diff --git a/api/src/engine/connectors/datashield/datashield.connector.ts b/api/src/engine/connectors/datashield/datashield.connector.ts
index d09e8f8dfbfa9995ad94384b79b9248bf17f0263..1f0cfd9000523cc293962565a26a4762fe6a1d19 100644
--- a/api/src/engine/connectors/datashield/datashield.connector.ts
+++ b/api/src/engine/connectors/datashield/datashield.connector.ts
@@ -260,6 +260,10 @@ export default class DataShieldConnector implements Connector {
datasets: data.datasets,
algorithm: {
name: data.algorithm.id,
+ parameters: data.algorithm.parameters.map((p) => ({
+ name: p.id,
+ value: p.value,
+ })),
},
};
@@ -319,21 +323,27 @@ export default class DataShieldConnector implements Connector {
const coVariable =
experiment.variables.length > 0 ? experiment.variables[0] : undefined;
+ const expToInput = {
+ algorithm: {
+ id: experiment.algorithm.name,
+ coVariable,
+ variables: experiment.coVariables,
+ },
+ datasets: experiment.datasets,
+ };
+
+ experiment.algorithm.parameters?.forEach((param) => {
+ if (!expToInput.algorithm[param.name]) {
+ // FIXME: the parameter should be added in a specific key entry (e.g. expToInput.algorithm.parameters')
+ // Should be fixed inside the Datashield API
+ expToInput.algorithm[param.name] = param.value;
+ }
+ });
+
const result = await firstValueFrom(
- this.httpService.post(
- path.href,
- {
- coVariable,
- variables: experiment.coVariables,
- algorithm: {
- id: experiment.algorithm.name,
- },
- datasets: experiment.datasets,
- },
- {
- headers: { cookie, 'Content-Type': 'application/json' },
- },
- ),
+ this.httpService.post(path.href, expToInput, {
+ headers: { cookie, 'Content-Type': 'application/json' },
+ }),
);
handlers(experiment, result.data, vars);
diff --git a/api/src/engine/connectors/datashield/handlers/algorithms/linear-regression.handler.spec.ts b/api/src/engine/connectors/datashield/handlers/algorithms/linear-regression.handler.spec.ts
index ca1f91e8b2e2d6de8af4ed0357420993d97531ea..962b13ac9c938ac539ea92e0eb57508be2a6cf04 100644
--- a/api/src/engine/connectors/datashield/handlers/algorithms/linear-regression.handler.spec.ts
+++ b/api/src/engine/connectors/datashield/handlers/algorithms/linear-regression.handler.spec.ts
@@ -87,22 +87,25 @@ describe('linear regression result handler', () => {
});
describe('Handle', () => {
- it('should output a tableResult', () => {
+ it('should output two TableResult', () => {
linearHandler.handle(experiment, data, vars);
- expect(experiment.results).toHaveLength(1);
+ expect(experiment.results).toHaveLength(2);
- const result = experiment.results[0] as TableResult;
+ const summary = experiment.results[0] as TableResult;
+ const coefs = experiment.results[1] as TableResult;
- expect(result.headers).toHaveLength(7);
+ expect(coefs.headers).toHaveLength(7);
data.coefficients.forEach((coef, index) => {
- expect(result.data[index][1]).toBe(coef.Estimate);
- expect(result.data[index][2]).toBe(coef['Std. Error']);
- expect(result.data[index][3]).toBe(coef['z-value']);
- expect(result.data[index][4]).toBe(coef['p-value']);
- expect(result.data[index][5]).toBe(coef['low0.95CI']);
- expect(result.data[index][6]).toBe(coef['high0.95CI']);
+ expect(coefs.data[index][1]).toBe(coef.Estimate);
+ expect(coefs.data[index][2]).toBe(coef['Std. Error']);
+ expect(coefs.data[index][3]).toBe(coef['z-value']);
+ expect(coefs.data[index][4]).toBe(coef['p-value']);
+ expect(coefs.data[index][5]).toBe(coef['low0.95CI']);
+ expect(coefs.data[index][6]).toBe(coef['high0.95CI']);
});
+
+ expect(summary.data.some((row) => !row[0] || !row[1])).toBeFalsy();
});
});
});
diff --git a/api/src/engine/connectors/datashield/handlers/algorithms/linear-regression.handler.ts b/api/src/engine/connectors/datashield/handlers/algorithms/linear-regression.handler.ts
index 623ca2190b5db5cf08c78e98f51ba76dcac0761e..8af3a9c6948820f2864d793868c5d0f49f017cfd 100644
--- a/api/src/engine/connectors/datashield/handlers/algorithms/linear-regression.handler.ts
+++ b/api/src/engine/connectors/datashield/handlers/algorithms/linear-regression.handler.ts
@@ -11,6 +11,10 @@ const lookupDict = {
'low0.95CI': 'Low 95% CI',
'high0.95CI': 'High 95% CI',
_row: '',
+ iter: 'Iteration(s)',
+ Nvalid: 'Valid observations',
+ Ntotal: 'Total observations',
+ df: 'Degrees of freedom',
};
const properties = [
@@ -23,6 +27,8 @@ const properties = [
'high0.95CI',
];
+const summaryProps = ['iter', 'Nvalid', 'Ntotal', 'df'];
+
export default class LinearRegressionHandler extends BaseHandler {
canHandle(algorithm: string, data: any): boolean {
return (
@@ -30,6 +36,19 @@ export default class LinearRegressionHandler extends BaseHandler {
);
}
+ getSummaryTable(data: any): TableResult {
+ const summaryTable: TableResult = {
+ name: 'Summary',
+ headers: [
+ { name: 'Name', type: 'string' },
+ { name: 'Value', type: 'string' },
+ ],
+ data: summaryProps.map((prop) => [lookupDict[prop], data[prop]]),
+ };
+
+ return summaryTable;
+ }
+
private getTableResult(data: any, vars: Variable[]): TableResult {
return {
name: 'Results',
@@ -50,9 +69,9 @@ export default class LinearRegressionHandler extends BaseHandler {
return this.next?.handle(experiment, data, vars);
const tableResult = this.getTableResult(data, vars);
+ const summaryResult = this.getSummaryTable(data);
- if (tableResult) {
- experiment.results.push(tableResult);
- }
+ if (summaryResult) experiment.results.push(summaryResult);
+ if (tableResult) experiment.results.push(tableResult);
}
}
diff --git a/api/src/engine/connectors/datashield/handlers/algorithms/logistic-regression.handler.spec.ts b/api/src/engine/connectors/datashield/handlers/algorithms/logistic-regression.handler.spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..c23fdf2b58af9e2cd0f32f273846937bff113ad4
--- /dev/null
+++ b/api/src/engine/connectors/datashield/handlers/algorithms/logistic-regression.handler.spec.ts
@@ -0,0 +1,102 @@
+import { Experiment } from '../../../../models/experiment/experiment.model';
+import { TableResult } from '../../../../models/result/table-result.model';
+import LogisticRegressionHandler from './logistic-regression.handler';
+
+const data = {
+ Nvalid: 214,
+ Nmissing: 0,
+ Ntotal: 214,
+ 'disclosure.risk': [[0], [0]],
+ errorMessage: [['No errors'], ['No errors']],
+ nsubs: 214,
+ iter: 6,
+ formula:
+ 'race ~ Urea.nitrogen..Mass.volume..in.Serum.or.Plasma + Albumin..Mass.volume..in.Serum.or.Plasma',
+ coefficients: [
+ {
+ Estimate: -4.53,
+ 'Std. Error': 3.4497,
+ 'z-value': -1.3132,
+ 'p-value': 0.1891,
+ 'low0.95CI.LP': -11.2914,
+ 'high0.95CI.LP': 2.2313,
+ P_OR: 0.0107,
+ 'low0.95CI.P_OR': 0,
+ 'high0.95CI.P_OR': 0.903,
+ _row: '(Intercept)',
+ },
+ {
+ Estimate: 0.0598,
+ 'Std. Error': 0.0663,
+ 'z-value': 0.9023,
+ 'p-value': 0.3669,
+ 'low0.95CI.LP': -0.0701,
+ 'high0.95CI.LP': 0.1898,
+ P_OR: 1.0617,
+ 'low0.95CI.P_OR': 0.9323,
+ 'high0.95CI.P_OR': 1.209,
+ _row: 'Urea.nitrogen..Mass.volume..in.Serum.or.Plasma',
+ },
+ {
+ Estimate: 0.4569,
+ 'Std. Error': 0.7518,
+ 'z-value': 0.6078,
+ 'p-value': 0.5433,
+ 'low0.95CI.LP': -1.0166,
+ 'high0.95CI.LP': 1.9304,
+ P_OR: 1.5792,
+ 'low0.95CI.P_OR': 0.3618,
+ 'high0.95CI.P_OR': 6.8926,
+ _row: 'Albumin..Mass.volume..in.Serum.or.Plasma',
+ },
+ ],
+ dev: 172.4603,
+ df: 211,
+ 'output.information':
+ 'SEE TOP OF OUTPUT FOR INFORMATION ON MISSING DATA AND ERROR MESSAGES',
+};
+
+const createExperiment = (): Experiment => ({
+ id: 'dummy-id',
+ name: 'Testing purpose',
+ algorithm: {
+ name: 'logistic-regression',
+ parameters: [
+ {
+ name: 'pos-level',
+ value: 'White',
+ },
+ ],
+ },
+ datasets: ['sophia.db'],
+ domain: 'dementia',
+ variables: ['race'],
+ coVariables: [
+ 'Urea.nitrogen..Mass.volume..in.Serum.or.Plasma',
+ 'Albumin..Mass.volume..in.Serum.or.Plasma',
+ ],
+ results: [],
+});
+
+describe('Logistic Regression Handler', () => {
+ describe('Normal usage', () => {
+ it('should return two TableResult', () => {
+ const experiment = createExperiment();
+ const handler = new LogisticRegressionHandler();
+ handler.handle(experiment, data, []);
+
+ expect(experiment.results).toHaveLength(2);
+
+ const summary = experiment.results[0] as TableResult;
+ const coefs = experiment.results[1] as TableResult;
+
+ expect(coefs.headers.length).toBeGreaterThan(0);
+ expect(coefs.data.length).toBeGreaterThan(0);
+ expect(coefs.data.some((row) => row.some((cell) => !cell)));
+
+ expect(summary.headers.length).toBe(2);
+ expect(summary.data.length).toBeGreaterThan(0);
+ expect(summary.data.some((row) => !row[0] || !row[1])).toBeFalsy();
+ });
+ });
+});
diff --git a/api/src/engine/connectors/datashield/handlers/algorithms/logistic-regression.handler.ts b/api/src/engine/connectors/datashield/handlers/algorithms/logistic-regression.handler.ts
new file mode 100644
index 0000000000000000000000000000000000000000..4dc980f4f875394216696e83d91f14fb7ed123e9
--- /dev/null
+++ b/api/src/engine/connectors/datashield/handlers/algorithms/logistic-regression.handler.ts
@@ -0,0 +1,82 @@
+import { Experiment } from '../../../../models/experiment/experiment.model';
+import { TableResult } from '../../../../models/result/table-result.model';
+import { Variable } from '../../../../models/variable.model';
+import BaseHandler from '../base.handler';
+
+const lookupDict = {
+ Estimate: 'Estimate',
+ 'Std. Error': 'Std. Error',
+ 'z-value': 'Z value',
+ 'p-value': 'P value',
+ 'low0.95CI.LP': 'Low 95% CI',
+ 'high0.95CI.LP': 'High 95% CI',
+ P_OR: 'P OR',
+ 'low0.95CI.P_OR': 'Low 95% CI P_OR',
+ 'high0.95CI.P_OR': 'High 95% CI P OR',
+ _row: '',
+ iter: 'Iteration(s)',
+ Nvalid: 'Valid observations',
+ Ntotal: 'Total observations',
+ df: 'Degrees of freedom',
+};
+
+const properties = [
+ '_row',
+ 'Estimate',
+ 'Std. Error',
+ 'z-value',
+ 'p-value',
+ 'low0.95CI.LP',
+ 'high0.95CI.LP',
+ // 'P_OR', // What is P_OR? Not defined in the ds' documentation
+ // 'low0.95CI.P_OR',
+ // 'high0.95CI.P_OR',
+];
+
+const summaryProps = ['iter', 'Nvalid', 'Ntotal', 'df'];
+
+export default class LogisticRegressionHandler extends BaseHandler {
+ canHandle(algorithm: string, data: any): boolean {
+ return (
+ algorithm.toLowerCase() === 'logistic-regression' &&
+ !!data['coefficients']
+ );
+ }
+
+ getSummaryTable(data: any): TableResult {
+ return {
+ name: 'Summary',
+ headers: [
+ { name: 'Name', type: 'string' },
+ { name: 'Value', type: 'string' },
+ ],
+ data: summaryProps.map((prop) => [lookupDict[prop], data[prop]]),
+ };
+ }
+
+ getTableResult(data: unknown, vars: Variable[]): TableResult {
+ return {
+ name: 'Results',
+ headers: properties.map((name) => ({
+ name: lookupDict[name],
+ type: 'string',
+ })),
+ data: data['coefficients'].map((row: any) => {
+ const variable = vars.find((v) => v.id === row['_row']);
+ if (variable) row['_row'] = variable.label ?? variable.id;
+ return properties.map((name) => row[name]);
+ }),
+ };
+ }
+
+ handle(experiment: Experiment, data: unknown, vars: Variable[]): void {
+ if (!this.canHandle(experiment.algorithm.name, data))
+ return this.next?.handle(experiment, data, vars);
+
+ const tableResult = this.getTableResult(data, vars);
+ const summaryTable = this.getSummaryTable(data);
+
+ if (summaryTable) experiment.results.push(summaryTable);
+ if (tableResult) experiment.results.push(tableResult);
+ }
+}
diff --git a/api/src/engine/connectors/datashield/handlers/algorithms/terminal-algorithm.handler.ts b/api/src/engine/connectors/datashield/handlers/algorithms/terminal-algorithm.handler.ts
index 17df4bf0962e99598383ed1403a8b99e77618338..289fcc6818dd72c8cdb263e606f908243138badd 100644
--- a/api/src/engine/connectors/datashield/handlers/algorithms/terminal-algorithm.handler.ts
+++ b/api/src/engine/connectors/datashield/handlers/algorithms/terminal-algorithm.handler.ts
@@ -17,6 +17,6 @@ export default class TerminalAlgorithmHandler extends BaseHandler {
};
experiment.results.push(alertResult);
- experiment.status = ExperimentStatus.WARN;
+ experiment.status = ExperimentStatus.ERROR;
}
}
diff --git a/api/src/engine/connectors/datashield/handlers/index.ts b/api/src/engine/connectors/datashield/handlers/index.ts
index 3275a8ea79c49c11a5cf32e8dc41da0f703b0115..9948a2fcf9d6e9a9c6db071210202530a7a418e1 100644
--- a/api/src/engine/connectors/datashield/handlers/index.ts
+++ b/api/src/engine/connectors/datashield/handlers/index.ts
@@ -2,12 +2,14 @@ import { Variable } from 'src/engine/models/variable.model';
import { Experiment } from '../../../../engine/models/experiment/experiment.model';
import ErrorAlgorithmHandler from './algorithms/error-algorithm.handler';
import LinearRegressionHandler from './algorithms/linear-regression.handler';
+import LogisticRegressionHandler from './algorithms/logistic-regression.handler';
import TerminalAlgorithmHandler from './algorithms/terminal-algorithm.handler';
const start = new ErrorAlgorithmHandler();
start
.setNext(new LinearRegressionHandler())
+ .setNext(new LogisticRegressionHandler())
.setNext(new TerminalAlgorithmHandler());
export default (
diff --git a/api/src/engine/models/experiment/experiment.model.ts b/api/src/engine/models/experiment/experiment.model.ts
index bffd7e8f9743716299aec5a22e4da335bdf10c60..fca29ffc178d065987211b4f1db150309fdb1ae3 100644
--- a/api/src/engine/models/experiment/experiment.model.ts
+++ b/api/src/engine/models/experiment/experiment.model.ts
@@ -12,7 +12,6 @@ export enum ExperimentStatus {
INIT = 'init',
PENDING = 'pending',
SUCCESS = 'success',
- WARN = 'warn',
ERROR = 'error',
}
diff --git a/api/src/schema.gql b/api/src/schema.gql
index 9ac6694a8a9c43a82c3770c9f4aa56cb1106dd3e..87e41eda3141dd8fd914a756e86362f7e68ecf4e 100644
--- a/api/src/schema.gql
+++ b/api/src/schema.gql
@@ -198,7 +198,6 @@ enum ExperimentStatus {
INIT
PENDING
SUCCESS
- WARN
ERROR
}