diff --git a/tests/test_assay.py b/tests/test_assay.py index 1de62161..dc186621 100644 --- a/tests/test_assay.py +++ b/tests/test_assay.py @@ -10,6 +10,7 @@ GDC_DATA_DICT = { "properties": { + "library_strategy": {"enum": ["value1", "value2"]}, "library_selection": {"enum": ["value1", "value2"]}, "platform": {"enum": ["value1", "value2"]}, "instrument_model": {"enum": ["value1", "value2"]}, @@ -169,7 +170,7 @@ def test__missingcols__validate(assay_info): expected_warnings = ( "Assay_information.yaml: Doesn't have variant_classifications column. " - "This column will be added.\n" + "This column will be added\n" "Assay_information.yaml: gene_padding is " "by default 10 if not specified.\n" ) @@ -261,39 +262,28 @@ def test_invalid__validate(assay_info): "center abbreviation.\n" "Assay_information.yaml: You are missing SEQ_ASSAY_IDs: SAGE-2\n" "Assay_information.yaml: " - "Please double check your is_paired_end column. " - "Valid values are True, False. " - "You have 1 row(s) in your file where is_paired_end column contains invalid values. " - "The row(s) this occurs in are: [1]. Please correct.\n" + "Please double check your is_paired_end column. " + "This column must only be these values: True, False\n" "Assay_information.yaml: " - "Please double check your library_selection column. " - "Valid values are value1, value2. " - "You have 2 row(s) in your file where library_selection column contains invalid values. " - "The row(s) this occurs in are: [0, 1]. Please correct.\n" + "Please double check your library_selection column. " + "This column must only be these values: value1, value2\n" "Assay_information.yaml: " - "Please double check your library_strategy column. " - "Valid values are Targeted Sequencing, WXS. " - "You have 1 row(s) in your file where library_strategy column contains invalid values. " - "The row(s) this occurs in are: [0]. Please correct.\n" + "Please double check your library_strategy column. " + "This column must only be these values: Targeted Sequencing, WXS\n" "Assay_information.yaml: " - "Please double check your platform column. " - "Valid values are value1, value2. " - "You have 2 row(s) in your file where platform column contains invalid values. " - "The row(s) this occurs in are: [0, 1]. Please correct.\n" + "Please double check your platform column. " + "This column must only be these values: value1, value2\n" "Assay_information.yaml: " - "Please double check your instrument_model column. " - "Valid values are value1, value2, Illumina NovaSeq 6000, None. " - "You have 2 row(s) in your file where instrument_model column contains invalid values. " - "The row(s) this occurs in are: [0, 1]. Please correct.\n" + "Please double check your instrument_model column. " + "This column must only be these values: value1, value2, " + "Illumina NovaSeq 6000, None\n" "Assay_information.yaml: " - "Please double check your variant_classifications column. " - "Valid values are Splice_Site, " + "Please double check your variant_classifications column. " + "This column must only be these values: Splice_Site, " "Nonsense_Mutation, Frame_Shift_Del, Frame_Shift_Ins, " "Nonstop_Mutation, Translation_Start_Site, In_Frame_Ins, " "In_Frame_Del, Missense_Mutation, Intron, Splice_Region, " - "Silent, RNA, 5'UTR, 3'UTR, IGR, 5'Flank, 3'Flank, None. " - "You have 1 row(s) in your file where variant_classifications column contains invalid values. " - "The row(s) this occurs in are: [0]. Please correct.\n" + "Silent, RNA, 5'UTR, 3'UTR, IGR, 5'Flank, 3'Flank, None\n" "Assay_information.yaml: " "Please double check your read_length. " "It must be an integer or null.\n" @@ -304,29 +294,23 @@ def test_invalid__validate(assay_info): "Please double check your gene_padding. " "It must be an integer or blank.\n" "Assay_information.yaml: " - "Please double check your calling_strategy column. " - "Valid values are tumor_only, tumor_normal, plasma_normal. " - "You have 1 row(s) in your file where calling_strategy column contains invalid values. " - "The row(s) this occurs in are: [0]. Please correct.\n" + "Please double check your calling_strategy column. This " + "column must only be these values: tumor_only, tumor_normal, " + "plasma_normal\n" "Assay_information.yaml: " "Please double check your specimen_tumor_cellularity. " "It must in this format >(num)%. ie. >10%\n" "Assay_information.yaml: " - "Please double check your alteration_types column. " - "Valid values are snv, small_indels, " - "gene_level_cna, intragenic_cna, structural_variants. " - "You have 1 row(s) in your file where alteration_types column contains invalid values. " - "The row(s) this occurs in are: [0]. Please correct.\n" + "Please double check your alteration_types column. " + "This column must only be these values: snv, small_indels, " + "gene_level_cna, intragenic_cna, structural_variants\n" "Assay_information.yaml: " - "Please double check your preservation_technique column. " - "Valid values are FFPE, fresh_frozen, NA. " - "You have 1 row(s) in your file where preservation_technique column contains invalid values. " - "The row(s) this occurs in are: [0]. Please correct.\n" + "Please double check your preservation_technique column. " + "This column must only be these values: FFPE, fresh_frozen, NA\n" "Assay_information.yaml: " - "Please double check your coverage column. " - "Valid values are hotspot_regions, coding_exons, introns, promoters. " - "You have 1 row(s) in your file where coverage column contains invalid values. " - "The row(s) this occurs in are: [0]. Please correct.\n" + "Please double check your coverage column. " + "This column must only be these values: " + "hotspot_regions, coding_exons, introns, promoters\n" ) patch_get_gdc.called_once_with("read_group")