@fnndsc/cumin 3.2.4

package/dist/filebrowser/chrisFileBrowser.d.ts

@@ -0,0 +1,77 @@
+/**
+ * @file ChRIS File Browser
+ *
+ * This module provides the ChRISFileBrowser class for browsing files, directories, and links
+ * within the ChRIS filesystem.
+ *
+ * @module
+ */
+import Client from "@fnndsc/chrisapi";
+import { FileBrowserFolder } from "@fnndsc/chrisapi";
+import { ChRISResource } from "../resources/chrisResources.js";
+/**
+ * Interface for boolean operations with a descriptive message.
+ */
+export interface BoolString {
+    status: boolean;
+    message: string;
+}
+/**
+ * Enum defining the types of ChRIS browsers.
+ */
+export declare enum BrowserType {
+    Files = "Files",
+    Links = "Links",
+    Dirs = "Dirs"
+}
+/**
+ * Class for browsing ChRIS filesystem objects.
+ */
+export declare class ChRISFileBrowser {
+    private _client;
+    private _chrisFileBrowserFolder;
+    private _resource;
+    private _bindOp;
+    constructor(variant: BrowserType | undefined, chrisObj: FileBrowserFolder);
+    /**
+     * Retrieves the ChRIS client instance asynchronously.
+     * @returns A Promise resolving to the Client instance or null.
+     */
+    client_get(): Promise<Client | null>;
+    /**
+     * Gets the status of the binding operation.
+     * @returns The binding operation status.
+     */
+    get bindOp_get(): BoolString;
+    /**
+     * Binds the `getFiles` method to the ChRIS resource.
+     * @returns The status of the binding operation.
+     */
+    files_bind(): BoolString;
+    /**
+     * Binds the `getLinkFiles` method to the ChRIS resource.
+     * @returns The status of the binding operation.
+     */
+    links_bind(): BoolString;
+    /**
+     * Binds the `getChildren` (dirs) method to the ChRIS resource.
+     * @returns The status of the binding operation.
+     */
+    dirs_bind(): BoolString;
+    /**
+     * Binds the appropriate method based on the browser variant.
+     * @param variant - The browser type (Files, Links, Dirs).
+     * @returns The status of the binding operation.
+     */
+    method_bind(variant: BrowserType): BoolString;
+    /**
+     * Gets the associated ChRIS resource.
+     * @returns The ChRISResource instance or null.
+     */
+    get resource_get(): ChRISResource | null;
+    /**
+     * Gets the underlying FileBrowserFolder object.
+     * @returns The FileBrowserFolder instance or null.
+     */
+    get fileBrowserFolder_get(): FileBrowserFolder | null;
+}

package/dist/filebrowser/chrisFileBrowser.js

@@ -0,0 +1,134 @@
+"use strict";
+/**
+ * @file ChRIS File Browser
+ *
+ * This module provides the ChRISFileBrowser class for browsing files, directories, and links
+ * within the ChRIS filesystem.
+ *
+ * @module
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ChRISFileBrowser = exports.BrowserType = void 0;
+const chrisConnection_js_1 = require("../connect/chrisConnection.js");
+const chrisResources_js_1 = require("../resources/chrisResources.js");
+/**
+ * Enum defining the types of ChRIS browsers.
+ */
+var BrowserType;
+(function (BrowserType) {
+    BrowserType["Files"] = "Files";
+    BrowserType["Links"] = "Links";
+    BrowserType["Dirs"] = "Dirs";
+})(BrowserType || (exports.BrowserType = BrowserType = {}));
+;
+/**
+ * Class for browsing ChRIS filesystem objects.
+ */
+class ChRISFileBrowser {
+    constructor(variant = BrowserType.Files, chrisObj) {
+        this._client = null;
+        this._chrisFileBrowserFolder = null;
+        this._resource = null;
+        this._bindOp = { "status": false, "message": "" };
+        this._chrisFileBrowserFolder = chrisObj;
+        this._resource = new chrisResources_js_1.ChRISResource();
+        this._bindOp = this.method_bind(variant);
+    }
+    /**
+     * Retrieves the ChRIS client instance asynchronously.
+     * @returns A Promise resolving to the Client instance or null.
+     */
+    async client_get() {
+        if (!this._client) {
+            this._client = await chrisConnection_js_1.chrisConnection.client_get();
+        }
+        return this._client;
+    }
+    /**
+     * Gets the status of the binding operation.
+     * @returns The binding operation status.
+     */
+    get bindOp_get() {
+        return this._bindOp;
+    }
+    /**
+     * Binds the `getFiles` method to the ChRIS resource.
+     * @returns The status of the binding operation.
+     */
+    files_bind() {
+        let bindOp = { "status": false, "message": "getFiles not bound" };
+        if (this._resource && this._chrisFileBrowserFolder) {
+            this._resource.binding_applyGet(this._chrisFileBrowserFolder, this._chrisFileBrowserFolder.getFiles, BrowserType.Files);
+            bindOp.status = true;
+            bindOp.message = "ChRISFileBrowser bound to fileBrowserFolder.getFiles";
+        }
+        return bindOp;
+    }
+    /**
+     * Binds the `getLinkFiles` method to the ChRIS resource.
+     * @returns The status of the binding operation.
+     */
+    links_bind() {
+        let bindOp = { "status": false, "message": "getLinks not bound" };
+        if (this._resource && this._chrisFileBrowserFolder) {
+            this._resource.binding_applyGet(this._chrisFileBrowserFolder, this._chrisFileBrowserFolder.getLinkFiles, BrowserType.Links);
+            bindOp.status = true;
+            bindOp.message = "ChRISFileBrowser bound to fileBrowserFolder.getLinkFiles";
+        }
+        return bindOp;
+    }
+    /**
+     * Binds the `getChildren` (dirs) method to the ChRIS resource.
+     * @returns The status of the binding operation.
+     */
+    dirs_bind() {
+        let bindOp = { "status": false, "message": "getDirs not bound" };
+        if (this._resource && this._chrisFileBrowserFolder) {
+            this._resource.binding_applyGet(this._chrisFileBrowserFolder, this._chrisFileBrowserFolder.getChildren, BrowserType.Dirs);
+            bindOp.status = true;
+            bindOp.message = "ChRISFileBrowser bound to fileBrowserFolder.getChildren";
+        }
+        return bindOp;
+    }
+    /**
+     * Binds the appropriate method based on the browser variant.
+     * @param variant - The browser type (Files, Links, Dirs).
+     * @returns The status of the binding operation.
+     */
+    method_bind(variant) {
+        let bindOp = { "status": false, "message": "" };
+        if (!this._resource || !this._chrisFileBrowserFolder) {
+            bindOp.message = "ChRISFileBrowesr resource or fileBrowserFolder is null";
+            return bindOp;
+        }
+        bindOp.status = true;
+        switch (variant) {
+            case BrowserType.Files:
+                bindOp = this.files_bind();
+                break;
+            case BrowserType.Links:
+                bindOp = this.links_bind();
+                break;
+            case BrowserType.Dirs:
+                bindOp = this.dirs_bind();
+                break;
+        }
+        return bindOp;
+    }
+    /**
+     * Gets the associated ChRIS resource.
+     * @returns The ChRISResource instance or null.
+     */
+    get resource_get() {
+        return this._resource;
+    }
+    /**
+     * Gets the underlying FileBrowserFolder object.
+     * @returns The FileBrowserFolder instance or null.
+     */
+    get fileBrowserFolder_get() {
+        return this._chrisFileBrowserFolder;
+    }
+}
+exports.ChRISFileBrowser = ChRISFileBrowser;
+//# sourceMappingURL=chrisFileBrowser.js.map

package/dist/filebrowser/chrisFileBrowser.js.map

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

@@ -0,0 +1,67 @@
+/**
+ * @file ChRIS Inode Management
+ *
+ * This module provides the ChRISinode class for managing inodes (files, directories, links)
+ * within the ChRIS filesystem. It acts as a facade for different browser types.
+ *
+ * @module
+ */
+import { ChRISFileBrowser, BrowserType } from "./chrisFileBrowser.js";
+import { FileBrowserFolder } from "@fnndsc/chrisapi";
+type ChRISBrowser = ChRISFileBrowser | null;
+/**
+ * Class representing an inode in the ChRIS filesystem.
+ */
+export declare class ChRISinode {
+    private _client;
+    private _fileBrowserFolderObj;
+    private _path;
+    private _browsers;
+    private constructor();
+    /**
+     * Factory method to create a new ChRISinode instance.
+     * @param path - The path to the inode.
+     * @returns A Promise resolving to a new ChRISinode instance.
+     */
+    static inode_create(path?: string): Promise<ChRISinode>;
+    /**
+     * Gets the file browser instance for this inode.
+     * @returns The file browser or null.
+     */
+    get fileBrowser_get(): ChRISFileBrowser | null;
+    /**
+     * Gets the link browser instance for this inode.
+     * @returns The link browser or null.
+     */
+    get linkBrowser_get(): ChRISFileBrowser | null;
+    /**
+     * Gets the directory browser instance for this inode.
+     * @returns The directory browser or null.
+     */
+    get dirBrowser_get(): ChRISFileBrowser | null;
+    /**
+     * Gets the path of this inode.
+     * @returns The path string.
+     */
+    get path_get(): string;
+    /**
+     * Gets the underlying FileBrowserFolder object.
+     * @returns The FileBrowserFolder instance or null.
+     */
+    get fileBrowserFolder_get(): FileBrowserFolder | null;
+    /**
+     * Retrieves a specific browser type for this inode.
+     * @param type - The type of browser to retrieve.
+     * @returns The requested browser or null.
+     */
+    browser_get(type: BrowserType): ChRISBrowser;
+    /**
+     * Initializes the inode and binds browsers.
+     */
+    private initAndBind;
+}
+/**
+ * @deprecated Use ChRISinode.inode_create instead.
+ */
+export declare function ChRISinode_create(path?: string): Promise<ChRISinode | null>;
+export {};

package/dist/filebrowser/chrisFiles.js

@@ -0,0 +1,130 @@
+"use strict";
+/**
+ * @file ChRIS Inode Management
+ *
+ * This module provides the ChRISinode class for managing inodes (files, directories, links)
+ * within the ChRIS filesystem. It acts as a facade for different browser types.
+ *
+ * @module
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ChRISinode = void 0;
+exports.ChRISinode_create = ChRISinode_create;
+const chrisFileBrowser_js_1 = require("./chrisFileBrowser.js");
+const chrisConnection_js_1 = require("../connect/chrisConnection.js");
+class ChRISConnectionError extends Error {
+    constructor(message) {
+        super(message);
+        this.name = "ChRISConnectionError";
+    }
+}
+class ChRISInitializationError extends Error {
+    constructor(message) {
+        super(message);
+        this.name = "ChRISInitializationError";
+    }
+}
+/**
+ * Class representing an inode in the ChRIS filesystem.
+ */
+class ChRISinode {
+    constructor(path = "") {
+        this._client = null;
+        this._fileBrowserFolderObj = null;
+        this._browsers = new Map();
+        this._path = path;
+    }
+    /**
+     * Factory method to create a new ChRISinode instance.
+     * @param path - The path to the inode.
+     * @returns A Promise resolving to a new ChRISinode instance.
+     */
+    static async inode_create(path = "") {
+        const instance = new ChRISinode(path);
+        await instance.initAndBind();
+        return instance;
+    }
+    /**
+     * Gets the file browser instance for this inode.
+     * @returns The file browser or null.
+     */
+    get fileBrowser_get() {
+        return this.browser_get(chrisFileBrowser_js_1.BrowserType.Files);
+    }
+    /**
+     * Gets the link browser instance for this inode.
+     * @returns The link browser or null.
+     */
+    get linkBrowser_get() {
+        return this.browser_get(chrisFileBrowser_js_1.BrowserType.Links);
+    }
+    /**
+     * Gets the directory browser instance for this inode.
+     * @returns The directory browser or null.
+     */
+    get dirBrowser_get() {
+        return this.browser_get(chrisFileBrowser_js_1.BrowserType.Dirs);
+    }
+    /**
+     * Gets the path of this inode.
+     * @returns The path string.
+     */
+    get path_get() {
+        return this._path;
+    }
+    /**
+     * Gets the underlying FileBrowserFolder object.
+     * @returns The FileBrowserFolder instance or null.
+     */
+    get fileBrowserFolder_get() {
+        return this._fileBrowserFolderObj;
+    }
+    /**
+     * Retrieves a specific browser type for this inode.
+     * @param type - The type of browser to retrieve.
+     * @returns The requested browser or null.
+     */
+    browser_get(type) {
+        return this._browsers.get(type) ?? null;
+    }
+    /**
+     * Initializes the inode and binds browsers.
+     */
+    async initAndBind() {
+        this._client = await chrisConnection_js_1.chrisConnection.client_get();
+        if (!this._client) {
+            throw new ChRISConnectionError("Could not access ChRIS. Have you connected with the 'connect' command?");
+        }
+        try {
+            this._fileBrowserFolderObj = await this._client.getFileBrowserFolderByPath(this._path);
+        }
+        catch (error) {
+            throw new ChRISInitializationError('Failed to get FileBrowserFolder: ' + (error instanceof Error ? error.message : String(error)));
+        }
+        if (!this._fileBrowserFolderObj) {
+            throw new ChRISInitializationError("Failed to initialize FileBrowserFolder");
+        }
+        this._browsers.set(chrisFileBrowser_js_1.BrowserType.Files, new chrisFileBrowser_js_1.ChRISFileBrowser(chrisFileBrowser_js_1.BrowserType.Files, this._fileBrowserFolderObj));
+        this._browsers.set(chrisFileBrowser_js_1.BrowserType.Links, new chrisFileBrowser_js_1.ChRISFileBrowser(chrisFileBrowser_js_1.BrowserType.Links, this._fileBrowserFolderObj));
+        this._browsers.set(chrisFileBrowser_js_1.BrowserType.Dirs, new chrisFileBrowser_js_1.ChRISFileBrowser(chrisFileBrowser_js_1.BrowserType.Dirs, this._fileBrowserFolderObj));
+        for (const [_, browser] of this._browsers) {
+            if (browser && !browser.bindOp_get.status) {
+                throw new ChRISInitializationError(`Failed to bind browser: ${browser.bindOp_get.message}`);
+            }
+        }
+    }
+}
+exports.ChRISinode = ChRISinode;
+/**
+ * @deprecated Use ChRISinode.inode_create instead.
+ */
+async function ChRISinode_create(path) {
+    try {
+        return await ChRISinode.inode_create(path);
+    }
+    catch (error) {
+        console.error("Failed to create ChRISinode:", error);
+        return null;
+    }
+}
+//# sourceMappingURL=chrisFiles.js.map

package/dist/filebrowser/chrisFiles.js.map

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

@@ -0,0 +1,43 @@
+/**
+ * @file ChRIS PACS File Operations
+ *
+ * This module provides functions for retrieving PACS files (DICOM medical imaging files)
+ * from the ChRIS backend. PACS files use a specialized API endpoint that differs from
+ * regular file downloads.
+ *
+ * @module
+ */
+import { Result } from "../utils/result.js";
+/**
+ * Downloads a PACS file (DICOM) by file ID and returns the raw binary content.
+ *
+ * PACS files must be downloaded using the PACSFile API instead of regular
+ * file download endpoints. This function handles binary data correctly,
+ * preserving DICOM file integrity.
+ *
+ * @param fileId - The numeric ID of the PACS file in ChRIS.
+ * @returns A Result containing the file content as a Buffer, or an error.
+ *
+ * @example
+ * ```typescript
+ * const result = await pacsFile_getBlob(12345);
+ * if (result.ok) {
+ *   const buffer: Buffer = result.value;
+ *   // Process DICOM data
+ * }
+ * ```
+ */
+export declare function pacsFile_getBlob(fileId: number): Promise<Result<Buffer>>;
+/**
+ * Downloads a PACS file and returns it as a UTF-8 string.
+ *
+ * **WARNING:** This function converts binary DICOM data to a UTF-8 string,
+ * which may corrupt the file if it contains non-text binary data.
+ * Use `pacsFile_getBlob()` instead for DICOM files to preserve data integrity.
+ *
+ * This function is provided for legacy compatibility only.
+ *
+ * @param fileId - The numeric ID of the PACS file in ChRIS.
+ * @returns A Result containing the file content as a string, or an error.
+ */
+export declare function pacsFile_getText(fileId: number): Promise<Result<string>>;

package/dist/filebrowser/chrisPACS.js

@@ -0,0 +1,103 @@
+"use strict";
+/**
+ * @file ChRIS PACS File Operations
+ *
+ * This module provides functions for retrieving PACS files (DICOM medical imaging files)
+ * from the ChRIS backend. PACS files use a specialized API endpoint that differs from
+ * regular file downloads.
+ *
+ * @module
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.pacsFile_getBlob = pacsFile_getBlob;
+exports.pacsFile_getText = pacsFile_getText;
+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 PACS file (DICOM) by file ID and returns the raw binary content.
+ *
+ * PACS files must be downloaded using the PACSFile API instead of regular
+ * file download endpoints. This function handles binary data correctly,
+ * preserving DICOM file integrity.
+ *
+ * @param fileId - The numeric ID of the PACS file in ChRIS.
+ * @returns A Result containing the file content as a Buffer, or an error.
+ *
+ * @example
+ * ```typescript
+ * const result = await pacsFile_getBlob(12345);
+ * if (result.ok) {
+ *   const buffer: Buffer = result.value;
+ *   // Process DICOM data
+ * }
+ * ```
+ */
+async function pacsFile_getBlob(fileId) {
+    const client = await chrisConnection_js_1.chrisConnection.client_get();
+    if (!client) {
+        errorStack_js_1.errorStack.stack_push("error", "Not connected to ChRIS. Cannot fetch PACS file.");
+        return (0, result_js_1.Err)();
+    }
+    try {
+        const pacsFile = await client.getPACSFile(fileId);
+        if (!pacsFile) {
+            errorStack_js_1.errorStack.stack_push("error", `Could not retrieve PACSFile resource for ID ${fileId}`);
+            return (0, result_js_1.Err)();
+        }
+        // Download the file blob using the PACS-specific method
+        const blob = await pacsFile.getFileBlob();
+        if (!blob) {
+            errorStack_js_1.errorStack.stack_push("error", `PACS file ID ${fileId} exists but returned no content/blob.`);
+            return (0, result_js_1.Err)();
+        }
+        // Convert blob to Buffer (handle different blob types)
+        // Note: In Node.js, chrisapi may return string/ArrayBuffer/Blob depending on axios config
+        let buffer;
+        if (typeof blob === "string") {
+            // Use 'binary' encoding to preserve binary data integrity
+            // This handles the case where axios returns a string in Node.js
+            buffer = Buffer.from(blob, 'binary');
+        }
+        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 PACS 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 PACS file for ID ${fileId}: ${msg}`);
+        return (0, result_js_1.Err)();
+    }
+}
+/**
+ * Downloads a PACS file and returns it as a UTF-8 string.
+ *
+ * **WARNING:** This function converts binary DICOM data to a UTF-8 string,
+ * which may corrupt the file if it contains non-text binary data.
+ * Use `pacsFile_getBlob()` instead for DICOM files to preserve data integrity.
+ *
+ * This function is provided for legacy compatibility only.
+ *
+ * @param fileId - The numeric ID of the PACS file in ChRIS.
+ * @returns A Result containing the file content as a string, or an error.
+ */
+async function pacsFile_getText(fileId) {
+    const result = await pacsFile_getBlob(fileId);
+    if (!result.ok) {
+        return (0, result_js_1.Err)();
+    }
+    // WARNING: This may corrupt binary DICOM data
+    return (0, result_js_1.Ok)(result.value.toString('utf-8'));
+}
+//# sourceMappingURL=chrisPACS.js.map

package/dist/filebrowser/chrisPACS.js.map

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

@@ -0,0 +1,47 @@
+/**
+ * @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
+ */
+import { Result } from "../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');
+ * }
+ * ```
+ */
+export declare function pipelineFile_getByPath(filePath: string): Promise<Result<Buffer>>;
+/**
+ * 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
+ * }
+ * ```
+ */
+export declare function pipelineFile_getTextByPath(filePath: string): Promise<Result<string>>;