Merge branch 'fix/hide-eori' into fix/lims-1980/keycloak-fixes

gfrn · gfrn · commit d8991e4b86da · 2025-12-11T17:02:21.000Z
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -7,6 +7,24 @@ All notable changes to this project will be documented in this file.
 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).
 
++++++++++
+v0.18.0 (21/11/2025)
++++++++++
+
+**Added**
+
+- Add sessions endpoint
+- Add endpoint to get shipments in a given proposal
+
++++++++++
+v0.17.0 (05/11/2025)
++++++++++
+
+**Added**
+
+- Push manufacturer serial number to ISPyB
+- Include more information when pushing shipment to shipping service
+
 +++++++++
 v0.16.1 (17/10/2025)
 +++++++++
diff --git a/src/scaup/auth/micro.py b/src/scaup/auth/micro.py
@@ -132,7 +132,9 @@ def proposal(
         proposalReference: str,
         token: HTTPAuthorizationCredentials = Depends(auth_scheme),
     ):
-        return _check_perms(proposalReference, "proposal", token.credentials)
+        proposal_reference = parse_proposal(proposal_reference=proposalReference)
+        _check_perms(proposalReference, "proposal", token.credentials)
+        return proposal_reference
 
     @staticmethod
     def session(
diff --git a/src/scaup/auth/template.py b/src/scaup/auth/template.py
@@ -7,7 +7,7 @@
 class GenericPermissions(Protocol):
     @staticmethod
     def proposal(proposalReference: str):
-        return proposalReference
+        return parse_proposal(proposal_reference=proposalReference)
 
     @staticmethod
     def session(proposalReference: str, visitNumber: int):
diff --git a/src/scaup/crud/proposals.py b/src/scaup/crud/proposals.py
@@ -35,9 +35,13 @@ def get_shipments(token: str, proposal_reference: ProposalReference, limit: int,
     query = select(Shipment).filter(
         Shipment.proposalCode == proposal_reference.code,
         Shipment.proposalNumber == proposal_reference.number,
-        Shipment.visitNumber == proposal_reference.visit_number,
     )
 
+    if proposal_reference.visit_number:
+        query = query.filter(Shipment.visitNumber == proposal_reference.visit_number)
+    else:
+        query = query.order_by(Shipment.visitNumber.desc(), Shipment.creationDate.desc())
+
     shipments: Paged[Shipment] = inner_db.paginate(query, limit, page, slow_count=False, scalar=False)
     shipments.items = update_shipment_statuses(shipments.items, token)
 
diff --git a/src/scaup/crud/shipments.py b/src/scaup/crud/shipments.py
@@ -167,6 +167,7 @@ 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}"
 
     packages: list[dict] = []
     for tlc in shipment.children:
@@ -192,16 +193,28 @@ def build_shipment_request(shipmentId: int, token: str):
 
         # Dewar cases do NOT include the dewar, this merely adds them to the outermost package
         if tlc.type == "dewar":
+            dewar_response = ExternalRequest.request(
+                token=token,
+                url=f"/proposals/{proposal_reference}/dewar-registry/{tlc.code}",
+            )
+
+            if dewar_response.status_code != 200:
+                app_logger.error(f"Error while getting dewar {tlc.code} from upstream: {dewar_response.text}")
+                raise HTTPException(
+                    status_code=status.HTTP_424_FAILED_DEPENDENCY,
+                    detail="Invalid facility code provided",
+                )
+
+            serial_number = dewar_response.json()["manufacturerSerialNumber"]
+
             line_items.append(
-                {
-                    "shippable_item_type": "CRYOGENIC_DRY_SHIPPER",
-                    "quantity": 1,
-                }
+                {"shippable_item_type": "CRYOGENIC_DRY_SHIPPER", "quantity": 1, "serial_number": serial_number}
             )
 
         if tlc.type in TYPE_TO_SHIPPING_SERVICE_TYPE:
             packages.append(
                 {
+                    "container_name": tlc.name,
                     "line_items": line_items,
                     "external_id": tlc.externalId,
                     "shippable_item_type": TYPE_TO_SHIPPING_SERVICE_TYPE[tlc.type],
@@ -237,7 +250,8 @@ def build_shipment_request(shipmentId: int, token: str):
 
     built_request_body = {
         # TODO: remove padding once shipping service removes regex check
-        "proposal": f"{shipment.proposalCode}{shipment.proposalNumber:06}",
+        "session_number": shipment.visitNumber,
+        "proposal": proposal_reference,
         "external_id": shipment.externalId,
         "origin_url": f"{Config.frontend_url}/proposals/{shipment.proposalCode}{shipment.proposalNumber}/sessions/"
         + f"{shipment.visitNumber}/shipments/{shipment.id}",
diff --git a/src/scaup/crud/top_level_containers.py b/src/scaup/crud/top_level_containers.py
@@ -21,6 +21,17 @@
 DEWAR_PREFIX = "DLS-BI-1"
 
 
+def _check_if_dls_code(code: str | None):
+    """Check if code is DLS barcode, or user provided serial number
+
+    Args:
+        code: User-provided code
+
+    Returns:
+        True if it is a DLS code, False otherwise"""
+    return code is not None and code[:3] == "DLS"
+
+
 def _check_fields(
     params: TopLevelContainerIn | OptionalTopLevelContainer,
     token: str,
@@ -38,7 +49,6 @@ def _check_fields(
         if params.code is None:
             # Perform no facility code check if code is not present
             return
-
         query = query.select_from(TopLevelContainer).filter(TopLevelContainer.id == item_id).join(Shipment)
 
     proposal_reference = inner_db.session.scalar(query)
@@ -72,7 +82,7 @@ def create_top_level_container(shipmentId: int | None, params: TopLevelContainer
         ).one()
     )
 
-    if params.code:
+    if _check_if_dls_code(params.code):
         _check_fields(params, token, shipmentId)
     elif params.type == "dewar" and autocreate:
         # Automatically register dewar if no code is provided
@@ -102,7 +112,10 @@ def create_top_level_container(shipmentId: int | None, params: TopLevelContainer
                 Config.ispyb_api.jwt,
                 method="POST",
                 url=f"/proposals/{proposal.reference}/dewar-registry",
-                json={"facilityCode": new_code},
+                json={
+                    "facilityCode": new_code,
+                    "manufacturerSerialNumber": (None if params.code.lower().strip() == "n/a" else params.code),
+                },
             )
 
             if ext_resp.status_code != 201:
diff --git a/src/scaup/main.py b/src/scaup/main.py
@@ -12,6 +12,7 @@
     internal,
     proposals,
     samples,
+    sessions,
     shipments,
     top_level_containers,
 )
@@ -72,5 +73,6 @@ async def general_exception_handler(request: Request, exc: Exception):
 api.include_router(containers.router)
 api.include_router(top_level_containers.router)
 api.include_router(internal.router)
+api.include_router(sessions.router)
 
 app.mount(os.getenv("MOUNT_POINT", "/api"), api)
diff --git a/src/scaup/models/sessions.py b/src/scaup/models/sessions.py
@@ -0,0 +1,44 @@
+from datetime import datetime
+from typing import Optional, Set
+
+from pydantic import AliasChoices, Field
+
+from ..utils.models import OrmBaseModel
+
+
+class SessionOut(OrmBaseModel):
+    beamLineSetupId: int | None = None
+    beamCalendarId: int | None = None
+    startDate: datetime | None = None
+    endDate: datetime | None = None
+    beamLineName: str | None = Field(None, max_length=45)
+    scheduled: int | None = Field(None, lt=10)
+    nbShifts: int | None = Field(None, lt=1e9)
+    comments: str | None = Field(None, max_length=2000)
+    visit_number: int | None = Field(
+        None,
+        lt=1e9,
+        serialization_alias="visitNumber",
+        validation_alias=AliasChoices("visitNumber", "visit_number"),
+    )
+    usedFlag: int | None = Field(
+        None,
+        lt=2,
+        description="Indicates if session has Datacollections or XFE or EnergyScans attached",  # noqa: E501
+    )
+    lastUpdate: datetime | None = Field(
+        None,
+        description="Last update timestamp: by default the end of the session, the last collect",  # noqa: E501
+    )
+    parentProposal: str | None = None
+    proposalId: int = Field(..., lt=1e9, description="Proposal ID")
+    sessionId: int = Field(..., lt=1e9, description="Session ID")
+    beamLineOperator: Set[str] | None = None
+    bltimeStamp: datetime
+    purgedProcessedData: bool
+    archived: int = Field(
+        ...,
+        lt=2,
+        description="The data for the session is archived and no longer available on disk",  # noqa: E501
+    )
+    collectionGroups: Optional[int] = None
diff --git a/src/scaup/models/top_level_containers.py b/src/scaup/models/top_level_containers.py
@@ -28,7 +28,7 @@ class BaseTopLevelContainer(BaseModel):
 
 class TopLevelContainerIn(BaseTopLevelContainer):
     type: str
-    code: str | None = None
+    code: str = "n/a"
     isInternal: bool = False
 
 
diff --git a/src/scaup/routes/proposals.py b/src/scaup/routes/proposals.py
@@ -103,6 +103,16 @@ def get_shipment_data(
     return ExternalRequest.request(token=token.credentials, url=f"/proposals/{proposalReference}/data").json()
 
 
+@router.get("/{proposalReference}/shipments")
+def get_proposal_shipments(
+    proposalReference: ProposalReference = Depends(Permissions.proposal),
+    token: HTTPAuthorizationCredentials = Depends(auth_scheme),
+    page: dict[str, int] = Depends(pagination),
+):
+    """Get shipments in proposal"""
+    return crud.get_shipments(token=token.credentials, proposal_reference=proposalReference, **page)
+
+
 @router.post(
     "/{proposalReference}/sessions/{visitNumber}/assign-data-collection-groups",
 )
diff --git a/src/scaup/routes/sessions.py b/src/scaup/routes/sessions.py
@@ -0,0 +1,40 @@
+from fastapi import APIRouter, Depends, HTTPException, Query
+from fastapi.security import HTTPAuthorizationCredentials
+from lims_utils.logging import app_logger
+from lims_utils.models import Paged, pagination
+
+from ..auth import auth_scheme
+from ..models.sessions import SessionOut
+from ..utils.external import ExternalRequest
+
+router = APIRouter(
+    tags=["Sessions"],
+    prefix="/sessions",
+)
+
+
+@router.get("", response_model=Paged[SessionOut])
+def get_sessions(
+    token: HTTPAuthorizationCredentials = Depends(auth_scheme),
+    page: dict[str, int] = Depends(pagination),
+    minEndDate: str | None = Query(default=None, description="Minimum session end date"),
+):
+    """Get sessions a user can view (wrapper for Expeye endpoint)"""
+    # TODO: replace search once Expeye supports filtering by beamline name
+    url = f"/sessions?limit={page['limit']}&page={page['page']}&search=m"
+    if minEndDate is not None:
+        url += f"&minEndDate={minEndDate}"
+
+    expeye_response = ExternalRequest.request(
+        token=token.credentials,
+        url=url,
+    )
+
+    if expeye_response.status_code != 200:
+        app_logger.warning(f"Failed to fetch proposals from Expeye: {expeye_response.text}")
+        raise HTTPException(
+            status_code=expeye_response.status_code,
+            detail="Failed to fetch proposals",
+        )
+
+    return expeye_response.json()
diff --git a/tests/proposals/test_get_session_shipments.py b/tests/proposals/test_get_session_shipments.py
@@ -5,7 +5,7 @@
 
 @responses.activate
 def test_get(client):
-    """Should get shipments in proposal"""
+    """Should get shipments in session"""
     responses.get(
         f"{Config.ispyb_api.url}/shipments/63975",
         status=200,
@@ -23,7 +23,7 @@ def test_get(client):
 
 @responses.activate
 def test_get_inexistent(client):
-    """Should return empty list if no shipments exist in proposal"""
+    """Should return empty list if no shipments exist in session"""
     resp = client.get("/proposals/cm55555/sessions/1/shipments")
 
     assert resp.status_code == 200
diff --git a/tests/proposals/test_get_shipments.py b/tests/proposals/test_get_shipments.py
@@ -0,0 +1,33 @@
+import responses
+
+from scaup.utils.config import Config
+
+
+@responses.activate
+def test_get(client):
+    """Should get shipments in proposal"""
+    responses.get(
+        f"{Config.ispyb_api.url}/shipments/63975",
+        status=200,
+        json={"shippingStatus": "opened"},
+    )
+
+    resp = client.get("/proposals/bi23047/shipments")
+
+    assert resp.status_code == 200
+
+    data = resp.json()
+
+    assert len(data["items"]) == 5
+
+
+@responses.activate
+def test_get_inexistent(client):
+    """Should return empty list if no shipments exist in proposal"""
+    resp = client.get("/proposals/cm55555/shipments")
+
+    assert resp.status_code == 200
+
+    data = resp.json()
+
+    assert len(data["items"]) == 0
diff --git a/tests/sessions/__init__.py b/tests/sessions/__init__.py
diff --git a/tests/sessions/test_get.py b/tests/sessions/test_get.py
diff --git a/tests/shipments/test_create_request.py b/tests/shipments/test_create_request.py
diff --git a/tests/shipments/top_level_containers/responses.py b/tests/shipments/top_level_containers/responses.py
diff --git a/tests/shipments/top_level_containers/test_create.py b/tests/shipments/top_level_containers/test_create.py
