Implement Phase 2 items and Phase 3 task 14 from plan.md

cbrain_cli/cli_utils.py

@@ -1,12 +1,13 @@
 import functools
+import importlib.metadata
 import json
 import re
+import socket
 import urllib.error
 import urllib.parse
 import urllib.request
 
-# import importlib.metadata
-from cbrain_cli.config import DEFAULT_HEADERS, auth_headers, load_credentials
+from cbrain_cli.config import DEFAULT_HEADERS, DEFAULT_TIMEOUT, auth_headers, load_credentials
 
 credentials = load_credentials() or {}
 cbrain_url = credentials.get("cbrain_url")
@@ -136,11 +137,11 @@ def handle_connection_error(error):
                     error_data = json.loads(error_response)
                     if isinstance(error_data, dict):
                         # Look for common error message fields
-                        error_msg = (
+                        error_msg = str(
                             error_data.get("message")
                             or error_data.get("error")
                             or error_data.get("notice")
-                            or str(error_data)
+                            or error_data
                         )
                         # Check if this looks like a password change redirect
                         if "change_password" in error_msg:
@@ -186,7 +187,12 @@ def handle_connection_error(error):
         else:
             print(f"{status_description}: {error.reason}")
     elif isinstance(error, urllib.error.URLError):
-        if "Connection refused" in str(error):
+        if isinstance(error.reason, socket.timeout):
+            print(
+                f"Error: Request timed out after {DEFAULT_TIMEOUT}s. "
+                "Check your connection or set CBRAIN_TIMEOUT env var."
+            )
+        elif "Connection refused" in str(error):
             print(f"Error: Cannot connect to CBRAIN server at {cbrain_url}")
             print("Please check if the CBRAIN server is running and accessible.")
         else:
@@ -215,6 +221,10 @@ def wrapper(*args, **kwargs):
         except urllib.error.URLError as e:
             handle_connection_error(e)
             return 1
+        except socket.timeout as e:
+            # Read-stage timeouts are raised bare, not wrapped in URLError.
+            handle_connection_error(urllib.error.URLError(e))
+            return 1
         except json.JSONDecodeError:
             print("Failed: Invalid response from server")
             return 1
@@ -245,14 +255,15 @@ def version_info(args):
     int
         Exit code (0 for success, 1 for failure)
     """
-    print("cbrain cli client version 1.0")
-    # try:
-    #     cbrain_cli_version = importlib.metadata.version('cbrain-cli')
-    #     print(f"cbrain cli client version {cbrain_cli_version}")
-    #     return 0
-    # except importlib.metadata.PackageNotFoundError:
-    #     print("Warning: Could not determine version. Package may not be installed properly.")
-    #     return 1
+    try:
+        cbrain_cli_version = importlib.metadata.version("cbrain-cli")
+        if output_json(args, {"version": cbrain_cli_version}):
+            return 0
+        print(f"cbrain cli client version {cbrain_cli_version}")
+        return 0
+    except importlib.metadata.PackageNotFoundError:
+        print("Warning: Could not determine version. Package may not be installed properly.")
+        return 1
 
 
 def api_get(url, token, params=None):
@@ -262,7 +273,7 @@ def api_get(url, token, params=None):
     if params:
         url = f"{url}?{urllib.parse.urlencode(params)}"
     req = urllib.request.Request(url, headers=auth_headers(token), method="GET")
-    with urllib.request.urlopen(req) as r:
+    with urllib.request.urlopen(req, timeout=DEFAULT_TIMEOUT) as r:
         return json.loads(r.read().decode())
 
 
@@ -273,7 +284,7 @@ def api_post_form(url, form_data, headers=None):
     headers = headers or DEFAULT_HEADERS
     body = urllib.parse.urlencode(form_data).encode()
     req = urllib.request.Request(url, data=body, headers=headers, method="POST")
-    with urllib.request.urlopen(req) as r:
+    with urllib.request.urlopen(req, timeout=DEFAULT_TIMEOUT) as r:
         return json.loads(r.read().decode())
 
 
@@ -287,7 +298,7 @@ def api_send(url, token, method="POST", payload=None):
         headers["Content-Type"] = "application/json"
         body = json.dumps(payload).encode()
     req = urllib.request.Request(url, data=body, headers=headers, method=method)
-    with urllib.request.urlopen(req) as r:
+    with urllib.request.urlopen(req, timeout=DEFAULT_TIMEOUT) as r:
         raw = r.read().decode()
         return (json.loads(raw) if raw.strip() else {}), r.status
 

cbrain_cli/config.py

@@ -15,6 +15,12 @@
 CREDENTIALS_FILE = SESSION_FILE_DIR / SESSION_FILE_NAME
 DEFAULT_CREDENTIALS_MODE = 0o600
 
+# HTTP request timeout in seconds; override with CBRAIN_TIMEOUT env var.
+try:
+    DEFAULT_TIMEOUT = max(1, int(os.environ.get("CBRAIN_TIMEOUT", "30")))
+except ValueError:
+    DEFAULT_TIMEOUT = 30
+
 # HTTP headers.
 DEFAULT_HEADERS = {
     "Content-Type": "application/x-www-form-urlencoded",

cbrain_cli/data/files.py

@@ -11,7 +11,7 @@
     cbrain_url,
     pagination,
 )
-from cbrain_cli.config import auth_headers
+from cbrain_cli.config import DEFAULT_TIMEOUT, auth_headers
 
 
 def show_file(args):
@@ -50,7 +50,7 @@ def upload_file(args):
         (response_data, response_status, file_name, file_size) or None if error
     """
     # Check if file exists.
-    if not os.path.exists(args.file_path):
+    if not os.path.isfile(args.file_path):
         raise CliValidationError(f"File not found: {args.file_path}", field="file_path")
 
     if args.group_id is None:
@@ -92,7 +92,7 @@ def upload_file(args):
     request = urllib.request.Request(
         f"{cbrain_url}/userfiles", data=body, headers=headers, method="POST"
     )
-    with urllib.request.urlopen(request) as response:
+    with urllib.request.urlopen(request, timeout=DEFAULT_TIMEOUT) as response:
         response_data = json.loads(response.read().decode("utf-8"))
         return response_data, response.status, file_name, file_size, args.data_provider
 

cbrain_cli/data/projects.py

@@ -42,7 +42,9 @@ def switch_project(args):
             f"Invalid group ID '{group_id}'. Must be a number or 'all'", field="group_id"
         ) from None
 
-    api_send(f"{cbrain_url}/groups/switch?id={group_id}", api_token)
+    _, switch_status = api_send(f"{cbrain_url}/groups/switch?id={group_id}", api_token)
+    if switch_status not in (200, 201, 204):
+        raise CliApiError(f"Failed to switch project (HTTP {switch_status})")
     group_data = api_get(f"{cbrain_url}/groups/{group_id}", api_token)
 
     credentials = load_credentials()

cbrain_cli/data/tools.py

@@ -35,10 +35,10 @@ def show_tool(args):
             api_token,
             {"page": str(page), "per_page": str(per_page)},
         )
-        if not tools_page:
+        if not tools_page or not isinstance(tools_page, list):
             break
         for tool in tools_page:
-            if tool.get("id") == tool_id:
+            if str(tool.get("id")) == str(tool_id):
                 return tool
         if len(tools_page) < per_page:
             break

cbrain_cli/formatter/background_activities_fmt.py

@@ -29,11 +29,7 @@ def print_activities_list(activities_data, args):
             "remote_resource_id": a.get("remote_resource_id", ""),
             "status": a.get("status", ""),
             "created_at": (
-                a.get("created_at", "").split("T")[0]
-                + " "
-                + a.get("created_at", "").split("T")[1].split(".")[0]
-                if a.get("created_at")
-                else ""
+                a["created_at"].replace("T", " ").split(".")[0] if a.get("created_at") else ""
             ),
             "items": ",".join(map(str, a.get("items", []))) if a.get("items") else "",
             "num_successes": a.get("num_successes", 0),

cbrain_cli/formatter/files_fmt.py

@@ -58,7 +58,9 @@ def print_files_list(files_data, args):
     dynamic_table_print(files_data, ["id", "type", "name"], ["ID", "Type", "File Name"])
 
 
-def print_upload_result(response_data, response_status, file_name, file_size, data_provider_id):
+def print_upload_result(
+    response_data, response_status, file_name, file_size, data_provider_id, args=None
+):
     """
     Print the result of a file upload operation.
 
@@ -74,7 +76,12 @@ def print_upload_result(response_data, response_status, file_name, file_size, da
         Size of the uploaded file in bytes
     data_provider_id : int
         ID of the data provider
+    args : argparse.Namespace, optional
+        Command line arguments, including the --json flag
     """
+    if args is not None and output_json(args, response_data):
+        return
+
     print(f"Uploading {file_name} ({file_size} bytes) to data provider {data_provider_id}...")
 
     if response_status == 200 or response_status == 201:
@@ -83,7 +90,7 @@ def print_upload_result(response_data, response_status, file_name, file_size, da
             print(f"Server response: {response_data['notice']}")
 
 
-def print_move_copy_result(response_data, response_status, operation="move"):
+def print_move_copy_result(response_data, response_status, operation="move", args=None):
     """
     Print the result of a file move or copy operation.
 
@@ -95,7 +102,12 @@ def print_move_copy_result(response_data, response_status, operation="move"):
         HTTP status code
     operation : str
         Operation type ("move" or "copy")
+    args : argparse.Namespace, optional
+        Command line arguments, including the --json flag
     """
+    if args is not None and output_json(args, response_data):
+        return
+
     if response_status == 200 or response_status == 201:
         # Show the message from the API response
         message = response_data.get("message", "").strip()

cbrain_cli/formatter/tags_fmt.py

@@ -58,7 +58,13 @@ def print_tag_details(tag_data, args):
 
 
 def print_tag_operation_result(
-    operation, tag_id=None, success=True, error_msg=None, response_status=None
+    operation,
+    tag_id=None,
+    success=True,
+    error_msg=None,
+    response_status=None,
+    args=None,
+    response_data=None,
 ):
     """
     Print result of a tag operation (create, update, delete).
@@ -75,7 +81,25 @@ def print_tag_operation_result(
         Error message if operation failed
     response_status : int, optional
         HTTP response status code if operation failed
+    args : argparse.Namespace, optional
+        Command line arguments, including the --json flag
+    response_data : dict, optional
+        Raw API response data for structured output
     """
+    if args is not None:
+        structured = (
+            response_data
+            if response_data
+            else {
+                "operation": operation,
+                "success": success,
+                "tag_id": tag_id,
+                "error": error_msg,
+            }
+        )
+        if output_json(args, structured):
+            return
+
     if success:
         if operation == "create":
             print("Tag created successfully!")

cbrain_cli/formatter/tasks_fmt.py

@@ -27,7 +27,7 @@ def print_task_data(tasks_data, args):
     formatted_tasks = [
         {
             "id": task.get("id", ""),
-            "type": task.get("type", "").replace("BoutiquesTask::", ""),
+            "type": (task.get("type") or "").replace("BoutiquesTask::", ""),
             "status": task.get("status", ""),
             "bourreau_id": task.get("bourreau_id", ""),
             "user_id": task.get("user_id", ""),
@@ -108,7 +108,7 @@ def print_task_details(task_data, args):
         print()
         print("DESCRIPTION")
         print("-" * 30)
-        for line in task_data.get("description").strip().split("\n"):
+        for line in str(task_data.get("description", "")).strip().split("\n"):
             print(line)
 
     # Display params if they exist.

cbrain_cli/formatter/tool_configs_fmt.py

@@ -88,4 +88,6 @@ def print_boutiques_descriptor(boutiques_descriptor, args):
         print("No Boutiques descriptor found.")
         return
 
+    if output_json(args, boutiques_descriptor):
+        return
     json_printer(boutiques_descriptor)

cbrain_cli/handlers.py

@@ -5,7 +5,7 @@
 and format their output appropriately.
 """
 
-from cbrain_cli.cli_utils import json_printer
+from cbrain_cli.cli_utils import json_printer, output_json
 from cbrain_cli.data import (
     background_activities,
     data_providers,
@@ -56,7 +56,7 @@ def handle_file_upload(args):
     result = files.upload_file(args)
     if result is None:
         return 1
-    files_fmt.print_upload_result(*result)
+    files_fmt.print_upload_result(*result, args=args)
     if result[1] not in (200, 201):
         return 1
 
@@ -66,7 +66,7 @@ def handle_file_copy(args):
     result = files.copy_file(args)
     if result is None:
         return 1
-    files_fmt.print_move_copy_result(*result, operation="copy")
+    files_fmt.print_move_copy_result(*result, operation="copy", args=args)
     if result[1] not in (200, 201):
         return 1
 
@@ -76,7 +76,7 @@ def handle_file_move(args):
     result = files.move_file(args)
     if result is None:
         return 1
-    files_fmt.print_move_copy_result(*result, operation="move")
+    files_fmt.print_move_copy_result(*result, operation="move", args=args)
     if result[1] not in (200, 201):
         return 1
 
@@ -111,6 +111,8 @@ def handle_dataprovider_is_alive(args):
     result = data_providers.is_alive(args)
     if result is None:
         return 1
+    if output_json(args, result):
+        return
     json_printer(result)
 
 
@@ -119,6 +121,8 @@ def handle_dataprovider_delete_unregistered(args):
     result = data_providers.delete_unregistered_files(args)
     if result is None:
         return 1
+    if output_json(args, result):
+        return
     json_printer(result)
 
 
@@ -161,6 +165,8 @@ def handle_project_show(args):
 def handle_project_unswitch(args):
     """Unswitch from current project context."""
     result = projects.unswitch_project(args)
+    if result is None:
+        return 1
     projects_fmt.print_unswitch_result(result, args)
 
 
@@ -229,7 +235,12 @@ def handle_tag_create(args):
     if result is None:
         return 1
     tags_fmt.print_tag_operation_result(
-        "create", success=result[1], error_msg=result[2], response_status=result[3]
+        "create",
+        success=result[1],
+        error_msg=result[2],
+        response_status=result[3],
+        args=args,
+        response_data=result[0],
     )
     if not result[1]:
         return 1
@@ -246,6 +257,8 @@ def handle_tag_update(args):
         success=result[1],
         error_msg=result[2],
         response_status=result[3],
+        args=args,
+        response_data=result[0],
     )
     if not result[1]:
         return 1
@@ -262,6 +275,7 @@ def handle_tag_delete(args):
         success=result[0],
         error_msg=result[1],
         response_status=result[2],
+        args=args,
     )
     if not result[0]:
         return 1