cBioPortal validation report: study in 'test_data/study_es

Validation status: Success

General

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Reading portal information from test_data/api_json_system_tests/cancer-types.json	–
Debug	–	–	Reading portal information from test_data/api_json_system_tests/genes.json	–
Debug	–	–	Reading portal information from test_data/api_json_system_tests/genesets.json	–
Debug	–	–	Reading portal information from test_data/api_json_system_tests/genesets_version.json	–
Debug	–	–	Reading portal information from test_data/api_json_system_tests/gene-panels.json	–
Debug	–	–	Reading portal information from test_data/api_json_system_tests/genesaliases.json	–
Debug	–	–	Retrieving chromosome lengths from '/cbioportal/core/src/main/resources/scripts/importer/chromosome_sizes.json'	–
Debug	–	–	Retrieving chromosome lengths from '/cbioportal/core/src/main/resources/scripts/importer/chromosome_sizes.json'	–
Debug	–	–	Study Tag file found. It will be validated.	–
Debug	–	–	Validating case lists	–
Info	–	–	Validation of case list folder complete	–
Info	–	–	Validation complete	–

case_lists/cases_cna.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

case_lists/cases_cnaseq.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

case_lists/cases_custom.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

case_lists/cases_sequenced.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

case_lists/cases_test.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

data_cancer_type.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 1 lines. Lines with warning: 0. Lines with error: 0	–

data_clinical_patients.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 846 lines. Lines with warning: 0. Lines with error: 0	–

data_clinical_samples.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 850 lines. Lines with warning: 0. Lines with error: 0	–

data_cna_discrete.txt

Line Number

Column Number

Message

Value Encountered

–

Starting validation of file

–

154, 155, 844…

Values contained in the column cbp_driver_tiers that will appear in the "Mutation Color" menu of the Oncoprint

Class 2, Class 1

See all 4 values

Line Number	Column Number	Value Encountered
154	6	Class 2
155	6	Class 1
844	6	Class 2
845	6	Class 1

–

Validation of file complete

–

Read 6305 lines. Lines with warning: 0. Lines with error: 0

–

data_cna_hg19.seg

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 10 lines. Lines with warning: 0. Lines with error: 0	–

data_cna_log2.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 8 lines. Lines with warning: 0. Lines with error: 0	–

data_expression_median.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 7 lines. Lines with warning: 0. Lines with error: 0	–

data_expression_median_Zscores.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 6 lines. Lines with warning: 0. Lines with error: 0	–

data_gene_panel_matrix.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	1	–	This column can be replaced by a 'gene_panel' property in the respective meta file	gistic
Info	–	–	Validation of file complete	–
Info	–	–	Read 21 lines. Lines with warning: 0. Lines with error: 0	–

data_generic_assay_patient_test.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 3 lines. Lines with warning: 0. Lines with error: 0	–

data_gistic_genes_amp.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 12 lines. Lines with warning: 0. Lines with error: 0	–

data_gsva_pvalues.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 8 lines. Lines with warning: 0. Lines with error: 0	–

data_gsva_scores.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 8 lines. Lines with warning: 0. Lines with error: 0	–

data_methylation_hm27.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 9 lines. Lines with warning: 0. Lines with error: 0	–

data_mutational_signature.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 61 lines. Lines with warning: 0. Lines with error: 0	–

data_mutations_extended.maf

Line Number

Column Number

Message

Value Encountered

–

Starting validation of file

–

4, 5, 6…

164

Values contained in the column cbp_driver_tiers that will appear in the "Mutation Color" menu of the Oncoprint

Class 2, Class 1, Class 4…

See all 11 values

Line Number	Column Number	Value Encountered
4	164	Class 2
5	164	Class 1
6	164	Class 4
7	164	Class 4
8	164	Class 1
9	164	Class 1
10	164	Class 3
12	164	Class 3
16	164	Class 1
17	164	Class 1
18	164	Class 1

7, 9

–

Line will not be loaded due to the variant classification filter. Filtered types: [Silent, Intron, 3'UTR, 3'Flank, 5'UTR, 5'Flank, IGR, RNA]

Silent

–

Validation of file complete

–

Read 38 lines. Lines with warning: 0. Lines with error: 0

–

data_resource_definition.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 4 lines. Lines with warning: 0. Lines with error: 0	–

data_resource_patient.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 4 lines. Lines with warning: 0. Lines with error: 0	–

data_resource_sample.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 4 lines. Lines with warning: 0. Lines with error: 0	–

data_resource_study.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 2 lines. Lines with warning: 0. Lines with error: 0	–

data_structural_variants.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	48	–	No Entrez gene id or gene symbol provided for site 2. Assuming either the intragenic, deletion, duplication, translocation or inversion variant	–
Info	49	–	No Entrez gene id or gene symbol provided for site 1. Assuming either the intragenic, deletion, duplication, translocation or inversion variant	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 49 lines. Lines with warning: 0. Lines with error: 0	–

data_treatment_ec50.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 11 lines. Lines with warning: 0. Lines with error: 0	–

data_treatment_ic50.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of file	–
Info	–	–	Validation of file complete	–
Info	–	–	Read 11 lines. Lines with warning: 0. Lines with error: 0	–

meta_cancer_type.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_clinical_patients.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_clinical_samples.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_cna_discrete.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_cna_hg19_seg.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_cna_log2.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_expression_median.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_expression_median_Zscores.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_gene_panel_matrix.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_generic_assay_patient_test.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_gistic_genes_amp.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_gsva_pvalues.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_gsva_scores.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_methylation_hm27.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_mutational_signature.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_mutations_extended.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_resource_definition.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_resource_patient.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_resource_sample.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_resource_study.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_structural_variants.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_study.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–
Info	–	–	Setting reference genome to human (GRCh37, hg19)	–

meta_treatment_ec50.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

meta_treatment_ic50.txt

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of meta file	–
Info	–	–	Validation of meta file complete	–

study_tags.yml

	Line Number	Column Number	Message	Value Encountered
Debug	–	–	Starting validation of study tags file	–
Info	–	–	Validation of study tags file complete.	–

Error	Error: cBioPortal will not know how to load this, please revise or remove
Warning	Warning: possible cause of confusion, please check whether this is intended
Info	Info: this looks good, no action required
Debug	Verbose output: details on the progress of the validation script

cBioPortal validation report