@jax-data-science/api-clients 0.0.1-0 → 0.0.1-a

package/lib/services/ontology/ontology.model.d.ts

@@ -0,0 +1,80 @@
+export interface OntologyConfig {
+    name: string;
+    prefix: string;
+    github: {
+        api: string;
+        home: string;
+    };
+    home: string;
+    api: {
+        docs: string;
+        base: string;
+    };
+    base_file: string;
+    international: boolean;
+    description: string;
+}
+export declare enum Ontology {
+    HP = "HP",
+    MONDO = "MONDO",
+    MP = "MP",
+    CL = "CL",
+    MAXO = "MAXO"
+}
+export interface OntologyTerm {
+    id: string;
+    name: string;
+}
+export interface OLSTerm {
+    appearsIn: string[];
+    curie: string;
+    definedBy: string[];
+    definition?: Array<{
+        type: string[];
+        value: string;
+        axioms?: Array<{
+            [key: string]: string;
+        }>;
+    }>;
+    definitionProperty?: string;
+    directAncestor?: string[];
+    directParent?: Array<string>;
+    hasDirectChildren?: boolean;
+    hasDirectParents?: boolean;
+    hasHierarchicalChildren?: boolean;
+    hasHierarchicalParents?: boolean;
+    hierarchicalAncestor?: string[];
+    hierarchicalParent?: Array<string | {
+        type: string[];
+        value: string;
+        axioms?: Array<{
+            [key: string]: string;
+        }>;
+    }>;
+    hierarchicalProperty?: string;
+    imported?: boolean;
+    iri: string;
+    isDefiningOntology?: boolean;
+    isObsolete?: boolean;
+    isPreferredRoot?: boolean;
+    label?: string[];
+    linkedEntities?: Record<string, any>;
+    linksTo?: string[];
+    numDescendants?: number;
+    numHierarchicalDescendants?: number;
+    ontologyId?: string;
+    ontologyIri?: string;
+    ontologyPreferredPrefix?: string;
+    searchableAnnotationValues?: any[];
+    shortForm?: string;
+    type?: string[];
+    [key: string]: any;
+}
+export interface OLSResponse {
+    page: number;
+    numElements: number;
+    totalPages: number;
+    totalElements: number;
+    elements: OLSTerm[];
+    facetFieldsToCounts?: Record<string, any>;
+}

package/lib/services/ontology/ontology.service.base.d.ts

@@ -0,0 +1,11 @@
+import { Observable } from 'rxjs';
+import { Ontology, OntologyTerm } from './ontology.model';
+import { CollectionResponse, Response } from '../../models/response';
+export declare abstract class OntologyService {
+    abstract search(query: string, limit: number, ontology: Ontology): Observable<CollectionResponse<OntologyTerm>>;
+    abstract term(id: string): Observable<Response<OntologyTerm>>;
+    abstract parents(id: string): Observable<CollectionResponse<OntologyTerm>>;
+    abstract children(id: string): Observable<CollectionResponse<OntologyTerm>>;
+    abstract ancestors(id: string): Observable<CollectionResponse<OntologyTerm>>;
+    abstract descendants(id: string): Observable<CollectionResponse<OntologyTerm>>;
+}

package/lib/{ontology/ontology.service.d.ts → services/ontology/ontology.service.jax.d.ts}

@@ -1,9 +1,10 @@
 import { HttpClient } from '@angular/common/http';
 import { Observable } from 'rxjs';
 import { Ontology, OntologyTerm } from './ontology.model';
-import { CollectionResponse, Response } from '../models/response';
+import { CollectionResponse, Response } from '../../models/response';
+import { OntologyService } from './ontology.service.base';
 import * as i0 from "@angular/core";
-export declare class OntologyService {
+export declare class JaxOntologyService extends OntologyService {
     private httpClient;
     config_location: string;
     private config;
@@ -43,14 +44,10 @@ export declare class OntologyService {
      * @param id - the term ID
      */
     descendants(id: string): Observable<CollectionResponse<OntologyTerm>>;
-    /**
-     * Get the ontology from curie
-     */
-    ontologyFromCurie(curie: string): Ontology;
     /**
      * Get the ontology api base url configuration
      **/
     ontologyBaseResolver(ontology: Ontology): string;
-    static ɵfac: i0.ɵɵFactoryDeclaration<OntologyService, never>;
-    static ɵprov: i0.ɵɵInjectableDeclaration<OntologyService>;
+    static ɵfac: i0.ɵɵFactoryDeclaration<JaxOntologyService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<JaxOntologyService>;
 }

package/lib/services/ontology/ontology.service.ols.d.ts

@@ -0,0 +1,22 @@
+import { HttpClient } from '@angular/common/http';
+import { OntologyService } from './ontology.service.base';
+import { Observable } from 'rxjs';
+import { OLSTerm, Ontology, OntologyTerm } from './ontology.model';
+import { CollectionResponse, Response } from '../../models/response';
+import * as i0 from "@angular/core";
+export declare class OLSOntologyService extends OntologyService {
+    private httpClient;
+    private OLS_SEARCH_BASE;
+    private OLS_ENTITY_BASE;
+    private PURL_BASE;
+    constructor(httpClient: HttpClient);
+    term(id: string): Observable<Response<OntologyTerm>>;
+    search(query: string, limit: number, ontology: Ontology): Observable<CollectionResponse<OntologyTerm>>;
+    parents(id: string): Observable<CollectionResponse<OntologyTerm>>;
+    children(id: string): Observable<CollectionResponse<OntologyTerm>>;
+    ancestors(id: string): Observable<CollectionResponse<OntologyTerm>>;
+    descendants(id: string): Observable<CollectionResponse<OntologyTerm>>;
+    mapOLSTermToOntologyTerm(olsTerm: OLSTerm): OntologyTerm;
+    static ɵfac: i0.ɵɵFactoryDeclaration<OLSOntologyService, never>;
+    static ɵprov: i0.ɵɵInjectableDeclaration<OLSOntologyService>;
+}

package/lib/services/ontology/ontology.shared.d.ts

@@ -0,0 +1,5 @@
+import { Ontology } from "./ontology.model";
+/**
+   * Get the ontology from curie
+   */
+export declare function ontologyFromCurie(curie: string): Ontology;

package/lib/tokens/isa-data-config.token.d.ts

@@ -0,0 +1,5 @@
+import { InjectionToken } from '@angular/core';
+export interface IsaDataServiceConfig {
+    baseUrl: string;
+}
+export declare const ISA_DATA_SERVICE_CONFIG: InjectionToken<IsaDataServiceConfig>;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jax-data-science/api-clients",
-  "version": "0.0.1-0",
+  "version": "0.0.1-a",
   "dependencies": {
     "@microsoft/fetch-event-source": "^2.0.1",
     "rxjs": "^7.8.0",

package/lib/ontology/ontology.model.d.ts

@@ -1,27 +0,0 @@
-export interface OntologyConfig {
-    name: string;
-    prefix: string;
-    github: {
-        api: string;
-        home: string;
-    };
-    home: string;
-    api: {
-        docs: string;
-        base: string;
-    };
-    base_file: string;
-    international: boolean;
-    description: string;
-}
-export declare enum Ontology {
-    HP = "HP",
-    MONDO = "MONDO",
-    MP = "MP",
-    CL = "CL",
-    MAXO = "MAXO"
-}
-export interface OntologyTerm {
-    id: string;
-    name: string;
-}