diff --git a/api/package.json b/api/package.json
index 481ac4aeefe16a08e350d7df20fbce7e2996b9f9..7e11e6620c4fd9c8cafe1ea3c5d93e90ee7d091d 100644
--- a/api/package.json
+++ b/api/package.json
@@ -14,7 +14,7 @@
"start:debug": "nest start --debug --watch",
"start:prod": "node dist/main",
"lint": "eslint \"{src,apps,libs,test}/**/*.ts\" --fix",
- "test": "jest",
+ "test": "jest --verbose",
"test:watch": "jest --watch",
"test:cov": "jest --coverage",
"test:debug": "node --inspect-brk -r tsconfig-paths/register -r ts-node/register node_modules/.bin/jest --runInBand",
diff --git a/api/src/engine/connectors/csv/main.connector.ts b/api/src/engine/connectors/csv/main.connector.ts
index d725496356e3133f54a364df1fa2158e13b14616..79c592b3f882ebf19e12df8e687990a72431ef28 100644
--- a/api/src/engine/connectors/csv/main.connector.ts
+++ b/api/src/engine/connectors/csv/main.connector.ts
@@ -37,8 +37,7 @@ export default class CSVService implements IEngineService {
domain: '',
datasets: [],
algorithm: {
- id: '',
- description: '',
+ name: '',
},
name: 'test',
variables: [],
diff --git a/api/src/engine/connectors/datashield/main.connector.ts b/api/src/engine/connectors/datashield/main.connector.ts
index 0055daa83b082ef08267e055ce79a36a91dbb8b9..f796f3c5a0427b895bdb56ab848eea74a2076983 100644
--- a/api/src/engine/connectors/datashield/main.connector.ts
+++ b/api/src/engine/connectors/datashield/main.connector.ts
@@ -159,7 +159,7 @@ export default class DataShieldService implements IEngineService {
domain: data.domain,
datasets: data.datasets,
algorithm: {
- id: data.algorithm.id,
+ name: data.algorithm.id,
},
};
diff --git a/api/src/engine/connectors/exareme/converters.ts b/api/src/engine/connectors/exareme/converters.ts
index 56f35ddcd2876a5cd6435cd3454c6fb414034923..4ba0bc25f7405d3a4a9031cf07c1d43f6aa4fe9b 100644
--- a/api/src/engine/connectors/exareme/converters.ts
+++ b/api/src/engine/connectors/exareme/converters.ts
@@ -1,7 +1,6 @@
import { MIME_TYPES } from 'src/common/interfaces/utilities.interface';
import { Category } from 'src/engine/models/category.model';
import { Dataset } from 'src/engine/models/dataset.model';
-import { Algorithm } from 'src/engine/models/experiment/algorithm.model';
import { Experiment } from 'src/engine/models/experiment/experiment.model';
import { AlgorithmParamInput } from 'src/engine/models/experiment/input/algorithm-parameter.input';
import { ExperimentCreateInput } from 'src/engine/models/experiment/input/experiment-create.input';
@@ -26,7 +25,6 @@ import {
dataToHeatmap,
descriptiveModelToTables,
descriptiveSingleToTables,
- transformToAlgorithms,
transformToExperiment,
} from './transformations';
@@ -45,7 +43,7 @@ export const dataToGroup = (data: Hierarchy): Group => {
export const dataToCategory = (data: Entity): Category => {
return {
- id: data.code,
+ value: data.code,
label: data.label,
};
};
@@ -215,7 +213,8 @@ export const dataToExperiment = (
exp.results = data.result
? data.result
- .map((result) => dataToResult(result, exp.algorithm.id))
+ .map((result) => dataToResult(result, exp.algorithm.name))
+ .filter((r) => r.length > 0)
.flat()
: [];
@@ -237,16 +236,12 @@ export const dataToExperiment = (
],
datasets: [],
algorithm: {
- id: 'unknown',
+ name: 'unknown',
},
};
}
};
-export const dataToAlgorithms = (data: string): Algorithm[] => {
- return transformToAlgorithms.evaluate(data);
-};
-
export const dataToRaw = (
algo: string,
result: ResultExperiment,
@@ -284,9 +279,11 @@ export const dataJSONtoResult = (
): Array<typeof ResultUnion> => {
switch (algo.toLowerCase()) {
case 'descriptive_stats':
+ case 'cart':
+ case 'id3':
return descriptiveDataToTableResult(result);
default:
- return dataToRaw(algo, result);
+ return [];
}
};
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 a7af56efcc46540e8565e6130e5d7c70e420ee8e..7b414bda9c4ae870c272c0c1fce525327fb613fa 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
@@ -7,7 +7,7 @@ const createExperiment = (): Experiment => ({
id: 'dummy-id',
name: 'Testing purpose',
algorithm: {
- id: 'PCA',
+ name: 'PCA',
},
datasets: ['desd-synthdata'],
domain: 'dementia',
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 64ff970285259fd69147fe2ff8fc0b3ca9eab668..61f82be6593f6165326387e228971236679e1d84 100644
--- a/api/src/engine/connectors/exareme/handlers/algorithms/PCA.handler.ts
+++ b/api/src/engine/connectors/exareme/handlers/algorithms/PCA.handler.ts
@@ -9,7 +9,8 @@ export default class PCAHandler extends BaseHandler {
}
handle(exp: Experiment, data: unknown): void {
- if (!this.canHandle(exp.algorithm.id)) return this.next?.handle(exp, data);
+ if (!this.canHandle(exp.algorithm.name))
+ return this.next?.handle(exp, data);
const barChar: BarChartResult = {
name: 'Eigen values',
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 c4cd6dcf6a9f3cd8c1d837b8a46b4d310842b874..bc55d0dc7b83b6c92f2ac6ce5ffa4d7831736d07 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
@@ -6,7 +6,7 @@ const createExperiment = (): Experiment => ({
id: 'dummy-id',
name: 'Testing purpose',
algorithm: {
- id: 'Anova_OnEway',
+ name: 'Anova_OnEway',
},
datasets: ['desd-synthdata'],
domain: 'dementia',
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 c8d9a6750785d57df2f2637572d306cd313935ee..5b25340ea67578d4367e003807f19a76f190fc59 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
@@ -98,7 +98,7 @@ export default class AnovaOneWayHandler extends BaseHandler {
}
handle(exp: Experiment, data: unknown): void {
- if (!this.canHandle(exp.algorithm.id)) return super.handle(exp, data);
+ if (!this.canHandle(exp.algorithm.name)) return super.handle(exp, data);
const summaryTable = this.getSummaryTable(data, exp.coVariables[0]);
if (summaryTable) exp.results.push(summaryTable);
diff --git a/api/src/engine/connectors/exareme/handlers/algorithms/descriptive.handler.ts b/api/src/engine/connectors/exareme/handlers/algorithms/descriptive.handler.ts
index d9fbc65f432ac29931d69428078d55e72eecd2a7..56396522d7a5504f218f586962d44cf81ac461b3 100644
--- a/api/src/engine/connectors/exareme/handlers/algorithms/descriptive.handler.ts
+++ b/api/src/engine/connectors/exareme/handlers/algorithms/descriptive.handler.ts
@@ -113,7 +113,7 @@ $fn := function($o, $prefix) {
handle(exp: Experiment, data: unknown): void {
let req = data;
- if (exp.algorithm.id.toLowerCase() === 'descriptive_stats') {
+ if (exp.algorithm.name.toLowerCase() === 'descriptive_stats') {
const inputs = data as ResultExperiment[];
if (inputs && Array.isArray(inputs)) {
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 f3ca9a5a31aae0db39f78813c63013071b840ce0..36a2759dff39197636dad6efbbaee39d37d2e7ce 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
@@ -6,7 +6,7 @@ const createExperiment = (): Experiment => ({
id: 'dummy-id',
name: 'Testing purpose',
algorithm: {
- id: 'pearson',
+ name: 'pearson',
},
datasets: ['desd-synthdata'],
domain: 'dementia',
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 0832d960e4ceb8bcf29551e6aaf98ebf9ffff2a5..40248088dcbb5aeff0a6b9b822d093743ed0607c 100644
--- a/api/src/engine/connectors/exareme/handlers/algorithms/pearson.handler.ts
+++ b/api/src/engine/connectors/exareme/handlers/algorithms/pearson.handler.ts
@@ -41,7 +41,7 @@ export default class PearsonHandler extends BaseHandler {
* @returns
*/
handle(exp: Experiment, data: unknown): void {
- if (this.canHandle(exp.algorithm.id)) {
+ if (this.canHandle(exp.algorithm.name)) {
try {
const results = PearsonHandler.transform.evaluate(
data,
diff --git a/api/src/engine/connectors/exareme/handlers/algorithms/raw.handler.ts b/api/src/engine/connectors/exareme/handlers/algorithms/raw.handler.ts
index 2e0dd77d9f86138dca531e1a0680286ba03fb40c..08cdac953300a1a06dee98568e37268a1999298c 100644
--- a/api/src/engine/connectors/exareme/handlers/algorithms/raw.handler.ts
+++ b/api/src/engine/connectors/exareme/handlers/algorithms/raw.handler.ts
@@ -21,7 +21,7 @@ export default class RawHandler extends BaseHandler {
if (inputs && Array.isArray(inputs))
inputs
.filter((input) => !!input.data && !!input.type)
- .map((input) => this.dataToRaw(exp.algorithm.id, input))
+ .map((input) => this.dataToRaw(exp.algorithm.name, input))
.forEach((input) => exp.results.push(input));
this.next?.handle(exp, data);
diff --git a/api/src/engine/connectors/exareme/main.connector.ts b/api/src/engine/connectors/exareme/main.connector.ts
index a87e303490c3338cf2b776a725cf28f74f2a8679..8a9d84b638329ee3d79c0a4d0267300127774860 100644
--- a/api/src/engine/connectors/exareme/main.connector.ts
+++ b/api/src/engine/connectors/exareme/main.connector.ts
@@ -31,7 +31,6 @@ import { UpdateUserInput } from 'src/users/inputs/update-user.input';
import { User } from 'src/users/models/user.model';
import { transformToUser } from '../datashield/transformations';
import {
- dataToAlgorithms,
dataToDataset,
dataToExperiment,
dataToGroup,
@@ -42,6 +41,7 @@ import { ExperimentData } from './interfaces/experiment/experiment.interface';
import { ExperimentsData } from './interfaces/experiment/experiments.interface';
import { Hierarchy } from './interfaces/hierarchy.interface';
import { Pathology } from './interfaces/pathology.interface';
+import transformToAlgorithms from './transformations/algorithms';
type Headers = Record<string, string>;
@@ -106,9 +106,8 @@ export default class ExaremeService implements IEngineService {
const resultAPI = await firstValueFrom(this.get<string>(request, path));
- return dataToAlgorithms(resultAPI.data);
+ return transformToAlgorithms.evaluate(resultAPI.data);
}
-
async getExperiment(id: string, request: Request): Promise<Experiment> {
const path = this.options.baseurl + `experiments/${id}`;
diff --git a/api/src/engine/connectors/exareme/transformations.ts b/api/src/engine/connectors/exareme/transformations.ts
index 07e59d977343342a6686f1f71ce936ee350cd7cd..19e33b3a5f40cc832e87b368b08ba68bda893962 100644
--- a/api/src/engine/connectors/exareme/transformations.ts
+++ b/api/src/engine/connectors/exareme/transformations.ts
@@ -3,31 +3,6 @@
import * as jsonata from 'jsonata'; // old import style needed due to 'export = jsonata'
-export const transformToAlgorithms = jsonata(`
-(
- $params := ["y", "pathology", "dataset", "filter", "x"];
-
- $toArray := function($x) { $type($x) = 'array' ? $x : [$x]};
-
- *.{
- 'id': name,
- 'label': label,
- 'description': desc,
- 'parameters': $toArray(parameters[$not(name in $params)].{
- 'id': name,
- 'description': desc,
- 'label': label,
- 'type': valueType,
- 'defaultValue': defaultValue,
- 'isMultiple': $boolean(valueMultiple),
- 'isRequired': $boolean(valueNotBlank),
- 'min': valueMin,
- 'max': valueMax
- })
-}
-)
-`);
-
export const transformToExperiment = jsonata(`
(
$params := ["y", "pathology", "dataset", "filter", "x", "formula"];
@@ -61,10 +36,10 @@ export const transformToExperiment = jsonata(`
"interactions" : $formula.interactions.[var1, var2][]
},
"algorithm": {
- "id": algorithm.name,
+ "name": algorithm.name,
"parameters" : $toArray(
algorithm.parameters[$not(name in $params)].({
- "id": name,
+ "name": name,
"label": label,
"value": value
})
diff --git a/api/src/engine/connectors/exareme/transformations/algorithms/algorithms.spec.ts b/api/src/engine/connectors/exareme/transformations/algorithms/algorithms.spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..1ed945272518d566d82debaff425b3b0dc148f20
--- /dev/null
+++ b/api/src/engine/connectors/exareme/transformations/algorithms/algorithms.spec.ts
@@ -0,0 +1,289 @@
+import { Algorithm } from 'src/engine/models/experiment/algorithm.model';
+import { NominalParameter } from 'src/engine/models/experiment/algorithm/nominal-parameter.model';
+import transformToAlgorithms from '.';
+
+describe('Algorithms', () => {
+ describe('when data is correct (Dummy Kaplan)', () => {
+ const data = [
+ {
+ name: 'KAPLAN_MEIER',
+ desc: 'Kaplan-Meier Estimator for the Survival Function',
+ label: 'Kaplan-Meier Estimator',
+ type: 'python_local_global',
+ parameters: [
+ {
+ name: 'y',
+ desc: 'A single categorical variable whose values describe a binary event.',
+ label: 'y',
+ type: 'column',
+ columnValuesSQLType: 'integer, text',
+ columnValuesIsCategorical: 'true',
+ value: 'alzheimerbroadcategory',
+ defaultValue: null,
+ valueType: 'string',
+ valueNotBlank: 'false',
+ valueMultiple: 'false',
+ valueMin: null,
+ valueMax: null,
+ valueEnumerations: null,
+ },
+ {
+ name: 'x',
+ desc: 'A single categorical variable based on which patients are grouped.',
+ label: 'x',
+ type: 'column',
+ columnValuesSQLType: 'integer, text',
+ columnValuesIsCategorical: 'false',
+ value: 'apoe4',
+ defaultValue: null,
+ valueType: 'string',
+ valueNotBlank: 'false',
+ valueMultiple: 'false',
+ valueMin: null,
+ valueMax: null,
+ valueEnumerations: null,
+ },
+ {
+ name: 'pathology',
+ desc: 'The name of the pathology that the dataset belongs to.',
+ label: 'pathology',
+ type: 'pathology',
+ columnValuesSQLType: null,
+ columnValuesIsCategorical: null,
+ value: 'dementia_longitudinal',
+ defaultValue: null,
+ valueType: 'string',
+ valueNotBlank: 'true',
+ valueMultiple: 'false',
+ valueMin: null,
+ valueMax: null,
+ valueEnumerations: null,
+ },
+ {
+ name: 'dataset',
+ desc: '',
+ label: 'dataset',
+ type: 'dataset',
+ columnValuesSQLType: null,
+ columnValuesIsCategorical: null,
+ value: 'alzheimer_fake_cohort',
+ defaultValue: null,
+ valueType: 'string',
+ valueNotBlank: 'true',
+ valueMultiple: 'true',
+ valueMin: null,
+ valueMax: null,
+ valueEnumerations: null,
+ },
+ {
+ name: 'filter',
+ desc: '',
+ label: 'filter',
+ type: 'filter',
+ columnValuesSQLType: null,
+ columnValuesIsCategorical: null,
+ value: '',
+ defaultValue: null,
+ valueType: 'string',
+ valueNotBlank: 'false',
+ valueMultiple: 'true',
+ valueMin: null,
+ valueMax: null,
+ valueEnumerations: null,
+ },
+ {
+ name: 'outcome_pos',
+ desc: '',
+ label: 'Positive outcome',
+ type: 'other',
+ columnValuesSQLType: null,
+ columnValuesIsCategorical: null,
+ value: 'AD',
+ defaultValue: null,
+ valueType: 'string',
+ valueNotBlank: 'true',
+ valueMultiple: 'false',
+ valueMin: null,
+ valueMax: null,
+ valueEnumerations: null,
+ },
+ {
+ name: 'outcome_neg',
+ desc: '',
+ label: 'Negative outcome',
+ type: 'other',
+ columnValuesSQLType: null,
+ columnValuesIsCategorical: null,
+ value: 'MCI',
+ defaultValue: null,
+ valueType: 'string',
+ valueNotBlank: 'true',
+ valueMultiple: 'false',
+ valueMin: null,
+ valueMax: null,
+ valueEnumerations: null,
+ },
+ {
+ name: 'test',
+ desc: '',
+ label: 'Total duration of experiment in days',
+ type: 'other',
+ columnValuesSQLType: null,
+ columnValuesIsCategorical: null,
+ value: '1100',
+ defaultValue: null,
+ valueType: 'real',
+ valueNotBlank: 'true',
+ valueMultiple: 'false',
+ valueMin: null,
+ valueMax: null,
+ valueEnumerations: ['test', 'test2'],
+ },
+ {
+ name: 'total_duration',
+ desc: '',
+ label: 'Total duration of experiment in days',
+ type: 'other',
+ columnValuesSQLType: null,
+ columnValuesIsCategorical: null,
+ value: '1100',
+ defaultValue: null,
+ valueType: 'real',
+ valueNotBlank: 'true',
+ valueMultiple: 'false',
+ valueMin: null,
+ valueMax: null,
+ valueEnumerations: null,
+ },
+ ],
+ },
+ ];
+
+ const algorithms: Algorithm[] = transformToAlgorithms.evaluate(data);
+ const kaplan = algorithms[0];
+
+ it('should produce one algorithm', () => {
+ expect(algorithms.length).toEqual(1);
+ });
+
+ it('should produce two algorithms', () => {
+ const algorithms: Algorithm[] = transformToAlgorithms.evaluate([
+ ...data,
+ ...data,
+ ]);
+ expect(algorithms.length).toEqual(2);
+ });
+
+ it('variable should be nominal', () => {
+ expect(kaplan.variable).not.toBeUndefined();
+ expect(kaplan.variable?.allowedTypes).toStrictEqual(['nominal']);
+ });
+
+ it('covariable should be integer or text', () => {
+ expect(kaplan.coVariable).not.toBeUndefined();
+ expect(kaplan.coVariable?.allowedTypes).toStrictEqual([
+ 'integer',
+ 'text',
+ ]);
+ });
+
+ it('should have 4 parameters', () => {
+ expect(kaplan.parameters.length).toBe(4);
+ });
+
+ it('nominal parameters should have values allowed', () => {
+ const nominalParam = kaplan.parameters.find(
+ (p) => p.name === 'test',
+ ) as NominalParameter;
+
+ expect(JSON.stringify(nominalParam.allowedValues)).toEqual(
+ JSON.stringify([
+ {
+ value: 'test',
+ label: 'test',
+ },
+ {
+ value: 'test2',
+ label: 'test2',
+ },
+ ]),
+ );
+ });
+
+ it('should have at least one linkedTo parameter', () => {
+ expect(kaplan.parameters.some((param) => param['linkedTo']));
+ });
+ });
+
+ describe('when data does not contains any parameters', () => {
+ const data = [
+ {
+ name: 'KAPLAN_MEIER',
+ desc: 'Kaplan-Meier Estimator for the Survival Function',
+ label: 'Kaplan-Meier Estimator',
+ type: 'python_local_global',
+ parameters: [
+ {
+ name: 'y',
+ desc: 'A single categorical variable whose values describe a binary event.',
+ label: 'y',
+ type: 'column',
+ columnValuesSQLType: 'integer, text',
+ columnValuesIsCategorical: 'true',
+ value: 'alzheimerbroadcategory',
+ defaultValue: null,
+ valueType: 'string',
+ valueNotBlank: 'false',
+ valueMultiple: 'false',
+ valueMin: null,
+ valueMax: null,
+ valueEnumerations: null,
+ },
+ {
+ name: 'x',
+ desc: 'A single categorical variable based on which patients are grouped.',
+ label: 'x',
+ type: 'column',
+ columnValuesSQLType: 'integer, text',
+ columnValuesIsCategorical: 'false',
+ value: 'apoe4',
+ defaultValue: null,
+ valueType: 'string',
+ valueNotBlank: 'false',
+ valueMultiple: 'false',
+ valueMin: null,
+ valueMax: null,
+ valueEnumerations: null,
+ },
+ ],
+ },
+ ];
+
+ const algorithms: Algorithm[] = transformToAlgorithms.evaluate(data);
+ const kaplan = algorithms[0];
+
+ it('Algo parameters should be undefined', () => {
+ expect(kaplan.parameters).toBeUndefined;
+ });
+ });
+
+ describe('when data is empty or undefined', () => {
+ it('should be undefined when data is undefined', () => {
+ const data = undefined;
+ const algorithms: Algorithm[] = transformToAlgorithms.evaluate(data);
+
+ expect(algorithms).toBeUndefined();
+ });
+
+ it('should be undefined when data is empty', () => {
+ const data = `
+ {
+ dummy:
+ }`;
+
+ const algorithms: Algorithm[] = transformToAlgorithms.evaluate(data);
+
+ expect(algorithms).toBeUndefined();
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/transformations/algorithms/index.ts b/api/src/engine/connectors/exareme/transformations/algorithms/index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..f177cbfdee60baf64000ad170a520fb097560b0f
--- /dev/null
+++ b/api/src/engine/connectors/exareme/transformations/algorithms/index.ts
@@ -0,0 +1,60 @@
+import * as jsonata from 'jsonata';
+
+const transformToAlgorithms = jsonata(`
+(
+ $dict:={
+ 'integer': 'NumberParameter',
+ 'real': 'NumberParameter'
+ };
+ $checkVal:= function($val) { $val ? $val : undefined};
+ $excludedParams:= ['centers', 'formula'];
+ $includes:= ['ANOVA_ONEWAY','ANOVA','LINEAR_REGRESSION',
+ 'LOGISTIC_REGRESSION','TTEST_INDEPENDENT','TTEST_PAIRED',
+ 'PEARSON_CORRELATION','ID3','KMEANS','NAIVE_BAYES',
+ 'TTEST_ONESAMPLE','PCA','CALIBRATION_BELT','CART',
+ 'KAPLAN_MEIER','THREE_C'];
+ $linkedVars:= ['positive_level', 'negative_level', 'outcome_neg', 'outcome_pos'];
+ $linkedCoVars:= ['referencevalues', 'xlevels'];
+ $truthy:= function($val) {(
+ $v:= $lowercase($val);
+ $v='true' ? true : ($v='false'? false : undefined)
+ )};
+ $extract:= function($v) {
+ $v?
+ {
+ "hint": $v.desc,
+ "isRequired": $truthy($checkVal($v.valueNotBlank)),
+ "hasMultiple": $truthy($checkVal($v.valueMultiple)),
+ "allowedTypes": $v.columnValuesIsCategorical = '' and $v.columnValuesSQLType = '' ?
+ undefined : $append($v.columnValuesIsCategorical = '' ?
+ ['nominal'] : [], $truthy($v.columnValuesIsCategorical) ? 'nominal' : $map(($checkVal($v.columnValuesSQLType) ~> $split(',')), $trim))
+ } : undefined
+ };
+
+ $[name in $includes].{
+ "id": name,
+ "label": $checkVal(label),
+ "type": type,
+ "description": $checkVal(desc),
+ "variable": parameters[(type='column' or type='formula') and name='y'] ~> $extract,
+ "coVariable": parameters[(type='column' or type='formula') and name='x'] ~> $extract,
+ "hasFormula": $boolean(parameters[(type='formula_description')]),
+ "parameters": parameters[type='other' and $not(name in $excludedParams)].{
+ "__typename": $lookup($dict, valueType),
+ "name": name,
+ "label": label,
+ "hint": $checkVal(desc),
+ "defaultValue": (name in $linkedCoVars) ? "[]" : (defaultValue ? defaultValue : value),
+ "isRequired": $truthy(valueNotBlank),
+ "hasMultiple": $truthy(valueMultiple),
+ "isReal": valueType = 'real' ? true : undefined,
+ "min": $checkVal(valueMin),
+ "max": $checkVal(valueMax),
+ "allowedValues": $checkVal(valueEnumerations).{'value':$, 'label': $}[],
+ "linkedTo": (name in $linkedVars) ? "VARIABLE" : ((name in $linkedCoVars) ? "COVARIABLE" : undefined)
+ }[]
+ }[]
+)
+`);
+
+export default transformToAlgorithms;
diff --git a/api/src/engine/engine.constants.ts b/api/src/engine/engine.constants.ts
index 3c9ae327491d37456964f9ce2cba8a7f04ecccf5..641ceed91bb4a29953fc558479f5b667fd112808 100644
--- a/api/src/engine/engine.constants.ts
+++ b/api/src/engine/engine.constants.ts
@@ -1,3 +1,4 @@
export const ENGINE_MODULE_OPTIONS = 'EngineModuleOption';
export const ENGINE_SERVICE = 'EngineService';
export const ENGINE_SKIP_TOS = 'TOS_SKIP';
+export const ENGINE_ONTOLOGY_URL = 'ONTOLOGY_URL';
diff --git a/api/src/engine/engine.controller.ts b/api/src/engine/engine.controller.ts
index f00a8e74803cc955fae75214d99bf561713e63cb..fc656aabb1d5d1c9f21e4a14af9cba01a5ee7440 100644
--- a/api/src/engine/engine.controller.ts
+++ b/api/src/engine/engine.controller.ts
@@ -12,11 +12,6 @@ export class EngineController {
@Inject(ENGINE_SERVICE) private readonly engineService: IEngineService,
) {}
- @Get('/algorithms')
- getAlgorithms(@Req() request: Request): Observable<string> | string {
- return this.engineService.getAlgorithmsREST(request);
- }
-
@Get('galaxy')
galaxy(@Req() request: Request): Observable<string> | string {
return this.engineService.getPassthrough?.('galaxy', request);
diff --git a/api/src/engine/engine.interfaces.ts b/api/src/engine/engine.interfaces.ts
index 3df6762aba25a3cb3cb5aedc6b8db07478f5f99e..8ca07651bcdc9883190d8ba7365546002c08ba1a 100644
--- a/api/src/engine/engine.interfaces.ts
+++ b/api/src/engine/engine.interfaces.ts
@@ -21,8 +21,6 @@ export interface IEngineOptions {
export type IConfiguration = Pick<Configuration, 'contactLink' | 'hasGalaxy'>;
export interface IEngineService {
- //GraphQL
-
/**
* Allow specific configuration for the engine
*
@@ -56,9 +54,6 @@ export interface IEngineService {
getAlgorithms(req?: Request): Promise<Algorithm[]>;
- // Standard REST API call
- getAlgorithmsREST(req?: Request): Observable<string> | string;
-
getActiveUser?(req?: Request): Promise<User>;
updateUser?(
diff --git a/api/src/engine/engine.resolver.ts b/api/src/engine/engine.resolver.ts
index 6260111702f3268881409f80f5db91cc197c1cba..d5acde6a200cda20f7105e610713c3cf407fac79 100644
--- a/api/src/engine/engine.resolver.ts
+++ b/api/src/engine/engine.resolver.ts
@@ -6,6 +6,7 @@ import { GQLRequest } from '../common/decorators/gql-request.decoractor';
import { Md5 } from 'ts-md5';
import {
ENGINE_MODULE_OPTIONS,
+ ENGINE_ONTOLOGY_URL,
ENGINE_SERVICE,
ENGINE_SKIP_TOS,
} from './engine.constants';
@@ -55,6 +56,7 @@ export class EngineResolver {
true,
),
matomo,
+ ontologyUrl: this.configSerivce.get(ENGINE_ONTOLOGY_URL),
};
const version = Md5.hashStr(JSON.stringify(data));
diff --git a/api/src/engine/models/category.model.ts b/api/src/engine/models/category.model.ts
index 2000d8f655368b17f99c6c7eee5540b32d94b9a0..4cb4460ffb878b00883419e1b34190b107882fbe 100644
--- a/api/src/engine/models/category.model.ts
+++ b/api/src/engine/models/category.model.ts
@@ -1,5 +1,10 @@
-import { ObjectType } from '@nestjs/graphql';
-import { BaseModel } from './entity.model';
+import { Field, ObjectType } from '@nestjs/graphql';
@ObjectType()
-export class Category extends BaseModel {}
+export class Category {
+ @Field()
+ value: string;
+
+ @Field({ nullable: true })
+ label?: string;
+}
diff --git a/api/src/engine/models/configuration.model.ts b/api/src/engine/models/configuration.model.ts
index 6ffe779cc55962c0dc0c20fd0e3d47c9e4d73348..9471881a191b9bdbc33a8d181487f6888d453fc3 100644
--- a/api/src/engine/models/configuration.model.ts
+++ b/api/src/engine/models/configuration.model.ts
@@ -25,4 +25,7 @@ export class Configuration {
@Field(() => Matomo, { nullable: true })
matomo?: Matomo;
+
+ @Field({ nullable: true })
+ ontologyUrl?: string;
}
diff --git a/api/src/engine/models/experiment/algorithm.model.ts b/api/src/engine/models/experiment/algorithm.model.ts
index 818b3c9d5c131a58625b3d724185cb6d87bc7827..761a0986d17aee99b192e939c9385637e0251f86 100644
--- a/api/src/engine/models/experiment/algorithm.model.ts
+++ b/api/src/engine/models/experiment/algorithm.model.ts
@@ -1,20 +1,30 @@
import { Field, ObjectType } from '@nestjs/graphql';
-import { AlgorithmParameter } from './algorithm-parameter.model';
+import { BaseParameter } from './algorithm/base-parameter.model';
+import { VariableParameter } from './algorithm/variable-parameter.model';
@ObjectType()
export class Algorithm {
@Field()
id: string;
- @Field(() => [AlgorithmParameter], { nullable: true, defaultValue: [] })
- parameters?: AlgorithmParameter[];
+ @Field(() => [BaseParameter], { nullable: true, defaultValue: [] })
+ parameters?: BaseParameter[];
- @Field({ nullable: true })
- label?: string;
+ @Field(() => VariableParameter)
+ variable?: VariableParameter;
+
+ @Field(() => VariableParameter, { nullable: true })
+ coVariable?: VariableParameter;
+
+ @Field({ nullable: true, defaultValue: false })
+ hasFormula?: boolean;
@Field({ nullable: true })
type?: string;
+ @Field({ nullable: true })
+ label?: string;
+
@Field({ nullable: true })
description?: string;
}
diff --git a/api/src/engine/models/experiment/algorithm/base-parameter.model.ts b/api/src/engine/models/experiment/algorithm/base-parameter.model.ts
new file mode 100644
index 0000000000000000000000000000000000000000..2b60e0806b187b1c5e37ee089dc9ce1e5f6f7713
--- /dev/null
+++ b/api/src/engine/models/experiment/algorithm/base-parameter.model.ts
@@ -0,0 +1,47 @@
+import { Field, InterfaceType } from '@nestjs/graphql';
+import { NominalParameter } from './nominal-parameter.model';
+import { NumberParameter } from './number-parameter.model';
+import { StringParameter } from './string-parameter.model';
+
+@InterfaceType({
+ resolveType(param) {
+ if (
+ param.min ||
+ param.max ||
+ param.isReal ||
+ param.__typename === 'NumberParameter'
+ )
+ return NumberParameter;
+
+ if (
+ param.allowedValues ||
+ param.linkedTo ||
+ param.__typename === 'NominalParameter'
+ )
+ return NominalParameter;
+
+ return StringParameter;
+ },
+})
+export abstract class BaseParameter {
+ @Field()
+ name: string;
+
+ @Field({ nullable: true })
+ label?: string;
+
+ @Field({
+ nullable: true,
+ description: 'Small hint (description) for the end user',
+ })
+ hint?: string;
+
+ @Field({ nullable: true, defaultValue: false })
+ isRequired?: boolean;
+
+ @Field({ nullable: true, defaultValue: false })
+ hasMultiple?: boolean;
+
+ @Field({ nullable: true })
+ defaultValue?: string;
+}
diff --git a/api/src/engine/models/experiment/algorithm/nominal-parameter.model.ts b/api/src/engine/models/experiment/algorithm/nominal-parameter.model.ts
new file mode 100644
index 0000000000000000000000000000000000000000..2008b60e545a5e91820295b5f285478df28e80fa
--- /dev/null
+++ b/api/src/engine/models/experiment/algorithm/nominal-parameter.model.ts
@@ -0,0 +1,40 @@
+import { Field, ObjectType, registerEnumType } from '@nestjs/graphql';
+import { BaseParameter } from './base-parameter.model';
+
+enum AllowedLink {
+ VARIABLE = 'VARIABLE',
+ COVARIABLE = 'COVARIABLE',
+}
+
+registerEnumType(AllowedLink, {
+ name: 'AllowedLink',
+ description: 'The supported links.',
+});
+
+@ObjectType()
+export class OptionValue {
+ @Field()
+ value: string;
+
+ @Field()
+ label: string;
+}
+
+@ObjectType({ implements: () => [BaseParameter] })
+export class NominalParameter implements BaseParameter {
+ name: string;
+ label?: string;
+ hint?: string;
+ isRequired?: boolean;
+ hasMultiple?: boolean;
+ defaultValue?: string;
+
+ @Field(() => AllowedLink, {
+ nullable: true,
+ description: 'Id of the parameter',
+ })
+ linkedTo?: AllowedLink;
+
+ @Field(() => [OptionValue], { defaultValue: [], nullable: true })
+ allowedValues?: OptionValue[];
+}
diff --git a/api/src/engine/models/experiment/algorithm/number-parameter.model.ts b/api/src/engine/models/experiment/algorithm/number-parameter.model.ts
new file mode 100644
index 0000000000000000000000000000000000000000..88b3604dcd4f8d2ac88bd2c422c5f67cf3d62fce
--- /dev/null
+++ b/api/src/engine/models/experiment/algorithm/number-parameter.model.ts
@@ -0,0 +1,20 @@
+import { Field, ObjectType } from '@nestjs/graphql';
+import { BaseParameter } from './base-parameter.model';
+@ObjectType({ implements: () => [BaseParameter] })
+export class NumberParameter implements BaseParameter {
+ name: string;
+ label?: string;
+ hint?: string;
+ isRequired?: boolean;
+ hasMultiple?: boolean;
+ defaultValue?: string;
+
+ @Field({ nullable: true })
+ min?: number;
+
+ @Field({ nullable: true })
+ max?: number;
+
+ @Field({ nullable: true, defaultValue: false })
+ isReal?: boolean;
+}
diff --git a/api/src/engine/models/experiment/algorithm/string-parameter.model.ts b/api/src/engine/models/experiment/algorithm/string-parameter.model.ts
new file mode 100644
index 0000000000000000000000000000000000000000..d7c2e40b16f64dc36d24c1c5d7283888a2d8cee8
--- /dev/null
+++ b/api/src/engine/models/experiment/algorithm/string-parameter.model.ts
@@ -0,0 +1,12 @@
+import { ObjectType } from '@nestjs/graphql';
+import { BaseParameter } from './base-parameter.model';
+
+@ObjectType({ implements: () => [BaseParameter] })
+export class StringParameter implements BaseParameter {
+ name: string;
+ label?: string;
+ hint?: string;
+ isRequired?: boolean;
+ hasMultiple?: boolean;
+ defaultValue?: string;
+}
diff --git a/api/src/engine/models/experiment/algorithm/variable-parameter.model.ts b/api/src/engine/models/experiment/algorithm/variable-parameter.model.ts
new file mode 100644
index 0000000000000000000000000000000000000000..0f9e55f7d4831de18538b3070b31bd8e390650e3
--- /dev/null
+++ b/api/src/engine/models/experiment/algorithm/variable-parameter.model.ts
@@ -0,0 +1,16 @@
+import { Field, ObjectType } from '@nestjs/graphql';
+
+@ObjectType()
+export class VariableParameter {
+ @Field({ nullable: true })
+ hint?: string;
+
+ @Field({ nullable: true, defaultValue: false })
+ isRequired: boolean;
+
+ @Field({ nullable: true, defaultValue: false })
+ hasMultiple: boolean;
+
+ @Field(() => [String], { nullable: true })
+ allowedTypes: string[];
+}
diff --git a/api/src/engine/models/experiment/experiment.model.ts b/api/src/engine/models/experiment/experiment.model.ts
index eb757d64d9444f4c505705d3d6faa2b7e32c4d72..b0fed2aa4bd3649d7f2c6f7bba4ce8601364b1c6 100644
--- a/api/src/engine/models/experiment/experiment.model.ts
+++ b/api/src/engine/models/experiment/experiment.model.ts
@@ -1,6 +1,5 @@
import { Field, ObjectType, PartialType } from '@nestjs/graphql';
import { ResultUnion } from '../result/common/result-union.model';
-import { Algorithm } from './algorithm.model';
import { Author } from './author.model';
@ObjectType()
@@ -21,6 +20,23 @@ export class Formula {
interactions: string[][];
}
+@ObjectType()
+export class ParamValue {
+ @Field()
+ name: string;
+
+ @Field()
+ value: string;
+}
+@ObjectType()
+export class AlgorithmResult {
+ @Field()
+ name: string;
+
+ @Field(() => [ParamValue], { nullable: true, defaultValue: [] })
+ parameters?: ParamValue[];
+}
+
@ObjectType()
export class Experiment {
@Field()
@@ -75,7 +91,7 @@ export class Experiment {
formula?: Formula;
@Field()
- algorithm: Algorithm;
+ algorithm: AlgorithmResult;
}
@ObjectType()
diff --git a/api/src/engine/models/experiment/input/algorithm-parameter.input.ts b/api/src/engine/models/experiment/input/algorithm-parameter.input.ts
index 8cd3ec29ddfecb22c1574ea339cd96b4a010f79a..62a0ab458497bbecc9387434f741821ddab9728a 100644
--- a/api/src/engine/models/experiment/input/algorithm-parameter.input.ts
+++ b/api/src/engine/models/experiment/input/algorithm-parameter.input.ts
@@ -1,25 +1,10 @@
-import { Field, InputType, registerEnumType } from '@nestjs/graphql';
-
-export enum ParamType {
- STRING,
- NUMBER,
-}
-
-registerEnumType(ParamType, {
- name: 'ParamType',
-});
+import { Field, InputType } from '@nestjs/graphql';
@InputType()
export class AlgorithmParamInput {
@Field()
id: string;
- @Field(() => ParamType, {
- nullable: true,
- defaultValue: ParamType.STRING,
- })
- type?: ParamType;
-
@Field(() => String)
value: string;
}
diff --git a/api/src/engine/models/experiment/input/algorithm.input.ts b/api/src/engine/models/experiment/input/algorithm.input.ts
index d87abd4561f975dbb9dfc00964f658265a340085..e815f47f2eee1d40781187d324be32df4d279399 100644
--- a/api/src/engine/models/experiment/input/algorithm.input.ts
+++ b/api/src/engine/models/experiment/input/algorithm.input.ts
@@ -9,6 +9,6 @@ export class AlgorithmInput {
@Field(() => [AlgorithmParamInput], { nullable: true, defaultValue: [] })
parameters: AlgorithmParamInput[];
- @Field()
- type: string;
+ @Field({ nullable: true })
+ type?: string;
}
diff --git a/api/src/schema.gql b/api/src/schema.gql
index 33142a24cc95cbc543605924b31ff76083003968..8265eb01a39457cb2d9420de4625a1b937ac26d7 100644
--- a/api/src/schema.gql
+++ b/api/src/schema.gql
@@ -2,6 +2,17 @@
# THIS FILE WAS AUTOMATICALLY GENERATED (DO NOT MODIFY)
# ------------------------------------------------------
+interface BaseParameter {
+ name: String!
+ label: String
+
+ """Small hint (description) for the end user"""
+ hint: String
+ isRequired: Boolean
+ hasMultiple: Boolean
+ defaultValue: String
+}
+
type User {
id: String!
username: String!
@@ -29,6 +40,7 @@ type Configuration {
skipTos: Boolean
enableSSO: Boolean
matomo: Matomo
+ ontologyUrl: String
}
type Dataset {
@@ -51,7 +63,7 @@ type Group {
}
type Category {
- id: String!
+ value: String!
label: String
}
@@ -77,24 +89,72 @@ type Domain {
rootGroup: Group!
}
-type AlgorithmParameter {
- id: String!
- value: String
+type OptionValue {
+ value: String!
+ label: String!
+}
+
+type NominalParameter implements BaseParameter {
+ name: String!
label: String
- description: String
+
+ """Small hint (description) for the end user"""
+ hint: String
+ isRequired: Boolean
+ hasMultiple: Boolean
defaultValue: String
- isMultiple: Boolean
+
+ """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
- min: String
- max: String
- type: String
+ 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
+ allowedTypes: [String!]
}
type Algorithm {
id: String!
- parameters: [AlgorithmParameter!]
- label: String
+ parameters: [BaseParameter!]
+ variable: VariableParameter!
+ coVariable: VariableParameter
+ hasFormula: Boolean
type: String
+ label: String
description: String
}
@@ -226,6 +286,16 @@ type Formula {
interactions: [[String!]!]
}
+type ParamValue {
+ name: String!
+ value: String!
+}
+
+type AlgorithmResult {
+ name: String!
+ parameters: [ParamValue!]
+}
+
type Experiment {
id: String!
name: String!
@@ -244,7 +314,7 @@ type Experiment {
coVariables: [String!]
filterVariables: [String!]
formula: Formula
- algorithm: Algorithm!
+ algorithm: AlgorithmResult!
}
type PartialExperiment {
@@ -265,7 +335,7 @@ type PartialExperiment {
coVariables: [String!]
filterVariables: [String!]
formula: Formula
- algorithm: Algorithm
+ algorithm: AlgorithmResult
}
type ListExperiments {
@@ -308,20 +378,14 @@ input ExperimentCreateInput {
input AlgorithmInput {
id: String!
parameters: [AlgorithmParamInput!] = []
- type: String!
+ type: String
}
input AlgorithmParamInput {
id: String!
- type: ParamType = STRING
value: String!
}
-enum ParamType {
- STRING
- NUMBER
-}
-
input FormulaTransformation {
id: String!
operation: String!
diff --git a/docs/for-developers/configuration/gateway.md b/docs/for-developers/configuration/gateway.md
index 2b16dacfcbdfbc415f9091c3086a000032787d21..7f879ca3369f383b0f2b26fbacc31d35d889258b 100644
--- a/docs/for-developers/configuration/gateway.md
+++ b/docs/for-developers/configuration/gateway.md
@@ -18,6 +18,7 @@ description: >-
| GATEWAY\_PORT | number | 8081 | Indicate the port that should be used by the gateway |
| NODE\_ENV | string | dev | Value can be `prod` or `dev` |
| BASE\_URL\_CONTEXT | string | null | Define context of the gateway. E.g. `api` if the api is under `http://127.0.0.1/api/` |
+| ONTOLOGY\_URL | string | null | Define ontology's url |
#### Authentication