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Update validator for generic assay binary and categorical data #7973
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4 changes: 4 additions & 0 deletions
4
core/src/test/scripts/test_data/data_generic_assay_empty_cell.txt
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ENTITY_STABLE_ID name description url TCGA-A1-A0SB-01 TCGA-A1-A0SD-01 TCGA-A1-A0SE-01 TCGA-A1-A0SH-01 TCGA-A2-A04U-01 TCGA-B6-A0RS-01 TCGA-BH-A0HP-01 TCGA-BH-A18P-01 | ||
mean_1 mean_1 mean_1 url_1 category_1 category_2 category_2 category_2 category_1 category_1 category_3 category_4 | ||
mean_2 mean_2 mean_2 url_2 category_1 category_1 category_2 category_1 category_2 category_3 category_4 | ||
mean_3 mean_3 mean_3 url_3 category_2 category_1 category_2 category_2 category_1 category_2 NA category_3 |
4 changes: 4 additions & 0 deletions
4
core/src/test/scripts/test_data/data_generic_assay_valid_binary.txt
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ENTITY_STABLE_ID name description url TCGA-A1-A0SB-01 TCGA-A1-A0SD-01 TCGA-A1-A0SE-01 TCGA-A1-A0SH-01 TCGA-A2-A04U-01 TCGA-B6-A0RS-01 TCGA-BH-A0HP-01 TCGA-BH-A18P-01 | ||
mean_1 mean_1 mean_1 url_1 true false false false true true yes no | ||
mean_2 mean_2 mean_2 url_2 false true true false true false yes no | ||
mean_3 mean_3 mean_3 url_3 false true false false true false NA yes |
4 changes: 4 additions & 0 deletions
4
core/src/test/scripts/test_data/data_generic_assay_valid_categorical.txt
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ENTITY_STABLE_ID name description url TCGA-A1-A0SB-01 TCGA-A1-A0SD-01 TCGA-A1-A0SE-01 TCGA-A1-A0SH-01 TCGA-A2-A04U-01 TCGA-B6-A0RS-01 TCGA-BH-A0HP-01 TCGA-BH-A18P-01 | ||
mean_1 mean_1 mean_1 url_1 category_1 category_2 category_2 category_2 category_1 category_1 category_3 category_4 | ||
mean_2 mean_2 mean_2 url_2 category_2 category_1 category_1 category_2 category_1 category_2 category_3 category_4 | ||
mean_3 mean_3 mean_3 url_3 category_2 category_1 category_2 category_2 category_1 category_2 NA category_3 |
4 changes: 4 additions & 0 deletions
4
core/src/test/scripts/test_data/data_generic_assay_valid_continuous.txt
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ENTITY_STABLE_ID name description url TCGA-A1-A0SB-01 TCGA-A1-A0SD-01 TCGA-A1-A0SE-01 TCGA-A1-A0SH-01 TCGA-A2-A04U-01 TCGA-B6-A0RS-01 TCGA-BH-A0HP-01 TCGA-BH-A18P-01 | ||
mean_1 mean_1 mean_1 url_1 NA 0.010373016 0.005419294 0.022753384 0.037687823 0.016708976 0.100042446 0.104214723 | ||
mean_2 mean_2 mean_2 url_2 0.002709404 0.009212318 0.002650657 <0.005475484 0.074175715 0.033049207 0.027323826 0.008861145 | ||
mean_3 mean_3 mean_3 url_3 0.006035782 >0.010095773 0.011926486 0.010637541 0.012168938 0.006641113 NA 0.020463421 |
4 changes: 4 additions & 0 deletions
4
core/src/test/scripts/test_data/data_generic_assay_with_non_numerical_data.txt
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ENTITY_STABLE_ID name description url TCGA-A1-A0SB-01 TCGA-A1-A0SD-01 TCGA-A1-A0SE-01 TCGA-A1-A0SH-01 TCGA-A2-A04U-01 TCGA-B6-A0RS-01 TCGA-BH-A0HP-01 TCGA-BH-A18P-01 | ||
mean_1 mean_1 mean_1 url_1 NA 0.010373016 0.005419294 0.022753384 0.037687823 0.016708976 0.100042446 0.104214723 | ||
mean_2 mean_2 mean_2 url_2 NON_NUMERIC 0.009212318 0.002650657 0.005475484 0.074175715 0.033049207 0.027323826 0.008861145 | ||
mean_3 mean_3 mean_3 url_3 0.006035782 0.010095773 0.011926486 0.010637541 0.012168938 0.006641113 0.025730547 0.020463421 |
4 changes: 4 additions & 0 deletions
4
core/src/test/scripts/test_data/data_generic_assay_with_not_defined_data.txt
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ENTITY_STABLE_ID name description url TCGA-A1-A0SB-01 TCGA-A1-A0SD-01 TCGA-A1-A0SE-01 TCGA-A1-A0SH-01 TCGA-A2-A04U-01 TCGA-B6-A0RS-01 TCGA-BH-A0HP-01 TCGA-BH-A18P-01 | ||
mean_1 mean_1 mean_1 url_1 true false false false true true yes no | ||
mean_2 mean_2 mean_2 url_2 false NOT_DEFINED true false true false yes no | ||
mean_3 mean_3 mean_3 url_3 false true false false true false NA yes |
4 changes: 4 additions & 0 deletions
4
core/src/test/scripts/test_data/data_generic_assay_without_entity_id_column.txt
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name description url TCGA-A1-A0SB-01 TCGA-A1-A0SD-01 TCGA-A1-A0SE-01 TCGA-A1-A0SH-01 TCGA-A2-A04U-01 TCGA-B6-A0RS-01 TCGA-BH-A0HP-01 TCGA-BH-A18P-01 | ||
mean_1 mean_1 url_1 0.370266873 0.010373016 0.005419294 0.022753384 0.037687823 0.016708976 0.100042446 0.104214723 | ||
mean_2 mean_2 url_2 0.002709404 0.009212318 0.002650657 0.005475484 0.074175715 0.033049207 0.027323826 0.008861145 | ||
mean_3 mean_3 url_3 0.006035782 0.010095773 0.011926486 0.010637541 0.012168938 0.006641113 0.025730547 0.020463421 |
2 changes: 0 additions & 2 deletions
2
core/src/test/scripts/test_data/data_treatment_ic50_different_name.txt
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core/src/test/scripts/test_data/data_treatment_ic50_duplicate_value.txt
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Just a small question. Are the binary values fixed?
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Yes, in the RFC, we planned to have a controlled vocabulary for binary type: https://docs.google.com/document/d/1-6O16_j5b5LeHA5SnChnlEKQTYhcwNh4AEwCxB8FwC8/edit?disco=AAAAHCuNjcs.
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Right. We can extend the list if we have to introduce other binary values.