fix( parsing no delivery option)

cg/apps/orderform/excel_orderform_parser.py

@@ -175,20 +175,13 @@ def parse_data_analysis(self) -> str:
         return data_analyses.pop().lower().replace(" ", "-")
 
     def get_data_delivery(self) -> str:
-        """Determine the order_data delivery type"""
-
-        data_delivery: str = self.parse_data_delivery()
-
-        try:
-            return DataDelivery(data_delivery)
-        except ValueError as error:
-            raise OrderFormError(f"Unsupported Data Delivery: {data_delivery}") from error
+        """Determine the order_data delivery type."""
+        return self.parse_data_delivery()
 
     def parse_data_delivery(self) -> str:
         data_deliveries: set[str] = {
             sample.data_delivery or self.NO_VALUE for sample in self.samples
         }
-
         if len(data_deliveries) > 1:
             raise OrderFormError(f"mixed 'Data Delivery' types: {', '.join(data_deliveries)}")
 
@@ -203,7 +196,7 @@ def get_customer_id(self) -> str:
         return customers.pop()
 
     def parse_orderform(self, excel_path: str) -> None:
-        """Parse out information from an order form"""
+        """Parse out information from an order form."""
 
         LOG.info(f"Open excel workbook from file {excel_path}")
         workbook: Workbook = openpyxl.load_workbook(
@@ -233,5 +226,24 @@ def parse_orderform(self, excel_path: str) -> None:
 
     @staticmethod
     def _transform_data_delivery(data_delivery: str) -> str:
-        """Transforms the data-delivery parsed in the excel file, to the ones used in cg"""
-        return data_delivery.lower().replace(" + ", "-").replace(" ", "_")
+        """Transforms the data-delivery parsed in the excel file, to the ones used in cg."""
+        try:
+            orderform_to_internal: dict = {
+                "analysis": DataDelivery.ANALYSIS_FILES,
+                "analysis + scout": DataDelivery.ANALYSIS_SCOUT,
+                "bam": DataDelivery.BAM,
+                "fastq": DataDelivery.FASTQ,
+                "fastq + analysis": DataDelivery.FASTQ_ANALYSIS,
+                "fastq + analysis + scout": DataDelivery.FASTQ_ANALYSIS_SCOUT,
+                "fastq + Scout": DataDelivery.FASTQ_SCOUT,
+                "fastq qc": DataDelivery.FASTQ_QC,
+                "fastq qc + analysis": DataDelivery.FASTQ_QC_ANALYSIS,
+                "no delivery": DataDelivery.NO_DELIVERY,
+                "scout": DataDelivery.SCOUT,
+                "nipt viewer": DataDelivery.NIPT_VIEWER,  # legacy option; keeping it for backward compatibility
+                "statina": DataDelivery.STATINA,
+                "fastq-analysis": DataDelivery.FASTQ_ANALYSIS,  # Sars Cov10 orderform does not have the same options as others
+            }
+            return orderform_to_internal[data_delivery]
+        except KeyError as error:
+            raise OrderFormError(f"Unsupported Data Delivery: {data_delivery}") from error

cg/models/orders/validators/excel_sample_validators.py

@@ -8,6 +8,8 @@ def parse_panels(panels: str) -> list[str] | None:
     separator = ";" if ";" in panels else None
     if ":" in panels:
         separator = ":"
+    if not separator:
+        return [panels]
     return panels.split(separator)
 
 

tests/apps/orderform/test_excel_orderform_parser.py

@@ -168,6 +168,30 @@ def test_parse_mip_orderform(mip_orderform: str, nr_samples_mip_orderform: int):
     assert order_form_parser.project_type == OrderType.MIP_DNA
 
 
+def test_parse_mip_orderform_no_delivery(
+    mip_orderform_no_delivery: str, nr_samples_mip_orderform: int
+):
+    """Test to parse a mip orderform in xlsx format"""
+    # GIVEN a orderform in excel format
+    assert is_excel(Path(mip_orderform_no_delivery))
+    # GIVEN a orderform API
+    order_form_parser = ExcelOrderformParser()
+    # GIVEN the correct orderform name
+    order_name: str = Path(mip_orderform_no_delivery).stem
+
+    # WHEN parsing the mip orderform
+    order_form_parser.parse_orderform(excel_path=mip_orderform_no_delivery)
+
+    # THEN assert that the correct name was set
+    assert order_form_parser.order_name == order_name
+
+    # THEN assert the number of samples parsed are correct
+    assert len(order_form_parser.samples) == nr_samples_mip_orderform
+    assert order_form_parser.samples[0].panels == ["Inherited cancer"]
+    # THEN assert that the project type is correct
+    assert order_form_parser.project_type == OrderType.MIP_DNA
+
+
 def test_parse_rml_orderform(rml_orderform: str, nr_samples_rml_orderform: int):
     """Test to parse an excel orderform in xlsx format"""
     # GIVEN a orderform in excel format
@@ -228,7 +252,7 @@ def test_fastq_samples_is_correct(fastq_order_parser: ExcelOrderformParser):
     assert tumour_sample and normal_sample
 
 
-def test_generate_parsed_rml_orderform(rml_order_parser: ExcelOrderformParser, caplog):
+def test_generate_parsed_rml_orderform(rml_order_parser: ExcelOrderformParser):
     """Test to generate a order from a parsed rml excel file"""
     # GIVEN a order form parser that have parsed an excel file
 

tests/fixture_plugins/orders_fixtures/order_form_fixtures.py

@@ -234,6 +234,15 @@ def mip_orderform(orderforms: Path) -> str:
     ).as_posix()
 
 
+@pytest.fixture(scope="session")
+def mip_orderform_no_delivery(orderforms: Path) -> str:
+    """Orderform fixture for MIP samples with delivery set to No delivery."""
+    return Path(
+        orderforms,
+        f"{Orderform.MIP_DNA}.{Orderform.get_current_orderform_version(Orderform.MIP_DNA)}.mip_no_delivery.xlsx",
+    ).as_posix()
+
+
 @pytest.fixture(scope="session")
 def mip_rna_orderform(orderforms: Path) -> str:
     """Orderform fixture for MIP RNA samples."""