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path: root/scripts/create_sra_metadata/create_sra_metadata.py
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-rw-r--r--scripts/create_sra_metadata/create_sra_metadata.py15
1 files changed, 9 insertions, 6 deletions
diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py
index f5dc0c8..89624fd 100644
--- a/scripts/create_sra_metadata/create_sra_metadata.py
+++ b/scripts/create_sra_metadata/create_sra_metadata.py
@@ -228,7 +228,7 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
taxon_id = SAMPLE.find('SAMPLE_NAME').find('TAXON_ID').text
- info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_"+taxon_id
+ info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_" + taxon_id
# This script download and prepare data and metadata for samples that will be mapepd againg a referenceT
info_for_yaml_dict['technology']['assembly_method'] = 'http://purl.obolibrary.org/obo/GENEPIO_0002028'
@@ -244,22 +244,25 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
#else:
# print(accession, 'Missing INSTRUMENT_MODEL', info_for_yaml_dict)
LIBRARY_DESCRIPTOR = EXPERIMENT.find('DESIGN').find('LIBRARY_DESCRIPTOR')
- if LIBRARY_DESCRIPTOR.text not in ['OTHER']:
+ if LIBRARY_DESCRIPTOR.text not in ['', 'OTHER']:
info_for_yaml_dict['technology']['additional_technology_information'] = 'LIBRARY_STRATEGY: {};'.format(LIBRARY_DESCRIPTOR.find('LIBRARY_STRATEGY').text)
SUBMISSION = EXPERIMENT_PACKAGE.find('SUBMISSION')
- info_for_yaml_dict['submitter']['submitter_sample_id'] = SUBMISSION.attrib['accession']
+ if SUBMISSION.attrib['accession']:
+ info_for_yaml_dict['submitter']['submitter_sample_id'] = SUBMISSION.attrib['accession']
- if SUBMISSION.attrib['lab_name'].lower() not in ['na']:
+ if SUBMISSION.attrib['lab_name'].lower() not in ['', 'na']:
info_for_yaml_dict['submitter']['originating_lab'] = SUBMISSION.attrib['lab_name']
STUDY = EXPERIMENT_PACKAGE.find('STUDY')
- info_for_yaml_dict['submitter']['publication'] = STUDY.attrib['alias']
+ if STUDY.attrib['alias']:
+ info_for_yaml_dict['submitter']['publication'] = STUDY.attrib['alias']
Organization = EXPERIMENT_PACKAGE.find('Organization')
Organization_Name = Organization.find('Name')
- info_for_yaml_dict['submitter']['authors'] = [Organization_Name.text]
+ if Organization_Name.text:
+ info_for_yaml_dict['submitter']['authors'] = [Organization_Name.text]
Organization_Contact = Organization.find('Contact')
if Organization_Contact is not None: