How to use test_required_column method in pandera

Best Python code snippet using pandera_python

test_inclusive_metrics_evaluator.py

Source:test_inclusive_metrics_evaluator.py

...31    # Should read: column with some nulls contains a null value32    assert InclusiveMetricsEvaluator(schema, Expressions.is_null("some_nulls")).eval(file)33    # Should skip: non-null column contains no null values34    assert not InclusiveMetricsEvaluator(schema, Expressions.is_null("no_nulls")).eval(file)35def test_required_column(schema, file):36    assert InclusiveMetricsEvaluator(schema, Expressions.not_null("required")).eval(file)37    assert not InclusiveMetricsEvaluator(schema, Expressions.is_null("required")).eval(file)38def test_missing_column(schema, file):39    with raises(RuntimeError):40        InclusiveMetricsEvaluator(schema, Expressions.less_than("missing", 5)).eval(file)41def test_missing_stats(schema, missing_stats, missing_stats_exprs):42    assert InclusiveMetricsEvaluator(schema, missing_stats_exprs).eval(missing_stats)43def test_zero_record_file(schema, empty, zero_rows_exprs):44    assert not InclusiveMetricsEvaluator(schema, zero_rows_exprs).eval(empty)45def test_not(schema, file):46    assert InclusiveMetricsEvaluator(schema, Expressions.not_(Expressions.less_than("id", 5))).eval(file)47    assert not InclusiveMetricsEvaluator(schema,48                                         Expressions.not_(Expressions.greater_than("id", 5))).eval(file)49def test_and(schema, file):...

test_input_validation.py

Source:test_input_validation.py

1import corna.constants as constant2import os3import pandas as pd4import pytest5from corna import custom_exception6from corna import dataframe_validator7from corna import input_validation8def test_check_if_file_exist():9    dir_path = os.path.dirname(os.path.abspath(__file__))10    file_not_exist_path = os.path.join(dir_path, "test_input_validation_data", "maven_data.py")11    assert dataframe_validator.check_if_file_exist(file_not_exist_path) == False12def test_check_file_empty():13    dir_path = os.path.dirname(os.path.abspath(__file__))14    empty_file_path = os.path.join(dir_path, "test_input_validation_data", "nacorr_test_1.txt")15    assert dataframe_validator.check_file_empty(empty_file_path) == True16def test_read_input_file():17    dir_path = os.path.dirname(os.path.abspath(__file__))18    other_extension_file_path = os.path.join(dir_path, "test_input_validation_data", "nacorr_test_1.pdf")19    with pytest.raises(custom_exception.FileExtensionError) as e:20        dataframe_validator.read_input_file(other_extension_file_path)21    assert e.value.message == 'Only CSV , TXT , XLS ,XLSX file extension are allowed.'22def test_data_frame_empty():23    data_frame=pd.DataFrame()24    assert dataframe_validator.check_df_empty(data_frame) == True25def test_required_column_missing():26    dir_path = os.path.dirname(os.path.abspath(__file__))27    file_path = os.path.join(dir_path, "test_input_validation_data", "test_maven_upload_acetic.csv")28    df = pd.read_csv(file_path)29    test_required_column = ['NaMe','LABEl','Formula','XYZ']30    assert dataframe_validator.check_required_column(df,*test_required_column)[0] == False31def test_check_positive_numerical_value():32    assert input_validation.check_intensity_value(14) == constant.VALID_STATE33    assert input_validation.check_intensity_value(-19) == constant.INTENSITY_STATE_NEGATIVE34    assert input_validation.check_intensity_value('test123') == constant.INTENSITY_STATE_INVALID35def test_check_label_column_format():36    assert input_validation.check_label_column_format('C12 PARENT') == constant.VALID_STATE37    assert input_validation.check_label_column_format('C13-label-2') == constant.VALID_STATE38    assert input_validation.check_label_column_format('C13-2') == constant.LABEL_STATE_INVALID39    assert input_validation.check_label_column_format('C13-label-a') == constant.LABEL_STATE_INVALID40    assert input_validation.check_label_column_format('C11-N15-label-1-2') == constant.LABEL_STATE_INVALID41def test_label_in_formula():42    assert input_validation.check_label_in_formula('C13-label-2','C10H12N5O6P') == constant.VALID_STATE43    assert input_validation.check_label_in_formula('C13-label-6', 'C5H12N5O6P') == constant.LABEL_STATE_NUMBER_MORE_FORMULA44    assert input_validation.check_label_in_formula('C13-label-6', 'H12N5O6P') == \45                                                                    constant.LABEL_STATE_NOT_FORMULA46def test_get_label():47    assert input_validation.get_label('C12 PARENT') == {'C': 0, 'N': 0}48    assert input_validation.get_label('C13-label-6') == {'C': 6}49    assert input_validation.get_label('C13N15-label-4-5') == {'C': 4, 'N': 5}50def test_check_formula_is_correct():51    assert input_validation.check_formula_is_correct('C5H12N5O6P') == constant.VALID_STATE52    assert input_validation.check_formula_is_correct('C5H12N5O6PLO') == constant.FORMULA_STATE_INVALID53def test_check_duplicate():54    dir_path = os.path.dirname(os.path.abspath(__file__))55    maven_correct_raw_file = os.path.join(dir_path, "test_input_validation_data",56                                          "test_maven_upload_acetic.csv")57    maven_df_correct = pd.read_csv(maven_correct_raw_file)58    maven_duplicate_entry_file=os.path.join(dir_path, "test_input_validation_data",59                                            "test_maven_upload_duplicate_entry.csv")60    maven_df_duplicate_entry=pd.read_csv(maven_duplicate_entry_file)61    print input_validation.check_duplicate(maven_df_duplicate_entry,0,[['Name','Label']])62    print input_validation.check_duplicate(maven_df_correct,0,[['Name','Label']]).empty63def test_check_missing():64    dir_path = os.path.dirname(os.path.abspath(__file__))65    maven_missing_entry_raw_file = os.path.join(dir_path, "test_input_validation_data",66                                                "test_maven_upload_missing_entry.csv")67    maven_missing_entry_df = pd.read_csv(maven_missing_entry_raw_file)68    assert len(input_validation.check_missing(maven_missing_entry_df)) == 269def test_validator_for_two_column():70    dir_path = os.path.dirname(os.path.abspath(__file__))71    maven_raw_label_not_in_formula_raw_file = os.path.join(dir_path, "test_input_validation_data",72                                                "test_maven_upload_acetic_label_incorrect.csv")73    maven_df = pd.read_csv(maven_raw_label_not_in_formula_raw_file)74    result_df = input_validation.validator_for_two_column(maven_df,constant.LABEL_COL,constant.FORMULA_COL,75                                                          input_validation.check_label_in_formula)76    assert result_df.iloc[0]['row_number'] == 177def test_validator_column_wise():78    dir_path = os.path.dirname(os.path.abspath(__file__))79    maven_raw_intensity_not_correct_raw_file = os.path.join(dir_path, "test_input_validation_data",80                                                           "test_maven_upload_acetic_intensity_incorrect.csv")81    maven_df = pd.read_csv(maven_raw_intensity_not_correct_raw_file)82    result_df = input_validation.validator_column_wise(maven_df,0,['sample_1'],83                                                       [input_validation.check_intensity_value])84    assert result_df.iloc[0]['state'] == 'negative'85    assert result_df.iloc[1]['state'] == 'invalid_intensity_value'86def test_get_isotope_name():87    assert input_validation.get_isotope_name(['C13','N15']) == ['C','N']88def test_get_istopes_name_and_number():89    label = 'C13N15-label-1-2'90    label_isotopes,label_number = input_validation.get_isotopes_name_and_number(label)91    assert label_isotopes == ['C','N']92    assert label_number == [1,2]93def test_get_split_isotopes():94    joined_isotopes = 'C13N15'...

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