curtain-web-api 1.0.60 → 1.0.62

package/.idea/compiler.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="TypeScriptCompiler">
+    <option name="useServicePoweredTypesWasEnabledByExperiment" value="true" />
+  </component>
+</project>

package/.idea/copilot.data.migration.agent.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="AgentMigrationStateService">
+    <option name="migrationStatus" value="COMPLETED" />
+  </component>
+</project>

package/.idea/copilot.data.migration.ask.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="AskMigrationStateService">
+    <option name="migrationStatus" value="COMPLETED" />
+  </component>
+</project>

package/.idea/copilot.data.migration.ask2agent.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="Ask2AgentMigrationStateService">
+    <option name="migrationStatus" value="COMPLETED" />
+  </component>
+</project>

package/.idea/copilot.data.migration.edit.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="EditMigrationStateService">
+    <option name="migrationStatus" value="COMPLETED" />
+  </component>
+</project>

package/build/classes/curtain-api.d.ts

@@ -18,49 +18,53 @@ export declare class CurtainWebAPI {
     login(username: string, password: string): Promise<User>;
     getUserInfo(): Promise<User>;
     logout(): Promise<void>;
-    refresh(): Promise<import("axios").AxiosResponse<any, any>>;
+    refresh(): Promise<import("axios").AxiosResponse<any, any, {}>>;
     ORCIDLogin(authorizationCode: string, redirectURI: string): Promise<User>;
     checkIfRefreshTokenExpired(): boolean;
-    deleteCurtainLink(curtainLinkID: string): Promise<import("axios").AxiosResponse<any, any>>;
-    putSettings(settings: any, enable?: boolean, description?: string, sessionType?: string, encryption?: CurtainEncryption, permanent?: boolean, onUploadProgress?: any): Promise<import("axios").AxiosResponse<any, any>>;
-    postSettings(id: string, token: string, onDownloadProgress?: any, url?: string | undefined): Promise<import("axios").AxiosResponse<any, any>>;
-    getPrideData(accession: string): Promise<import("axios").AxiosResponse<any, any>>;
-    generateTemporarySession(linkId: string, lifetime: number): Promise<import("axios").AxiosResponse<any, any>>;
-    updateSession(sessionData: any, linkId: string, encryption?: CurtainEncryption): Promise<import("axios").AxiosResponse<any, any>>;
-    getSessionSettings(linkId: string): Promise<import("axios").AxiosResponse<any, any>>;
-    getOwnership(linkId: string): Promise<import("axios").AxiosResponse<any, any>>;
-    getOwners(linkId: string): Promise<import("axios").AxiosResponse<any, any>>;
-    addOwner(linkId: string, owner: string): Promise<import("axios").AxiosResponse<any, any>>;
-    getCurtainLinks(username: string, sessionDescription?: string, offset?: number, sessionType?: string): Promise<import("axios").AxiosResponse<any, any>>;
-    getSiteProperties(): Promise<import("axios").AxiosResponse<any, any>>;
-    saveDataFilterList(name: string, data: string, category?: string): Promise<import("axios").AxiosResponse<any, any>>;
-    getDataFilterListByID(id: number, limit?: number): Promise<import("axios").AxiosResponse<any, any>>;
-    getDataFilterList(title?: string, searchTerm?: string, category?: string, limit?: number): Promise<import("axios").AxiosResponse<any, any>>;
-    getDataFilterListByCategory(category: string): Promise<import("axios").AxiosResponse<any, any>>;
-    deleteDataFilterList(id: number): Promise<import("axios").AxiosResponse<any, any>>;
-    downloadStats(): Promise<import("axios").AxiosResponse<any, any>>;
-    postInteractomeAtlasProxy(genes: string[], filterParameter: string): Promise<import("axios").AxiosResponse<any, any>>;
-    postPrimitiveStatsTest(data: any, type?: string): Promise<import("axios").AxiosResponse<any, any>>;
-    getDataAllListCategory(): Promise<import("axios").AxiosResponse<any, any>>;
-    postCompareSession(idList: string[], matchType: string, studyList: string[], sessionId: string): Promise<import("axios").AxiosResponse<any, any>>;
-    getStatsSummary(lastNDays: number): Promise<import("axios").AxiosResponse<any, any>>;
-    postEncryptionFactors(encryptedAESKey: string, encryptedIV: string, linkId: string): Promise<import("axios").AxiosResponse<any, any>>;
-    getEncryptionFactors(linkId: string): Promise<import("axios").AxiosResponse<any, any>>;
-    createCurtainAPIKey(name: string): Promise<import("axios").AxiosResponse<any, any>>;
-    getCurtainAPIKeys(): Promise<import("axios").AxiosResponse<any, any>>;
-    deleteCurtainAPIKey(id: number): Promise<import("axios").AxiosResponse<any, any>>;
-    getRandomDataCiteSuffix(): Promise<import("axios").AxiosResponse<any, any>>;
-    submitDataCite(data: any): Promise<import("axios").AxiosResponse<any, any>>;
-    getDataCite(id: number): Promise<import("axios").AxiosResponse<any, any>>;
-    getDataCites(url?: string, title?: string, status?: string, limit?: number, offset?: number, manage?: boolean, curtain_type?: string): Promise<import("axios").AxiosResponse<any, any>>;
-    getDataCiteTimeLimitedPermissionToken(suffix: string): Promise<import("axios").AxiosResponse<any, any>>;
-    getDataCiteProxyOrcidPublicRecord(orcid: string): Promise<import("axios").AxiosResponse<any, any>>;
+    deleteCurtainLink(curtainLinkID: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    putSettings(settings: any, enable?: boolean, description?: string, sessionType?: string, encryption?: CurtainEncryption, permanent?: boolean, onUploadProgress?: any): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    postSettings(id: string, token: string, onDownloadProgress?: any, url?: string | undefined): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getPrideData(accession: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    generateTemporarySession(linkId: string, lifetime: number): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    updateSession(sessionData: any, linkId: string, encryption?: CurtainEncryption): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getSessionSettings(linkId: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getOwnership(linkId: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getOwners(linkId: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    addOwner(linkId: string, owner: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getCurtainLinks(username: string, sessionDescription?: string, offset?: number, sessionType?: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getSiteProperties(): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    saveDataFilterList(name: string, data: string, category?: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getDataFilterListByID(id: number, limit?: number): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getDataFilterList(title?: string, searchTerm?: string, category?: string, limit?: number, offset?: number): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getDataFilterListByCategory(category: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    deleteDataFilterList(id: number): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    updateDataFilterList(id: number, name?: string, data?: string, category?: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    downloadStats(): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    postInteractomeAtlasProxy(genes: string[], filterParameter: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    postPrimitiveStatsTest(data: any, type?: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getDataAllListCategory(): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    postCompareSession(idList: string[], matchType: string, studyList: string[], sessionId: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getStatsSummary(lastNDays: number): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    postEncryptionFactors(encryptedAESKey: string, encryptedIV: string, linkId: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getEncryptionFactors(linkId: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    createCurtainAPIKey(name: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getCurtainAPIKeys(): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    deleteCurtainAPIKey(id: number): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getRandomDataCiteSuffix(): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    submitDataCite(data: any): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getDataCite(id: number): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getDataCites(url?: string, title?: string, status?: string, limit?: number, offset?: number, manage?: boolean, curtain_type?: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getDataCiteTimeLimitedPermissionToken(suffix: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getDataCiteProxyOrcidPublicRecord(orcid: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
     getDataCiteQuota(): Promise<import("axios").AxiosResponse<{
         quota: number;
         max_quota: number;
-    }, any>>;
-    updateDataCite(id: number, data: any): Promise<import("axios").AxiosResponse<any, any>>;
-    deleteDataCite(id: number): Promise<import("axios").AxiosResponse<any, any>>;
-    changeDataCiteStatus(id: number, status: string): Promise<import("axios").AxiosResponse<any, any>>;
-    lockDataCite(id: number, lock: boolean): Promise<import("axios").AxiosResponse<any, any>>;
+    }, any, {}>>;
+    updateDataCite(id: number, data: any): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    deleteDataCite(id: number): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    changeDataCiteStatus(id: number, status: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    lockDataCite(id: number, lock: boolean): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getKinaseLibraryProxy(sequence: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getJobResult(job_id: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+    getDataCiteFile(datacite_id: number): Promise<import("axios").AxiosResponse<any, any, {}>>;
 }

package/build/classes/curtain-api.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
     function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
     return new (P || (P = Promise))(function (resolve, reject) {
@@ -452,7 +462,7 @@ class CurtainWebAPI {
             return response;
         });
     }
-    getDataFilterList(title = "", searchTerm = "", category = "", limit = 99999999) {
+    getDataFilterList(title = "", searchTerm = "", category = "", limit = 99999999, offset = 0) {
         let params = new URLSearchParams();
         if (title != "") {
             params.append("name", title);
@@ -464,6 +474,7 @@ class CurtainWebAPI {
             params.append("category", category);
         }
         params.append("limit", limit.toString());
+        params.append("offset", offset.toString());
         return this.axiosInstance.get(this.baseURL + "data_filter_list/", { responseType: "json", params });
     }
     getDataFilterListByCategory(category) {
@@ -478,6 +489,21 @@ class CurtainWebAPI {
             return response;
         });
     }
+    updateDataFilterList(id, name, data, category) {
+        let headers = new axios_1.AxiosHeaders();
+        headers["Accept"] = "application/json";
+        headers["Content-Type"] = "application/json";
+        const updateData = {};
+        if (name !== undefined)
+            updateData.name = name;
+        if (data !== undefined)
+            updateData.data = data;
+        if (category !== undefined)
+            updateData.category = category;
+        return this.axiosInstance.patch(this.baseURL + "data_filter_list/" + id + "/", updateData, { headers: headers, responseType: "json" }).then((response) => {
+            return response;
+        });
+    }
     downloadStats() {
         let headers = new axios_1.AxiosHeaders();
         headers["Accept"] = "application/json";
@@ -638,5 +664,22 @@ class CurtainWebAPI {
         headers["Content-Type"] = "application/json";
         return this.axiosInstance.post(this.baseURL + "datacite/" + id + "/lock/", { lock: lock }, { headers: headers, responseType: "json" });
     }
+    getKinaseLibraryProxy(sequence) {
+        let headers = new axios_1.AxiosHeaders();
+        headers["Accept"] = "application/json";
+        let params = new URLSearchParams();
+        params.append("sequence", sequence);
+        return this.axiosInstance.get(this.baseURL + "kinase_library_proxy/", { headers: headers, params: params, responseType: "json" });
+    }
+    getJobResult(job_id) {
+        let headers = new axios_1.AxiosHeaders();
+        headers["Accept"] = "application/json";
+        return this.axiosInstance.get(this.baseURL + "job/" + job_id + "/", { headers: headers, responseType: "json" });
+    }
+    getDataCiteFile(datacite_id) {
+        let headers = new axios_1.AxiosHeaders();
+        headers["Accept"] = "application/json";
+        return this.axiosInstance.get(this.baseURL + "datacite/file/" + datacite_id + "/", { headers: headers, responseType: "blob" });
+    }
 }
 exports.CurtainWebAPI = CurtainWebAPI;

package/build/classes/curtain-encryption.d.ts

@@ -16,8 +16,8 @@ export interface CurtainEncryption {
 }
 export declare function arrayBufferToBase64String(arrayBuffer: ArrayBuffer): string;
 export declare function removeLines(str_data: string): string;
-export declare function base64ToArrayBuffer(b64: string): Uint8Array;
-export declare function pemToArrayBuffer(pem: string): Uint8Array;
+export declare function base64ToArrayBuffer(b64: string): ArrayBuffer;
+export declare function pemToArrayBuffer(pem: string): ArrayBuffer;
 export declare function encryptAESKey(publicKey: CryptoKey, aesKey: ArrayBuffer): Promise<ArrayBuffer>;
 export declare function generateAESKey(): Promise<CryptoKey>;
 export declare function encryptAESData(aesKey: CryptoKey, data: string): Promise<{

package/build/classes/curtain-encryption.js

@@ -124,7 +124,7 @@ function base64ToArrayBuffer(b64) {
     for (let i = 0; i < byteString.length; i++) {
         byteArray[i] = byteString.charCodeAt(i);
     }
-    return byteArray;
+    return byteArray.buffer;
 }
 function pemToArrayBuffer(pem) {
     const b64Lines = removeLines(pem);
@@ -156,7 +156,7 @@ function encryptAESData(aesKey, data) {
         const enc = new TextEncoder();
         const encoded = enc.encode(data);
         const encrypted = yield crypto.subtle.encrypt({ name: "AES-GCM", iv: iv }, aesKey, encoded);
-        return { encrypted: arrayBufferToBase64String(encrypted), iv: arrayBufferToBase64String(iv) };
+        return { encrypted: arrayBufferToBase64String(encrypted), iv: arrayBufferToBase64String(iv.buffer) };
     });
 }
 // a function to decrypt a string with an aes key

package/build/utilities.d.ts

@@ -1,5 +1,5 @@
-export declare function getProteomicsData(acc: string, tissueType: string): Promise<import("axios").AxiosResponse<any, any>>;
-export declare function getPrideData(acc: string): Promise<import("axios").AxiosResponse<any, any>>;
-export declare function getEBIAlpha(id: string): Promise<import("axios").AxiosResponse<any, any>>;
-export declare function getStringDBInteractions(genes: string[], organism: string, score?: number, networkType?: string): Promise<import("axios").AxiosResponse<any, any>>;
+export declare function getProteomicsData(acc: string, tissueType: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+export declare function getPrideData(acc: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+export declare function getEBIAlpha(id: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
+export declare function getStringDBInteractions(genes: string[], organism: string, score?: number, networkType?: string): Promise<import("axios").AxiosResponse<any, any, {}>>;
 export declare function getInteractomeAtlas(genes: string[], filterParameter?: string): Promise<any>;

package/build/utilities.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getProteomicsData = getProteomicsData;
 exports.getPrideData = getPrideData;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "curtain-web-api",
-  "version": "1.0.60",
+  "version": "1.0.62",
   "description": "",
   "main": "./build/index.js",
   "types": "./build/index.d.ts",

package/src/classes/curtain-api.ts

@@ -449,7 +449,8 @@ export class CurtainWebAPI {
         title: string = "",
         searchTerm: string = "",
         category: string = "",
-        limit: number = 99999999
+        limit: number = 99999999,
+        offset: number = 0
     ) {
         let params = new URLSearchParams();
         if (title != "") {
@@ -463,6 +464,7 @@ export class CurtainWebAPI {
         }
 
         params.append("limit", limit.toString())
+        params.append("offset", offset.toString())
         return this.axiosInstance.get(this.baseURL + "data_filter_list/", {responseType:"json", params})
     }
 
@@ -480,6 +482,19 @@ export class CurtainWebAPI {
         });
     }
 
+    updateDataFilterList(id: number, name?: string, data?: string, category?: string) {
+        let headers = new AxiosHeaders();
+        headers["Accept"] = "application/json";
+        headers["Content-Type"] = "application/json";
+        const updateData: {name?: string, data?: string, category?: string} = {};
+        if (name !== undefined) updateData.name = name;
+        if (data !== undefined) updateData.data = data;
+        if (category !== undefined) updateData.category = category;
+        return this.axiosInstance.patch(this.baseURL + "data_filter_list/" + id + "/", updateData, {headers: headers, responseType:"json"}).then((response) => {
+            return response;
+        });
+    }
+
     downloadStats() {
         let headers = new AxiosHeaders();
         headers["Accept"] = "application/json";
@@ -659,5 +674,25 @@ export class CurtainWebAPI {
         headers["Content-Type"] = "application/json"
         return this.axiosInstance.post(this.baseURL + "datacite/" + id + "/lock/", {lock: lock}, {headers: headers, responseType: "json"})
     }
+
+    getKinaseLibraryProxy(sequence: string) {
+        let headers = new AxiosHeaders();
+        headers["Accept"] = "application/json";
+        let params = new URLSearchParams();
+        params.append("sequence", sequence);
+        return this.axiosInstance.get(this.baseURL + "kinase_library_proxy/", {headers: headers, params: params, responseType: "json"});
+    }
+
+    getJobResult(job_id: string) {
+        let headers = new AxiosHeaders();
+        headers["Accept"] = "application/json";
+        return this.axiosInstance.get(this.baseURL + "job/" + job_id + "/", {headers: headers, responseType: "json"});
+    }
+
+    getDataCiteFile(datacite_id: number) {
+        let headers = new AxiosHeaders();
+        headers["Accept"] = "application/json";
+        return this.axiosInstance.get(this.baseURL + "datacite/file/" + datacite_id + "/", {headers: headers, responseType: "blob"});
+    }
 }
 

package/src/classes/curtain-encryption.ts

@@ -21,7 +21,7 @@ export async function generateKeyPair(modulusLength: number = 2048, publicExpone
       modulusLength: modulusLength,
       publicExponent: publicExponent,
       hash: "SHA-256",
-    },
+    } as RsaHashedKeyGenParams,
     true,
     ["encrypt", "decrypt"],
   )
@@ -85,14 +85,14 @@ export function removeLines(str_data: string) {
   return str_data.replace("\n", "");
 }
 
-export function base64ToArrayBuffer(b64: string) {
+export function base64ToArrayBuffer(b64: string): ArrayBuffer {
   const byteString = atob(b64);
   const byteArray = new Uint8Array(byteString.length);
   for(let i=0; i < byteString.length; i++) {
     byteArray[i] = byteString.charCodeAt(i);
   }
 
-  return byteArray;
+  return byteArray.buffer;
 }
 
 export function pemToArrayBuffer(pem: string) {
@@ -128,7 +128,7 @@ export async function encryptAESData(aesKey: CryptoKey, data: string) {
   const enc = new TextEncoder()
   const encoded = enc.encode(data)
   const encrypted = await crypto.subtle.encrypt({name: "AES-GCM", iv: iv}, aesKey, encoded)
-  return {encrypted: arrayBufferToBase64String(encrypted), iv: arrayBufferToBase64String(iv)}
+  return {encrypted: arrayBufferToBase64String(encrypted), iv: arrayBufferToBase64String(iv.buffer)}
 }
 
 // a function to decrypt a string with an aes key