Add Taxprofiler ordering support (#3935) (minor)

### Added

- Taxprofiler excel order form test fixture

### Changed

- 1508 orderforms need to be version 32

cg/apps/orderform/excel_orderform_parser.py

@@ -22,7 +22,7 @@ class ExcelOrderformParser(OrderformParser):
     model_config = ConfigDict(arbitrary_types_allowed=True)
     NO_ANALYSIS: str = "no-analysis"
     NO_VALUE: str = "no_value"
-    SHEET_NAMES: list[str] = ["Orderform", "orderform", "order form"]
+    SHEET_NAMES: list[str] = ["Orderform", "orderform", "order form", "Order Form"]
     VALID_ORDERFORMS: list[str] = [
         f"{Orderform.MIP_DNA}:{Orderform.get_current_orderform_version(Orderform.MIP_DNA)}",  # Orderform MIP-DNA, Balsamic, sequencing only, MIP-RNA
         f"{Orderform.MICROSALT}:{Orderform.get_current_orderform_version(Orderform.MICROSALT)}",  # Microbial WGS

cg/constants/orderforms.py

@@ -30,12 +30,13 @@ class Orderform(StrEnum):
     SARS_COV_2: str = "2184"
     MICROBIAL_FASTQ: str = "microbial_sequencing"
     PACBIO_LONG_READ: str = "pacbio_revio_sequencing"
+    TAXPROFILER: str = "1508"
 
     @staticmethod
     def get_current_orderform_version(order_form: str) -> str:
         """Returns the current version of the given order form."""
         current_order_form_versions = {
-            Orderform.MIP_DNA: "31",
+            Orderform.MIP_DNA: "32",
             Orderform.RML: "19",
             Orderform.MICROSALT: "11",
             Orderform.SARS_COV_2: "9",

cg/models/orders/samples.py

@@ -252,6 +252,10 @@ def required_for_new_samples(cls, v: str) -> None:
         return None
 
 
+class TaxprofilerSample(MetagenomeSample):
+    _suitable_project = OrderType.TAXPROFILER
+
+
 class MicrobialSample(OrderInSample):
     # 1603 Orderform Microbial WGS
     # "These fields are required"

cg/models/orders/validators/excel_sample_validators.py

@@ -23,6 +23,7 @@ def validate_data_analysis(data_analysis):
         "MIP RNA",  # OF 1508
         "RNAfusion",  # OF 1508
         "Mutant",  # OF 2184
+        "Taxprofiler",  # OF 1508
         "Tomte",  # OF 1508
         "No analysis",  # OF 1508, 1604, 2184
     ]

tests/apps/orderform/test_excel_orderform_parser.py

@@ -277,3 +277,19 @@ def test_parse_microbial_sequencing_orderform(microbial_sequencing_orderform: st
     assert order_form_parser.project_type == OrderType.MICROBIAL_FASTQ
     # THEN assert that samples are parsed
     assert order_form_parser.samples
+
+
+def test_parse_taxprofiler_orderform(taxprofiler_orderform: str):
+    """Test to parse a Taxprofiler orderform in excel format"""
+
+    # GIVEN an order form in Excel format
+    assert is_excel(Path(taxprofiler_orderform))
+
+    # GIVEN an ExcelOrderformParser
+    orderform_parser: ExcelOrderformParser = ExcelOrderformParser()
+
+    # WHEN parsing the orderform
+    orderform_parser.parse_orderform(excel_path=taxprofiler_orderform)
+
+    # THEN assert that the project type is correct
+    assert orderform_parser.project_type == OrderType.TAXPROFILER

tests/fixture_plugins/orders_fixtures/order_form_fixtures.py

@@ -261,6 +261,15 @@ def rnafusion_orderform(orderforms: Path) -> str:
     ).as_posix()
 
 
+@pytest.fixture
+def taxprofiler_orderform(orderforms: Path) -> str:
+    """Orderform fixture for sarscov2 samples."""
+    return Path(
+        orderforms,
+        f"{Orderform.TAXPROFILER}.{Orderform.get_current_orderform_version(Orderform.TAXPROFILER)}.taxprofiler.xlsx",
+    ).as_posix()
+
+
 @pytest.fixture(scope="session")
 def mip_uploaded_json_order(orderforms: Path) -> str:
     """JSON orderform fixture for MIP DNA samples."""