@fnndsc/chili 3.4.0 → 3.5.0

package/dist/chefs/chefs.js

@@ -9,6 +9,7 @@ import { files_rm } from '../commands/fs/rm.js';
 import { files_cp } from '../commands/fs/cp.js';
 import { files_mv } from '../commands/fs/mv.js';
 import { mkdir_render, touch_render, upload_render, cat_render, rm_render, cp_render, mv_render } from '../views/fs.js';
+import { chiliLog } from "../screen/output.js";
 /**
  * Lists directory contents.
  *
@@ -21,10 +22,10 @@ async function chefs_ls(options, pathStr = "") {
         return;
     }
     if (options.long) {
-        console.log(long_render(items, { human: !!options.human }));
+        chiliLog(long_render(items, { human: !!options.human }));
     }
     else {
-        console.log(grid_render(items));
+        chiliLog(grid_render(items));
     }
 }
 /**
@@ -36,7 +37,7 @@ async function chefs_ls(options, pathStr = "") {
  */
 async function chefs_cp(src, dest, options) {
     const success = await files_cp(src, dest, options);
-    console.log(cp_render(src, dest, success));
+    chiliLog(cp_render(src, dest, success));
 }
 /**
  * Moves a file or directory.
@@ -47,7 +48,7 @@ async function chefs_cp(src, dest, options) {
  */
 async function chefs_mv(src, dest, _options) {
     const success = await files_mv(src, dest);
-    console.log(mv_render(src, dest, success));
+    chiliLog(mv_render(src, dest, success));
 }
 /**
  * Creates a directory.
@@ -56,7 +57,7 @@ async function chefs_mv(src, dest, _options) {
  */
 async function chefs_mkdir(dirPath) {
     const success = await files_mkdir(dirPath);
-    console.log(mkdir_render(dirPath, success));
+    chiliLog(mkdir_render(dirPath, success));
 }
 /**
  * Creates an empty file.
@@ -65,7 +66,7 @@ async function chefs_mkdir(dirPath) {
  */
 async function chefs_touch(filePath) {
     const success = await files_touch(filePath);
-    console.log(touch_render(filePath, success));
+    chiliLog(touch_render(filePath, success));
 }
 /**
  * Uploads a local file or directory to ChRIS.
@@ -74,9 +75,9 @@ async function chefs_touch(filePath) {
  * @param remotePath - Remote ChRIS path.
  */
 async function chefs_upload(localPath, remotePath) {
-    console.log(`Uploading ${localPath} to ${remotePath}...`);
+    chiliLog(`Uploading ${localPath} to ${remotePath}...`);
     const success = await files_upload(localPath, remotePath);
-    console.log(upload_render(localPath, remotePath, success));
+    chiliLog(upload_render(localPath, remotePath, success));
 }
 /**
  * Changes the current working directory.
@@ -96,7 +97,7 @@ async function chefs_cd(path) {
  */
 async function chefs_pwd() {
     const current = await chrisContext.current_get(Context.ChRISfolder);
-    console.log(current || "/");
+    chiliLog(current || "/");
 }
 /**
  * Displays file content.
@@ -106,7 +107,7 @@ async function chefs_pwd() {
 async function chefs_cat(filePath) {
     const result = await files_cat(filePath);
     const content = result.ok ? result.value : null;
-    console.log(cat_render(content, filePath));
+    chiliLog(cat_render(content, filePath));
 }
 /**
  * Removes a file or directory.
@@ -116,7 +117,7 @@ async function chefs_cat(filePath) {
  */
 async function chefs_rm(targetPath, options) {
     const result = await files_rm(targetPath, options);
-    console.log(rm_render(result));
+    chiliLog(rm_render(result));
 }
 /**
  * Sets up the 'chefs' command group in Commander.

package/dist/commands/fs/download.js

@@ -10,6 +10,7 @@ import chalk from "chalk";
 import { pipeline } from "stream/promises";
 import { bytes_format } from "./upload.js";
 import { prompt_confirmOrThrow } from "../../utils/input_format.js";
+import { chiliLog } from "../../screen/output.js";
 export { bytes_format };
 /**
  * Recursively creates a directory and all parent directories.
@@ -141,7 +142,7 @@ export async function files_downloadWithProgress(chrisPath, localPath, options =
         }
     }
     // Download directory
-    console.log(chalk.cyan("Scanning files to download..."));
+    chiliLog(chalk.cyan("Scanning files to download..."));
     options.onProgress?.({
         operation: "download",
         kind: "transfer",
@@ -190,7 +191,7 @@ export async function files_downloadWithProgress(chrisPath, localPath, options =
             const result = await fileContent_getBinaryStream(file.path);
             if (!result.ok) {
                 summary.failedCount++;
-                console.log(chalk.yellow(`\nFailed to download: ${file.path}`));
+                chiliLog(chalk.yellow(`\nFailed to download: ${file.path}`));
                 continue;
             }
             const { stream, size } = result.value;
@@ -212,7 +213,7 @@ export async function files_downloadWithProgress(chrisPath, localPath, options =
         catch (error) {
             summary.failedCount++;
             const msg = error instanceof Error ? error.message : String(error);
-            console.log(chalk.red(`\nError downloading ${file.path}: ${msg}`));
+            chiliLog(chalk.red(`\nError downloading ${file.path}: ${msg}`));
         }
         options.onProgress?.({
             operation: "download",

package/dist/commands/fs/upload.js

@@ -9,6 +9,7 @@ import fs from "fs";
 import path from "path";
 import chalk from "chalk";
 import { prompt_confirmOrThrow } from "../../utils/input_format.js";
+import { chiliLog } from "../../screen/output.js";
 /**
  * Formats bytes into human-readable format.
  * @param bytes - Number of bytes.
@@ -109,7 +110,7 @@ async function localFiles_scan(localPath, remotePath) {
 export async function files_uploadWithProgress(localPath, remotePath, options = {}) {
     const resolvedRemote = await path_resolveChrisFs(remotePath, {});
     // Scan files
-    console.log(chalk.cyan("Scanning files to upload..."));
+    chiliLog(chalk.cyan("Scanning files to upload..."));
     options.onProgress?.({
         operation: "upload",
         kind: "transfer",
@@ -184,12 +185,12 @@ export async function files_uploadWithProgress(localPath, remotePath, options =
             }
             else {
                 summary.failedCount++;
-                console.log(chalk.yellow(`Failed to upload: ${file.hostPath}`));
+                chiliLog(chalk.yellow(`Failed to upload: ${file.hostPath}`));
             }
         }
         catch (error) {
             summary.failedCount++;
-            console.log(chalk.red(`Error uploading ${file.hostPath}: ${error instanceof Error ? error.message : String(error)}`));
+            chiliLog(chalk.red(`Error uploading ${file.hostPath}: ${error instanceof Error ? error.message : String(error)}`));
         }
         options.onProgress?.({
             operation: "upload",

package/dist/commands/man/doc.js

@@ -9,6 +9,7 @@
 import fs from "fs";
 import path from "path";
 import { projectDir_get, browser_open, asciidoc_render } from "../../man/renderer.js";
+import { chiliErrLog, chiliLog } from "../../screen/output.js";
 /**
  * Displays a documentation page for a specific topic.
  *
@@ -19,7 +20,7 @@ export async function manPage_display(options) {
     const docDir = path.join(projectDir_get(), "doc");
     const docPath = path.join(docDir, `${options.topic}.adoc`);
     if (!fs.existsSync(docPath)) {
-        console.error(`Documentation for '${options.topic}' not found.`);
+        chiliErrLog(`Documentation for '${options.topic}' not found.`);
         return;
     }
     if (options.browser) {
@@ -27,6 +28,6 @@ export async function manPage_display(options) {
     }
     else {
         const content = fs.readFileSync(docPath, "utf-8");
-        console.log(await asciidoc_render(content, options.style, options.width));
+        chiliLog(await asciidoc_render(content, options.style, options.width));
     }
 }

package/dist/commands/plugins/add.js

@@ -14,13 +14,14 @@ import { computeResources_validate, computeResourceNames_parse, computeResources
 import path from 'path';
 import { input_detectFormat, PluginInputFormat, } from '../../utils/input_format.js';
 import { adminCredentials_prompt, } from '../../utils/admin_prompt.js';
+import { chiliErrLog, chiliLog } from "../../screen/output.js";
 async function computeResources_resolve(options) {
     if (options.compute) {
         const names = computeResourceNames_parse(options.compute);
         const validationResult = await computeResources_validate(names);
         if (!validationResult.ok) {
             const errors = errorStack.allOfType_get('error');
-            errors.forEach((err) => console.error(err));
+            errors.forEach((err) => chiliErrLog(err));
             return { ok: false };
         }
         return { ok: true, value: names };
@@ -28,7 +29,7 @@ async function computeResources_resolve(options) {
     const allResult = await computeResources_getAll();
     if (allResult.ok && allResult.value.length > 0) {
         const names = allResult.value.map((r) => r.name);
-        console.log(`Using compute resources: ${names.join(', ')}`);
+        chiliLog(`Using compute resources: ${names.join(', ')}`);
         return { ok: true, value: names };
     }
     return { ok: true, value: ['host'] };
@@ -42,13 +43,13 @@ async function computeResources_resolve(options) {
  */
 export async function plugin_add(input, options) {
     const detected = input_detectFormat(input);
-    console.log(`Detected input format: ${detected.format}`);
+    chiliLog(`Detected input format: ${detected.format}`);
     const resourcesResult = await computeResources_resolve(options);
     if (!resourcesResult.ok)
         return 'failed';
     const computeResources = resourcesResult.value;
     // Phase 1: Check if plugin exists in current CUBE
-    console.log('\n=== Phase 1: Checking current CUBE ===');
+    chiliLog('\n=== Phase 1: Checking current CUBE ===');
     const searchTerm = detected.format === PluginInputFormat.DOCKER_IMAGE
         ? detected.pluginName || detected.value
         : detected.value;
@@ -56,10 +57,10 @@ export async function plugin_add(input, options) {
     if (existingPlugin) {
         return 'already_exists';
     }
-    console.log('Plugin not found in current CUBE.');
+    chiliLog('Plugin not found in current CUBE.');
     // Phase 2: Search peer stores (skip if input is store URL)
     if (detected.format !== PluginInputFormat.STORE_URL) {
-        console.log('\n=== Phase 2: Searching peer stores ===');
+        chiliLog('\n=== Phase 2: Searching peer stores ===');
         const peerStoreUrls = options.store
             ? [options.store]
             : ['https://cube.chrisproject.org/api/v1/'];
@@ -71,15 +72,15 @@ export async function plugin_add(input, options) {
             : undefined;
         const peerResult = await plugins_searchPeers(searchName, searchVersion, peerStoreUrls);
         if (peerResult) {
-            console.log(`Found plugin in peer store: ${peerResult.storeName}`);
+            chiliLog(`Found plugin in peer store: ${peerResult.storeName}`);
             const ok = await pluginFromStore_register(peerResult.plugin, computeResources, options);
             return ok ? 'installed' : 'failed';
         }
-        console.log('Plugin not found in peer stores.');
+        chiliLog('Plugin not found in peer stores.');
     }
     // Phase 3: Docker extraction (only for Docker images or plugin names)
     if (detected.format !== PluginInputFormat.STORE_URL) {
-        console.log('\n=== Phase 3: Docker extraction ===');
+        chiliLog('\n=== Phase 3: Docker extraction ===');
         const dockerImage = detected.format === PluginInputFormat.DOCKER_IMAGE
             ? detected.value
             : `${detected.value}:latest`; // Assume latest tag for plugin names
@@ -87,7 +88,7 @@ export async function plugin_add(input, options) {
         return ok ? 'installed' : 'failed';
     }
     // If we get here with a store URL, we couldn't process it
-    console.error('Store URL import not yet fully supported.');
+    chiliErrLog('Store URL import not yet fully supported.');
     return 'failed';
 }
 /**
@@ -101,7 +102,7 @@ export async function plugin_add(input, options) {
  * @returns Promise resolving to success boolean.
  */
 async function pluginFromStore_register(pluginData, computeResources, options) {
-    console.log('Importing plugin from peer store...');
+    chiliLog('Importing plugin from peer store...');
     const initialCreds = options.adminUser && options.adminPassword
         ? { username: options.adminUser, password: options.adminPassword }
         : undefined;
@@ -109,11 +110,11 @@ async function pluginFromStore_register(pluginData, computeResources, options) {
     const result = await plugin_importFromStore('', // Store URL not needed when we have plugin data
     pluginData, computeResources, initialCreds);
     if (result.success) {
-        console.log(`Plugin '${result.plugin?.name}' registered successfully.`);
+        chiliLog(`Plugin '${result.plugin?.name}' registered successfully.`);
         return true;
     }
     if (!result.requiresAuth) {
-        console.error(result.errorMessage || 'Failed to import plugin from store.');
+        chiliErrLog(result.errorMessage || 'Failed to import plugin from store.');
         return false;
     }
     // Admin auth required - try with interactive credentials
@@ -122,16 +123,16 @@ async function pluginFromStore_register(pluginData, computeResources, options) {
         return retryResult.success;
     }, options);
     if (!retrySuccess) {
-        console.error('Failed to import plugin from store (authentication failed or rejected).');
+        chiliErrLog('Failed to import plugin from store (authentication failed or rejected).');
         const errors = errorStack.allOfType_get('error');
         if (errors.length > 0) {
-            console.error('Errors:');
-            errors.forEach((e) => console.error(`- ${e}`));
+            chiliErrLog('Errors:');
+            errors.forEach((e) => chiliErrLog(`- ${e}`));
         }
         const warnings = errorStack.allOfType_get('warning');
         if (warnings.length > 0) {
-            console.error('Warnings:');
-            warnings.forEach((e) => console.error(`- ${e}`));
+            chiliErrLog('Warnings:');
+            warnings.forEach((e) => chiliErrLog(`- ${e}`));
         }
     }
     return retrySuccess;
@@ -155,11 +156,11 @@ async function pluginFromDocker_register(image, computeResources, options) {
     if (!pulled) {
         return false;
     }
-    console.log('Extracting plugin descriptor from image...');
+    chiliLog('Extracting plugin descriptor from image...');
     const pluginData = await pluginJSON_extractFromImage(image, options);
     if (!pluginData) {
         const msg = 'Failed to extract plugin descriptor from image.';
-        console.error(msg);
+        chiliErrLog(msg);
         errorStack.stack_push('error', msg);
         return false;
     }
@@ -169,10 +170,10 @@ async function pluginFromDocker_register(image, computeResources, options) {
         ? { username: options.adminUser, password: options.adminPassword }
         : undefined;
     // Register with admin API
-    console.log('Registering plugin with ChRIS CUBE...');
+    chiliLog('Registering plugin with ChRIS CUBE...');
     const registered = await plugin_registerWithAdmin(pluginData, computeResources, initialCreds);
     if (registered) {
-        console.log(`Plugin '${registered.name}' registered successfully.`);
+        chiliLog(`Plugin '${registered.name}' registered successfully.`);
         return true;
     }
     // Check if failure was due to admin auth
@@ -187,7 +188,7 @@ async function pluginFromDocker_register(image, computeResources, options) {
             lowerE.includes('admin credentials required');
     });
     if (!authError) {
-        console.error('Failed to register plugin.');
+        chiliErrLog('Failed to register plugin.');
         return false;
     }
     // Retry with admin credentials
@@ -224,17 +225,17 @@ async function pluginJSON_extractFromImage(image, options) {
         },
     ];
     for (const method of methods) {
-        console.log(`Trying ${method.name}...`);
+        chiliLog(`Trying ${method.name}...`);
         const jsonString = await method.fn();
         if (jsonString && jsonString.trim() !== '') {
             try {
                 const parsed = JSON.parse(jsonString);
-                console.log(`Successfully extracted plugin descriptor using ${method.name}`);
+                chiliLog(`Successfully extracted plugin descriptor using ${method.name}`);
                 return parsed;
             }
             catch (e) {
                 const msg = `Failed to parse JSON from ${method.name}`;
-                console.error(msg);
+                chiliErrLog(msg);
                 errorStack.stack_push('error', msg);
             }
         }
@@ -296,7 +297,7 @@ async function pluginJSON_tryOldChrisapp(image) {
         return null;
     }
     const command = `docker run --rm ${image} ${cmd[0]} --json`;
-    console.log(`  Running: ${cmd[0]} --json`);
+    chiliLog(`  Running: ${cmd[0]} --json`);
     const result = await shellCommand_runWithDetails(command);
     if (!result.success || !result.stdout || result.stdout.trim() === '') {
         if (result.error || result.stderr) {
@@ -319,20 +320,20 @@ function pluginData_inferMissingFields(pluginData, image, options) {
     if (!pluginData.name) {
         const imageNameWithoutTag = image.split(':')[0];
         pluginData.name = path.basename(imageNameWithoutTag);
-        console.log(`Inferred plugin name: ${pluginData.name}`);
+        chiliLog(`Inferred plugin name: ${pluginData.name}`);
     }
     if (!pluginData.dock_image) {
         pluginData.dock_image = image;
-        console.log(`Inferred dock_image: ${pluginData.dock_image}`);
+        chiliLog(`Inferred dock_image: ${pluginData.dock_image}`);
     }
     if (!pluginData.public_repo && options.public_repo) {
         pluginData.public_repo = options.public_repo;
-        console.log(`Using provided public_repo: ${pluginData.public_repo}`);
+        chiliLog(`Using provided public_repo: ${pluginData.public_repo}`);
     }
     else if (!pluginData.public_repo && image.includes('/')) {
         const repoGuess = image.split('/')[0] + '/' + path.basename(image.split(':')[0]);
         pluginData.public_repo = `https://github.com/${repoGuess}`;
-        console.log(`Inferred public_repo: ${pluginData.public_repo}`);
+        chiliLog(`Inferred public_repo: ${pluginData.public_repo}`);
     }
 }
 /**
@@ -358,7 +359,7 @@ async function registrationWithAuth_retry(registrationFn, options) {
     for (let attempt = 1; attempt <= MAX_ATTEMPTS; attempt++) {
         const creds = await adminCredentials_prompt(attempt, MAX_ATTEMPTS);
         if (!creds) {
-            console.log('Authentication cancelled.');
+            chiliLog('Authentication cancelled.');
             return false;
         }
         const success = await registrationFn(creds);
@@ -366,9 +367,9 @@ async function registrationWithAuth_retry(registrationFn, options) {
             return true;
         }
         if (attempt < MAX_ATTEMPTS) {
-            console.log('Authentication failed.');
+            chiliLog('Authentication failed.');
         }
     }
-    console.error(`Authentication failed after ${MAX_ATTEMPTS} attempts.`);
+    chiliErrLog(`Authentication failed after ${MAX_ATTEMPTS} attempts.`);
     return false;
 }

package/dist/config/colorConfig.js

@@ -11,6 +11,7 @@ import * as fs from 'fs';
 import * as path from 'path';
 import { fileURLToPath } from 'url';
 import chalk from 'chalk';
+import { chiliErrLog } from "../screen/output.js";
 let cachedConfig = null;
 /**
  * Loads the color configuration from colors.yml.
@@ -32,7 +33,7 @@ function colorConfig_load() {
     }
     catch (e) {
         const msg = e instanceof Error ? e.message : String(e);
-        console.error(`Warning: Could not load color config: ${msg}`);
+        chiliErrLog(`Warning: Could not load color config: ${msg}`);
         return {
             icons: {
                 enabled: true,

package/dist/connect/connectHandler.js

@@ -2,6 +2,7 @@ import { connect_login } from "../commands/connect/login.js";
 import { connect_logout } from "../commands/connect/logout.js";
 import { login_render, logout_render } from "../views/connect.js";
 import chalk from "chalk";
+import { chiliErrLog, chiliLog } from "../screen/output.js";
 /**
  * Sets up the 'connect' and 'logout' commands for the CLI program.
  *
@@ -23,12 +24,12 @@ export function connectCommand_setup(program) {
         };
         try {
             const success = await connect_login(connectOptions);
-            console.log(login_render(success, url, user));
+            chiliLog(login_render(success, url, user));
         }
         catch (error) {
-            console.log(login_render(false, url, user));
+            chiliLog(login_render(false, url, user));
             const msg = error instanceof Error ? error.message : String(error);
-            console.error(chalk.red(`Error: ${msg}`));
+            chiliErrLog(chalk.red(`Error: ${msg}`));
         }
     });
     program
@@ -37,12 +38,12 @@ export function connectCommand_setup(program) {
         .action(async () => {
         try {
             await connect_logout();
-            console.log(logout_render(true));
+            chiliLog(logout_render(true));
         }
         catch (error) {
-            console.log(logout_render(false));
+            chiliLog(logout_render(false));
             const msg = error instanceof Error ? error.message : String(error);
-            console.error(chalk.red(`Error: ${msg}`));
+            chiliErrLog(chalk.red(`Error: ${msg}`));
         }
     });
 }

package/dist/context/contextCommand.js

@@ -8,6 +8,7 @@ import { context_getFull, context_getSingle, context_set as salsa_context_set }
 import chalk from "chalk";
 // import Table from "cli-table3";
 import { screen, border_draw, table_display } from "../screen/screen.js";
+import { chiliLog } from "../screen/output.js";
 /**
  * Retrieves and formats ChRIS context information based on CLI options.
  *
@@ -94,7 +95,7 @@ async function context_displaySingle(options) {
                 Value: singleContext.pacsserver || "Not set",
             },
         ];
-        console.log(screen.table_output(tableData, {
+        chiliLog(screen.table_output(tableData, {
             head: ["Context", "Value"],
             columns: [
                 { color: "yellow", justification: "right" },
@@ -174,7 +175,7 @@ export async function contextCommand_setup(program) {
         .option("--all", "get all contexts for current session")
         .action(async (options) => {
         const result = await context_get(options);
-        console.log(result);
+        chiliLog(result);
     });
     contextCommand
         .command("set")

package/dist/controllers/fileController.js

@@ -7,6 +7,7 @@ import { errorStack } from "@fnndsc/cumin";
 import chalk from 'chalk';
 import { BaseController } from "./baseController.js";
 import { files_getGroup, files_getSingle, files_share as salsaFiles_share, fileContent_get } from "@fnndsc/salsa";
+import { chiliErrLog, chiliLog } from "../screen/output.js";
 /**
  * Controller for managing ChRIS file system resources (files, links, directories).
  * Extends BaseController to provide file-specific functionality.
@@ -62,7 +63,7 @@ export class FileController extends BaseController {
     async files_share(options) {
         const fileId = options.fileId; // Assuming CLIoptions has a fileId property
         if (fileId === undefined) {
-            console.error("Error: fileId is required for sharing.");
+            chiliErrLog("Error: fileId is required for sharing.");
             return;
         }
         const shareOptions = { ...options }; // Pass all CLI options as share options for now
@@ -78,10 +79,10 @@ export class FileController extends BaseController {
         const result = await fileContent_get(filePath);
         if (!result.ok) {
             const error = errorStack.stack_pop();
-            console.error(chalk.red(`Error viewing file: ${error?.message || 'Unknown error'}`));
+            chiliErrLog(chalk.red(`Error viewing file: ${error?.message || 'Unknown error'}`));
             return;
         }
-        console.log(result.value);
+        chiliLog(result.value);
     }
     /**
      * Gets the current path associated with this controller.

package/dist/controllers/pluginController.js

@@ -6,6 +6,7 @@
 import { ChRISPluginGroup, dictionary_fromCLI } from "@fnndsc/cumin";
 import { BaseController } from "./baseController.js";
 import { plugin_run as salsaPlugin_run, plugins_searchableToIDs as salsaPlugins_searchableToIDs, pluginMeta_readmeContentFetch, pluginMeta_documentationUrlGet, pluginMeta_pluginIDFromSearch } from "@fnndsc/salsa";
+import { chiliErrLog } from "../screen/output.js";
 /**
  * Controller for managing ChRIS plugins.
  * Handles plugin searching, running, and group operations.
@@ -54,7 +55,7 @@ export class PluginController extends BaseController {
             parsedParams = dictionary_fromCLI(params);
         }
         catch (e) {
-            console.error("Error parsing plugin parameters:", e);
+            chiliErrLog("Error parsing plugin parameters:", e);
             return null;
         }
         return await salsaPlugin_run(searchable, parsedParams);