@cirrobio/sdk 0.0.1 → 0.1.29

package/dist/api.d.ts

@@ -1,8 +1,8 @@
-import { Middleware, ResponseContext } from "@cirrobio/api-client";
-export declare class ApiError extends Error {
-    errors: string[];
-    constructor(message: string, errors: string[]);
-}
-export declare class PortalErrorHandler implements Middleware {
-    post(context: ResponseContext): Promise<Response | void>;
-}
+import { Middleware, ResponseContext } from "@cirrobio/api-client";
+export declare class ApiError extends Error {
+    errors: string[];
+    constructor(message: string, errors: string[]);
+}
+export declare class PortalErrorHandler implements Middleware {
+    post(context: ResponseContext): Promise<Response | void>;
+}

package/dist/api.js

@@ -1,105 +1,105 @@
-"use strict";
-var __extends = (this && this.__extends) || (function () {
-    var extendStatics = function (d, b) {
-        extendStatics = Object.setPrototypeOf ||
-            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
-            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
-        return extendStatics(d, b);
-    };
-    return function (d, b) {
-        if (typeof b !== "function" && b !== null)
-            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
-        extendStatics(d, b);
-        function __() { this.constructor = d; }
-        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
-    };
-})();
-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) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (g && (g = 0, op[0] && (_ = 0)), _) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.PortalErrorHandler = exports.ApiError = void 0;
-var ApiError = /** @class */ (function (_super) {
-    __extends(ApiError, _super);
-    function ApiError(message, errors) {
-        var _this = _super.call(this, message) || this;
-        _this.errors = errors;
-        return _this;
-    }
-    return ApiError;
-}(Error));
-exports.ApiError = ApiError;
-var PortalErrorHandler = /** @class */ (function () {
-    function PortalErrorHandler() {
-    }
-    PortalErrorHandler.prototype.post = function (context) {
-        return __awaiter(this, void 0, void 0, function () {
-            var response, errorMessage, errors, err, ignore_1;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        response = context.response;
-                        if (response && (response.status >= 200 && response.status < 300)) {
-                            return [2 /*return*/, response];
-                        }
-                        errors = [];
-                        _a.label = 1;
-                    case 1:
-                        _a.trys.push([1, 3, , 4]);
-                        return [4 /*yield*/, response.json()];
-                    case 2:
-                        err = _a.sent();
-                        console.warn(err);
-                        if ('errorDetail' in err) {
-                            errorMessage = err.errorDetail;
-                            errors.push(err.errors.map(function (e) { return e.message; }));
-                        }
-                        else {
-                            errorMessage = err.message;
-                        }
-                        return [3 /*break*/, 4];
-                    case 3:
-                        ignore_1 = _a.sent();
-                        errorMessage = "Unknown Error";
-                        return [3 /*break*/, 4];
-                    case 4: throw new ApiError(errorMessage, errors);
-                }
-            });
-        });
-    };
-    return PortalErrorHandler;
-}());
-exports.PortalErrorHandler = PortalErrorHandler;
+"use strict";
+var __extends = (this && this.__extends) || (function () {
+    var extendStatics = function (d, b) {
+        extendStatics = Object.setPrototypeOf ||
+            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
+            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
+        return extendStatics(d, b);
+    };
+    return function (d, b) {
+        if (typeof b !== "function" && b !== null)
+            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
+        extendStatics(d, b);
+        function __() { this.constructor = d; }
+        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+    };
+})();
+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) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (g && (g = 0, op[0] && (_ = 0)), _) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
+            }
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
+    }
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.PortalErrorHandler = exports.ApiError = void 0;
+var ApiError = /** @class */ (function (_super) {
+    __extends(ApiError, _super);
+    function ApiError(message, errors) {
+        var _this = _super.call(this, message) || this;
+        _this.errors = errors;
+        return _this;
+    }
+    return ApiError;
+}(Error));
+exports.ApiError = ApiError;
+var PortalErrorHandler = /** @class */ (function () {
+    function PortalErrorHandler() {
+    }
+    PortalErrorHandler.prototype.post = function (context) {
+        return __awaiter(this, void 0, void 0, function () {
+            var response, errorMessage, errors, err, ignore_1;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        response = context.response;
+                        if (response && (response.status >= 200 && response.status < 300)) {
+                            return [2 /*return*/, response];
+                        }
+                        errors = [];
+                        _a.label = 1;
+                    case 1:
+                        _a.trys.push([1, 3, , 4]);
+                        return [4 /*yield*/, response.json()];
+                    case 2:
+                        err = _a.sent();
+                        console.warn(err);
+                        if ('errorDetail' in err) {
+                            errorMessage = err.errorDetail;
+                            errors.push(err.errors.map(function (e) { return e.message; }));
+                        }
+                        else {
+                            errorMessage = err.message;
+                        }
+                        return [3 /*break*/, 4];
+                    case 3:
+                        ignore_1 = _a.sent();
+                        errorMessage = "Unknown Error";
+                        return [3 /*break*/, 4];
+                    case 4: throw new ApiError(errorMessage, errors);
+                }
+            });
+        });
+    };
+    return PortalErrorHandler;
+}());
+exports.PortalErrorHandler = PortalErrorHandler;

package/dist/extensions.fn.d.ts

@@ -0,0 +1,49 @@
+/**
+ * An array of file extensions that can be rendered in a genome viewer
+ */
+export declare const FILE_TRACK_ANNOTATION: string[];
+export declare const FILE_TRACK_ALIGNMENTS: string[];
+export declare const FILE_TRACK_VARIANT: string[];
+export declare const FILE_TRACK_WIG: string[];
+export declare const FILE_TRACK_SEG: string[];
+export declare const FILE_TRACK_INDEX_EXTENSIONS: string[];
+export declare const FILE_VITESSCE_EXTENSIONS: string[];
+export declare const FILE_TRACK_EXTENSIONS_NO_INDEX: string[];
+export declare const FILE_TRACK_EXTENSIONS: string[];
+export declare const FILE_BROWSER_EXTENSIONS: string[];
+/**
+ * An array of file extensions that are protein structure files.
+ */
+export declare const FILE_PROTEIN_STRUCTURE_EXTENSIONS: string[];
+/**
+ * An array of file extensions that are considered tabular files.
+ */
+export declare const FILE_DSV_EXTENSIONS: string[];
+/**
+ * An array of file extensions that contain genomic sequence content.
+ */
+export declare const FILE_TXT_GENOMICS_EXTENSIONS: string[];
+/**
+ * An array of file extensions that are considered TXT files.
+ */
+export declare const FILE_TXT_EXTENSIONS: string[];
+/**
+ * An array of file extensions that are considered image files.
+ */
+export declare const FILE_IMAGE_EXTENSIONS: string[];
+/**
+ * An array of file extensions that are considered OME (Open Microscopy Environment) files.
+ */
+export declare const FILE_OME_EXTENSIONS: string[];
+/**
+ * An array of file extensions that can be opened in the browser.
+ * Includes common document formats such as HTML, PDF, and JSON, as well as image, DSV, TXT, and OME file formats.
+ */
+export declare const FILE_EXTENSIONS_TO_OPEN: string[];
+/**
+ * Checks if a file has an extension that matches one in the provided list.
+ * @param filePath The file to check the extension of.
+ * @param extensions A list of file endings to check the file against.
+ * @returns True or false if the file has an ending in the extensions list.
+ */
+export declare function matchesExtension(filePath: string, extensions: string[]): boolean;

package/dist/extensions.fn.js

@@ -0,0 +1,72 @@
+"use strict";
+/**
+ * An array of file extensions that can be rendered in a genome viewer
+ */
+var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
+    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
+        if (ar || !(i in from)) {
+            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
+            ar[i] = from[i];
+        }
+    }
+    return to.concat(ar || Array.prototype.slice.call(from));
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.matchesExtension = exports.FILE_EXTENSIONS_TO_OPEN = exports.FILE_OME_EXTENSIONS = exports.FILE_IMAGE_EXTENSIONS = exports.FILE_TXT_EXTENSIONS = exports.FILE_TXT_GENOMICS_EXTENSIONS = exports.FILE_DSV_EXTENSIONS = exports.FILE_PROTEIN_STRUCTURE_EXTENSIONS = exports.FILE_BROWSER_EXTENSIONS = exports.FILE_TRACK_EXTENSIONS = exports.FILE_TRACK_EXTENSIONS_NO_INDEX = exports.FILE_VITESSCE_EXTENSIONS = exports.FILE_TRACK_INDEX_EXTENSIONS = exports.FILE_TRACK_SEG = exports.FILE_TRACK_WIG = exports.FILE_TRACK_VARIANT = exports.FILE_TRACK_ALIGNMENTS = exports.FILE_TRACK_ANNOTATION = void 0;
+exports.FILE_TRACK_ANNOTATION = ['bed', 'bed.gz', 'gtf', 'gtf.gz'];
+exports.FILE_TRACK_ALIGNMENTS = ['cram', 'cram.gz']; // TODO: put back bam
+exports.FILE_TRACK_VARIANT = ['vcf', 'vcf.gz'];
+exports.FILE_TRACK_WIG = ['wig', 'wig.gz', 'bw', 'bw.gz', 'bigwig', 'bigwig.gz'];
+exports.FILE_TRACK_SEG = ['seg', 'seg.gz'];
+exports.FILE_TRACK_INDEX_EXTENSIONS = ['tbi', 'bai', 'crai', 'csi'];
+exports.FILE_VITESSCE_EXTENSIONS = ['hdf5', 'h5ad', 'loom'];
+exports.FILE_TRACK_EXTENSIONS_NO_INDEX = __spreadArray(__spreadArray(__spreadArray(__spreadArray(__spreadArray([], exports.FILE_TRACK_ANNOTATION, true), exports.FILE_TRACK_ALIGNMENTS, true), exports.FILE_TRACK_VARIANT, true), exports.FILE_TRACK_WIG, true), exports.FILE_TRACK_SEG, true);
+exports.FILE_TRACK_EXTENSIONS = __spreadArray(__spreadArray([], exports.FILE_TRACK_EXTENSIONS_NO_INDEX, true), exports.FILE_TRACK_INDEX_EXTENSIONS, true);
+exports.FILE_BROWSER_EXTENSIONS = ['html', 'pdf'];
+/**
+ * An array of file extensions that are protein structure files.
+ */
+exports.FILE_PROTEIN_STRUCTURE_EXTENSIONS = ['pdb', 'pdb.gz', 'cif', 'cif.gz', 'ent', 'ent.gz', 'mmtf', 'mmtf.gz'];
+/**
+ * An array of file extensions that are considered tabular files.
+ */
+exports.FILE_DSV_EXTENSIONS = ['tab', 'csv', 'tsv', 'dsv'];
+/**
+ * An array of file extensions that contain genomic sequence content.
+ */
+exports.FILE_TXT_GENOMICS_EXTENSIONS = ['fasta', 'fna', 'fsa', 'fa', 'fastp', 'fastq', 'faa', 'gbk', 'gff', 'vcf', 'seq'];
+/**
+ * An array of file extensions that are considered TXT files.
+ */
+exports.FILE_TXT_EXTENSIONS = __spreadArray(__spreadArray(['txt', 'log', 'yml', 'cfg', 'xml', 'yaml'], exports.FILE_DSV_EXTENSIONS, true), exports.FILE_TXT_GENOMICS_EXTENSIONS, true);
+/**
+ * An array of file extensions that are considered image files.
+ */
+exports.FILE_IMAGE_EXTENSIONS = ['jpg', 'jpeg', 'png', 'svg'];
+/**
+ * An array of file extensions that are considered OME (Open Microscopy Environment) files.
+ */
+exports.FILE_OME_EXTENSIONS = ['tif', 'ome.tif', 'ome.tiff', 'ome.tif.gz', 'ome.tiff.gz'];
+/**
+ * An array of file extensions that can be opened in the browser.
+ * Includes common document formats such as HTML, PDF, and JSON, as well as image, DSV, TXT, and OME file formats.
+ */
+exports.FILE_EXTENSIONS_TO_OPEN = __spreadArray(__spreadArray(__spreadArray(__spreadArray(['html', 'pdf', 'json', 'fcs'], exports.FILE_IMAGE_EXTENSIONS, true), exports.FILE_TXT_EXTENSIONS, true), exports.FILE_TRACK_EXTENSIONS, true), exports.FILE_PROTEIN_STRUCTURE_EXTENSIONS, true);
+/**
+ * Checks if a file has an extension that matches one in the provided list.
+ * @param filePath The file to check the extension of.
+ * @param extensions A list of file endings to check the file against.
+ * @returns True or false if the file has an ending in the extensions list.
+ */
+function matchesExtension(filePath, extensions) {
+    filePath = filePath.toLowerCase();
+    // Decompress the filePath if it ends with .gz
+    if (filePath.endsWith('.gz')) {
+        filePath = filePath.slice(0, -3); // remove the .gz extension
+    }
+    // Now, get the extension of the file
+    var fileExtension = filePath.slice(filePath.lastIndexOf('.') + 1);
+    // Check if the fileExtension is in the list of extensions
+    return extensions.includes(fileExtension);
+}
+exports.matchesExtension = matchesExtension;

package/dist/index.d.ts

@@ -1 +1,2 @@
-export * from './api';
+export * from './api';
+export * from './extensions.fn';

package/dist/index.js

@@ -1,17 +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("./api"), exports);
+"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("./api"), exports);
+__exportStar(require("./extensions.fn"), exports);

package/package.json

@@ -1,25 +1,25 @@
-{
-  "name": "@cirrobio/sdk",
-  "version": "0.0.1",
-  "description": "SDK for Cirro",
-  "author": "CirroBio",
-  "repository": {
-    "type": "git",
-    "url": "https://github.com/CirroBio/Cirro-client-ts.git",
-    "directory": "packages/sdk"
-  },
-  "license": "MIT",
-  "homepage": "https://cirro.bio",
-  "main": "./dist/index.js",
-  "typings": "./dist/index.d.ts",
-  "scripts": {
-    "build": "tsc",
-    "prepare": "npm run build"
-  },
-  "devDependencies": {
-    "typescript": "^4.0"
-  },
-  "dependencies": {
-    "@cirrobio/api-client": "^0.1"
-  }
-}
+{
+  "name": "@cirrobio/sdk",
+  "version": "0.1.29",
+  "description": "SDK for Cirro",
+  "author": "CirroBio",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/CirroBio/Cirro-client-ts.git",
+    "directory": "packages/sdk"
+  },
+  "license": "MIT",
+  "homepage": "https://cirro.bio",
+  "main": "./dist/index.js",
+  "typings": "./dist/index.d.ts",
+  "scripts": {
+    "build": "tsc",
+    "prepare": "npm run build"
+  },
+  "devDependencies": {
+    "typescript": "^4.0"
+  },
+  "dependencies": {
+    "@cirrobio/api-client": "^0.1"
+  }
+}

package/src/api.ts

@@ -1,36 +1,36 @@
-import { Middleware, ResponseContext } from "@cirrobio/api-client";
-
-export class ApiError extends Error {
-  errors: string[];
-
-  constructor(message: string, errors: string[]) {
-    super(message);
-    this.errors = errors;
-  }
-}
-
-export class PortalErrorHandler implements Middleware {
-  async post(context: ResponseContext): Promise<Response | void> {
-    const { response } = context;
-    if (response && (response.status >= 200 && response.status < 300)) {
-      return response;
-    }
-
-    // Handle Error
-    let errorMessage: string;
-    const errors = [];
-    try {
-      const err = await response.json();
-      console.warn(err);
-      if ('errorDetail' in err) {
-        errorMessage = err.errorDetail;
-        errors.push(err.errors.map((e: any) => e.message));
-      } else {
-        errorMessage = err.message;
-      }
-    } catch (ignore) {
-      errorMessage = "Unknown Error";
-    }
-    throw new ApiError(errorMessage, errors);
-  }
-}
+import { Middleware, ResponseContext } from "@cirrobio/api-client";
+
+export class ApiError extends Error {
+  errors: string[];
+
+  constructor(message: string, errors: string[]) {
+    super(message);
+    this.errors = errors;
+  }
+}
+
+export class PortalErrorHandler implements Middleware {
+  async post(context: ResponseContext): Promise<Response | void> {
+    const { response } = context;
+    if (response && (response.status >= 200 && response.status < 300)) {
+      return response;
+    }
+
+    // Handle Error
+    let errorMessage: string;
+    const errors = [];
+    try {
+      const err = await response.json();
+      console.warn(err);
+      if ('errorDetail' in err) {
+        errorMessage = err.errorDetail;
+        errors.push(err.errors.map((e: any) => e.message));
+      } else {
+        errorMessage = err.message;
+      }
+    } catch (ignore) {
+      errorMessage = "Unknown Error";
+    }
+    throw new ApiError(errorMessage, errors);
+  }
+}

package/src/extensions.fn.ts

@@ -0,0 +1,89 @@
+
+/**
+ * An array of file extensions that can be rendered in a genome viewer
+ */
+
+export const FILE_TRACK_ANNOTATION = ['bed', 'bed.gz', 'gtf', 'gtf.gz'];
+export const FILE_TRACK_ALIGNMENTS = ['cram', 'cram.gz'];  // TODO: put back bam
+export const FILE_TRACK_VARIANT = ['vcf', 'vcf.gz'];
+export const FILE_TRACK_WIG = ['wig', 'wig.gz', 'bw', 'bw.gz', 'bigwig', 'bigwig.gz'];
+export const FILE_TRACK_SEG = ['seg', 'seg.gz'];
+export const FILE_TRACK_INDEX_EXTENSIONS = ['tbi', 'bai', 'crai', 'csi'];
+export const FILE_VITESSCE_EXTENSIONS = ['hdf5', 'h5ad', 'loom'];
+export const FILE_TRACK_EXTENSIONS_NO_INDEX = [
+    ...FILE_TRACK_ANNOTATION,
+    ...FILE_TRACK_ALIGNMENTS,
+    ...FILE_TRACK_VARIANT,
+    ...FILE_TRACK_WIG,
+    ...FILE_TRACK_SEG
+];
+export const FILE_TRACK_EXTENSIONS = [
+    ...FILE_TRACK_EXTENSIONS_NO_INDEX,
+    ...FILE_TRACK_INDEX_EXTENSIONS
+]
+
+
+export const FILE_BROWSER_EXTENSIONS = ['html', 'pdf'];
+
+
+/**
+ * An array of file extensions that are protein structure files.
+ */
+export const FILE_PROTEIN_STRUCTURE_EXTENSIONS = ['pdb', 'pdb.gz', 'cif', 'cif.gz', 'ent', 'ent.gz', 'mmtf', 'mmtf.gz'];
+/**
+ * An array of file extensions that are considered tabular files.
+ */
+export const FILE_DSV_EXTENSIONS = ['tab', 'csv', 'tsv', 'dsv'];
+/**
+ * An array of file extensions that contain genomic sequence content.
+ */
+export const FILE_TXT_GENOMICS_EXTENSIONS = ['fasta', 'fna', 'fsa', 'fa', 'fastp', 'fastq', 'faa', 'gbk', 'gff', 'vcf', 'seq'];
+
+/**
+ * An array of file extensions that are considered TXT files.
+ */
+export const FILE_TXT_EXTENSIONS = ['txt', 'log', 'yml', 'cfg', 'xml', 'yaml', ...FILE_DSV_EXTENSIONS, ...FILE_TXT_GENOMICS_EXTENSIONS];
+
+
+/**
+ * An array of file extensions that are considered image files.
+ */
+export const FILE_IMAGE_EXTENSIONS = ['jpg', 'jpeg', 'png', 'svg'];
+
+/**
+ * An array of file extensions that are considered OME (Open Microscopy Environment) files.
+ */
+export const FILE_OME_EXTENSIONS = ['tif', 'ome.tif', 'ome.tiff', 'ome.tif.gz', 'ome.tiff.gz'];
+
+/**
+ * An array of file extensions that can be opened in the browser.
+ * Includes common document formats such as HTML, PDF, and JSON, as well as image, DSV, TXT, and OME file formats.
+ */
+export const FILE_EXTENSIONS_TO_OPEN = ['html', 'pdf', 'json', 'fcs',
+    ...FILE_IMAGE_EXTENSIONS,
+    ...FILE_TXT_EXTENSIONS,
+    ...FILE_TRACK_EXTENSIONS,
+    ...FILE_PROTEIN_STRUCTURE_EXTENSIONS
+];
+
+
+/**
+ * Checks if a file has an extension that matches one in the provided list.
+ * @param filePath The file to check the extension of.
+ * @param extensions A list of file endings to check the file against.
+ * @returns True or false if the file has an ending in the extensions list.
+ */
+export function matchesExtension(filePath: string, extensions: string[]): boolean {
+    filePath = filePath.toLowerCase();
+
+    // Decompress the filePath if it ends with .gz
+    if (filePath.endsWith('.gz')) {
+        filePath = filePath.slice(0, -3);  // remove the .gz extension
+    }
+
+    // Now, get the extension of the file
+    const fileExtension = filePath.slice(filePath.lastIndexOf('.') + 1);
+
+    // Check if the fileExtension is in the list of extensions
+    return extensions.includes(fileExtension);
+}

package/src/index.ts

@@ -1 +1,2 @@
-export * from './api'
+export * from './api'
+export * from './extensions.fn'

package/tsconfig.json

@@ -6,7 +6,7 @@
     "moduleResolution": "node",
     "outDir": "dist",
     "lib": [
-      "es6",
+      "es2016",
       "dom"
     ],
     "typeRoots": [
@@ -17,4 +17,4 @@
     "dist",
     "node_modules"
   ]
-}
+}