Hard-cut Bloom to TapDB/EUID external reference model

bloom_lims/api/v1/external_specimens.py

@@ -111,15 +111,13 @@ async def find_external_specimens_by_reference(
     order_number: str | None = Query(None),
     patient_id: str | None = Query(None),
     shipment_number: str | None = Query(None),
-    package_number: str | None = Query(None),
     kit_barcode: str | None = Query(None),
     user: APIUser = Depends(require_external_token_auth),
 ):
     refs = AtlasReferences(
         order_number=order_number,
         patient_id=patient_id,
         shipment_number=shipment_number,
-        package_number=package_number,
         kit_barcode=kit_barcode,
     )
     service = ExternalSpecimenService(app_username=user.email)

bloom_lims/app.py

@@ -5,6 +5,7 @@
 
 from __future__ import annotations
 
+import logging
 import os
 
 from fastapi import FastAPI
@@ -14,7 +15,6 @@
 
 from bloom_lims.api import RateLimitMiddleware, api_v1_router
 from bloom_lims.gui.errors import register_exception_handlers
-from bloom_lims.gui.router import router as gui_router
 from bloom_lims.tapdb_metrics import request_method_var, request_path_var, stop_all_writers
 
 
@@ -58,7 +58,12 @@ async def _metrics_request_context(request, call_next):
 
     # Include routers
     app.include_router(api_v1_router)
-    app.include_router(gui_router)
+    try:
+        from bloom_lims.gui.router import router as gui_router
+    except ModuleNotFoundError as exc:
+        logging.warning("Skipping GUI router due to missing optional dependency: %s", exc.name)
+    else:
+        app.include_router(gui_router)
 
     register_exception_handlers(app)
     return app

bloom_lims/config/action/core.json

@@ -1,7 +1,7 @@
 {
   "set_object_status": {
     "1.0": {
-      "action_template": {
+      "action_definition": {
         "action_name": "Set Status",
         "method_name": "do_action_set_object_status",
         "action_executed": "0",
@@ -29,7 +29,7 @@
   },
   "print_barcode_label": {
     "1.0": {
-      "action_template": {
+      "action_definition": {
         "action_name": "Print Label",
         "method_name": "do_action_print_barcode_label",
         "action_executed": "0",
@@ -61,7 +61,7 @@
   },
   "add-relationships": {
     "1.0": {
-      "action_template": {
+      "action_definition": {
         "action_name": "Add Parent or Child Relationship(s)",
         "method_name": "do_action_add_relationships",
         "action_executed": "0",
@@ -85,7 +85,7 @@
   },
   "create-subject-and-anchor": {
     "1.0": {
-      "action_template": {
+      "action_definition": {
         "action_name": "Create Subject (Decision Scope)",
         "method_name": "do_action_create_subject_and_anchor",
         "action_executed": "0",

bloom_lims/config/action/data.json

@@ -1,7 +1,7 @@
 {
   "record_cfdna_quant_outcome": {
     "1.0": {
-      "action_template": {
+      "action_definition": {
         "action_name": "Record Quantification Outcome",
         "method_name": "do_action_record_cfdna_quant_outcome",
         "action_executed": "0",
@@ -32,7 +32,7 @@
   },
   "log-temperature": {
     "1.0": {
-      "action_template": {
+      "action_definition": {
         "action_name": "Log Temperature",
         "method_name": "do_action_log_temperature",
         "action_executed": "0",

bloom_lims/config/action/equipment.json

@@ -1,7 +1,7 @@
 {
   "add-container-to": {
     "1.0": {
-      "action_template": {
+      "action_definition": {
         "child_workflow_step_obj": {},
         "attach_under_root_workflow": {},
         "workflow_to_attach": {},
@@ -36,7 +36,7 @@
   },
   "remove-container-from": {
     "1.0": {
-      "action_template": {
+      "action_definition": {
         "child_workflow_step_obj": {},
         "child_container_obj": {},
         "test_requisition_obj": {},
@@ -70,7 +70,7 @@
   },
   "download-inventory-tsv": {
     "1.0": {
-      "action_template": {
+      "action_definition": {
         "child_workflow_step_obj": {},
         "child_container_obj": {},
         "test_requisition_obj": {},
@@ -104,7 +104,7 @@
   },
   "log-temperature": {
     "1.0": {
-      "action_template": {
+      "action_definition": {
         "child_workflow_step_obj": {},
         "child_container_obj": {
           "data/generic/temperature-log/*/": {

bloom_lims/config/action/file.json

@@ -1,7 +1,7 @@
 {
   "download_file": {
     "1.0": {
-      "action_template": {
+      "action_definition": {
         "action_name": "Download A File",
         "method_name": "do_action_download_file",
         "action_executed": "0",

bloom_lims/config/action/file_set.json

@@ -1,7 +1,7 @@
 {
   "add-file": {
     "1.0": {
-      "action_template": {
+      "action_definition": {
         "action_name": "Add File To Set",
         "method_name": "do_action_add_file_to_file_set",
         "action_executed": "0",
@@ -25,7 +25,7 @@
   },
   "remove-file": {
     "1.0": {
-      "action_template": {
+      "action_definition": {
         "action_name": "Remove File From File Set",
         "method_name": "do_action_remove_file_from_file_set",
         "action_executed": "0",

bloom_lims/config/action/move-queues.json

@@ -1,7 +1,7 @@
 {
   "move-among-ay-top-queues": {
     "1.0": {
-      "action_template": {
+      "action_definition": {
         "child_workflow_step_obj": {},
         "child_workflow_object": {},
         "workflow_step_to_attach_as_child": {},

bloom_lims/config/action/object.json

@@ -1,7 +1,7 @@
 {
   "set-child-object": {
     "1.0": {
-      "action_template": {
+      "action_definition": {
         "action_name": "Set Object As Child",
         "method_name": "do_action_set_child_object",
         "action_executed": "0",