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Parse new concentration field #2740

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merged 13 commits into from
Dec 20, 2023
Merged

Parse new concentration field #2740

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3f48d9d
Parse new concentration field
islean Dec 6, 2023
c229c98
Merge branch 'master' into parse-concentration
islean Dec 6, 2023
b9e2e56
Add default
islean Dec 6, 2023
7ebd1b1
Merge remote-tracking branch 'origin/parse-concentration' into parse-…
islean Dec 6, 2023
181b497
Add default
islean Dec 6, 2023
6bcb7c8
Add default
islean Dec 6, 2023
29699bd
Add support for json
islean Dec 6, 2023
03192f2
Merge branch 'master' into parse-concentration
islean Dec 6, 2023
6dbd602
Merge branch 'master' into parse-concentration
islean Dec 6, 2023
1166284
Merge branch 'master' into parse-concentration
islean Dec 13, 2023
7bae2a9
Merge branch 'master' into parse-concentration
islean Dec 14, 2023
e6a9ff5
Merge branch 'master' into parse-concentration
islean Dec 15, 2023
7c1f385
Merge branch 'master' into parse-concentration
islean Dec 19, 2023
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1 change: 1 addition & 0 deletions cg/models/orders/constants.py
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Expand Up @@ -26,6 +26,7 @@ class ExcelSampleAliases(StrEnum):
COLLECTION_DATE = "UDF/Collection Date"
COMMENT = "UDF/Comment"
CONCENTRATION = "UDF/Concentration (nM)"
CONCENTRATION_NG_UL = "UDF/Concentration (ng/ul)"
CONCENTRATION_SAMPLE = "UDF/Sample Conc."
CONTAINER = "Container/Type"
CONTAINER_NAME = "Container/Name"
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1 change: 1 addition & 0 deletions cg/models/orders/excel_sample.py
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Expand Up @@ -29,6 +29,7 @@ class ExcelSample(OrderSample):
concentration: Annotated[str, AfterValidator(numeric_value)] = Field(
None, alias=ExcelSampleAliases.CONCENTRATION
)
concentration_ng_ul: str = Field(None, alias=ExcelSampleAliases.CONCENTRATION_NG_UL)
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concentration_sample: Annotated[str, AfterValidator(numeric_value)] = Field(
None, alias=ExcelSampleAliases.CONCENTRATION_SAMPLE
)
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1 change: 1 addition & 0 deletions cg/models/orders/json_sample.py
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Expand Up @@ -9,6 +9,7 @@
class JsonSample(OrderSample):
cohorts: list[str] | None = None
concentration: str | None = None
concentration_ng_ul: str | None = None
concentration_sample: str | None = None
control: str | None = None
data_analysis: Pipeline = Pipeline.MIP_DNA
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1 change: 1 addition & 0 deletions cg/models/orders/sample_base.py
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Expand Up @@ -53,6 +53,7 @@ class OrderSample(BaseModel):
collection_date: str | None = None
comment: constr(max_length=Sample.comment.property.columns[0].type.length) | None = None
concentration: float | None = None
concentration_ng_ul: float | None = None
concentration_sample: float | None = None
container: ContainerEnum | None = None
container_name: str | None = None
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