Merge branch 'master' into improvement/lims-2051/pdf-report

Author: gfrn

CHANGELOG.rst

@@ -8,7 +8,20 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 +++++++++
-v0.18.2 (09/01/2025)
+v0.19.0 (16/01/2026)
++++++++++
+
+**Changed**
+
+- All grids are now displayed in PDF reports, even if they don't have a cassette slot assigned
+
+**Added**
+
+- Perform manufacturer serial number check when creating dewars
+- Add endpoint for creating inventory dewar
+
++++++++++
+v0.18.2 (09/01/2026)
 +++++++++
 
 **Changed**

alembic/versions/31b603858335_increase_name_character_limit.py

@@ -0,0 +1,60 @@
+"""Increase name character limit
+
+Revision ID: 31b603858335
+Revises: 730f6f07da68
+Create Date: 2026-01-23 14:09:57.262059
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = '31b603858335'
+down_revision: Union[str, None] = '730f6f07da68'
+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('Container', 'name',
+               existing_type=sa.VARCHAR(length=40),
+               type_=sa.String(length=80),
+               existing_nullable=False)
+    op.alter_column('Sample', 'name',
+               existing_type=sa.VARCHAR(length=40),
+               type_=sa.String(length=80),
+               existing_nullable=False)
+    op.alter_column('Shipment', 'name',
+               existing_type=sa.VARCHAR(length=40),
+               type_=sa.String(length=80),
+               existing_nullable=False)
+    op.alter_column('TopLevelContainer', 'name',
+               existing_type=sa.VARCHAR(length=40),
+               type_=sa.String(length=80),
+               existing_nullable=False)
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column('TopLevelContainer', 'name',
+               existing_type=sa.String(length=80),
+               type_=sa.VARCHAR(length=40),
+               existing_nullable=False)
+    op.alter_column('Shipment', 'name',
+               existing_type=sa.String(length=80),
+               type_=sa.VARCHAR(length=40),
+               existing_nullable=False)
+    op.alter_column('Sample', 'name',
+               existing_type=sa.String(length=80),
+               type_=sa.VARCHAR(length=40),
+               existing_nullable=False)
+    op.alter_column('Container', 'name',
+               existing_type=sa.String(length=80),
+               type_=sa.VARCHAR(length=40),
+               existing_nullable=False)
+    # ### end Alembic commands ###

database/data.sql

@@ -2,8 +2,10 @@
 -- PostgreSQL database dump
 --
 
--- Dumped from database version 17.5
--- Dumped by pg_dump version 17.4
+\restrict U6bOmzaZYjYIO0Hg2gWsqgE5LjK1vVHNNCtv3caSVlfRNEoi3Gvy4hpNaeUfHGq
+
+-- Dumped from database version 17.6 (Debian 17.6-2.pgdg13+1)
+-- Dumped by pg_dump version 18.0
 
 SET statement_timeout = 0;
 SET lock_timeout = 0;
@@ -45,7 +47,7 @@ CREATE TABLE public."Container" (
     details json,
     "requestedReturn" boolean NOT NULL,
     "registeredContainer" character varying,
-    name character varying(40) NOT NULL,
+    name character varying(80) NOT NULL,
     "externalId" integer,
     comments character varying(255),
     "isInternal" boolean NOT NULL,
@@ -161,7 +163,7 @@ CREATE TABLE public."Sample" (
     location smallint,
     details json,
     "containerId" integer,
-    name character varying(40) NOT NULL,
+    name character varying(80) NOT NULL,
     "externalId" integer,
     comments character varying(255),
     "subLocation" smallint,
@@ -250,7 +252,7 @@ CREATE TABLE public."Shipment" (
     "creationDate" timestamp with time zone DEFAULT now() NOT NULL,
     "shipmentRequest" integer,
     status character varying(25) DEFAULT 'Created'::character varying,
-    name character varying(40) NOT NULL,
+    name character varying(80) NOT NULL,
     "externalId" integer,
     comments character varying(255),
     "proposalCode" character varying(2) NOT NULL,
@@ -301,7 +303,7 @@ CREATE TABLE public."TopLevelContainer" (
     details json,
     code character varying(20) NOT NULL,
     type character varying(40) DEFAULT 'dewar'::character varying NOT NULL,
-    name character varying(40) NOT NULL,
+    name character varying(80) NOT NULL,
     "externalId" integer,
     comments character varying(255),
     "isInternal" boolean NOT NULL,
@@ -498,7 +500,7 @@ COPY public."TopLevelContainer" ("topLevelContainerId", "shipmentId", details, c
 --
 
 COPY public.alembic_version (version_num) FROM stdin;
-730f6f07da68
+31b603858335
 \.
 
 
@@ -861,3 +863,5 @@ GRANT ALL ON SCHEMA public TO PUBLIC;
 -- PostgreSQL database dump complete
 --
 
+\unrestrict U6bOmzaZYjYIO0Hg2gWsqgE5LjK1vVHNNCtv3caSVlfRNEoi3Gvy4hpNaeUfHGq
+

src/scaup/crud/samples.py

@@ -3,12 +3,14 @@
 from fastapi import HTTPException, status
 from lims_utils.logging import app_logger
 from lims_utils.models import Paged, ProposalReference
+from psycopg.errors import ForeignKeyViolation
 from sqlalchemy import and_, insert, select
+from sqlalchemy.exc import IntegrityError
 
 from ..models.inner_db.tables import Container, Sample, SampleParentChild, Shipment
 from ..models.samples import OptionalSample, SampleIn, SampleOut
 from ..utils.config import Config
-from ..utils.crud import assert_not_booked, edit_item
+from ..utils.crud import assert_not_booked, delete_item, edit_item
 from ..utils.database import inner_db
 from ..utils.external import Expeye, ExternalRequest
 from ..utils.session import retry_if_exists
@@ -189,3 +191,16 @@ def get_samples(
                 pass
 
     return validated_samples
+
+
+def delete_sample(sample_id: int):
+    try:
+        delete_item(table=Sample, item_id=sample_id)
+    except IntegrityError as e:
+        if isinstance(e.__cause__, ForeignKeyViolation):
+            # If a foreign key violation occurs, that's because the sample is in SampleParentChild
+            raise HTTPException(
+                status_code=status.HTTP_409_CONFLICT,
+                detail="Sample is linked to a different session and cannot be deleted",
+            )
+        raise

src/scaup/crud/shipments.py

@@ -170,7 +170,7 @@ def _get_children(
 @assert_no_unassigned
 def build_shipment_request(shipmentId: int, token: str):
     shipment = _get_shipment_tree(shipmentId)
-    proposal_reference = f"{shipment.proposalCode}{shipment.proposalNumber:06}"
+    proposal_reference = f"{shipment.proposalCode}{shipment.proposalNumber}"
 
     packages: list[dict] = []
     for tlc in shipment.children:
@@ -252,7 +252,6 @@ def build_shipment_request(shipmentId: int, token: str):
     )
 
     built_request_body = {
-        # TODO: remove padding once shipping service removes regex check
         "session_number": shipment.visitNumber,
         "proposal": proposal_reference,
         "external_id": shipment.externalId,

src/scaup/models/inner_db/tables.py

@@ -22,7 +22,7 @@ class Base(DeclarativeBase):
 
 
 class BaseColumns:
-    name: Mapped[str] = mapped_column(String(40))
+    name: Mapped[str] = mapped_column(String(80))
     externalId: Mapped[int | None] = mapped_column(unique=True, comment="Item ID in ISPyB")
     comments: Mapped[str | None] = mapped_column(String(255))
     creationDate: Mapped[datetime] = mapped_column(DateTime(timezone=True), server_default=func.now())

src/scaup/routes/samples.py

@@ -3,9 +3,7 @@
 
 from ..auth import Permissions, auth_scheme
 from ..crud import samples as crud
-from ..models.inner_db.tables import Sample
 from ..models.samples import OptionalSample, SampleOut
-from ..utils.crud import delete_item
 
 auth_sample = Permissions.sample
 
@@ -29,4 +27,4 @@ def edit_sample(
 @router.delete("/{sampleId}", status_code=status.HTTP_204_NO_CONTENT)
 def delete_sample(sampleId=Depends(auth_sample)):
     """Create new sample in shipment"""
-    return delete_item(table=Sample, item_id=sampleId)
+    return crud.delete_sample(sample_id=sampleId)

tests/shipments/samples/test_delete.py

@@ -0,0 +1,8 @@
+def test_delete_with_parent(client):
+    """Should fail if sample is referenced in SampleParentChild"""
+
+    resp = client.delete(
+        "/samples/1877",
+    )
+
+    assert resp.status_code == 409

tests/shipments/test_create_request.py

@@ -188,7 +188,7 @@ def test_request_fail(client):
 def test_invalid_dewar_response_from_ispyb(client):
     """Should throw error if ISPyB returns error when getting dewar from dewar registry"""
     responses.get(
-        f"{Config.ispyb_api.url}/proposals/cm000003/dewar-registry/DLS-4",
+        f"{Config.ispyb_api.url}/proposals/cm3/dewar-registry/DLS-4",
         status=404,
         json={},
     )