@fnndsc/cumin 3.2.4

package/dist/filebrowser/chrisPipeline.js

@@ -0,0 +1,118 @@
+"use strict";
+/**
+ * @file ChRIS Pipeline Source File Operations
+ *
+ * This module provides functions for retrieving pipeline source files (YAML configuration files)
+ * from the ChRIS backend. Pipeline files are stored under /PIPELINES/<owner>/<filename>.
+ *
+ * @module
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.pipelineFile_getByPath = pipelineFile_getByPath;
+exports.pipelineFile_getTextByPath = pipelineFile_getTextByPath;
+const chrisConnection_js_1 = require("../connect/chrisConnection.js");
+const errorStack_js_1 = require("../error/errorStack.js");
+const result_js_1 = require("../utils/result.js");
+/**
+ * Downloads a pipeline source file by path and returns the raw binary content.
+ *
+ * Pipeline source files are typically YAML configuration files stored under /PIPELINES/<owner>/<filename>.
+ * The API returns fname as the full path like "PIPELINES/user/file.yml" (without leading slash).
+ *
+ * @param filePath - The full path to the pipeline file, e.g., /PIPELINES/user/pipeline.yml
+ * @returns A Result containing the file content as a Buffer, or an error.
+ *
+ * @example
+ * ```typescript
+ * const result = await pipelineFile_getByPath('/PIPELINES/user/config.yml');
+ * if (result.ok) {
+ *   const buffer: Buffer = result.value;
+ *   const yamlContent = buffer.toString('utf-8');
+ * }
+ * ```
+ */
+async function pipelineFile_getByPath(filePath) {
+    const client = await chrisConnection_js_1.chrisConnection.client_get();
+    if (!client) {
+        errorStack_js_1.errorStack.stack_push("error", "Not connected to ChRIS. Cannot fetch pipeline file.");
+        return (0, result_js_1.Err)();
+    }
+    // The API returns fname as the full path like "PIPELINES/sandip.samal/PHI_detection.yml"
+    // So we need to match against the full path minus the leading slash
+    const expectedFname = filePath.startsWith('/') ? filePath.substring(1) : filePath;
+    try {
+        // Filter server-side by fname; fall back to client-side filter on the returned items
+        // in case the backend does not support fname as a query param.
+        const pipelineSourceFileListResult = await client.getPipelineSourceFiles({ fname: expectedFname, limit: 1000 });
+        if (pipelineSourceFileListResult === null) {
+            errorStack_js_1.errorStack.stack_push("error", `Failed to retrieve pipeline source file list.`);
+            return (0, result_js_1.Err)();
+        }
+        const allItems = pipelineSourceFileListResult.getItems();
+        // Filter by full fname path (API returns full path like "PIPELINES/user/file.yml")
+        const matchingPipelineFiles = allItems.filter((item) => {
+            const itemData = item.data;
+            return itemData.fname === expectedFname;
+        });
+        if (matchingPipelineFiles.length === 0) {
+            errorStack_js_1.errorStack.stack_push("error", `Pipeline source file not found: ${filePath}`);
+            return (0, result_js_1.Err)();
+        }
+        const pipelineSourceFile = matchingPipelineFiles[0];
+        const blob = await pipelineSourceFile.getFileBlob();
+        if (!blob) {
+            errorStack_js_1.errorStack.stack_push("error", `Pipeline source file ${filePath} exists but returned no content/blob.`);
+            return (0, result_js_1.Err)();
+        }
+        // Convert blob to Buffer (handle different blob types)
+        let buffer;
+        if (typeof blob === "string") {
+            buffer = Buffer.from(blob);
+        }
+        else if (blob instanceof ArrayBuffer) {
+            buffer = Buffer.from(blob);
+        }
+        else if (blob instanceof Blob) {
+            const arrayBuffer = await blob.arrayBuffer();
+            buffer = Buffer.from(arrayBuffer);
+        }
+        else if (Buffer.isBuffer(blob)) {
+            buffer = blob;
+        }
+        else {
+            throw new Error(`Unexpected blob type for pipeline file: ${typeof blob}`);
+        }
+        return (0, result_js_1.Ok)(buffer);
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        errorStack_js_1.errorStack.stack_push("error", `Failed to fetch pipeline file for ${filePath}: ${msg}`);
+        return (0, result_js_1.Err)();
+    }
+}
+/**
+ * Downloads a pipeline source file and returns it as a UTF-8 string.
+ *
+ * This is a convenience wrapper around `pipelineFile_getByPath()` that converts
+ * the Buffer to a string. Suitable for YAML/text files.
+ *
+ * @param filePath - The full path to the pipeline file, e.g., /PIPELINES/user/pipeline.yml
+ * @returns A Result containing the file content as a string, or an error.
+ *
+ * @example
+ * ```typescript
+ * const result = await pipelineFile_getTextByPath('/PIPELINES/user/config.yml');
+ * if (result.ok) {
+ *   const yamlContent: string = result.value;
+ *   // Parse YAML content
+ * }
+ * ```
+ */
+async function pipelineFile_getTextByPath(filePath) {
+    const result = await pipelineFile_getByPath(filePath);
+    if (!result.ok) {
+        return (0, result_js_1.Err)();
+    }
+    return (0, result_js_1.Ok)(result.value.toString('utf-8'));
+}
+//# sourceMappingURL=chrisPipeline.js.map

package/dist/filebrowser/chrisPipeline.js.map

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package/dist/groups/chrisGroups.d.ts

@@ -0,0 +1,11 @@
+/**
+ * @file ChRIS Group resources.
+ * @module
+ */
+import { ChRISResourceGroup } from '../resources/chrisResourceGroup.js';
+/**
+ * Group handler for ChRIS user groups.
+ */
+export declare class ChRISGroupGroup extends ChRISResourceGroup {
+    constructor();
+}

package/dist/groups/chrisGroups.js

@@ -0,0 +1,18 @@
+"use strict";
+/**
+ * @file ChRIS Group resources.
+ * @module
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ChRISGroupGroup = void 0;
+const chrisResourceGroup_js_1 = require("../resources/chrisResourceGroup.js");
+/**
+ * Group handler for ChRIS user groups.
+ */
+class ChRISGroupGroup extends chrisResourceGroup_js_1.ChRISResourceGroup {
+    constructor() {
+        super('Groups', 'getGroups');
+    }
+}
+exports.ChRISGroupGroup = ChRISGroupGroup;
+//# sourceMappingURL=chrisGroups.js.map

package/dist/groups/chrisGroups.js.map

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -0,0 +1,68 @@
+#!/usr/bin/env node
+/**
+ * @file Cumin Package Main Entry Point.
+ *
+ * This file serves as the main entry point and export aggregator for the Cumin infrastructure
+ * library. It exports error stacks, config utilities, PACs handlers, connections, file browsers,
+ * and result Monads for downstream consumption by Salsa, Chili, and Chell.
+ *
+ * @module
+ */
+export * from "./";
+export * from "./error/errorStack";
+export * from "./config/config";
+export * from "./feeds/chrisFeed";
+export * from "./connect/chrisConnection";
+export * from "./context/chrisContext";
+export * from "./plugins/chrisPlugins";
+export * from "./plugins/chrisPluginMetaPlugins";
+export * from "./compute/computeResources";
+export * from "./pacs/chrisPACS";
+export * from "./resources/chrisResources";
+export * from "./resources/chrisResourceGroup";
+export * from "./resources/chrisObjContext";
+export * from "./resources/chrisEmbeddedResourceGroup";
+export * from "./filebrowser/chrisFileBrowser";
+export * from "./filebrowser/chrisFiles";
+export * from "./filebrowser/chrisPACS";
+export * from "./filebrowser/chrisPipeline";
+export * from "./io/chrisIO";
+export * from "./io/io";
+export * from "./io/node_io";
+export * from "./utils/keypair";
+export * from "./utils/searchable";
+export * from "./utils/result";
+export * from "./cache";
+export * from "./path/chrisPath";
+export * from "./pipelines/chrisPipeline";
+export * from "./users/chrisUsers";
+export * from "./tags/chrisTags";
+export * from "./groups/chrisGroups";
+export * from "./pluginmetas/chrisPluginMetas";
+export * from "./workflows/chrisWorkflows";
+/**
+ * Shape of a single node (file, directory, or link) in a ChRIS path listing.
+ */
+export interface ChrisPathNode {
+    path: string;
+    fname?: string;
+    fsize?: number;
+    id?: number;
+    isDir?: boolean;
+    isLink?: boolean;
+    linkTarget?: string;
+}
+/**
+ * Summary metadata describing a ChRIS plugin.
+ */
+export interface ChrisPluginSummary {
+    id?: number;
+    name?: string;
+}
+/**
+ * Gets the ChRIS version from the given URL.
+ *
+ * @param url - The URL of the ChRIS instance.
+ * @returns A Promise resolving to the version string.
+ */
+export declare function chrisVersion_get(url: string): Promise<string>;

package/dist/index.js

@@ -0,0 +1,86 @@
+#!/usr/bin/env node
+"use strict";
+/**
+ * @file Cumin Package Main Entry Point.
+ *
+ * This file serves as the main entry point and export aggregator for the Cumin infrastructure
+ * library. It exports error stacks, config utilities, PACs handlers, connections, file browsers,
+ * and result Monads for downstream consumption by Salsa, Chili, and Chell.
+ *
+ * @module
+ */
+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 });
+exports.chrisVersion_get = chrisVersion_get;
+__exportStar(require("./"), exports);
+__exportStar(require("./error/errorStack"), exports);
+__exportStar(require("./config/config"), exports);
+__exportStar(require("./feeds/chrisFeed"), exports);
+__exportStar(require("./connect/chrisConnection"), exports);
+__exportStar(require("./context/chrisContext"), exports);
+__exportStar(require("./plugins/chrisPlugins"), exports);
+__exportStar(require("./plugins/chrisPluginMetaPlugins"), exports);
+__exportStar(require("./compute/computeResources"), exports);
+__exportStar(require("./pacs/chrisPACS"), exports);
+__exportStar(require("./resources/chrisResources"), exports);
+__exportStar(require("./resources/chrisResourceGroup"), exports);
+__exportStar(require("./resources/chrisObjContext"), exports);
+__exportStar(require("./resources/chrisEmbeddedResourceGroup"), exports);
+__exportStar(require("./filebrowser/chrisFileBrowser"), exports);
+__exportStar(require("./filebrowser/chrisFiles"), exports);
+__exportStar(require("./filebrowser/chrisPACS"), exports);
+__exportStar(require("./filebrowser/chrisPipeline"), exports);
+__exportStar(require("./io/chrisIO"), exports);
+__exportStar(require("./io/io"), exports);
+__exportStar(require("./io/node_io"), exports);
+__exportStar(require("./utils/keypair"), exports);
+__exportStar(require("./utils/searchable"), exports);
+__exportStar(require("./utils/result"), exports);
+__exportStar(require("./cache"), exports);
+__exportStar(require("./path/chrisPath"), exports);
+__exportStar(require("./pipelines/chrisPipeline"), exports);
+__exportStar(require("./users/chrisUsers"), exports);
+__exportStar(require("./tags/chrisTags"), exports);
+__exportStar(require("./groups/chrisGroups"), exports);
+__exportStar(require("./pluginmetas/chrisPluginMetas"), exports);
+__exportStar(require("./workflows/chrisWorkflows"), exports);
+/**
+ * Gets the ChRIS version from the given URL.
+ *
+ * @param url - The URL of the ChRIS instance.
+ * @returns A Promise resolving to the version string.
+ */
+async function chrisVersion_get(url) {
+    const version = "1.0.0";
+    // const client = Client.getClient(url);
+    // const version = await client.getVersion();
+    return version;
+}
+/**
+ * Main entry point for the module when run directly.
+ */
+async function main() {
+    console.log("In main...");
+}
+// Only run the main function if this file is being run directly
+// Use CommonJS check for main module
+if (require.main === module) {
+    main().catch((error) => {
+        console.error("An error occurred:", error);
+        process.exit(1);
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

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package/dist/io/browser_io.d.ts

@@ -0,0 +1,97 @@
+/**
+ * @file Browser localStorage implementation of IStorageProvider.
+ *
+ * @module
+ */
+import { IStorageProvider } from "./io.js";
+/**
+ * An in-memory, non-persisting storage provider suitable for browser environments
+ * where persistence is managed by the host application (GUI).
+ *
+ * This provider satisfies the `IStorageProvider` interface but does not
+ * store any data persistently. All data is held in-memory and reset
+ * when the application (e.g., browser tab) is refreshed.
+ *
+ * It effectively acts as a dummy or passthrough for storage operations,
+ * relying on the external environment to provide necessary context.
+ */
+export declare class BrowserStorageProvider implements IStorageProvider {
+    private store;
+    constructor();
+    /**
+     * Reads data associated with a path from the in-memory store.
+     *
+     * @param path - The virtual path of the data.
+     * @returns A Promise resolving to the data string or null if not found.
+     */
+    read(path: string): Promise<string | null>;
+    /**
+     * Reads binary data associated with a path.
+     *
+     * @param path - The virtual path.
+     * @returns A Promise resolving to ArrayBuffer or null.
+     */
+    readBinary(path: string): Promise<ArrayBuffer | null>;
+    /**
+     * Writes data to the in-memory store associated with a path.
+     *
+     * @param path - The virtual path to write to.
+     * @param data - The string data to write.
+     * @returns A Promise that resolves when the operation is complete.
+     */
+    write(path: string, data: string): Promise<void>;
+    /**
+     * Removes data associated with a path from the in-memory store.
+     *
+     * @param path - The virtual path to remove.
+     * @returns A Promise that resolves when the operation is complete.
+     */
+    remove(path: string): Promise<void>;
+    /**
+     * Creates a "directory" in the in-memory store.
+     * For this non-persisting provider, this is a no-op as directories are not physically managed.
+     *
+     * @param path - The virtual path of the directory.
+     * @param options - Optional recursive creation (ignored).
+     * @returns A Promise that resolves when the operation is complete.
+     */
+    mkdir(path: string, options?: {
+        recursive?: boolean;
+    }): Promise<void>;
+    /**
+     * Checks if a path exists in the in-memory store.
+     *
+     * @param path - The virtual path to check.
+     * @returns A Promise resolving to true if the path exists, false otherwise.
+     */
+    exists(path: string): Promise<boolean>;
+    /**
+     * Reads the contents of a "directory" in the in-memory store.
+     * For this non-persisting provider, it simulates by returning keys that start with the path prefix.
+     * This is a simplified simulation and does not represent a true filesystem.
+     *
+     * @param path - The virtual path of the directory.
+     * @returns A Promise resolving to an array of file/directory names within the path.
+     */
+    readdir(path: string): Promise<string[]>;
+    /**
+     * Checks if a path represents a "directory" in the in-memory store.
+     * For this non-persisting provider, it checks if any keys start with the path as a prefix.
+     *
+     * @param path - The virtual path to check.
+     * @returns A Promise resolving to true if it appears to be a directory, false otherwise.
+     */
+    isDirectory(path: string): Promise<boolean>;
+    /**
+     * Joins path segments.
+     * @param paths - The path segments.
+     * @returns Joined path.
+     */
+    join(...paths: string[]): string;
+    /**
+     * Returns the last portion of a path.
+     * @param path - The path to extract the basename from.
+     * @returns The basename.
+     */
+    basename(path: string): string;
+}

package/dist/io/browser_io.js

@@ -0,0 +1,149 @@
+"use strict";
+/**
+ * @file Browser localStorage implementation of IStorageProvider.
+ *
+ * @module
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.BrowserStorageProvider = void 0;
+/**
+ * An in-memory, non-persisting storage provider suitable for browser environments
+ * where persistence is managed by the host application (GUI).
+ *
+ * This provider satisfies the `IStorageProvider` interface but does not
+ * store any data persistently. All data is held in-memory and reset
+ * when the application (e.g., browser tab) is refreshed.
+ *
+ * It effectively acts as a dummy or passthrough for storage operations,
+ * relying on the external environment to provide necessary context.
+ */
+class BrowserStorageProvider {
+    constructor() {
+        // A simple in-memory store for demonstration/testing purposes
+        this.store = new Map();
+        console.log("BrowserStorageProvider initialized (in-memory, non-persisting).");
+    }
+    /**
+     * Reads data associated with a path from the in-memory store.
+     *
+     * @param path - The virtual path of the data.
+     * @returns A Promise resolving to the data string or null if not found.
+     */
+    async read(path) {
+        const data = this.store.get(path);
+        return data === undefined ? null : data;
+    }
+    /**
+     * Reads binary data associated with a path.
+     *
+     * @param path - The virtual path.
+     * @returns A Promise resolving to ArrayBuffer or null.
+     */
+    async readBinary(path) {
+        console.warn("[BrowserStorageProvider] readBinary not implemented for in-memory store.");
+        return null;
+    }
+    /**
+     * Writes data to the in-memory store associated with a path.
+     *
+     * @param path - The virtual path to write to.
+     * @param data - The string data to write.
+     * @returns A Promise that resolves when the operation is complete.
+     */
+    async write(path, data) {
+        this.store.set(path, data);
+        console.debug(`[BrowserStorageProvider] Wrote to: ${path}`);
+    }
+    /**
+     * Removes data associated with a path from the in-memory store.
+     *
+     * @param path - The virtual path to remove.
+     * @returns A Promise that resolves when the operation is complete.
+     */
+    async remove(path) {
+        this.store.delete(path);
+        console.debug(`[BrowserStorageProvider] Removed: ${path}`);
+    }
+    /**
+     * Creates a "directory" in the in-memory store.
+     * For this non-persisting provider, this is a no-op as directories are not physically managed.
+     *
+     * @param path - The virtual path of the directory.
+     * @param options - Optional recursive creation (ignored).
+     * @returns A Promise that resolves when the operation is complete.
+     */
+    async mkdir(path, options) {
+        // No-op for a non-persisting in-memory store
+        console.debug(`[BrowserStorageProvider] mkdir (no-op): ${path}`);
+    }
+    /**
+     * Checks if a path exists in the in-memory store.
+     *
+     * @param path - The virtual path to check.
+     * @returns A Promise resolving to true if the path exists, false otherwise.
+     */
+    async exists(path) {
+        return this.store.has(path);
+    }
+    /**
+     * Reads the contents of a "directory" in the in-memory store.
+     * For this non-persisting provider, it simulates by returning keys that start with the path prefix.
+     * This is a simplified simulation and does not represent a true filesystem.
+     *
+     * @param path - The virtual path of the directory.
+     * @returns A Promise resolving to an array of file/directory names within the path.
+     */
+    async readdir(path) {
+        const prefixedPath = path.endsWith('/') ? path : `${path}/`;
+        const entries = [];
+        for (const key of this.store.keys()) {
+            if (key.startsWith(prefixedPath)) {
+                let relativePath = key.substring(prefixedPath.length);
+                // Only add the immediate child part
+                const firstSlashIndex = relativePath.indexOf('/');
+                if (firstSlashIndex !== -1) {
+                    relativePath = relativePath.substring(0, firstSlashIndex);
+                }
+                if (!entries.includes(relativePath)) {
+                    entries.push(relativePath);
+                }
+            }
+        }
+        return entries;
+    }
+    /**
+     * Checks if a path represents a "directory" in the in-memory store.
+     * For this non-persisting provider, it checks if any keys start with the path as a prefix.
+     *
+     * @param path - The virtual path to check.
+     * @returns A Promise resolving to true if it appears to be a directory, false otherwise.
+     */
+    async isDirectory(path) {
+        const prefixedPath = path.endsWith('/') ? path : `${path}/`;
+        for (const key of this.store.keys()) {
+            if (key.startsWith(prefixedPath)) {
+                return true;
+            }
+        }
+        return false;
+    }
+    /**
+     * Joins path segments.
+     * @param paths - The path segments.
+     * @returns Joined path.
+     */
+    join(...paths) {
+        return paths.join('/');
+    }
+    /**
+     * Returns the last portion of a path.
+     * @param path - The path to extract the basename from.
+     * @returns The basename.
+     */
+    basename(path) {
+        const parts = path.split('/');
+        return parts[parts.length - 1] || '';
+    }
+}
+exports.BrowserStorageProvider = BrowserStorageProvider;
+//# sourceMappingURL=browser_io.js.map

package/dist/io/browser_io.js.map

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