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Fix tests from improve order flow #4152

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Fix tests from improve order flow #4152

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25c5aee
fix failing tests
diitaz93 Jan 23, 2025
1987cd9
new test for parsing skip reception control
diitaz93 Jan 23, 2025
8b2c4d2
Merge branch 'master' into fix-remaining-tests
diitaz93 Jan 23, 2025
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101 changes: 57 additions & 44 deletions tests/services/orders/lims_service/test_order_lims_service.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,3 @@
import pytest

from cg.constants import Workflow
from cg.models.lims.sample import LimsSample
from cg.services.orders.lims_service.service import OrderLimsService
Expand All @@ -12,17 +10,17 @@
from cg.services.orders.validation.workflows.rml.models.order import RmlOrder


def test_to_lims_mip(mip_dna_order_to_submit):
def test_to_lims_mip(mip_dna_order: MipDnaOrder):
# GIVEN a scout order for a trio
order_data = MipDnaOrder.model_validate(mip_dna_order_to_submit)

# WHEN parsing the order to format for LIMS import
new_samples = [sample for _, _, sample in order_data.enumerated_new_samples]
new_samples = [sample for _, _, sample in mip_dna_order.enumerated_new_samples]
samples: list[LimsSample] = OrderLimsService._build_lims_sample(
customer="cust003",
samples=new_samples,
workflow=Workflow.MIP_DNA,
delivery_type=order_data.delivery_type,
skip_reception_control=order_data.skip_reception_control,
delivery_type=mip_dna_order.delivery_type,
skip_reception_control=mip_dna_order.skip_reception_control,
)

# THEN it should list all samples
Expand All @@ -35,7 +33,7 @@ def test_to_lims_mip(mip_dna_order_to_submit):
container_names = {sample.container_name for sample in samples if sample.container_name}
assert container_names == {"MipPlate"}

# ... and pick out relevant UDFs
# THEN it should pick out relevant UDFs
first_sample: LimsSample = samples[0]
assert first_sample.well_position == "A:1"
assert first_sample.udfs.priority == "standard"
Expand All @@ -48,40 +46,39 @@ def test_to_lims_mip(mip_dna_order_to_submit):
assert isinstance(samples[1].udfs.comment, str)


def test_to_lims_fastq(fastq_order_to_submit):
def test_to_lims_fastq(fastq_order: FastqOrder):
# GIVEN a fastq order for two samples; normal vs. tumour
order_data = FastqOrder.model_validate(fastq_order_to_submit)

# WHEN parsing the order to format for LIMS
samples: list[LimsSample] = OrderLimsService._build_lims_sample(
customer="dummyCust",
samples=order_data.samples,
samples=fastq_order.samples,
workflow=Workflow.RAW_DATA,
delivery_type=order_data.delivery_type,
skip_reception_control=order_data.skip_reception_control,
delivery_type=fastq_order.delivery_type,
skip_reception_control=fastq_order.skip_reception_control,
)

# THEN should "work"
# THEN two samples should be parsed, one normal and one tumour
assert len(samples) == 2
normal_sample = samples[0]
tumour_sample = samples[1]
# ... and pick out relevant UDF values

# THEN it should pick out relevant UDFs
assert normal_sample.udfs.tumour is False
assert tumour_sample.udfs.tumour is True
assert normal_sample.udfs.volume == "54"


@pytest.mark.xfail(reason="RML sample container validation not working")
def test_to_lims_rml(rml_order_to_submit: dict):
def test_to_lims_rml(rml_order: RmlOrder):
# GIVEN a rml order for four samples
order_data = RmlOrder.model_validate(rml_order_to_submit)

# WHEN parsing for LIMS
samples: list[LimsSample] = OrderLimsService._build_lims_sample(
customer="cust000",
samples=order_data.samples,
samples=rml_order.samples,
workflow=Workflow.RAW_DATA,
delivery_type=order_data.delivery_type,
delivery_type=rml_order.delivery_type,
skip_reception_control=rml_order.skip_reception_control,
)

# THEN it should have found the same number of samples
Expand All @@ -97,17 +94,16 @@ def test_to_lims_rml(rml_order_to_submit: dict):
assert first_sample.udfs.well_position_rml == "A:1"


@pytest.mark.xfail(reason="Fluffy sample container validation not working")
def test_to_lims_fluffy(fluffy_order_to_submit: dict):
def test_to_lims_fluffy(fluffy_order: FluffyOrder):
# GIVEN a Fluffy order for four samples
order_data = FluffyOrder.model_validate(fluffy_order_to_submit)

# WHEN parsing for LIMS
samples: list[LimsSample] = OrderLimsService._build_lims_sample(
customer="cust000",
samples=order_data.samples,
samples=fluffy_order.samples,
workflow=Workflow.FLUFFY,
delivery_type=order_data.delivery_type,
delivery_type=fluffy_order.delivery_type,
skip_reception_control=fluffy_order.skip_reception_control,
)

# THEN it should have found the same number of samples
Expand All @@ -123,22 +119,22 @@ def test_to_lims_fluffy(fluffy_order_to_submit: dict):
assert first_sample.udfs.well_position_rml == "A:1"


def test_to_lims_microbial(microbial_order_to_submit: dict):
def test_to_lims_microbial(microsalt_order: MicrosaltOrder):
# GIVEN a microbial order for three samples
order_data = MicrosaltOrder.model_validate(microbial_order_to_submit)

# WHEN parsing for LIMS
samples: list[LimsSample] = OrderLimsService._build_lims_sample(
customer="cust000",
samples=order_data.samples,
samples=microsalt_order.samples,
workflow=Workflow.MICROSALT,
delivery_type=order_data.delivery_type,
skip_reception_control=order_data.skip_reception_control,
delivery_type=microsalt_order.delivery_type,
skip_reception_control=microsalt_order.skip_reception_control,
)
# THEN it should "work"

# THEN 5 samples should be parsed
assert len(samples) == 5
# ... and pick out relevant UDFs

# THEN it should pick out relevant UDFs
first_sample = samples[0].dict()
assert first_sample["udfs"]["priority"] == "research"
assert first_sample["udfs"]["organism"] == "C. jejuni"
Expand All @@ -161,7 +157,8 @@ def test_to_lims_sarscov2(mutant_order: MutantOrder):

# THEN it should have found the same number of samples
assert len(samples) == 6
# ... and pick out relevant UDFs

# THEN it should pick out relevant UDFs
first_sample = samples[0].dict()
assert first_sample["udfs"]["collection_date"] == "2021-05-05"
assert first_sample["udfs"]["extraction_method"] == "MagNaPure 96"
Expand All @@ -178,27 +175,26 @@ def test_to_lims_sarscov2(mutant_order: MutantOrder):
assert first_sample["udfs"]["volume"] == "20"


def test_to_lims_balsamic(balsamic_order_to_submit: dict):
def test_to_lims_balsamic(balsamic_order: BalsamicOrder):
# GIVEN a cancer order for a sample
order_data = BalsamicOrder.model_validate(balsamic_order_to_submit)

new_samples = [sample for _, _, sample in order_data.enumerated_new_samples]
new_samples = [sample for _, _, sample in balsamic_order.enumerated_new_samples]
# WHEN parsing the order to format for LIMS import
samples: list[LimsSample] = OrderLimsService._build_lims_sample(
customer="cust000",
samples=new_samples,
workflow=Workflow.BALSAMIC,
delivery_type=order_data.delivery_type,
skip_reception_control=order_data.skip_reception_control,
delivery_type=balsamic_order.delivery_type,
skip_reception_control=balsamic_order.skip_reception_control,
)
# THEN it should list all samples

# THEN it should list all samples
assert len(samples) == 1
# ... and determine the container, container name, and well position

# THEN it should determine the container, container name, and well position
container_names = {sample.container_name for sample in samples if sample.container_name}

# ... and pick out relevant UDFs
# THEN it should pick out relevant UDFs
first_sample = samples[0].dict()
assert first_sample["name"] == "BalsamicSample"
assert {sample.container for sample in samples} == set(["96 well plate"])
Expand All @@ -209,15 +205,32 @@ def test_to_lims_balsamic(balsamic_order_to_submit: dict):
assert first_sample["udfs"]["source"] == "cytology (FFPE)"
assert first_sample["udfs"]["volume"] == "42"
assert first_sample["udfs"]["priority"] == "standard"

assert container_names == set(["BalsamicPlate"])
assert first_sample["well_position"] == "A:1"
assert first_sample["udfs"]["tumour"] is True
assert first_sample["udfs"]["capture_kit"] == "GMCKsolid"
assert first_sample["udfs"]["tumour_purity"] == "13"

assert first_sample["udfs"]["formalin_fixation_time"] == "15"
assert first_sample["udfs"]["post_formalin_fixation_time"] == "3"
assert first_sample["udfs"]["tissue_block_size"] == "large"

assert first_sample["udfs"]["comment"] == "This is a sample comment"


def test_order_with_skip_reception_control(balsamic_order: BalsamicOrder):
"""Test that an order set to skip reception control can be parsed correctly by LIMS."""
# GIVEN a Balsamic order with one case and one sample set to skip reception control
balsamic_order.skip_reception_control = True

# WHEN parsing the order to format for LIMS import
new_samples = [sample for _, _, sample in balsamic_order.enumerated_new_samples]
samples: list[LimsSample] = OrderLimsService._build_lims_sample(
customer="cust000",
samples=new_samples,
workflow=Workflow.BALSAMIC,
delivery_type=balsamic_order.delivery_type,
skip_reception_control=balsamic_order.skip_reception_control,
)

# THEN the parsed samples should have the skip reception control flag set
first_sample = samples[0].dict()
assert first_sample["udfs"]["skip_reception_control"] is True
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