original_docstring: 
          Convert the valid entry in the config to the one that should be created after brokering.
          This is only useful after we merged the vcf files otherwise this function will not do anything.
          
docstring: Convert the valid entry in the config to the one that should be created after brokering.
  This is only useful after we merged the vcf files otherwise this function will not do anything.
docstring_tokens: Convert the valid entry in the config to the one that should be created after brokering . This is only useful after we merged the vcf files otherwise this function will not do anything .
code: def copy_valid_config_to_brokering_after_merge(self):
          """
          Convert the valid entry in the config to the one that should be created after brokering.
          This is only useful after we merged the vcf files otherwise this function will not do anything.
          """
          if not self.eload_cfg.query('validation', 'valid', 'analyses'):
              raise ValueError('Merge did not complete, most likely because one of the validation did not pass.')
          for analysis_alias, analysis_data in self.eload_cfg.query('validation', 'valid', 'analyses').items():
              self.eload_cfg.set('brokering', 'analyses', analysis_alias, 'assembly_accession',
                                 value=analysis_data.get('assembly_accession'))
              self.eload_cfg.set('brokering', 'analyses', analysis_alias, 'assembly_fasta',
                                 value=analysis_data.get('assembly_fasta'))
              self.eload_cfg.set('brokering', 'analyses', analysis_alias, 'assembly_report',
                                 value=analysis_data.get('assembly_report'))
              vcf_files_dict = {}
              for vcf_file in analysis_data.get('vcf_files'):
                  vcf_files_dict[vcf_file] = {}
                  if os.path.exists(vcf_file + '.tbi'):
                      vcf_files_dict[vcf_file]['index'] = vcf_file + '.tbi'
                  else:
                      self.warning(f'Cannot find the tbi index for {vcf_file}')
                  if os.path.exists(vcf_file + '.csi'):
                      vcf_files_dict[vcf_file]['csi'] = vcf_file + '.csi'
                  else:
                      self.warning(f'Cannot find the csi index for {vcf_file}')
              self.eload_cfg.set('brokering', 'analyses', analysis_alias, 'vcf_files', value=vcf_files_dict)
code_tokens: def copy_valid_config_to_brokering_after_merge ( self ) : if not self . eload_cfg . query ( 'validation' , 'valid' , 'analyses' ) : raise ValueError ( 'Merge did not complete, most likely because one of the validation did not pass.' ) for analysis_alias , analysis_data in self . eload_cfg . query ( 'validation' , 'valid' , 'analyses' ) . items ( ) : self . eload_cfg . set ( 'brokering' , 'analyses' , analysis_alias , 'assembly_accession' , value = analysis_data . get ( 'assembly_accession' ) ) self . eload_cfg . set ( 'brokering' , 'analyses' , analysis_alias , 'assembly_fasta' , value = analysis_data . get ( 'assembly_fasta' ) ) self . eload_cfg . set ( 'brokering' , 'analyses' , analysis_alias , 'assembly_report' , value = analysis_data . get ( 'assembly_report' ) ) vcf_files_dict = { } for vcf_file in analysis_data . get ( 'vcf_files' ) : vcf_files_dict [ vcf_file ] = { } if os . path . exists ( vcf_file + '.tbi' ) : vcf_files_dict [ vcf_file ] [ 'index' ] = vcf_file + '.tbi' else : self . warning ( f'Cannot find the tbi index for {vcf_file}' ) if os . path . exists ( vcf_file + '.csi' ) : vcf_files_dict [ vcf_file ] [ 'csi' ] = vcf_file + '.csi' else : self . warning ( f'Cannot find the csi index for {vcf_file}' ) self . eload_cfg . set ( 'brokering' , 'analyses' , analysis_alias , 'vcf_files' , value = vcf_files_dict )
short_docstring: Convert the valid entry in the config to the one that should be created after brokering.
short_docstring_tokens: Convert the valid entry in the config to the one that should be created after brokering .
comment: """
          Convert the valid entry in the config to the one that should be created after brokering.
          This is only useful after we merged the vcf files otherwise this function will not do anything.
          """