@fnndsc/cumin 3.2.4

package/dist/plugins/chrisPlugins.js

@@ -0,0 +1,528 @@
+"use strict";
+/**
+ * @file ChRIS Plugin Management
+ *
+ * This module provides classes for managing ChRIS plugins.
+ * It includes the `ChRISPluginGroup` for collection operations and `ChRISPlugin` for individual plugin operations,
+ * such as searching for plugins and creating plugin instances.
+ *
+ * @module
+ */
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ChRISPlugin = exports.ChRISPluginInstanceGroup = exports.ChRISPluginGroup = void 0;
+exports.plugin_registerDirect = plugin_registerDirect;
+const chrisapi_1 = __importDefault(require("@fnndsc/chrisapi"));
+const chrisConnection_js_1 = require("../connect/chrisConnection.js");
+const chrisContext_js_1 = require("../context/chrisContext.js");
+const chrisResources_js_1 = require("../resources/chrisResources.js");
+const chrisResourceGroup_js_1 = require("../resources/chrisResourceGroup.js");
+const keypair_js_1 = require("../utils/keypair.js");
+const searchable_js_1 = require("../utils/searchable.js");
+const errorStack_js_1 = require("../error/errorStack.js");
+const result_js_1 = require("../utils/result.js");
+/**
+ * Group handler for ChRIS plugins.
+ */
+class ChRISPluginGroup extends chrisResourceGroup_js_1.ChRISResourceGroup {
+    constructor() {
+        super("Plugins", "getPlugins");
+    }
+}
+exports.ChRISPluginGroup = ChRISPluginGroup;
+/**
+ * Group handler for ChRIS plugin instances.
+ */
+class ChRISPluginInstanceGroup extends chrisResourceGroup_js_1.ChRISResourceGroup {
+    constructor() {
+        super("PluginInstances", "getPluginInstances");
+    }
+}
+exports.ChRISPluginInstanceGroup = ChRISPluginInstanceGroup;
+/**
+ * Type guard for CollectionJson.
+ */
+function collectionJson_is(data) {
+    return (typeof data === 'object' &&
+        data !== null &&
+        'collection' in data &&
+        typeof data.collection === 'object');
+}
+function collectionItem_toData(item) {
+    const data = {};
+    item.data?.forEach((datum) => { data[datum.name] = datum.value; });
+    return data;
+}
+function collectionItem_selectBest(items, pluginName, version) {
+    const exactNameMatches = [];
+    let targetItem = null;
+    for (const item of items) {
+        const itemData = collectionItem_toData(item);
+        if (itemData['name'] === pluginName) {
+            exactNameMatches.push(item);
+            if (version && itemData['version'] === version) {
+                targetItem = item;
+                break;
+            }
+        }
+    }
+    if (targetItem)
+        return targetItem;
+    if (exactNameMatches.length > 0 && !version)
+        return exactNameMatches[0];
+    const fallback = items[0];
+    const fallbackData = collectionItem_toData(fallback);
+    if (fallbackData['name'] !== pluginName) {
+        errorStack_js_1.errorStack.stack_push('warning', `Peer store search for exact plugin name '${pluginName}' returned '${fallbackData['name']}'. Exact name not found, using first result.`);
+    }
+    return fallback;
+}
+function collectionItem_toPluginData(item) {
+    const pluginData = collectionItem_toData(item);
+    if (item.href)
+        pluginData['url'] = item.href;
+    if (item.links)
+        pluginData['links'] = item.links;
+    return pluginData;
+}
+/**
+ * Class for managing individual ChRIS plugins.
+ */
+class ChRISPlugin {
+    constructor() {
+        this._client = null;
+        // Client is fetched lazily
+    }
+    /**
+     * 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;
+    }
+    /**
+     * Converts a plain string to a searchable format.
+     * @deprecated Use Searchable.from() instead.
+     */
+    pluginString_makeSearchable(plugin) {
+        const searchable = searchable_js_1.Searchable.from(plugin);
+        return searchable.toNormalizedString();
+    }
+    /**
+     * Resolves a searchable string or object to plugin IDs.
+     * @param pluginSearchable - A searchable string or Searchable object.
+     * @returns A Promise resolving to QueryHits containing matching plugin IDs.
+     */
+    async pluginIDs_resolve(pluginSearchable) {
+        const searchable = typeof pluginSearchable === 'string'
+            ? searchable_js_1.Searchable.from(pluginSearchable)
+            : pluginSearchable;
+        if (!searchable.validate()) {
+            errorStack_js_1.errorStack.stack_push("error", "Invalid searchable format");
+            return null;
+        }
+        const pluginList = await this.pluginIDs_getFromSearchable(searchable);
+        if (!pluginList || pluginList.hits.length === 0) {
+            errorStack_js_1.errorStack.stack_push("error", "No matching plugins found");
+            return null;
+        }
+        return pluginList;
+    }
+    async previousID_get() {
+        const previousIDstring = await chrisContext_js_1.chrisContext.ChRISplugin_get();
+        if (!previousIDstring) {
+            errorStack_js_1.errorStack.stack_push("error", "Could not resolve a previous plugin ID context");
+            return null;
+        }
+        return Number(previousIDstring);
+    }
+    async plugin_runOnCUBE(pluginID, previousID, options) {
+        const client = await this.client_get();
+        if (!client) {
+            console.error("Could not access ChRIS. Client is not initialized.");
+            return null;
+        }
+        const combinedParams = {
+            ...options,
+            previous_id: previousID,
+        };
+        const pluginInstance = await client.createPluginInstance(pluginID, combinedParams);
+        if (!pluginInstance) {
+            errorStack_js_1.errorStack.stack_push("error", "Failed to create plugin instance");
+            return null;
+        }
+        return pluginInstance;
+    }
+    pluginInstance_toDict(pluginInstance) {
+        if (!pluginInstance) {
+            return null;
+        }
+        const chrisResource = new chrisResources_js_1.ChRISResource();
+        chrisResource.resourceCollection = pluginInstance;
+        const items = chrisResource.resourceItems_buildFromCollection(pluginInstance);
+        if (!items) {
+            errorStack_js_1.errorStack.stack_push("error", "Could not convert pluginInstance resource into dictionary");
+            return null;
+        }
+        const dict = chrisResource.resourceItems_toDicts(items)[0];
+        return dict;
+    }
+    async plugin_run(plugin, params) {
+        let pluginList;
+        if ((pluginList = await this.pluginIDs_resolve(plugin)) === null) {
+            return null;
+        }
+        const pluginID = pluginList.hits[0];
+        // Parse params first to check for explicit previous_id
+        const pluginParams = (0, keypair_js_1.dictionary_fromCLI)(params);
+        // Prioritize explicit previous_id from params, fall back to context
+        let previousID;
+        if (pluginParams.previous_id !== undefined) {
+            // Explicit value provided in params - use it!
+            previousID = Number(pluginParams.previous_id);
+        }
+        else {
+            // Fall back to context
+            const contextPreviousID = await this.previousID_get();
+            if (contextPreviousID === null) {
+                return null;
+            }
+            previousID = contextPreviousID;
+        }
+        try {
+            const dict = this.pluginInstance_toDict(await this.plugin_runOnCUBE(pluginID, previousID, pluginParams));
+            return dict;
+        }
+        catch (error) {
+            if (error instanceof Error) {
+                errorStack_js_1.errorStack.stack_push("error", `Error running plugin instance | ${error.message}`);
+            }
+            else {
+                errorStack_js_1.errorStack.stack_push("error", "An unknown error occurred while running plugin instance");
+            }
+            return null;
+        }
+    }
+    async pluginData_getFromSearch(searchOptions, dataField) {
+        const chrisPluginGroup = new ChRISPluginGroup();
+        // We rely on lazy initialization of ChRISResourceGroup
+        const searchParams = (0, keypair_js_1.listParams_fromOptions)(searchOptions);
+        const searchResults = await chrisPluginGroup.asset.resources_listAndFilterByOptions(searchParams);
+        if (!searchResults) {
+            return null;
+        }
+        const queryHits = (0, keypair_js_1.record_extract)(searchResults.tableData, dataField);
+        return queryHits;
+    }
+    /**
+     * Gets plugin IDs from a searchable.
+     * @param searchable - A searchable string or Searchable object.
+     * @returns A Promise resolving to QueryHits containing matching plugin IDs.
+     */
+    async pluginIDs_getFromSearchable(searchable) {
+        const searchableObj = typeof searchable === 'string'
+            ? searchable_js_1.Searchable.from(searchable)
+            : searchable;
+        const seachParams = {
+            search: searchableObj.toNormalizedString(),
+        };
+        const pluginList = await this.pluginData_getFromSearch(seachParams, "id");
+        if (!pluginList) {
+            errorStack_js_1.errorStack.stack_push("error", `A plugin conforming to "${searchableObj.raw}" was not found.`);
+            return null;
+        }
+        if (pluginList.hits.length > 1) {
+            errorStack_js_1.errorStack.stack_push("warning", `Multiple plugins conformed to "${searchableObj.raw}".`);
+        }
+        return pluginList;
+    }
+    async pluginIDs_get(name_exact) {
+        return await this.pluginData_getFromSearch({ search: "name_exact: " + name_exact }, "id");
+    }
+    /**
+     * Uploads a plugin representation file to create a new plugin admin resource.
+     *
+     * Requires admin credentials. Will push error to errorStack if authentication fails.
+     *
+     * @param pluginData - Plugin descriptor JSON data.
+     * @param computeResources - Array of compute resource names to assign plugin to.
+     * @param adminToken - Optional admin authentication token (if different from current user).
+     * @returns Promise resolving to the created plugin data or null on failure.
+     */
+    async plugin_registerWithAdmin(pluginData, computeResources = ['host'], adminToken) {
+        try {
+            let client;
+            if (adminToken) {
+                const url = await chrisConnection_js_1.chrisConnection.chrisURL_get();
+                if (!url) {
+                    errorStack_js_1.errorStack.stack_push('error', 'ChRIS URL not found. Cannot create admin client.');
+                    return null;
+                }
+                client = new chrisapi_1.default(url, { token: adminToken });
+            }
+            else {
+                client = await this.client_get();
+            }
+            if (!client) {
+                errorStack_js_1.errorStack.stack_push('error', 'Not connected to ChRIS. Please log in.');
+                return null;
+            }
+            // Verify admin URL is available — non-admin users won't have this link
+            const clientAny = client;
+            if (!clientAny.adminUrl && clientAny.setUrls) {
+                await clientAny.setUrls().catch(() => undefined);
+            }
+            if (!clientAny.adminUrl) {
+                errorStack_js_1.errorStack.stack_push('error', 'Admin credentials required to register plugins. Authentication failed.');
+                return null;
+            }
+            // Create plugin representation as JSON string (ChRIS expects a file upload)
+            const pluginJson = JSON.stringify(pluginData, null, 2);
+            const pluginBlob = new Blob([pluginJson], { type: 'application/json' });
+            const computeNames = computeResources.join(',');
+            const pluginFileObj = { fname: pluginBlob };
+            const pluginAdmin = await client.adminUploadPlugin({ compute_names: computeNames }, pluginFileObj);
+            if (pluginAdmin && pluginAdmin.data) {
+                return pluginAdmin.data;
+            }
+            errorStack_js_1.errorStack.stack_push('error', 'Failed to register plugin. No data in response.');
+            return null;
+        }
+        catch (error) {
+            const errorMessage = error instanceof Error ? error.message : String(error);
+            const errorString = errorMessage.toLowerCase();
+            if (errorString.includes('403') || errorString.includes('forbidden') ||
+                errorString.includes('401') || errorString.includes('unauthorized') ||
+                errorString.includes('permission denied')) {
+                errorStack_js_1.errorStack.stack_push('error', 'Admin credentials required to register plugins. Authentication failed.');
+            }
+            else {
+                errorStack_js_1.errorStack.stack_push('error', `Failed to register plugin: ${errorMessage}`);
+            }
+            return null;
+        }
+    }
+    /**
+     * Searches for a plugin in a peer ChRIS store (public plugin repository).
+     *
+     * Uses anonymous client to query public plugin stores without authentication.
+     *
+     * @param pluginName - Name of the plugin to search for.
+     * @param version - Optional version of the plugin to search for.
+     * @param peerStoreUrl - URL of the peer ChRIS store (default: cube.chrisproject.org).
+     * @returns Promise resolving to plugin data and store URL, or null if not found.
+     */
+    async plugin_searchPeerStore(pluginName, version, peerStoreUrl = 'https://cube.chrisproject.org/api/v1/') {
+        try {
+            let searchUrl = `${peerStoreUrl}plugins/search/?name_exact=${encodeURIComponent(pluginName)}`;
+            if (version)
+                searchUrl += `&version=${encodeURIComponent(version)}`;
+            const response = await fetch(searchUrl, {
+                headers: { 'Accept': 'application/vnd.collection+json' },
+            });
+            if (!response.ok) {
+                errorStack_js_1.errorStack.stack_push('error', `Failed to search peer store: ${response.status} ${response.statusText}`);
+                return null;
+            }
+            const data = await response.json();
+            if (collectionJson_is(data) && data.collection?.items) {
+                const items = data.collection.items;
+                if (items.length === 0)
+                    return null;
+                const targetItem = collectionItem_selectBest(items, pluginName, version);
+                const pluginData = collectionItem_toPluginData(targetItem);
+                return { plugin: pluginData, storeUrl: targetItem.href };
+            }
+            if (typeof data === 'object' && data !== null && 'results' in data) {
+                const results = data.results || [];
+                if (results.length === 0)
+                    return null;
+                const plugin = results[0];
+                return { plugin, storeUrl: plugin.url || `${peerStoreUrl}plugins/${plugin.id}/` };
+            }
+            return null;
+        }
+        catch (error) {
+            const errorMessage = error instanceof Error ? error.message : String(error);
+            errorStack_js_1.errorStack.stack_push('error', `Failed to search peer store: ${errorMessage}`);
+            return null;
+        }
+    }
+    /**
+     * Checks if a plugin with given name or dock_image already exists in current CUBE.
+     *
+     * @param nameOrImage - Plugin name or docker image to search for.
+     * @returns Promise resolving to plugin data if found, null otherwise.
+     */
+    async plugin_existsInCube(nameOrImage) {
+        try {
+            const client = await this.client_get();
+            if (!client) {
+                return null;
+            }
+            // Try searching by name first
+            let pluginList = await client.getPlugins({ name_exact: nameOrImage, limit: 1 });
+            if (pluginList && pluginList.data && pluginList.data.length > 0) {
+                return pluginList.data[0];
+            }
+            // Try searching by dock_image
+            pluginList = await client.getPlugins({ dock_image: nameOrImage, limit: 1 });
+            if (pluginList && pluginList.data && pluginList.data.length > 0) {
+                return pluginList.data[0];
+            }
+            return null;
+        }
+        catch (error) {
+            const errorMessage = error instanceof Error ? error.message : String(error);
+            errorStack_js_1.errorStack.stack_push('error', `Failed to check if plugin exists: ${errorMessage}`);
+            return null;
+        }
+    }
+    /**
+     * Lists plugins from a peer ChRIS store.
+     * Handles pagination to fetch all results.
+     *
+     * @param peerStoreUrl - URL of the peer store.
+     * @param searchParams - Optional search parameters.
+     * @returns Promise resolving to array of plugin data objects.
+     */
+    async plugin_listPeerStore(peerStoreUrl = 'https://cube.chrisproject.org/api/v1/', searchParams) {
+        try {
+            let url;
+            if (searchParams && Object.keys(searchParams).length > 0) {
+                url = `${peerStoreUrl}plugins/search/`;
+            }
+            else {
+                url = `${peerStoreUrl}plugins/`;
+            }
+            const params = new URLSearchParams();
+            params.append('limit', '100'); // Efficient pagination
+            if (searchParams) {
+                for (const [key, value] of Object.entries(searchParams)) {
+                    params.append(key, value);
+                }
+            }
+            url += `?${params.toString()}`;
+            const allPlugins = [];
+            let nextUrl = url;
+            while (nextUrl) {
+                const response = await fetch(nextUrl, {
+                    headers: { 'Accept': 'application/vnd.collection+json' }
+                });
+                if (!response.ok) {
+                    errorStack_js_1.errorStack.stack_push('error', `Failed to fetch from peer store: ${response.statusText}`);
+                    return null;
+                }
+                const data = await response.json();
+                if (collectionJson_is(data) && data.collection.items) {
+                    const items = data.collection.items;
+                    items.forEach(item => {
+                        const pluginData = {};
+                        if (item.data) {
+                            item.data.forEach((datum) => {
+                                pluginData[datum.name] = datum.value;
+                            });
+                        }
+                        if (item.href)
+                            pluginData['url'] = item.href;
+                        allPlugins.push(pluginData);
+                    });
+                    nextUrl = null;
+                    if (data.collection.links) {
+                        const nextLink = data.collection.links.find(l => l.rel === 'next');
+                        if (nextLink) {
+                            nextUrl = nextLink.href;
+                        }
+                    }
+                }
+                else {
+                    break;
+                }
+            }
+            return allPlugins;
+        }
+        catch (error) {
+            const msg = error instanceof Error ? error.message : String(error);
+            errorStack_js_1.errorStack.stack_push('error', `Error listing peer store: ${msg}`);
+            return null;
+        }
+    }
+    /**
+     * Gets the compute resources currently assigned to a plugin.
+     *
+     * @param pluginId - ID of the plugin.
+     * @returns Promise resolving to array of compute resource names.
+     */
+    async plugin_getComputeResources(pluginId) {
+        try {
+            const client = await this.client_get();
+            if (!client) {
+                return [];
+            }
+            const plugin = await client.getPlugin(pluginId);
+            if (!plugin) {
+                return [];
+            }
+            const computeResourceList = await plugin.getPluginComputeResources();
+            const resources = computeResourceList.data || [];
+            return resources.map((r) => r.name);
+        }
+        catch (error) {
+            const errorMessage = error instanceof Error ? error.message : String(error);
+            errorStack_js_1.errorStack.stack_push('error', `Failed to get plugin compute resources: ${errorMessage}`);
+            return [];
+        }
+    }
+}
+exports.ChRISPlugin = ChRISPlugin;
+/**
+ * Registers a plugin using the legacy non-admin PluginList._post() method.
+ *
+ * **DEPRECATED:** This method uses the legacy non-admin plugin registration endpoint
+ * which may not be available in modern ChRIS CUBE installations. Prefer using
+ * ChRISPlugin.plugin_registerWithAdmin() instead.
+ *
+ * This function is provided for backward compatibility only and will be removed
+ * in a future release.
+ *
+ * @param pluginData - Plugin descriptor data (name, dock_image, etc.).
+ * @param computeResources - Optional array of compute resource names to assign.
+ * @returns A Result containing the registered plugin data, or an error.
+ *
+ * @deprecated Use ChRISPlugin.plugin_registerWithAdmin() instead.
+ */
+async function plugin_registerDirect(pluginData, computeResources) {
+    const client = await chrisConnection_js_1.chrisConnection.client_get();
+    if (!client) {
+        errorStack_js_1.errorStack.stack_push("error", "Not connected to ChRIS. Cannot register plugin.");
+        return (0, result_js_1.Err)();
+    }
+    try {
+        const pluginList = await client.getPlugins();
+        // Prepare data for POST request
+        const data = {
+            ...pluginData,
+        };
+        if (computeResources && computeResources.length > 0) {
+            data.compute_resources = computeResources;
+        }
+        // Call the internal _post method directly (legacy API)
+        const response = await pluginList._post(data);
+        if (response && response.data) {
+            return (0, result_js_1.Ok)(response.data);
+        }
+        errorStack_js_1.errorStack.stack_push("error", "Failed to register plugin. No data in response.");
+        return (0, result_js_1.Err)();
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        errorStack_js_1.errorStack.stack_push("error", `Failed to register plugin: ${msg}`);
+        return (0, result_js_1.Err)();
+    }
+}
+//# sourceMappingURL=chrisPlugins.js.map

package/dist/plugins/chrisPlugins.js.map

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

@@ -0,0 +1,73 @@
+/**
+ * @file ChRIS Embedded Resource Group
+ *
+ * This module manages groups of ChRIS resources that are embedded within other resources
+ * (e.g., files within a folder, parameters of a plugin). It handles context-aware initialization.
+ *
+ * @module
+ */
+import { ChRISResourceGroup } from "../resources/chrisResourceGroup.js";
+/**
+ * Error thrown when the ChRIS client is not connected.
+ */
+export declare class ChRISConnectionError extends Error {
+    constructor(message: string);
+}
+/**
+ * Error thrown when ChRIS initialization fails.
+ */
+export declare class ChRISInitializationError extends Error {
+    constructor(message: string);
+}
+/**
+ * Error thrown when a context specification is invalid.
+ */
+export declare class ChRISContextSpecError extends Error {
+    constructor(message: string);
+}
+/**
+ * Specification representing the parsed components of a context string.
+ */
+export interface ContextSpec {
+    /**
+     * The type of context (e.g., 'folder', 'plugin', 'feed').
+     */
+    type: string;
+    /**
+     * The value or path associated with the context.
+     */
+    value: string;
+}
+/**
+ * Splits a context string into its type and value components on the first occurrence of a delimiter.
+ *
+ * This function parses strings like "folder:/path/to/folder" or "plugin:123" into an object
+ * containing the type (the prefix before the first delimiter) and the value (the rest of the string).
+ * If the path contains extra delimiters (e.g. "/pacs/queries/2601_AccessionNumber:22548684"), this
+ * function correctly preserves those extra delimiters in the value component.
+ *
+ * @param context - The context string to be split. Must be a string.
+ * @param delimiter - The delimiter character to split on. Defaults to ":".
+ * @returns An object conforming to ContextSpec with the split components.
+ * @throws ChRISContextSpecError If the input is not a string or the delimiter is not found.
+ */
+export declare function context_split(context: unknown, delimiter?: string): ContextSpec;
+/**
+ * Parameters for creating a ChRISEmbeddedResourceGroup.
+ */
+export interface ChRISEmbeddedResourceGroupParams<T = unknown> {
+    resourceName: string;
+    getMethod: string;
+    chrisContext: T;
+    context: string;
+}
+/**
+ * Group of ChRIS resources embedded within a specific context.
+ */
+export declare class ChRISEmbeddedResourceGroup<T = unknown> extends ChRISResourceGroup {
+    readonly context: string;
+    readonly chrisContextObj: T;
+    private constructor();
+    static create<T = unknown>(resourceName: string, getMethod: string, context: string): Promise<ChRISEmbeddedResourceGroup<T> | null>;
+    private static context_init;
+}