feat(update): Pydantic model

cg/models/lims/sample.py

@@ -1,4 +1,5 @@
-from pydantic.v1 import BaseModel, validator
+from pydantic import BaseModel, field_validator
+from pydantic_core.core_schema import ValidationInfo
 from typing_extensions import Literal
 
 from cg.constants import Priority
@@ -8,69 +9,70 @@
 
 class Udf(BaseModel):
     application: str
-    capture_kit: str | None
-    collection_date: str | None
-    comment: str | None
-    concentration: str | None
-    concentration_sample: str | None
-    concentration_ng_ul: str | None
+    capture_kit: str | None = None
+    collection_date: str | None = None
+    comment: str | None = None
+    concentration: float | None = None
+    concentration_ng_ul: str | None = None
+    concentration_sample: float | None = None
+    control: str | None = None
     customer: str
-    control: str | None
-    data_analysis: str | None
-    data_delivery: str | None
-    elution_buffer: str | None
-    extraction_method: str | None
+    data_analysis: str | None = None
+    data_delivery: str | None = None
+    elution_buffer: str | None = None
+    extraction_method: str | None = None
     family_name: str | None = "NA"
-    formalin_fixation_time: str | None
-    index: str | None
-    index_number: str | None
-    lab_code: str | None
-    organism: str | None
-    organism_other: str | None
-    original_lab: str | None
-    original_lab_address: str | None
-    pool: str | None
-    post_formalin_fixation_time: str | None
-    pre_processing_method: str | None
-    primer: str | None
+    formalin_fixation_time: float | None = None
+    index: str | None = None
+    index_number: str | None = None
+    lab_code: str | None = None
+    organism: str | None = None
+    organism_other: str | None = None
+    original_lab: str | None = None
+    original_lab_address: str | None = None
+    pool: str | None = None
+    post_formalin_fixation_time: float | None = None
+    pre_processing_method: str | None = None
+    primer: str | None = None
     priority: str = Priority.standard.name
-    quantity: str | None
-    reference_genome: str | None
-    region: str | None
-    region_code: str | None
+    quantity: float | None = None
+    reference_genome: str | None = None
+    region: str | None = None
+    region_code: str | None = None
     require_qc_ok: bool = False
-    rml_plate_name: str | None
-    selection_criteria: str | None
+    rml_plate_name: str | None = None
+    selection_criteria: str | None = None
     sex: Literal["M", "F", "unknown"] = "unknown"
     skip_reception_control: bool | None = None
     source: str = "NA"
-    tissue_block_size: str | None
+    tissue_block_size: str | None = None
     tumour: bool | None = False
-    tumour_purity: str | None
-    volume: str | None
-    well_position_rml: str | None
-    verified_organism: bool | None
+    tumour_purity: float | None = None
+    verified_organism: bool | None = None
+    volume: str | None = None
+    well_position_rml: str | None = None
 
-    @validator("sex", pre=True)
+    @field_validator("sex", mode="before")
+    @classmethod
     def validate_sex(cls, value: str):
         return SEX_MAP.get(value, "unknown")
 
 
 class LimsSample(BaseModel):
-    name: str
     container: str = "Tube"
-    container_name: str | None
-    well_position: str | None
-    index_sequence: str | None
-    udfs: Udf | None
+    container_name: str | None = None
+    index_sequence: str | None = None
+    name: str
+    udfs: Udf | None = None
+    well_position: str | None = None
 
-    @validator("well_position", pre=False)
-    def reset_well_positions_for_tubes(cls, value: str, values: dict[str, str]):
-        return None if values["container"] == "Tube" else value
+    @field_validator("well_position", mode="before")
+    def reset_well_positions_for_tubes(cls, value: str, info: ValidationInfo):
+        return None if info.data.get("container") == "Tube" else value
 
     @classmethod
     def parse_obj(cls, obj: dict):
-        parsed_obj: LimsSample = super().parse_obj(obj)
-        udf: Udf = Udf.parse_obj(obj)
-        parsed_obj.udfs = udf
-        return parsed_obj
+        lims_sample: LimsSample = super().model_validate(obj)
+        udf: Udf = Udf.model_validate(obj)
+        lims_sample.udfs = udf
+        return lims_sample

tests/fixtures/cgweb_orders/balsamic.json

@@ -18,15 +18,15 @@
       "data_delivery": "fastq-analysis-scout",
       "elution_buffer": "Other (specify in 'Comments')",
       "family_name": "family1",
-      "formalin_fixation_time": "1",
+      "formalin_fixation_time": 1,
       "name": "s1",
       "phenotype_groups": [
         ""
       ],
       "phenotype_terms": [
         ""
       ],
-      "post_formalin_fixation_time": "2",
+      "post_formalin_fixation_time": 2,
       "priority": "standard",
       "quantity": "2",
       "sex": "male",
@@ -35,7 +35,7 @@
       "synopsis": "",
       "tissue_block_size": "small",
       "tumour": true,
-      "tumour_purity": "75",
+      "tumour_purity": 75,
       "volume": "1",
       "well_position": "A:1"
     }

tests/services/orders/order_lims_service/test_order_lims_service.py

@@ -1,3 +1,5 @@
+import math
+
 import pytest
 
 from cg.constants import Workflow
@@ -32,7 +34,7 @@ def test_to_lims_mip(mip_order_to_submit):
     assert first_sample.udfs.priority == "standard"
     assert first_sample.udfs.application == "WGSPCFC030"
     assert first_sample.udfs.source == "tissue (fresh frozen)"
-    assert first_sample.udfs.quantity == "220"
+    assert first_sample.udfs.quantity == 220
     assert first_sample.udfs.customer == "cust003"
     assert first_sample.udfs.volume == "1.0"
 
@@ -74,7 +76,7 @@ def test_to_lims_rml(rml_order_to_submit):
     first_sample = samples[0]
     assert first_sample.udfs.pool == "pool-1"
     assert first_sample.udfs.volume == "30"
-    assert first_sample.udfs.concentration == "5.0"
+    assert math.isclose(first_sample.udfs.concentration, 5.0, rel_tol=1e-09, abs_tol=1e-09)
     assert first_sample.udfs.index == "IDT DupSeq 10 bp Set B"
     assert first_sample.udfs.index_number == "1"
 
@@ -151,7 +153,7 @@ def test_to_lims_balsamic(balsamic_order_to_submit, project):
     # ... and pick out relevant UDFs
     first_sample = samples[0].dict()
     assert first_sample["name"] == "s1"
-    assert {sample.container for sample in samples} == set(["96 well plate"])
+    assert {sample.container for sample in samples} == {"96 well plate"}
     assert first_sample["udfs"]["data_analysis"] in [
         Workflow.BALSAMIC,
         Workflow.BALSAMIC_QC,
@@ -165,15 +167,15 @@ def test_to_lims_balsamic(balsamic_order_to_submit, project):
     assert first_sample["udfs"]["volume"] == "1.0"
     assert first_sample["udfs"]["priority"] == "standard"
 
-    assert container_names == set(["p1"])
+    assert container_names == {"p1"}
     assert first_sample["well_position"] == "A:1"
     assert first_sample["udfs"]["tumour"] is True
     assert first_sample["udfs"]["capture_kit"] == "other"
-    assert first_sample["udfs"]["tumour_purity"] == "75"
+    assert first_sample["udfs"]["tumour_purity"] == 75
 
-    assert first_sample["udfs"]["formalin_fixation_time"] == "1"
-    assert first_sample["udfs"]["post_formalin_fixation_time"] == "2"
+    assert first_sample["udfs"]["formalin_fixation_time"] == 1
+    assert first_sample["udfs"]["post_formalin_fixation_time"] == 2
     assert first_sample["udfs"]["tissue_block_size"] == "small"
 
-    assert first_sample["udfs"]["quantity"] == "2"
+    assert first_sample["udfs"]["quantity"] == 2
     assert first_sample["udfs"]["comment"] == "other Elution buffer"