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

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
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

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
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

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  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

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
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

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  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

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
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

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end