Merge branch '38-add-algorithm-resources-in-graphql' into 'develop'

Resolve "Add Algorithm resources in GraphQL"

Closes #38

See merge request sibmip/gateway!16

api/src/engine/connectors/datashield/main.connector.ts

@@ -8,8 +8,12 @@ import {
 } from 'src/engine/models/experiment/experiment.model';
 import { ListExperiments } from 'src/engine/models/experiment/list-experiments.model';
 import { ExperimentEditInput } from 'src/engine/models/experiment/input/experiment-edit.input';
+import { Algorithm } from 'src/engine/models/experiment/algorithm.model';
 
 export default class DataShieldService implements IEngineService {
+  getAlgorithms(): Algorithm[] | Promise<Algorithm[]> {
+    throw new Error('Method not implemented.');
+  }
   createExperiment(
     data: ExperimentCreateInput,
     isTransient: boolean,
@@ -48,7 +52,7 @@ export default class DataShieldService implements IEngineService {
     throw new Error('Method not implemented.');
   }
 
-  getExperimentAPI(): Observable<string> {
+  getExperimentREST(): Observable<string> {
     throw new Error('Method not implemented.');
   }
 
@@ -56,7 +60,7 @@ export default class DataShieldService implements IEngineService {
     throw new Error('Method not implemented.');
   }
 
-  editExperimentAPI(): Observable<string> {
+  editExperimentREST(): Observable<string> {
     throw new Error('Method not implemented.');
   }
 
@@ -72,7 +76,7 @@ export default class DataShieldService implements IEngineService {
     throw new Error('Method not implemented.');
   }
 
-  getAlgorithms(): Observable<string> {
+  getAlgorithmsREST(): Observable<string> {
     throw new Error('Method not implemented.');
   }
 }

api/src/engine/connectors/exareme/converters.ts

 import { Category } from 'src/engine/models/category.model';
 import { AlgorithmParameter } from 'src/engine/models/experiment/algorithm-parameter.model';
+import { Algorithm } from 'src/engine/models/experiment/algorithm.model';
 import { Experiment } from 'src/engine/models/experiment/experiment.model';
 import { ExperimentCreateInput } from 'src/engine/models/experiment/input/experiment-create.input';
 import { Group } from 'src/engine/models/group.model';
@@ -18,6 +19,7 @@ import { VariableEntity } from './interfaces/variable-entity.interface';
 import {
   descriptiveModelToTables,
   descriptiveSingleToTables,
+  transformToAlgorithms,
   transformToExperiment,
 } from './transformations';
 
@@ -92,7 +94,8 @@ export const descriptiveDataToTableResult = (
 
   result.groups = [
     new GroupResult({
-      name: 'Single',
+      name: 'Variables',
+      description: 'Descriptive statistics for the variables of interest.',
       results: descriptiveSingleToTables.evaluate(data),
     }),
   ];
@@ -100,6 +103,8 @@ export const descriptiveDataToTableResult = (
   result.groups.push(
     new GroupResult({
       name: 'Model',
+      description:
+        'Intersection table for the variables of interest as it appears in the experiment.',
       results: descriptiveModelToTables.evaluate(data),
     }),
   );
@@ -124,10 +129,14 @@ export const dataToExperiment = (data: ExperimentData): Experiment => {
   return exp;
 };
 
+export const dataToAlgorithms = (data: string): Algorithm[] => {
+  return transformToAlgorithms.evaluate(data);
+};
+
 export const dataToRaw = (result: ResultExperiment): RawResult[] => {
   return [
     {
-      data: result.data,
+      rawdata: result.data,
     },
   ];
 };

api/src/engine/connectors/exareme/main.connector.ts

@@ -4,6 +4,7 @@ import { Request } from 'express';
 import { firstValueFrom, map, Observable } from 'rxjs';
 import { IEngineOptions, IEngineService } from 'src/engine/engine.interfaces';
 import { Domain } from 'src/engine/models/domain.model';
+import { Algorithm } from 'src/engine/models/experiment/algorithm.model';
 import {
   Experiment,
   PartialExperiment,
@@ -14,6 +15,7 @@ import { ListExperiments } from 'src/engine/models/experiment/list-experiments.m
 import { Group } from 'src/engine/models/group.model';
 import { Variable } from 'src/engine/models/variable.model';
 import {
+  dataToAlgorithms,
   dataToCategory,
   dataToExperiment,
   dataToGroup,
@@ -60,6 +62,14 @@ export default class ExaremeService implements IEngineService {
     };
   }
 
+  async getAlgorithms(): Promise<Algorithm[]> {
+    const path = this.options.baseurl + 'algorithms';
+
+    const resultAPI = await firstValueFrom(this.httpService.get<string>(path));
+
+    return dataToAlgorithms(resultAPI.data);
+  }
+
   async getExperiment(uuid: string): Promise<Experiment> {
     const path = this.options.baseurl + `experiments/${uuid}`;
 
@@ -144,7 +154,7 @@ export default class ExaremeService implements IEngineService {
       .pipe(map((response) => response.data));
   }
 
-  getExperimentAPI(uuid: string): Observable<string> {
+  getExperimentREST(uuid: string): Observable<string> {
     const path = this.options.baseurl + `experiments/${uuid}`;
 
     return this.httpService
@@ -158,7 +168,7 @@ export default class ExaremeService implements IEngineService {
     return this.httpService.delete(path).pipe(map((response) => response.data));
   }
 
-  editExperimentAPI(uuid: string, request: Request): Observable<string> {
+  editExperimentREST(uuid: string, request: Request): Observable<string> {
     const path = this.options.baseurl + `experiments/${uuid}`;
 
     return this.httpService
@@ -190,7 +200,7 @@ export default class ExaremeService implements IEngineService {
       .pipe(map((response) => response.data));
   }
 
-  getAlgorithms(request: Request): Observable<string> {
+  getAlgorithmsREST(request: Request): Observable<string> {
     const path = this.options.baseurl + 'algorithms';
 
     return this.httpService

api/src/engine/connectors/exareme/transformations.ts

@@ -3,6 +3,31 @@
 
 import * as jsonata from 'jsonata'; // old import style needed due to 'export = jsonata'
 
+export const transformToAlgorithms = jsonata(`
+(
+    $params := ["y", "pathology", "dataset", "filter"];
+
+    $toArray := function($x) { $type($x) = 'array' ? $x : [$x]};
+
+    *.{
+    'name': name,
+    'label': label,
+    'description': desc,
+    'parameters': $toArray(parameters[$not(name in $params)].{
+        'name': 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"];

api/src/engine/engine.controller.ts

@@ -21,7 +21,7 @@ export class EngineController {
 
   @Get('/algorithms')
   getAlgorithms(@Req() request: Request): Observable<string> {
-    return this.engineService.getAlgorithms(request);
+    return this.engineService.getAlgorithmsREST(request);
   }
 
   @Get('/experiments')
@@ -31,7 +31,7 @@ export class EngineController {
 
   @Get('/experiments/:uuid')
   getExperiment(@Param('uuid') uuid: string): Observable<string> {
-    return this.engineService.getExperimentAPI(uuid);
+    return this.engineService.getExperimentREST(uuid);
   }
 
   @Delete('/experiments/:uuid')
@@ -47,7 +47,7 @@ export class EngineController {
     @Param('uuid') uuid: string,
     @Req() request: Request,
   ): Observable<string> {
-    return this.engineService.editExperimentAPI(uuid, request);
+    return this.engineService.editExperimentREST(uuid, request);
   }
 
   @Post('experiments/transient')

api/src/engine/engine.interfaces.ts

 import { Request } from 'express';
 import { Observable } from 'rxjs';
 import { Domain } from './models/domain.model';
+import { Algorithm } from './models/experiment/algorithm.model';
 import {
   Experiment,
   PartialExperiment,
@@ -39,16 +40,18 @@ export interface IEngineService {
     expriment: ExperimentEditInput,
   ): Promise<Experiment> | Experiment;
 
+  getAlgorithms(): Promise<Algorithm[]> | Algorithm[];
+
   // Standard REST API call
-  getAlgorithms(request: Request): Observable<string>;
+  getAlgorithmsREST(request: Request): Observable<string>;
 
   getExperiments(request: Request): Observable<string>;
 
-  getExperimentAPI(uuid: string): Observable<string>;
+  getExperimentREST(uuid: string): Observable<string>;
 
   deleteExperiment(uuid: string, request: Request): Observable<string>;
 
-  editExperimentAPI(uuid: string, request: Request): Observable<string>;
+  editExperimentREST(uuid: string, request: Request): Observable<string>;
 
   startExperimentTransient(request: Request): Observable<string>;
 

api/src/engine/engine.resolver.ts

@@ -3,6 +3,7 @@ import { Args, Mutation, Query, Resolver } from '@nestjs/graphql';
 import { ENGINE_SERVICE } from './engine.constants';
 import { IEngineService } from './engine.interfaces';
 import { Domain } from './models/domain.model';
+import { Algorithm } from './models/experiment/algorithm.model';
 import {
   Experiment,
   PartialExperiment,
@@ -38,6 +39,11 @@ export class EngineResolver {
     return this.engineService.getExperiment(uuid);
   }
 
+  @Query(() => [Algorithm])
+  async algorithms() {
+    return this.engineService.getAlgorithms();
+  }
+
   @Mutation(() => Experiment)
   async createExperiment(
     @Args('data') experimentCreateInput: ExperimentCreateInput,

api/src/engine/models/experiment/algorithm-parameter.model.ts

@@ -5,6 +5,30 @@ export class AlgorithmParameter {
   @Field()
   name: string;
 
-  @Field(() => [String])
-  value: string[];
+  @Field(() => [String], { nullable: true })
+  value?: string[];
+
+  @Field({ nullable: true })
+  label?: string;
+
+  @Field({ nullable: true })
+  description?: string;
+
+  @Field({ nullable: true })
+  defaultValue?: string;
+
+  @Field({ defaultValue: false, nullable: true })
+  isMultiple?: boolean;
+
+  @Field({ defaultValue: false, nullable: true })
+  isRequired?: boolean;
+
+  @Field({ nullable: true })
+  min?: string;
+
+  @Field({ nullable: true })
+  max?: string;
+
+  @Field({ nullable: true })
+  type?: string;
 }

api/src/engine/models/experiment/algorithm.model.ts

@@ -7,8 +7,14 @@ export class Algorithm {
   name: string;
 
   @Field(() => [AlgorithmParameter], { nullable: true, defaultValue: [] })
-  parameters: AlgorithmParameter[];
+  parameters?: AlgorithmParameter[];
 
-  @Field()
-  type: string;
+  @Field({ nullable: true })
+  label?: string;
+
+  @Field({ nullable: true })
+  type?: string;
+
+  @Field({ nullable: true })
+  description?: string;
 }

api/src/engine/models/result/common/result-union.model.ts

@@ -11,7 +11,7 @@ export const ResultUnion = createUnionType({
       return TableResult;
     }
 
-    if (value.listMax) {
+    if (value.rawdata) {
       return RawResult;
     }
 

api/src/engine/models/result/groups-result.model.ts

@@ -11,6 +11,9 @@ export class GroupResult {
   @Field()
   name: string;
 
+  @Field({ nullable: true })
+  description?: string;
+
   @Field(() => [ResultUnion])
   results: Array<typeof ResultUnion>;
 }

api/src/engine/models/result/raw-result.model.ts

 import { Field, ObjectType } from '@nestjs/graphql';
-import { GraphQLJSONObject } from 'graphql-type-json';
+import GraphQLJSON from 'graphql-type-json';
 import { Result } from './common/result.model';
 
+// field name 'rawdata' was used instead of 'data' because of typing problem on union with same field name
+// see :https://stackoverflow.com/questions/44170603/graphql-using-same-field-names-in-different-types-within-union
+
 @ObjectType()
 export class RawResult extends Result {
-  @Field(() => GraphQLJSONObject)
-  data: unknown;
-
-  @Field(() => [String], { defaultValue: [] })
-  listMax?: string[];
+  @Field(() => GraphQLJSON)
+  rawdata: unknown;
 }

api/src/schema.gql

@@ -34,8 +34,30 @@ type Domain {
   rootGroup: Group!
 }
 
+type AlgorithmParameter {
+  name: String!
+  value: [String!]
+  label: String
+  description: String
+  defaultValue: String
+  isMultiple: Boolean
+  isRequired: Boolean
+  min: String
+  max: String
+  type: String
+}
+
+type Algorithm {
+  name: String!
+  parameters: [AlgorithmParameter!]
+  label: String
+  type: String
+  description: String
+}
+
 type GroupResult {
   name: String!
+  description: String
   results: [ResultUnion!]!
 }
 
@@ -48,14 +70,13 @@ type TableResult {
 }
 
 type RawResult {
-  data: JSONObject!
-  listMax: [String!]!
+  rawdata: JSON!
 }
 
 """
-The `JSONObject` scalar type represents JSON objects as specified by [ECMA-404](http://www.ecma-international.org/publications/files/ECMA-ST/ECMA-404.pdf).
+The `JSON` scalar type represents JSON values as specified by [ECMA-404](http://www.ecma-international.org/publications/files/ECMA-ST/ECMA-404.pdf).
 """
-scalar JSONObject @specifiedBy(url: "http://www.ecma-international.org/publications/files/ECMA-ST/ECMA-404.pdf")
+scalar JSON @specifiedBy(url: "http://www.ecma-international.org/publications/files/ECMA-ST/ECMA-404.pdf")
 
 type GroupsResult {
   groups: [GroupResult!]!
@@ -66,17 +87,6 @@ type Header {
   type: String!
 }
 
-type AlgorithmParameter {
-  name: String!
-  value: [String!]!
-}
-
-type Algorithm {
-  name: String!
-  parameters: [AlgorithmParameter!]
-  type: String!
-}
-
 type Experiment {
   uuid: String
   author: String
@@ -124,6 +134,7 @@ type Query {
   domains(ids: [String!] = []): [Domain!]!
   experiments(name: String = "", page: Float = 0): ListExperiments!
   expriment(uuid: String!): Experiment!
+  algorithms: [Algorithm!]!
 }
 
 type Mutation {