diff --git a/api/src/engine/connectors/csv/csv.connector.ts b/api/src/engine/connectors/csv/csv.connector.ts
index 9d1e2e7a4697ec6faf9edefe4372c8f41fe78b04..9397ddbc7ddc31fbc3b2d9d8d2fdd7358850405b 100644
--- a/api/src/engine/connectors/csv/csv.connector.ts
+++ b/api/src/engine/connectors/csv/csv.connector.ts
@@ -1,11 +1,10 @@
import { HttpService } from '@nestjs/axios';
import { NotImplementedException } from '@nestjs/common';
import { firstValueFrom } from 'rxjs';
-import {
- Dictionary,
- ExperimentResult,
-} from '../../../common/interfaces/utilities.interface';
-import Connector from '../../../engine/interfaces/connector.interface';
+import { Dictionary } from '../../../common/interfaces/utilities.interface';
+import Connector, {
+ RunResult,
+} from '../../../engine/interfaces/connector.interface';
import EngineOptions from '../../../engine/interfaces/engine-options.interface';
import { Domain } from '../../../engine/models/domain.model';
import { Algorithm } from '../../../engine/models/experiment/algorithm.model';
@@ -26,7 +25,7 @@ export default class CSVConnector implements Connector {
throw new NotImplementedException();
}
- async runExperiment(): Promise<ExperimentResult[]> {
+ async runExperiment(): Promise<RunResult> {
throw new NotImplementedException();
}
diff --git a/api/src/engine/connectors/datashield/datashield.connector.ts b/api/src/engine/connectors/datashield/datashield.connector.ts
index 135d72682a0b5b35c6fce8b8406d218226c50749..d09e8f8dfbfa9995ad94384b79b9248bf17f0263 100644
--- a/api/src/engine/connectors/datashield/datashield.connector.ts
+++ b/api/src/engine/connectors/datashield/datashield.connector.ts
@@ -2,20 +2,19 @@ import { HttpService } from '@nestjs/axios';
import { InternalServerErrorException, Logger } from '@nestjs/common';
import { Request } from 'express';
import { catchError, firstValueFrom } from 'rxjs';
-import {
- ExperimentResult,
- MIME_TYPES,
-} from '../../../common/interfaces/utilities.interface';
+import { ExperimentResult } from '../../../common/interfaces/utilities.interface';
import { errorAxiosHandler } from '../../../common/utils/shared.utils';
import EngineService from '../../../engine/engine.service';
import ConnectorConfiguration from '../../../engine/interfaces/connector-configuration.interface';
-import Connector from '../../../engine/interfaces/connector.interface';
+import Connector, {
+ RunResult,
+} from '../../../engine/interfaces/connector.interface';
import EngineOptions from '../../../engine/interfaces/engine-options.interface';
import { Domain } from '../../../engine/models/domain.model';
import { Algorithm } from '../../../engine/models/experiment/algorithm.model';
import { AllowedLink } from '../../../engine/models/experiment/algorithm/nominal-parameter.model';
import { Experiment } from '../../../engine/models/experiment/experiment.model';
-import { RawResult } from '../../../engine/models/result/raw-result.model';
+import { AlertLevel } from '../../../engine/models/result/alert-result.model';
import {
TableResult,
TableStyle,
@@ -23,6 +22,7 @@ import {
import { Variable } from '../../../engine/models/variable.model';
import { ExperimentCreateInput } from '../../../experiments/models/input/experiment-create.input';
import { User } from '../../../users/models/user.model';
+import handlers from './handlers';
import {
dataToGroups,
dsGroup,
@@ -120,12 +120,7 @@ export default class DataShieldConnector implements Connector {
{
name: 'pos-level',
label: 'Positive level',
- linkedTo: AllowedLink.VARIABLE,
- isRequired: true,
- },
- {
- name: 'neg-level',
- label: 'Negative level',
+ hint: 'All other categories will be considered negative',
linkedTo: AllowedLink.VARIABLE,
isRequired: true,
},
@@ -138,7 +133,7 @@ export default class DataShieldConnector implements Connector {
variable: Variable,
datasets: string[],
cookie?: string,
- ): Promise<RawResult> {
+ ): Promise<ExperimentResult> {
const url = new URL(this.options.baseurl + `histogram`);
url.searchParams.append('var', variable.id);
@@ -159,12 +154,9 @@ export default class DataShieldConnector implements Connector {
DataShieldConnector.logger.warn('Cannot parse histogram result');
DataShieldConnector.logger.verbose(path);
return {
- rawdata: {
- data:
- 'Engine error when processing the request. Reason: ' +
- response.data,
- type: MIME_TYPES.ERROR,
- },
+ level: AlertLevel.ERROR,
+ message:
+ 'Engine error when processing the request. Reason: ' + response.data,
};
}
@@ -250,7 +242,7 @@ export default class DataShieldConnector implements Connector {
async runExperiment(
data: ExperimentCreateInput,
request: Request,
- ): Promise<ExperimentResult[]> {
+ ): Promise<RunResult> {
const user = request.user as User;
const cookie = [`sid=${user.extraFields['sid']}`, `user=${user.id}`].join(
';',
@@ -281,7 +273,7 @@ export default class DataShieldConnector implements Connector {
switch (data.algorithm.id) {
case 'MULTIPLE_HISTOGRAMS': {
- expResult.results = await Promise.all<RawResult>(
+ expResult.results = await Promise.all<ExperimentResult>(
allVariables.map((variable) =>
this.getHistogram(variable, expResult.datasets, cookie),
),
@@ -304,9 +296,47 @@ export default class DataShieldConnector implements Connector {
expResult.results = results;
break;
}
+ default: {
+ expResult.results = [];
+ await this.runAlgorithm(expResult, allVariables, cookie);
+ }
}
- return expResult.results;
+ return {
+ results: expResult.results,
+ status: expResult.status,
+ };
+ }
+
+ private async runAlgorithm(
+ experiment: Experiment,
+ vars: Variable[],
+ cookie?: string,
+ ) {
+ const path = new URL('/runAlgorithm', this.options.baseurl);
+
+ // Covariable and variable are inversed in Datashield API
+ const coVariable =
+ experiment.variables.length > 0 ? experiment.variables[0] : undefined;
+
+ 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' },
+ },
+ ),
+ );
+
+ handlers(experiment, result.data, vars);
}
async logout(request: Request): Promise<void> {
diff --git a/api/src/engine/connectors/datashield/handlers/algorithms/error-algorithm.handler.spec.ts b/api/src/engine/connectors/datashield/handlers/algorithms/error-algorithm.handler.spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..c98aac3c296578a453816679b11688ec9da6aa98
--- /dev/null
+++ b/api/src/engine/connectors/datashield/handlers/algorithms/error-algorithm.handler.spec.ts
@@ -0,0 +1,44 @@
+import { AlertResult } from '../../../../models/result/alert-result.model';
+import { Experiment } from '../../../../models/experiment/experiment.model';
+import ErrorAlgorithmHandler from './error-algorithm.handler';
+
+const vars = [];
+
+const createExperiment = (): Experiment => ({
+ id: 'dummy-id',
+ name: 'Testing purpose',
+ algorithm: {
+ name: 'LINEAR_REGRESSION',
+ },
+ datasets: ['desd-synthdata'],
+ domain: 'dementia',
+ variables: ['lefthippocampus'],
+ coVariables: ['righthippocampus', 'leftamygdala'],
+ results: [],
+});
+
+const data = {
+ errorMessage: [['There is an error']],
+};
+
+describe('Error handler', () => {
+ let errorHandler: ErrorAlgorithmHandler;
+ let exp: Experiment;
+
+ beforeEach(() => {
+ errorHandler = new ErrorAlgorithmHandler();
+ exp = createExperiment();
+ });
+
+ describe('Handle', () => {
+ it('should output an error message', () => {
+ errorHandler.handle(exp, data, vars);
+
+ expect(exp.results).toHaveLength(1);
+
+ const result = exp.results[0] as AlertResult;
+
+ expect(result.message).toBe(data.errorMessage[0][0]);
+ });
+ });
+});
diff --git a/api/src/engine/connectors/datashield/handlers/algorithms/error-algorithm.handler.ts b/api/src/engine/connectors/datashield/handlers/algorithms/error-algorithm.handler.ts
new file mode 100644
index 0000000000000000000000000000000000000000..5332b195c2e3b18b9be2cf3ded1198de4f85db00
--- /dev/null
+++ b/api/src/engine/connectors/datashield/handlers/algorithms/error-algorithm.handler.ts
@@ -0,0 +1,34 @@
+import { Variable } from '../../../../models/variable.model';
+
+import { AlertLevel } from '../../../../models/result/alert-result.model';
+import {
+ Experiment,
+ ExperimentStatus,
+} from '../../../../models/experiment/experiment.model';
+import BaseHandler from '../base.handler';
+
+export default class ErrorAlgorithmHandler extends BaseHandler {
+ canHandle(data: any) {
+ const errors = data.errorMessage;
+
+ return errors && errors[0] && errors[0][0] && errors[0][0] !== 'No errors';
+ }
+
+ handle(experiment: Experiment, data: any, vars: Variable[]): void {
+ if (!this.canHandle(data)) {
+ return this.next?.handle(experiment, data, vars);
+ }
+
+ const errors = data.errorMessage as string[][];
+
+ errors
+ .filter((err) => err)
+ .map((error) => ({
+ level: AlertLevel.ERROR,
+ message: error.join(' '),
+ }))
+ .forEach((error) => experiment.results.push(error));
+
+ experiment.status = ExperimentStatus.ERROR;
+ }
+}
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
new file mode 100644
index 0000000000000000000000000000000000000000..ca1f91e8b2e2d6de8af4ed0357420993d97531ea
--- /dev/null
+++ b/api/src/engine/connectors/datashield/handlers/algorithms/linear-regression.handler.spec.ts
@@ -0,0 +1,108 @@
+import { Experiment } from '../../../../models/experiment/experiment.model';
+import { TableResult } from '../../../../models/result/table-result.model';
+import { Variable } from '../../../../models/variable.model';
+import LinearRegressionHandler from './linear-regression.handler';
+
+const data = {
+ Nvalid: 107,
+ Nmissing: 506,
+ Ntotal: 613,
+ 'disclosure.risk': [[0]],
+ errorMessage: [['No errors']],
+ nsubs: 107,
+ iter: 3,
+ formula:
+ 'Alanine.aminotransferase..Enzymatic.activity.volume..in.Serum.or.Plasma ~ Urea.nitrogen..Mass.volume..in.Serum.or.Plasma + Albumin..Mass.volume..in.Serum.or.Plasma',
+ coefficients: [
+ {
+ Estimate: -0.2119,
+ 'Std. Error': 30.8718,
+ 'z-value': -0.0069,
+ 'p-value': 0.9945,
+ 'low0.95CI': -60.7195,
+ 'high0.95CI': 60.2956,
+ _row: '(Intercept)',
+ },
+ {
+ Estimate: 0.1606,
+ 'Std. Error': 0.4521,
+ 'z-value': 0.3553,
+ 'p-value': 0.7224,
+ 'low0.95CI': -0.7255,
+ 'high0.95CI': 1.0468,
+ _row: 'Urea.nitrogen..Mass.volume..in.Serum.or.Plasma',
+ },
+ {
+ Estimate: 3.7592,
+ 'Std. Error': 6.8887,
+ 'z-value': 0.5457,
+ 'p-value': 0.5853,
+ 'low0.95CI': -9.7423,
+ 'high0.95CI': 17.2608,
+ _row: 'Albumin..Mass.volume..in.Serum.or.Plasma',
+ },
+ ],
+ dev: 15817.4616,
+ df: 104,
+ '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: 'linear-regression',
+ },
+ datasets: ['sophia.db'],
+ domain: 'dementia',
+ variables: ['lefthippocampus'],
+ coVariables: ['righthippocampus', 'leftamygdala'],
+ results: [],
+});
+
+const vars: Variable[] = [
+ {
+ id: 'Alanine.aminotransferase..Enzymatic.activity.volume..in.Serum.or.Plasma',
+ label:
+ 'Alanine aminotransferase Enzymatic activity volume in Serum or Plasma',
+ },
+ {
+ id: 'Urea.nitrogen..Mass.volume..in.Serum.or.Plasma',
+ label: 'Urea nitrogen Mass volume in Serum or Plasma',
+ },
+ {
+ id: 'Albumin..Mass.volume..in.Serum.or.Plasma',
+ label: 'Albumin Mass volume in Serum or Plasma',
+ },
+];
+
+describe('linear regression result handler', () => {
+ let linearHandler: LinearRegressionHandler;
+ let experiment: Experiment;
+
+ beforeEach(() => {
+ linearHandler = new LinearRegressionHandler();
+ experiment = createExperiment();
+ });
+
+ describe('Handle', () => {
+ it('should output a tableResult', () => {
+ linearHandler.handle(experiment, data, vars);
+
+ expect(experiment.results).toHaveLength(1);
+
+ const result = experiment.results[0] as TableResult;
+
+ expect(result.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']);
+ });
+ });
+ });
+});
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
new file mode 100644
index 0000000000000000000000000000000000000000..623ca2190b5db5cf08c78e98f51ba76dcac0761e
--- /dev/null
+++ b/api/src/engine/connectors/datashield/handlers/algorithms/linear-regression.handler.ts
@@ -0,0 +1,58 @@
+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': 'Low 95% CI',
+ 'high0.95CI': 'High 95% CI',
+ _row: '',
+};
+
+const properties = [
+ '_row',
+ 'Estimate',
+ 'Std. Error',
+ 'z-value',
+ 'p-value',
+ 'low0.95CI',
+ 'high0.95CI',
+];
+
+export default class LinearRegressionHandler extends BaseHandler {
+ canHandle(algorithm: string, data: any): boolean {
+ return (
+ algorithm.toLowerCase() === 'linear-regression' && data['coefficients']
+ );
+ }
+
+ private getTableResult(data: any, 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);
+
+ 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
new file mode 100644
index 0000000000000000000000000000000000000000..17df4bf0962e99598383ed1403a8b99e77618338
--- /dev/null
+++ b/api/src/engine/connectors/datashield/handlers/algorithms/terminal-algorithm.handler.ts
@@ -0,0 +1,22 @@
+import {
+ AlertLevel,
+ AlertResult,
+} from '../../../../models/result/alert-result.model';
+import {
+ Experiment,
+ ExperimentStatus,
+} from '../../../../models/experiment/experiment.model';
+import BaseHandler from '../base.handler';
+
+export default class TerminalAlgorithmHandler extends BaseHandler {
+ handle(experiment: Experiment): void {
+ const alertResult: AlertResult = {
+ level: AlertLevel.ERROR,
+ message:
+ "The algorithm's result cannot be processed by the engine. Either the algorithm is not supported or the result is not in the expected format.",
+ };
+
+ experiment.results.push(alertResult);
+ experiment.status = ExperimentStatus.WARN;
+ }
+}
diff --git a/api/src/engine/connectors/datashield/handlers/base.handler.ts b/api/src/engine/connectors/datashield/handlers/base.handler.ts
new file mode 100644
index 0000000000000000000000000000000000000000..f90c575e1f2f06935046608e6fb60d161d1e4f86
--- /dev/null
+++ b/api/src/engine/connectors/datashield/handlers/base.handler.ts
@@ -0,0 +1,19 @@
+import { Logger } from '@nestjs/common';
+import { Variable } from '../../../models/variable.model';
+import { Experiment } from '../../../models/experiment/experiment.model';
+import ResultHandler from './result-handler.interface';
+
+export default abstract class BaseHandler implements ResultHandler {
+ protected static readonly logger = new Logger(this.name);
+
+ next: ResultHandler = null;
+
+ setNext(h: ResultHandler): ResultHandler {
+ this.next = h;
+ return h;
+ }
+
+ handle(experiment: Experiment, data: unknown, vars: Variable[]): void {
+ this.next?.handle(experiment, data, vars);
+ }
+}
diff --git a/api/src/engine/connectors/datashield/handlers/index.ts b/api/src/engine/connectors/datashield/handlers/index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..3275a8ea79c49c11a5cf32e8dc41da0f703b0115
--- /dev/null
+++ b/api/src/engine/connectors/datashield/handlers/index.ts
@@ -0,0 +1,20 @@
+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 TerminalAlgorithmHandler from './algorithms/terminal-algorithm.handler';
+
+const start = new ErrorAlgorithmHandler();
+
+start
+ .setNext(new LinearRegressionHandler())
+ .setNext(new TerminalAlgorithmHandler());
+
+export default (
+ exp: Experiment,
+ data: unknown,
+ vars: Variable[],
+): Experiment => {
+ start.handle(exp, data, vars);
+ return exp;
+};
diff --git a/api/src/engine/connectors/datashield/handlers/result-handler.interface.ts b/api/src/engine/connectors/datashield/handlers/result-handler.interface.ts
new file mode 100644
index 0000000000000000000000000000000000000000..94f16bf04cd8a66822e63a91d56faf9d4ee66eb7
--- /dev/null
+++ b/api/src/engine/connectors/datashield/handlers/result-handler.interface.ts
@@ -0,0 +1,8 @@
+import { Experiment } from '../../../models/experiment/experiment.model';
+import { Variable } from '../../../models/variable.model';
+
+// produce algo handler
+export default interface ResultHandler {
+ setNext(h: ResultHandler): ResultHandler;
+ handle(partialExperiment: Experiment, data: unknown, vars: Variable[]): void;
+}
diff --git a/api/src/engine/connectors/local/local.connector.ts b/api/src/engine/connectors/local/local.connector.ts
index bfc517a33c9d32bcf27a1db48ab50daefdd14a27..5c0d749734a9d6f9f559f98e3cc72210ae23f1e8 100644
--- a/api/src/engine/connectors/local/local.connector.ts
+++ b/api/src/engine/connectors/local/local.connector.ts
@@ -1,8 +1,7 @@
-import Connector from '../../interfaces/connector.interface';
+import { User } from '../../../users/models/user.model';
+import Connector, { RunResult } from '../../interfaces/connector.interface';
import { Domain } from '../../models/domain.model';
import { Algorithm } from '../../models/experiment/algorithm.model';
-import { ResultUnion } from '../../models/result/common/result-union.model';
-import { User } from '../../../users/models/user.model';
export default class LocalConnector implements Connector {
async login(): Promise<User> {
@@ -16,7 +15,7 @@ export default class LocalConnector implements Connector {
throw new Error('Method not implemented.');
}
- async runExperiment(): Promise<Array<typeof ResultUnion>> {
+ async runExperiment(): Promise<RunResult> {
throw new Error('Method not implemented.');
}
diff --git a/api/src/engine/engine.service.ts b/api/src/engine/engine.service.ts
index c9661520f1cb929da165e584eced8f43bb1b3ebb..b4b1824e94b1a2b53c1caf13430b92c3a8a57bfa 100644
--- a/api/src/engine/engine.service.ts
+++ b/api/src/engine/engine.service.ts
@@ -10,7 +10,6 @@ import { ConfigType } from '@nestjs/config';
import { Cache } from 'cache-manager';
import { Request } from 'express';
import { Observable } from 'rxjs';
-import { ExperimentResult } from '../common/interfaces/utilities.interface';
import cacheConfig from '../config/cache.config';
import { ExperimentCreateInput } from '../experiments/models/input/experiment-create.input';
import { ExperimentEditInput } from '../experiments/models/input/experiment-edit.input';
@@ -18,17 +17,19 @@ import { UpdateUserInput } from '../users/inputs/update-user.input';
import { User } from '../users/models/user.model';
import { ENGINE_MODULE_OPTIONS } from './engine.constants';
import ConnectorConfiguration from './interfaces/connector-configuration.interface';
-import Connector from './interfaces/connector.interface';
+import Connector, { RunResult } from './interfaces/connector.interface';
import EngineOptions from './interfaces/engine-options.interface';
import { Domain } from './models/domain.model';
import { Algorithm } from './models/experiment/algorithm.model';
import {
Experiment,
+ ExperimentStatus,
PartialExperiment,
} from './models/experiment/experiment.model';
import { ListExperiments } from './models/experiment/list-experiments.model';
import { FilterConfiguration } from './models/filter/filter-configuration';
import { FormulaOperation } from './models/formula/formula-operation.model';
+import { AlertLevel } from './models/result/alert-result.model';
import { Variable } from './models/variable.model';
const DOMAINS_CACHE_KEY = 'domains';
@@ -161,9 +162,17 @@ export default class EngineService implements Connector {
async runExperiment(
data: ExperimentCreateInput,
req?: Request,
- ): Promise<ExperimentResult[]> {
+ ): Promise<RunResult> {
if (!this.connector.runExperiment) throw new NotImplementedException();
- return this.connector.runExperiment(data, req);
+ return this.connector.runExperiment(data, req).catch((err) => ({
+ results: [
+ {
+ level: AlertLevel.ERROR,
+ message: `Error while running experiment, details '${err}'`,
+ },
+ ],
+ status: ExperimentStatus.ERROR,
+ }));
}
async listExperiments?(
diff --git a/api/src/engine/interfaces/connector.interface.ts b/api/src/engine/interfaces/connector.interface.ts
index f1cd94914674d242cd7967861f9355fb2ab3809f..bca83dfda48fa27a7cef0538ea9f581e6e33c78e 100644
--- a/api/src/engine/interfaces/connector.interface.ts
+++ b/api/src/engine/interfaces/connector.interface.ts
@@ -9,6 +9,7 @@ import { Domain } from '../models/domain.model';
import { Algorithm } from '../models/experiment/algorithm.model';
import {
Experiment,
+ ExperimentStatus,
PartialExperiment,
} from '../models/experiment/experiment.model';
import { ListExperiments } from '../models/experiment/list-experiments.model';
@@ -16,6 +17,10 @@ import { FilterConfiguration } from '../models/filter/filter-configuration';
import { FormulaOperation } from '../models/formula/formula-operation.model';
import ConnectorConfiguration from './connector-configuration.interface';
+export type RunResult = {
+ results: ExperimentResult[];
+ status?: ExperimentStatus;
+};
export default interface Connector {
/**
* Allow specific configuration for the engine
@@ -51,7 +56,7 @@ export default interface Connector {
runExperiment?(
data: ExperimentCreateInput,
req?: Request,
- ): Promise<ExperimentResult[]>;
+ ): Promise<RunResult>;
/**
* Get a list of experiment (limited to 10 per page)
diff --git a/api/src/experiments/experiments.resolver.ts b/api/src/experiments/experiments.resolver.ts
index 3739933dfa2c2b736f4851375afc0f272e456b3c..c96416a187c23e2a1e304bc681db99fb8ce8fa4f 100644
--- a/api/src/experiments/experiments.resolver.ts
+++ b/api/src/experiments/experiments.resolver.ts
@@ -1,10 +1,10 @@
import { Logger, UseGuards } from '@nestjs/common';
import { Args, Mutation, Query, Resolver } from '@nestjs/graphql';
import { Request } from 'express';
-import EngineService from '../engine/engine.service';
import { GlobalAuthGuard } from '../auth/guards/global-auth.guard';
import { GQLRequest } from '../common/decorators/gql-request.decoractor';
import { CurrentUser } from '../common/decorators/user.decorator';
+import EngineService from '../engine/engine.service';
import {
Experiment,
ExperimentStatus,
@@ -77,14 +77,14 @@ export class ExperimentsResolver {
return this.engineService.createExperiment(data, isTransient, req);
}
- //if the experiment is transient we wait a response before returning a response
+ //if the experiment is transient we wait a connector's response before returning a client's response
if (isTransient) {
const results = await this.engineService.runExperiment(data, req);
const expTransient = this.experimentService.dataToExperiment(data, user);
return { ...expTransient, results, status: ExperimentStatus.SUCCESS };
}
- //if not we will create an experiment in local db
+ //if not transient we will create an experiment in local db
const experiment = await this.experimentService.create(
data,
user,
@@ -92,13 +92,13 @@ export class ExperimentsResolver {
);
//create an async query that will update the result when it's done
- this.engineService.runExperiment(data, req).then((results) => {
+ this.engineService.runExperiment(data, req).then((runResult) => {
this.experimentService.update(
experiment.id,
{
- results,
+ status: ExperimentStatus.SUCCESS, // default status
+ ...runResult,
finishedAt: new Date().toISOString(),
- status: ExperimentStatus.SUCCESS,
},
user,
);
diff --git a/api/src/schema.gql b/api/src/schema.gql
index 88e2456ea1e31782c278e0e2b1bebb63c59502bd..9ac6694a8a9c43a82c3770c9f4aa56cb1106dd3e 100644
--- a/api/src/schema.gql
+++ b/api/src/schema.gql
@@ -21,157 +21,6 @@ type User {
agreeNDA: Boolean
}
-type AuthenticationOutput {
- accessToken: String!
- refreshToken: String!
-}
-
-type Configuration {
- connectorId: String!
- hasGalaxy: Boolean @deprecated(reason: "Only used for legacy reason should be avoided")
-
- """Indicates if histograms can handle grouping"""
- hasGrouping: Boolean
-
- """Indicates if filters and formula are enabled"""
- hasFilters: Boolean
- version: String!
- skipAuth: Boolean
- skipTos: Boolean
- enableSSO: Boolean
-}
-
-type Dataset {
- id: String!
- label: String
- isLongitudinal: Boolean
-}
-
-type Group {
- id: String!
- label: String
- description: String
- groups: [String!]
-
- """List of variable's ids"""
- variables: [String!]
-
- """List of datasets avalaible, set null if all datasets allowed"""
- datasets: [String!]
-}
-
-type Category {
- value: String!
- label: String
-}
-
-type Variable {
- id: String!
- label: String
- type: String
- description: String
- enumerations: [Category!]
- groups: [Group!]
-
- """List of datasets avalaible, set null if all datasets allowed"""
- datasets: [String!]
-}
-
-type Domain {
- id: String!
- label: String
- description: String
- version: String
- groups: [Group!]!
- variables: [Variable!]!
- datasets: [Dataset!]!
- rootGroup: Group!
-}
-
-type OptionValue {
- value: String!
- label: String!
-}
-
-type NominalParameter implements BaseParameter {
- name: String!
- label: String
-
- """Small hint (description) for the end user"""
- hint: String
- isRequired: Boolean
- hasMultiple: Boolean
- defaultValue: String
-
- """Id of the parameter"""
- linkedTo: AllowedLink
- allowedValues: [OptionValue!]
-}
-
-"""The supported links."""
-enum AllowedLink {
- VARIABLE
- COVARIABLE
-}
-
-type NumberParameter implements BaseParameter {
- name: String!
- label: String
-
- """Small hint (description) for the end user"""
- hint: String
- isRequired: Boolean
- hasMultiple: Boolean
- defaultValue: String
- min: Float
- max: Float
- isReal: Boolean
-}
-
-type StringParameter implements BaseParameter {
- name: String!
- label: String
-
- """Small hint (description) for the end user"""
- hint: String
- isRequired: Boolean
- hasMultiple: Boolean
- defaultValue: String
-}
-
-type VariableParameter {
- hint: String
- isRequired: Boolean
- hasMultiple: Boolean
-
- """If undefined, all types are allowed"""
- allowedTypes: [String!]
-}
-
-type Algorithm {
- id: String!
- parameters: [BaseParameter!]
- variable: VariableParameter!
- coVariable: VariableParameter
- hasFormula: Boolean
- type: String
- label: String
- description: String
-}
-
-type FilterConfiguration {
- """List of types that can considered as number"""
- numberTypes: [String!]
-}
-
-type FormulaOperation {
- """Type name of the variable"""
- variableType: String!
-
- """List of operation available for this type"""
- operationTypes: [String!]!
-}
-
type ChartAxis {
"""label of the Axis"""
label: String
@@ -374,6 +223,157 @@ type PartialExperiment {
algorithm: AlgorithmResult
}
+type AuthenticationOutput {
+ accessToken: String!
+ refreshToken: String!
+}
+
+type Configuration {
+ connectorId: String!
+ hasGalaxy: Boolean @deprecated(reason: "Only used for legacy reason should be avoided")
+
+ """Indicates if histograms can handle grouping"""
+ hasGrouping: Boolean
+
+ """Indicates if filters and formula are enabled"""
+ hasFilters: Boolean
+ version: String!
+ skipAuth: Boolean
+ skipTos: Boolean
+ enableSSO: Boolean
+}
+
+type Dataset {
+ id: String!
+ label: String
+ isLongitudinal: Boolean
+}
+
+type Group {
+ id: String!
+ label: String
+ description: String
+ groups: [String!]
+
+ """List of variable's ids"""
+ variables: [String!]
+
+ """List of datasets avalaible, set null if all datasets allowed"""
+ datasets: [String!]
+}
+
+type Category {
+ value: String!
+ label: String
+}
+
+type Variable {
+ id: String!
+ label: String
+ type: String
+ description: String
+ enumerations: [Category!]
+ groups: [Group!]
+
+ """List of datasets avalaible, set null if all datasets allowed"""
+ datasets: [String!]
+}
+
+type Domain {
+ id: String!
+ label: String
+ description: String
+ version: String
+ groups: [Group!]!
+ variables: [Variable!]!
+ datasets: [Dataset!]!
+ rootGroup: Group!
+}
+
+type OptionValue {
+ value: String!
+ label: String!
+}
+
+type NominalParameter implements BaseParameter {
+ name: String!
+ label: String
+
+ """Small hint (description) for the end user"""
+ hint: String
+ isRequired: Boolean
+ hasMultiple: Boolean
+ defaultValue: String
+
+ """Id of the parameter"""
+ linkedTo: AllowedLink
+ allowedValues: [OptionValue!]
+}
+
+"""The supported links."""
+enum AllowedLink {
+ VARIABLE
+ COVARIABLE
+}
+
+type NumberParameter implements BaseParameter {
+ name: String!
+ label: String
+
+ """Small hint (description) for the end user"""
+ hint: String
+ isRequired: Boolean
+ hasMultiple: Boolean
+ defaultValue: String
+ min: Float
+ max: Float
+ isReal: Boolean
+}
+
+type StringParameter implements BaseParameter {
+ name: String!
+ label: String
+
+ """Small hint (description) for the end user"""
+ hint: String
+ isRequired: Boolean
+ hasMultiple: Boolean
+ defaultValue: String
+}
+
+type VariableParameter {
+ hint: String
+ isRequired: Boolean
+ hasMultiple: Boolean
+
+ """If undefined, all types are allowed"""
+ allowedTypes: [String!]
+}
+
+type Algorithm {
+ id: String!
+ parameters: [BaseParameter!]
+ variable: VariableParameter!
+ coVariable: VariableParameter
+ hasFormula: Boolean
+ type: String
+ label: String
+ description: String
+}
+
+type FilterConfiguration {
+ """List of types that can considered as number"""
+ numberTypes: [String!]
+}
+
+type FormulaOperation {
+ """Type name of the variable"""
+ variableType: String!
+
+ """List of operation available for this type"""
+ operationTypes: [String!]!
+}
+
type ListExperiments {
currentPage: Float
totalPages: Float