@galaxyproject/galaxy-api-client 25.0.0-dev.0

package/dist/index.js

@@ -0,0 +1,87 @@
+import createClient from 'openapi-fetch';
+
+// src/client.ts
+
+// src/api-types.ts
+function isHDA(entry) {
+  return entry !== void 0 && "history_content_type" in entry && entry.history_content_type === "dataset";
+}
+function isHDCA(entry) {
+  return entry !== void 0 && "history_content_type" in entry && entry.history_content_type === "dataset_collection";
+}
+function isDCE(item) {
+  return item && "element_type" in item;
+}
+function isCollectionElement(element) {
+  return element.element_type === "dataset_collection";
+}
+function isDatasetElement(element) {
+  return element.element_type === "hda";
+}
+function hasDetails(entry) {
+  return "peek" in entry;
+}
+function isInaccessible(entry) {
+  return "accessible" in entry && !entry.accessible;
+}
+
+// src/client.ts
+function createGalaxyApi(options = {}) {
+  const opts = typeof options === "string" ? { baseUrl: options } : options;
+  const baseUrl = opts.baseUrl || window.location.origin;
+  const normalizedBaseUrl = baseUrl.endsWith("/") ? baseUrl.slice(0, -1) : baseUrl;
+  const headers = {
+    ...opts.headers || {}
+  };
+  if (opts.apiKey) {
+    headers["x-api-key"] = opts.apiKey;
+  }
+  return createClient({
+    baseUrl: normalizedBaseUrl,
+    headers,
+    // Pass any custom fetchOptions directly to createClient
+    ...opts.fetchOptions ? { fetchOptions: opts.fetchOptions } : {}
+  });
+}
+
+// src/utils/error.ts
+function errorMessageAsString(error) {
+  if (typeof error === "string") {
+    return error;
+  }
+  if (error instanceof Error) {
+    return error.message;
+  }
+  if (error && typeof error === "object") {
+    if (error.status && error.error) {
+      return `API Error (${error.status}): ${error.error}`;
+    }
+    if (error.message) {
+      return error.message;
+    }
+    try {
+      return JSON.stringify(error);
+    } catch (e) {
+      return String(error);
+    }
+  }
+  return "Unknown error";
+}
+
+// src/index.ts
+var SimpleError = class extends Error {
+  constructor(message) {
+    super(message);
+    this.name = "GalaxyApiError";
+  }
+};
+function GalaxyApi() {
+  return createGalaxyApi();
+}
+function formatErrorMessage(error) {
+  return errorMessageAsString(error);
+}
+
+export { GalaxyApi, SimpleError, createGalaxyApi, formatErrorMessage, hasDetails, isCollectionElement, isDCE, isDatasetElement, isHDA, isHDCA, isInaccessible };
+//# sourceMappingURL=index.js.map
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
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* This file re-exports the types we want to use from the Galaxy API.\n * It serves as a compatibility layer to avoid importing directly from the\n * symlinked files, which would require all of Galaxy's dependencies.\n */\n\n// Import types from the symlinked files\nimport { type components, type GalaxyApiPaths } from \"./api/schema\";\n\n// We only need the types, not the code that depends on Galaxy's implementation\nexport type { components, GalaxyApiPaths };\n\n// Re-export specific types\nexport type HistorySummary = components[\"schemas\"][\"HistorySummary\"];\nexport type HistoryDetailed = components[\"schemas\"][\"HistoryDetailed\"];\nexport type HDASummary = components[\"schemas\"][\"HDASummary\"];\nexport type HDADetailed = components[\"schemas\"][\"HDADetailed\"];\nexport type DCESummary = components[\"schemas\"][\"DCESummary\"];\nexport type HDCASummary = components[\"schemas\"][\"HDCASummary\"];\nexport type HDCADetailed = components[\"schemas\"][\"HDCADetailed\"];\nexport type DCObject = components[\"schemas\"][\"DCObject\"];\nexport type HDAObject = components[\"schemas\"][\"HDAObject\"];\nexport type HDAInaccessible = components[\"schemas\"][\"HDAInaccessible\"];\nexport type DatasetTextContentDetails = components[\"schemas\"][\"DatasetTextContentDetails\"];\nexport type DatasetStorageDetails = components[\"schemas\"][\"DatasetStorageDetails\"];\nexport type DatasetCollectionAttributes = components[\"schemas\"][\"DatasetCollectionAttributesResult\"];\nexport type ConcreteObjectStoreModel = components[\"schemas\"][\"ConcreteObjectStoreModel\"];\nexport type MessageException = components[\"schemas\"][\"MessageExceptionModel\"];\nexport type DatasetHash = components[\"schemas\"][\"DatasetHash\"];\nexport type DatasetSource = components[\"schemas\"][\"DatasetSource\"];\nexport type DatasetTransform = components[\"schemas\"][\"DatasetSourceTransform\"];\nexport type StoreExportPayload = components[\"schemas\"][\"StoreExportPayload\"];\nexport type ModelStoreFormat = components[\"schemas\"][\"ModelStoreFormat\"];\nexport type ObjectExportTaskResponse = components[\"schemas\"][\"ObjectExportTaskResponse\"];\nexport type ExportObjectRequestMetadata = components[\"schemas\"][\"ExportObjectRequestMetadata\"];\nexport type ExportObjectResultMetadata = components[\"schemas\"][\"ExportObjectResultMetadata\"];\nexport type AsyncTaskResultSummary = components[\"schemas\"][\"AsyncTaskResultSummary\"];\n\n// Define utility types that may be used in the client\nexport type HistorySortByLiteral = \"create_time\" | \"name\" | \"update_time\" | \"username\" | undefined;\n\nexport interface HistoryContentsStats {\n    id: string;\n    update_time: string;\n    size: number;\n    contents_active: components[\"schemas\"][\"HistoryActiveContentCounts\"];\n}\n\nexport interface HistorySummaryExtended extends HistorySummary, HistoryContentsStats {\n    user_id: string | null;\n}\n\nexport interface SelectableObjectStore extends ConcreteObjectStoreModel {\n    object_store_id: string;\n}\n\nexport type DatasetEntry = HDASummary | HDADetailed | HDAInaccessible;\n\nexport interface DCECollection extends DCESummary {\n    element_type: \"dataset_collection\";\n    object: DCObject;\n}\n\nexport interface DCEDataset extends DCESummary {\n    element_type: \"hda\";\n    object: HDAObject;\n}\n\nexport interface SubCollection extends DCObject {\n    name: string;\n    hdca_id: string;\n}\n\nexport type CollectionEntry = HDCASummary | SubCollection;\nexport type HistoryItemSummary = HDASummary | HDCASummary;\n\n// Utility functions\nexport function isHDA(entry?: HistoryItemSummary): entry is HDASummary {\n    return entry !== undefined && \"history_content_type\" in entry && entry.history_content_type === \"dataset\";\n}\n\nexport function isHDCA(entry?: HistoryItemSummary | CollectionEntry): entry is HDCASummary {\n    return (\n        entry !== undefined && \"history_content_type\" in entry && entry.history_content_type === \"dataset_collection\"\n    );\n}\n\nexport function isDCE(item: object): item is DCESummary {\n    return item && \"element_type\" in item;\n}\n\nexport function isCollectionElement(element: DCESummary): element is DCECollection {\n    return element.element_type === \"dataset_collection\";\n}\n\nexport function isDatasetElement(element: DCESummary): element is DCEDataset {\n    return element.element_type === \"hda\";\n}\n\nexport function hasDetails(entry: DatasetEntry): entry is HDADetailed {\n    return \"peek\" in entry;\n}\n\nexport function isInaccessible(entry: DatasetEntry): entry is HDAInaccessible {\n    return \"accessible\" in entry && !entry.accessible;\n}\n","import createClient from \"openapi-fetch\";\nimport { type GalaxyApiPaths } from \"./api-types\";\n\n/**\n * Options for creating a Galaxy API client\n */\nexport interface GalaxyApiOptions {\n    /**\n     * The base URL of the Galaxy server (e.g., \"https://usegalaxy.org\")\n     * @default window.location.origin\n     */\n    baseUrl?: string;\n\n    /**\n     * API key for authentication\n     */\n    apiKey?: string;\n\n    /**\n     * Custom headers to include with each request\n     */\n    headers?: Record<string, string>;\n\n    /**\n     * Custom fetch options that will be passed to all requests\n     */\n    fetchOptions?: RequestInit;\n}\n\n/**\n * Creates a Galaxy API client with the specified options\n * @param options Configuration options for the Galaxy API client\n * @returns The Galaxy API client\n */\nexport function createGalaxyApi(options: GalaxyApiOptions | string = {}) {\n    // Handle the case where baseUrl is passed as a string for backward compatibility\n    const opts = typeof options === \"string\" ? { baseUrl: options } : options;\n\n    // Default to window.location.origin if no baseUrl is provided\n    const baseUrl = opts.baseUrl || window.location.origin;\n    const normalizedBaseUrl = baseUrl.endsWith(\"/\") ? baseUrl.slice(0, -1) : baseUrl;\n\n    // Build headers object\n    const headers: Record<string, string> = {\n        ...(opts.headers || {}),\n    };\n\n    // Add API key header if provided\n    if (opts.apiKey) {\n        headers[\"x-api-key\"] = opts.apiKey;\n    }\n\n    // Create the client with all options\n    return createClient<GalaxyApiPaths>({\n        baseUrl: normalizedBaseUrl,\n        headers,\n        // Pass any custom fetchOptions directly to createClient\n        ...(opts.fetchOptions ? { fetchOptions: opts.fetchOptions } : {}),\n    });\n}\n\nexport type GalaxyApiClient = ReturnType<typeof createGalaxyApi>;\n","/**\n * Simple error handling utilities for Galaxy Client API\n */\n\n/**\n * Convert various error formats to a readable string message\n */\nexport function errorMessageAsString(error: any): string {\n    if (typeof error === \"string\") {\n        return error;\n    }\n\n    if (error instanceof Error) {\n        return error.message;\n    }\n\n    if (error && typeof error === \"object\") {\n        // Handle API response errors\n        if (error.status && error.error) {\n            return `API Error (${error.status}): ${error.error}`;\n        }\n\n        // Handle response objects with error message\n        if (error.message) {\n            return error.message;\n        }\n\n        // Try to stringify the error object\n        try {\n            return JSON.stringify(error);\n        } catch (e) {\n            // Fall back to object inspection\n            return String(error);\n        }\n    }\n\n    return \"Unknown error\";\n}\n","/**\n * Galaxy Client API\n * A client library for the Galaxy API\n */\n\nimport { createGalaxyApi, type GalaxyApiClient } from \"./client\";\nimport { errorMessageAsString } from \"./utils/error\";\n\n// Re-export all the types from our type compatibility layer\nexport * from \"./api-types\";\n\n// SimpleError class for error handling\nexport class SimpleError extends Error {\n    constructor(message: string) {\n        super(message);\n        this.name = \"GalaxyApiError\";\n    }\n}\n\n// Re-export the client functions\nexport { createGalaxyApi, type GalaxyApiClient };\n\n// For backward compatibility - creates a client with default settings\nexport function GalaxyApi() {\n    return createGalaxyApi();\n}\n\n// Utility function to format error messages\nexport function formatErrorMessage(error: any): string {\n    return errorMessageAsString(error);\n}\n"]}

package/package.json

@@ -0,0 +1,51 @@
+{
+  "name": "@galaxyproject/galaxy-api-client",
+  "version": "25.0.0-dev.0",
+  "description": "A client library for the Galaxy API",
+  "type": "module",
+  "main": "./dist/index.js",
+  "module": "./dist/index.js",
+  "types": "./dist/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./dist/index.d.ts",
+      "import": "./dist/index.js",
+      "require": "./dist/index.cjs"
+    }
+  },
+  "files": [
+    "dist",
+    "src"
+  ],
+  "scripts": {
+    "build": "tsup",
+    "dev": "tsup --watch",
+    "clean": "rimraf dist",
+    "prepublishOnly": "npm run clean && npm run build",
+    "test": "vitest run",
+    "test:watch": "vitest",
+    "test:coverage": "vitest run --coverage",
+    "sync-version": "node scripts/sync-version.js"
+  },
+  "keywords": [
+    "galaxy",
+    "api",
+    "client"
+  ],
+  "author": "Galaxy Community",
+  "license": "MIT",
+  "dependencies": {
+    "openapi-fetch": "^0.12.0"
+  },
+  "peerDependencies": {
+    "typescript": ">=4.5.0"
+  },
+  "devDependencies": {
+    "jsdom": "^26.1.0",
+    "rimraf": "^6.0.1",
+    "ts-node": "^10.9.2",
+    "tsup": "^8.4.0",
+    "typescript": "^5.8.3",
+    "vitest": "^3.1.3"
+  }
+}

package/src/api-types.ts

@@ -0,0 +1,106 @@
+/**
+ * This file re-exports the types we want to use from the Galaxy API.
+ * It serves as a compatibility layer to avoid importing directly from the
+ * symlinked files, which would require all of Galaxy's dependencies.
+ */
+
+// Import types from the symlinked files
+import { type components, type GalaxyApiPaths } from "./api/schema";
+
+// We only need the types, not the code that depends on Galaxy's implementation
+export type { components, GalaxyApiPaths };
+
+// Re-export specific types
+export type HistorySummary = components["schemas"]["HistorySummary"];
+export type HistoryDetailed = components["schemas"]["HistoryDetailed"];
+export type HDASummary = components["schemas"]["HDASummary"];
+export type HDADetailed = components["schemas"]["HDADetailed"];
+export type DCESummary = components["schemas"]["DCESummary"];
+export type HDCASummary = components["schemas"]["HDCASummary"];
+export type HDCADetailed = components["schemas"]["HDCADetailed"];
+export type DCObject = components["schemas"]["DCObject"];
+export type HDAObject = components["schemas"]["HDAObject"];
+export type HDAInaccessible = components["schemas"]["HDAInaccessible"];
+export type DatasetTextContentDetails = components["schemas"]["DatasetTextContentDetails"];
+export type DatasetStorageDetails = components["schemas"]["DatasetStorageDetails"];
+export type DatasetCollectionAttributes = components["schemas"]["DatasetCollectionAttributesResult"];
+export type ConcreteObjectStoreModel = components["schemas"]["ConcreteObjectStoreModel"];
+export type MessageException = components["schemas"]["MessageExceptionModel"];
+export type DatasetHash = components["schemas"]["DatasetHash"];
+export type DatasetSource = components["schemas"]["DatasetSource"];
+export type DatasetTransform = components["schemas"]["DatasetSourceTransform"];
+export type StoreExportPayload = components["schemas"]["StoreExportPayload"];
+export type ModelStoreFormat = components["schemas"]["ModelStoreFormat"];
+export type ObjectExportTaskResponse = components["schemas"]["ObjectExportTaskResponse"];
+export type ExportObjectRequestMetadata = components["schemas"]["ExportObjectRequestMetadata"];
+export type ExportObjectResultMetadata = components["schemas"]["ExportObjectResultMetadata"];
+export type AsyncTaskResultSummary = components["schemas"]["AsyncTaskResultSummary"];
+
+// Define utility types that may be used in the client
+export type HistorySortByLiteral = "create_time" | "name" | "update_time" | "username" | undefined;
+
+export interface HistoryContentsStats {
+    id: string;
+    update_time: string;
+    size: number;
+    contents_active: components["schemas"]["HistoryActiveContentCounts"];
+}
+
+export interface HistorySummaryExtended extends HistorySummary, HistoryContentsStats {
+    user_id: string | null;
+}
+
+export interface SelectableObjectStore extends ConcreteObjectStoreModel {
+    object_store_id: string;
+}
+
+export type DatasetEntry = HDASummary | HDADetailed | HDAInaccessible;
+
+export interface DCECollection extends DCESummary {
+    element_type: "dataset_collection";
+    object: DCObject;
+}
+
+export interface DCEDataset extends DCESummary {
+    element_type: "hda";
+    object: HDAObject;
+}
+
+export interface SubCollection extends DCObject {
+    name: string;
+    hdca_id: string;
+}
+
+export type CollectionEntry = HDCASummary | SubCollection;
+export type HistoryItemSummary = HDASummary | HDCASummary;
+
+// Utility functions
+export function isHDA(entry?: HistoryItemSummary): entry is HDASummary {
+    return entry !== undefined && "history_content_type" in entry && entry.history_content_type === "dataset";
+}
+
+export function isHDCA(entry?: HistoryItemSummary | CollectionEntry): entry is HDCASummary {
+    return (
+        entry !== undefined && "history_content_type" in entry && entry.history_content_type === "dataset_collection"
+    );
+}
+
+export function isDCE(item: object): item is DCESummary {
+    return item && "element_type" in item;
+}
+
+export function isCollectionElement(element: DCESummary): element is DCECollection {
+    return element.element_type === "dataset_collection";
+}
+
+export function isDatasetElement(element: DCESummary): element is DCEDataset {
+    return element.element_type === "hda";
+}
+
+export function hasDetails(entry: DatasetEntry): entry is HDADetailed {
+    return "peek" in entry;
+}
+
+export function isInaccessible(entry: DatasetEntry): entry is HDAInaccessible {
+    return "accessible" in entry && !entry.accessible;
+}

package/src/client.test.ts

@@ -0,0 +1,68 @@
+import { describe, it, expect, vi, beforeEach } from "vitest";
+import { createGalaxyApi } from "./client";
+
+// Create a mock API client for testing
+const mockApiClient = {
+    GET: vi.fn(),
+    POST: vi.fn(),
+    PUT: vi.fn(),
+    DELETE: vi.fn(),
+    PATCH: vi.fn(),
+};
+
+// Mock createClient before importing
+vi.mock("openapi-fetch", () => {
+    return {
+        default: vi.fn().mockImplementation(() => mockApiClient),
+    };
+});
+
+import createClient from "openapi-fetch";
+
+describe("Galaxy API Client", () => {
+    beforeEach(() => {
+        // Reset mock function calls before each test
+        vi.clearAllMocks();
+    });
+
+    it("creates a client with the default base URL", () => {
+        // Set up window.location.origin for testing
+        const originalLocation = window.location;
+        delete (window as any).location;
+        window.location = { ...originalLocation, origin: "https://test-galaxy.org" } as any;
+
+        const api = createGalaxyApi();
+
+        expect(createClient).toHaveBeenCalledWith({ baseUrl: "https://test-galaxy.org" });
+
+        // Restore window.location
+        window.location = originalLocation;
+    });
+
+    it("creates a client with a custom base URL", () => {
+        const customUrl = "https://usegalaxy.org";
+        const api = createGalaxyApi(customUrl);
+
+        expect(createClient).toHaveBeenCalledWith({ baseUrl: customUrl });
+    });
+
+    it("strips trailing slash from base URL", () => {
+        const customUrl = "https://usegalaxy.org/";
+        const expectedUrl = "https://usegalaxy.org";
+        const api = createGalaxyApi(customUrl);
+
+        expect(createClient).toHaveBeenCalledWith({ baseUrl: expectedUrl });
+    });
+
+    it("returns the configured client", () => {
+        const api = createGalaxyApi();
+
+        // Should have all the HTTP methods
+        expect(api).toEqual(mockApiClient);
+        expect(api).toHaveProperty("GET");
+        expect(api).toHaveProperty("POST");
+        expect(api).toHaveProperty("PUT");
+        expect(api).toHaveProperty("DELETE");
+        expect(api).toHaveProperty("PATCH");
+    });
+});

package/src/client.ts

@@ -0,0 +1,62 @@
+import createClient from "openapi-fetch";
+import { type GalaxyApiPaths } from "./api-types";
+
+/**
+ * Options for creating a Galaxy API client
+ */
+export interface GalaxyApiOptions {
+    /**
+     * The base URL of the Galaxy server (e.g., "https://usegalaxy.org")
+     * @default window.location.origin
+     */
+    baseUrl?: string;
+
+    /**
+     * API key for authentication
+     */
+    apiKey?: string;
+
+    /**
+     * Custom headers to include with each request
+     */
+    headers?: Record<string, string>;
+
+    /**
+     * Custom fetch options that will be passed to all requests
+     */
+    fetchOptions?: RequestInit;
+}
+
+/**
+ * Creates a Galaxy API client with the specified options
+ * @param options Configuration options for the Galaxy API client
+ * @returns The Galaxy API client
+ */
+export function createGalaxyApi(options: GalaxyApiOptions | string = {}) {
+    // Handle the case where baseUrl is passed as a string for backward compatibility
+    const opts = typeof options === "string" ? { baseUrl: options } : options;
+
+    // Default to window.location.origin if no baseUrl is provided
+    const baseUrl = opts.baseUrl || window.location.origin;
+    const normalizedBaseUrl = baseUrl.endsWith("/") ? baseUrl.slice(0, -1) : baseUrl;
+
+    // Build headers object
+    const headers: Record<string, string> = {
+        ...(opts.headers || {}),
+    };
+
+    // Add API key header if provided
+    if (opts.apiKey) {
+        headers["x-api-key"] = opts.apiKey;
+    }
+
+    // Create the client with all options
+    return createClient<GalaxyApiPaths>({
+        baseUrl: normalizedBaseUrl,
+        headers,
+        // Pass any custom fetchOptions directly to createClient
+        ...(opts.fetchOptions ? { fetchOptions: opts.fetchOptions } : {}),
+    });
+}
+
+export type GalaxyApiClient = ReturnType<typeof createGalaxyApi>;

package/src/dist/api-types.js

@@ -0,0 +1,46 @@
+"use strict";
+/**
+ * This file re-exports the types we want to use from the Galaxy API.
+ * It serves as a compatibility layer to avoid importing directly from the
+ * symlinked files, which would require all of Galaxy's dependencies.
+ */
+exports.__esModule = true;
+exports.isInaccessible =
+    exports.hasDetails =
+    exports.isDatasetElement =
+    exports.isCollectionElement =
+    exports.isDCE =
+    exports.isHDCA =
+    exports.isHDA =
+        void 0;
+// Utility functions
+function isHDA(entry) {
+    return entry !== undefined && "history_content_type" in entry && entry.history_content_type === "dataset";
+}
+exports.isHDA = isHDA;
+function isHDCA(entry) {
+    return (
+        entry !== undefined && "history_content_type" in entry && entry.history_content_type === "dataset_collection"
+    );
+}
+exports.isHDCA = isHDCA;
+function isDCE(item) {
+    return item && "element_type" in item;
+}
+exports.isDCE = isDCE;
+function isCollectionElement(element) {
+    return element.element_type === "dataset_collection";
+}
+exports.isCollectionElement = isCollectionElement;
+function isDatasetElement(element) {
+    return element.element_type === "hda";
+}
+exports.isDatasetElement = isDatasetElement;
+function hasDetails(entry) {
+    return "peek" in entry;
+}
+exports.hasDetails = hasDetails;
+function isInaccessible(entry) {
+    return "accessible" in entry && !entry.accessible;
+}
+exports.isInaccessible = isInaccessible;