validation_schema.py

from pandas_schema import Column, Schema
from pandas_schema.validation import (
    LeadingWhitespaceValidation,
    TrailingWhitespaceValidation,
    CanConvertValidation,
    InListValidation,
    CustomElementValidation,
)

EmptyStringValidation = CustomElementValidation(
    lambda d: d != "", "This field cannot be empty"
)

nipt_results_schema = Schema(
    [
        Column("SampleID", [TrailingWhitespaceValidation(), EmptyStringValidation]),
        Column("SampleType", []),
        Column("Description", []),
        Column(
            "SampleProject", [TrailingWhitespaceValidation(), EmptyStringValidation]
        ),
        Column("Index1", []),
        Column("Index2", []),
        Column("Library_nM", []),
        Column("QCFlag", []),
        Column("Zscore_13", [CanConvertValidation(float)]),
        Column("Zscore_18", [CanConvertValidation(float)]),
        Column("Zscore_21", [CanConvertValidation(float)]),
        Column("Zscore_X", [CanConvertValidation(float)]),
        Column("Ratio_13", [CanConvertValidation(float)]),
        Column("Ratio_18", [CanConvertValidation(float)]),
        Column("Ratio_21", [CanConvertValidation(float)]),
        Column("Ratio_X", [CanConvertValidation(float)]),
        Column("Ratio_Y", [CanConvertValidation(float)]),
        Column("MappedReads", [CanConvertValidation(int)]),
        Column("GC_Dropout", [CanConvertValidation(float)]),
        Column("AT_Dropout", [CanConvertValidation(float)]),
        Column("Chr1_Ratio", [CanConvertValidation(float)]),
        Column("Chr2_Ratio", [CanConvertValidation(float)]),
        Column("Chr3_Ratio", [CanConvertValidation(float)]),
        Column("Chr4_Ratio", [CanConvertValidation(float)]),
        Column("Chr5_Ratio", [CanConvertValidation(float)]),
        Column("Chr6_Ratio", [CanConvertValidation(float)]),
        Column("Chr7_Ratio", [CanConvertValidation(float)]),
        Column("Chr8_Ratio", [CanConvertValidation(float)]),
        Column("Chr9_Ratio", [CanConvertValidation(float)]),
        Column("Chr10_Ratio", [CanConvertValidation(float)]),
        Column("Chr11_Ratio", [CanConvertValidation(float)]),
        Column("Chr12_Ratio", [CanConvertValidation(float)]),
        Column("Chr14_Ratio", [CanConvertValidation(float)]),
        Column("Chr15_Ratio", [CanConvertValidation(float)]),
        Column("Chr16_Ratio", [CanConvertValidation(float)]),
        Column("Chr17_Ratio", [CanConvertValidation(float)]),
        Column("Chr19_Ratio", [CanConvertValidation(float)]),
        Column("Chr20_Ratio", [CanConvertValidation(float)]),
        Column("Chr22_Ratio", [CanConvertValidation(float)]),
        Column("Chr1", [CanConvertValidation(float)]),
        Column("Chr2", [CanConvertValidation(float)]),
        Column("Chr3", [CanConvertValidation(float)]),
        Column("Chr4", [CanConvertValidation(float)]),
        Column("Chr5", [CanConvertValidation(float)]),
        Column("Chr6", [CanConvertValidation(float)]),
        Column("Chr7", [CanConvertValidation(float)]),
        Column("Chr8", [CanConvertValidation(float)]),
        Column("Chr9", [CanConvertValidation(float)]),
        Column("Chr10", [CanConvertValidation(float)]),
        Column("Chr11", [CanConvertValidation(float)]),
        Column("Chr12", [CanConvertValidation(float)]),
        Column("Chr13", [CanConvertValidation(float)]),
        Column("Chr14", [CanConvertValidation(float)]),
        Column("Chr15", [CanConvertValidation(float)]),
        Column("Chr16", [CanConvertValidation(float)]),
        Column("Chr17", [CanConvertValidation(float)]),
        Column("Chr18", [CanConvertValidation(float)]),
        Column("Chr19", [CanConvertValidation(float)]),
        Column("Chr20", [CanConvertValidation(float)]),
        Column("Chr21", [CanConvertValidation(float)]),
        Column("Chr22", [CanConvertValidation(float)]),
        Column("ChrX", [CanConvertValidation(float)]),
        Column("ChrY", [CanConvertValidation(float)]),
        Column("FF_Formatted", [CanConvertValidation(float)]),
        Column("FFY", [CanConvertValidation(float)]),
        Column("FFX", [CanConvertValidation(float)]),
        Column("DuplicationRate", [CanConvertValidation(float)]),
        Column("Bin2BinVariance", [CanConvertValidation(float)]),
        Column("UnfilteredCNVcalls", [CanConvertValidation(float)]),
        Column("CNVSegment", [InListValidation(["Found"])]),
        Column("Flowcell", []),
        Column("SequencingDate", []),
        Column("Median_13", [CanConvertValidation(float)]),
        Column("Median_18", [CanConvertValidation(float)]),
        Column("Median_21", [CanConvertValidation(float)]),
        Column("Median_X", [CanConvertValidation(float)]),
        Column("Median_Y", [CanConvertValidation(float)]),
        Column("Stdev_13", [CanConvertValidation(float)]),
        Column("Stdev_18", [CanConvertValidation(float)]),
        Column("Stdev_21", [CanConvertValidation(float)]),
        Column("Stdev_X", [CanConvertValidation(float)]),
        Column("Stdev_Y", [CanConvertValidation(float)]),
    ]
)