From 96359f5e0aa5250c797e25223be1d1b3f36e606b Mon Sep 17 00:00:00 2001 From: Sebastian Diaz Date: Fri, 17 Jan 2025 13:29:38 +0100 Subject: [PATCH] move new validation service to orders --- tests/fixtures/cgweb_orders/sarscov2.json | 16 ++++++++-------- .../lims_service/test_order_lims_service.py | 16 +++++++--------- 2 files changed, 15 insertions(+), 17 deletions(-) diff --git a/tests/fixtures/cgweb_orders/sarscov2.json b/tests/fixtures/cgweb_orders/sarscov2.json index 9a1402a603..4def8c2d39 100644 --- a/tests/fixtures/cgweb_orders/sarscov2.json +++ b/tests/fixtures/cgweb_orders/sarscov2.json @@ -36,20 +36,20 @@ "lab_code": null, "mother": null, "name": "sarscov2sample1", - "organism": "other", - "organism_other": "unknown", - "original_lab": "Unilabs Stockholm", - "original_lab_address": "171 54 Solna", + "organism": "SARS-CoV-2", + "organism_other": "", + "original_lab": "Karolinska University Hospital Solna", + "original_lab_address": "171 76 Solna", "phenotype_groups": null, "phenotype_terms": null, "pool": null, "post_formalin_fixation_time": null, - "pre_processing_method": "Other (specify in \"Comments\")", + "pre_processing_method": "COVIDSeq", "primer": "Illumina Artic V3", "priority": "research", "quantity": "3", "reagent_label": null, - "reference_genome": "NC_000001", + "reference_genome": "NC_111", "region": "Stockholm", "region_code": "01", "require_qc_ok": null, @@ -331,8 +331,8 @@ "lab_code": null, "mother": null, "name": "sarscov2sample6", - "organism": "SARS-CoV-2", - "organism_other": "", + "organism": "other", + "organism_other": "unknown", "original_lab": "LaboratorieMedicinskt Centrum Gotland", "original_lab_address": "621 84 Visby", "phenotype_groups": null, diff --git a/tests/services/orders/lims_service/test_order_lims_service.py b/tests/services/orders/lims_service/test_order_lims_service.py index 9394191fc4..86f850027a 100644 --- a/tests/services/orders/lims_service/test_order_lims_service.py +++ b/tests/services/orders/lims_service/test_order_lims_service.py @@ -144,17 +144,15 @@ def test_to_lims_microbial(microbial_order_to_submit: dict): assert first_sample["udfs"]["volume"] == "20" -@pytest.mark.xfail(reason="Mutant extraction methods need a new enum") -def test_to_lims_sarscov2(sarscov2_order_to_submit: dict): +def test_to_lims_sarscov2(mutant_order: MutantOrder): # GIVEN a sarscov2 order for samples - order_data = MutantOrder.model_validate(sarscov2_order_to_submit) # WHEN parsing for LIMS samples: list[LimsSample] = OrderLimsService._build_lims_sample( customer="cust000", - samples=order_data.samples, + samples=mutant_order.samples, workflow=Workflow.MUTANT, - delivery_type=order_data.delivery_type, + delivery_type=mutant_order.delivery_type, ) # THEN it should have found the same number of samples @@ -164,16 +162,16 @@ def test_to_lims_sarscov2(sarscov2_order_to_submit: dict): assert first_sample["udfs"]["collection_date"] == "2021-05-05" assert first_sample["udfs"]["extraction_method"] == "MagNaPure 96" assert first_sample["udfs"]["lab_code"] == "SE100 Karolinska" - assert first_sample["udfs"]["organism"] == "SARS CoV-2" + assert first_sample["udfs"]["organism"] == "SARS-CoV-2" assert first_sample["udfs"]["original_lab"] == "Karolinska University Hospital Solna" - assert first_sample["udfs"]["original_lab_address"] == "171 76 Stockholm" + assert first_sample["udfs"]["original_lab_address"] == "171 76 Solna" assert first_sample["udfs"]["pre_processing_method"] == "COVIDSeq" assert first_sample["udfs"]["priority"] == "research" assert first_sample["udfs"]["reference_genome"] == "NC_111" assert first_sample["udfs"]["region"] == "Stockholm" assert first_sample["udfs"]["region_code"] == "01" - assert first_sample["udfs"]["selection_criteria"] == "1. Allmän övervakning" - assert first_sample["udfs"]["volume"] == "1" + assert first_sample["udfs"]["selection_criteria"] == "Allmän övervakning" + assert first_sample["udfs"]["volume"] == "20" def test_to_lims_balsamic(balsamic_order_to_submit: dict):