From f69b78aef6c6d28106de76b86fbb59c7005feb62 Mon Sep 17 00:00:00 2001
From: Steve Reis <stevereis@gmail.com>
Date: Wed, 15 Sep 2021 17:00:31 +0200
Subject: [PATCH] WIP graphql pathologies Added flatten groups
---
.../common/interfaces/utilities.interface.ts | 1 +
.../connectors/datashield/main.connector.ts | 5 +
.../exareme/interfaces/hierarchy.interface.ts | 8 ++
.../exareme/interfaces/pathology.interface.ts | 9 ++
.../interfaces/variable-entity.interface.ts | 9 ++
.../exareme/interfaces/variable.interface.ts | 4 +
.../connectors/exareme/main.connector.ts | 93 ++++++++++++++++++-
api/src/engine/engine.interfaces.ts | 3 +
api/src/engine/engine.resolver.ts | 17 +---
9 files changed, 134 insertions(+), 15 deletions(-)
create mode 100644 api/src/common/interfaces/utilities.interface.ts
create mode 100644 api/src/engine/connectors/exareme/interfaces/hierarchy.interface.ts
create mode 100644 api/src/engine/connectors/exareme/interfaces/pathology.interface.ts
create mode 100644 api/src/engine/connectors/exareme/interfaces/variable-entity.interface.ts
create mode 100644 api/src/engine/connectors/exareme/interfaces/variable.interface.ts
diff --git a/api/src/common/interfaces/utilities.interface.ts b/api/src/common/interfaces/utilities.interface.ts
new file mode 100644
index 0000000..f226c24
--- /dev/null
+++ b/api/src/common/interfaces/utilities.interface.ts
@@ -0,0 +1 @@
+export type Dictionary<T> = { [key: string]: T };
\ No newline at end of file
diff --git a/api/src/engine/connectors/datashield/main.connector.ts b/api/src/engine/connectors/datashield/main.connector.ts
index a362265..104a4fe 100644
--- a/api/src/engine/connectors/datashield/main.connector.ts
+++ b/api/src/engine/connectors/datashield/main.connector.ts
@@ -1,7 +1,12 @@
import { Observable } from 'rxjs';
import { IEngineService } from 'src/engine/engine.interfaces';
+import { Domain } from 'src/engine/models/domain.model';
export default class DataShieldService implements IEngineService {
+ getDomain(): Domain[] {
+ throw new Error('Method not implemented.');
+ }
+
demo(): string {
return 'datashield';
}
diff --git a/api/src/engine/connectors/exareme/interfaces/hierarchy.interface.ts b/api/src/engine/connectors/exareme/interfaces/hierarchy.interface.ts
new file mode 100644
index 0000000..6d0f02b
--- /dev/null
+++ b/api/src/engine/connectors/exareme/interfaces/hierarchy.interface.ts
@@ -0,0 +1,8 @@
+import { VariableEntity } from "./variable-entity.interface";
+
+export interface Hierarchy {
+ code: string;
+ label: string;
+ groups: Hierarchy[];
+ variables: VariableEntity[];
+}
\ No newline at end of file
diff --git a/api/src/engine/connectors/exareme/interfaces/pathology.interface.ts b/api/src/engine/connectors/exareme/interfaces/pathology.interface.ts
new file mode 100644
index 0000000..d9dbea5
--- /dev/null
+++ b/api/src/engine/connectors/exareme/interfaces/pathology.interface.ts
@@ -0,0 +1,9 @@
+import { Hierarchy } from "./Hierarchy.interface";
+import { VariableEntity } from "./variable-entity.interface";
+
+export interface Pathology {
+ code: string;
+ label: string;
+ datasets: VariableEntity[];
+ metadataHierarchy: Hierarchy;
+}
\ No newline at end of file
diff --git a/api/src/engine/connectors/exareme/interfaces/variable-entity.interface.ts b/api/src/engine/connectors/exareme/interfaces/variable-entity.interface.ts
new file mode 100644
index 0000000..ce1ce25
--- /dev/null
+++ b/api/src/engine/connectors/exareme/interfaces/variable-entity.interface.ts
@@ -0,0 +1,9 @@
+import { Variable } from "./variable.interface";
+
+export interface VariableEntity extends Variable {
+ type?: 'nominal' | 'ordinal' | 'real' | 'integer' | 'text' | 'date';
+ description?: string;
+ enumerations?: Variable[];
+ group?: Variable[];
+ info?: string;
+}
\ No newline at end of file
diff --git a/api/src/engine/connectors/exareme/interfaces/variable.interface.ts b/api/src/engine/connectors/exareme/interfaces/variable.interface.ts
new file mode 100644
index 0000000..85174c8
--- /dev/null
+++ b/api/src/engine/connectors/exareme/interfaces/variable.interface.ts
@@ -0,0 +1,4 @@
+export interface Variable {
+ code: string;
+ label?: string;
+}
\ No newline at end of file
diff --git a/api/src/engine/connectors/exareme/main.connector.ts b/api/src/engine/connectors/exareme/main.connector.ts
index b85b494..ae59036 100644
--- a/api/src/engine/connectors/exareme/main.connector.ts
+++ b/api/src/engine/connectors/exareme/main.connector.ts
@@ -1,13 +1,57 @@
import { HttpService } from '@nestjs/axios';
import { Request } from 'express';
-import { map, Observable } from 'rxjs';
+import { firstValueFrom, map, Observable } from 'rxjs';
+import { Dictionary } from 'src/common/interfaces/utilities.interface';
import { IEngineOptions, IEngineService } from 'src/engine/engine.interfaces';
+import { Domain } from 'src/engine/models/domain.model';
+import { Group } from 'src/engine/models/group.model';
+import { Hierarchy } from './interfaces/Hierarchy.interface';
+import { Pathology } from './interfaces/pathology.interface';
+import { VariableEntity } from './interfaces/variable-entity.interface';
export default class ExaremeService implements IEngineService {
constructor(
private readonly options: IEngineOptions,
private readonly httpService: HttpService,
- ) {}
+ ) { }
+
+ private hierarchyToGroup = (data: Hierarchy): Group => {
+ return {
+ id: data.code,
+ label: data.label,
+ groups: data.groups ? data.groups.map((child: Hierarchy) => this.hierarchyToGroup(child)) : [],
+ variables: []
+ }
+ }
+
+ private flattenGroups = (data: Hierarchy): Group[] => {
+ let groups: Group[] = [this.hierarchyToGroup(data)];
+
+ if (data.groups) {
+ groups = groups.concat(data.groups.flatMap(this.flattenGroups));
+ }
+
+ return groups;
+ }
+
+
+ async getDomain(): Promise<Domain[]> {
+ const path = this.options.baseurl + 'pathologies';
+
+ const data = await firstValueFrom(this.httpService.get(path));
+
+ const domains = data.data.map((data: Pathology): Domain => {
+ return {
+ id: data.code,
+ label: data.label,
+ groups: data.metadataHierarchy.groups.flatMap(this.flattenGroups),
+ datasets: [],
+ variables: [],
+ }
+ })
+
+ return domains;
+ }
demo(): string {
return 'exareme';
@@ -82,4 +126,49 @@ export default class ExaremeService implements IEngineService {
.get<string>(path)
.pipe(map((response) => response.data));
}
+
+ private pathologiesHierarchies = (
+ json: Pathology[]
+ ): Dictionary<Hierarchy> => {
+ const pathologiesDatasets: Dictionary<Hierarchy> = {};
+ json.forEach(pathology => {
+ pathologiesDatasets[pathology.code] = pathology.metadataHierarchy;
+ });
+
+ return pathologiesDatasets;
+ };
+
+ private pathologiesVariables = (json: Pathology[]): Dictionary<VariableEntity[]> => {
+ const pathologiesVariables: Dictionary<VariableEntity[]> = {};
+ json.forEach(pathology => {
+ let variables: VariableEntity[] = [];
+
+ const dummyAccumulator = (node: any): void => {
+ if (node.variables) {
+ variables = [...variables, ...node.variables];
+ }
+
+ if (node.groups) {
+ return node.groups.map(dummyAccumulator);
+ }
+ };
+
+ if (pathology) {
+ dummyAccumulator(pathology.metadataHierarchy);
+ }
+
+ pathologiesVariables[pathology.code] = variables;
+ });
+
+ return pathologiesVariables;
+ };
+
+ private pathologiesDatasets = (json: Pathology[]): Dictionary<VariableEntity[]> => {
+ const pathologiesDatasets: Dictionary<VariableEntity[]> = {};
+ json.forEach(pathology => {
+ pathologiesDatasets[pathology.code] = pathology.datasets;
+ });
+
+ return pathologiesDatasets;
+ };
}
diff --git a/api/src/engine/engine.interfaces.ts b/api/src/engine/engine.interfaces.ts
index 22f4a54..17db7ff 100644
--- a/api/src/engine/engine.interfaces.ts
+++ b/api/src/engine/engine.interfaces.ts
@@ -1,5 +1,6 @@
import { Request } from 'express';
import { Observable } from 'rxjs';
+import { Domain } from './models/domain.model';
export interface IEngineOptions {
type: string;
@@ -9,6 +10,8 @@ export interface IEngineOptions {
export interface IEngineService {
demo(): string;
+ getDomain(): Domain[] | Promise<Domain[]>;
+
getAlgorithms(request: Request): Observable<string>;
getExperiments(request: Request): Observable<string>;
diff --git a/api/src/engine/engine.resolver.ts b/api/src/engine/engine.resolver.ts
index 0e4687c..6adcf0d 100644
--- a/api/src/engine/engine.resolver.ts
+++ b/api/src/engine/engine.resolver.ts
@@ -8,19 +8,10 @@ import { Domain } from './models/domain.model';
export class EngineResolver {
constructor(
@Inject(ENGINE_SERVICE) private readonly engineService: IEngineService,
- ) {}
+ ) { }
- @Query(() => Domain)
- async hello() {
- const dummy: Domain = {
- id: 'test',
- label: 'test',
- description: 'test',
- groups: [],
- variables: [],
- datasets: [],
- };
-
- return dummy;
+ @Query(() => [Domain])
+ async domain() {
+ return this.engineService.getDomain();
}
}
--
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