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| author | lltommy | 2020-11-11 11:53:19 +0100 |
|---|---|---|
| committer | lltommy | 2020-11-11 11:53:19 +0100 |
| commit | 17847c35bf6050f5d3715eda615e4a612425a58a (patch) | |
| tree | 32628509164d93e8f85c97f4b1ccabcd26faeca3 /scripts/create_sra_metadata | |
| parent | 94e54badc0dae2071772fb695328416734a8a029 (diff) | |
| parent | 8d3e9971edebcf6ae3ef80cddf2fe2142c628875 (diff) | |
| download | bh20-seq-resource-17847c35bf6050f5d3715eda615e4a612425a58a.tar.gz bh20-seq-resource-17847c35bf6050f5d3715eda615e4a612425a58a.tar.lz bh20-seq-resource-17847c35bf6050f5d3715eda615e4a612425a58a.zip | |
Merge branch 'master' of https://github.com/arvados/bh20-seq-resource
Diffstat (limited to 'scripts/create_sra_metadata')
| -rw-r--r-- | scripts/create_sra_metadata/create_sra_metadata.py | 14 |
1 files changed, 10 insertions, 4 deletions
diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py index 59218e9..2aac0e5 100644 --- a/scripts/create_sra_metadata/create_sra_metadata.py +++ b/scripts/create_sra_metadata/create_sra_metadata.py @@ -270,12 +270,18 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): if Organization_Address is not None: info_for_yaml_dict['submitter']['lab_address'] = '; '.join([x.text for x in Organization_Address] + ['Postal code ' + Organization_Address.attrib['postal_code']]) - if 'collection_date' not in info_for_yaml_dict['sample']: - info_for_yaml_dict['sample']['collection_date'] = '1970-01-01' - info_for_yaml_dict['sample']['additional_collection_information'] = "The real 'collection_date' is missing" - + # Do not trick the quality control! + #if 'collection_date' not in info_for_yaml_dict['sample']: + # info_for_yaml_dict['sample']['collection_date'] = '1970-01-01' + # info_for_yaml_dict['sample']['additional_collection_information'] = "The real 'collection_date' is missing" # Check if mandatory fields are missing + if 'collection_date' not in info_for_yaml_dict['sample']: + # print(accession_version, ' - collection_date not found') + if accession not in not_created_accession_dict: + not_created_accession_dict[accession] = [] + not_created_accession_dict[accession].append('collection_date not found') + if 'sample_sequencing_technology' not in info_for_yaml_dict['technology']: # print(accession_version, ' - technology not found') if accession not in not_created_accession_dict: |