add(pacbio orderform parsing) (#3899) (patch)

# Description

add pacbio orderform parsing

cg/apps/orderform/excel_orderform_parser.py

@@ -30,6 +30,7 @@ class ExcelOrderformParser(OrderformParser):
         f"{Orderform.METAGENOME}:{Orderform.get_current_orderform_version(Orderform.METAGENOME)}",  # Microbial meta genomes
         f"{Orderform.SARS_COV_2}:{Orderform.get_current_orderform_version(Orderform.SARS_COV_2)}",  # Orderform SARS-CoV-2
         f"{Orderform.MICROBIAL_FASTQ}:{Orderform.get_current_orderform_version(Orderform.MICROBIAL_FASTQ)}",  # Microbial FASTQ
+        f"{Orderform.PACBIO_LONG_READ}:{Orderform.get_current_orderform_version(Orderform.PACBIO_LONG_READ)}",
     ]
     samples: list[ExcelSample] = []
 
@@ -145,6 +146,7 @@ def get_project_type(self, document_title: str) -> str:
             Orderform.MICROSALT: OrderType.MICROSALT,
             Orderform.SARS_COV_2: OrderType.SARS_COV_2,
             Orderform.MICROBIAL_FASTQ: OrderType.MICROBIAL_FASTQ,
+            Orderform.PACBIO_LONG_READ: OrderType.PACBIO_LONG_READ,
         }
         for document_number, value in document_number_to_project_type.items():
             if document_number in document_title:

cg/constants/orderforms.py

@@ -29,6 +29,7 @@ class Orderform(StrEnum):
     RML: str = "1604"
     SARS_COV_2: str = "2184"
     MICROBIAL_FASTQ: str = "microbial_sequencing"
+    PACBIO_LONG_READ: str = "pacbio_revio_sequencing"
 
     @staticmethod
     def get_current_orderform_version(order_form: str) -> str:
@@ -39,6 +40,7 @@ def get_current_orderform_version(order_form: str) -> str:
             Orderform.MICROSALT: "11",
             Orderform.SARS_COV_2: "9",
             Orderform.MICROBIAL_FASTQ: "1",
+            Orderform.PACBIO_LONG_READ: "1",
         }
         return current_order_form_versions[order_form]
 

tests/apps/orderform/test_excel_orderform_parser.py

@@ -100,6 +100,20 @@ def test_parse_microbial_orderform(microsalt_orderform: str):
     assert orderform_parser.project_type == OrderType.MICROSALT
 
 
+def test_parse_pacbio_sequencing_orderform(pacbio_revio_sequencing_orderform: str):
+    """Test to parse a pacbio orderform in excel format"""
+    # GIVEN a order form in excel format
+    assert is_excel(Path(pacbio_revio_sequencing_orderform))
+    # GIVEN a orderform API
+    orderform_parser: ExcelOrderformParser = ExcelOrderformParser()
+
+    # WHEN parsing the orderform
+    orderform_parser.parse_orderform(excel_path=pacbio_revio_sequencing_orderform)
+
+    # THEN assert that the project type is correct
+    assert orderform_parser.project_type == OrderType.PACBIO_LONG_READ
+
+
 def test_parse_sarscov2_orderform(sarscov2_orderform: str):
     """Test to parse a sarscov2 orderform in excel format"""
 

tests/fixture_plugins/orders_fixtures/order_form_fixtures.py

@@ -162,6 +162,15 @@ def microbial_sequencing_orderform(orderforms: Path) -> str:
     ).as_posix()
 
 
+@pytest.fixture(scope="session")
+def pacbio_revio_sequencing_orderform(orderforms: Path) -> str:
+    """Orderform fixture for pacbio samples."""
+    return Path(
+        orderforms,
+        f"{Orderform.PACBIO_LONG_READ}_{Orderform.get_current_orderform_version(Orderform.PACBIO_LONG_READ)}.xlsx",
+    ).as_posix()
+
+
 @pytest.fixture
 def sarscov2_orderform(orderforms: Path) -> str:
     """Orderform fixture for sarscov2 samples."""