From 12b9afda4164b4f4a2774097b05f51ad63033d34 Mon Sep 17 00:00:00 2001
From: Steve Reis <stevereis93@gmail.com>
Date: Tue, 23 Aug 2022 10:18:10 +0200
Subject: [PATCH] feat(exareme2): Ttest onesample and paired integration
---
.../ttest-onesample.handler.spec.ts | 24 ++++++++++---------
.../algorithms/ttest-onesample.handler.ts | 17 +++++++++----
.../algorithms/ttest-paired.handler.spec.ts | 24 ++++++++++---------
.../algorithms/ttest-paired.handler.ts | 21 +++++++++++-----
.../connectors/exareme/handlers/index.ts | 5 ++--
.../transformations/algorithms/index.ts | 2 +-
6 files changed, 57 insertions(+), 36 deletions(-)
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 258f810..4713037 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 0cb7bb1..be893f5 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 b1e0629..1797524 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 f7196ee..10ca096 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 c3041fe..a101809 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/transformations/algorithms/index.ts b/api/src/engine/connectors/exareme/transformations/algorithms/index.ts
index 6d71217..e32d56f 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_CORRELATION', '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) {(
--
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