Hard-retire assay and legacy file_set surfaces

Author: iamh2o

bloom_lims/api/v1/stats.py

@@ -46,7 +46,7 @@ async def get_dashboard_stats(user: APIUser = Depends(require_api_auth)):
     """
     Get dashboard statistics and recent activity.
 
-    Returns aggregated counts for assays, workflows, equipment, reagents,
+    Returns aggregated counts for queue runtime, workflows, equipment, reagents,
     and recent activity across all object types.
     """
     try:
@@ -74,7 +74,21 @@ async def get_dashboard_stats(user: APIUser = Depends(require_api_auth)):
                 if str(getattr(row, "bstatus", "") or "").strip().lower() in {"open", "active"}
             ]
 
-            stats.assays_total = len(queue_definitions)
+            queue_statuses = [
+                str(getattr(row, "bstatus", "") or "").strip().lower()
+                for row in queue_definitions
+            ]
+
+            stats.queue_runtime_total = len(queue_definitions)
+            stats.queue_runtime_in_progress = len(
+                [status for status in queue_statuses if status in {"active", "open", "in_progress"}]
+            )
+            stats.queue_runtime_complete = len(
+                [status for status in queue_statuses if status in {"complete", "completed"}]
+            )
+            stats.queue_runtime_exception = len(
+                [status for status in queue_statuses if status in {"exception", "failed", "error"}]
+            )
             stats.workflows_total = len(work_items)
             stats.workflows_active = len(open_work_items)
 
@@ -112,12 +126,12 @@ async def get_dashboard_stats(user: APIUser = Depends(require_api_auth)):
         recent_activity = RecentActivitySchema()
 
         try:
-            recent_assays = sorted(
+            recent_queue_runtime = sorted(
                 [row for row in generic_rows if _beta_kind(row) == "queue_definition"],
                 key=lambda row: row.created_dt or datetime.min.replace(tzinfo=UTC),
                 reverse=True,
             )[:5]
-            recent_activity.recent_assays = [
+            recent_activity.recent_queue_runtime = [
                 RecentActivityItem(
                     euid=a.euid,
                     name=a.name,
@@ -126,7 +140,7 @@ async def get_dashboard_stats(user: APIUser = Depends(require_api_auth)):
                     status=a.bstatus,
                     created_dt=a.created_dt,
                 )
-                for a in recent_assays
+                for a in recent_queue_runtime
             ]
 
             recent_workflows = sorted(

bloom_lims/config/action/file_set.json

@@ -1,50 +1 @@
-{
-  "add-file": {
-    "1.0": {
-      "action_definition": {
-        "action_name": "Add File To Set",
-        "method_name": "do_action_add_file_to_file_set",
-        "action_executed": "0",
-        "max_executions": "-1",
-        "action_enabled": "1",
-        "capture_data": "yes",
-        "captured_data": {},
-        "deactivate_actions_when_executed": [],
-        "executed_datetime": [],
-        "action_order": "0",
-        "action_simple_value": "",
-        "action_user": [],
-        "curr_user": "",
-        "description": "Add a file to a file set.",
-        "ui_schema": {
-          "title": "Add File To Set",
-          "fields": []
-        }
-      }
-    }
-  },
-  "remove-file": {
-    "1.0": {
-      "action_definition": {
-        "action_name": "Remove File From File Set",
-        "method_name": "do_action_remove_file_from_file_set",
-        "action_executed": "0",
-        "max_executions": "-1",
-        "action_enabled": "1",
-        "capture_data": "yes",
-        "captured_data": {},
-        "deactivate_actions_when_executed": [],
-        "executed_datetime": [],
-        "action_order": "0",
-        "action_simple_value": "",
-        "action_user": [],
-        "curr_user": "",
-        "description": "Remove a file from a file set.",
-        "ui_schema": {
-          "title": "Remove File From File Set",
-          "fields": []
-        }
-      }
-    }
-  }
-}
+{}

bloom_lims/config/action/test_requisitions.json

@@ -1,98 +1,4 @@
 {
-  "add_container_to_assay_q": {
-    "1.0": {
-      "action_definition": {
-        "action_enabled": "1",
-        "action_executed": "0",
-        "action_name": "Add Specimen to Assay Queue",
-        "action_order": "0",
-        "action_simple_value": "",
-        "action_user": [],
-        "capture_data": "yes",
-        "captured_data": {},
-        "curr_user": "",
-        "deactivate_actions_when_executed": [],
-        "executed_datetime": [],
-        "max_executions": "-1",
-        "method_name": "do_action_add_container_to_assay_q",
-        "printer_opts": {
-          "label_style": "",
-          "printer_name": ""
-        },
-        "workflow_obj": {
-          "workflow/assay/generic/1.0": {
-            "json_addl": {
-              "properties": {
-                "step_number": "1"
-              }
-            }
-          }
-        },
-        "ui_schema": {
-          "title": "Add Specimen to Assay Queue",
-          "fields": [
-            {
-              "name": "assay_selection",
-              "type": "select",
-              "required": true,
-              "options_source": "workflow_assays"
-            }
-          ]
-        }
-      },
-      "properties": {
-        "comments": "",
-        "name": ""
-      }
-    }
-  },
-  "add_container_to_assay_q__pan_cancer_panel": {
-    "1.0": {
-      "action_definition": {
-        "action_enabled": "1",
-        "action_executed": "0",
-        "action_name": "Add Specimen to Assay Queue",
-        "action_order": "0",
-        "action_simple_value": "",
-        "action_user": [],
-        "capture_data": "yes",
-        "captured_data": {},
-        "curr_user": "",
-        "deactivate_actions_when_executed": [],
-        "executed_datetime": [],
-        "max_executions": "-1",
-        "method_name": "do_action_add_container_to_assay_q",
-        "printer_opts": {
-          "label_style": "",
-          "printer_name": ""
-        },
-        "workflow_obj": {
-          "workflow/assay/generic/1.0": {
-            "json_addl": {
-              "properties": {
-                "step_number": "1"
-              }
-            }
-          }
-        },
-        "ui_schema": {
-          "title": "Add Specimen to Assay Queue",
-          "fields": [
-            {
-              "name": "assay_selection",
-              "type": "select",
-              "required": true,
-              "options_source": "workflow_assays"
-            }
-          ]
-        }
-      },
-      "properties": {
-        "comments": "",
-        "name": ""
-      }
-    }
-  },
   "set_verification_state": {
     "1.0": {
       "action_definition": {

bloom_lims/config/test_requisition/clinical.json

@@ -3,7 +3,6 @@
     "1.0": {
       "action_groups": {},
       "action_imports": {
-        "add_container_to_assay_q": "action/test_requisitions/add_container_to_assay_q__pan_cancer_panel/1.0",
         "add_relationships": "action/core/add-relationships/1.0",
         "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
         "print_barcode_label": "action/core/print_barcode_label/1.0",
@@ -28,14 +27,7 @@
         "name": "pan-cancer 239 Gene Panel Requisition"
       },
       "singleton": "0",
-      "valid_parents": [
-        {
-          "workflow/assay/hla-typing/1.2/": {}
-        },
-        {
-          "workflow/assay/carrier-screen/3.9/": {}
-        }
-      ]
+      "valid_parents": []
     }
   }
 }

bloom_lims/config/test_requisition/research.json

@@ -3,8 +3,6 @@
     "1.0": {
       "action_groups": {},
       "action_imports": {
-        "add_container_to_assay_q": "action/test_requisitions/add_container_to_assay_q/1.0",
-        "add_container_to_assay_q_pan_cancer_panel": "action/test_requisitions/add_container_to_assay_q__pan_cancer_panel/1.0",
         "add_relationships": "action/core/add-relationships/1.0",
         "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
         "print_barcode_label": "action/core/print_barcode_label/1.0",

bloom_lims/gui/actions.py

@@ -1,16 +1,10 @@
 from __future__ import annotations
 
 import copy
-from html import escape as html_escape
 
 from bloom_lims.bobjs import BloomObj
 
 
-def _build_assay_selection_options(_bobdb: BloomObj) -> list[dict]:
-    """Workflow-backed assay selection is retired in queue-centric Bloom beta."""
-    return []
-
-
 def _normalize_action_slug(action_data: dict) -> str:
     method_name = str(action_data.get("method_name") or "").strip()
     if method_name.startswith("do_action_"):
@@ -66,27 +60,13 @@ def _default_ui_fields_for_action(action_data: dict) -> list[dict]:
     return []
 
 
-def _build_assay_selection_html(options: list[dict]) -> str:
-    rendered_options = []
-    for option in options:
-        option_value = html_escape(str(option.get("value", "")), quote=True)
-        option_label = html_escape(str(option.get("label", "")))
-        rendered_options.append(f'<option value="{option_value}">{option_label}</option>')
-
-    if not rendered_options:
-        rendered_options.append('<option value="" disabled selected>No assay workflows available</option>')
-
-    return '<select name="assay_selection" required>' + "".join(rendered_options) + "</select>"
-
-
 def hydrate_dynamic_action_groups(action_groups: dict, bobdb: BloomObj) -> dict:
-    """Hydrate dynamic UI bits inside action groups (assay dropdown, etc)."""
+    """Hydrate dynamic UI bits for active action surfaces only."""
+    del bobdb  # Legacy assay/workflow hydration is retired.
     if not isinstance(action_groups, dict):
         return {}
 
     hydrated = copy.deepcopy(action_groups)
-    assay_selection_options = None
-    assay_selection_html = None
 
     for group_data in hydrated.values():
         if not isinstance(group_data, dict):
@@ -117,23 +97,14 @@ def hydrate_dynamic_action_groups(action_groups: dict, bobdb: BloomObj) -> dict:
                     ui_schema["fields"] = copy.deepcopy(default_fields)
                     fields = ui_schema["fields"]
 
-            if isinstance(captured, dict) and "___workflow/assay/" in captured:
-                if assay_selection_options is None:
-                    assay_selection_options = _build_assay_selection_options(bobdb)
-                if assay_selection_html is None:
-                    assay_selection_html = _build_assay_selection_html(assay_selection_options)
-                captured["___workflow/assay/"] = assay_selection_html
-
-            for field in fields:
-                if not isinstance(field, dict):
-                    continue
-                if field.get("options_source") == "workflow_assays":
-                    if assay_selection_options is None:
-                        assay_selection_options = _build_assay_selection_options(bobdb)
-                    if assay_selection_html is None:
-                        assay_selection_html = _build_assay_selection_html(assay_selection_options)
-                    field["options"] = copy.deepcopy(assay_selection_options)
-                    if field.get("name") == "assay_selection":
-                        captured.setdefault("___workflow/assay/", assay_selection_html)
+            # Hard-cut: remove retired assay/workflow-assay capture/UI selectors.
+            captured.pop("___workflow/assay/", None)
+            ui_schema["fields"] = [
+                field
+                for field in fields
+                if isinstance(field, dict)
+                and field.get("options_source") != "workflow_assays"
+                and field.get("name") != "assay_selection"
+            ]
 
     return hydrated

bloom_lims/gui/routes/operations.py

@@ -250,14 +250,6 @@ async def lims(request: Request, _=Depends(require_auth)):
     return RedirectResponse(url="/", status_code=303)
 
 
-@router.get("/assays", response_class=HTMLResponse)
-async def assays(request: Request, show_type: str = "all", _auth=Depends(require_auth)):
-    raise HTTPException(
-        status_code=410,
-        detail="Assay workflow pages are retired in queue-centric Bloom beta.",
-    )
-
-
 @router.get("/calculate_cogs_children")
 async def Acalculate_cogs_children(euid, request: Request, _auth=Depends(require_auth)):
     try:

bloom_lims/schemas/base.py

@@ -153,10 +153,14 @@ class ErrorResponse(BloomBaseSchema):
 class DashboardStatsSchema(BloomBaseSchema):
     """Dashboard statistics response schema."""
 
-    assays_total: int = Field(default=0, description="Total number of assays")
-    assays_in_progress: int = Field(default=0, description="Assays in progress")
-    assays_complete: int = Field(default=0, description="Completed assays")
-    assays_exception: int = Field(default=0, description="Assays with exceptions")
+    queue_runtime_total: int = Field(default=0, description="Total queue runtime objects")
+    queue_runtime_in_progress: int = Field(
+        default=0, description="Queue runtime objects in progress"
+    )
+    queue_runtime_complete: int = Field(default=0, description="Completed queue runtime objects")
+    queue_runtime_exception: int = Field(
+        default=0, description="Queue runtime objects with exceptions"
+    )
 
     workflows_total: int = Field(default=0, description="Total number of workflows")
     workflows_active: int = Field(default=0, description="Active workflows")
@@ -188,8 +192,8 @@ class RecentActivityItem(BloomBaseSchema):
 class RecentActivitySchema(BloomBaseSchema):
     """Recent activity response schema."""
 
-    recent_assays: List[RecentActivityItem] = Field(
-        default_factory=list, description="Recent assay activities"
+    recent_queue_runtime: List[RecentActivityItem] = Field(
+        default_factory=list, description="Recent queue runtime activities"
     )
     recent_workflows: List[RecentActivityItem] = Field(
         default_factory=list, description="Recent workflow activities"