@fnndsc/chili 3.2.5 → 3.3.0

package/README.md

@@ -42,27 +42,34 @@ Designed for developers and power-users who want to script and control a ChRIS i
 2.  **[`salsa`](https://github.com/FNNDSC/salsa) (Logic)**: Shared Application Logic and Service Assets — high-level business intents.
 3.  **[`cumin`](https://github.com/FNNDSC/cumin) (Infrastructure)**: State and connection layer — authentication, context persistence, low-level API.
 
-## Installation & Development
+## Development
 
-### Full build (all layers)
+`chili` lives in the [`mise` monorepo](https://github.com/FNNDSC/mise) alongside
+`cumin`, `salsa`, and `chell`. Build the whole stack from the repository root —
+npm workspaces links the four packages together, so there is nothing to clone or
+hand-link:
 
 ```bash
-cd chili
-make meal
+git clone https://github.com/FNNDSC/mise
+cd mise
+make taco            # scrub → prep → cook → taste → serve (the full course)
 ```
 
-### Individual steps
+### Individual steps (run from the repo root)
 
 | Target | Action |
 |--------|--------|
-| `make shop` | Clone `cumin` and `salsa` if missing |
-| `make prep` | `npm install` across all packages |
-| `make cook` | Build (compile TypeScript) all packages |
-| `make taste` | Run tests |
-| `make serve` | Link packages globally |
+| `make prep` | `npm install` — install deps and link all four workspaces |
+| `make cook` | Build (compile TypeScript) all packages in dependency order |
+| `make taste` | Run the full test suite |
+| `make serve` | Link `chell` globally |
 | `make scrub` | Clean build artifacts and `node_modules` |
 
-> Use [NVM](https://github.com/nvm-sh/nvm) to avoid needing `sudo` for global links.
+To build or test just this package: `npm run build -w @fnndsc/chili` /
+`npm test -w @fnndsc/chili`.
+
+> Use [NVM](https://github.com/nvm-sh/nvm) and Node 22.x to avoid needing `sudo`
+> for the global link in `make serve`.
 
 ## Core Features
 

package/dist/commands/man/doc.js

@@ -23,7 +23,7 @@ export async function manPage_display(options) {
         return;
     }
     if (options.browser) {
-        browser_open(docPath);
+        await browser_open(docPath);
     }
     else {
         const content = fs.readFileSync(docPath, "utf-8");

package/dist/commands/plugin/readme.js

@@ -11,6 +11,9 @@ import { marked } from "marked";
 import TerminalRenderer from "marked-terminal";
 import chalk from "chalk";
 marked.setOptions({
+    // @ts-expect-error marked-terminal@6 ships .d.ts that drift from marked@9's
+    // Renderer type at this runtime-compatible version pair. (Tracked: align the
+    // marked / marked-terminal versions across chili & chell.)
     renderer: new TerminalRenderer({
         code: chalk.yellow,
         blockquote: chalk.gray.italic,

package/dist/filesystem/fileGroupHandler.d.ts

@@ -25,11 +25,6 @@ export declare class FileGroupHandler {
      * @returns A Promise resolving to a new FileGroupHandler instance.
      */
     static handler_create(assetName: string, path?: string): Promise<FileGroupHandler>;
-    /**
-     * Removes duplicate column headers from FilteredResourceData results.
-     * Copied from BaseGroupHandler to support local listing logic.
-     */
-    private columns_removeDuplicates;
     /**
      * Lists files, links, or directories using the new command logic.
      */

package/dist/filesystem/fileGroupHandler.js

@@ -4,6 +4,7 @@ import { path_resolveChrisFs } from "../utils/cli.js";
 import { FileController } from "../controllers/fileController.js";
 import { files_create } from "../commands/fs/create.js";
 import { errorStack } from "@fnndsc/cumin";
+import { resourceColumns_removeDuplicates } from "../utils/resourceData.js";
 import { table_display } from "../screen/screen.js";
 import { files_fetchList } from "../commands/files/list.js";
 import { fileFields_fetch } from "../commands/files/fields.js";
@@ -41,24 +42,6 @@ export class FileGroupHandler {
             throw new Error(`Failed to initialize FileGroupHandler for ${assetName}: ${errorMessage}`);
         }
     }
-    /**
-     * Removes duplicate column headers from FilteredResourceData results.
-     * Copied from BaseGroupHandler to support local listing logic.
-     */
-    columns_removeDuplicates(results) {
-        const uniqueHeaders = Array.from(new Set(results.selectedFields));
-        const uniqueTableData = results.tableData.map((row) => uniqueHeaders.reduce((acc, header) => {
-            if (typeof header === "string" && header in row) {
-                acc[header] = row[header];
-            }
-            return acc;
-        }, {}));
-        return {
-            ...results,
-            selectedFields: uniqueHeaders,
-            tableData: uniqueTableData,
-        };
-    }
     /**
      * Lists files, links, or directories using the new command logic.
      */
@@ -73,7 +56,7 @@ export class FileGroupHandler {
                 console.log(`No ${this.assetName} found matching the criteria.`);
             }
             else {
-                const uniqueResults = this.columns_removeDuplicates(results);
+                const uniqueResults = resourceColumns_removeDuplicates(results);
                 // cumin returns dynamic table rows (Record<string, unknown>[]);
                 // narrow to the FileResource view model at this boundary.
                 console.log(fileList_render(uniqueResults.tableData, uniqueResults.selectedFields, { table: options.table, csv: options.csv }));

package/dist/handlers/baseGroupHandler.d.ts

@@ -16,13 +16,6 @@ export declare class BaseGroupHandler {
     displayOptions: TableOptions;
     chrisObject: ChRISPluginGroup | ChRISFeedGroup | ChRISEmbeddedResourceGroup<unknown> | ChRISPACSGroup;
     constructor(assetName: string, chrisObject: ChRISPluginGroup | ChRISFeedGroup | ChRISEmbeddedResourceGroup<unknown> | ChRISPACSGroup);
-    /**
-     * Removes duplicate column headers from FilteredResourceData results.
-     *
-     * @param results - The FilteredResourceData to process.
-     * @returns FilteredResourceData with unique headers and corresponding data.
-     */
-    private columns_removeDuplicates;
     /**
      * Lists ChRIS resources based on provided CLI options.
      *

package/dist/handlers/baseGroupHandler.js

@@ -6,6 +6,7 @@
 import { Command } from "commander";
 import { ChRISFeedGroup, record_extract, errorStack, } from "@fnndsc/cumin";
 import { options_toParams } from "../utils/cli.js";
+import { resourceColumns_removeDuplicates } from "../utils/resourceData.js";
 import { table_display, border_draw } from "../screen/screen.js";
 import * as readline from "readline";
 /**
@@ -21,26 +22,6 @@ export class BaseGroupHandler {
             title: { title: this.assetName, justification: "center" },
         };
     }
-    /**
-     * Removes duplicate column headers from FilteredResourceData results.
-     *
-     * @param results - The FilteredResourceData to process.
-     * @returns FilteredResourceData with unique headers and corresponding data.
-     */
-    columns_removeDuplicates(results) {
-        const uniqueHeaders = Array.from(new Set(results.selectedFields));
-        const uniqueTableData = results.tableData.map((row) => uniqueHeaders.reduce((acc, header) => {
-            if (typeof header === "string" && header in row) {
-                acc[header] = row[header];
-            }
-            return acc;
-        }, {}));
-        return {
-            ...results,
-            selectedFields: uniqueHeaders,
-            tableData: uniqueTableData,
-        };
-    }
     /**
      * Lists ChRIS resources based on provided CLI options.
      *
@@ -77,7 +58,7 @@ export class BaseGroupHandler {
                 console.log(`No ${this.assetName} found matching the criteria.`);
             }
             else {
-                const uniqueResults = this.columns_removeDuplicates(results);
+                const uniqueResults = resourceColumns_removeDuplicates(results);
                 // Construct column options based on parsed widths
                 const columns = uniqueResults.selectedFields.map(field => {
                     const width = columnWidths[field];

package/dist/index.d.ts

@@ -2,6 +2,11 @@
 /**
  * @file Command-line entry point for the chili (ChILI) CLI.
  *
+ * This is a thin wrapper: all command wiring and execution live in {@link run}
+ * (./run.js) so the same logic can be driven in-process by a host such as chell
+ * without spawning a separate `node` subprocess. This file only adds the
+ * bin-only concerns — shell completion and fatal-exit handling.
+ *
  * @module
  */
-export { logical_toPhysical } from './utils/cli.js';
+export { logical_toPhysical } from "./utils/cli.js";

package/dist/index.js

@@ -2,62 +2,18 @@
 /**
  * @file Command-line entry point for the chili (ChILI) CLI.
  *
- * @module
- */
-/**
- * Suppress DEP0169 warning from axios/proxy-from-env dependency.
- *
- * This warning originates from the `proxy-from-env` package (version 1.1.0)
- * used by axios for proxy configuration. The package uses the legacy `url.parse()`
- * API which is deprecated in favor of the WHATWG URL API.
+ * This is a thin wrapper: all command wiring and execution live in {@link run}
+ * (./run.js) so the same logic can be driven in-process by a host such as chell
+ * without spawning a separate `node` subprocess. This file only adds the
+ * bin-only concerns — shell completion and fatal-exit handling.
  *
- * Why we suppress it:
- * - It's a transitive dependency (axios → proxy-from-env) we don't control
- * - proxy-from-env 1.1.0 is the latest version and hasn't been updated
- * - According to the warning: "CVEs are not issued for url.parse() vulnerabilities"
- * - The warning doesn't affect functionality, only console output
- * - This is a well-known issue in the Node.js ecosystem
- *
- * This can be removed once:
- * - proxy-from-env migrates to WHATWG URL API, OR
- * - axios replaces proxy-from-env with an alternative
- *
- * Tracking: https://github.com/Rob--W/proxy-from-env/issues/51
+ * @module
  */
-const originalEmitWarning = process.emitWarning;
-process.emitWarning = function (warning, ...args) {
-    // Suppress only the specific DEP0169 warning
-    if (typeof warning === 'string' &&
-        (warning.includes('DEP0169') || warning.includes('url.parse()'))) {
-        return;
-    }
-    // Allow all other warnings through
-    return originalEmitWarning.call(process, warning, ...args);
-};
-import { Command } from "commander";
-import figlet from "figlet";
 import omelette from "omelette";
-import { connectCommand_setup } from "./connect/connectHandler.js";
-import { FeedGroupHandler, FeedMemberHandler } from "./feeds/feedHandler.js";
-import { PluginGroupHandler, PluginMemberHandler, } from "./plugins/pluginHandler.js";
-import { PluginMetaGroupHandler } from "./plugins/pluginMetaHandler.js";
-import { PluginContextGroupHandler } from "./plugins/pluginGroupHandler.js";
-import { inodeCommand_setup } from "./filesystem/inodeCommand.js";
-import { contextCommand_setup } from "./context/contextCommand.js";
-import { pathCommand_setup } from "./path/pathCommand.js";
-import { fileBrowserCommand_setup } from "./filesystem/filesystemHandler.js";
-import { manCommand_setup } from "./man/man.js";
-import { chefsCommand_setup } from "./chefs/chefs.js";
-import { PACSServerGroupHandler } from "./pacs/pacsServerHandler.js";
-import { PACSQueryGroupHandler } from "./pacs/pacsQueryHandler.js";
-import { PACSRetrieveGroupHandler } from "./pacs/pacsRetrieveHandler.js";
-import { chrisConnection_init, NodeStorageProvider, errorStack_getAllOfType } from "@fnndsc/cumin";
-import { FileGroupHandler } from "./filesystem/fileGroupHandler.js";
-const program = new Command();
-program.version("1.0.1").description("A CLI for ChRIS");
+import { run } from "./run.js";
 /**
- * Sets up command completion for the ChILI CLI using omelette.
- * This provides auto-completion suggestions in the shell.
+ * Sets up shell command completion for the standalone chili CLI using omelette.
+ * This is a bin-only concern; in-process hosts provide their own completion.
  */
 function commandCompletion_setup() {
     const completion = omelette(`chili|chili`);
@@ -95,7 +51,6 @@ function commandCompletion_setup() {
     });
     completion.on("man.doc", ({ reply }) => {
         console.log("Autocomplete triggered for man doc command");
-        // We'll implement actual topic retrieval here later
         reply([]);
     });
     completion.init();
@@ -104,136 +59,15 @@ function commandCompletion_setup() {
     }
 }
 /**
- * Initializes and sets up all command handlers for the ChILI CLI.
- *
- * @param program - The Commander.js program instance.
- */
-async function handlers_initialize() {
-    // const client = await chrisConnection.client_get(); 
-    // We don't enforce connection here to allow --help to work. 
-    // Commands will fail individually if not connected.
-    fileBrowserCommand_setup(program);
-    contextCommand_setup(program);
-    pathCommand_setup(program);
-    manCommand_setup(program);
-    chefsCommand_setup(program);
-    const pacsServerHandler = new PACSServerGroupHandler();
-    pacsServerHandler.pacsServerCommand_setup(program);
-    const pacsQueryHandler = new PACSQueryGroupHandler();
-    pacsQueryHandler.pacsQueryCommand_setup(program);
-    const pacsRetrieveHandler = new PACSRetrieveGroupHandler();
-    pacsRetrieveHandler.pacsRetrieveCommand_setup(program);
-    await inodeCommand_setup(program);
-    const pluginGroupHandler = new PluginGroupHandler();
-    pluginGroupHandler.pluginGroupCommand_setup(program);
-    const pluginMetaGroupHandler = new PluginMetaGroupHandler();
-    pluginMetaGroupHandler.pluginMetaGroupCommand_setup(program);
-    const feedGroupHandler = new FeedGroupHandler();
-    feedGroupHandler.feedGroupCommand_setup(program);
-    const feedMemberHandler = new FeedMemberHandler();
-    feedMemberHandler.feedCommand_setup(program);
-    const pluginMemberHandler = new PluginMemberHandler();
-    pluginMemberHandler.pluginCommand_setup(program);
-    try {
-        const filesGroupHandler = await FileGroupHandler.handler_create("files");
-        filesGroupHandler.fileGroupCommand_setup(program);
-        const linksGroupHandler = await FileGroupHandler.handler_create("links");
-        linksGroupHandler.fileGroupCommand_setup(program);
-        const dirsGroupHandler = await FileGroupHandler.handler_create("dirs");
-        dirsGroupHandler.fileGroupCommand_setup(program);
-    }
-    catch (e) {
-        const err = e instanceof Error ? e.message : String(e);
-        const errors = errorStack_getAllOfType("error");
-        const warnings = errorStack_getAllOfType("warning");
-        console.log(`Note: File group commands (files, dirs, links) are unavailable. Reason: ${err}`);
-        if (errors.length > 0) {
-            console.log("Errors:");
-            errors.forEach(msg => console.log(`  - ${msg}`));
-        }
-        if (warnings.length > 0) {
-            console.log("Warnings:");
-            warnings.forEach(msg => console.log(`  - ${msg}`));
-        }
-    }
-    try {
-        const computesOfPluginHandler = await PluginContextGroupHandler.handler_create("computesofplugin");
-        computesOfPluginHandler.pluginContextGroupCommand_setup(program);
-        const pluginInstancesHandler = await PluginContextGroupHandler.handler_create("instancesofplugin");
-        pluginInstancesHandler.pluginContextGroupCommand_setup(program);
-        const pluginParametersHandler = await PluginContextGroupHandler.handler_create("parametersofplugin");
-        pluginParametersHandler.pluginContextGroupCommand_setup(program);
-    }
-    catch (e) {
-        const err = e instanceof Error ? e.message : String(e);
-        const errors = errorStack_getAllOfType("error");
-        const warnings = errorStack_getAllOfType("warning");
-        console.log(`Note: Plugin context commands are unavailable. Reason: ${err}`);
-        if (errors.length > 0) {
-            console.log("Errors:");
-            errors.forEach(msg => console.log(`  - ${msg}`));
-        }
-        if (warnings.length > 0) {
-            console.log("Warnings:");
-            warnings.forEach(msg => console.log(`  - ${msg}`));
-        }
-    }
-    commandCompletion_setup();
-}
-/**
- * Parses the command line arguments to extract context information.
- *
- * @param args - The command line arguments array (process.argv).
- * @returns A tuple containing the context string (if found) and the remaining arguments.
- */
-function context_parse(args) {
-    // Find the first argument that looks like a context string (contains "=" but doesn't start with "-")
-    for (let i = 2; i < args.length; i++) {
-        const arg = args[i];
-        if (arg.includes("=") && !arg.startsWith("-")) {
-            const context = arg;
-            // Reconstruct args without the context string
-            const newArgs = [...args.slice(0, i), ...args.slice(i + 1)];
-            return [context, newArgs];
-        }
-    }
-    return [undefined, args];
-}
-/**
- * Main function to run the ChILI CLI.
- * Handles initialization, context parsing, and command execution.
+ * Bin entry: register shell completion, then run the requested chili command.
  */
 async function main() {
-    const nodeStorageProvider = new NodeStorageProvider();
-    const connection = await chrisConnection_init(nodeStorageProvider);
-    const [context, newArgs] = context_parse(process.argv);
-    if (context) {
-        const contextSetSuccess = await connection.context_set(context);
-        if (!contextSetSuccess) {
-            console.error("Failed to set context. Exiting.");
-            process.exit(1);
-        }
-        process.argv = newArgs;
-    }
-    program
-        .name("chili")
-        .description("ChILI handles Intelligent Line Interactions")
-        .option("-v, --verbose", "enable verbose output")
-        .option("-c, --config <path>", "path to config file")
-        .option("-s, --nosplash", "disable splash screen");
-    connectCommand_setup(program);
-    await handlers_initialize(); // Call handlers_initialize here
-    program.parseOptions(process.argv);
-    const options = program.opts();
-    if (!options.nosplash) {
-        console.log(figlet.textSync("ChILI"));
-        console.log("ChILI handles Intelligent Line Interactions");
-    }
-    program.parse(process.argv);
+    commandCompletion_setup();
+    await run(process.argv.slice(2));
 }
 main().catch((error) => {
     console.error("An error occurred:", error);
     process.exit(1);
 });
-// Export utilities for use by other packages (e.g., chell)
-export { logical_toPhysical } from './utils/cli.js';
+// Re-export library utilities for consumers that import the package root.
+export { logical_toPhysical } from "./utils/cli.js";

package/dist/man/renderer.d.ts

@@ -23,4 +23,4 @@ export declare function asciidoc_render(content: string, style: "figlet" | "asci
  *
  * @param filePath - The path to the file to open.
  */
-export declare function browser_open(filePath: string): void;
+export declare function browser_open(filePath: string): Promise<void>;

package/dist/man/renderer.js

@@ -6,7 +6,7 @@
 import fs from "fs";
 import path from "path";
 import chalk from "chalk";
-import asciidoctor from "asciidoctor";
+import { convert as adoc_convert } from "asciidoctor";
 import { exec } from "child_process";
 import os from "os";
 const headingStyles = [
@@ -63,9 +63,8 @@ export function projectDir_get() {
  * @param content - The AsciiDoc content string.
  * @returns The converted HTML string.
  */
-function adoc_htmlConvert(content) {
-    const ascii = asciidoctor();
-    let result = ascii.convert(content, {
+async function adoc_htmlConvert(content) {
+    let result = await adoc_convert(content, {
         standalone: false,
         attributes: {
             showtitle: "",
@@ -107,7 +106,7 @@ function text_wrap(text, width) {
  * @returns A Promise resolving to the formatted string.
  */
 export async function asciidoc_render(content, style, width) {
-    let result = adoc_htmlConvert(content);
+    let result = await adoc_htmlConvert(content);
     function ASCII_create(text, style) {
         const transformedText = style.textTransform(text);
         return style.color(transformedText);
@@ -159,12 +158,11 @@ export async function asciidoc_render(content, style, width) {
  *
  * @param filePath - The path to the file to open.
  */
-export function browser_open(filePath) {
-    const ascii = asciidoctor();
+export async function browser_open(filePath) {
     const tempHtmlPath = path.join(os.tmpdir(), path.basename(filePath).replace(".adoc", ".html"));
     try {
         const content = fs.readFileSync(filePath, "utf-8");
-        const html = ascii.convert(content, {
+        const html = await adoc_convert(content, {
             safe: "safe",
             standalone: true,
             attributes: { showtitle: true },

package/dist/path/pathCommand.js

@@ -13,7 +13,7 @@ import { table_display, border_draw } from "../screen/screen.js";
 import { options_toParams } from "../utils/cli.js";
 import archy from "archy";
 import open from "open";
-import { exec } from "child_process";
+import { execFile } from "child_process";
 import os from "os";
 import { files_downloadWithProgress } from "../commands/fs/download.js";
 /**
@@ -160,10 +160,13 @@ async function mermaid_renderServerSide(mermaidDefinition, outputFile) {
     const tempDir = os.tmpdir();
     const inputFile = path.join(tempDir, "input.mmd");
     fs.writeFileSync(inputFile, mermaidDefinition);
+    // Pass args as an array (execFile, no shell) so a user-supplied --save path
+    // cannot inject shell commands. Requires `mmdc` (@mermaid-js/mermaid-cli),
+    // which is fetched on demand via npx and is not a hard dependency.
     return new Promise((resolve, reject) => {
-        exec(`npx mmdc -i ${inputFile} -o ${outputFile}`, (error, stdout, stderr) => {
+        execFile("npx", ["mmdc", "-i", inputFile, "-o", outputFile], (error) => {
             if (error) {
-                console.error(`exec error: ${error}`);
+                console.error(`Mermaid render failed. Ensure @mermaid-js/mermaid-cli is available (npx mmdc): ${error.message}`);
                 reject(error);
                 return;
             }

package/dist/run.d.ts

@@ -0,0 +1,24 @@
+/**
+ * @file In-process library entry for the chili (ChILI) CLI.
+ *
+ * Exposes {@link run}, which builds a fresh Commander program and executes a
+ * single chili command, returning when it completes. Unlike the bin entry
+ * (`index.ts`), importing this module has no side effect of running the CLI and
+ * never calls `process.exit`, so a host process such as chell can drive chili
+ * in-process instead of spawning a separate `node` subprocess.
+ *
+ * @module
+ */
+/**
+ * Executes a single chili command in the current process.
+ *
+ * Builds a fresh Commander program (so repeated calls do not share parser
+ * state), wires all command handlers, and parses the supplied arguments. Help,
+ * version and usage errors are handled gracefully (Commander's message is
+ * already written) instead of terminating the process; genuine errors thrown by
+ * a command action propagate to the caller.
+ *
+ * @param argv - The chili arguments, e.g. `["feeds", "list", "-s"]` (without
+ *   the leading `node`/script entries).
+ */
+export declare function run(argv: string[]): Promise<void>;

package/dist/run.js

@@ -0,0 +1,192 @@
+/**
+ * @file In-process library entry for the chili (ChILI) CLI.
+ *
+ * Exposes {@link run}, which builds a fresh Commander program and executes a
+ * single chili command, returning when it completes. Unlike the bin entry
+ * (`index.ts`), importing this module has no side effect of running the CLI and
+ * never calls `process.exit`, so a host process such as chell can drive chili
+ * in-process instead of spawning a separate `node` subprocess.
+ *
+ * @module
+ */
+import { Command, CommanderError } from "commander";
+import figlet from "figlet";
+import { connectCommand_setup } from "./connect/connectHandler.js";
+import { FeedGroupHandler, FeedMemberHandler } from "./feeds/feedHandler.js";
+import { PluginGroupHandler, PluginMemberHandler, } from "./plugins/pluginHandler.js";
+import { PluginMetaGroupHandler } from "./plugins/pluginMetaHandler.js";
+import { PluginContextGroupHandler } from "./plugins/pluginGroupHandler.js";
+import { inodeCommand_setup } from "./filesystem/inodeCommand.js";
+import { contextCommand_setup } from "./context/contextCommand.js";
+import { pathCommand_setup } from "./path/pathCommand.js";
+import { fileBrowserCommand_setup } from "./filesystem/filesystemHandler.js";
+import { manCommand_setup } from "./man/man.js";
+import { chefsCommand_setup } from "./chefs/chefs.js";
+import { PACSServerGroupHandler } from "./pacs/pacsServerHandler.js";
+import { PACSQueryGroupHandler } from "./pacs/pacsQueryHandler.js";
+import { PACSRetrieveGroupHandler } from "./pacs/pacsRetrieveHandler.js";
+import { chrisConnection_init, NodeStorageProvider, errorStack_getAllOfType, } from "@fnndsc/cumin";
+import { FileGroupHandler } from "./filesystem/fileGroupHandler.js";
+/**
+ * Suppress the DEP0169 (`url.parse()`) warning emitted transitively by
+ * axios -> proxy-from-env, which we do not control. Installed once at import.
+ * See the tracking note in the original bin entry for context.
+ */
+const originalEmitWarning = process.emitWarning;
+process.emitWarning = function (warning, ...args) {
+    if (typeof warning === "string" &&
+        (warning.includes("DEP0169") || warning.includes("url.parse()"))) {
+        return;
+    }
+    return originalEmitWarning.call(process, warning, ...args);
+};
+/**
+ * Registers every chili command handler on the supplied program. The handler
+ * setup functions are program-parameterised, so a fresh program can be wired on
+ * each call without sharing Commander state across invocations.
+ *
+ * @param program - The Commander program to register commands on.
+ */
+async function handlers_initialize(program) {
+    // Connection is intentionally not enforced here so that `--help` works; each
+    // command fails individually if it needs a connection that is not present.
+    fileBrowserCommand_setup(program);
+    contextCommand_setup(program);
+    pathCommand_setup(program);
+    manCommand_setup(program);
+    chefsCommand_setup(program);
+    const pacsServerHandler = new PACSServerGroupHandler();
+    pacsServerHandler.pacsServerCommand_setup(program);
+    const pacsQueryHandler = new PACSQueryGroupHandler();
+    pacsQueryHandler.pacsQueryCommand_setup(program);
+    const pacsRetrieveHandler = new PACSRetrieveGroupHandler();
+    pacsRetrieveHandler.pacsRetrieveCommand_setup(program);
+    await inodeCommand_setup(program);
+    const pluginGroupHandler = new PluginGroupHandler();
+    pluginGroupHandler.pluginGroupCommand_setup(program);
+    const pluginMetaGroupHandler = new PluginMetaGroupHandler();
+    pluginMetaGroupHandler.pluginMetaGroupCommand_setup(program);
+    const feedGroupHandler = new FeedGroupHandler();
+    feedGroupHandler.feedGroupCommand_setup(program);
+    const feedMemberHandler = new FeedMemberHandler();
+    feedMemberHandler.feedCommand_setup(program);
+    const pluginMemberHandler = new PluginMemberHandler();
+    pluginMemberHandler.pluginCommand_setup(program);
+    try {
+        const filesGroupHandler = await FileGroupHandler.handler_create("files");
+        filesGroupHandler.fileGroupCommand_setup(program);
+        const linksGroupHandler = await FileGroupHandler.handler_create("links");
+        linksGroupHandler.fileGroupCommand_setup(program);
+        const dirsGroupHandler = await FileGroupHandler.handler_create("dirs");
+        dirsGroupHandler.fileGroupCommand_setup(program);
+    }
+    catch (e) {
+        const err = e instanceof Error ? e.message : String(e);
+        const errors = errorStack_getAllOfType("error");
+        const warnings = errorStack_getAllOfType("warning");
+        console.log(`Note: File group commands (files, dirs, links) are unavailable. Reason: ${err}`);
+        if (errors.length > 0) {
+            console.log("Errors:");
+            errors.forEach((msg) => console.log(`  - ${msg}`));
+        }
+        if (warnings.length > 0) {
+            console.log("Warnings:");
+            warnings.forEach((msg) => console.log(`  - ${msg}`));
+        }
+    }
+    try {
+        const computesOfPluginHandler = await PluginContextGroupHandler.handler_create("computesofplugin");
+        computesOfPluginHandler.pluginContextGroupCommand_setup(program);
+        const pluginInstancesHandler = await PluginContextGroupHandler.handler_create("instancesofplugin");
+        pluginInstancesHandler.pluginContextGroupCommand_setup(program);
+        const pluginParametersHandler = await PluginContextGroupHandler.handler_create("parametersofplugin");
+        pluginParametersHandler.pluginContextGroupCommand_setup(program);
+    }
+    catch (e) {
+        const err = e instanceof Error ? e.message : String(e);
+        const errors = errorStack_getAllOfType("error");
+        const warnings = errorStack_getAllOfType("warning");
+        console.log(`Note: Plugin context commands are unavailable. Reason: ${err}`);
+        if (errors.length > 0) {
+            console.log("Errors:");
+            errors.forEach((msg) => console.log(`  - ${msg}`));
+        }
+        if (warnings.length > 0) {
+            console.log("Warnings:");
+            warnings.forEach((msg) => console.log(`  - ${msg}`));
+        }
+    }
+}
+/**
+ * Extracts a leading `key=value` context string from an argv array.
+ *
+ * @param args - An argv array shaped like `process.argv` (exec, script, ...).
+ * @returns A tuple of the context string (if any) and argv with it removed.
+ */
+function context_parse(args) {
+    for (let i = 2; i < args.length; i++) {
+        const arg = args[i];
+        if (arg.includes("=") && !arg.startsWith("-")) {
+            const context = arg;
+            const newArgs = [...args.slice(0, i), ...args.slice(i + 1)];
+            return [context, newArgs];
+        }
+    }
+    return [undefined, args];
+}
+/**
+ * Executes a single chili command in the current process.
+ *
+ * Builds a fresh Commander program (so repeated calls do not share parser
+ * state), wires all command handlers, and parses the supplied arguments. Help,
+ * version and usage errors are handled gracefully (Commander's message is
+ * already written) instead of terminating the process; genuine errors thrown by
+ * a command action propagate to the caller.
+ *
+ * @param argv - The chili arguments, e.g. `["feeds", "list", "-s"]` (without
+ *   the leading `node`/script entries).
+ */
+export async function run(argv) {
+    const nodeStorageProvider = new NodeStorageProvider();
+    const connection = await chrisConnection_init(nodeStorageProvider);
+    // Commander's default parsing expects argv[0]/argv[1] to be exec/script.
+    let fullArgv = ["node", "chili", ...argv];
+    const [context, newArgs] = context_parse(fullArgv);
+    if (context) {
+        const contextSetSuccess = await connection.context_set(context);
+        if (!contextSetSuccess) {
+            console.error("Failed to set context.");
+            return;
+        }
+        fullArgv = newArgs;
+    }
+    const program = new Command();
+    program
+        .name("chili")
+        .description("ChILI handles Intelligent Line Interactions")
+        .version("1.0.1")
+        .option("-v, --verbose", "enable verbose output")
+        .option("-c, --config <path>", "path to config file")
+        .option("-s, --nosplash", "disable splash screen")
+        .exitOverride();
+    connectCommand_setup(program);
+    await handlers_initialize(program);
+    program.parseOptions(fullArgv);
+    const options = program.opts();
+    if (!options.nosplash) {
+        console.log(figlet.textSync("ChILI"));
+        console.log("ChILI handles Intelligent Line Interactions");
+    }
+    try {
+        await program.parseAsync(fullArgv);
+    }
+    catch (err) {
+        // Under exitOverride, --help/--version/usage errors throw a CommanderError
+        // whose message Commander has already written. Swallow these so the host
+        // (e.g. a chell REPL) is not torn down; rethrow anything else.
+        if (err instanceof CommanderError) {
+            return;
+        }
+        throw err;
+    }
+}

package/dist/utils/resourceData.d.ts

@@ -0,0 +1,16 @@
+/**
+ * @file Shared shaping helpers for FilteredResourceData prior to display.
+ *
+ * @module
+ */
+import { FilteredResourceData } from "@fnndsc/cumin";
+/**
+ * Removes duplicate column headers from a FilteredResourceData result.
+ *
+ * Keeps each selected field once (preserving first-seen order) and projects
+ * every table row onto that unique header set.
+ *
+ * @param results - The resource data to de-duplicate.
+ * @returns A new FilteredResourceData with unique selectedFields and matching rows.
+ */
+export declare function resourceColumns_removeDuplicates(results: FilteredResourceData): FilteredResourceData;

package/dist/utils/resourceData.js

@@ -0,0 +1,23 @@
+/**
+ * Removes duplicate column headers from a FilteredResourceData result.
+ *
+ * Keeps each selected field once (preserving first-seen order) and projects
+ * every table row onto that unique header set.
+ *
+ * @param results - The resource data to de-duplicate.
+ * @returns A new FilteredResourceData with unique selectedFields and matching rows.
+ */
+export function resourceColumns_removeDuplicates(results) {
+    const uniqueHeaders = Array.from(new Set(results.selectedFields));
+    const uniqueTableData = results.tableData.map((row) => uniqueHeaders.reduce((acc, header) => {
+        if (typeof header === "string" && header in row) {
+            acc[header] = row[header];
+        }
+        return acc;
+    }, {}));
+    return {
+        ...results,
+        selectedFields: uniqueHeaders,
+        tableData: uniqueTableData,
+    };
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@fnndsc/chili",
-  "version": "3.2.5",
+  "version": "3.3.0",
   "description": "ChILI handles Intelligent Line Interactions: A CLI and library for ChRIS, acting as the controller layer for business logic and user presentation.",
   "repository": {
     "type": "git",
@@ -25,7 +25,7 @@
   "scripts": {
     "build": "tsc && chmod +x ./dist/index.js",
     "start": "node dist/index.js",
-    "test": "jest",
+    "test": "jest --coverage",
     "test:coverage": "jest --coverage --coverageProvider=v8",
     "clean": "rm -rf dist types fnndsc-chili*tgz",
     "build:cumin": "cd ../cumin && npm run build",
@@ -47,14 +47,13 @@
   "author": "FNNDSC <dev@babyMRI.org>",
   "license": "MIT",
   "dependencies": {
-    "@fnndsc/cumin": "^3.2.4",
-    "@fnndsc/salsa": "^3.2.4",
+    "@fnndsc/cumin": "^3.4.0",
+    "@fnndsc/salsa": "^3.2.5",
     "@fortawesome/fontawesome-free": "^6.6.0",
     "@fortawesome/fontawesome-svg-core": "^6.6.0",
     "@fortawesome/free-solid-svg-icons": "^6.6.0",
-    "@mermaid-js/mermaid-cli": "^11.12.0",
     "archy": "^1.0.0",
-    "asciidoctor": "^3.0.4",
+    "asciidoctor": "^4.0.1",
     "axios": "^1.6.0",
     "chalk": "^4.1.2",
     "cli-highlight": "^2.1.11",
@@ -65,7 +64,6 @@
     "js-yaml": "^4.1.0",
     "marked": "^9.1.0",
     "marked-terminal": "^6.1.0",
-    "node-fetch": "^3.3.2",
     "omelette": "^0.4.17",
     "open": "^10.1.0",
     "table": "^6.8.1"
@@ -77,7 +75,7 @@
     "@types/jest": "^30.0.0",
     "@types/js-yaml": "^4.0.5",
     "@types/marked-terminal": "^6.1.1",
-    "@types/node": "^24.10.1",
+    "@types/node": "^22.0.0",
     "@types/node-fetch": "^2.6.11",
     "@types/omelette": "^0.4.4",
     "jest": "^30.2.0",