Error encountered while executing validateData.py
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v.jlak...@gmail.com
Apr 3, 2019, 4:58:23 AM4/3/19
to cBioPortal for Cancer Genomics Discussion Group
Hi,
I am trying to run the following command but I am encountering an issue with this:
./validateData.py -s /home/bioinfo/cbioportal/core/src/test/scripts/test_data/study_es_0 -n
and the output is
./validateData.py:3770: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
parsedYaml = yaml.load(stream)
INFO: -: Running validation from cBioPortal version 0-unknown-version-SNAPSHOT
WARNING: -: Skipping validations relating to cancer types defined in the portal
WARNING: -: Skipping validations relating to gene identifiers and aliases defined in the portal
WARNING: -: Skipping validations relating to gene set identifiers
WARNING: -: Skipping validations relating to gene panel identifiers
INFO: meta_cancer_type.txt: Validation of meta file complete
INFO: meta_clinical_patients.txt: Validation of meta file complete
INFO: meta_clinical_samples.txt: Validation of meta file complete
INFO: meta_cna_discrete.txt: Validation of meta file complete
INFO: meta_cna_hg19_seg.txt: Validation of meta file complete
INFO: meta_cna_log2.txt: Validation of meta file complete
INFO: meta_expression_median.txt: Validation of meta file complete
INFO: meta_expression_median_Zscores.txt: Validation of meta file complete
INFO: meta_fusions.txt: Validation of meta file complete
INFO: meta_gene_panel_matrix.txt: Validation of meta file complete
INFO: meta_gistic_genes_amp.txt: Validation of meta file complete
INFO: meta_gsva_pvalues.txt: Validation of meta file complete
INFO: meta_gsva_scores.txt: Validation of meta file complete
INFO: meta_methylation_hm27.txt: Validation of meta file complete
INFO: meta_mutations_extended.txt: Validation of meta file complete
INFO: meta_study.txt: Validation of meta file complete
INFO: data_cancer_type.txt: Validation of file complete
INFO: data_cancer_type.txt: Read 1 lines. Lines with warning: 0. Lines with error: 0
INFO: data_clinical_samples.txt: Validation of file complete
INFO: data_clinical_samples.txt: Read 846 lines. Lines with warning: 0. Lines with error: 0
INFO: study_tags.yml: Validation of study tags file complete.
INFO: data_cna_discrete.txt: Validation of file complete
INFO: data_cna_discrete.txt: Read 9 lines. Lines with warning: 0. Lines with error: 0
INFO: data_clinical_patients.txt: Validation of file complete
INFO: data_clinical_patients.txt: Read 845 lines. Lines with warning: 0. Lines with error: 0
INFO: data_expression_median.txt: Validation of file complete
INFO: data_expression_median.txt: Read 7 lines. Lines with warning: 0. Lines with error: 0
INFO: data_expression_median_Zscores.txt: Validation of file complete
INFO: data_expression_median_Zscores.txt: Read 6 lines. Lines with warning: 0. Lines with error: 0
INFO: data_fusions.txt: Validation of file complete
INFO: data_fusions.txt: Read 6 lines. Lines with warning: 0. Lines with error: 0
INFO: data_gistic_genes_amp.txt: Validation of file complete
INFO: data_gistic_genes_amp.txt: Read 15 lines. Lines with warning: 0. Lines with error: 0
INFO: data_gsva_pvalues.txt: Validation of file complete
INFO: data_gsva_pvalues.txt: Read 8 lines. Lines with warning: 0. Lines with error: 0
INFO: data_gsva_scores.txt: Validation of file complete
INFO: data_gsva_scores.txt: Read 8 lines. Lines with warning: 0. Lines with error: 0
INFO: data_cna_log2.txt: Validation of file complete
INFO: data_cna_log2.txt: Read 8 lines. Lines with warning: 0. Lines with error: 0
INFO: data_methylation_hm27.txt: Validation of file complete
INFO: data_methylation_hm27.txt: Read 9 lines. Lines with warning: 0. Lines with error: 0
INFO: data_mutations_extended.maf: lines [4, 5, 6, (5 more)]: column 164: Values contained in the column cbp_driver_tiers that will appear in the "Mutation Color" menu of the Oncoprint; values encountered: ['Class 2', 'Class 1', 'Class 4', '(1 more)']
INFO: data_mutations_extended.maf: lines [7, 9, 14]: 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]; value encountered: 'Silent'
INFO: data_mutations_extended.maf: Validation of file complete
INFO: data_mutations_extended.maf: Read 38 lines. Lines with warning: 0. Lines with error: 0
INFO: data_cna_hg19.seg: Validation of file complete
INFO: data_cna_hg19.seg: Read 10 lines. Lines with warning: 0. Lines with error: 0
INFO: case_lists/cases_sequenced.txt: Validation of meta file complete
INFO: case_lists/cases_custom.txt: Validation of meta file complete
INFO: case_lists/cases_cnaseq.txt: Validation of meta file complete
INFO: case_lists/cases_cna.txt: Validation of meta file complete
INFO: case_lists/cases_test.txt: Validation of meta file complete
INFO: -: Validation of case list folder complete
INFO: data_gene_panel_matrix.txt: line 1: This column can be replaced by a 'gene_panel' property in the respective meta file; value encountered: 'gistic'
Traceback (most recent call last):
File "./validateData.py", line 4352, in <module>
exit_status = main_validate(parsed_args)
File "./validateData.py", line 4335, in main_validate
validate_study(study_dir, portal_instance, logger, relaxed_mode, strict_maf_checks)
File "./validateData.py", line 4210, in validate_study
validators_by_meta_type[cbioportal_common.MetaFileTypes.GENE_PANEL_MATRIX][0].validate()
File "./validateData.py", line 366, in validate
self._validate_file()
File "./validateData.py", line 479, in _validate_file
self.checkLine(fields)
File "./validateData.py", line 2811, in checkLine
if gene_panel_id not in self.portal.gene_panel_list and gene_panel_id != 'NA':
TypeError: argument of type 'NoneType' is not iterable
I think I got one clue here:
when I run the following command, I could see it's a connection issue. Can you please help ?
bioinfo@bioinfo-pc:~/cbioportal/core/src/main/scripts/importer$ ./validateData.py -s ../../../test/scripts/test_data/study_es_0/ -v
INFO: -: Running validation from cBioPortal version 0-unknown-version-SNAPSHOT
DEBUG: -: Requesting cancertypes from portal at 'http://localhost:8080/cbioportal'
Traceback (most recent call last):
File "./validateData.py", line 3877, in request_from_portal_api
response.raise_for_status()
File "/usr/lib/python3/dist-packages/requests/models.py", line 840, in raise_for_status
raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 404 Client Error: for url: http://localhost:8080/cbioportal/api-legacy/cancertypes
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "./validateData.py", line 4352, in <module>
exit_status = main_validate(parsed_args)
File "./validateData.py", line 4330, in main_validate
portal_instance = load_portal_info(server_url, logger)
File "./validateData.py", line 3994, in load_portal_info
parsed_json = request_from_portal_api(path, api_name, logger)
File "./validateData.py", line 3881, in request_from_portal_api
) from e
ConnectionError: Failed to fetch metadata from the portal at [http://localhost:8080/cbioportal/api-legacy/cancertypes]Can you please help ?
Pieter Lukasse
Apr 3, 2019, 5:28:28 AM4/3/19
to v.jlak...@gmail.com, cBioPortal for Cancer Genomics Discussion Group
Hi,
can you please try to open the URL http://localhost:8080/cbioportal/api-legacy/cancertypes in a browser on the same machine you are executing the .py script?
Thanks,
Pieter Lukasse
Op wo 3 apr. 2019 om 10:58 schreef <v.jlak...@gmail.com>:
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