Class: Dratools::RunRecordCollector

Inherits:
Object
  • Object
show all
Defined in:
lib/dratools/run_record_collector.rb

Overview

BioProject などの上位レコードから DDBJ sra-run レコードを集める。

Constant Summary collapse

XREF_URL_PATTERN = 
%r{/(?:resource|search/entry)/([^/]+)/([^/?#.]+)}
TRAVERSABLE_XREF_TYPES = 
[
  DdbjRecordFields::SRA_RUN_RESOURCE_TYPE,
  DdbjRecordFields::SRA_EXPERIMENT_RESOURCE_TYPE,
  DdbjRecordFields::SRA_SAMPLE_RESOURCE_TYPE,
  DdbjRecordFields::SRA_STUDY_RESOURCE_TYPE,
  DdbjRecordFields::SRA_SUBMISSION_RESOURCE_TYPE,
  DdbjRecordFields::BIOPROJECT_RESOURCE_TYPE,
  DdbjRecordFields::BIOSAMPLE_RESOURCE_TYPE
].freeze

Instance Method Summary collapse

Constructor Details

#initialize(client:) ⇒ RunRecordCollector

Returns a new instance of RunRecordCollector.



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# File 'lib/dratools/run_record_collector.rb', line 23

def initialize(client:)
  @client = client
end

Instance Method Details

#collect_run_records(ddbj_record, seen_keys = Set.new) ⇒ Object 



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# File 'lib/dratools/run_record_collector.rb', line 27

def collect_run_records(ddbj_record, seen_keys = Set.new)
  explore(ddbj_record, seen_keys: seen_keys).run_records
end

#explore(ddbj_record, seen_keys: Set.new, relation: TraversalNode::ROOT_RELATION, tolerant: false, direct_run_fetch_limit: nil) ⇒ Object 



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# File 'lib/dratools/run_record_collector.rb', line 31

def explore(ddbj_record, seen_keys: Set.new, relation: TraversalNode::ROOT_RELATION,
            tolerant: false, direct_run_fetch_limit: nil)
  node = node_from_record(ddbj_record, relation: relation)
  return node if run_record?(ddbj_record)

  xrefs = ddbj_record.fetch(DdbjRecordFields::DB_XREFS_KEY, [])
  run_xrefs = xrefs.select { |xref| sra_run_xref?(xref) }
  if (lightweight_children = lightweight_direct_run_nodes(run_xrefs, direct_run_fetch_limit))
    node.children.concat(lightweight_children)
    return node
  end

  direct_children = explore_edges(run_xrefs, TraversalNode::DB_XREF_RELATION, seen_keys,
                                  tolerant: tolerant,
                                  direct_run_fetch_limit: direct_run_fetch_limit)
  if direct_children.any? { |child| child.run? || child.run_records.any? }
    node.children.concat(direct_children)
    return node
  end

  recursive_xrefs = xrefs.select { |xref| traversable_xref?(xref) }
  validate_recursive_non_run_xref_count!(ddbj_record, recursive_xrefs)
  db_xref_edges = explore_edges(
    recursive_xrefs,
    TraversalNode::DB_XREF_RELATION,
    seen_keys,
    tolerant: tolerant,
    direct_run_fetch_limit: direct_run_fetch_limit
  )
  child_edges = explore_edges(
    child_bioprojects(ddbj_record),
    TraversalNode::CHILD_BIOPROJECT_RELATION,
    seen_keys,
    tolerant: tolerant,
    direct_run_fetch_limit: direct_run_fetch_limit
  )
  node.children.concat(db_xref_edges + child_edges)
  node
end