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diff --git a/api/assets/engines/default/logo_small.png b/api/assets/engines/default/logo_small.png
index 1adc2e10f5c6b802fa4479df95ff8c75735e42ce..65080c251bca424f5ba18bd0b3063755ec6eb07c 100644
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diff --git a/api/src/common/utils/shared.utils.ts b/api/src/common/utils/shared.utils.ts
index 8d9b507a16f8e293fd2bacf76542981e1962c6eb..a696ec7c804388a17266564531ee3a3dec16e22b 100644
--- a/api/src/common/utils/shared.utils.ts
+++ b/api/src/common/utils/shared.utils.ts
@@ -111,6 +111,8 @@ export const isPlainObject = (fn: any): fn is object => {
export const isFunction = (val: any): boolean => typeof val === 'function';
export const isString = (val: any): val is string => typeof val === 'string';
export const isNumber = (val: any): val is number => typeof val === 'number';
+export const formatNumber = (val: any, precision = 4): number | string =>
+ isNumber(val) ? val.toPrecision(precision) : val;
export const isConstructor = (val: any): boolean => val === 'constructor';
export const isNil = (val: any): val is null | undefined =>
isUndefined(val) || val === null;
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 fd0a46d6d38f19e9dfac67bf3ec798431ff503a8..4f360a0d0461623bb0eab626ce9954405594229b 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
@@ -2,6 +2,7 @@ import { Experiment } from '../../../../models/experiment/experiment.model';
import { HeatMapResult } from '../../../../models/result/heat-map-result.model';
import handlers from '..';
import { BarChartResult } from '../../../../models/result/bar-chart-result.model';
+import { Domain } from '../../../../models/domain.model';
const createExperiment = (): Experiment => ({
id: 'dummy-id',
@@ -24,6 +25,16 @@ const createExperiment = (): Experiment => ({
results: [],
});
+const domain: Domain = {
+ id: 'dummy-id',
+ groups: [],
+ rootGroup: {
+ id: 'dummy-id',
+ },
+ datasets: [{ id: 'desd-synthdata', label: 'Dead Synthdata' }],
+ variables: [],
+};
+
const data = [
{
n_obs: 920,
@@ -80,7 +91,7 @@ const data = [
describe('PCA result handler', () => {
it('Test PCA handler with regular data (no edge cases)', () => {
const exp = createExperiment();
- handlers(exp, data, null);
+ handlers(exp, data, domain);
expect(exp.results.length).toBeGreaterThanOrEqual(2);
exp.results.forEach((result) => {
diff --git a/api/src/engine/connectors/exareme/handlers/algorithms/PCA.handler.ts b/api/src/engine/connectors/exareme/handlers/algorithms/PCA.handler.ts
index 32f08a02deb817ca2078c07774e39ac06a26f041..23884d9a71a456cabc1eedb13d14aa3eeb92fc34 100644
--- a/api/src/engine/connectors/exareme/handlers/algorithms/PCA.handler.ts
+++ b/api/src/engine/connectors/exareme/handlers/algorithms/PCA.handler.ts
@@ -1,4 +1,5 @@
-import { Domain } from 'src/engine/models/domain.model';
+import { Variable } from 'src/engine/models/variable.model';
+import { Domain } from '../../../../models/domain.model';
import { Experiment } from '../../../../models/experiment/experiment.model';
import { BarChartResult } from '../../../../models/result/bar-chart-result.model';
import {
@@ -18,18 +19,13 @@ export default class PCAHandler extends BaseHandler {
);
}
- handle(exp: Experiment, data: any, domain?: Domain): void {
- if (!this.canHandle(exp.algorithm.name, data))
- return this.next?.handle(exp, data, domain);
-
- const extractedData = data[0];
-
- const barChar: BarChartResult = {
+ private getBarChartResult(data: any): BarChartResult {
+ const barChart: BarChartResult = {
name: 'Eigen values',
- barValues: extractedData['eigenvalues'],
+ barValues: data['eigenvalues'],
xAxis: {
label: 'Dimensions',
- categories: exp.variables.map((_, i) => i + 1).map(String),
+ categories: data['eigenvalues'].map((_: unknown, i: number) => i + 1),
},
hasConnectedBars: true,
yAxis: {
@@ -37,17 +33,18 @@ export default class PCAHandler extends BaseHandler {
},
};
- if (barChar.barValues && barChar.barValues.length > 0)
- exp.results.push(barChar);
+ return barChart;
+ }
- const matrix = extractedData['eigenvectors'] as number[][];
+ private getHeatMapResult(data: any, variables: Variable[]): HeatMapResult {
+ const matrix = data['eigenvectors'] as number[][];
const heatMapChart: HeatMapResult = {
name: 'Eigen vectors',
matrix,
heatMapStyle: HeatMapStyle.BUBBLE,
yAxis: {
- categories: exp.variables,
+ categories: variables.map((v) => v.label ?? v.id),
},
xAxis: {
categories: [...Array(matrix.length).keys()]
@@ -62,8 +59,27 @@ export default class PCAHandler extends BaseHandler {
);
}
+ return heatMapChart;
+ }
+
+ handle(exp: Experiment, data: any, domain: Domain): void {
+ if (!this.canHandle(exp.algorithm.name, data))
+ return this.next?.handle(exp, data, domain);
+
+ const extractedData = data[0];
+
+ const variables =
+ exp.variables
+ ?.map((v) => domain.variables.find((v2) => v2.id === v) ?? { id: v })
+ .filter((v) => v) ?? [];
+
+ const barChart = this.getBarChartResult(extractedData);
+ if (barChart.barValues && barChart.barValues.length > 0)
+ exp.results.push(barChart);
+
+ const heatMapChart = this.getHeatMapResult(extractedData, variables);
if (heatMapChart.matrix) exp.results.push(heatMapChart);
- this.next?.handle(exp, data);
+ this.next?.handle(exp, data, domain);
}
}
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
index 1f286bfc9edd64f51a5d11810931c6591d2e0f72..77d8232e46f772a3d84eefa8f7573bea7e383068 100644
--- 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
@@ -1,3 +1,4 @@
+import { Domain } from '../../../../models/domain.model';
import handlers from '..';
import { Experiment } from '../../../../models/experiment/experiment.model';
import AnovaOneWayHandler from './anova-one-way.handler';
@@ -15,11 +16,24 @@ const createExperiment = (): Experiment => ({
results: [],
});
+const domain: Domain = {
+ id: 'dummy-id',
+ groups: [],
+ rootGroup: {
+ id: 'dummy-id',
+ },
+ datasets: [{ id: 'desd-synthdata', label: 'Dead Synthdata' }],
+ variables: [
+ { id: 'rightcerebralwhitematter', label: 'Example label' },
+ { id: 'ppmicategory', label: 'Example label 2' },
+ ],
+};
+
const data = [
{
anova_table: {
- x_label: 'Variable X',
- y_label: 'Variable Y',
+ x_label: 'Example label 2',
+ y_label: 'Example label',
df_residual: 1424.0,
df_explained: 3.0,
ss_residual: 1941.1517872154072,
@@ -130,16 +144,16 @@ describe('Anova oneway result handler', () => {
it('Test anova 1 way handler', () => {
const exp = createExperiment();
- const table1 = anovaHandler.getSummaryTable(data[0], exp.coVariables[0]);
+ const table1 = anovaHandler.getSummaryTable(
+ data[0],
+ data[0].anova_table.x_label,
+ );
const table2 = anovaHandler.getTuckeyTable(data[0]);
const meanPlot = anovaHandler.getMeanPlot(data[0]);
- handlers(exp, data, null);
+ handlers(exp, data, domain);
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);
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
index 2b6fa2d7628c010e98be1c552d566c29ec5e4799..b464ea1320ecd7b1189b64ab8fc6951e06400fdb 100644
--- 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
@@ -1,16 +1,20 @@
import * as jsonata from 'jsonata'; // old import style needed due to 'export = jsonata'
-import { Domain } from 'src/engine/models/domain.model';
-import { MeanChartResult } from 'src/engine/models/result/means-chart-result.model';
+import { formatNumber } from '../../../../../common/utils/shared.utils';
+import { Domain } from '../../../../models/domain.model';
+import { MeanChartResult } from '../../../../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 {
public static readonly ALGO_NAME = 'anova_oneway';
private static readonly tuckeyTransform = jsonata(`
- {
+ (
+ $format:= "#0.0000";
+ {
"name": 'Tuckey Honest Significant Differences',
"headers": [
{"name": 'A', "type": 'string'},
@@ -22,18 +26,27 @@ export default class AnovaOneWayHandler extends BaseHandler {
{"name": 'T value', "type": 'string'},
{"name": 'P value', "type": 'string'}
],
- "data": tuckey_test.[$.groupA, $.groupB, $.meanA, $.meanB, $.diff, $.se, $.t_stat, $.p_tuckey][]
- }
+ "data": tuckey_test.[$lookup($$.categories, $.groupA),
+ $lookup($$.categories, $.groupB),
+ $formatNumber($.meanA, $format),
+ $formatNumber($.meanB, $format),
+ $formatNumber($.diff, $format),
+ $formatNumber($.se, $format),
+ $formatNumber($.t_stat, $format),
+ $formatNumber($.p_tuckey, $format)
+ ][]
+ })
`);
private static readonly meanPlotTransform = jsonata(`
(
$cats:= $keys(ci_info.means);
+
{
"name": "Mean Plot: " & anova_table.y_label & ' ~ ' & anova_table.x_label,
"xAxis": {
"label": anova_table.x_label,
- "categories": $cats
+ "categories": $cats.($lookup($$.categories, $))
},
"yAxis": {
"label": '95% CI: ' & anova_table.y_label
@@ -46,8 +59,13 @@ export default class AnovaOneWayHandler extends BaseHandler {
})
`);
- canHandle(algorithm: string): boolean {
- return algorithm.toLocaleLowerCase() === AnovaOneWayHandler.ALGO_NAME;
+ canHandle(algorithm: string, data: any): boolean {
+ return (
+ data &&
+ data.length !== 0 &&
+ data[0]['anova_table'] &&
+ algorithm.toLocaleLowerCase() === AnovaOneWayHandler.ALGO_NAME
+ );
}
getTuckeyTable(data: unknown): TableResult | undefined {
@@ -75,18 +93,18 @@ export default class AnovaOneWayHandler extends BaseHandler {
[
varname,
data['anova_table']['df_explained'],
- data['anova_table']['ss_explained'],
- data['anova_table']['ms_explained'],
- data['anova_table']['p_value'],
- data['anova_table']['f_stat'],
+ formatNumber(data['anova_table']['ss_explained']),
+ formatNumber(data['anova_table']['ms_explained']),
+ formatNumber(data['anova_table']['f_stat']),
+ formatNumber(data['anova_table']['p_value']),
],
[
'Residual',
data['anova_table']['df_residual'],
- data['anova_table']['ss_residual'],
- data['anova_table']['ms_residual'],
- '',
- '',
+ formatNumber(data['anova_table']['ss_residual']),
+ formatNumber(data['anova_table']['ms_residual']),
+ 'N/A',
+ 'N/A',
],
],
};
@@ -99,14 +117,38 @@ export default class AnovaOneWayHandler extends BaseHandler {
}
handle(exp: Experiment, data: any, domain: Domain): void {
- if (!data || data.length === 0) return super.handle(exp, data, domain);
-
- if (!this.canHandle(exp.algorithm.name))
+ if (!this.canHandle(exp.algorithm.name, data))
return super.handle(exp, data, domain);
const result = data[0];
- const summaryTable = this.getSummaryTable(result, exp.coVariables[0]);
+ const varIds = [...exp.variables, ...(exp.coVariables ?? [])];
+ const variables = domain.variables.filter((v) => varIds.includes(v.id));
+
+ const [variable, coVariate] = variables;
+
+ if (variable) result.anova_table.y_label = variable.label ?? variable.id;
+ if (coVariate) result.anova_table.x_label = coVariate.label ?? coVariate.id;
+
+ if (coVariate && coVariate.enumerations) {
+ result.categories = coVariate.enumerations.reduce((p, e) => {
+ p[e.value] = e.label ?? e.value;
+ return p;
+ }, {});
+ } else {
+ result.categories = result['min_max_per_group']['categories'].reduce(
+ (p: { [x: string]: string }, e: string) => {
+ p[e] = e;
+ return p;
+ },
+ {},
+ );
+ }
+
+ const summaryTable = this.getSummaryTable(
+ result,
+ result.anova_table.x_label,
+ );
if (summaryTable) exp.results.push(summaryTable);
const tuckeyTable = this.getTuckeyTable(result);
diff --git a/api/src/engine/connectors/exareme/handlers/algorithms/pearson.handler.spec.ts b/api/src/engine/connectors/exareme/handlers/algorithms/pearson.handler.spec.ts
index 1ec54c8b8c69ebae7d7b00262e6b772ff28054d6..1fe22eb459b05e20e97085b69271330bf2431428 100644
--- a/api/src/engine/connectors/exareme/handlers/algorithms/pearson.handler.spec.ts
+++ b/api/src/engine/connectors/exareme/handlers/algorithms/pearson.handler.spec.ts
@@ -1,4 +1,4 @@
-import { HeatMapResult } from 'src/engine/models/result/heat-map-result.model';
+import { Domain } from '../../../../models/domain.model';
import handlers from '..';
import { Experiment } from '../../../../models/experiment/experiment.model';
import PearsonHandler from './pearson.handler';
@@ -42,8 +42,21 @@ const createExperiment = (): Experiment => ({
results: [],
});
-describe('Pearson result handler', () => {
- const data = {
+const domain: Domain = {
+ id: 'dummy-id',
+ groups: [],
+ rootGroup: {
+ id: 'dummy-id',
+ },
+ datasets: [{ id: 'desd-synthdata', label: 'Dead Synthdata' }],
+ variables: [
+ { id: 'rightcerebralwhitematter', label: 'Example label' },
+ { id: 'ppmicategory', label: 'Example label 2' },
+ ],
+};
+
+const data = [
+ {
n_obs: 1840,
correlations: {
variables: [
@@ -413,24 +426,16 @@ describe('Pearson result handler', () => {
0.5096526209667468, 0.5533006654400224,
],
},
- };
+ },
+];
+describe('Pearson result handler', () => {
it('Test pearson handler with regular data', () => {
const exp = createExperiment();
- const names = [
- 'correlations',
- 'p_values',
- 'low_confidence_intervals',
- 'high_confidence_intervals',
- ];
-
- handlers(exp, data, null);
- const results = exp.results as HeatMapResult[];
- const heatmaps = names.map((name) =>
- results.find((it) => it.name === name),
- );
+ handlers(exp, data, domain);
+ const results = exp.results;
- expect(heatmaps.length).toBeGreaterThanOrEqual(4);
+ expect(results.length).toBe(2);
});
});
diff --git a/api/src/engine/connectors/exareme/handlers/algorithms/pearson.handler.ts b/api/src/engine/connectors/exareme/handlers/algorithms/pearson.handler.ts
index cff25e2cf307aec468a7b050c33af97f646e02f0..098950d835d25c66702909a200250a6653a302a3 100644
--- a/api/src/engine/connectors/exareme/handlers/algorithms/pearson.handler.ts
+++ b/api/src/engine/connectors/exareme/handlers/algorithms/pearson.handler.ts
@@ -1,16 +1,24 @@
import * as jsonata from 'jsonata'; // old import style needed due to 'export = jsonata'
import { Expression } from 'jsonata';
-import { Domain } from 'src/engine/models/domain.model';
+import { formatNumber } from '../../../../../common/utils/shared.utils';
+import { Domain } from '../../../../models/domain.model';
+import {
+ TableResult,
+ TableStyle,
+} from '../../../../models/result/table-result.model';
import { Experiment } from '../../../../models/experiment/experiment.model';
import { HeatMapResult } from '../../../../models/result/heat-map-result.model';
import BaseHandler from '../base.handler';
+type Lookup = {
+ [key: string]: string;
+};
export default class PearsonHandler extends BaseHandler {
public static readonly ALGO_NAME = 'pearson_correlation';
private static readonly transform: Expression = jsonata(`
(
- $params := ['correlations', 'p_values', 'ci_lo', 'ci_hi'];
+ $params := ['correlations'];
$dictName := {
"correlations": "Correlations",
"p_values": "P values",
@@ -22,16 +30,58 @@ export default class PearsonHandler extends BaseHandler {
{
'name': $lookup($dictName, $k),
'xAxis': {
- 'categories': $v.variables
+ 'categories': $v.variables.($lookup($$.lookupVars, $))
},
'yAxis': {
- 'categories': $reverse($v.variables)
+ 'categories': $reverse($keys($v.$sift(function($val, $key) {$key ~> /^(?!variables$)/}))).($lookup($$.lookupVars, $))
},
'matrix': $v.$sift(function($val, $key) {$key ~> /^(?!variables$)/}).$each(function($val, $key) {$val})[]
}
- })
+ })[]
)`);
+ private getTableResult(data: any, lookup: Lookup): TableResult {
+ const elements = [...data['correlations']['variables']];
+ const keys = [
+ ...Object.keys(data['correlations']).filter((k) => k !== 'variables'),
+ ];
+ const tableData = [];
+ const doneMap = {};
+
+ while (keys.length > 0) {
+ const key = keys.shift();
+ elements.forEach((elem, i) => {
+ const token = [key, elem].sort().join();
+ if (elem === key || doneMap[token]) return;
+ doneMap[token] = true;
+ tableData.push([
+ lookup[key] ?? key,
+ lookup[elem] ?? elem,
+ formatNumber(data['correlations'][key][i]),
+ formatNumber(data['p_values'][key][i]),
+ formatNumber(data['ci_lo'][key][i]),
+ formatNumber(data['ci_hi'][key][i]),
+ ]);
+ });
+ }
+
+ const tableResult: TableResult = {
+ name: 'Pearson summary',
+ tableStyle: TableStyle.DEFAULT,
+ headers: [
+ { name: 'Variable 1', type: 'string' },
+ { name: 'Variable 2', type: 'string' },
+ { name: 'Correlation', type: 'string' },
+ { name: 'P value', type: 'string' },
+ { name: 'Low CI', type: 'string' },
+ { name: 'High CI', type: 'string' },
+ ],
+ data: tableData,
+ };
+
+ return tableResult;
+ }
+
/**
* This function returns true if the algorithm is Pearson.
* @param {string} algorithm - The name of the algorithm to use.
@@ -47,12 +97,28 @@ export default class PearsonHandler extends BaseHandler {
);
}
- handle(exp: Experiment, data: any, domain?: Domain): void {
+ handle(exp: Experiment, data: any, domain: Domain): void {
if (!this.canHandle(exp.algorithm.name, data))
return super.handle(exp, data, domain);
const extData = data[0];
+ const varIds = [...exp.variables, ...(exp.coVariables ?? [])];
+ const lookup: Lookup = varIds.reduce((acc, curr) => {
+ acc[curr] = curr;
+ return acc;
+ }, {}); // fallback to original ids if domain is empty
+
+ domain.variables
+ .filter((v) => varIds.includes(v.id))
+ .forEach((v) => {
+ lookup[v.id] = v.label ?? v.id;
+ });
+
+ extData.lookupVars = lookup;
+ const tableResult = this.getTableResult(extData, lookup);
+ if (tableResult.data.length > 0) exp.results.push(tableResult);
+
const results = PearsonHandler.transform.evaluate(
extData,
) as HeatMapResult[];
@@ -60,6 +126,6 @@ export default class PearsonHandler extends BaseHandler {
.filter((heatMap) => heatMap.matrix.length > 0 && heatMap.name)
.forEach((heatMap) => exp.results.push(heatMap));
- this.next?.handle(exp, data);
+ this.next?.handle(exp, data, domain);
}
}
diff --git a/api/src/engine/connectors/exareme/handlers/algorithms/ttest-onesample.handler.spec.ts b/api/src/engine/connectors/exareme/handlers/algorithms/ttest-onesample.handler.spec.ts
index 258f8106788321276cbdce6aa785190d44a307fc..4713037aacbb3d41a783318c5084809bba822b27 100644
--- a/api/src/engine/connectors/exareme/handlers/algorithms/ttest-onesample.handler.spec.ts
+++ b/api/src/engine/connectors/exareme/handlers/algorithms/ttest-onesample.handler.spec.ts
@@ -2,17 +2,19 @@ import { TableResult } from '../../../../models/result/table-result.model';
import { Experiment } from '../../../../models/experiment/experiment.model';
import TtestOnesampleHandler from './ttest-onesample.handler';
-const data = {
- n_obs: 1991,
- t_value: 304.98272738655413,
- p_value: 0.0,
- df: 1990.0,
- mean_diff: 220.17867654445,
- se_diff: 0.7464781919192859,
- ci_upper: 221.64263732187715,
- ci_lower: 218.71471576702288,
- cohens_d: 6.835017232945105,
-};
+const data = [
+ {
+ n_obs: 1991,
+ t_value: 304.98272738655413,
+ p_value: 0.0,
+ df: 1990.0,
+ mean_diff: 220.17867654445,
+ se_diff: 0.7464781919192859,
+ ci_upper: 221.64263732187715,
+ ci_lower: 218.71471576702288,
+ cohens_d: 6.835017232945105,
+ },
+];
const createExperiment = (): Experiment => ({
id: 'dummy-id',
diff --git a/api/src/engine/connectors/exareme/handlers/algorithms/ttest-onesample.handler.ts b/api/src/engine/connectors/exareme/handlers/algorithms/ttest-onesample.handler.ts
index 0cb7bb1903e8e49f68820f5fe337c5353175cc4f..be893f5444f1f1559de4f0d5c8c71603f3842cba 100644
--- a/api/src/engine/connectors/exareme/handlers/algorithms/ttest-onesample.handler.ts
+++ b/api/src/engine/connectors/exareme/handlers/algorithms/ttest-onesample.handler.ts
@@ -31,13 +31,18 @@ const isNumberPrecision = (value: any, name: string) => {
export default class TtestOnesampleHandler extends BaseHandler {
public static readonly ALGO_NAME = 'ttest_onesample';
- private canHandle(algoId: string) {
- return algoId.toLocaleLowerCase() === TtestOnesampleHandler.ALGO_NAME;
+ private canHandle(algoId: string, data: any) {
+ return (
+ data &&
+ data[0] &&
+ data[0]['t_value'] &&
+ algoId.toLowerCase() === TtestOnesampleHandler.ALGO_NAME
+ );
}
private getTable(data: any): TableResult {
const tableModel: TableResult = {
- name: 'T-test',
+ name: 'Results',
tableStyle: TableStyle.NORMAL,
headers: ['name', 'value'].map((name) => ({ name, type: 'string' })),
data: [
@@ -62,10 +67,12 @@ export default class TtestOnesampleHandler extends BaseHandler {
}
handle(experiment: Experiment, data: any, domain?: Domain): void {
- if (!this.canHandle(experiment.algorithm.name))
+ if (!this.canHandle(experiment.algorithm.name, data))
return super.handle(experiment, data, domain);
- const tableModel = this.getTable(data);
+ const extData = data[0];
+
+ const tableModel = this.getTable(extData);
if (tableModel) experiment.results.push(tableModel);
}
diff --git a/api/src/engine/connectors/exareme/handlers/algorithms/ttest-paired.handler.spec.ts b/api/src/engine/connectors/exareme/handlers/algorithms/ttest-paired.handler.spec.ts
index b1e0629051c6a34941173ec2d56eb04b47560045..1797524ebd33ea552b613597811ad14d672d8c6d 100644
--- a/api/src/engine/connectors/exareme/handlers/algorithms/ttest-paired.handler.spec.ts
+++ b/api/src/engine/connectors/exareme/handlers/algorithms/ttest-paired.handler.spec.ts
@@ -2,22 +2,24 @@ import { TableResult } from '../../../../models/result/table-result.model';
import { Experiment } from '../../../../models/experiment/experiment.model';
import TTestPairedHandler from './ttest-paired.handler';
-const data = {
- t_stat: -97.35410837992711,
- p: 1.0,
- df: 144.0,
- mean_diff: -66.00088551724139,
- se_diff: 0.6779465871093092,
- ci_upper: 'Infinity',
- ci_lower: -67.12322892404309,
- cohens_d: -11.456478738682357,
-};
+const data = [
+ {
+ t_stat: -97.35410837992711,
+ p: 1.0,
+ df: 144.0,
+ mean_diff: -66.00088551724139,
+ se_diff: 0.6779465871093092,
+ ci_upper: 'Infinity',
+ ci_lower: -67.12322892404309,
+ cohens_d: -11.456478738682357,
+ },
+];
const createExperiment = (): Experiment => ({
id: 'dummy-id',
name: 'Testing purpose',
algorithm: {
- name: 'TTEST_PAIRED',
+ name: TTestPairedHandler.ALGO_NAME.toUpperCase(),
},
datasets: ['desd-synthdata'],
domain: 'dementia',
diff --git a/api/src/engine/connectors/exareme/handlers/algorithms/ttest-paired.handler.ts b/api/src/engine/connectors/exareme/handlers/algorithms/ttest-paired.handler.ts
index f7196ee295154f399f64c888d5228424f9403f54..10ca096c455e37dcc904636c29349ce4497d6bf1 100644
--- a/api/src/engine/connectors/exareme/handlers/algorithms/ttest-paired.handler.ts
+++ b/api/src/engine/connectors/exareme/handlers/algorithms/ttest-paired.handler.ts
@@ -20,14 +20,21 @@ const lookupDict = {
const NUMBER_PRECISION = 4;
export default class TTestPairedHandler extends BaseHandler {
- private canHandle(experimentId: string) {
- return experimentId.toLocaleLowerCase() === 'ttest_paired';
+ public static readonly ALGO_NAME = 'paired_ttest';
+
+ private canHandle(algoName: string, data: any) {
+ return (
+ data &&
+ data[0] &&
+ data[0]['t_stat'] &&
+ algoName.toLowerCase() === TTestPairedHandler.ALGO_NAME
+ );
}
private getTable(data: any): TableResult {
const tableModel: TableResult = {
- name: 'T-test',
- tableStyle: TableStyle.NORMAL,
+ name: 'Results',
+ tableStyle: TableStyle.DEFAULT,
headers: ['name', 'value'].map((name) => ({ name, type: 'string' })),
data: [
't_stat',
@@ -50,10 +57,12 @@ export default class TTestPairedHandler extends BaseHandler {
}
handle(experiment: Experiment, data: any, domain?: Domain): void {
- if (!this.canHandle(experiment.algorithm.name))
+ if (!this.canHandle(experiment.algorithm.name, data))
return super.handle(experiment, data, domain);
- const tableModel = this.getTable(data);
+ const extData = data[0];
+
+ const tableModel = this.getTable(extData);
if (tableModel) experiment.results.push(tableModel);
}
diff --git a/api/src/engine/connectors/exareme/handlers/index.ts b/api/src/engine/connectors/exareme/handlers/index.ts
index c3041feb05df727b30a27a3589afbee533893f8f..a1018098456f7d9a6fec1016d8f3cc26e1404c17 100644
--- a/api/src/engine/connectors/exareme/handlers/index.ts
+++ b/api/src/engine/connectors/exareme/handlers/index.ts
@@ -8,10 +8,10 @@ import LogisticRegressionHandler from './algorithms/logistic-regression.handler'
import PCAHandler from './algorithms/PCA.handler';
import PearsonHandler from './algorithms/pearson.handler';
import RawHandler from './algorithms/raw.handler';
+import TtestOnesampleHandler from './algorithms/ttest-onesample.handler';
import TTestPairedHandler from './algorithms/ttest-paired.handler';
-import ResultHandler from './result-handler.interface';
-const start = new PearsonHandler() as ResultHandler;
+const start = new PearsonHandler();
start
.setNext(new DescriptiveHandler())
@@ -21,6 +21,7 @@ start
.setNext(new LinearRegressionCVHandler())
.setNext(new LogisticRegressionHandler())
.setNext(new TTestPairedHandler())
+ .setNext(new TtestOnesampleHandler())
.setNext(new RawHandler()); // should be last handler as it works as a fallback (if other handlers could not process the results)
export default (exp: Experiment, data: unknown, domain: Domain): Experiment => {
diff --git a/api/src/engine/connectors/exareme/handlers/result-handler.interface.ts b/api/src/engine/connectors/exareme/handlers/result-handler.interface.ts
index 3c82f7d32ca56246281bcb09c996565d77a518eb..f5b363c6e10f31d7d2536ee058d6378627c8249a 100644
--- a/api/src/engine/connectors/exareme/handlers/result-handler.interface.ts
+++ b/api/src/engine/connectors/exareme/handlers/result-handler.interface.ts
@@ -1,8 +1,8 @@
-import { Domain } from 'src/engine/models/domain.model';
+import { Domain } from '../../../models/domain.model';
import { Experiment } from '../../../models/experiment/experiment.model';
// produce algo handler
export default interface ResultHandler {
setNext(h: ResultHandler): ResultHandler;
- handle(partialExperiment: Experiment, data: unknown, domain?: Domain): void;
+ handle(partialExperiment: Experiment, data: unknown, domain: Domain): void;
}
diff --git a/api/src/engine/connectors/exareme/transformations/algorithms/index.ts b/api/src/engine/connectors/exareme/transformations/algorithms/index.ts
index c723ebab7f62915d8c71f4e1e8a28a8a96c2fd2e..e32d56fdc6239581684c2123caaf24d88cae290d 100644
--- a/api/src/engine/connectors/exareme/transformations/algorithms/index.ts
+++ b/api/src/engine/connectors/exareme/transformations/algorithms/index.ts
@@ -12,7 +12,7 @@ const transformToAlgorithms = jsonata(`
'LOGISTIC_REGRESSION','TTEST_INDEPENDENT','TTEST_PAIRED',
'PEARSON','ID3','KMEANS','NAIVE_BAYES',
'TTEST_ONESAMPLE','PCA','CALIBRATION_BELT','CART',
- 'KAPLAN_MEIER','THREE_C', 'ONE_WAY_ANOVA', 'PEARSON', 'LINEAR_REGRESSION_CV'];
+ 'KAPLAN_MEIER','THREE_C', 'ONE_WAY_ANOVA', 'PEARSON_CORRELATION', 'LINEAR_REGRESSION_CV', 'TTEST_ONESAMPLE', 'PAIRED_TTEST'];
$linkedVars:= ['positive_class', 'positive_level', 'negative_level', 'outcome_neg', 'outcome_pos'];
$linkedCoVars:= ['referencevalues', 'xlevels'];
$truthy:= function($val) {(