Generate barcodes using old ISPyB standard

Author: gfrn

alembic/versions/730f6f07da68_make_barcode_column_string.py

@@ -0,0 +1,35 @@
+"""Make barcode column string
+
+Revision ID: 730f6f07da68
+Revises: dea9c772d734
+Create Date: 2025-07-17 15:50:30.406046
+
+"""
+from typing import Sequence, Union
+
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision: str = '730f6f07da68'
+down_revision: Union[str, None] = 'dea9c772d734'
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column('TopLevelContainer', 'barCode',
+               existing_type=sa.UUID(),
+               type_=sa.String(length=40),
+               existing_nullable=True)
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column('TopLevelContainer', 'barCode',
+               existing_type=sa.String(length=40),
+               type_=sa.UUID(),
+               existing_nullable=True)
+    # ### end Alembic commands ###

database/data.sql

@@ -2,7 +2,7 @@
 -- PostgreSQL database dump
 --
 
--- Dumped from database version 17.4
+-- Dumped from database version 17.5
 -- Dumped by pg_dump version 17.4
 
 SET statement_timeout = 0;
@@ -305,7 +305,7 @@ CREATE TABLE public."TopLevelContainer" (
     "externalId" integer,
     comments character varying(255),
     "isInternal" boolean NOT NULL,
-    "barCode" uuid,
+    "barCode" character varying(40),
     "creationDate" timestamp with time zone DEFAULT now() NOT NULL
 );
 
@@ -498,43 +498,43 @@ COPY public."TopLevelContainer" ("topLevelContainerId", "shipmentId", details, c
 --
 
 COPY public.alembic_version (version_num) FROM stdin;
-dea9c772d734
+730f6f07da68
 \.
 
 
 --
 -- Name: Container_containerId_seq; Type: SEQUENCE SET; Schema: public; Owner: sample_handling
 --
 
-SELECT pg_catalog.setval('public."Container_containerId_seq"', 2238, true);
+SELECT pg_catalog.setval('public."Container_containerId_seq"', 2247, true);
 
 
 --
 -- Name: PreSession_preSessionId_seq; Type: SEQUENCE SET; Schema: public; Owner: sample_handling
 --
 
-SELECT pg_catalog.setval('public."PreSession_preSessionId_seq"', 423, true);
+SELECT pg_catalog.setval('public."PreSession_preSessionId_seq"', 427, true);
 
 
 --
 -- Name: Sample_sampleId_seq; Type: SEQUENCE SET; Schema: public; Owner: sample_handling
 --
 
-SELECT pg_catalog.setval('public."Sample_sampleId_seq"', 2558, true);
+SELECT pg_catalog.setval('public."Sample_sampleId_seq"', 2579, true);
 
 
 --
 -- Name: Shipment_shipmentId_seq; Type: SEQUENCE SET; Schema: public; Owner: sample_handling
 --
 
-SELECT pg_catalog.setval('public."Shipment_shipmentId_seq"', 307, true);
+SELECT pg_catalog.setval('public."Shipment_shipmentId_seq"', 308, true);
 
 
 --
 -- Name: TopLevelContainer_topLevelContainerId_seq; Type: SEQUENCE SET; Schema: public; Owner: sample_handling
 --
 
-SELECT pg_catalog.setval('public."TopLevelContainer_topLevelContainerId_seq"', 980, true);
+SELECT pg_catalog.setval('public."TopLevelContainer_topLevelContainerId_seq"', 987, true);
 
 
 --

src/scaup/crud/top_level_containers.py

@@ -1,7 +1,7 @@
 from fastapi import HTTPException, status
 from lims_utils.logging import app_logger
 from lims_utils.models import Paged
-from sqlalchemy import func, insert, select
+from sqlalchemy import func, insert, select, update
 
 from ..models.inner_db.tables import Shipment, TopLevelContainer
 from ..models.top_level_containers import (
@@ -59,6 +59,17 @@ def _check_fields(
 @assert_not_booked
 @retry_if_exists
 def create_top_level_container(shipmentId: int | None, params: TopLevelContainerIn, token: str, autocreate=True):
+    proposal = (
+        None
+        if shipmentId is None
+        else inner_db.session.execute(
+            select(
+                func.concat(Shipment.proposalCode, Shipment.proposalNumber).label("reference"),
+                Shipment.visitNumber,
+            ).filter(Shipment.id == shipmentId)
+        ).one()
+    )
+
     if params.code:
         _check_fields(params, token, shipmentId)
     elif params.type == "dewar" and autocreate:
@@ -84,28 +95,25 @@ def create_top_level_container(shipmentId: int | None, params: TopLevelContainer
 
         new_code = f"DLS-BI-{dewar_number:04}"
 
-        proposal_reference = inner_db.session.scalar(
-            select(func.concat(Shipment.proposalCode, Shipment.proposalNumber)).filter(Shipment.id == shipmentId)
-        )
-
-        ext_resp = ExternalRequest.request(
-            Config.ispyb_api.jwt,
-            method="POST",
-            url=f"/proposals/{proposal_reference}/dewar-registry",
-            json={"facilityCode": new_code},
-        )
-
-        if ext_resp.status_code != 201:
-            app_logger.warning(
-                "Error from Expeye while creating dewar registry entry with code %s: %s",
-                new_code,
-                ext_resp.text,
-            )
-            raise HTTPException(
-                status_code=status.HTTP_424_FAILED_DEPENDENCY,
-                detail="Invalid response while creating top level container in ISPyB",
+        if proposal:
+            ext_resp = ExternalRequest.request(
+                Config.ispyb_api.jwt,
+                method="POST",
+                url=f"/proposals/{proposal.reference}/dewar-registry",
+                json={"facilityCode": new_code},
             )
 
+            if ext_resp.status_code != 201:
+                app_logger.warning(
+                    "Error from Expeye while creating dewar registry entry with code %s: %s",
+                    new_code,
+                    ext_resp.text,
+                )
+                raise HTTPException(
+                    status_code=status.HTTP_424_FAILED_DEPENDENCY,
+                    detail="Invalid response while creating top level container in ISPyB",
+                )
+
         params.code = new_code
 
     if not params.name:
@@ -116,6 +124,17 @@ def create_top_level_container(shipmentId: int | None, params: TopLevelContainer
         {"shipmentId": shipmentId, **params.model_dump(exclude_unset=True)},
     )
 
+    if proposal:
+        bar_code = f"{proposal.reference}-{proposal.visitNumber}-{container.id:07}"
+
+        # This is because some users expect a sequential numeric ID to make tracking how old a dewar is easier,
+        # and because of historical reasons, some users are used to seeing the proposal/session number on there
+        # as well, so I have to create barcodes this way.
+        container = inner_db.session.scalar(
+            update(TopLevelContainer).returning(TopLevelContainer).filter(TopLevelContainer.id == container.id),
+            {"barCode": bar_code},
+        )
+
     inner_db.session.commit()
     return container
 

src/scaup/models/inner_db/tables.py

@@ -1,10 +1,8 @@
-import uuid
 from datetime import datetime
 from typing import Any, List, Literal, Optional
 
 from sqlalchemy import (
     JSON,
-    UUID,
     DateTime,
     ForeignKey,
     PrimaryKeyConstraint,
@@ -55,7 +53,7 @@ class TopLevelContainer(Base, BaseColumns):
 
     details: Mapped[dict[str, Any] | None] = mapped_column(JSON)
     code: Mapped[str] = mapped_column(String(20))
-    barCode: Mapped[UUID | None] = mapped_column(UUID(as_uuid=True), default=uuid.uuid4)
+    barCode: Mapped[str | None] = mapped_column(String(40))
     type: Mapped[str] = mapped_column(String(40), server_default="dewar")
     isInternal: Mapped[bool] = mapped_column(
         default=False,

src/scaup/models/top_level_containers.py

@@ -1,5 +1,4 @@
 import json
-import uuid
 from datetime import datetime
 from typing import Any, List, Optional
 
@@ -44,14 +43,14 @@ class TopLevelContainerOut(BaseTopLevelContainer):
     type: str
     model_config = ConfigDict(from_attributes=True, arbitrary_types_allowed=True)
     externalId: int | None = None
-    barCode: uuid.UUID
+    barCode: str | None = None
     history: List[TopLevelContainerHistory] | None = None
 
 
 class TopLevelContainerExternal(BaseExternal):
     comments: str
     code: str
-    barCode: uuid.UUID
+    barCode: str | None = None
     firstExperimentId: int | None = None
     weight: float = 18
     dewarRegistryId: int | None = None

tests/shipments/top_level_containers/test_create.py

@@ -40,6 +40,26 @@ def test_create_no_name(client):
     )
 
 
+@responses.activate
+def test_create_auto_barcode(client):
+    """Should automatically generate barcode if not provided in request"""
+
+    resp = client.post(
+        "/shipments/1/topLevelContainers",
+        json={
+            "type": "dewar",
+            "code": "DLS-EM-0001",
+        },
+    )
+
+    assert resp.status_code == 201
+
+    new_tlc = resp.json()["id"]
+    assert "cm1-1-" in inner_db.session.scalar(
+        select(TopLevelContainer.barCode).filter(TopLevelContainer.id == new_tlc)
+    )
+
+
 @responses.activate
 def test_create_duplicate_name(client):
     """Should not allow creation if name is already present in shipment"""

tests/utils/external/test_external_object.py

@@ -1,6 +1,5 @@
 import copy
 from datetime import datetime
-from uuid import UUID
 
 import pytest
 import responses
@@ -16,7 +15,7 @@
     shipmentId=1,
     type="dewar",
     name="Test_Dewar",
-    barCode=UUID(bytes=b"ffffffffffffffff"),
+    barCode="barCode",
     creationDate=datetime.now(),
 )