From 9957f40f1c809d6e3725397ae5281193eeaa8290 Mon Sep 17 00:00:00 2001
From: "Hartung, Michael" <michael.hartung@uni-hamburg.de>
Date: Fri, 15 Jul 2022 11:57:54 +0200
Subject: [PATCH] selection of algorithms available to user
---
src/app/config.ts | 13 +++++--
.../launch-analysis.component.ts | 34 +++++++++++--------
src/app/interfaces.ts | 21 ++++++++++--
.../explorer-page.component.html | 1 -
src/app/services/analysis/analysis.service.ts | 17 +---------
.../netex-controller.service.ts | 3 +-
6 files changed, 49 insertions(+), 40 deletions(-)
diff --git a/src/app/config.ts b/src/app/config.ts
index 13229016..c575eae9 100644
--- a/src/app/config.ts
+++ b/src/app/config.ts
@@ -1,3 +1,5 @@
+import { AlgorithmTarget, AlgorithmType, QuickAlgorithmType } from "./interfaces";
+
// https://visjs.github.io/vis-network/docs/network/nodes.html
export interface NodeGroup {
groupName?: string;
@@ -24,9 +26,9 @@ export interface EdgeGroup {
shadow?: any;
}
-export type Identifier = 'symbol'|'uniprot'|'ensg';
-export type InteractionDrugProteinDB = 'DrugBank'|'Chembl'|'DGIdb' | 'NeDRex';
-export type InteractionProteinProteinDB = 'STRING'|'BioGRID'|'APID' | 'NeDRex';
+export type Identifier = 'symbol' | 'uniprot' | 'ensg';
+export type InteractionDrugProteinDB = 'DrugBank' | 'Chembl' | 'DGIdb' | 'NeDRex';
+export type InteractionProteinProteinDB = 'STRING' | 'BioGRID' | 'APID' | 'NeDRex';
export type IndicationDrugDisorderDB = 'DrugBank' | 'NeDRex';
export type AssociatedProteinDisorderDB = 'NeDRex' | 'DisGeNET';
@@ -79,6 +81,7 @@ export interface IConfig {
nodeShadow?: boolean;
edgeShadow?: boolean;
useNedrexLicensed?: boolean;
+ algorithms: { [key in AlgorithmTarget]: Array<AlgorithmType | QuickAlgorithmType> }
}
/**
@@ -126,6 +129,10 @@ export const defaultConfig: IConfig = {
physicsOn: false,
useNedrexLicensed: true,
selfReferences: false,
+ algorithms: {
+ 'drug': ['trustrank', 'closeness', 'degree', 'proximity'],
+ 'drug-target': ['trustrank', 'multisteiner', 'keypathwayminer', 'degree', 'closeness', 'betweenness']
+ },
nodeGroups: {
// all NodeGroups but the default group must be set, if not provided by the user, they will be taken from here
// IMPORTANT: node color must be hexacode!
diff --git a/src/app/dialogs/launch-analysis/launch-analysis.component.ts b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
index bf4637eb..2810fcc7 100644
--- a/src/app/dialogs/launch-analysis/launch-analysis.component.ts
+++ b/src/app/dialogs/launch-analysis/launch-analysis.component.ts
@@ -1,15 +1,13 @@
-import {Component, EventEmitter, Input, OnChanges, OnInit, Output, SimpleChanges} from '@angular/core';
+import { Component, EventEmitter, Input, OnChanges, OnInit, Output, SimpleChanges } from '@angular/core';
import {
- Algorithm,
- AlgorithmType,
AnalysisService, BETWEENNESS_CENTRALITY, CLOSENESS_CENTRALITY,
DEGREE_CENTRALITY,
KEYPATHWAYMINER, MAX_TASKS,
MULTISTEINER, NETWORK_PROXIMITY,
- QuickAlgorithmType,
TRUSTRANK
} from '../../services/analysis/analysis.service';
-import { IConfig } from 'src/app/config';
+import { Algorithm, AlgorithmType, QuickAlgorithmType } from 'src/app/interfaces';
+import { DrugstoneConfigService } from 'src/app/services/drugstone-config/drugstone-config.service';
@Component({
selector: 'app-launch-analysis',
@@ -23,9 +21,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
@Input()
public target: 'drug' | 'drug-target';
@Input()
- public inputNetwork: {nodes: any, edges: any};
- @Input()
- public config: IConfig;
+ public inputNetwork: { nodes: any, edges: any };
@Output()
public showChange = new EventEmitter<boolean>();
@Output()
@@ -82,7 +78,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
public maxTasks = MAX_TASKS;
- constructor(public analysis: AnalysisService) {
+ constructor(public analysis: AnalysisService, public drugstoneConfig: DrugstoneConfigService) {
}
ngOnInit(): void {
@@ -91,10 +87,18 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
ngOnChanges(changes: SimpleChanges): void {
if (this.target === 'drug-target') {
this.algorithms = [MULTISTEINER, KEYPATHWAYMINER, TRUSTRANK, CLOSENESS_CENTRALITY, DEGREE_CENTRALITY, BETWEENNESS_CENTRALITY];
- this.algorithm = MULTISTEINER.slug;
} else if (this.target === 'drug') {
this.algorithms = [TRUSTRANK, CLOSENESS_CENTRALITY, DEGREE_CENTRALITY, NETWORK_PROXIMITY];
- this.algorithm = TRUSTRANK.slug;
+ } else {
+ // return because this.target === undefined
+ return
+ }
+ this.algorithms = this.algorithms.filter(algorithm => this.drugstoneConfig.config.algorithms[this.target].includes(algorithm.slug));
+ // sanity check to fallback algorithm, trustrank works on all targets
+ if (!this.algorithms.length) {
+ this.algorithms = [TRUSTRANK];
+ } else {
+ this.algorithm = this.algorithms[0].slug;
}
}
@@ -111,12 +115,12 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
});
const parameters: any = {
seeds: seedsFiltered,
- config: this.config,
+ config: this.drugstoneConfig.config,
input_network: this.inputNetwork
};
- parameters.ppi_dataset = this.config.interactionProteinProtein;
- parameters.pdi_dataset = this.config.interactionDrugProtein;
+ parameters.ppi_dataset = this.drugstoneConfig.config.interactionProteinProtein;
+ parameters.pdi_dataset = this.drugstoneConfig.config.interactionDrugProtein;
parameters.target = this.target === 'drug' ? 'drug' : 'drug-target';
// pass network data to reconstruct network in analysis result to connect non-proteins to results
// drop interactions in nodes beforehand to no cause cyclic error, information is contained in edges
@@ -176,7 +180,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
parameters.hub_penalty = this.multisteinerHubPenalty;
}
const token = await this.analysis.startAnalysis(this.algorithm, this.target, parameters);
- const object = {taskId: token, algorithm: this.algorithm, target: this.target, params: parameters};
+ const object = { taskId: token, algorithm: this.algorithm, target: this.target, params: parameters };
this.taskEvent.emit(object);
}
diff --git a/src/app/interfaces.ts b/src/app/interfaces.ts
index 8f5eacee..16048966 100644
--- a/src/app/interfaces.ts
+++ b/src/app/interfaces.ts
@@ -1,5 +1,3 @@
-import {AlgorithmType, QuickAlgorithmType} from './services/analysis/analysis.service';
-
export interface Node {
ctxRenderer?: any;
label: string;
@@ -67,10 +65,12 @@ export interface NetworkEdge {
label: string;
}
+export type AlgorithmTarget = 'drug' | 'drug-target'
+
export interface Task {
token: string;
info: {
- target: 'drug' | 'drug-target',
+ target: AlgorithmTarget,
algorithm: AlgorithmType | QuickAlgorithmType;
parameters?: { [key: string]: any };
@@ -231,3 +231,18 @@ export interface Dataset {
id: string;
data: Array<[string, string]>;
}
+
+export type AlgorithmType =
+ 'trustrank'
+ | 'keypathwayminer'
+ | 'multisteiner'
+ | 'closeness'
+ | 'degree'
+ | 'proximity'
+ | 'betweenness';
+export type QuickAlgorithmType = 'quick' | 'super';
+
+export interface Algorithm {
+ slug: AlgorithmType | QuickAlgorithmType;
+ name: string;
+}
diff --git a/src/app/pages/explorer-page/explorer-page.component.html b/src/app/pages/explorer-page/explorer-page.component.html
index fbeb61c7..2bc4959d 100644
--- a/src/app/pages/explorer-page/explorer-page.component.html
+++ b/src/app/pages/explorer-page/explorer-page.component.html
@@ -6,7 +6,6 @@
<app-launch-analysis
[(show)]="showAnalysisDialog"
[target]="analysisDialogTarget"
- [config]="drugstoneConfig.config"
[inputNetwork]="{ nodes: proteins, edges: edges }"
(taskEvent)="emitTaskEvent($event)"
>
diff --git a/src/app/services/analysis/analysis.service.ts b/src/app/services/analysis/analysis.service.ts
index 96030cbf..f85cb23f 100644
--- a/src/app/services/analysis/analysis.service.ts
+++ b/src/app/services/analysis/analysis.service.ts
@@ -1,4 +1,4 @@
-import {Wrapper, Task, getWrapperFromNode, Node, Dataset, Tissue} from '../../interfaces';
+import {Wrapper, Task, getWrapperFromNode, Node, Dataset, Tissue, Algorithm} from '../../interfaces';
import {Subject} from 'rxjs';
import {HttpClient} from '@angular/common/http';
import {environment} from '../../../environments/environment';
@@ -6,16 +6,6 @@ import {toast} from 'bulma-toast';
import {Injectable} from '@angular/core';
import {NetexControllerService} from '../netex-controller/netex-controller.service';
-export type AlgorithmType =
- 'trustrank'
- | 'keypathwayminer'
- | 'multisteiner'
- | 'closeness'
- | 'degree'
- | 'proximity'
- | 'betweenness';
-export type QuickAlgorithmType = 'quick' | 'super';
-
export const algorithmNames = {
trustrank: 'TrustRank',
keypathwayminer: 'KeyPathwayMiner',
@@ -28,11 +18,6 @@ export const algorithmNames = {
super: 'Quick-Start',
};
-export interface Algorithm {
- slug: AlgorithmType | QuickAlgorithmType;
- name: string;
-}
-
export const TRUSTRANK: Algorithm = {slug: 'trustrank', name: algorithmNames.trustrank};
export const CLOSENESS_CENTRALITY: Algorithm = {slug: 'closeness', name: algorithmNames.closeness};
export const DEGREE_CENTRALITY: Algorithm = {slug: 'degree', name: algorithmNames.degree};
diff --git a/src/app/services/netex-controller/netex-controller.service.ts b/src/app/services/netex-controller/netex-controller.service.ts
index 81c3d7bd..64d13472 100644
--- a/src/app/services/netex-controller/netex-controller.service.ts
+++ b/src/app/services/netex-controller/netex-controller.service.ts
@@ -1,9 +1,8 @@
import {Injectable} from '@angular/core';
import {environment} from '../../../environments/environment';
import {HttpClient, HttpParams} from '@angular/common/http';
-import {AlgorithmType, QuickAlgorithmType} from '../analysis/analysis.service';
import {Observable} from 'rxjs';
-import {Tissue, Node, EdgeType} from 'src/app/interfaces';
+import {Tissue, Node, EdgeType, QuickAlgorithmType, AlgorithmType} from 'src/app/interfaces';
import {InteractionDrugProteinDB, InteractionProteinProteinDB} from 'src/app/config';
@Injectable({
--
GitLab