Datahub Studies Validation Fixes- 1

public/blca_tcga_pub/case_lists/cases_all.txt

@@ -3,4 +3,4 @@ stable_id: blca_tcga_pub_all
 case_list_name: All samples
 case_list_description: All samples (131 samples)
 case_list_category: all_cases_in_study
-case_list_ids: TCGA-GD-A3OP-01	TCGA-GD-A3OQ-01	TCGA-BT-A20Q-01	TCGA-FD-A3SS-01	TCGA-CF-A3MI-01	TCGA-DK-A3IN-01	TCGA-BT-A20U-01	TCGA-E5-A2PC-01	TCGA-G2-A3IE-01	TCGA-FD-A3SL-01	TCGA-DK-A1A5-01	TCGA-BT-A20O-01	TCGA-BT-A42C-01	TCGA-FD-A3SQ-01	TCGA-G2-A2EK-01	TCGA-GV-A3JZ-01	TCGA-CU-A3YL-01	TCGA-BT-A3PH-01	TCGA-GV-A3JW-01	TCGA-BL-A13J-01	TCGA-DK-A1A3-01	TCGA-H4-A2HO-01	TCGA-FD-A3SO-01	TCGA-GD-A2C5-01	TCGA-GC-A3OO-01	TCGA-FD-A3SR-01	TCGA-GC-A3WC-01	TCGA-G2-A2EC-01	TCGA-BT-A20N-01	TCGA-G2-A2EO-01	TCGA-G2-A2EJ-01	TCGA-FD-A3SJ-01	TCGA-BT-A2LD-01	TCGA-GC-A3RB-01	TCGA-FD-A3N5-01	TCGA-FD-A3NA-01	TCGA-FD-A3SN-01	TCGA-G2-A3IB-01	TCGA-DK-A1AC-01	TCGA-CU-A0YR-01	TCGA-BT-A42B-01	TCGA-DK-A3WX-01	TCGA-G2-A2EF-01	TCGA-BT-A3PJ-01	TCGA-CU-A3KJ-01	TCGA-DK-A3WW-01	TCGA-CF-A3MH-01	TCGA-GV-A3QK-01	TCGA-GV-A40E-01	TCGA-DK-A1A6-01	TCGA-DK-A1A7-01	TCGA-G2-A2ES-01	TCGA-DK-A2I4-01	TCGA-BT-A2LB-01	TCGA-DK-A2HX-01	TCGA-DK-A1AG-01	TCGA-DK-A2I1-01	TCGA-DK-A1AD-01	TCGA-C4-A0F6-01	TCGA-GV-A3QF-01	TCGA-CU-A0YO-01	TCGA-CU-A3QU-01	TCGA-DK-A2I2-01	TCGA-CF-A1HS-01	TCGA-DK-A3IQ-01	TCGA-CF-A27C-01	TCGA-BL-A3JM-01	TCGA-BL-A13I-01	TCGA-GD-A3OS-01	TCGA-FD-A3B8-01	TCGA-DK-A3WY-01	TCGA-BL-A0C8-01	TCGA-GC-A3RC-01	TCGA-G2-A3VY-01	TCGA-BT-A3PK-01	TCGA-HQ-A2OE-01	TCGA-E7-A3Y1-01	TCGA-C4-A0F1-01	TCGA-DK-A1AA-01	TCGA-DK-A1AF-01	TCGA-GV-A3QG-01	TCGA-H4-A2HQ-01	TCGA-C4-A0F7-01	TCGA-FT-A3EE-01	TCGA-FD-A3B7-01	TCGA-GC-A3RD-01	TCGA-DK-A3IV-01	TCGA-DK-A1AB-01	TCGA-DK-A1AE-01	TCGA-K4-A3WU-01	TCGA-K4-A3WV-01	TCGA-C4-A0F0-01	TCGA-E7-A3X6-01	TCGA-DK-A3IU-01	TCGA-DK-A3IS-01	TCGA-BT-A20P-01	TCGA-DK-A3IT-01	TCGA-BT-A0YX-01	TCGA-GC-A3I6-01	TCGA-GC-A3YS-01	TCGA-DK-A3IM-01	TCGA-GC-A3BM-01	TCGA-BT-A20T-01	TCGA-GV-A3JV-01	TCGA-FD-A3B3-01	TCGA-FD-A3B5-01	TCGA-DK-A3X2-01	TCGA-DK-A3IL-01	TCGA-CF-A3MF-01	TCGA-DK-A3IK-01	TCGA-BT-A20W-01	TCGA-GV-A40G-01	TCGA-BT-A0S7-01	TCGA-BT-A20J-01	TCGA-DK-A2I6-01	TCGA-K4-A3WS-01	TCGA-DK-A3X1-01	TCGA-CU-A0YN-01	TCGA-FJ-A3Z7-01	TCGA-BT-A20R-01	TCGA-FJ-A3ZF-01	TCGA-FD-A3SM-01	TCGA-GV-A3QI-01	TCGA-CF-A1HR-01	TCGA-GV-A3JX-01	TCGA-FD-A3B6-01	TCGA-CF-A3MG-01	TCGA-GV-A3QH-01	TCGA-FD-A3SP-01	TCGA-FJ-A3ZE-01	TCGA-GU-A42R-01
+case_list_ids: TCGA-GD-A3OP-01	TCGA-GD-A3OQ-01	TCGA-BT-A20Q-01	TCGA-FD-A3SS-01	TCGA-CF-A3MI-01	TCGA-DK-A3IN-01	TCGA-BT-A20U-01	TCGA-E5-A2PC-01	TCGA-G2-A3IE-01	TCGA-FD-A3SL-01	TCGA-DK-A1A5-01	TCGA-BT-A20O-01	TCGA-BT-A42C-01	TCGA-FD-A3SQ-01	TCGA-G2-A2EK-01	TCGA-GV-A3JZ-01	TCGA-CU-A3YL-01	TCGA-BT-A3PH-01	TCGA-GV-A3JW-01	TCGA-BL-A13J-01	TCGA-DK-A1A3-01	TCGA-H4-A2HO-01	TCGA-FD-A3SO-01	TCGA-GD-A2C5-01	TCGA-GC-A3OO-01	TCGA-FD-A3SR-01	TCGA-GC-A3WC-01	TCGA-G2-A2EC-01	TCGA-BT-A20N-01	TCGA-G2-A2EO-01	TCGA-G2-A2EJ-01	TCGA-FD-A3SJ-01	TCGA-BT-A2LD-01	TCGA-GC-A3RB-01	TCGA-FD-A3N5-01	TCGA-FD-A3NA-01	TCGA-FD-A3SN-01	TCGA-G2-A3IB-01	TCGA-DK-A1AC-01	TCGA-CU-A0YR-01	TCGA-BT-A42B-01	TCGA-DK-A3WX-01	TCGA-G2-A2EF-01	TCGA-BT-A3PJ-01	TCGA-CU-A3KJ-01	TCGA-DK-A3WW-01	TCGA-CF-A3MH-01	TCGA-GV-A3QK-01	TCGA-GV-A40E-01	TCGA-DK-A1A6-01	TCGA-DK-A1A7-01	TCGA-G2-A2ES-01	TCGA-DK-A2I4-01	TCGA-BT-A2LB-01	TCGA-DK-A2HX-01	TCGA-DK-A1AG-01	TCGA-DK-A2I1-01	TCGA-DK-A1AD-01	TCGA-C4-A0F6-01	TCGA-GV-A3QF-01	TCGA-CU-A0YO-01	TCGA-CU-A3QU-01	TCGA-DK-A2I2-01	TCGA-CF-A1HS-01	TCGA-DK-A3IQ-01	TCGA-CF-A27C-01	TCGA-BL-A3JM-01	TCGA-BL-A13I-01	TCGA-GD-A3OS-01	TCGA-FD-A3B8-01	TCGA-DK-A3WY-01	TCGA-BL-A0C8-01	TCGA-GC-A3RC-01	TCGA-G2-A3VY-01	TCGA-BT-A3PK-01	TCGA-HQ-A2OE-01	TCGA-E7-A3Y1-01	TCGA-C4-A0F1-01	TCGA-DK-A1AA-01	TCGA-DK-A1AF-01	TCGA-GV-A3QG-01	TCGA-H4-A2HQ-01	TCGA-C4-A0F7-01	TCGA-FT-A3EE-01	TCGA-FD-A3B7-01	TCGA-GC-A3RD-01	TCGA-DK-A3IV-01	TCGA-DK-A1AB-01	TCGA-DK-A1AE-01	TCGA-K4-A3WU-01	TCGA-K4-A3WV-01	TCGA-C4-A0F0-01	TCGA-E7-A3X6-01	TCGA-DK-A3IU-01	TCGA-DK-A3IS-01	TCGA-BT-A20P-01	TCGA-DK-A3IT-01	TCGA-BT-A0YX-01	TCGA-GC-A3I6-01	TCGA-GC-A3YS-01	TCGA-DK-A3IM-01	TCGA-GC-A3BM-01	TCGA-BT-A20T-01	TCGA-GV-A3JV-01	TCGA-FD-A3B3-01	TCGA-FD-A3B5-01	TCGA-DK-A3X2-01	TCGA-DK-A3IL-01	TCGA-CF-A3MF-01	TCGA-DK-A3IK-01	TCGA-BT-A20W-01	TCGA-GV-A40G-01	TCGA-BT-A0S7-01	TCGA-BT-A20J-01	TCGA-DK-A2I6-01	TCGA-K4-A3WS-01	TCGA-DK-A3X1-01	TCGA-CU-A0YN-01	TCGA-FJ-A3Z7-01	TCGA-BT-A20R-01	TCGA-FJ-A3ZF-01	TCGA-FD-A3SM-01	TCGA-GV-A3QI-01	TCGA-CF-A1HR-01	TCGA-GV-A3JX-01	TCGA-FD-A3B6-01	TCGA-CF-A3MG-01	TCGA-GV-A3QH-01	TCGA-FD-A3SP-01	TCGA-FJ-A3ZE-01	TCGA-GU-A42R-01

public/brca_aurora_2023/meta_log2_cna.txt

@@ -2,7 +2,7 @@ cancer_study_identifier: brca_aurora_2023
 genetic_alteration_type: COPY_NUMBER_ALTERATION
 datatype: LOG2-VALUE
 stable_id: log2CNA
-show_profile_in_analysis_tab: true
+show_profile_in_analysis_tab: false
 profile_description: Log2 copy-number values for each gene
 profile_name: Copy-number alterations (log2)
 data_filename: data_log2_cna.txt

public/brca_aurora_2023/meta_study.txt

@@ -1,7 +1,7 @@
 type_of_cancer: brca
 cancer_study_identifier: brca_aurora_2023
 name: Metastatic Breast Cancer (AURORA US Network, Nat Cancer 2023)
-description: Whole exome and low-pass whole genome sequencing of 55 patients with metastatic breast cancer (53 primary cancers and 102 metastases) and their matched normals. Retrospective Tissue Collection; an initiative of the Breast Cancer Research Foundation.
+description: Whole-exome and low-pass whole genome sequencing of 55 patients with metastatic breast cancer (53 primary cancers and 102 metastases) and their matched normals. Retrospective Tissue Collection; an initiative of the Breast Cancer Research Foundation.
 reference_genome: hg38
 pmid: 36585450
 citation: Garcia-Recio et al. Nat Cancer 2023

public/crc_orion_2024/meta_clinical_patient.txt

@@ -1,4 +1,4 @@
 cancer_study_identifier: crc_orion_2024
 genetic_alteration_type: CLINICAL
 datatype: PATIENT_ATTRIBUTES
-data_filename: data_patients.txt
+data_filename: data_clinical_patient.txt

public/crc_orion_2024/meta_clinical_sample.txt

@@ -1,4 +1,4 @@
 cancer_study_identifier: crc_orion_2024
 genetic_alteration_type: CLINICAL
 datatype: SAMPLE_ATTRIBUTES
-data_filename: data_samples.txt
+data_filename: data_clinical_sample.txt