add tests for parse and validate

tests/conftest.py

@@ -123,7 +123,7 @@
     "tests.fixture_plugins.orders_fixtures.order_form_fixtures",
     "tests.fixture_plugins.orders_fixtures.order_to_submit_fixtures",
     "tests.fixture_plugins.orders_fixtures.order_fixtures",
-    "tests.fixture_plugins.orders_fixtures.services_and_api_fixtures",
+    "tests.fixture_plugins.orders_fixtures.services_fixtures",
     "tests.fixture_plugins.orders_fixtures.store_fixtures",
     "tests.fixture_plugins.orders_fixtures.store_service_fixtures",
     "tests.fixture_plugins.pacbio_fixtures.context_fixtures",

tests/fixture_plugins/orders_fixtures/order_to_submit_fixtures.py

@@ -7,18 +7,20 @@
 from cg.constants.constants import FileFormat
 from cg.io.controller import ReadFile
 
+# Valid orders
+
 
 @pytest.fixture(scope="session")
 def balsamic_order_to_submit(cgweb_orders_dir: Path) -> dict:
-    """Load an example cancer order."""
+    """Load an example Balsamic order."""
     return ReadFile.get_content_from_file(
         file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "balsamic.json")
     )
 
 
 @pytest.fixture(scope="session")
 def fastq_order_to_submit(cgweb_orders_dir) -> dict:
-    """Load an example FASTQ order."""
+    """Load an example Fastq order."""
     return ReadFile.get_content_from_file(
         file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "fastq.json")
     )
@@ -34,23 +36,23 @@ def fluffy_order_to_submit(cgweb_orders_dir: Path) -> dict:
 
 @pytest.fixture(scope="session")
 def metagenome_order_to_submit(cgweb_orders_dir: Path) -> dict:
-    """Load an example metagenome order."""
+    """Load an example Metagenome order."""
     return ReadFile.get_content_from_file(
         file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "metagenome.json")
     )
 
 
 @pytest.fixture(scope="session")
 def microbial_fastq_order_to_submit(cgweb_orders_dir: Path) -> dict:
-    """Load an example microbial order."""
+    """Load an example Microbial fastq order."""
     return ReadFile.get_content_from_file(
         file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "microbial_fastq.json")
     )
 
 
 @pytest.fixture(scope="session")
 def microbial_order_to_submit(cgweb_orders_dir: Path) -> dict:
-    """Load an example microbial order."""
+    """Load an example Microsalt order."""
     return ReadFile.get_content_from_file(
         file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "microsalt.json")
     )
@@ -66,7 +68,7 @@ def mip_dna_order_to_submit(cgweb_orders_dir: Path) -> dict:
 
 @pytest.fixture(scope="session")
 def mip_rna_order_to_submit(cgweb_orders_dir: Path) -> dict:
-    """Load an example RNA order."""
+    """Load an example MIP-RNA order."""
     return ReadFile.get_content_from_file(
         file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "mip_rna.json")
     )
@@ -90,15 +92,15 @@ def rml_order_to_submit(cgweb_orders_dir: Path) -> dict:
 
 @pytest.fixture(scope="session")
 def rnafusion_order_to_submit(cgweb_orders_dir: Path) -> dict:
-    """Load an example RNA order."""
+    """Load an example RNA Fusion order."""
     return ReadFile.get_content_from_file(
         file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "rnafusion.json")
     )
 
 
 @pytest.fixture(scope="session")
 def sarscov2_order_to_submit(cgweb_orders_dir: Path) -> dict:
-    """Load an example sarscov2 order."""
+    """Load an example Mutant order."""
     return ReadFile.get_content_from_file(
         file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "sarscov2.json")
     )
@@ -114,7 +116,18 @@ def taxprofiler_order_to_submit(cgweb_orders_dir: Path) -> dict:
 
 @pytest.fixture(scope="session")
 def tomte_order_to_submit(cgweb_orders_dir: Path) -> dict:
-    """Load an example TOMTE order."""
+    """Load an example Tomte order."""
     return ReadFile.get_content_from_file(
         file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "tomte.json")
     )
+
+
+# Invalid orders
+
+
+@pytest.fixture(scope="session")
+def invalid_balsamic_order_to_submit(cgweb_orders_dir: Path) -> dict:
+    """Load an invalid example Balsamic order."""
+    return ReadFile.get_content_from_file(
+        file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "FAIL_balsamic.json")
+    )

tests/fixtures/cgweb_orders/FAIL_balsamic.json

@@ -0,0 +1,61 @@
+{
+	"cases": [
+		{
+			"cohorts": null,
+			"name": "B",
+			"panels": null,
+			"priority": "FAIL",
+			"samples": [
+				{
+					"age_at_sampling": "17.2",
+					"application": "PANKTTR100",
+					"capture_kit": "GMCKsolid",
+					"comment": "This is a sample comment",
+					"concentration_ng_ul": null,
+					"container": "96 well plate",
+					"container_name": "BalsamicPlate",
+					"control": "FAIL",
+					"data_analysis": null,
+					"data_delivery": null,
+					"elution_buffer": "Tris-HCl",
+					"family_name": null,
+					"father": null,
+					"formalin_fixation_time": "15",
+					"mother": null,
+					"name": "BalsamicSample",
+					"phenotype_groups": [
+						"PhGroup"
+					],
+					"phenotype_terms": [
+						"PhTerm"
+					],
+					"post_formalin_fixation_time": "3",
+					"priority": null,
+					"quantity": null,
+					"reference_genome": null,
+					"require_qc_ok": false,
+					"sex": "male",
+					"source": "cytology (FFPE)",
+					"source_comment": null,
+					"status": null,
+					"subject_id": "Subject1",
+					"tissue_block_size": "large",
+					"tumour": true,
+					"tumour_purity": "13",
+					"volume": 42,
+					"well_position": "A:1"
+				}
+			],
+			"synopsis": "A synopsis"
+		}
+	],
+	"comment": null,
+	"customer": "cust000",
+	"data_analysis": "balsamic",
+	"data_delivery": null,
+	"delivery_type": "analysis-scout",
+	"name": "BalsamicOrder",
+	"project_type": "balsamic",
+	"ticket": null,
+	"user_id": 1
+}

tests/services/orders/validation_service/test_validation_service.py

@@ -0,0 +1,21 @@
+import pytest
+
+from cg.exc import OrderError
+from cg.models.orders.constants import OrderType
+from cg.services.orders.validation.service import OrderValidationService
+
+
+def test_parse_and_validate_pydantic_error(
+    order_validation_service: OrderValidationService, invalid_balsamic_order_to_submit: dict
+):
+    # GIVEN a raw order that will fail validation and a validation service
+
+    # WHEN parsing and validating the order
+
+    # THEN an OrderError should be raised
+    with pytest.raises(OrderError):
+        order_validation_service.parse_and_validate(
+            raw_order=invalid_balsamic_order_to_submit,
+            order_type=OrderType.BALSAMIC,
+            user_id=1,
+        )