Use paginate function from lims-utils (#12)

* Use paginate function from lims-utils

* Revert Expeye access changes

Author: gfrn

src/scaup/crud/containers.py

@@ -6,7 +6,7 @@
 from ..models.containers import ContainerIn, ContainerOut, OptionalContainer
 from ..models.inner_db.tables import Container, Sample, Shipment
 from ..utils.crud import assert_not_booked, edit_item
-from ..utils.database import inner_db, paginate
+from ..utils.database import inner_db
 from ..utils.session import retry_if_exists
 
 
@@ -81,7 +81,7 @@ def get_containers(
     if container_type:
         query = query.filter(Container.type == container_type)
 
-    return paginate(query, limit, page, slow_count=True, scalar=False)
+    return inner_db.paginate(query, limit, page, slow_count=True, scalar=False)
 
 
 def update_container(

src/scaup/crud/internal.py

@@ -4,7 +4,7 @@
 from ..models.inner_db.tables import Container, TopLevelContainer
 from ..models.shipments import ShipmentChildren
 from ..models.top_level_containers import TopLevelContainerOut
-from ..utils.database import inner_db, paginate
+from ..utils.database import inner_db
 from ..utils.query import query_result_to_object
 
 
@@ -15,7 +15,7 @@ def get_unassigned(limit: int, page: int):
         Container.parentId.is_(None),
     )
 
-    paged_result = paginate(query, limit, page, slow_count=False, scalar=False)
+    paged_result = inner_db.paginate(query, limit, page, slow_count=False, scalar=False)
     paged_result.items = query_result_to_object(paged_result.items)
     return paged_result
 
@@ -42,4 +42,4 @@ def get_internal_container_tree(top_level_container_id: int):
 def get_internal_containers(limit: int, page: int):
     query = select(TopLevelContainer).filter(TopLevelContainer.isInternal.is_(True))
 
-    return paginate(query, limit, page, slow_count=False, scalar=False)
+    return inner_db.paginate(query, limit, page, slow_count=False, scalar=False)

src/scaup/crud/samples.py

@@ -9,7 +9,7 @@
 from ..models.samples import OptionalSample, SampleIn, SampleOut
 from ..utils.config import Config
 from ..utils.crud import assert_not_booked, edit_item
-from ..utils.database import inner_db, paginate
+from ..utils.database import inner_db
 from ..utils.external import ExternalRequest
 from ..utils.session import retry_if_exists
 
@@ -140,7 +140,7 @@ def get_samples(
         query = query.filter(Container.isInternal.is_not(True))
 
     query = query.order_by(Container.name, Container.location, Sample.location)
-    samples = paginate(query, limit, page, slow_count=True, scalar=True)
+    samples = inner_db.paginate(query, limit, page, slow_count=True, scalar=True)
 
     if ignore_external or token is None:
         return samples

src/scaup/routes/internal.py

@@ -1,6 +1,6 @@
 from fastapi import APIRouter, Body, Depends, status
 from fastapi.security import HTTPAuthorizationCredentials
-from lims_utils.models import pagination
+from lims_utils.models import Paged, pagination
 
 from ..auth import User, auth_scheme
 from ..crud import internal as crud
@@ -10,7 +10,6 @@
 from ..models.shipments import GenericItem, ShipmentChildren
 from ..models.top_level_containers import TopLevelContainerIn, TopLevelContainerOut
 from ..utils.auth import check_em_staff
-from ..utils.database import Paged
 
 
 def _internal_check_em_staff(user=Depends(User)):

src/scaup/routes/proposals.py

@@ -2,7 +2,7 @@
 
 from fastapi import APIRouter, Body, Depends, Query, status
 from fastapi.security import HTTPAuthorizationCredentials
-from lims_utils.models import ProposalReference, pagination
+from lims_utils.models import Paged, ProposalReference, pagination
 
 from ..auth import Permissions, auth_scheme
 from ..crud import containers as containers_crud
@@ -11,7 +11,6 @@
 from ..models.containers import ContainerOut
 from ..models.samples import SampleOut, SublocationAssignment
 from ..models.shipments import ShipmentIn, ShipmentOut
-from ..utils.database import Paged
 from ..utils.external import ExternalRequest
 
 auth = Permissions.session
@@ -32,7 +31,7 @@ def create_shipment(
     parameters: ShipmentIn = Body(),
 ):
     """Create new shipment in session"""
-    return crud.create_shipment(proposalReference, params=parameters)
+    return crud.create_shipment(proposal_reference=proposalReference, params=parameters)
 
 
 @router.get(