From 0ada968d28b1d43c5068b89f86dc71f4fe6f4fd7 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Mon, 11 Dec 2023 12:57:08 -0700 Subject: [PATCH 1/3] Add new study dataset --- .../data_clinical_patient.txt | 3 + .../data_clinical_sample.txt | 3 + .../data_expression_raw.txt | 3 + .../data_expression_tpm.txt | 3 + .../log-validate-studies-2023-12-11_19:54.txt | 55 + .../serra_pnf_ntap_2023-validation.html | 240400 +++++++++++++++ .../meta_clinical_patient.txt | 4 + .../meta_clinical_sample.txt | 4 + .../meta_expression_raw.txt | 8 + .../meta_expression_tpm.txt | 8 + public/serra_pnf_ntap_2023/meta_study.txt | 8 + 11 files changed, 240499 insertions(+) create mode 100644 public/serra_pnf_ntap_2023/data_clinical_patient.txt create mode 100644 public/serra_pnf_ntap_2023/data_clinical_sample.txt create mode 100644 public/serra_pnf_ntap_2023/data_expression_raw.txt create mode 100644 public/serra_pnf_ntap_2023/data_expression_tpm.txt create mode 100644 public/serra_pnf_ntap_2023/html_report/log-validate-studies-2023-12-11_19:54.txt create mode 100644 public/serra_pnf_ntap_2023/html_report/serra_pnf_ntap_2023-validation.html create mode 100644 public/serra_pnf_ntap_2023/meta_clinical_patient.txt create mode 100644 public/serra_pnf_ntap_2023/meta_clinical_sample.txt create mode 100644 public/serra_pnf_ntap_2023/meta_expression_raw.txt create mode 100644 public/serra_pnf_ntap_2023/meta_expression_tpm.txt create mode 100644 public/serra_pnf_ntap_2023/meta_study.txt diff --git a/public/serra_pnf_ntap_2023/data_clinical_patient.txt b/public/serra_pnf_ntap_2023/data_clinical_patient.txt new file mode 100644 index 0000000000..f7ba73886d --- /dev/null +++ b/public/serra_pnf_ntap_2023/data_clinical_patient.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:80db27442923770389c7801f6c59b6c9d17d2756d3468df68a37d548151238aa +size 369 diff --git a/public/serra_pnf_ntap_2023/data_clinical_sample.txt b/public/serra_pnf_ntap_2023/data_clinical_sample.txt new file mode 100644 index 0000000000..ce6778125c --- /dev/null +++ b/public/serra_pnf_ntap_2023/data_clinical_sample.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ee7780781e90f44203ec6ebf48b3ed6a34cf4950fd9fc7ff1ee6f6dcf171b36c +size 1312 diff --git a/public/serra_pnf_ntap_2023/data_expression_raw.txt b/public/serra_pnf_ntap_2023/data_expression_raw.txt new file mode 100644 index 0000000000..02ab117dcf --- /dev/null +++ b/public/serra_pnf_ntap_2023/data_expression_raw.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5e8ff8e0fbdf7b53f338b9b8b1b2bc6f90546ea0fc0c79ec534eeff22e7da190 +size 5536549 diff --git a/public/serra_pnf_ntap_2023/data_expression_tpm.txt b/public/serra_pnf_ntap_2023/data_expression_tpm.txt new file mode 100644 index 0000000000..05b0d9f5c1 --- /dev/null +++ b/public/serra_pnf_ntap_2023/data_expression_tpm.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8ccdc7a4625e0028da01035fde170739926e9a8941cb3b3059cacb5bc239da75 +size 8611497 diff --git a/public/serra_pnf_ntap_2023/html_report/log-validate-studies-2023-12-11_19:54.txt b/public/serra_pnf_ntap_2023/html_report/log-validate-studies-2023-12-11_19:54.txt new file mode 100644 index 0000000000..c9cd627786 --- /dev/null +++ b/public/serra_pnf_ntap_2023/html_report/log-validate-studies-2023-12-11_19:54.txt @@ -0,0 +1,55 @@ +=== Validation study: /datahub/serra_pnf_ntap_2023 +DEBUG: -: Requesting info from portal at 'http://cbioportal.org' +DEBUG: -: Requesting cancer-types from portal at 'http://cbioportal.org' +DEBUG: -: Requesting genes from portal at 'http://cbioportal.org' +DEBUG: -: Requesting genesets from portal at 'http://cbioportal.org' +DEBUG: -: Requesting genesets_version from portal at 'http://cbioportal.org' +DEBUG: -: Requesting gene-panels from portal at 'http://cbioportal.org' + +DEBUG: meta_clinical_patient.txt: Starting validation of meta file +INFO: meta_clinical_patient.txt: Validation of meta file complete + +DEBUG: meta_clinical_sample.txt: Starting validation of meta file +INFO: meta_clinical_sample.txt: Validation of meta file complete + +DEBUG: meta_expression_raw.txt: Starting validation of meta file +INFO: meta_expression_raw.txt: Validation of meta file complete + +DEBUG: meta_expression_tpm.txt: Starting validation of meta file +INFO: meta_expression_tpm.txt: Validation of meta file complete + +DEBUG: meta_study.txt: Starting validation of meta file +INFO: meta_study.txt: Validation of meta file complete +INFO: meta_study.txt: No reference genome specified -- using default (hg19) + +ERROR: -: Cancer type of study is neither known to the portal nor defined in a cancer_type file; value encountered: 'pnf' + +DEBUG: data_clinical_sample.txt: Starting validation of file +INFO: data_clinical_sample.txt: Validation of file complete +INFO: data_clinical_sample.txt: Read 32 lines. Lines with warning: 0. Lines with error: 0 + +INFO: -: No directory named 'case_lists' found, so assuming no custom case lists. + +DEBUG: data_clinical_patient.txt: Starting validation of file +WARNING: data_clinical_patient.txt: Columns OS_MONTHS and/or OS_STATUS not found. Overall survival analysis feature will not be available for this study. +WARNING: data_clinical_patient.txt: Columns DFS_MONTHS and/or DFS_STATUS not found. Disease free analysis feature will not be available for this study. +INFO: data_clinical_patient.txt: Validation of file complete +INFO: data_clinical_patient.txt: Read 9 lines. Lines with warning: 0. Lines with error: 0 + +DEBUG: data_expression_raw.txt: Starting validation of file +WARNING: data_expression_raw.txt: line 1: The recommended column Entrez_Gene_Id was not found. Using Hugo_Symbol for all gene parsing. +WARNING: data_expression_raw.txt: lines [6, 91, 174, (23791 more)]: Gene symbol not known to the cBioPortal instance. This record will not be loaded.; values encountered: ['C1ORF112', 'FAM214B', 'KIAA0100', '(22668 more)'] +WARNING: data_expression_raw.txt: lines [26, 5510, 5512, (125 more)]: Duplicate line for a previously listed feature/gene, this line will be ignored.; values encountered: ['4267 (already defined on line 25)', '6845 (already defined on line 5509)', '3581 (already defined on line 5511)', '(76 more)'] +WARNING: data_expression_raw.txt: lines [19371, 51127, 52334, (23 more)]: Hugo Symbol is not in gene or alias table and starts with a number. This can be caused by unintentional gene conversion in Excel.; values encountered: ['7SK', '5_8S_RRNA', '5S_RRNA'] +INFO: data_expression_raw.txt: Validation of file complete +INFO: data_expression_raw.txt: Read 61599 lines. Lines with warning: 23923. Lines with error: 0 + +DEBUG: data_expression_tpm.txt: Starting validation of file +WARNING: data_expression_tpm.txt: line 1: The recommended column Entrez_Gene_Id was not found. Using Hugo_Symbol for all gene parsing. +WARNING: data_expression_tpm.txt: lines [6, 91, 174, (23791 more)]: Gene symbol not known to the cBioPortal instance. This record will not be loaded.; values encountered: ['C1ORF112', 'FAM214B', 'KIAA0100', '(22668 more)'] +WARNING: data_expression_tpm.txt: lines [26, 5510, 5512, (125 more)]: Duplicate line for a previously listed feature/gene, this line will be ignored.; values encountered: ['4267 (already defined on line 25)', '6845 (already defined on line 5509)', '3581 (already defined on line 5511)', '(76 more)'] +WARNING: data_expression_tpm.txt: lines [19371, 51127, 52334, (23 more)]: Hugo Symbol is not in gene or alias table and starts with a number. This can be caused by unintentional gene conversion in Excel.; values encountered: ['7SK', '5_8S_RRNA', '5S_RRNA'] +INFO: data_expression_tpm.txt: Validation of file complete +INFO: data_expression_tpm.txt: Read 61599 lines. Lines with warning: 23923. Lines with error: 0 + +INFO: -: Validation complete diff --git a/public/serra_pnf_ntap_2023/html_report/serra_pnf_ntap_2023-validation.html b/public/serra_pnf_ntap_2023/html_report/serra_pnf_ntap_2023-validation.html new file mode 100644 index 0000000000..0dea04b3aa --- /dev/null +++ b/public/serra_pnf_ntap_2023/html_report/serra_pnf_ntap_2023-validation.html @@ -0,0 +1,240400 @@ + + + + + + + + + + + + + cBioPortal validation report: study in '/datahub/serra_pnf_ntap_2023' + + + + + +
+
+
+

cBioPortal validation report

+

Study directory:
/datahub/serra_pnf_ntap_2023

+

For details, please see the documentation on file formats supported by cBioPortal

+

cBioPortal version 5.4.7-dirty-SNAPSHOT

+
+
+ + +
+
+
+ Validation status: + + Failed + +
+ +
+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Line NumberColumn NumberMessageValue Encountered
DebugRequesting info from portal at 'http://cbioportal.org'
DebugRequesting cancer-types from portal at 'http://cbioportal.org'
DebugRequesting genes from portal at 'http://cbioportal.org'
DebugRequesting genesets from portal at 'http://cbioportal.org'
DebugRequesting genesets_version from portal at 'http://cbioportal.org'
DebugRequesting gene-panels from portal at 'http://cbioportal.org'
ErrorCancer type of study is neither known to the portal nor defined in a cancer_type filepnf
InfoNo directory named 'case_lists' found, so assuming no custom case lists.
InfoValidation complete
+
+
+
+ + +
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Line NumberColumn NumberMessageValue Encountered
DebugStarting validation of file
WarningColumns OS_MONTHS and/or OS_STATUS not found. Overall survival analysis feature will not be available for this study.
WarningColumns DFS_MONTHS and/or DFS_STATUS not found. Disease free analysis feature will not be available for this study.
InfoValidation of file complete
InfoRead 9 lines. Lines with warning: 0. Lines with error: 0
+
+
+
+ +
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Line NumberColumn NumberMessageValue Encountered
DebugStarting validation of file
InfoValidation of file complete
InfoRead 32 lines. Lines with warning: 0. Lines with error: 0
+
+
+
+ +
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Line NumberColumn NumberMessageValue Encountered
DebugStarting validation of file
Warning1The recommended column Entrez_Gene_Id was not found. Using Hugo_Symbol for all gene parsing.
Warning6, 91, 174…Gene symbol not known to the cBioPortal instance. This record will not be loaded.C1ORF112, FAM214B, KIAA0100… + See all 23794 values + +
Warning26, 5510, 5512…Duplicate line for a previously listed feature/gene, this line will be ignored.4267 (already defined on line 25), 6845 (already defined on line 5509), 3581 (already defined on line 5511)… + See all 128 values + +
Warning19371, 51127, 52334…Hugo Symbol is not in gene or alias table and starts with a number. This can be caused by unintentional gene conversion in Excel.7SK, 5_8S_RRNA, 5S_RRNA + See all 26 values + +
InfoValidation of file complete
InfoRead 61599 lines. Lines with warning: 23923. Lines with error: 0
+
+
+
+ +
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Line NumberColumn NumberMessageValue Encountered
DebugStarting validation of file
Warning1The recommended column Entrez_Gene_Id was not found. Using Hugo_Symbol for all gene parsing.
Warning6, 91, 174…Gene symbol not known to the cBioPortal instance. This record will not be loaded.C1ORF112, FAM214B, KIAA0100… + See all 23794 values + +
Warning26, 5510, 5512…Duplicate line for a previously listed feature/gene, this line will be ignored.4267 (already defined on line 25), 6845 (already defined on line 5509), 3581 (already defined on line 5511)… + See all 128 values + +
Warning19371, 51127, 52334…Hugo Symbol is not in gene or alias table and starts with a number. This can be caused by unintentional gene conversion in Excel.7SK, 5_8S_RRNA, 5S_RRNA + See all 26 values + +
InfoValidation of file complete
InfoRead 61599 lines. Lines with warning: 23923. Lines with error: 0
+
+
+
+ +
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Line NumberColumn NumberMessageValue Encountered
DebugStarting validation of meta file
InfoValidation of meta file complete
+
+
+
+ +
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Line NumberColumn NumberMessageValue Encountered
DebugStarting validation of meta file
InfoValidation of meta file complete
+
+
+
+ +
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Line NumberColumn NumberMessageValue Encountered
DebugStarting validation of meta file
InfoValidation of meta file complete
+
+
+
+ +
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Line NumberColumn NumberMessageValue Encountered
DebugStarting validation of meta file
InfoValidation of meta file complete
+
+
+
+ +
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Line NumberColumn NumberMessageValue Encountered
DebugStarting validation of meta file
InfoValidation of meta file complete
InfoNo reference genome specified -- using default (hg19)
+
+
+
+ + +
+
+
+
+
+

Legend

+
+
+

+ Click on a filename below to see a table of messages about the data + in the file. The colors in the tables have the following meanings: +

+ + + + + + + + + + + + + + + + + + + +
ErrorError: cBioPortal will not know how to load this, please revise or remove
WarningWarning: possible cause of confusion, please check whether this is intended
InfoInfo: this looks good, no action required
DebugVerbose output: details on the progress of the validation script
+
+
+
+ + \ No newline at end of file diff --git a/public/serra_pnf_ntap_2023/meta_clinical_patient.txt b/public/serra_pnf_ntap_2023/meta_clinical_patient.txt new file mode 100644 index 0000000000..6e9d74026a --- /dev/null +++ b/public/serra_pnf_ntap_2023/meta_clinical_patient.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: serra_pnf_ntap_2023 +genetic_alteration_type: CLINICAL +datatype: PATIENT_ATTRIBUTES +data_filename: data_clinical_patient.txt diff --git a/public/serra_pnf_ntap_2023/meta_clinical_sample.txt b/public/serra_pnf_ntap_2023/meta_clinical_sample.txt new file mode 100644 index 0000000000..aa8a3d1e64 --- /dev/null +++ b/public/serra_pnf_ntap_2023/meta_clinical_sample.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: serra_pnf_ntap_2023 +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES +data_filename: data_clinical_sample.txt diff --git a/public/serra_pnf_ntap_2023/meta_expression_raw.txt b/public/serra_pnf_ntap_2023/meta_expression_raw.txt new file mode 100644 index 0000000000..46185b9d78 --- /dev/null +++ b/public/serra_pnf_ntap_2023/meta_expression_raw.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: serra_pnf_ntap_2023 +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: rna_seq_mrna +show_profile_in_analysis_tab: true +profile_name: mRNA expression +profile_description: Expression levels +data_filename: data_expression_raw.txt diff --git a/public/serra_pnf_ntap_2023/meta_expression_tpm.txt b/public/serra_pnf_ntap_2023/meta_expression_tpm.txt new file mode 100644 index 0000000000..9efb3b46fe --- /dev/null +++ b/public/serra_pnf_ntap_2023/meta_expression_tpm.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: serra_pnf_ntap_2023 +genetic_alteration_type: MRNA_EXPRESSION +datatype: CONTINUOUS +stable_id: mrna_seq_tpm +show_profile_in_analysis_tab: true +profile_name: Normalized gene expression +profile_description: Normalized gene expression levels (TPM) +data_filename: data_expression_tpm.txt diff --git a/public/serra_pnf_ntap_2023/meta_study.txt b/public/serra_pnf_ntap_2023/meta_study.txt new file mode 100644 index 0000000000..0a294af770 --- /dev/null +++ b/public/serra_pnf_ntap_2023/meta_study.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: serra_pnf_ntap_2023 +type_of_cancer: pnf +name: 'Reprogramming Captures the Genetic and Tumorigenic Properties of Neurofibromatosis Type 1 Plexiform Neurofibromas' +description: Neurofibromatosis type 1 iPSCs gene expression profiling +citation: 'Carrió M et al. Reprogramming Captures the Genetic and Tumorigenic Properties of Neurofibromatosis Type 1 Plexiform Neurofibromas. Stem Cell Reports. doi: 10.1016/j.stemcr.2019.01.001.' +pmid: 30713041 +groups: PUBLIC +add_global_case_list: true From d5765c74a80b7b1573826b047e1ecaf337aa8afc Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Fri, 15 Dec 2023 13:15:56 -0700 Subject: [PATCH 2/3] Add reference for new cancer type --- public/pnf_serra_nfosi_2023/cancer_type.txt | 1 + .../data_clinical_patient.txt | 0 .../data_clinical_sample.txt | 0 .../data_expression_raw.txt | 0 .../data_expression_tpm.txt | 0 ...log-validate-studies-2023-12-15_20:12.txt} | 10 +- .../pnf_serra_nfosi_2023-validation.html} | 132 ++++++++++++++++-- .../pnf_serra_nfosi_2023/meta_cancer_type.txt | 3 + .../meta_clinical_patient.txt | 2 +- .../meta_clinical_sample.txt | 2 +- .../meta_expression_raw.txt | 2 +- .../meta_expression_tpm.txt | 2 +- .../meta_study.txt | 2 +- 13 files changed, 136 insertions(+), 20 deletions(-) create mode 100644 public/pnf_serra_nfosi_2023/cancer_type.txt rename public/{serra_pnf_ntap_2023 => pnf_serra_nfosi_2023}/data_clinical_patient.txt (100%) rename public/{serra_pnf_ntap_2023 => pnf_serra_nfosi_2023}/data_clinical_sample.txt (100%) rename public/{serra_pnf_ntap_2023 => pnf_serra_nfosi_2023}/data_expression_raw.txt (100%) rename public/{serra_pnf_ntap_2023 => pnf_serra_nfosi_2023}/data_expression_tpm.txt (100%) rename public/{serra_pnf_ntap_2023/html_report/log-validate-studies-2023-12-11_19:54.txt => pnf_serra_nfosi_2023/html_report/log-validate-studies-2023-12-15_20:12.txt} (90%) rename public/{serra_pnf_ntap_2023/html_report/serra_pnf_ntap_2023-validation.html => pnf_serra_nfosi_2023/html_report/pnf_serra_nfosi_2023-validation.html} (99%) create mode 100644 public/pnf_serra_nfosi_2023/meta_cancer_type.txt rename public/{serra_pnf_ntap_2023 => pnf_serra_nfosi_2023}/meta_clinical_patient.txt (69%) rename public/{serra_pnf_ntap_2023 => pnf_serra_nfosi_2023}/meta_clinical_sample.txt (68%) rename public/{serra_pnf_ntap_2023 => pnf_serra_nfosi_2023}/meta_expression_raw.txt (83%) rename public/{serra_pnf_ntap_2023 => pnf_serra_nfosi_2023}/meta_expression_tpm.txt (85%) rename public/{serra_pnf_ntap_2023 => pnf_serra_nfosi_2023}/meta_study.txt (91%) diff --git a/public/pnf_serra_nfosi_2023/cancer_type.txt b/public/pnf_serra_nfosi_2023/cancer_type.txt new file mode 100644 index 0000000000..dd9092d1b0 --- /dev/null +++ b/public/pnf_serra_nfosi_2023/cancer_type.txt @@ -0,0 +1 @@ +pnf Plexiforme Neurofibroma DarkOrchid nfib diff --git a/public/serra_pnf_ntap_2023/data_clinical_patient.txt b/public/pnf_serra_nfosi_2023/data_clinical_patient.txt similarity index 100% rename from public/serra_pnf_ntap_2023/data_clinical_patient.txt rename to public/pnf_serra_nfosi_2023/data_clinical_patient.txt diff --git a/public/serra_pnf_ntap_2023/data_clinical_sample.txt b/public/pnf_serra_nfosi_2023/data_clinical_sample.txt similarity index 100% rename from public/serra_pnf_ntap_2023/data_clinical_sample.txt rename to public/pnf_serra_nfosi_2023/data_clinical_sample.txt diff --git a/public/serra_pnf_ntap_2023/data_expression_raw.txt b/public/pnf_serra_nfosi_2023/data_expression_raw.txt similarity index 100% rename from public/serra_pnf_ntap_2023/data_expression_raw.txt rename to public/pnf_serra_nfosi_2023/data_expression_raw.txt diff --git a/public/serra_pnf_ntap_2023/data_expression_tpm.txt b/public/pnf_serra_nfosi_2023/data_expression_tpm.txt similarity index 100% rename from public/serra_pnf_ntap_2023/data_expression_tpm.txt rename to public/pnf_serra_nfosi_2023/data_expression_tpm.txt diff --git a/public/serra_pnf_ntap_2023/html_report/log-validate-studies-2023-12-11_19:54.txt b/public/pnf_serra_nfosi_2023/html_report/log-validate-studies-2023-12-15_20:12.txt similarity index 90% rename from public/serra_pnf_ntap_2023/html_report/log-validate-studies-2023-12-11_19:54.txt rename to public/pnf_serra_nfosi_2023/html_report/log-validate-studies-2023-12-15_20:12.txt index c9cd627786..ba8d775c2d 100644 --- a/public/serra_pnf_ntap_2023/html_report/log-validate-studies-2023-12-11_19:54.txt +++ b/public/pnf_serra_nfosi_2023/html_report/log-validate-studies-2023-12-15_20:12.txt @@ -1,4 +1,4 @@ -=== Validation study: /datahub/serra_pnf_ntap_2023 +=== Validation study: /datahub/pnf_serra_nfosi_2023 DEBUG: -: Requesting info from portal at 'http://cbioportal.org' DEBUG: -: Requesting cancer-types from portal at 'http://cbioportal.org' DEBUG: -: Requesting genes from portal at 'http://cbioportal.org' @@ -6,6 +6,9 @@ DEBUG: -: Requesting genesets from portal at 'http://cbioportal.org' DEBUG: -: Requesting genesets_version from portal at 'http://cbioportal.org' DEBUG: -: Requesting gene-panels from portal at 'http://cbioportal.org' +DEBUG: meta_cancer_type.txt: Starting validation of meta file +INFO: meta_cancer_type.txt: Validation of meta file complete + DEBUG: meta_clinical_patient.txt: Starting validation of meta file INFO: meta_clinical_patient.txt: Validation of meta file complete @@ -22,7 +25,10 @@ DEBUG: meta_study.txt: Starting validation of meta file INFO: meta_study.txt: Validation of meta file complete INFO: meta_study.txt: No reference genome specified -- using default (hg19) -ERROR: -: Cancer type of study is neither known to the portal nor defined in a cancer_type file; value encountered: 'pnf' +DEBUG: cancer_type.txt: Starting validation of file +INFO: cancer_type.txt: line 1: New disease type will be added to the portal; value encountered: 'pnf' +INFO: cancer_type.txt: Validation of file complete +INFO: cancer_type.txt: Read 1 lines. Lines with warning: 0. Lines with error: 0 DEBUG: data_clinical_sample.txt: Starting validation of file INFO: data_clinical_sample.txt: Validation of file complete diff --git a/public/serra_pnf_ntap_2023/html_report/serra_pnf_ntap_2023-validation.html b/public/pnf_serra_nfosi_2023/html_report/pnf_serra_nfosi_2023-validation.html similarity index 99% rename from public/serra_pnf_ntap_2023/html_report/serra_pnf_ntap_2023-validation.html rename to public/pnf_serra_nfosi_2023/html_report/pnf_serra_nfosi_2023-validation.html index 0dea04b3aa..b6dd85782f 100644 --- a/public/serra_pnf_ntap_2023/html_report/serra_pnf_ntap_2023-validation.html +++ b/public/pnf_serra_nfosi_2023/html_report/pnf_serra_nfosi_2023-validation.html @@ -36,7 +36,7 @@ - cBioPortal validation report: study in '/datahub/serra_pnf_ntap_2023' + cBioPortal validation report: study in '/datahub/pnf_serra_nfosi_2023' @@ -46,7 +46,7 @@

cBioPortal validation report

-

Study directory:
/datahub/serra_pnf_ntap_2023

+

Study directory:
/datahub/pnf_serra_nfosi_2023

For details, please see the documentation on file formats supported by cBioPortal

cBioPortal version 5.4.7-dirty-SNAPSHOT

@@ -55,22 +55,22 @@

cBioPortal validation report

-
+
Validation status: - Failed + Please check
-
+
@@ -138,11 +138,69 @@

General

– - - Error + + Info + – + – + No directory named 'case_lists' found, so assuming no custom case lists. + – + + + + Info + – – + Validation complete + – + + + + +
+
+
+ + +
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + - + @@ -150,7 +208,7 @@

General

- + @@ -158,7 +216,7 @@

General

- + @@ -168,7 +226,6 @@

General

-
+
Line NumberColumn NumberMessageValue Encountered
DebugStarting validation of file
Info1 Cancer type of study is neither known to the portal nor defined in a cancer_type fileNew disease type will be added to the portal pnf
Info No directory named 'case_lists' found, so assuming no custom case lists.Validation of file complete
Info Validation completeRead 1 lines. Lines with warning: 0. Lines with error: 0
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Line NumberColumn NumberMessageValue Encountered
DebugStarting validation of meta file
InfoValidation of meta file complete
+
+
+
+