@fnndsc/salsa 3.2.4

package/dist/files/index.js

@@ -0,0 +1,562 @@
+"use strict";
+/**
+ * @file File group resolution and content dispatch across file source types.
+ *
+ * @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 __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.files_listRecursive = files_listRecursive;
+exports.files_copyRecursively = files_copyRecursively;
+exports.files_create = files_create;
+exports.files_touch = files_touch;
+exports.files_copy = files_copy;
+exports.files_move = files_move;
+exports.files_uploadPath = files_uploadPath;
+exports.files_mkdir = files_mkdir;
+exports.files_getGroup = files_getGroup;
+exports.files_list = files_list;
+exports.files_listAll = files_listAll;
+exports.fileFields_get = fileFields_get;
+exports.files_delete = files_delete;
+exports.files_getSingle = files_getSingle;
+exports.files_share = files_share;
+exports.fileContent_get = fileContent_get;
+exports.fileContent_getBinary = fileContent_getBinary;
+exports.fileContent_getBinaryStream = fileContent_getBinaryStream;
+const path = __importStar(require("path"));
+const cumin_1 = require("@fnndsc/cumin");
+const pipeline_content_1 = require("./pipeline_content");
+const regular_content_1 = require("./regular_content");
+const pacs_content_1 = require("./pacs_content");
+const dispatcher_js_1 = require("../vfs/dispatcher.js");
+/**
+ * Recursively lists all files and directories under a given ChRIS path.
+ *
+ * @param rootPath - The starting directory path.
+ * @returns A Promise resolving to an array of FsItem objects.
+ */
+async function files_listRecursive(rootPath) {
+    let items = [];
+    // 1. List files in current directory
+    const filesGroup = await files_getGroup('files', rootPath);
+    if (filesGroup) {
+        const fileResults = await filesGroup.asset.resources_getAll();
+        if (fileResults && fileResults.tableData) {
+            fileResults.tableData.forEach((f) => {
+                items.push({
+                    path: f['fname'] || '', // fname is the full path
+                    type: 'file',
+                    size: f['fsize'] || 0
+                });
+            });
+        }
+    }
+    // 2. List subdirectories
+    const dirsGroup = await files_getGroup('dirs', rootPath);
+    if (dirsGroup) {
+        const dirResults = await dirsGroup.asset.resources_getAll();
+        if (dirResults && dirResults.tableData) {
+            for (const d of dirResults.tableData) {
+                const dirPath = d.path;
+                items.push({ path: dirPath, type: 'dir' });
+                // Recurse
+                const subItems = await files_listRecursive(dirPath);
+                items = items.concat(subItems);
+            }
+        }
+    }
+    return items;
+}
+/**
+ * Recursively copies a directory from source to destination within ChRIS.
+ *
+ * @param srcPath - The source directory path.
+ * @param destPath - The destination directory path (the parent + new dir name).
+ * @returns A Promise resolving to true on success, false on failure.
+ */
+async function files_copyRecursively(srcPath, destPath) {
+    try {
+        // Ensure destination directory exists (mkdir -p behavior ideally, but files_mkdir is shallow?)
+        // Actually files_mkdir assumes parent exists.
+        // For a copy, we create the target root first.
+        await files_mkdir(destPath);
+        const items = await files_listRecursive(srcPath);
+        let successCount = 0;
+        let failCount = 0;
+        for (const item of items) {
+            // Normalize item.path to ensure it has a leading slash
+            const normalizedItemPath = item.path.startsWith('/') ? item.path : '/' + item.path;
+            const relativePath = normalizedItemPath.substring(srcPath.length).replace(/^\//, '');
+            const targetPath = path.posix.join(destPath, relativePath); // Use posix for ChRIS paths
+            if (item.type === 'dir') {
+                console.log(`  Creating directory: ${targetPath}`);
+                const created = await files_mkdir(targetPath);
+                if (!created) {
+                    console.warn(`  Warning: Failed to create directory ${targetPath}`);
+                    failCount++;
+                }
+                else {
+                    successCount++;
+                }
+            }
+            else if (item.type === 'file') {
+                console.log(`  Copying file: ${path.posix.basename(normalizedItemPath)}`);
+                const copied = await files_copy(normalizedItemPath, targetPath);
+                if (!copied) {
+                    console.warn(`  Warning: Failed to copy file ${normalizedItemPath}`);
+                    failCount++;
+                    // Continue trying to copy other files instead of aborting
+                }
+                else {
+                    successCount++;
+                }
+            }
+        }
+        console.log(`Copied ${successCount} items, ${failCount} failed`);
+        return failCount === 0;
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        cumin_1.errorStack.stack_push("error", `Recursive copy failed: ${msg}`);
+        return false;
+    }
+}
+/**
+ * Resolves a file ID from a ChRIS path.
+ *
+ * @param srcPath - The absolute ChRIS file path.
+ * @returns Result containing the file ID or Err on failure.
+ */
+async function fileId_resolve(srcPath) {
+    const srcDir = path.posix.dirname(srcPath);
+    const srcName = path.posix.basename(srcPath);
+    const group = await files_getGroup('files', srcDir);
+    if (!group) {
+        cumin_1.errorStack.stack_push("error", `Could not access source directory: ${srcDir}`);
+        return (0, cumin_1.Err)();
+    }
+    const results = await group.asset.resources_getAll();
+    let fileId;
+    if (results && results.tableData) {
+        const match = results.tableData.find((f) => {
+            const fname = f.fname || '';
+            return fname === srcPath || path.posix.basename(fname) === srcName;
+        });
+        if (match && match.id !== undefined) {
+            fileId = Number(match.id);
+        }
+    }
+    if (fileId === undefined) {
+        cumin_1.errorStack.stack_push("error", `Source file not found: ${srcPath}`);
+        return (0, cumin_1.Err)();
+    }
+    return (0, cumin_1.Ok)(fileId);
+}
+/**
+ * Determines whether a given ChRIS path refers to a directory.
+ *
+ * @param targetPath - The absolute ChRIS path to check.
+ * @returns Promise resolving to true if the path is a directory, false otherwise.
+ */
+async function path_isDir(targetPath) {
+    const parent = path.posix.dirname(targetPath);
+    const name = path.posix.basename(targetPath);
+    const results = await files_listAll({ limit: 1000, offset: 0 }, "dirs", parent);
+    if (!results || !results.tableData) {
+        return false;
+    }
+    return results.tableData.some((entry) => {
+        const candidate = entry.path || entry.fname || "";
+        return candidate === targetPath || path.posix.basename(candidate) === name;
+    });
+}
+/**
+ * Uploads content to a specified ChRIS path, effectively creating or overwriting a file.
+ *
+ * @param content - The content to upload (string, Buffer, or Blob).
+ * @param pathStr - The ChRIS path for the new file.
+ * @returns A Promise resolving to true on success, false on failure.
+ */
+async function files_create(content, pathStr) {
+    try {
+        let uploadContent;
+        if (typeof content === 'string') {
+            uploadContent = new Blob([content]);
+        }
+        else if (Buffer.isBuffer(content)) {
+            uploadContent = new Blob([new Uint8Array(content)]); // Convert Buffer to Uint8Array for Blob
+        }
+        else {
+            uploadContent = content; // Assume it's already a Blob
+        }
+        // Split path into directory and filename
+        const dir = path.posix.dirname(pathStr);
+        const name = path.posix.basename(pathStr);
+        const success = await cumin_1.chrisIO.file_upload(uploadContent, dir, name);
+        if (!success) {
+            cumin_1.errorStack.stack_push("error", `File upload failed for ${pathStr}.`);
+        }
+        return success;
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        cumin_1.errorStack.stack_push("error", `File creation failed for ${pathStr}: ${msg}`);
+        return false;
+    }
+}
+/**
+ * Creates a new empty file at the specified path (like Unix touch).
+ * Optionally creates the file with specified content.
+ *
+ * @param path - The ChRIS path for the new file.
+ * @param content - Optional content to write to the file (string, Buffer, or Blob).
+ * @returns A Promise resolving to true on success, false on failure.
+ */
+async function files_touch(path, content) {
+    const fileContent = content ?? new Blob([""]);
+    return await files_create(fileContent, path);
+}
+/**
+ * Copies a single file from one ChRIS path to another.
+ *
+ * @param srcPath - The full path to the source file.
+ * @param destPath - The full path to the destination file (including filename).
+ * @returns A Promise resolving to true on success, false on failure.
+ */
+async function files_copy(srcPath, destPath) {
+    try {
+        // 1. Resolve source file to get ID (needed for download)
+        const fileIdResult = await fileId_resolve(srcPath);
+        if (!fileIdResult.ok) {
+            return false;
+        }
+        const fileId = fileIdResult.value;
+        // 2. Download content
+        const content = await cumin_1.chrisIO.file_download(fileId);
+        if (content === null) {
+            cumin_1.errorStack.stack_push("error", `Failed to download source file (ID: ${fileId}): ${srcPath}`);
+            return false;
+        }
+        // 3. Upload to destination
+        // files_create handles Blob/Buffer conversion and path splitting
+        const uploadSuccess = await files_create(content, destPath);
+        if (!uploadSuccess) {
+            const lastError = cumin_1.errorStack.stack_pop();
+            if (lastError) {
+                console.error(`    Error: ${lastError.message}`);
+            }
+        }
+        return uploadSuccess;
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        cumin_1.errorStack.stack_push("error", `Copy failed from ${srcPath} to ${destPath}: ${msg}`);
+        return false;
+    }
+}
+/**
+ * Moves a file or directory by updating its path on the server.
+ *
+ * For directories, this performs a server-side rename without data transfer.
+ * For files, the file ID is resolved and the path is updated.
+ *
+ * @param srcPath - The source file or directory path.
+ * @param destPath - The target path. If an existing directory or trailing slash is provided,
+ *                   the source basename is appended.
+ * @returns Promise resolving to true on success, false on failure.
+ */
+async function files_move(srcPath, destPath) {
+    try {
+        const srcIsDir = await path_isDir(srcPath);
+        const destIsDir = await path_isDir(destPath);
+        const destLooksDir = destPath.endsWith("/");
+        const finalDest = (destIsDir || destLooksDir)
+            ? path.posix.join(destPath, path.posix.basename(srcPath))
+            : destPath;
+        if (srcIsDir) {
+            const moveResult = await cumin_1.chrisIO.folder_moveByPath(srcPath, finalDest);
+            return moveResult.ok && moveResult.value;
+        }
+        const fileIdResult = await fileId_resolve(srcPath);
+        if (!fileIdResult.ok) {
+            return false;
+        }
+        const moveResult = await cumin_1.chrisIO.file_moveById(fileIdResult.value, finalDest);
+        return moveResult.ok && moveResult.value;
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        cumin_1.errorStack.stack_push("error", `Move failed from ${srcPath} to ${destPath}: ${msg}`);
+        return false;
+    }
+}
+/**
+ * Uploads a local file or directory to ChRIS recursively.
+ *
+ * @param localPath - The local filesystem path.
+ * @param remotePath - The ChRIS destination path.
+ * @returns Promise<boolean> success.
+ */
+async function files_uploadPath(localPath, remotePath) {
+    return await cumin_1.chrisIO.uploadLocalPath(localPath, remotePath);
+}
+/**
+ * Creates a new folder (directory) at the specified ChRIS path.
+ *
+ * @param folderPath - The full ChRIS path for the new folder.
+ * @returns A Promise resolving to true on success, false on failure.
+ */
+async function files_mkdir(folderPath) {
+    const result = await cumin_1.chrisIO.folder_create(folderPath);
+    if (!result.ok) {
+        return false;
+    }
+    // result.value is true if created, false if already exists
+    // Both cases are considered success
+    return true;
+}
+/**
+ * Creates a ChRISEmbeddedResourceGroup for a specific asset type (files, links, dirs).
+ * This function encapsulates the logic from `FileController.handler_create`.
+ *
+ * @param assetName - The type of asset ('files', 'links', 'dirs').
+ * @param path - Optional ChRIS path. Defaults to current folder context.
+ * @returns A Promise resolving to a ChRISEmbeddedResourceGroup instance, or null on error.
+ */
+async function files_getGroup(assetName, path) {
+    if (!path) {
+        const fileContext = await cumin_1.chrisContext.current_get(cumin_1.Context.ChRISfolder);
+        path = fileContext ? fileContext : "/";
+    }
+    let chrisFileSystemGroup = null;
+    try {
+        switch (assetName) {
+            case "files":
+                chrisFileSystemGroup = (await (0, cumin_1.objContext_create)("ChRISFilesContext", `folder:${path}`));
+                break;
+            case "links":
+                chrisFileSystemGroup = (await (0, cumin_1.objContext_create)("ChRISLinksContext", `folder:${path}`));
+                break;
+            case "dirs":
+                chrisFileSystemGroup = (await (0, cumin_1.objContext_create)("ChRISDirsContext", `folder:${path}`));
+                break;
+            default:
+                cumin_1.errorStack.stack_push("error", `Unsupported asset type: ${assetName}`);
+                return null;
+        }
+        if (!chrisFileSystemGroup) {
+            cumin_1.errorStack.stack_push("error", `Failed to initialize ChRIS context for ${assetName} at ${path}`);
+            return null;
+        }
+    }
+    catch (error) {
+        cumin_1.errorStack.stack_push("error", `Error creating ChRISEmbeddedResourceGroup for ${assetName}: ${error}`);
+        return null;
+    }
+    return chrisFileSystemGroup;
+}
+/**
+ * List files, links, or directories based on options.
+ *
+ * @param options - Search and pagination options.
+ * @param assetName - The type of asset to list ('files', 'links', 'dirs').
+ * @param path - Optional ChRIS path. Defaults to current folder context.
+ * @returns A Promise resolving to FilteredResourceData or null.
+ */
+async function files_list(options, assetName = "files", path) {
+    const group = await files_getGroup(assetName, path);
+    if (!group) {
+        return null;
+    }
+    return await group.asset.resources_listAndFilterByOptions(options);
+}
+/**
+ * List *all* files, links, or directories by automatically handling pagination.
+ *
+ * @param options - Search options (limit and offset will be managed internally).
+ * @param assetName - The type of asset to list ('files', 'links', 'dirs').
+ * @param path - Optional ChRIS path. Defaults to current folder context.
+ * @returns A Promise resolving to FilteredResourceData containing all matching assets, or null.
+ */
+async function files_listAll(options, assetName = "files", path) {
+    const group = await files_getGroup(assetName, path);
+    if (!group) {
+        return null;
+    }
+    return await group.asset.resources_getAll(options);
+}
+/**
+ * Get the list of available fields for files, links, or directories.
+ *
+ * @param assetName - The type of asset ('files', 'links', 'dirs').
+ * @returns A Promise resolving to an array of field names or null.
+ */
+async function fileFields_get(assetName = "files") {
+    const group = await files_getGroup(assetName);
+    if (!group) {
+        return null;
+    }
+    const results = await group.asset.resourceFields_get();
+    return results ? results.fields : null;
+}
+/**
+ * Deletes a file, link, or directory by its ID.
+ *
+ * @param id - The ID of the asset to delete.
+ * @param assetName - The type of asset ('files', 'links', 'dirs').
+ * @returns A Promise resolving to true on success, false on failure.
+ */
+async function files_delete(id, assetName = "files") {
+    const group = await files_getGroup(assetName);
+    if (!group) {
+        return false;
+    }
+    return await group.asset.resourceItem_delete(id);
+}
+/**
+ * Creates a ChRISEmbeddedResourceGroup for a single file.
+ * This function encapsulates the logic from `FileController.member_create`.
+ *
+ * @param path - The ChRIS path to the file.
+ * @returns A Promise resolving to a ChRISEmbeddedResourceGroup instance, or null on error.
+ */
+async function files_getSingle(path) {
+    let chrisFilesGroup = null;
+    try {
+        chrisFilesGroup = (await (0, cumin_1.objContext_create)("ChRISFilesContext", `folder:${path}`));
+        if (!chrisFilesGroup) {
+            cumin_1.errorStack.stack_push("error", `Failed to create ChRISFilesContext for path: ${path}`);
+            return null;
+        }
+    }
+    catch (error) {
+        cumin_1.errorStack.stack_push("error", `Error creating ChRISFilesContext for path ${path}: ${error}`);
+        return null;
+    }
+    return chrisFilesGroup;
+}
+/**
+ * Shares files in ChRIS.
+ *
+ * @param fileId - The ID of the file to share.
+ * @param options - Options for sharing (e.g., user, permissions).
+ * @returns A Promise resolving to true.
+ */
+async function files_share(fileId, options) {
+    // Implement actual sharing logic using cumin/chrisapi
+    console.log(`Sharing file ${fileId} with options:`, options);
+    return Promise.resolve(true);
+}
+/**
+ * Retrieves the content of a file by its path.
+ *
+ * Router function that delegates to specialized handlers based on path type.
+ *
+ * @param filePath - The full ChRIS path to the file.
+ * @returns A Result containing the content string or error.
+ */
+async function fileContent_get(filePath) {
+    const provider = dispatcher_js_1.vfsDispatcher.provider_get(filePath);
+    if (provider && provider.prefix !== '') {
+        return dispatcher_js_1.vfsDispatcher.read(filePath);
+    }
+    if (filePath.startsWith('/PIPELINES/')) {
+        return (0, pipeline_content_1.fileContent_getPipeline)(filePath);
+    }
+    if (filePath.startsWith('/SERVICES/PACS/')) {
+        return (0, pacs_content_1.fileContent_getPACS)(filePath);
+    }
+    return (0, regular_content_1.fileContent_getRegular)(filePath);
+}
+/**
+ * Retrieves the binary content of a file by its path.
+ *
+ * Router function that delegates to specialized handlers based on path type.
+ * Returns raw Buffer instead of converting to UTF-8 string.
+ *
+ * @param filePath - The full ChRIS path to the file.
+ * @returns A Result containing the content Buffer or error.
+ */
+async function fileContent_getBinary(filePath) {
+    const provider = dispatcher_js_1.vfsDispatcher.provider_get(filePath);
+    if (provider && provider.prefix !== '') {
+        return dispatcher_js_1.vfsDispatcher.readBinary(filePath);
+    }
+    if (filePath.startsWith('/PIPELINES/')) {
+        return (0, pipeline_content_1.fileContent_getPipelineBinary)(filePath);
+    }
+    if (filePath.startsWith('/SERVICES/PACS/')) {
+        return (0, pacs_content_1.fileContent_getPACSBinary)(filePath);
+    }
+    return (0, regular_content_1.fileContent_getRegularBinary)(filePath);
+}
+/**
+ * Retrieves the binary content of a file by its path as a stream/blob.
+ *
+ * Router function that delegates to specialized handlers based on path type.
+ *
+ * @param filePath - The full ChRIS path to the file.
+ * @returns A Result containing the stream/blob and metadata or error.
+ */
+async function fileContent_getBinaryStream(filePath) {
+    const provider = dispatcher_js_1.vfsDispatcher.provider_get(filePath);
+    if (provider && provider.prefix !== '/') {
+        return dispatcher_js_1.vfsDispatcher.readBinary(filePath).then((res) => {
+            if (res.ok) {
+                return (0, cumin_1.Ok)({ stream: res.value, size: res.value.length });
+            }
+            return (0, cumin_1.Err)();
+        });
+    }
+    if (filePath.startsWith('/PIPELINES/')) {
+        return (0, pipeline_content_1.fileContent_getPipelineBinary)(filePath).then((res) => {
+            if (res.ok) {
+                return (0, cumin_1.Ok)({ stream: res.value, size: res.value.length });
+            }
+            return (0, cumin_1.Err)();
+        });
+    }
+    if (filePath.startsWith('/SERVICES/PACS/')) {
+        return (0, pacs_content_1.fileContent_getPACSBinary)(filePath).then((res) => {
+            if (res.ok) {
+                return (0, cumin_1.Ok)({ stream: res.value, size: res.value.length });
+            }
+            return (0, cumin_1.Err)();
+        });
+    }
+    return (0, regular_content_1.fileContent_getRegularStream)(filePath);
+}
+//# sourceMappingURL=index.js.map

package/dist/files/index.js.map

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

@@ -0,0 +1,29 @@
+/**
+ * @file Content retrieval for PACS-backed files (text and binary).
+ *
+ * @module
+ */
+import { Result } from "@fnndsc/cumin";
+/**
+ * Fetches the content of a PACS file (DICOM).
+ *
+ * Path structure: /SERVICES/PACS/<service>/<patient>/<study>/<series>/<file>.dcm
+ * Example: /SERVICES/PACS/PACSDCM/7654321-EVANS-19861111/.../0168-1.3...dcm
+ *
+ * PACS files appear in directory listings but must be downloaded through
+ * the PACSFile API instead of the regular file download endpoint.
+ *
+ * @param filePath - The full path to the PACS file.
+ * @returns A Result containing the file content as a string, or an error.
+ */
+export declare function fileContent_getPACS(filePath: string): Promise<Result<string>>;
+/**
+ * Fetches the binary content of a PACS file (DICOM).
+ *
+ * Same as fileContent_getPACS but returns raw Buffer instead of string.
+ * Use this for binary files like DICOM (.dcm) that should not be converted to UTF-8.
+ *
+ * @param filePath - The full path to the PACS file.
+ * @returns A Result containing the file content as a Buffer, or an error.
+ */
+export declare function fileContent_getPACSBinary(filePath: string): Promise<Result<Buffer>>;