@nextage/omics-lib 1.0.2

package/build/models/variant.d.ts

@@ -0,0 +1,19 @@
+import mongoose from 'mongoose';
+import { IVariant } from '../types';
+export interface VariantAttrs extends IVariant {
+    createdAt?: Date;
+    updatedAt?: Date;
+    deletedAt?: Date;
+    version?: number;
+}
+export interface VariantDoc extends mongoose.Document {
+    createdAt?: Date;
+    updatedAt?: Date;
+    deletedAt?: Date;
+    version: number;
+}
+export interface VariantModel extends mongoose.Model<VariantDoc> {
+    build(attrs: VariantAttrs): VariantDoc;
+}
+export declare const Variant: VariantModel;
+//# sourceMappingURL=variant.d.ts.map

package/build/models/variant.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"variant.d.ts","sourceRoot":"","sources":["../../src/models/variant.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAuB,UAAU,CAAC;AAEjD,OAAO,EAAE,QAAQ,EAAE,MAAkB,UAAU,CAAC;AAEhD,MAAM,WAAW,YAAa,SAAQ,QAAQ;IAC5C,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,OAAO,CAAC,EAAI,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,UAAW,SAAQ,QAAQ,CAAC,QAAQ;IACnD,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,OAAO,EAAK,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,YAAa,SAAQ,QAAQ,CAAC,KAAK,CAAC,UAAU,CAAC;IAC9D,KAAK,CAAC,KAAK,EAAE,YAAY,GAAG,UAAU,CAAC;CACxC;AA4CD,eAAO,MAAM,OAAO,cAA8D,CAAC"}

package/build/models/variant.js

@@ -0,0 +1,45 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.Variant = void 0;
+const mongoose_1 = __importDefault(require("mongoose"));
+const mongoose_update_if_current_1 = require("mongoose-update-if-current");
+const AnnotationSchema = new mongoose_1.default.Schema({
+    gene: { type: String },
+    consequence: { type: String },
+    transcript: { type: String },
+    hgvsc: { type: String },
+    hgvsp: { type: String },
+    proteinPosition: { type: String },
+    codons: { type: String },
+    exon: { type: String }
+}, { _id: false });
+const schema = new mongoose_1.default.Schema({
+    variantId: { type: String, required: true, unique: true },
+    chrom: { type: String },
+    pos: { type: Number },
+    ref: { type: String },
+    alt: { type: [String] },
+    type: { type: String },
+    classification: { type: String },
+    annotations: { type: AnnotationSchema },
+    createdAt: { type: Date },
+    updatedAt: { type: Date },
+    deletedAt: { type: Date }
+}, {
+    toJSON: {
+        transform(doc, ret) {
+            ret.id = ret._id;
+            delete ret._id;
+        },
+    },
+});
+schema.set('versionKey', 'version');
+schema.plugin(mongoose_update_if_current_1.updateIfCurrentPlugin);
+schema.statics.build = (attrs) => {
+    return new exports.Variant(attrs);
+};
+exports.Variant = mongoose_1.default.model('Variant', schema);
+//# sourceMappingURL=variant.js.map

package/build/models/variant.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"variant.js","sourceRoot":"","sources":["../../src/models/variant.ts"],"names":[],"mappings":";;;;;;AAAA,wDAAiD;AACjD,2EAAmE;AAqBnE,MAAM,gBAAgB,GAAG,IAAI,kBAAQ,CAAC,MAAM,CAAC;IAC3C,IAAI,EAAa,EAAE,IAAI,EAAE,MAAM,EAAE;IACjC,WAAW,EAAM,EAAE,IAAI,EAAE,MAAM,EAAE;IACjC,UAAU,EAAO,EAAE,IAAI,EAAE,MAAM,EAAE;IACjC,KAAK,EAAY,EAAE,IAAI,EAAE,MAAM,EAAE;IACjC,KAAK,EAAY,EAAE,IAAI,EAAE,MAAM,EAAE;IACjC,eAAe,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE;IACjC,MAAM,EAAW,EAAE,IAAI,EAAE,MAAM,EAAE;IACjC,IAAI,EAAa,EAAE,IAAI,EAAE,MAAM,EAAE;CAClC,EAAE,EAAE,GAAG,EAAE,KAAK,EAAE,CAAC,CAAC;AAEnB,MAAM,MAAM,GAAG,IAAI,kBAAQ,CAAC,MAAM,CAChC;IACE,SAAS,EAAO,EAAE,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE;IAC9D,KAAK,EAAW,EAAE,IAAI,EAAE,MAAM,EAAE;IAChC,GAAG,EAAa,EAAE,IAAI,EAAE,MAAM,EAAE;IAChC,GAAG,EAAa,EAAE,IAAI,EAAE,MAAM,EAAE;IAChC,GAAG,EAAa,EAAE,IAAI,EAAE,CAAC,MAAM,CAAC,EAAE;IAClC,IAAI,EAAY,EAAE,IAAI,EAAE,MAAM,EAAE;IAChC,cAAc,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE;IAChC,WAAW,EAAK,EAAE,IAAI,EAAE,gBAAgB,EAAE;IAC1C,SAAS,EAAO,EAAE,IAAI,EAAE,IAAI,EAAE;IAC9B,SAAS,EAAO,EAAE,IAAI,EAAE,IAAI,EAAE;IAC9B,SAAS,EAAO,EAAE,IAAI,EAAE,IAAI,EAAE;CAC/B,EACD;IACE,MAAM,EAAE;QACN,SAAS,CAAC,GAAG,EAAE,GAAQ;YACrB,GAAG,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,CAAC;YACjB,OAAO,GAAG,CAAC,GAAG,CAAC;QACjB,CAAC;KACF;CACF,CACF,CAAC;AAEF,MAAM,CAAC,GAAG,CAAC,YAAY,EAAE,SAAS,CAAC,CAAC;AACpC,MAAM,CAAC,MAAM,CAAC,kDAAqB,CAAC,CAAC;AAErC,MAAM,CAAC,OAAO,CAAC,KAAK,GAAG,CAAC,KAAmB,EAAE,EAAE;IAC7C,OAAO,IAAI,eAAO,CAAC,KAAK,CAAC,CAAC;AAC5B,CAAC,CAAC;AAEW,QAAA,OAAO,GAAG,kBAAQ,CAAC,KAAK,CAA2B,SAAS,EAAE,MAAM,CAAC,CAAC"}

package/build/routes/express.interfaces.d.ts

@@ -0,0 +1,11 @@
+export interface ErrorResponse extends Error {
+    status?: number;
+}
+export interface ExpressErrorResult {
+    result: {
+        fields: string[];
+        code: number;
+        message: string;
+    };
+}
+//# sourceMappingURL=express.interfaces.d.ts.map

package/build/routes/express.interfaces.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"express.interfaces.d.ts","sourceRoot":"","sources":["../../src/routes/express.interfaces.ts"],"names":[],"mappings":"AAGA,MAAM,WAAW,aAAc,SAAQ,KAAK;IAC1C,MAAM,CAAC,EAAG,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,kBAAkB;IACjC,MAAM,EAAE;QAAE,MAAM,EAAE,MAAM,EAAE,CAAC;QAAC,IAAI,EAAE,MAAM,CAAC;QAAC,OAAO,EAAE,MAAM,CAAC;KAAE,CAAC;CAC9D"}

package/build/routes/express.interfaces.js

@@ -0,0 +1,10 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+// export interface AuthRequest extends Request {
+//   auth? : AuthRequestContext;
+// }
+// export interface AuthRequestContext extends JwtPayload {
+//   user?: UserDoc | null;
+//   err? : ErrorResponse;
+// }
+//# sourceMappingURL=express.interfaces.js.map

package/build/routes/express.interfaces.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"express.interfaces.js","sourceRoot":"","sources":["../../src/routes/express.interfaces.ts"],"names":[],"mappings":";;AAWA,iDAAiD;AACjD,gCAAgC;AAChC,IAAI;AAEJ,2DAA2D;AAC3D,2BAA2B;AAC3B,0BAA0B;AAC1B,IAAI"}

package/build/routes/index.d.ts

@@ -0,0 +1,3 @@
+export * from './swagger';
+export * from './validators';
+//# sourceMappingURL=index.d.ts.map

package/build/routes/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/routes/index.ts"],"names":[],"mappings":"AAAA,cAAc,WAAW,CAAC;AAC1B,cAAc,cAAc,CAAC"}

package/build/routes/index.js

@@ -0,0 +1,19 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+__exportStar(require("./swagger"), exports);
+__exportStar(require("./validators"), exports);
+//# sourceMappingURL=index.js.map

package/build/routes/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/routes/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,4CAA0B;AAC1B,+CAA6B"}

package/build/routes/swagger.d.ts

@@ -0,0 +1,13 @@
+export declare const definitions: {
+    AppStatus: {
+        type: string;
+        properties: {
+            status: {
+                type: string;
+                example: string;
+            };
+        };
+    };
+};
+export declare const examples: {};
+//# sourceMappingURL=swagger.d.ts.map

package/build/routes/swagger.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"swagger.d.ts","sourceRoot":"","sources":["../../src/routes/swagger.ts"],"names":[],"mappings":"AAAA,eAAO,MAAM,WAAW;;;;;;;;;;CAOvB,CAAC;AAEF,eAAO,MAAM,QAAQ,IAAK,CAAA"}

package/build/routes/swagger.js

@@ -0,0 +1,13 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.examples = exports.definitions = void 0;
+exports.definitions = {
+    AppStatus: {
+        type: 'object',
+        properties: {
+            status: { type: 'string', example: 'OK' },
+        }
+    }
+};
+exports.examples = {};
+//# sourceMappingURL=swagger.js.map

package/build/routes/swagger.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"swagger.js","sourceRoot":"","sources":["../../src/routes/swagger.ts"],"names":[],"mappings":";;;AAAa,QAAA,WAAW,GAAG;IACzB,SAAS,EAAE;QACT,IAAI,EAAQ,QAAQ;QACpB,UAAU,EAAE;YACV,MAAM,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,OAAO,EAAE,IAAI,EAAE;SAC1C;KACF;CACF,CAAC;AAEW,QAAA,QAAQ,GAAG,EAAE,CAAA"}

package/build/routes/validators.d.ts

@@ -0,0 +1,11 @@
+import { Result, Schema, ValidationError } from 'express-validator';
+import { DefaultSchemaKeys } from 'express-validator/lib/middlewares/schema';
+import { ExpressErrorResult } from './express.interfaces';
+export declare const idSchema: Schema<DefaultSchemaKeys>;
+/**
+ *
+ * @param {*} errors
+ * @returns
+ */
+export declare function formatErrors(errors: Result<ValidationError>): ExpressErrorResult;
+//# sourceMappingURL=validators.d.ts.map

package/build/routes/validators.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"validators.d.ts","sourceRoot":"","sources":["../../src/routes/validators.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AACpE,OAAO,EAAE,iBAAiB,EAAE,MAAoB,0CAA0C,CAAC;AAE3F,OAAO,EAAE,kBAAkB,EAAE,MAAmB,sBAAsB,CAAC;AAEvE,eAAO,MAAM,QAAQ,EAAE,MAAM,CAAC,iBAAiB,CAE9C,CAAC;AAIF;;;;GAIG;AACF,wBAAgB,YAAY,CAAC,MAAM,EAAE,MAAM,CAAC,eAAe,CAAC,GAAG,kBAAkB,CAGjF"}

package/build/routes/validators.js

@@ -0,0 +1,17 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.idSchema = void 0;
+exports.formatErrors = formatErrors;
+const constants_1 = require("../constants");
+exports.idSchema = {
+    id: { in: ['body', 'params', 'query'], isMongoId: true }
+};
+/**
+ *
+ * @param {*} errors
+ * @returns
+ */
+function formatErrors(errors) {
+    return { result: Object.assign({ fields: errors.array().map((e) => e.params) }, constants_1.RES_CODE.INCORRECT_DATA) };
+}
+//# sourceMappingURL=validators.js.map

package/build/routes/validators.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"validators.js","sourceRoot":"","sources":["../../src/routes/validators.ts"],"names":[],"mappings":";;;AAiBC,oCAGA;AAjBD,4CAA+D;AAGlD,QAAA,QAAQ,GAA8B;IACjD,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,MAAM,EAAE,QAAQ,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE;CACzD,CAAC;AAIF;;;;GAIG;AACF,SAAgB,YAAY,CAAC,MAA+B;IAE3D,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,KAAK,EAAE,CAAC,GAAG,CAAC,CAAC,CAAM,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,EAAE,EAAE,oBAAQ,CAAC,cAAc,CAAC,EAAE,CAAC;AAClH,CAAC"}

package/build/services/index.d.ts

@@ -0,0 +1,2 @@
+export * from './password';
+//# sourceMappingURL=index.d.ts.map

package/build/services/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/services/index.ts"],"names":[],"mappings":"AAAA,cAAc,YAAY,CAAC"}

package/build/services/index.js

@@ -0,0 +1,18 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+__exportStar(require("./password"), exports);
+//# sourceMappingURL=index.js.map

package/build/services/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/services/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,6CAA2B"}

package/build/services/password.d.ts

@@ -0,0 +1,5 @@
+export declare class Password {
+    static toHash(password: string): Promise<string>;
+    static compare(storedPassword: string, suppliedPassword: string): Promise<boolean>;
+}
+//# sourceMappingURL=password.d.ts.map

package/build/services/password.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"password.d.ts","sourceRoot":"","sources":["../../src/services/password.ts"],"names":[],"mappings":"AAKA,qBAAa,QAAQ;WAEN,MAAM,CAAC,QAAQ,EAAE,MAAM;WAQvB,OAAO,CAAC,cAAc,EAAE,MAAM,EAAE,gBAAgB,EAAE,MAAM;CAMtE"}

package/build/services/password.js

@@ -0,0 +1,20 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.Password = void 0;
+const crypto_1 = require("crypto");
+const util_1 = require("util");
+const scriptAsync = (0, util_1.promisify)(crypto_1.scrypt);
+class Password {
+    static async toHash(password) {
+        const salt = (0, crypto_1.randomBytes)(8).toString('hex');
+        const buf = (await scriptAsync(password, salt, 64));
+        return `${buf.toString('hex')}.${salt}`;
+    }
+    static async compare(storedPassword, suppliedPassword) {
+        const [hashedPassword, salt] = storedPassword.split('.');
+        const buf = (await scriptAsync(suppliedPassword, salt, 64));
+        return buf.toString('hex') === hashedPassword;
+    }
+}
+exports.Password = Password;
+//# sourceMappingURL=password.js.map

package/build/services/password.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"password.js","sourceRoot":"","sources":["../../src/services/password.ts"],"names":[],"mappings":";;;AAAA,mCAA6C;AAC7C,+BAA2C;AAE3C,MAAM,WAAW,GAAG,IAAA,gBAAS,EAAC,eAAM,CAAC,CAAC;AAEtC,MAAa,QAAQ;IAEnB,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,QAAgB;QAElC,MAAM,IAAI,GAAG,IAAA,oBAAW,EAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;QAC5C,MAAM,GAAG,GAAI,CAAC,MAAM,WAAW,CAAC,QAAQ,EAAE,IAAI,EAAE,EAAE,CAAC,CAAW,CAAC;QAE/D,OAAO,GAAG,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,IAAI,IAAI,EAAE,CAAC;IAC1C,CAAC;IAED,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,cAAsB,EAAE,gBAAwB;QACnE,MAAM,CAAC,cAAc,EAAE,IAAI,CAAC,GAAG,cAAc,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;QACzD,MAAM,GAAG,GAAsB,CAAC,MAAM,WAAW,CAAC,gBAAgB,EAAE,IAAI,EAAE,EAAE,CAAC,CAAW,CAAC;QAEzF,OAAO,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,KAAK,cAAc,CAAC;IAChD,CAAC;CACF;AAhBD,4BAgBC"}

package/build/types/genotype.d.ts

@@ -0,0 +1,11 @@
+import { BaseDBItem } from '../interfaces';
+export interface IGenotype extends BaseDBItem {
+    variantId: string;
+    sampleId: string;
+    sequencingSampleId: string;
+    GT: string;
+    VAF: number;
+    DP: number;
+    alleles: string[];
+}
+//# sourceMappingURL=genotype.d.ts.map

package/build/types/genotype.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"genotype.d.ts","sourceRoot":"","sources":["../../src/types/genotype.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,WAAW,SAAU,SAAQ,UAAU;IAC3C,SAAS,EAAW,MAAM,CAAC;IAC3B,QAAQ,EAAY,MAAM,CAAC;IAC3B,kBAAkB,EAAE,MAAM,CAAC;IAC3B,EAAE,EAAkB,MAAM,CAAC;IAC3B,GAAG,EAAiB,MAAM,CAAC;IAC3B,EAAE,EAAkB,MAAM,CAAC;IAC3B,OAAO,EAAa,MAAM,EAAE,CAAC;CAC9B"}

package/build/types/genotype.js

@@ -0,0 +1,3 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=genotype.js.map

package/build/types/genotype.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"genotype.js","sourceRoot":"","sources":["../../src/types/genotype.ts"],"names":[],"mappings":""}

package/build/types/index.d.ts

@@ -0,0 +1,4 @@
+export * from './genotype';
+export * from './sample';
+export * from './variant';
+//# sourceMappingURL=index.d.ts.map

package/build/types/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/types/index.ts"],"names":[],"mappings":"AAAA,cAAc,YAAY,CAAC;AAC3B,cAAc,UAAU,CAAC;AACzB,cAAc,WAAW,CAAC"}

package/build/types/index.js

@@ -0,0 +1,20 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+__exportStar(require("./genotype"), exports);
+__exportStar(require("./sample"), exports);
+__exportStar(require("./variant"), exports);
+//# sourceMappingURL=index.js.map

package/build/types/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/types/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,6CAA2B;AAC3B,2CAAyB;AACzB,4CAA0B"}

package/build/types/sample.d.ts

@@ -0,0 +1,13 @@
+import { BaseDBItem } from '../interfaces';
+export interface ISample extends BaseDBItem {
+    biobankSampleId: string;
+    sequencingSampleId: string;
+    clinical: SampleClinicalData;
+}
+export interface SampleClinicalData {
+    diagnosis: string;
+    snomedM: string;
+    snomedT: string;
+    tumorSite: string;
+}
+//# sourceMappingURL=sample.d.ts.map

package/build/types/sample.d.ts.map

@@ -0,0 +1 @@
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package/build/types/sample.js

@@ -0,0 +1,3 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=sample.js.map

package/build/types/sample.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"sample.js","sourceRoot":"","sources":["../../src/types/sample.ts"],"names":[],"mappings":""}

package/build/types/variant.d.ts

@@ -0,0 +1,22 @@
+import { BaseDBItem } from '../interfaces';
+export interface IVariant extends BaseDBItem {
+    variantId: string;
+    chrom: string;
+    pos: number;
+    ref: string;
+    alt: string[];
+    type: string;
+    classification: string;
+    annotations: VariantAnnotation;
+}
+export interface VariantAnnotation {
+    gene: string;
+    consequence: string;
+    transcript: string;
+    hgvsc: string;
+    hgvsp: string;
+    proteinPosition: string;
+    codons: string;
+    exon: string;
+}
+//# sourceMappingURL=variant.d.ts.map

package/build/types/variant.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"variant.d.ts","sourceRoot":"","sources":["../../src/types/variant.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,WAAW,QAAS,SAAQ,UAAU;IAC1C,SAAS,EAAO,MAAM,CAAC;IACvB,KAAK,EAAW,MAAM,CAAC;IACvB,GAAG,EAAa,MAAM,CAAC;IACvB,GAAG,EAAa,MAAM,CAAC;IACvB,GAAG,EAAa,MAAM,EAAE,CAAC;IACzB,IAAI,EAAY,MAAM,CAAC;IACvB,cAAc,EAAE,MAAM,CAAC;IACvB,WAAW,EAAK,iBAAiB,CAAC;CACnC;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAa,MAAM,CAAC;IACxB,WAAW,EAAM,MAAM,CAAC;IACxB,UAAU,EAAO,MAAM,CAAC;IACxB,KAAK,EAAY,MAAM,CAAC;IACxB,KAAK,EAAY,MAAM,CAAC;IACxB,eAAe,EAAE,MAAM,CAAC;IACxB,MAAM,EAAW,MAAM,CAAC;IACxB,IAAI,EAAa,MAAM,CAAC;CACzB"}

package/build/types/variant.js

@@ -0,0 +1,3 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=variant.js.map

package/build/types/variant.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"variant.js","sourceRoot":"","sources":["../../src/types/variant.ts"],"names":[],"mappings":""}

package/build/utils/express.d.ts

@@ -0,0 +1,37 @@
+import { Request, Response, NextFunction, Handler } from 'express';
+import { ValidationError, Result, Schema } from 'express-validator';
+import { DefaultSchemaKeys } from 'express-validator/lib/middlewares/schema';
+/**
+ *
+ * @param schema
+ * @param errorFormatter
+ * @returns
+ */
+export declare function validateSchema(schema: Schema<DefaultSchemaKeys>, errorFormatter?: (err: Result<ValidationError>, req: Request) => Result<ValidationError>): (req: Request, res: Response, next: NextFunction) => void;
+/**
+ *
+ * @param {*} res
+ * @param {*} status
+ * @param {*} content
+ * @returns
+ */
+export declare function sendJSONResponse(res: Response, status?: number, content?: Object): void;
+/**
+ * Create an Express middleware function which errors if an HTTP method is not allowed.
+ *
+ * @access public
+ * @param {Array<string>} [methods=[]]
+ *     The HTTP methods which will not throw 405 errors.
+ * @param {string} [message]
+ *     The error message text to use if a disallowed method is used.
+ * @returns {import('express').Handler}
+ *     Returns a middleware function.
+ */
+export declare function allowMethods(methods?: string[], message?: string): Handler;
+/**
+ *
+ * @param {*} roles
+ * @param {*} condition
+ */
+export declare function authHandler(roles?: string[], condition?: string): (req: Request, res: Response, next: NextFunction) => void;
+//# sourceMappingURL=express.d.ts.map

package/build/utils/express.d.ts.map

@@ -0,0 +1 @@
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package/build/utils/express.js

@@ -0,0 +1,114 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.validateSchema = validateSchema;
+exports.sendJSONResponse = sendJSONResponse;
+exports.allowMethods = allowMethods;
+exports.authHandler = authHandler;
+const http_errors_1 = __importDefault(require("http-errors"));
+const express_validator_1 = require("express-validator");
+const constants_1 = require("../constants");
+const functs_1 = require("./functs");
+const authentication_error_1 = require("../errors/authentication-error");
+const forbidden_error_1 = require("../errors/forbidden-error");
+/**
+ *
+ * @param schema
+ * @param errorFormatter
+ * @returns
+ */
+function validateSchema(schema, errorFormatter = (err, req) => err) {
+    return (req, res, next) => {
+        (0, express_validator_1.checkSchema)(schema).run(req).then((aaa) => {
+            const errors = (0, express_validator_1.validationResult)(req);
+            if (errors.isEmpty())
+                return next();
+            res.status(400).json(errorFormatter(errors, req));
+        });
+    };
+}
+/**
+ *
+ * @param {*} res
+ * @param {*} status
+ * @param {*} content
+ * @returns
+ */
+function sendJSONResponse(res, status = 200, content = {}) {
+    if (!res)
+        return;
+    res.status(status);
+    res.json(content);
+}
+/**
+ * Create an Express middleware function which errors if an HTTP method is not allowed.
+ *
+ * @access public
+ * @param {Array<string>} [methods=[]]
+ *     The HTTP methods which will not throw 405 errors.
+ * @param {string} [message]
+ *     The error message text to use if a disallowed method is used.
+ * @returns {import('express').Handler}
+ *     Returns a middleware function.
+ */
+function allowMethods(methods = [], message = 'Method Not Allowed') {
+    const normalizedMethods = normalizeAllowedMethods(methods);
+    return (request, response, next) => {
+        if (!normalizedMethods.includes(request.method.toUpperCase())) {
+            response.header('Allow', normalizedMethods.join(', '));
+            return next((0, http_errors_1.default)(405, message));
+        }
+        next();
+    };
+}
+;
+/**
+ * Normalise an array of HTTP methods.
+ *
+ * @access private
+ * @param {Array<string>} methods
+ *     The HTTP methods to normalise.
+ * @returns {Array<string>}
+ *     Returns an array of capitalised HTTP methods.
+ */
+function normalizeAllowedMethods(methods) {
+    if (!Array.isArray(methods))
+        return [];
+    return methods.filter(method => typeof method === 'string')
+        .map(method => method.toUpperCase());
+}
+/**
+ *
+ * @param {*} roles
+ * @param {*} condition
+ */
+function authHandler(roles, condition) {
+    return (req, res, next) => {
+        const user = (0, functs_1.getAttr)(req, 'context.user');
+        if (!user) {
+            sendJSONResponse(res, 401, constants_1.RES_CODE.AUTH_REQUIRED);
+            next(new authentication_error_1.AuthenticationError('messages.authentication.required'));
+            return;
+        }
+        if (roles) {
+            let hasRoles = true;
+            switch (condition) {
+                case '&&':
+                    hasRoles = roles.every(role => user.roles.indexOf(role) >= 0);
+                    break;
+                case '||':
+                default:
+                    hasRoles = roles.some(role => user.roles.indexOf(role) >= 0);
+                    break;
+            }
+            if (!hasRoles) {
+                sendJSONResponse(res, 401, constants_1.RES_CODE.FORBIDDEN);
+                throw new forbidden_error_1.ForbiddenError('messages.authorization.failed');
+            }
+        }
+        next();
+    };
+}
+//# sourceMappingURL=express.js.map

package/build/utils/express.js.map

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package/build/utils/functs.d.ts

@@ -0,0 +1,46 @@
+import { AppObject, BaseUser } from '../interfaces';
+/**
+ *
+ * @param path
+ * @returns
+ */
+export declare function pathExists(path?: string): Promise<boolean>;
+/**
+ *
+ * @param object
+ * @param path
+ */
+export declare function getAttr(object: any, path: string): any;
+/**
+ *
+ * @param object
+ * @param path
+ * @param value
+ */
+export declare function setAttr(object: any, path: string, value: any): any;
+/**
+ * Scan recoursively a directory to find files ending with fname
+ * @param dir Directory to use to explore
+ */
+export declare function findFilesRecursive(dir: string, fname: string): string[];
+/**
+ * Sets the tenantId on the given payload based on the user's role and organizations.
+ * - Normal users: tenantId is always set to their first organization
+ * - Admin users (CONFIG_ROLES):
+ *     - If applyDefaultForAdmin = false → can access all tenants
+ *     - If applyDefaultForAdmin = true and tenantId not provided → tenantId set to first org (subset view)
+ */
+export declare function setTenant(item: AppObject, user?: BaseUser, applyDefaultForAdmin?: boolean): void;
+/**
+ *
+ * @param user
+ * @returns
+ */
+export declare function getTenant(user?: BaseUser): string | undefined;
+/**
+ *
+ * @param input
+ * @returns
+ */
+export declare function validateUrl(input: string): string;
+//# sourceMappingURL=functs.d.ts.map

package/build/utils/functs.d.ts.map

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