Implement Phase 2 items and Phase 3 task 14 & task 17 from plan.md

capture_tests/cbrain_cli_commands

@@ -96,7 +96,7 @@ cbrain --jsonl tag show 21
 cbrain         tag show   99
 cbrain         tag update 99 --name Renamed --user-id 2 --group-id 3
 cbrain         tag show   99
-cbrain         tag delete 99
+cbrain         tag delete 99 --yes
 
 cbrain         tag create --name NewTag1 --user-id 2 --group-id 3
 cbrain --json  tag create --name NewTag2 --user-id 2 --group-id 3
@@ -165,7 +165,7 @@ cbrain         file show 2
 cbrain --json  file show 2
 cbrain --jsonl file show 2
 
-cbrain         file delete 5
+cbrain         file delete 5 --yes
 
 cbrain         file move --file-id 2 --dp-id 15
 #cbrain --json  file move --file-id 2 --dp-id 15

capture_tests/expected_captures.txt

@@ -16,22 +16,24 @@ Stderr:
 ############################
 Command: cbrain        version
 Status: 0
-Stdout: 30 bytes
+Stdout: 32 bytes
 Stderr: 0 bytes
 
 Stdout:
-cbrain cli client version 1.0
+cbrain cli client version 0.1.0
 Stderr:
 (No output)
 
 ############################
 Command: cbrain --json version
 Status: 0
-Stdout: 30 bytes
+Stdout: 25 bytes
 Stderr: 0 bytes
 
 Stdout:
-cbrain cli client version 1.0
+{
+  "version": "0.1.0"
+}
 Stderr:
 (No output)
 
@@ -74,22 +76,24 @@ Stderr:
 ############################
 Command: cbrain        version
 Status: 0
-Stdout: 30 bytes
+Stdout: 32 bytes
 Stderr: 0 bytes
 
 Stdout:
-cbrain cli client version 1.0
+cbrain cli client version 0.1.0
 Stderr:
 (No output)
 
 ############################
 Command: cbrain --json version
 Status: 0
-Stdout: 30 bytes
+Stdout: 25 bytes
 Stderr: 0 bytes
 
 Stdout:
-cbrain cli client version 1.0
+{
+  "version": "0.1.0"
+}
 Stderr:
 (No output)
 
@@ -744,7 +748,7 @@ Stderr:
 (No output)
 
 ############################
-Command: cbrain         tag delete 99
+Command: cbrain         tag delete 99 --yes
 Status: 0
 Stdout: 29 bytes
 Stderr: 0 bytes
@@ -1638,7 +1642,7 @@ Stderr:
 (No output)
 
 ############################
-Command: cbrain         file delete 5
+Command: cbrain         file delete 5 --yes
 Status: 0
 Stdout: 71 bytes
 Stderr: 0 bytes

cbrain_cli/cli_utils.py

@@ -1,12 +1,16 @@
+import configparser
 import functools
+import importlib.metadata
 import json
 import re
+import socket
+import sys
 import urllib.error
 import urllib.parse
 import urllib.request
+from pathlib import Path
 
-# 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 +140,11 @@ 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 +190,12 @@ 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 +224,10 @@ 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
@@ -235,6 +248,9 @@ def version_info(args):
     """
     Display the CLI version information.
 
+    Prefer installed package metadata; fall back to setup.cfg when running
+    from a source tree without install.
+
     Parameters
     ----------
     args : argparse.Namespace
@@ -245,14 +261,17 @@ 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")
+    except importlib.metadata.PackageNotFoundError:
+        cfg = configparser.ConfigParser()
+        cfg.read(Path(__file__).resolve().parents[1] / "setup.cfg")
+        cbrain_cli_version = cfg["metadata"]["version"]
+
+    if output_json(args, {"version": cbrain_cli_version}):
+        return 0
+    print(f"cbrain cli client version {cbrain_cli_version}")
+    return 0
 
 
 def api_get(url, token, params=None):
@@ -262,7 +281,7 @@ 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 +292,7 @@ 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 +306,7 @@ 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
 
@@ -305,6 +324,34 @@ def output_json(args, data):
     return False
 
 
+def confirm_destructive(args, prompt):
+    """
+    Gate destructive actions: ``--yes`` skips, TTY asks, otherwise refuse.
+
+    Returns
+    -------
+    bool
+        True to proceed, False if the user declined an interactive prompt.
+    """
+    if getattr(args, "yes", False):
+        return True
+    # JSON/JSONL must not mix with a prompt; pipes/EOF also never auto-confirm.
+    if getattr(args, "json", False) or getattr(args, "jsonl", False) or not sys.stdin.isatty():
+        raise CliValidationError(
+            "Refusing destructive action without confirmation; pass --yes",
+            field="--yes",
+        )
+    try:
+        answer = input(f"{prompt} [y/N]: ").strip().lower()
+    except EOFError:
+        print("Aborted.")
+        return False
+    if answer in ("y", "yes"):
+        return True
+    print("Aborted.")
+    return False
+
+
 def display_key_value_table(pairs):
     """
     Print a (key-value) two-column Field/Value table from a list of (field, value) tuples.

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()