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

package/README.md

@@ -5,3 +5,17 @@ This library was generated with [Nx](https://nx.dev).
 ## Running unit tests
 
 Run `nx test api-clients` to execute the unit tests.
+
+
+## Ontology Service
+
+Ontology Service has two implementations JAXOntologyService & OLS Ontology Service. Both converge on the same model that is
+subject to change in releases.
+
+To use any particular implementation
+
+```
+    providers: [
+        {provide: OntologyService, useClass: JAXOntologyService}
+    ]
+```

package/fesm2022/jax-data-science-api-clients.mjs

@@ -1,5 +1,5 @@
 import * as i0 from '@angular/core';
-import { Injectable, inject, Inject, NgModule } from '@angular/core';
+import { Injectable, inject, InjectionToken, Inject, NgModule } from '@angular/core';
 import { throwError, map, catchError, Observable, BehaviorSubject, combineLatest, tap } from 'rxjs';
 import { fetchEventSource } from '@microsoft/fetch-event-source';
 import * as i1 from '@angular/common/http';
@@ -370,133 +370,134 @@ var WorkflowExecutionStatus;
     WorkflowExecutionStatus[WorkflowExecutionStatus["TIMED_OUT"] = 7] = "TIMED_OUT";
 })(WorkflowExecutionStatus || (WorkflowExecutionStatus = {}));
 
-var Ontology;
-(function (Ontology) {
-    Ontology["HP"] = "HP";
-    Ontology["MONDO"] = "MONDO";
-    Ontology["MP"] = "MP";
-    Ontology["CL"] = "CL";
-    Ontology["MAXO"] = "MAXO";
-})(Ontology || (Ontology = {}));
+const ISA_DATA_SERVICE_CONFIG = new InjectionToken('ISA_DATA_SERVICE_CONFIG');
 
-class OntologyService {
-    httpClient;
-    config_location = 'https://raw.githubusercontent.com/TheJacksonLaboratory/ontology-service/refs/heads/main/config/ontologies-internal.json';
-    config;
-    /**
-     * Get the configuration file from the source for the backend api service
-     */
-    constructor(httpClient) {
-        this.httpClient = httpClient;
-        this.httpClient.get(this.config_location).subscribe({
-            next: (config) => this.config = config,
-            error: () => {
-                this.config = [];
-            }
-        });
+/**
+ * service for interacting with ISA (Investigation-Study-Assay) data model API.
+ */
+class ISADataService {
+    apiConfig = inject(ISA_DATA_SERVICE_CONFIG);
+    apiServiceFactory = inject(ApiBaseServiceFactory);
+    apiBaseService;
+    constructor() {
+        this.apiBaseService = this.apiServiceFactory.create(this.apiConfig.baseUrl);
     }
-    /**
-     * Search for terms in an ontology
-     * @param query - the search query
-     * @param limit - the number of results to return
-     * @param ontology - the ontology to search
-     */
-    search(query, limit, ontology) {
-        return this.httpClient.get(`${this.ontologyBaseResolver(ontology)}/search?q=${query}&limit=${limit}`);
+    getApiBaseUrl() {
+        return this.apiConfig.baseUrl;
     }
+    // measure operations
     /**
-     * Get a term by its ID
-     * @param id - the term ID
+     * Fetches measure series metadata for the given measure series IDs and study IDs.
+     *
+     * @param measureSeriesIds - measure series identifiers to fetch metadata for. ONLY ONE ID IS SUPPORTED.
+     * @param studyIds - ONLY ONE ID IS SUPPORTED. REQUIRED!! WILL BE REMOVED IN THE FUTURE.
+     *
+     * @return Observable<Response<MeasureSeriesMetadata>> - an observable containing the measure series metadata.
      */
-    term(id) {
-        try {
-            const url = `${this.ontologyBaseResolver(this.ontologyFromCurie(id))}/${id}`;
-            return this.httpClient.get(url);
-        }
-        catch (error) {
-            return throwError(error);
+    getMeasureSeriesMetadata(measureSeriesIds, studyIds) {
+        if (!measureSeriesIds?.length) {
+            const errorResponse = {
+                code: 'BAD_REQUEST',
+                num_code: 400,
+                message: 'missing required parameter: measureSeriesIds',
+            };
+            throw errorResponse;
         }
+        const url = this.buildUrl('/visualization/measures/metadata', {
+            measureSeriesIds: measureSeriesIds.join(','),
+            studyId: studyIds.join(',')
+        });
+        return this.apiBaseService.get(url);
     }
     /**
-     * Get the parents of a term
-     * @param id - the term ID
+     * THIS METHOD SHOULD NOT BE USED. PLACEHOLDER FOR FUTURE IMPLEMENTATION ONCE THE API GROWS.
      */
-    parents(id) {
-        try {
-            const url = `${this.ontologyBaseResolver(this.ontologyFromCurie(id))}/${id}/parents`;
-            return this.httpClient.get(url);
-        }
-        catch (error) {
-            return throwError(error);
-        }
+    getMeasuresMetadata(measureIds, studyIds) {
+        const reqUrl = '';
+        return this.apiBaseService.get(reqUrl);
     }
     /**
-     * Get the children of a term
-     * @param id - the term ID
+     * Fetches measure series characteristics for the given measure series IDs and study IDs.
+     *
+     * @param measureSeriesIds - measure series identifiers to fetch metadata for. ONLY ONE ID IS SUPPORTED.
+     * @param studyIds - ONLY ONE ID IS SUPPORTED. REQUIRED!! WILL BE REMOVED IN THE FUTURE.
+     *
+     * @return Observable<Response<MeasureSeriesMetadata>> - an observable containing the measure series metadata.
      */
-    children(id) {
-        try {
-            const url = `${this.ontologyBaseResolver(this.ontologyFromCurie(id))}/${id}/children`;
-            return this.httpClient.get(url);
-        }
-        catch (error) {
-            return throwError(error);
+    getMeasureSeriesCharacteristics(measureSeriesIds, studyIds) {
+        if (!measureSeriesIds?.length) {
+            const errorResponse = {
+                code: 'BAD_REQUEST',
+                num_code: 400,
+                message: 'missing required parameter: measureSeriesIds',
+            };
+            throw errorResponse;
         }
+        const url = this.buildUrl('/visualization/measures/characteristics', {
+            measureSeriesIds: measureSeriesIds.join(','),
+            studyIds: studyIds.join(',')
+        });
+        return this.apiBaseService.get(url);
     }
+    // ASSAYS: to-be-implemented
     /**
-     * Get the ancestors of a term
-     * @param id - the term ID
+     * Placeholder for assay operations
+     * TODO: Implement assay-related methods
      */
-    ancestors(id) {
-        try {
-            const url = `${this.ontologyBaseResolver(this.ontologyFromCurie(id))}/${id}/ancestors`;
-            return this.httpClient.get(url);
-        }
-        catch (error) {
-            return throwError(error);
-        }
-    }
+    // STUDIES: to-be-implemented
     /**
-     * Get the descendants of a term
-     * @param id - the term ID
+     * Placeholder for study operations
+     * TODO: Implement study-related methods
      */
-    descendants(id) {
-        try {
-            const url = `${this.ontologyBaseResolver(this.ontologyFromCurie(id))}/${id}/descendants`;
-            return this.httpClient.get(url);
-        }
-        catch (error) {
-            return throwError(error);
-        }
-    }
+    // INVESTIGATIONS: to-be-implemented
     /**
-     * Get the ontology from curie
+     * Placeholder for investigation operations
+     * TODO: Implement investigation-related methods
      */
-    ontologyFromCurie(curie) {
-        return Ontology[curie.split(':')[0]];
-    }
     /**
-     * Get the ontology api base url configuration
-     **/
-    ontologyBaseResolver(ontology) {
-        if (!this.config || this.config.length === 0) {
-            throw new Error('No ontology configuration found.');
-        }
-        const ontology_config = this.config.find((config) => config.prefix.toUpperCase() === ontology);
-        if (!ontology_config) {
-            throw new Error('Ontology not found in configuration.');
-        }
-        return ontology_config.api.base;
+     * Builds the URL for the ISA data service.
+     *
+     * @param endpoint - the API endpoint path.
+     * @param params - optional query parameters as key-value pairs.
+     *
+     * @return complete URL with query string parameters.
+     */
+    buildUrl(endpoint, params) {
+        const queryParams = new URLSearchParams(params).toString();
+        return queryParams ? `${endpoint}?${queryParams}` : endpoint;
     }
-    static ɵfac = i0.ɵɵngDeclareFactory({ minVersion: "12.0.0", version: "19.1.5", ngImport: i0, type: OntologyService, deps: [{ token: i1.HttpClient }], target: i0.ɵɵFactoryTarget.Injectable });
-    static ɵprov = i0.ɵɵngDeclareInjectable({ minVersion: "12.0.0", version: "19.1.5", ngImport: i0, type: OntologyService, providedIn: 'root' });
+    // HEALTH CHECK
+    // TO-DO [GIK 05/30/2025]: should be moved outside this service
+    getHealthCheck() {
+        return this.apiBaseService.get('/monitors/servers/health');
+    }
+    static ɵfac = i0.ɵɵngDeclareFactory({ minVersion: "12.0.0", version: "19.1.5", ngImport: i0, type: ISADataService, deps: [], target: i0.ɵɵFactoryTarget.Injectable });
+    static ɵprov = i0.ɵɵngDeclareInjectable({ minVersion: "12.0.0", version: "19.1.5", ngImport: i0, type: ISADataService, providedIn: 'root' });
 }
-i0.ɵɵngDeclareClassMetadata({ minVersion: "12.0.0", version: "19.1.5", ngImport: i0, type: OntologyService, decorators: [{
+i0.ɵɵngDeclareClassMetadata({ minVersion: "12.0.0", version: "19.1.5", ngImport: i0, type: ISADataService, decorators: [{
             type: Injectable,
             args: [{
                     providedIn: 'root'
                 }]
-        }], ctorParameters: () => [{ type: i1.HttpClient }] });
+        }], ctorParameters: () => [] });
+
+/**
+ * This module defines the data models for representing the Investigation-Study-Assay (ISA)
+ * data model, which is a standard for describing life science experiments and their results.
+ *
+ * Key Concepts:
+ * - Investigation: The overall research project or study.
+ * - Study: A specific experimental design within an investigation.
+ * - Assay: A specific test or measurement performed on samples within a study.
+ *
+ * Measures represent the actual data points collected from assay executions, including:
+ * - Measure: a single assay results with unique identifier
+ * - MeasureSeries: a collection of measures that share common metadata and characteristics
+ *
+ * Each measure/series contains values, metadata about the experimental conditions,
+ * and characteristics that describe sample properties or experimental parameters.
+ */
+;
 
 // TODO - move to constants file/library
 const MUS_CHRS = [
@@ -670,6 +671,272 @@ i0.ɵɵngDeclareClassMetadata({ minVersion: "12.0.0", version: "19.1.5", ngImpor
                 }]
         }] });
 
+class OntologyService {
+}
+
+var Ontology;
+(function (Ontology) {
+    Ontology["HP"] = "HP";
+    Ontology["MONDO"] = "MONDO";
+    Ontology["MP"] = "MP";
+    Ontology["CL"] = "CL";
+    Ontology["MAXO"] = "MAXO";
+})(Ontology || (Ontology = {}));
+
+/**
+   * Get the ontology from curie
+   */
+function ontologyFromCurie(curie) {
+    return Ontology[curie.split(':')[0]];
+}
+
+class JaxOntologyService extends OntologyService {
+    httpClient;
+    config_location = 'https://raw.githubusercontent.com/TheJacksonLaboratory/ontology-service/refs/heads/main/config/ontologies-internal.json';
+    config;
+    /**
+     * Get the configuration file from the source for the backend api service
+     */
+    constructor(httpClient) {
+        super();
+        this.httpClient = httpClient;
+        this.httpClient.get(this.config_location).subscribe({
+            next: (config) => this.config = config,
+            error: () => {
+                this.config = [];
+            }
+        });
+    }
+    /**
+     * Search for terms in an ontology
+     * @param query - the search query
+     * @param limit - the number of results to return
+     * @param ontology - the ontology to search
+     */
+    search(query, limit, ontology) {
+        return this.httpClient.get(`${this.ontologyBaseResolver(ontology)}/search?q=${query}&limit=${limit}`);
+    }
+    /**
+     * Get a term by its ID
+     * @param id - the term ID
+     */
+    term(id) {
+        try {
+            const url = `${this.ontologyBaseResolver(ontologyFromCurie(id))}/${id}`;
+            return this.httpClient.get(url);
+        }
+        catch (error) {
+            return throwError(() => error);
+        }
+    }
+    /**
+     * Get the parents of a term
+     * @param id - the term ID
+     */
+    parents(id) {
+        try {
+            const url = `${this.ontologyBaseResolver(ontologyFromCurie(id))}/${id}/parents`;
+            return this.httpClient.get(url);
+        }
+        catch (error) {
+            return throwError(() => error);
+        }
+    }
+    /**
+     * Get the children of a term
+     * @param id - the term ID
+     */
+    children(id) {
+        try {
+            const url = `${this.ontologyBaseResolver(ontologyFromCurie(id))}/${id}/children`;
+            return this.httpClient.get(url);
+        }
+        catch (error) {
+            return throwError(() => error);
+        }
+    }
+    /**
+     * Get the ancestors of a term
+     * @param id - the term ID
+     */
+    ancestors(id) {
+        try {
+            const url = `${this.ontologyBaseResolver(ontologyFromCurie(id))}/${id}/ancestors`;
+            return this.httpClient.get(url);
+        }
+        catch (error) {
+            return throwError(() => error);
+        }
+    }
+    /**
+     * Get the descendants of a term
+     * @param id - the term ID
+     */
+    descendants(id) {
+        try {
+            const url = `${this.ontologyBaseResolver(ontologyFromCurie(id))}/${id}/descendants`;
+            return this.httpClient.get(url);
+        }
+        catch (error) {
+            return throwError(() => error);
+        }
+    }
+    /**
+     * Get the ontology api base url configuration
+     **/
+    ontologyBaseResolver(ontology) {
+        if (!this.config || this.config.length === 0) {
+            throw new Error('No ontology configuration found.');
+        }
+        const ontology_config = this.config.find((config) => config.prefix.toUpperCase() === ontology);
+        if (!ontology_config) {
+            throw new Error('Ontology not found in configuration.');
+        }
+        return ontology_config.api.base;
+    }
+    static ɵfac = i0.ɵɵngDeclareFactory({ minVersion: "12.0.0", version: "19.1.5", ngImport: i0, type: JaxOntologyService, deps: [{ token: i1.HttpClient }], target: i0.ɵɵFactoryTarget.Injectable });
+    static ɵprov = i0.ɵɵngDeclareInjectable({ minVersion: "12.0.0", version: "19.1.5", ngImport: i0, type: JaxOntologyService, providedIn: 'root' });
+}
+i0.ɵɵngDeclareClassMetadata({ minVersion: "12.0.0", version: "19.1.5", ngImport: i0, type: JaxOntologyService, decorators: [{
+            type: Injectable,
+            args: [{
+                    providedIn: 'root'
+                }]
+        }], ctorParameters: () => [{ type: i1.HttpClient }] });
+
+// ols-ontology.service.ts
+class OLSOntologyService extends OntologyService {
+    httpClient;
+    OLS_SEARCH_BASE = 'https://www.ebi.ac.uk/ols4/api/v2/entities';
+    OLS_ENTITY_BASE = 'https://www.ebi.ac.uk/ols4/api/v2/ontologies';
+    PURL_BASE = 'http://purl.obolibrary.org/obo';
+    constructor(httpClient) {
+        super();
+        this.httpClient = httpClient;
+    }
+    term(id) {
+        const ontology = ontologyFromCurie(id);
+        const params = new URLSearchParams;
+        params.set('includeObsoleteEntities', 'false');
+        return this.httpClient.get(`${this.OLS_ENTITY_BASE}/${ontology.toLowerCase()}/classes/${this.PURL_BASE}/${id.replace(':', '_')}?${params.toString()}`).pipe(map(olsResponse => {
+            return {
+                object: this.mapOLSTermToOntologyTerm(olsResponse)
+            };
+        }));
+    }
+    search(query, limit, ontology) {
+        const params = new URLSearchParams;
+        params.set('search', query);
+        params.set('size', limit.toString());
+        params.set('ontologyId', ontology.toLowerCase());
+        params.set('includeObsoleteEntities', 'false');
+        return this.httpClient.get(`${this.OLS_SEARCH_BASE}?${params.toString()}`).pipe(map(olsResponse => {
+            const collectionResponse = {
+                data: olsResponse.elements.filter((olsTerm) => olsTerm.definedBy.includes(ontology.toLowerCase())).map(olsTerm => this.mapOLSTermToOntologyTerm(olsTerm)),
+                paging: {
+                    page: olsResponse.page,
+                    total_pages: olsResponse.totalPages,
+                    total_items: olsResponse.totalElements
+                }
+            };
+            return collectionResponse;
+        }));
+    }
+    parents(id) {
+        const ontology = ontologyFromCurie(id);
+        const params = new URLSearchParams;
+        params.set('includeObsoleteEntities', 'false');
+        return this.httpClient.get(`${this.OLS_ENTITY_BASE}/${ontology.toLowerCase()}/classes/${this.PURL_BASE}/${id.replace(':', '_')}?${params.toString()}`).pipe(map(olsTerm => {
+            const data = olsTerm.directParent
+                ? olsTerm.directParent
+                    .map(parent => olsTerm.linkedEntities && olsTerm.linkedEntities[parent]
+                    ? this.mapOLSTermToOntologyTerm(olsTerm.linkedEntities[parent])
+                    : "").filter(parent => parent !== "")
+                : [];
+            return {
+                data: data,
+                paging: {
+                    page: 1,
+                    total_pages: 1,
+                    total_items: data.length
+                }
+            };
+        }));
+    }
+    children(id) {
+        const ontology = ontologyFromCurie(id);
+        const params = new URLSearchParams;
+        params.set('includeObsoleteEntities', 'false');
+        params.set('size', '100');
+        params.set('lang', 'en');
+        return this.httpClient.get(`${this.OLS_ENTITY_BASE}/${ontology.toLowerCase()}/classes/${this.PURL_BASE}/${id.replace(':', '_')}/children?${params.toString()}`).pipe(map(childrenResponse => {
+            const data = childrenResponse.elements.map(olsTerm => this.mapOLSTermToOntologyTerm(olsTerm));
+            return {
+                data: data,
+                paging: {
+                    page: childrenResponse.page,
+                    total_pages: childrenResponse.totalPages,
+                    total_items: data.length
+                }
+            };
+        }));
+    }
+    ancestors(id) {
+        const ontology = ontologyFromCurie(id);
+        const params = new URLSearchParams;
+        params.set('includeObsoleteEntities', 'false');
+        return this.httpClient.get(`${this.OLS_ENTITY_BASE}/${ontology.toLowerCase()}/classes/${this.PURL_BASE}/${id.replace(':', '_')}?${params.toString()}`).pipe(map(olsTerm => {
+            const data = olsTerm.directAncestor
+                ? olsTerm.directAncestor
+                    .map(ancestor => olsTerm.linkedEntities && olsTerm.linkedEntities[ancestor]
+                    ? this.mapOLSTermToOntologyTerm(olsTerm.linkedEntities[ancestor])
+                    : "").filter(ancestor => ancestor !== "")
+                : [];
+            return {
+                data: data,
+                paging: {
+                    page: 1,
+                    total_pages: 1,
+                    total_items: data.length
+                }
+            };
+        }));
+    }
+    // finish testing this method
+    descendants(id) {
+        const ontology = ontologyFromCurie(id);
+        const params = new URLSearchParams;
+        params.set('includeObsoleteEntities', 'false');
+        params.set('size', '100'); // max size for children endpoint
+        params.set('lang', 'en');
+        return this.httpClient.get(`${this.OLS_ENTITY_BASE}/${ontology.toLowerCase()}/classes/${this.PURL_BASE}/${id.replace(':', '_')}/hierarchicalChildren?${params.toString()}`).pipe(map(childrenResponse => {
+            const data = childrenResponse.elements.map(olsTerm => this.mapOLSTermToOntologyTerm(olsTerm));
+            return {
+                data: data,
+                paging: {
+                    page: childrenResponse.page,
+                    total_pages: childrenResponse.totalPages,
+                    total_items: data.length
+                }
+            };
+        }));
+    }
+    mapOLSTermToOntologyTerm(olsTerm) {
+        return {
+            id: olsTerm.curie,
+            name: olsTerm.label && olsTerm.label.length > 0 ? olsTerm.label[0] : 'No label'
+        };
+    }
+    static ɵfac = i0.ɵɵngDeclareFactory({ minVersion: "12.0.0", version: "19.1.5", ngImport: i0, type: OLSOntologyService, deps: [{ token: i1.HttpClient }], target: i0.ɵɵFactoryTarget.Injectable });
+    static ɵprov = i0.ɵɵngDeclareInjectable({ minVersion: "12.0.0", version: "19.1.5", ngImport: i0, type: OLSOntologyService, providedIn: 'root' });
+}
+i0.ɵɵngDeclareClassMetadata({ minVersion: "12.0.0", version: "19.1.5", ngImport: i0, type: OLSOntologyService, decorators: [{
+            type: Injectable,
+            args: [{
+                    providedIn: 'root'
+                }]
+        }], ctorParameters: () => [{ type: i1.HttpClient }] });
+
 class SnpGridService {
     http;
     environment;
@@ -907,5 +1174,5 @@ var DatasetStatus;
  * Generated bundle index. Do not edit.
  */
 
-export { AsyncTaskService, DatasetStatus, MUS_CHRS, MVarService, MvarClientModule, OntologyService, SnpGridClientModule, SnpGridService, WorkflowExecutionStatus };
+export { AsyncTaskService, DatasetStatus, ISADataService, ISA_DATA_SERVICE_CONFIG, JaxOntologyService, MUS_CHRS, MVarService, MvarClientModule, OLSOntologyService, OntologyService, SnpGridClientModule, SnpGridService, WorkflowExecutionStatus };
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