from './common/header.model';
import { Result } from './common/result.model';
-export enum ThemeType {
+export enum TableStyle {
DEFAULT,
NORMAL,
}
-registerEnumType(ThemeType, {
- name: 'ThemeType',
+registerEnumType(TableStyle, {
+ name: 'TableStyle',
});
@ObjectType()
@@ -22,6 +22,6 @@ export class TableResult extends Result {
@Field(() => [Header])
headers: Header[];
- @Field(() => ThemeType, { defaultValue: ThemeType.DEFAULT, nullable: true })
- theme?: ThemeType;
+ @Field(() => TableStyle, { defaultValue: TableStyle.DEFAULT, nullable: true })
+ tableStyle?: TableStyle;
}
diff --git a/api/src/main/app.module.ts b/api/src/main/app.module.ts
index 56ef2df..4f784ef 100644
--- a/api/src/main/app.module.ts
+++ b/api/src/main/app.module.ts
@@ -53,7 +53,6 @@ import { AppService } from './app.service';
migrations: ['dist/migrations/*{.ts,.js}'],
migrationsRun: process.env.NODE_ENV !== 'dev',
synchronize: process.env.NODE_ENV === 'dev',
- loggerLevel: 'debug',
autoLoadEntities: true,
}),
}),
diff --git a/api/src/schema.gql b/api/src/schema.gql
index 8a0e240..95da149 100644
--- a/api/src/schema.gql
+++ b/api/src/schema.gql
@@ -85,30 +85,22 @@ type Algorithm {
description: String
}
-type ChartAxis {
- """label of the Axis"""
- label: String
-
- """label of each element on this Axis"""
- categories: [String!]
-}
-
type GroupResult {
name: String!
description: String
results: [ResultUnion!]!
}
-union ResultUnion = TableResult | RawResult | GroupsResult | HeatMapResult | LineChartResult | BarChartResult
+union ResultUnion = TableResult | RawResult | GroupsResult | HeatMapResult | LineChartResult | BarChartResult | MeanChartResult
type TableResult {
name: String!
data: [[String!]!]!
headers: [Header!]!
- theme: ThemeType
+ tableStyle: TableStyle
}
-enum ThemeType {
+enum TableStyle {
DEFAULT
NORMAL
}
@@ -157,6 +149,23 @@ type BarChartResult {
hasConnectedBars: Boolean
}
+type MeanChartResult {
+ name: String!
+ xAxis: ChartAxis
+ yAxis: ChartAxis
+
+ """List of points with confidence information: min, mean, max"""
+ pointCIs: [PointCI!]!
+}
+
+type ChartAxis {
+ """label of the Axis"""
+ label: String
+
+ """label of each element on this Axis"""
+ categories: [String!]
+}
+
type ExtraLineInfo {
label: String!
values: [String!]!
@@ -180,6 +189,12 @@ type Header {
type: String!
}
+type PointCI {
+ min: Float
+ mean: Float!
+ max: Float
+}
+
type Author {
username: String
fullname: String
--
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