Release Bloom 8.0.0 with TapDB 9.0.10

Author: iamh2o

README.md

@@ -21,7 +21,7 @@
 
 Bloom is the LSMC internal material and container graph service. It owns laboratory containers, materials/content, equipment, lineage, recursive template creation, search, and graph views. Atlas owns orders and customer-facing accession context; Bloom owns the physical/material execution graph.
 
-Current Dayhoff pin: `7.0.22`. Current TapDB dependency: `daylily-tapdb @ ...@9.0.9`.
+Current Dayhoff pin: `8.0.0`. Current TapDB dependency: `daylily-tapdb @ ...@9.0.10`.
 
 Bloom is internal-only in Dayhoff exposure policy. It must be reachable only through approved LSMC networks and Dayhoff-generated service credentials.
 

bloom_lims/ai_agent_access.py

@@ -78,9 +78,13 @@ def _endpoint_id_for_request(method: str, path: str) -> str:
     resolved_method = str(method or "").upper()
     resolved_path = str(path or "").split("?", 1)[0].rstrip("/") or "/"
     for spec in ENDPOINT_CATALOG:
-        if spec.method == resolved_method and _template_matches(spec.path_template, resolved_path):
+        if spec.method == resolved_method and _template_matches(
+            spec.path_template, resolved_path
+        ):
             return spec.endpoint_id
-    raise AgentTokenError("AI-agent token is not authorized for this endpoint", status_code=403)
+    raise AgentTokenError(
+        "AI-agent token is not authorized for this endpoint", status_code=403
+    )
 
 
 def _parse_expiry(value: str) -> datetime:
@@ -95,15 +99,21 @@ def _parse_expiry(value: str) -> datetime:
 
 def _load_grants(path: Path) -> list[dict[str, Any]]:
     if not path.is_absolute():
-        raise AgentTokenError("AI-agent grant store path must be absolute", status_code=500)
+        raise AgentTokenError(
+            "AI-agent grant store path must be absolute", status_code=500
+        )
     if not path.exists():
         raise AgentTokenError("AI-agent grant store is missing", status_code=500)
     try:
         payload = json.loads(path.read_text(encoding="utf-8"))
     except json.JSONDecodeError as exc:
-        raise AgentTokenError("AI-agent grant store is malformed", status_code=500) from exc
+        raise AgentTokenError(
+            "AI-agent grant store is malformed", status_code=500
+        ) from exc
     if not isinstance(payload, dict) or not isinstance(payload.get("tokens"), list):
-        raise AgentTokenError("AI-agent grant store must contain a tokens list", status_code=500)
+        raise AgentTokenError(
+            "AI-agent grant store must contain a tokens list", status_code=500
+        )
     return [record for record in payload["tokens"] if isinstance(record, dict)]
 
 
@@ -119,7 +129,9 @@ def validate_ai_agent_request(request: Request, token: str) -> ValidatedAgentAcc
     endpoint_id = _endpoint_id_for_request(request.method, request.url.path)
     token_digest = hashlib.sha256(token.encode("utf-8")).hexdigest()
     for record in _load_grants(Path(raw_path)):
-        if not secrets.compare_digest(str(record.get("token_hash") or ""), token_digest):
+        if not secrets.compare_digest(
+            str(record.get("token_hash") or ""), token_digest
+        ):
             continue
         if record.get("revoked_at"):
             raise AgentTokenError("AI-agent token has been revoked")
@@ -128,7 +140,9 @@ def validate_ai_agent_request(request: Request, token: str) -> ValidatedAgentAcc
             raise AgentTokenError("AI-agent token has expired")
         endpoint_ids = [str(item) for item in record.get("endpoint_ids") or []]
         if endpoint_id not in endpoint_ids:
-            raise AgentTokenError("AI-agent token is not authorized for this endpoint", status_code=403)
+            raise AgentTokenError(
+                "AI-agent token is not authorized for this endpoint", status_code=403
+            )
         validated = ValidatedAgentAccess(
             token_id=str(record.get("token_id") or ""),
             agent_id=str(record.get("agent_id") or ""),

bloom_lims/api/v1/__init__.py

@@ -20,8 +20,8 @@
 from .auth import router as auth_router
 from .batch import router as batch_router
 from .beta_lab import router as beta_lab_router
-from .containers import router as containers_router
 from .container_actions import router as container_actions_router
+from .containers import router as containers_router
 from .content import router as content_router
 from .equipment import router as equipment_router
 from .execution_queue import router as execution_queue_router

bloom_lims/api/v1/auth.py

@@ -25,9 +25,13 @@ def _broker_preferences_contract(email: str) -> tuple[str, dict[str, str]]:
     token = str(os.environ.get("LSMC_AUTH_BROKER_SERVICE_TOKEN") or "").strip()
     service_id = str(os.environ.get("LSMC_AUTH_BROKER_SERVICE_ID") or "bloom").strip()
     if not raw_url:
-        raise HTTPException(status_code=503, detail="Broker user preferences URL is not configured")
+        raise HTTPException(
+            status_code=503, detail="Broker user preferences URL is not configured"
+        )
     if not token:
-        raise HTTPException(status_code=503, detail="Broker service token is not configured")
+        raise HTTPException(
+            status_code=503, detail="Broker service token is not configured"
+        )
     if "{email}" not in raw_url:
         raise HTTPException(
             status_code=503,
@@ -58,7 +62,9 @@ async def get_current_user(user: APIUser = Depends(require_api_auth)):
 @preferences_router.get("/me/preferences")
 async def current_user_preferences(user: APIUser = Depends(require_api_auth)):
     if not user.email:
-        raise HTTPException(status_code=400, detail="Authenticated user email is required")
+        raise HTTPException(
+            status_code=400, detail="Authenticated user email is required"
+        )
     url, headers = _broker_preferences_contract(user.email)
     with httpx.Client(timeout=5.0) as client:
         response = client.get(url, headers=headers)
@@ -73,17 +79,24 @@ async def update_current_user_preferences(
     user: APIUser = Depends(require_api_auth),
 ):
     if not user.email:
-        raise HTTPException(status_code=400, detail="Authenticated user email is required")
+        raise HTTPException(
+            status_code=400, detail="Authenticated user email is required"
+        )
     payload = await request.json()
     theme = str(payload.get("theme") or "").strip()
     if theme and theme not in THEME_NAMES:
         raise HTTPException(status_code=400, detail="Unknown theme")
     service_themes = payload.get("service_themes")
     if service_themes is not None:
         if not isinstance(service_themes, dict):
-            raise HTTPException(status_code=400, detail="service_themes must be an object")
+            raise HTTPException(
+                status_code=400, detail="service_themes must be an object"
+            )
         for service_theme in service_themes.values():
-            if service_theme is not None and str(service_theme).strip() not in THEME_NAMES:
+            if (
+                service_theme is not None
+                and str(service_theme).strip() not in THEME_NAMES
+            ):
                 raise HTTPException(status_code=400, detail="Unknown theme")
     forward_payload = {}
     if "theme" in payload:

bloom_lims/api/v1/container_actions.py

@@ -10,7 +10,6 @@
 from pydantic import BaseModel, Field, ValidationError
 from sqlalchemy import select
 
-from bloom_lims.tapdb_adapter import BLOOMdb3, generic_instance
 from bloom_lims.domain.lab_actions import LabActionsService
 from bloom_lims.schemas.lab_actions import (
     ExtractionPlateRequest,
@@ -22,6 +21,7 @@
     SeqLibraryPoolRequest,
     SeqRunSetRequest,
 )
+from bloom_lims.tapdb_adapter import BLOOMdb3, generic_instance
 
 from .dependencies import APIUser, require_write
 
@@ -76,8 +76,12 @@ def _split_source(value: str) -> tuple[str, str | None]:
     return euid, well
 
 
-def _normalize_record(row: dict[str, Any], default_target: str | None) -> dict[str, Any]:
-    source = row.get("source") or row.get("source_euid") or row.get("euid") or row.get("0")
+def _normalize_record(
+    row: dict[str, Any], default_target: str | None
+) -> dict[str, Any]:
+    source = (
+        row.get("source") or row.get("source_euid") or row.get("euid") or row.get("0")
+    )
     target = (
         row.get("target")
         or row.get("target_container_euid")
@@ -159,7 +163,10 @@ async def validate_container_action(
 ):
     try:
         planned = _parse_rows(payload)
-        source_types = {row["source_euid"]: _object_kind(row["source_euid"], user) for row in planned}
+        source_types = {
+            row["source_euid"]: _object_kind(row["source_euid"], user)
+            for row in planned
+        }
         target_types = {
             row["target_euid"]: _object_kind(row["target_euid"], user)
             for row in planned
@@ -232,9 +239,13 @@ async def execute_container_action(
                 SeqRunSetRequest.model_validate(operation_payload)
             )
         elif payload.operation_type == "lab_set":
-            result = service.create_lab_set(LabSetRequest.model_validate(operation_payload))
+            result = service.create_lab_set(
+                LabSetRequest.model_validate(operation_payload)
+            )
         elif payload.operation_type == "print_euids":
-            result = service.print_euids(PrintEuidRequest.model_validate(operation_payload))
+            result = service.print_euids(
+                PrintEuidRequest.model_validate(operation_payload)
+            )
         else:  # pragma: no cover - Literal validation should prevent this.
             raise HTTPException(status_code=400, detail="Unsupported operation_type")
         return {

bloom_lims/api/v1/lab_actions.py

@@ -177,13 +177,13 @@ async def download_seq_run_sample_sheet(
 ):
     service = _service_for_user(user)
     try:
-        content, filename, media_type = service.sequencing_sample_sheet_download(set_euid)
+        content, filename, media_type = service.sequencing_sample_sheet_download(
+            set_euid
+        )
         return PlainTextResponse(
             content,
             media_type=media_type,
-            headers={
-                "Content-Disposition": f'attachment; filename="{filename}"'
-            },
+            headers={"Content-Disposition": f'attachment; filename="{filename}"'},
         )
     except Exception as exc:
         _raise_http(exc)

bloom_lims/cli/db.py

@@ -383,6 +383,20 @@ def _retire_obsolete_template_variants(
     domain_code: str,
 ) -> int:
     current = _active_template_categories_by_semantic_key(templates)
+    current_semantic_types = {
+        (
+            str((template.get("json_addl") or {}).get("semantic_category") or "")
+            .strip()
+            .lower(),
+            str(template.get("type") or "").strip(),
+        )
+        for template in templates
+        if isinstance(template.get("json_addl"), dict)
+        and str(
+            (template.get("json_addl") or {}).get("semantic_category") or ""
+        ).strip()
+        and str(template.get("type") or "").strip()
+    }
     current_prefixes = {
         str(template.get("instance_prefix") or "").strip().upper()
         for template in templates
@@ -411,18 +425,16 @@ def _retire_obsolete_template_variants(
             )
             expected_category = current.get(key)
             actual_category = str(row.category or "").strip().upper()
-            semantic_category = template_semantic_category(row).strip().upper()
-            if semantic_category and actual_category != semantic_category:
-                row.is_deleted = True
-                row.bstatus = "retired"
-                retired += 1
-                continue
             if actual_category in current_prefixes:
                 row.is_deleted = True
                 row.bstatus = "retired"
                 retired += 1
                 continue
             if expected_category is None:
+                if (key[0], key[1]) in current_semantic_types:
+                    row.is_deleted = True
+                    row.bstatus = "retired"
+                    retired += 1
                 continue
             if actual_category == expected_category:
                 continue

bloom_lims/domain/beta_actions.py

@@ -187,9 +187,7 @@ def record(
         return action_record
 
     def _ensure_action_template(self, action_key: str) -> generic_template:
-        template_code = (
-            f"{BETA_ACTION_TEMPLATE_PREFIX}/{BETA_ACTION_GROUP}/{action_key}/1.0/"
-        )
+        template_code = f"action/{BETA_ACTION_GROUP}/{action_key}/1.0/"
         return require_seeded_template(
             self.session,
             template_code,

bloom_lims/domain/beta_lab_refs.py

@@ -172,9 +172,7 @@ def _fulfillment_item_refs_for_instance(self, instance) -> list[dict[str, str]]:
             ).strip()
             atlas_tenant_id = str(payload.get("atlas_tenant_id") or "").strip()
             atlas_trf_euid = str(
-                payload.get("atlas_trf_euid")
-                or payload.get("atlas_order_euid")
-                or ""
+                payload.get("atlas_trf_euid") or payload.get("atlas_order_euid") or ""
             ).strip()
             if not (
                 fulfillment_item_euid
@@ -195,8 +193,7 @@ def _fulfillment_item_refs_for_instance(self, instance) -> list[dict[str, str]]:
                     payload.get("atlas_order_test_euid") or atlas_test_euid
                 ).strip(),
                 "atlas_fulfillment_slot_euid": str(
-                    payload.get("atlas_fulfillment_slot_euid")
-                    or fulfillment_item_euid
+                    payload.get("atlas_fulfillment_slot_euid") or fulfillment_item_euid
                 ).strip(),
             }
         return list(refs.values())
@@ -366,7 +363,9 @@ def _replace_fulfillment_item_references(
         atlas_tenant_id = str(atlas_context.get("atlas_tenant_id") or "").strip()
         atlas_trf_euid = str(atlas_context.get("atlas_trf_euid") or "").strip()
         atlas_order_euid = str(
-            atlas_context.get("atlas_order_euid") or atlas_context.get("order_euid") or ""
+            atlas_context.get("atlas_order_euid")
+            or atlas_context.get("order_euid")
+            or ""
         ).strip()
         fulfillment_items = list(atlas_context.get("fulfillment_items") or [])
         for fulfillment_slot in list(atlas_context.get("fulfillment_slots") or []):
@@ -464,8 +463,7 @@ def _replace_fulfillment_item_references(
                     object_evidence(ref_obj.euid, role="atlas_reference_link"),
                 ],
                 correlation_id=(
-                    f"SLOT_SATISFIED_BY:{atlas_fulfillment_slot_euid}:"
-                    f"{instance.euid}"
+                    f"SLOT_SATISFIED_BY:{atlas_fulfillment_slot_euid}:{instance.euid}"
                 ),
                 causation_id=(
                     f"bloom:atlas_fulfillment_reference:"
@@ -484,7 +482,9 @@ def _replace_container_entity_references(
     ) -> None:
         atlas_tenant_id = str(atlas_context.get("atlas_tenant_id") or "").strip()
         atlas_order_euid = str(
-            atlas_context.get("atlas_order_euid") or atlas_context.get("order_euid") or ""
+            atlas_context.get("atlas_order_euid")
+            or atlas_context.get("order_euid")
+            or ""
         ).strip()
         atlas_order_test_euid = str(
             atlas_context.get("atlas_order_test_euid")

bloom_lims/domain/beta_lab_stages.py

@@ -409,9 +409,7 @@ def record_post_extract_qc(
                 "idempotency_key": idempotency_key or "",
                 "occurred_at": self._timestamp(),
             },
-            template_code=self.DATA_TEMPLATE_BY_BETA_KIND.get(
-                "post_extract_qc_result"
-            ),
+            template_code=self.DATA_TEMPLATE_BY_BETA_KIND.get("post_extract_qc_result"),
         )
         if payload.quant_artifact_euid:
             qc_props = self._props(qc_record)