Merge pull request #51 from RafsanNeloy/remaining_phaseworks

Implement Remaining `plan.md` Tasks (16, 18, 19 & 21)

Author: dlq

capture_tests/cbrain_cli_commands

@@ -79,10 +79,10 @@ cbrain --json  project unswitch
 cbrain --jsonl project switch 10
 cbrain --jsonl project unswitch
 
-cbrain         project switch all  # 'all' not yet implemented as of Aug 2025
+cbrain         project switch all
 cbrain --json  project switch all
 cbrain --jsonl project switch all
-cbrain         project switch 3 # need to reset for rest of test to work
+cbrain         project switch 3 # reset project filter for task list below
 
 # Tags
 cbrain         tag list
@@ -103,10 +103,7 @@ cbrain --json  tag create --name NewTag2 --user-id 2 --group-id 3
 cbrain --jsonl tag create --name NewTag3 --user-id 2 --group-id 3
 
 # Tasks
-# NOTE: we needed to reset the current project to 3 above,
-# until 'group switch all' is implemented; this means only
-# tasks in group 3 are shown below, but that's OK, that's
-# what's in the test DB anyway
+# Reset above to project 3 so task list matches seeded DB view.
 cbrain         task list
 cbrain --json  task list
 cbrain --jsonl task list
@@ -115,8 +112,11 @@ cbrain         task show 2
 cbrain --json  task show 2
 cbrain --jsonl task show 2
 
-# Not yet implemented
-cbrain         task operation   # should provide error message
+# Task operations (hold on Completed task → skipped; deterministic, no BAC)
+cbrain         task operation hold --task-id 2
+cbrain --json  task operation hold --task-id 2
+cbrain --jsonl task operation hold --task-id 2
+cbrain         task operation hold  # missing --task-id / --batch-id
 
 # ToolConfigs, as admin user
 ./switch_session admin

capture_tests/expected_captures.txt

@@ -558,40 +558,43 @@ Stderr:
 (No output)
 
 ############################
-Command: cbrain         project switch all  # 'all' not yet implemented as of Aug 2025
-Status: 1
-Stdout: 74 bytes
+Command: cbrain         project switch all
+Status: 0
+Stdout: 32 bytes
 Stderr: 0 bytes
 
 Stdout:
-Error: Project switch 'all' not yet implemented as of Aug 2025 (group_id)
+Current project is "all" ID=all
 Stderr:
 (No output)
 
 ############################
 Command: cbrain --json  project switch all
-Status: 1
-Stdout: 74 bytes
+Status: 0
+Stdout: 35 bytes
 Stderr: 0 bytes
 
 Stdout:
-Error: Project switch 'all' not yet implemented as of Aug 2025 (group_id)
+{
+  "id": "all",
+  "name": "all"
+}
 Stderr:
 (No output)
 
 ############################
 Command: cbrain --jsonl project switch all
-Status: 1
-Stdout: 74 bytes
+Status: 0
+Stdout: 26 bytes
 Stderr: 0 bytes
 
 Stdout:
-Error: Project switch 'all' not yet implemented as of Aug 2025 (group_id)
+{"id":"all","name":"all"}
 Stderr:
 (No output)
 
 ############################
-Command: cbrain         project switch 3 # need to reset for rest of test to work
+Command: cbrain         project switch 3 # reset project filter for task list below
 Status: 0
 Stdout: 31 bytes
 Stderr: 0 bytes
@@ -998,18 +1001,67 @@ Stderr:
 (No output)
 
 ############################
-Command: cbrain         task operation   # should provide error message
+Command: cbrain         task operation hold --task-id 2
 Status: 0
-Stdout: 41 bytes
+Stdout: 182 bytes
+Stderr: 0 bytes
+
+Stdout:
+TASK OPERATION RESULT
+------------------------------
+Operation: hold
+Succeeded: 0
+Skipped:   1
+Failed:    0
+
+SKIPPED
+------------------------------
+Tasks have incompatible states: 2
+Stderr:
+(No output)
+
+############################
+Command: cbrain --json  task operation hold --task-id 2
+Status: 0
+Stdout: 142 bytes
 Stderr: 0 bytes
 
 Stdout:
 {
-  "message": "No operation selected"
+  "skipped_list": {
+    "Tasks have incompatible states": [
+      2
+    ]
+  },
+  "success_list": [],
+  "failed_list": {},
+  "bac_ids": []
 }
 Stderr:
 (No output)
 
+############################
+Command: cbrain --jsonl task operation hold --task-id 2
+Status: 0
+Stdout: 104 bytes
+Stderr: 0 bytes
+
+Stdout:
+{"skipped_list":{"Tasks have incompatible states":[2]},"success_list":[],"failed_list":{},"bac_ids":[]}
+Stderr:
+(No output)
+
+############################
+Command: cbrain         task operation hold  # missing --task-id / --batch-id
+Status: 1
+Stdout: 68 bytes
+Stderr: 0 bytes
+
+Stdout:
+Error: At least one --task-id or --batch-id is required (--task-id)
+Stderr:
+(No output)
+
 ############################
 Command: ./switch_session admin
 Status: 0
@@ -1187,36 +1239,36 @@ Stderr:
 ############################
 Command: cbrain         tool-config show 19 # visible to user admin
 Status: 1
-Stdout: 107 bytes
+Stdout: 117 bytes
 Stderr: 0 bytes
 
 Stdout:
 Authentication error (401): Unauthorized
-Error: Access denied. Please log in using authorized credentials.
+Error: Session expired or invalid. Run 'cbrain logout' then 'cbrain login'.
 Stderr:
 (No output)
 
 ############################
 Command: cbrain --json  tool-config show 19
 Status: 1
-Stdout: 107 bytes
+Stdout: 117 bytes
 Stderr: 0 bytes
 
 Stdout:
 Authentication error (401): Unauthorized
-Error: Access denied. Please log in using authorized credentials.
+Error: Session expired or invalid. Run 'cbrain logout' then 'cbrain login'.
 Stderr:
 (No output)
 
 ############################
 Command: cbrain --jsonl tool-config show 19
 Status: 1
-Stdout: 107 bytes
+Stdout: 117 bytes
 Stderr: 0 bytes
 
 Stdout:
 Authentication error (401): Unauthorized
-Error: Access denied. Please log in using authorized credentials.
+Error: Session expired or invalid. Run 'cbrain logout' then 'cbrain login'.
 Stderr:
 (No output)
 

cbrain_cli/cli_utils.py

@@ -13,6 +13,20 @@
 from cbrain_cli import config as cbrain_config
 from cbrain_cli.config import DEFAULT_HEADERS, DEFAULT_TIMEOUT, auth_headers
 
+_debug = False
+
+
+def set_debug(flag: bool) -> None:
+    """Enable or disable debug output."""
+    global _debug
+    _debug = bool(flag)
+
+
+def debug_log(message: str) -> None:
+    """Print a debug line to stderr when debug mode is active."""
+    if _debug:
+        print(f"[DEBUG] {message}", file=sys.stderr)
+
 
 class CbrainClient:
     """
@@ -46,11 +60,23 @@ def _request(self, method, path, *, headers=None, body=None, params=None):
         if params:
             target = f"{target}?{urllib.parse.urlencode(params)}"
         hdrs = headers or auth_headers(self.token)
+        # strip host from full URL for debug display; preserve all query params
+        parsed = urllib.parse.urlsplit(target)
+        display_path = parsed.path
+        if display_path.startswith(self.base_url):
+            display_path = display_path[len(self.base_url) :]
+        query = urllib.parse.urlencode(params) if params else parsed.query
+        if query:
+            display_path = f"{display_path}?{query}"
+        debug_log(f"{method} {display_path}")
         req = urllib.request.Request(target, data=body, headers=hdrs, method=method)
         try:
             with urllib.request.urlopen(req, timeout=self.timeout) as r:
-                return r.read(), r.status
+                status = r.status
+                debug_log(f"→ HTTP {status}")
+                return r.read(), status
         except urllib.error.HTTPError as e:
+            debug_log(f"→ HTTP {e.code} ({e.reason})")
             raise CliApiError(e.reason or f"HTTP {e.code}", status=e.code) from e
 
     def get(self, path, params=None):
@@ -95,7 +121,7 @@ def post_multipart(self, path, body, content_type):
 
 PAGINATABLE_ACTIONS = {
     ("file", "list"),
-    ("dataprovider", "list"),
+    ("data-provider", "list"),
     ("tool", "list"),
     ("tool-config", "list"),
     ("tag", "list"),
@@ -204,7 +230,7 @@ def handle_connection_error(error):
 
         if error.code == 401:
             print(f"{status_description}: {error.reason}")
-            print("Error: Access denied. Please log in using authorized credentials.")
+            print("Error: Session expired or invalid. Run 'cbrain logout' then 'cbrain login'.")
         elif error.code in (400, 404, 422, 500):
             # Try to extract specific error message from response
             try:

cbrain_cli/data/files.py

@@ -92,7 +92,9 @@ def _change_provider(args, operation):
     if not file_ids:
         raise CliValidationError("File ID(s) are required", field="--file-id")
     if not dest_provider_id:
-        raise CliValidationError("Destination data provider ID is required", field="--dp-id")
+        raise CliValidationError(
+            "Destination data provider ID is required", field="--data-provider-id"
+        )
     payload = {
         "file_ids": file_ids,
         "data_provider_id_for_mv_cp": dest_provider_id,

cbrain_cli/data/projects.py

@@ -25,23 +25,25 @@ def switch_project(args):
     if not group_id:
         raise CliValidationError("Group ID is required", field="group_id")
 
-    if group_id == "all":
-        raise CliValidationError(
-            "Project switch 'all' not yet implemented as of Aug 2025", field="group_id"
-        )
-
-    try:
-        group_id = int(group_id)
-    except ValueError:
-        raise CliValidationError(
-            f"Invalid group ID '{group_id}'. Must be a number or 'all'", field="group_id"
-        ) from None
+    # Server accepts numeric id or "all" (no single project filter).
+    if group_id != "all":
+        try:
+            group_id = int(group_id)
+        except ValueError:
+            raise CliValidationError(
+                f"Invalid group ID '{group_id}'. Must be a number or 'all'", field="group_id"
+            ) from None
 
     client = CbrainClient.from_credentials()
     _, switch_status = client.send("POST", f"/groups/switch?id={group_id}")
     if switch_status not in (200, 201, 204):
         raise CliApiError(f"Failed to switch project (HTTP {switch_status})")
-    group_data = client.get(f"/groups/{group_id}")
+
+    # "all" is session state only — no /groups/all resource.
+    if group_id == "all":
+        group_data = {"id": "all", "name": "all"}
+    else:
+        group_data = client.get(f"/groups/{group_id}")
 
     credentials = load_credentials()
     if credentials is not None:
@@ -124,6 +126,13 @@ def show_project(args):
     if not current_group_id:
         return None
 
+    # Session "all" has no Group row; mirror switch_project synthetic result.
+    if current_group_id == "all":
+        return {
+            "id": "all",
+            "name": credentials.get("current_group_name") or "all",
+        }
+
     try:
         return CbrainClient.from_credentials().get(f"/groups/{current_group_id}")
     except CliApiError as e: