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Finish integration tests #4107

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merged 2 commits into from
Jan 16, 2025
+30 −26
Merged

Finish integration tests #4107

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11d8617
finish integration tests for orders
diitaz93 Jan 16, 2025
6bb26a0
docstring
diitaz93 Jan 16, 2025
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2 changes: 2 additions & 0 deletions tests/fixture_plugins/orders_fixtures/store_fixtures.py
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Original file line number Diff line number Diff line change
Expand Up @@ -96,6 +96,8 @@ def store_with_all_test_applications(store: Store, helpers: StoreHelpers) -> Sto
helpers.ensure_user(store=store, customer=customer)
helpers.ensure_panel(store=store, panel_abbreviation="AID")
helpers.ensure_panel(store=store, panel_abbreviation="Ataxi")
helpers.ensure_panel(store=store, panel_abbreviation="IEM")
helpers.ensure_panel(store=store, panel_abbreviation="OMIM-AUTO")
order = Order(customer_id=1, id=MAF_ORDER_ID, ticket_id=100000000)
store.add_item_to_store(order)
store.commit_to_store()
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15 changes: 12 additions & 3 deletions tests/fixtures/cgweb_orders/rnafusion.json
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Expand Up @@ -29,9 +29,18 @@
"source": "tissue (fresh frozen)",
"synopsis": "",
"subject_id": "subject-sample1-rna-t1",
"volume": "1",
"volume": "120",
"well_position": "A:1"
},
}
],
"synopsis": "A synopsis"
},
{
"cohorts": null,
"name": "RnaFusionCase2",
"panels": null,
"priority": "standard",
"samples": [
{
"application": "RNAPOAR025",
"cohorts": [""],
Expand All @@ -51,7 +60,7 @@
"source": "tissue (fresh frozen)",
"synopsis": "",
"subject_id": "subject-sample1-rna-t2",
"volume": "2",
"volume": "20",
"well_position": "B:1"
}
],
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4 changes: 2 additions & 2 deletions tests/fixtures/cgweb_orders/taxprofiler.json
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Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,7 @@
"tumour_purity": null,
"verified_organism": null,
"volume": 25,
"well_position": "A:1",
"well_position": "B:2",
"well_position_rml": null
},
{
Expand Down Expand Up @@ -182,7 +182,7 @@
"tumour_purity": null,
"verified_organism": null,
"volume": 22,
"well_position": "A:1",
"well_position": "C:3",
"well_position_rml": null
}
],
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26 changes: 9 additions & 17 deletions tests/fixtures/cgweb_orders/tomte.json
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Expand Up @@ -8,7 +8,7 @@
{
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"cohorts": null,
"name": "TomteCase",
"panels": [""],
"panels": ["OMIM-AUTO"],
"priority": "standard",
"samples": [
{
Expand All @@ -26,9 +26,7 @@
"father": "sample3",
"mother": "sample2",
"name": "sample1",
"panels": [
"IEM"
],
"panels": ["IEM"],
"phenotype_groups": [
"Phenotype-group"
],
Expand All @@ -46,7 +44,7 @@
"subject_id": "subject1",
"synopsis": "As for the synopsis it will be this overly complex sentence to prove that the synopsis field might in fact be a very long string, which we should be prepared for.",
"tumour": true,
"volume": "1",
"volume": "110",
"well_position": "A:1"
},
{
Expand All @@ -62,9 +60,7 @@
"data_delivery": "scout",
"family_name": "family1",
"name": "sample2",
"panels": [
"IEM"
],
"panels": ["IEM"],
"synopsis": "As for the synopsis it will be this overly complex sentence to prove that the synopsis field might in fact be a very long string, which we should be prepared for.",
"phenotype_groups": [
""
Expand All @@ -81,7 +77,7 @@
"status": "affected",
"subject_id": "subject2",
"tumour": false,
"volume": "2",
"volume": "25",
"well_position": "B:1"
},
{
Expand All @@ -96,9 +92,7 @@
"data_delivery": "scout",
"family_name": "family1",
"name": "sample3",
"panels": [
"IEM"
],
"panels": ["OMIM-AUTO"],
"phenotype_groups": [
""
],
Expand All @@ -115,7 +109,7 @@
"subject_id": "subject3",
"synopsis": "As for the synopsis it will be this overly complex sentence to prove that the synopsis field might in fact be a very long string, which we should be prepared for.",
"tumour": false,
"volume": "3",
"volume": "30",
"well_position": "C:1"
},
{
Expand All @@ -130,9 +124,7 @@
"data_delivery": "scout",
"family_name": "family2",
"name": "sample4",
"panels": [
"IEM"
],
"panels": ["OMIM-AUTO"],
"phenotype_groups": [
""
],
Expand All @@ -149,7 +141,7 @@
"subject_id": "subjectsample4",
"synopsis": "As for the synopsis it will be this overly complex sentence to prove that the synopsis field might in fact be a very long string, which we should be prepared for.",
"tumour": false,
"volume": "4",
"volume": "45",
"well_position": "D:1"
}
]
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9 changes: 5 additions & 4 deletions tests/meta/orders/test_meta_orders_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -78,10 +78,10 @@ def test_too_long_order_name():
OrderType.MIP_RNA,
OrderType.PACBIO_LONG_READ,
OrderType.RML,
# OrderType.RNAFUSION,
# OrderType.SARS_COV_2,
# OrderType.TAXPROFILER,
# OrderType.TOMTE,
OrderType.RNAFUSION,
OrderType.SARS_COV_2,
OrderType.TAXPROFILER,
OrderType.TOMTE,
],
)
def test_submit_order(
Expand All @@ -94,6 +94,7 @@ def test_submit_order(
email_address: str,
helpers: StoreHelpers,
):
"""Test submitting a valid order of each ordertype."""
# GIVEN an order
order: Order = all_orders_to_submit[order_type]

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