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stephen-riggsstephen-riggs
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Add some tests for the api dcg insert
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‎tests/server/api/test_workflow.py‎

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from unittest import mock
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from sqlmodel import Session, select
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from murfey.server.api.workflow import register_dc_group
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from murfey.util.db import DataCollectionGroup, SearchMap
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from tests.conftest import ExampleVisit
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@mock.patch("murfey.server.workflow._transport_object")
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def test_register_dc_group_new_dcg(mock_transport, murfey_db_session: Session):
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"""Test the request for a completely new data collection group"""
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mock_transport.feedback_queue = "mock_feedback_queue"
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# Request new dcg registration
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dcg_params = {
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"experiment_type_id": 44,
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"tag": "atlas_tag",
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"atlas": "/path/to/Atlas_1.jpg",
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"sample": 1,
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"atlas_pixel_size": 1e-5,
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}
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register_dc_group(
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visit_name="cm12345-6",
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session_id=ExampleVisit.murfey_session_id,
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dcg_params=dcg_params,
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db=murfey_db_session,
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)
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# Check request for registering dcg in ispyb and murfey
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mock_transport.send.assert_called_once_with(
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"mock_feedback_queue",
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{
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"register": "data_collection_group",
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"start_time": mock.ANY,
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"experiment_type_id": dcg_params["experiment_type_id"],
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"tag": dcg_params["tag"],
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"session_id": ExampleVisit.murfey_session_id,
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"atlas": dcg_params["atlas"],
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"sample": dcg_params["sample"],
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"atlas_pixel_size": dcg_params["atlas_pixel_size"],
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"microscope": ExampleVisit.instrument_name,
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"proposal_code": ExampleVisit.proposal_code,
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"proposal_number": ExampleVisit.proposal_number,
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"visit_number": ExampleVisit.visit_number,
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},
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)
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@mock.patch("murfey.server.workflow._transport_object")
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def test_register_dc_group_atlas_to_processing(
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mock_transport, murfey_db_session: Session
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):
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"""
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Test the request to update an existing data collection group
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from atlas type 44 to a processing type with a different tag
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"""
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mock_transport.feedback_queue = "mock_feedback_queue"
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# Make sure dcg is present
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dcg = DataCollectionGroup(
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id=1,
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session_id=ExampleVisit.murfey_session_id,
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tag="atlas_tag",
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atlas_id=90,
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atlas_pixel_size=1e-5,
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sample=1,
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atlas="/path/to/Atlas_1.jpg",
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)
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murfey_db_session.add(dcg)
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murfey_db_session.commit()
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# Request new dcg registration with processing experiment type and tag
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dcg_params = {
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"experiment_type_id": 36,
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"tag": "processing_tag",
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"atlas": "/path/to/Atlas_1.jpg",
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"sample": 1,
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"atlas_pixel_size": 1e-5,
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}
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register_dc_group(
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visit_name="cm12345-6",
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session_id=ExampleVisit.murfey_session_id,
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dcg_params=dcg_params,
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db=murfey_db_session,
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)
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# Check request to ispyb for updating the experiment type
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mock_transport.send.assert_called_once_with(
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"mock_feedback_queue",
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{
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"register": "experiment_type_update",
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"experiment_type_id": dcg_params["experiment_type_id"],
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"dcgid": dcg.id,
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},
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)
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# Check that the tag of the data collection group was updated
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new_dcg = murfey_db_session.exec(
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select(DataCollectionGroup).where(DataCollectionGroup.id == dcg.id)
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).one()
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assert new_dcg.tag == dcg_params["tag"]
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@mock.patch("murfey.server.workflow._transport_object")
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def test_register_dc_group_processing_to_atlas(
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mock_transport, murfey_db_session: Session
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):
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"""
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Test the request to update an existing data collection group
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of processing type with a new atlas type 44, which should leave the tag unchanged
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"""
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mock_transport.feedback_queue = "mock_feedback_queue"
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# Make sure dcg is present
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dcg = DataCollectionGroup(
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id=1,
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session_id=ExampleVisit.murfey_session_id,
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tag="processing_tag",
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atlas_id=90,
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atlas_pixel_size=1e-5,
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sample=1,
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atlas="/path/to/Atlas_1.jpg",
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)
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murfey_db_session.add(dcg)
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murfey_db_session.commit()
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# Request new dcg registration with atlas experiment type and tag
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dcg_params = {
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"experiment_type_id": 44,
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"tag": "atlas_tag",
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"atlas": "/path/to/Atlas_2.jpg",
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"sample": 1,
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"atlas_pixel_size": 1e-4,
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}
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register_dc_group(
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visit_name="cm12345-6",
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session_id=ExampleVisit.murfey_session_id,
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dcg_params=dcg_params,
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db=murfey_db_session,
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)
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# Check request to ispyb for updating the experiment type
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mock_transport.send.assert_called_once_with(
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"mock_feedback_queue",
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{
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"register": "atlas_update",
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"atlas_id": dcg.atlas_id,
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"atlas": dcg_params["atlas"],
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"sample": dcg_params["sample"],
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"atlas_pixel_size": dcg_params["atlas_pixel_size"],
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"dcgid": dcg.id,
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"session_id": ExampleVisit.murfey_session_id,
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},
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)
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# Check the data collection group atlas was updated
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new_dcg = murfey_db_session.exec(
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select(DataCollectionGroup).where(DataCollectionGroup.id == dcg.id)
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).one()
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assert new_dcg.atlas == dcg_params["atlas"]
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assert new_dcg.atlas_pixel_size == dcg_params["atlas_pixel_size"]
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# Check the tag of the data collection group was not updated
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assert new_dcg.tag != dcg_params["tag"]
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@mock.patch("murfey.server.workflow._transport_object")
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def test_register_dc_group_new_atlas(mock_transport, murfey_db_session: Session):
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"""
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Test the request to update an existing data collection group
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by adding an atlas, using the same tag
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"""
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mock_transport.feedback_queue = "mock_feedback_queue"
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mock_transport.do_insert_atlas.return_value = 5
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# Make sure dcg is present without an atlas id
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dcg = DataCollectionGroup(
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id=1,
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session_id=ExampleVisit.murfey_session_id,
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tag="processing_tag",
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)
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murfey_db_session.add(dcg)
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murfey_db_session.commit()
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# Request new dcg registration with atlas and exisiting tag
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dcg_params = {
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"experiment_type_id": 36,
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"tag": "processing_tag",
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"atlas": "/path/to/Atlas_2.jpg",
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"sample": 1,
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"atlas_pixel_size": 1e-4,
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}
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register_dc_group(
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visit_name="cm12345-6",
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session_id=ExampleVisit.murfey_session_id,
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dcg_params=dcg_params,
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db=murfey_db_session,
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)
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# Check no sends are made by the transport object
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mock_transport.send.assert_not_called()
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# Check the call to insert the atlas into ispyb
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atlas_args = mock_transport.do_insert_atlas.call_args_list
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assert len(atlas_args) == 1
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assert atlas_args[0].dataCollectionGroupId == dcg.id
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assert atlas_args[0].atlasImage == dcg_params["atlas"]
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assert atlas_args[0].pixelSize == dcg_params["atlas_pixel_size"]
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assert atlas_args[0].cassetteSlot == dcg_params["sample"]
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# Check the data collection group atlas was updated
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new_dcg = murfey_db_session.exec(
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select(DataCollectionGroup).where(DataCollectionGroup.id == dcg.id)
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).one()
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assert new_dcg.atlas == dcg_params["atlas"]
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assert new_dcg.sample == dcg_params["sample"]
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assert new_dcg.atlas_pixel_size == dcg_params["atlas_pixel_size"]
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assert new_dcg.tag == dcg_params["tag"]
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assert new_dcg.atlas_id == 5
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@mock.patch("murfey.server.workflow.register_search_map_in_database")
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@mock.patch("murfey.server.workflow._transport_object")
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def test_register_dc_group_new_atlas_with_searchmaps(
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mock_register_search_map, mock_transport, murfey_db_session: Session
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):
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"""
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Test the request to update an existing data collection group
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by adding an atlas, using the same tag, and also update search maps
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"""
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mock_transport.feedback_queue = "mock_feedback_queue"
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# Make sure dcg is present with an atlas id
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dcg = DataCollectionGroup(
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id=1,
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session_id=ExampleVisit.murfey_session_id,
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tag="processing_tag",
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atlas_id=90,
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atlas_pixel_size=1e-5,
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sample=1,
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atlas="/path/to/Atlas_1.jpg",
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)
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murfey_db_session.add(dcg)
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murfey_db_session.commit()
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# Add some search maps with the dcg tag and one with a different tag
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sm1 = SearchMap(
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id=1,
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session_id=ExampleVisit.murfey_session_id,
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tag="processing_tag",
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name="searchmap1",
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)
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sm2 = SearchMap(
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id=2,
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session_id=ExampleVisit.murfey_session_id,
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tag="processing_tag",
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name="searchmap2",
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)
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sm3 = SearchMap(
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id=3,
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session_id=ExampleVisit.murfey_session_id,
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tag="different_tag",
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name="searchmap3",
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)
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murfey_db_session.add(sm1)
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murfey_db_session.add(sm2)
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murfey_db_session.add(sm3)
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murfey_db_session.commit()
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# Request new dcg registration with new atlas tag and sample
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dcg_params = {
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"experiment_type_id": 37,
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"tag": "processing_tag",
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"atlas": "/path/to/Atlas_2.jpg",
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"sample": 2,
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"atlas_pixel_size": 1e-4,
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}
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register_dc_group(
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visit_name="cm12345-6",
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session_id=ExampleVisit.murfey_session_id,
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dcg_params=dcg_params,
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db=murfey_db_session,
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)
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# Check request to ispyb for updating the experiment type
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mock_transport.send.assert_called_once_with(
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"mock_feedback_queue",
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{
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"register": "atlas_update",
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"atlas_id": dcg.atlas_id,
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"atlas": dcg_params["atlas"],
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"sample": dcg_params["sample"],
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"atlas_pixel_size": dcg_params["atlas_pixel_size"],
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"dcgid": dcg.id,
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"session_id": ExampleVisit.murfey_session_id,
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},
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)
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# Check the data collection group atlas was updated
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new_dcg = murfey_db_session.exec(
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select(DataCollectionGroup).where(DataCollectionGroup.id == dcg.id)
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).one()
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assert new_dcg.atlas == dcg_params["atlas"]
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assert new_dcg.sample == dcg_params["sample"]
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assert new_dcg.atlas_pixel_size == dcg_params["atlas_pixel_size"]
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assert new_dcg.tag == dcg_params["tag"]
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assert new_dcg.atlas_id == dcg.atlas_id
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# Check the search map update calls
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assert mock_register_search_map.call_count == 2
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mock_register_search_map.assert_any_call(
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ExampleVisit.murfey_session_id,
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"searchmap1",
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mock.ANY,
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murfey_db_session,
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close_db=False,
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)
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mock_register_search_map.assert_any_call(
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ExampleVisit.murfey_session_id,
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"searchmap2",
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mock.ANY,
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murfey_db_session,
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close_db=False,
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)

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