Class: EBICheck::Process

Inherits:
Object
  • Object
show all
Defined in:
lib/ebi_check/process.rb

Overview

rubocop:disable Metrics/ClassLength

Constant Summary collapse

EGA =

Service names to identify EGA and ENA accessions

'EGA'
ENA = 
'ENA'
TEMPLATE_STUDY_INFO =

Templates for printing information

'Study ID: %s, EBI Accession Number: %s'
TEMPLATE_STUDY_ERROR = 
' Error retrieving study XML - %s'
TEMPLATE_SAMPLE_INFO = 
' Sample ID: %s, EBI Accession Number: %s'
TEMPLATE_SAMPLE_ERROR = 
'  Error retrieving sample XML - %s'
TEMPLATE_SC =

SC = Sequencescape side

'  SC:  %s=%s'
TEMPLATE_EBI =

EBI = EBI EGA / ENA side

'  EBI: %s=%s'

Instance Method Summary collapse

Constructor Details

#initialize(out = $stdout) ⇒ Process

Initializes a new EBICheck::Process instance.

Parameters:

  • out (IO) (defaults to: $stdout) —

    The output stream for printing results (default: $stdout).



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# File 'lib/ebi_check/process.rb', line 44

def initialize(out = $stdout)
  @out = out
end

Instance Method Details

#samples_by_accession_numbers(sample_numbers) ⇒ void

This method returns an undefined value.

Compares local and remote sample XML data for the given sample accession numbers.

Parameters:

  • sample_numbers (Array<String>) —

    The accession numbers of the samples to check.



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# File 'lib/ebi_check/process.rb', line 115

def samples_by_accession_numbers(sample_numbers)
  sample_ids = Sample::Metadata.where(sample_ebi_accession_number: sample_numbers).pluck(:sample_id)
  samples_by_ids(sample_ids)
end

#samples_by_ids(sample_ids) ⇒ void

This method returns an undefined value.

Compares local and remote sample XML data for the given sample IDs.

Parameters:

  • sample_ids (Array<Integer>) —

    The IDs of the samples to check.



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# File 'lib/ebi_check/process.rb', line 96

def samples_by_ids(sample_ids) # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
  samples = Sample.where(id: sample_ids)
  samples_by_study = samples.group_by { |sample| sample.studies.first }

  samples_by_study.each do |study, samples|
    print_study_info(study)
    samples.each do |sample|
      check_sample(sample)
    rescue StandardError, Faraday::Error => e
      out.puts format(TEMPLATE_SAMPLE_ERROR, e.message)
    end
  rescue Faraday::Error => e
    out.puts format(TEMPLATE_STUDY_ERROR, e.message)
  end
end

#samples_by_study_accession_numbers(study_numbers) ⇒ void

This method returns an undefined value.

Compares local and remote sample XML data for the given study accession numbers.

Parameters:

  • study_numbers (Array<String>) —

    The accession numbers of the studies whose samples to check.



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# File 'lib/ebi_check/process.rb', line 123

def samples_by_study_accession_numbers(study_numbers)
  study_ids = Study::Metadata.where(study_ebi_accession_number: study_numbers).pluck(:study_id)
  samples_by_study_ids(study_ids)
end

#samples_by_study_ids(study_ids) ⇒ void

This method returns an undefined value.

Compares local and remote sample XML data for the given study IDs.

Parameters:

  • study_ids (Array<Integer>) —

    The IDs of the studies whose samples to check.



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# File 'lib/ebi_check/process.rb', line 79

def samples_by_study_ids(study_ids) # rubocop:disable Metrics/MethodLength
  study_ids.each do |study_id|
    study = Study.find_by(id: study_id)
    print_study_info(study)
    study.samples.each do |sample|
      check_sample(sample)
    rescue StandardError, Faraday::Error => e
      out.puts format(TEMPLATE_SAMPLE_ERROR, e.message)
    end
  rescue Faraday::Error => e
    out.puts format(TEMPLATE_STUDY_ERROR, e.message)
  end
end

#studies_by_accession_numbers(study_numbers) ⇒ void

This method returns an undefined value.

Compares local and remote study XML data for the given study accession numbers.

Parameters:

  • study_numbers (Array<String>) —

    The accession numbers of the studies to check.



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# File 'lib/ebi_check/process.rb', line 71

def studies_by_accession_numbers(study_numbers)
  study_ids = Study::Metadata.where(study_ebi_accession_number: study_numbers).pluck(:study_id)
  studies_by_ids(study_ids)
end

#studies_by_ids(study_ids) ⇒ void

This method returns an undefined value.

Compares local and remote study XML data for the given study IDs.

Parameters:

  • study_ids (Array<Integer>) —

    The IDs of the studies to check.



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# File 'lib/ebi_check/process.rb', line 51

def studies_by_ids(study_ids) # rubocop:disable Metrics/MethodLength
  study_ids.each do |study_id|
    study = Study.find_by(id: study_id)
    print_study_info(study)

    xml = local_study_xml(study)
    local = extract_study_fields(xml)

    xml = remote_study_xml(study)
    remote = extract_study_fields(xml)

    print_differences(local, remote)
  rescue Faraday::Error => e
    out.puts format(TEMPLATE_STUDY_ERROR, e.message)
  end
end