From e981261a9ba5cd0fb9dcb24e39f1298bd18d3e73 Mon Sep 17 00:00:00 2001
From: stevereis <stevereis93@gmail.com>
Date: Tue, 28 Sep 2021 11:45:05 +0200
Subject: [PATCH] Refactor Transient to Experiment
---
.../connectors/datashield/main.connector.ts | 9 ++---
.../engine/connectors/exareme/converters.ts | 13 +++----
.../connectors/exareme/main.connector.ts | 11 +++---
api/src/engine/engine.interfaces.ts | 8 +++--
api/src/engine/engine.resolver.ts | 10 +++---
.../experiment-create.input.ts} | 9 +++--
.../models/experiment/experiment.model.ts | 23 +++++++++++++
.../models/transient/transient.model.ts | 11 ------
.../engine/models/utility/extrafield.input.ts | 12 -------
api/src/schema.gql | 34 ++++++++++++-------
10 files changed, 78 insertions(+), 62 deletions(-)
rename api/src/engine/models/{transient/transient-create.input.ts => experiment/experiment-create.input.ts} (69%)
create mode 100644 api/src/engine/models/experiment/experiment.model.ts
delete mode 100644 api/src/engine/models/transient/transient.model.ts
delete mode 100644 api/src/engine/models/utility/extrafield.input.ts
diff --git a/api/src/engine/connectors/datashield/main.connector.ts b/api/src/engine/connectors/datashield/main.connector.ts
index cfa03be..1cdbb50 100644
--- a/api/src/engine/connectors/datashield/main.connector.ts
+++ b/api/src/engine/connectors/datashield/main.connector.ts
@@ -1,14 +1,15 @@
import { Observable } from 'rxjs';
import { IEngineService } from 'src/engine/engine.interfaces';
import { Domain } from 'src/engine/models/domain.model';
-import { TransientCreateInput } from 'src/engine/models/transient/transient-create.input';
-import { Transient } from 'src/engine/models/transient/transient.model';
+import { ExperimentCreateInput } from 'src/engine/models/experiment/experiment-create.input';
+import { Experiment } from 'src/engine/models/experiment/experiment.model';
export default class DataShieldService implements IEngineService {
- createTransient(data: TransientCreateInput): Promise<Transient> | Transient {
+ createTransient(
+ data: ExperimentCreateInput,
+ ): Experiment | Promise<Experiment> {
throw new Error('Method not implemented.');
}
-
getDomains(): Domain[] {
throw new Error('Method not implemented.');
}
diff --git a/api/src/engine/connectors/exareme/converters.ts b/api/src/engine/connectors/exareme/converters.ts
index 5a77920..ba948ad 100644
--- a/api/src/engine/connectors/exareme/converters.ts
+++ b/api/src/engine/connectors/exareme/converters.ts
@@ -4,9 +4,9 @@ import { Variable } from 'src/engine/models/variable.model';
import { Hierarchy } from './interfaces/hierarchy.interface';
import { VariableEntity } from './interfaces/variable-entity.interface';
import { Entity } from './interfaces/entity.interface';
-import { TransientCreateInput } from 'src/engine/models/transient/transient-create.input';
+import { ExperimentCreateInput } from 'src/engine/models/experiment/experiment-create.input';
import { TransientDataResult } from './interfaces/transient/transient-data-result.interface';
-import { Transient } from 'src/engine/models/transient/transient.model';
+import { Experiment } from 'src/engine/models/experiment/experiment.model';
import { MetaData } from 'src/engine/models/result/common/metadata.model';
import { TableResult } from 'src/engine/models/result/table-result.model';
import { Dictionary } from 'src/common/interfaces/utilities.interface';
@@ -40,7 +40,7 @@ export const dataToVariable = (data: VariableEntity): Variable => {
};
};
-export const transientInputToData = (data: TransientCreateInput) => {
+export const experimentInputToData = (data: ExperimentCreateInput) => {
return {
algorithm: {
parameters: [
@@ -62,9 +62,9 @@ export const transientInputToData = (data: TransientCreateInput) => {
},
],
type: 'string',
- name: 'DESCRIPTIVE_STATS',
+ name: data.algorithm,
},
- name: 'Descriptive statistics',
+ name: data.name,
};
};
@@ -80,7 +80,7 @@ const dictToTable = (dict: Dictionary<string[]>, rows: number): string[][] => {
});
};
-export const dataToTransient = (data: TransientDataResult): Transient => {
+export const dataToTransient = (data: TransientDataResult): Experiment => {
const result = data.result[0];
const tables = Object.keys(result.data.single).map((varKey): TableResult => {
const variable = result.data.single[varKey];
@@ -116,6 +116,7 @@ export const dataToTransient = (data: TransientDataResult): Transient => {
data: dictToTable(rows, count),
metadatas: domains,
name: varKey,
+ groupBy: 'single',
};
});
diff --git a/api/src/engine/connectors/exareme/main.connector.ts b/api/src/engine/connectors/exareme/main.connector.ts
index a4ecf13..d9a772d 100644
--- a/api/src/engine/connectors/exareme/main.connector.ts
+++ b/api/src/engine/connectors/exareme/main.connector.ts
@@ -5,15 +5,15 @@ import { firstValueFrom, map, Observable } from 'rxjs';
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 { TransientCreateInput } from 'src/engine/models/transient/transient-create.input';
-import { Transient } from 'src/engine/models/transient/transient.model';
+import { ExperimentCreateInput } from 'src/engine/models/experiment/experiment-create.input';
+import { Experiment } from 'src/engine/models/experiment/experiment.model';
import { Variable } from 'src/engine/models/variable.model';
import {
dataToCategory,
dataToGroup,
dataToTransient,
dataToVariable,
- transientInputToData,
+ experimentInputToData,
} from './converters';
import { Hierarchy } from './interfaces/hierarchy.interface';
import { Pathology } from './interfaces/pathology.interface';
@@ -25,8 +25,8 @@ export default class ExaremeService implements IEngineService {
private readonly httpService: HttpService,
) {}
- async createTransient(data: TransientCreateInput): Promise<Transient> {
- const form = transientInputToData(data);
+ async createTransient(data: ExperimentCreateInput): Promise<Experiment> {
+ const form = experimentInputToData(data);
const path = this.options.baseurl + 'experiments/transient';
@@ -40,7 +40,6 @@ export default class ExaremeService implements IEngineService {
ppmi: {
data: {
std: 1.2048783713787277,
- max: 15.0815,
min: 7.6335,
mean: 11.38076218487395,
},
diff --git a/api/src/engine/engine.interfaces.ts b/api/src/engine/engine.interfaces.ts
index 323e65e..0d90e92 100644
--- a/api/src/engine/engine.interfaces.ts
+++ b/api/src/engine/engine.interfaces.ts
@@ -1,8 +1,8 @@
import { Request } from 'express';
import { Observable } from 'rxjs';
import { Domain } from './models/domain.model';
-import { TransientCreateInput } from './models/transient/transient-create.input';
-import { Transient } from './models/transient/transient.model';
+import { ExperimentCreateInput } from './models/experiment/experiment-create.input';
+import { Experiment } from './models/experiment/experiment.model';
export interface IEngineOptions {
type: string;
@@ -24,7 +24,9 @@ export interface IEngineService {
startExperimentTransient(request: Request): Observable<string>;
- createTransient(data: TransientCreateInput): Promise<Transient> | Transient;
+ createTransient(
+ data: ExperimentCreateInput,
+ ): Promise<Experiment> | Experiment;
startExperiment(request: Request): Observable<string>;
diff --git a/api/src/engine/engine.resolver.ts b/api/src/engine/engine.resolver.ts
index 750a2d6..e3de433 100644
--- a/api/src/engine/engine.resolver.ts
+++ b/api/src/engine/engine.resolver.ts
@@ -3,8 +3,8 @@ 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 { TransientCreateInput } from './models/transient/transient-create.input';
-import { Transient } from './models/transient/transient.model';
+import { ExperimentCreateInput } from './models/experiment/experiment-create.input';
+import { Experiment } from './models/experiment/experiment.model';
@Resolver()
export class EngineResolver {
@@ -20,10 +20,10 @@ export class EngineResolver {
return this.engineService.getDomains(ids);
}
- @Mutation(() => Transient)
+ @Mutation(() => Experiment)
async createTransient(
- @Args('data') transientCreateInput: TransientCreateInput,
+ @Args('data') experimentCreateInput: ExperimentCreateInput,
) {
- return this.engineService.createTransient(transientCreateInput);
+ return this.engineService.createTransient(experimentCreateInput);
}
}
diff --git a/api/src/engine/models/transient/transient-create.input.ts b/api/src/engine/models/experiment/experiment-create.input.ts
similarity index 69%
rename from api/src/engine/models/transient/transient-create.input.ts
rename to api/src/engine/models/experiment/experiment-create.input.ts
index 0a2827e..d871eea 100644
--- a/api/src/engine/models/transient/transient-create.input.ts
+++ b/api/src/engine/models/experiment/experiment-create.input.ts
@@ -1,8 +1,7 @@
import { Field, InputType } from '@nestjs/graphql';
-import { Extrafield } from '../utility/extrafield.input';
@InputType()
-export class TransientCreateInput extends Extrafield {
+export class ExperimentCreateInput {
@Field(() => [String])
datasets: string[];
@@ -14,4 +13,10 @@ export class TransientCreateInput extends Extrafield {
@Field()
domain: string;
+
+ @Field()
+ algorithm: string;
+
+ @Field()
+ name: string;
}
diff --git a/api/src/engine/models/experiment/experiment.model.ts b/api/src/engine/models/experiment/experiment.model.ts
new file mode 100644
index 0000000..42dd04f
--- /dev/null
+++ b/api/src/engine/models/experiment/experiment.model.ts
@@ -0,0 +1,23 @@
+import { Field, GraphQLISODateTime, ObjectType } from '@nestjs/graphql';
+import { Result } from '../result/result.model';
+
+@ObjectType()
+export class Experiment {
+ @Field()
+ title: string;
+
+ @Field({ nullable: true })
+ uuid?: string;
+
+ @Field(() => GraphQLISODateTime, { nullable: true })
+ created_at?: Date;
+
+ @Field(() => GraphQLISODateTime, { nullable: true })
+ update_at?: Date;
+
+ @Field(() => GraphQLISODateTime, { nullable: true })
+ finished_at?: Date;
+
+ @Field(() => [Result])
+ result: Result[];
+}
diff --git a/api/src/engine/models/transient/transient.model.ts b/api/src/engine/models/transient/transient.model.ts
deleted file mode 100644
index 54d8e10..0000000
--- a/api/src/engine/models/transient/transient.model.ts
+++ /dev/null
@@ -1,11 +0,0 @@
-import { Field, ObjectType } from '@nestjs/graphql';
-import { TableResult } from '../result/table-result.model';
-
-@ObjectType()
-export class Transient {
- @Field()
- title: string;
-
- @Field(() => [TableResult])
- result: TableResult[];
-}
diff --git a/api/src/engine/models/utility/extrafield.input.ts b/api/src/engine/models/utility/extrafield.input.ts
deleted file mode 100644
index 22f9172..0000000
--- a/api/src/engine/models/utility/extrafield.input.ts
+++ /dev/null
@@ -1,12 +0,0 @@
-import { Field, InputType } from '@nestjs/graphql';
-
-/**
- * This class is used to add a common extra field to
- * an input class in order to provide specific
- * information for a connector
- */
-@InputType()
-export class Extrafield {
- @Field({ nullable: true })
- extradata: string;
-}
diff --git a/api/src/schema.gql b/api/src/schema.gql
index e0d4db8..8d97521 100644
--- a/api/src/schema.gql
+++ b/api/src/schema.gql
@@ -34,20 +34,27 @@ type Domain {
rootGroup: Group!
}
-type MetaData {
- name: String!
- type: String!
+type Result {
+ groupBy: String
}
-type TableResult {
- name: String!
- data: [[String!]!]!
- metadatas: [MetaData!]!
+type Experiment {
+ title: String!
+ uuid: String
+ created_at: DateTime
+ update_at: DateTime
+ finished_at: DateTime
+ result: [Result!]!
}
-type Transient {
- title: String!
- result: [TableResult!]!
+"""
+A date-time string at UTC, such as 2019-12-03T09:54:33Z, compliant with the date-time format.
+"""
+scalar DateTime
+
+type MetaData {
+ name: String!
+ type: String!
}
type Query {
@@ -55,13 +62,14 @@ type Query {
}
type Mutation {
- createTransient(data: TransientCreateInput!): Transient!
+ createTransient(data: ExperimentCreateInput!): Experiment!
}
-input TransientCreateInput {
- extradata: String
+input ExperimentCreateInput {
datasets: [String!]!
variables: [String!]!
filter: String
domain: String!
+ algorithm: String!
+ name: String!
}
--
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