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Error while importing data into cbioportal #71

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lakhujanivijay opened this issue Aug 7, 2019 · 0 comments
Open

Error while importing data into cbioportal #71

lakhujanivijay opened this issue Aug 7, 2019 · 0 comments

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@lakhujanivijay
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Hi

I am trying to import data into cbioportal and my command is this:

docker run -it --rm --net cbio-net \
     -v "/media/bioinfo/primary1/data_set:/study:ro" \
     -v "$PWD:/outdir" \
     -v "$PWD/portal.properties:/cbioportal/portal.properties:ro" \
     thehyve/cbioportal:v2.0.1-iss5758 \
     metaImport.py \
        -u http://cbioportal-container:8080/cbioportal \
        -s /study --html=/outdir/.html -v -o

I encounter the following error:

INFO: -: Running validation from cBioPortal version 0-unknown-version-SNAPSHOT
DEBUG: -: Requesting cancertypes from portal at 'http://cbioportal-container:8080/cbioportal'
DEBUG: -: Requesting genes from portal at 'http://cbioportal-container:8080/cbioportal'
DEBUG: -: Requesting genesaliases from portal at 'http://cbioportal-container:8080/cbioportal'
DEBUG: -: Requesting genesets from portal at 'http://cbioportal-container:8080/cbioportal'

DEBUG: meta_study.txt: Starting validation of meta file
INFO: meta_study.txt: Validation of meta file complete

DEBUG: meta_fusion.txt: Starting validation of meta file
INFO: meta_fusion.txt: Validation of meta file complete

DEBUG: meta_mutation_file.txt: Starting validation of meta file
INFO: meta_mutation_file.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_clinical_patient.txt: Starting validation of meta file
INFO: meta_clinical_patient.txt: Validation of meta file complete

ERROR: -: **Cancer type of study is neither known to the portal nor defined in a cancer_type file; value encountered: 'mixed**'

my meta_study.txt file looks like this:

type_of_cancer: mixed
cancer_study_identifier: test_2019
name: test_2019
short_name: test_2019
description: test_2019
groups: PUBLIC
add_global_case_list: true

It is weird that I was able to upload the exact same data set with mixed cancer type and now it says that "Cancer type of study is neither known to the portal nor defined in a cancer_type file"

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