Hard-cut fulfillment contract rename across Bloom surfaces

Author: iamh2o

ATLAS_BLOOM_API_GUIDANCE.md

@@ -23,7 +23,7 @@ Beta contract guardrails:
 
 1. The atomic business/fulfillment/reporting unit is `TRF.test`; `TRF` is rollup context only.
 2. External contracts are EUID-only (do not depend on UUIDs).
-3. Container context may link to multiple tests on the same TRF; direct container-linked tests/process-items are the authoritative processing set.
+3. Container context may link to multiple tests on the same TRF; direct container-linked tests/fulfillment-items are the authoritative processing set.
 
 Beta work-control endpoints (queue claim/reservation/consume):
 

README.md

@@ -46,7 +46,7 @@ Canonical queues:
 - `ilmn_start_seq_run`
 - `ont_start_seq_run`
 
-Atlas records intake outcomes first. Bloom accepts only Atlas-approved material, links that material to Atlas TRF/Test/process-item context through explicit graph-linked reference objects, and preserves lineage from specimen/container through plate and well placement, library prep, pooling, sequencing run creation, and sequenced library assignment.
+Atlas records intake outcomes first. Bloom accepts only Atlas-approved material, links that material to Atlas TRF/Test/fulfillment-item context through explicit graph-linked reference objects, and preserves lineage from specimen/container through plate and well placement, library prep, pooling, sequencing run creation, and sequenced library assignment.
 The atomic business/fulfillment/reporting unit is `TRF.test`; `TRF` is a rollup container across child tests.
 Accepted-material ingress queue membership is applied to the physical container (`container_euid`), with specimen queue reads falling back to containing-container queue state when needed.
 
@@ -63,7 +63,7 @@ Bloom returns:
 - `atlas_tenant_id`
 - `atlas_trf_euid`
 - `atlas_test_euid`
-- `atlas_test_process_item_euid`
+- `atlas_test_fulfillment_item_euid`
 
 Public beta APIs return EUIDs only. Internal UUIDs are not part of the supported contract.
 
@@ -137,7 +137,7 @@ Workflow/workset runtime surfaces are retired from active API/GUI mounts for the
 
 ## Development
 
-Bloom runs on the TapDB-backed adapter layer used across the LSMC refactor. The beta queue flow uses explicit object creation, lineage writes, targeted lookup queries, process-item references, and idempotency keys on direct integration calls.
+Bloom runs on the TapDB-backed adapter layer used across the LSMC refactor. The beta queue flow uses explicit object creation, lineage writes, targeted lookup queries, fulfillment-item references, and idempotency keys on direct integration calls.
 
 Focused validation commands for the beta path:
 

bloom_lims/domain/beta_actions.py

@@ -21,7 +21,7 @@
 _ACTION_TEMPLATE_DEFINITIONS: dict[str, dict[str, Any]] = {
     "register_accepted_material": {
         "name": "Register Accepted Material",
-        "description": "Creates accepted Bloom beta material and links Atlas process-item references.",
+        "description": "Creates accepted Bloom beta material and links Atlas fulfillment-item references.",
     },
     "create_empty_tube": {
         "name": "Create Empty Tube",

bloom_lims/domain/beta_lab.py

@@ -64,20 +64,20 @@ def _render_search_page(
 async def modern_dashboard(request: Request, _=Depends(require_auth)):
     user_data = request.session.get("user_data", {})
     stats = {
-        "assays_total": 0,
+        "queue_runtime_total": 0,
         "objects_total": 0,
         "equipment_total": 0,
         "reagents_total": 0,
     }
-    recent_assays = []
+    recent_queue_runtime = []
     recent_objects = []
     db_unavailable = not _is_tapdb_reachable()
 
     if not db_unavailable:
         try:
             bobdb = BloomObj(BLOOMdb3(app_username=user_data.get("email", "anonymous")))
             stats = {
-                "assays_total": bobdb.session.query(bobdb.Base.classes.workflow_instance)
+                "queue_runtime_total": bobdb.session.query(bobdb.Base.classes.workflow_instance)
                 .filter_by(is_deleted=False, is_singleton=True)
                 .count(),
                 "objects_total": bobdb.session.query(bobdb.Base.classes.generic_instance)
@@ -93,7 +93,7 @@ async def modern_dashboard(request: Request, _=Depends(require_auth)):
                 )
                 .count(),
             }
-            recent_assays = (
+            recent_queue_runtime = (
                 bobdb.session.query(bobdb.Base.classes.workflow_instance)
                 .filter_by(is_deleted=False, is_singleton=True)
                 .order_by(bobdb.Base.classes.workflow_instance.created_dt.desc())
@@ -115,7 +115,7 @@ async def modern_dashboard(request: Request, _=Depends(require_auth)):
         "request": request,
         "udat": user_data,
         "stats": stats,
-        "recent_assays": recent_assays,
+        "recent_queue_runtime": recent_queue_runtime,
         "recent_objects": recent_objects,
         "db_unavailable": db_unavailable,
     }

bloom_lims/gui/routes/modern.py

@@ -275,9 +275,9 @@ async def assays(request: Request, show_type: str = "all", _auth=Depends(require
     atype = {}
 
     if show_type == "assay":
-        atype["type"] = "Assays"
+        atype["type"] = "Queue Runtime"
     else:
-        atype["type"] = "All Assays, etc"
+        atype["type"] = "All Queue Runtime Objects"
 
     for i in sorted(ay_ds.keys()):
         assays.append(ay_ds[i])

bloom_lims/gui/routes/operations.py

@@ -19,9 +19,9 @@
 ]
 
 
-class AtlasProcessItemReference(BaseModel):
+class AtlasFulfillmentItemReference(BaseModel):
     atlas_test_euid: str
-    atlas_test_process_item_euid: str
+    atlas_test_fulfillment_item_euid: str
 
 
 class AtlasCollectionEventSnapshot(BaseModel):
@@ -36,7 +36,7 @@ class AtlasCollectionEventSnapshot(BaseModel):
     expected_label_text: str | None = None
 
 
-class AtlasProcessContext(BaseModel):
+class AtlasFulfillmentContext(BaseModel):
     atlas_tenant_id: str
     atlas_trf_euid: str | None = None
     atlas_test_euid: str | None = None
@@ -47,10 +47,10 @@ class AtlasProcessContext(BaseModel):
     atlas_organization_site_euid: str | None = None
     atlas_collection_event_euid: str | None = None
     collection_event_snapshot: AtlasCollectionEventSnapshot | None = None
-    process_items: list[AtlasProcessItemReference] = Field(default_factory=list)
+    fulfillment_items: list[AtlasFulfillmentItemReference] = Field(default_factory=list)
 
     @model_validator(mode="after")
-    def validate_context(self) -> "AtlasProcessContext":
+    def validate_context(self) -> "AtlasFulfillmentContext":
         if not self.atlas_tenant_id.strip():
             raise ValueError("atlas_tenant_id is required")
         if self.atlas_trf_euid is not None and not self.atlas_trf_euid.strip():
@@ -100,9 +100,9 @@ def validate_context(self) -> "AtlasProcessContext":
                     "collection_event_snapshot.collection_event_euid must match "
                     "atlas_collection_event_euid"
                 )
-        if self.process_items:
+        if self.fulfillment_items:
             if not (self.atlas_trf_euid and self.atlas_trf_euid.strip()):
-                raise ValueError("atlas_trf_euid is required when process_items are provided")
+                raise ValueError("atlas_trf_euid is required when fulfillment_items are provided")
         elif (self.atlas_test_euid is not None or self.atlas_test_euids) and not self.atlas_trf_euid:
             raise ValueError("atlas_trf_euid is required when atlas_test_euid is provided")
         return self
@@ -115,26 +115,26 @@ class BetaAcceptedMaterialCreateRequest(BaseModel):
     container_template_code: str = Field(default="container/tube/tube-generic-10ml/1.0")
     status: str = Field(default="active")
     properties: dict[str, Any] = Field(default_factory=dict)
-    atlas_context: AtlasProcessContext
+    atlas_context: AtlasFulfillmentContext
 
 
 class BetaTubeCreateRequest(BaseModel):
     container_template_code: str = Field(default="container/tube/tube-generic-10ml/1.0")
     status: str = Field(default="active")
     properties: dict[str, Any] = Field(default_factory=dict)
-    atlas_context: AtlasProcessContext
+    atlas_context: AtlasFulfillmentContext
 
 
 class BetaTubeUpdateRequest(BaseModel):
     status: str | None = None
     properties: dict[str, Any] | None = None
-    atlas_context: AtlasProcessContext | None = None
+    atlas_context: AtlasFulfillmentContext | None = None
 
 
 class BetaSpecimenUpdateRequest(BaseModel):
     status: str | None = None
     properties: dict[str, Any] | None = None
-    atlas_context: AtlasProcessContext | None = None
+    atlas_context: AtlasFulfillmentContext | None = None
 
 
 class BetaMaterialResponse(BaseModel):
@@ -179,7 +179,7 @@ class BetaExtractionCreateRequest(BaseModel):
     well_name: str
     extraction_type: Literal["cfdna", "gdna"] = Field(default="cfdna")
     output_name: str | None = None
-    atlas_test_process_item_euid: str | None = None
+    atlas_test_fulfillment_item_euid: str | None = None
     claim_euid: str | None = None
     consume_source: bool = False
     metadata: dict[str, Any] = Field(default_factory=dict)
@@ -191,7 +191,7 @@ class BetaExtractionResponse(BaseModel):
     well_euid: str
     well_name: str
     extraction_output_euid: str
-    atlas_test_process_item_euid: str
+    atlas_test_fulfillment_item_euid: str
     current_queue: str
     idempotent_replay: bool = False
 
@@ -229,7 +229,7 @@ class BetaLibraryPrepCreateRequest(BaseModel):
 class BetaLibraryPrepResponse(BaseModel):
     source_extraction_output_euid: str
     library_prep_output_euid: str
-    atlas_test_process_item_euid: str
+    atlas_test_fulfillment_item_euid: str
     current_queue: str
     idempotent_replay: bool = False
 
@@ -316,7 +316,7 @@ class BetaRunResolutionResponse(BaseModel):
     atlas_tenant_id: str
     atlas_trf_euid: str
     atlas_test_euid: str
-    atlas_test_process_item_euid: str
+    atlas_test_fulfillment_item_euid: str
 
 
 class BetaClaimCreateRequest(BaseModel):

bloom_lims/schemas/beta_lab.py

@@ -2,20 +2,20 @@
 
 ## Accepted Material Registration
 
-Bloom accepts Atlas-approved material only after Atlas records an `ACCEPTED` intake outcome and materializes one or more test process items.
+Bloom accepts Atlas-approved material only after Atlas records an `ACCEPTED` intake outcome and materializes one or more test fulfillment items.
 
 Minimum request context:
 
 - `atlas_context.atlas_trf_euid`
 - `atlas_context.atlas_patient_euid`
-- `atlas_context.process_items[].atlas_test_euid`
-- `atlas_context.process_items[].atlas_test_process_item_euid`
+- `atlas_context.fulfillment_items[].atlas_test_euid`
+- `atlas_context.fulfillment_items[].atlas_test_fulfillment_item_euid`
 - patient context
 - shipment or test kit context
 - queue intent
 - idempotency key
 
-Bloom persists Atlas linkage through graph-linked reference objects and returns EUID-only identifiers for created material plus `process_item_euids[]`.
+Bloom persists Atlas linkage through graph-linked reference objects and returns EUID-only identifiers for created material plus `fulfillment_item_euids[]`.
 
 For accepted-material ingress, queue transitions are expected on `container_euid` (container-first lab movement).
 
@@ -52,7 +52,7 @@ Output:
 - `atlas_tenant_id`
 - `atlas_trf_euid`
 - `atlas_test_euid`
-- `atlas_test_process_item_euid`
+- `atlas_test_fulfillment_item_euid`
 
 Rules:
 

docs/bloom_beta_api_contracts.md

@@ -11,12 +11,12 @@ Align accepted-material ingestion so queue ingress and cross-system linkage are
 1. Atlas bridge and external-object graph updates
 - Queue accepted material by `container_euid`.
 - Persist container mapping before specimen mapping.
-- Keep container relations to TRF/Test/TestProcessItem + Shipment/TestKit.
+- Keep container relations to TRF/Test/TestFulfillmentItem + Shipment/TestKit.
 - Keep specimen relations to Patient + containment only.
 
 2. Bloom accepted-material behavior updates
 - Resolve/create container before specimen creation.
-- Attach process-item reference links to container.
+- Attach fulfillment-item reference links to container.
 - Attach patient-only reference link to specimen.
 - Add patient EUID to accepted-material Atlas context contract.
 - Add queue-resolution fallback: specimen can resolve queue from containing container.
@@ -33,11 +33,11 @@ Align accepted-material ingestion so queue ingress and cross-system linkage are
 
 ## Acceptance Checks
 - Atlas accepted-material handoff calls Bloom queue endpoint with `container_euid`.
-- Atlas specimen external-object mapping has no test/test-process-item relations.
-- Bloom accepted-material creation stores process-item refs on container and patient ref on specimen.
+- Atlas specimen external-object mapping has no test/test-fulfillment-item relations.
+- Bloom accepted-material creation stores fulfillment-item refs on container and patient ref on specimen.
 - Bloom extraction succeeds when only container has ingress queue membership.
 - Resolver and downstream beta flow remain unchanged.
 
 ## Breaking-Change Notes
 - `POST /api/v1/external/atlas/beta/materials` accepted-material context now carries Atlas patient EUID.
-- Specimen external-object relation semantics changed: no direct test/test-process-item relation projection.
+- Specimen external-object relation semantics changed: no direct test/test-fulfillment-item relation projection.

docs/container_first_handoff_execplan.md

@@ -1,12 +1,12 @@
 {% extends "modern/base.html" %}
 
-{% block title %}Assays - BLOOM LIMS{% endblock %}
+{% block title %}Queue Runtime - BLOOM LIMS{% endblock %}
 
 {% block content %}
 <div class="page-header">
   <div>
-    <h1>Assays</h1>
-    <p class="text-muted">Manage laboratory assay objects</p>
+    <h1>Queue Runtime</h1>
+    <p class="text-muted">Queue/material/run-centric operational objects</p>
   </div>
   <div class="page-actions">
   </div>
@@ -15,9 +15,9 @@ <h1>Assays</h1>
 <!-- Filter Bar -->
 <div class="filter-bar mb-lg">
   <div class="filter-group">
-    <label class="filter-label">Type:</label>
+    <label class="filter-label">Runtime Type:</label>
     <select class="form-select" id="filter-type" onchange="filterAssays()">
-      <option value="all" {% if show_type == 'all' %}selected{% endif %}>All Types</option>
+      <option value="all" {% if show_type == 'all' %}selected{% endif %}>All Runtime Types</option>
       {% for atype in assay_types %}
       <option value="{{ atype }}" {% if show_type == atype %}selected{% endif %}>{{ atype }}</option>
       {% endfor %}
@@ -33,12 +33,12 @@ <h1>Assays</h1>
     </select>
   </div>
   <div class="filter-search">
-    <input type="text" class="form-input" placeholder="Search assays..." id="search-input" onkeyup="searchAssays(this.value)">
+    <input type="text" class="form-input" placeholder="Search queue runtime objects..." id="search-input" onkeyup="searchAssays(this.value)">
     <i class="fas fa-search"></i>
   </div>
 </div>
 
-<!-- Assays Grid -->
+<!-- Queue Runtime Grid -->
 <div class="grid grid-3" id="assays-grid">
   {% if assays %}
     {% for assay in assays %}
@@ -69,7 +69,7 @@ <h4 class="assay-name">{{ assay.name | default(assay.subtype) }}</h4>
     <div class="empty-state" style="grid-column: 1 / -1;">
       <div class="empty-state-icon"><i class="fas fa-flask"></i></div>
       <p>No assays found</p>
-      <p class="text-muted text-sm">Create a new assay to get started</p>
+      <p class="text-muted text-sm">Queue runtime objects appear as material and run operations progress</p>
     </div>
   {% endif %}
 </div>