Module: GraphHelper

Defined in:
app/helpers/graph_helper.rb

Instance Method Summary collapse

Instance Method Details

#biological_association_graph(biological_association, graph: nil, target: nil) ⇒ Object 



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# File 'app/helpers/graph_helper.rb', line 215

def biological_association_graph(biological_association, graph: nil, target: nil)
  b = biological_association
  return nil if b.nil?

  g = initialize_graph(graph, nil, target)

  g.add_node(b.biological_association_subject, citations: false)
  g.add_node(b.biological_association_object, citations: false)

  g.add_edge(b.biological_association_subject, b.biological_association_object, edge_label: b.biological_relationship.name)
  g
end

#citation_graph(citation, graph: nil, target: nil, source: false, citation_object: false, topics: true) ⇒ Object 



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# File 'app/helpers/graph_helper.rb', line 144

def citation_graph(citation, graph: nil, target: nil, source: false, citation_object: false, topics: true)
  c = citation
  return nil if c.nil?

  g = initialize_graph(graph, c, target)

  if source
    source_graph(c.source, graph: g, target: c, authors: true, editors: true)
  end

  if citation_object
    g.add_node(c.citation_object, citations: false, identifiers: true)
    g.add_edge(c, c.citation_object)
  end

  if topics
    c.topics.each do |t|
      g.add(t, c)
    end
  end
  g
end

#collecting_event_graph(collecting_event, graph: nil, target: nil, collection_objects: false) ⇒ Object 



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# File 'app/helpers/graph_helper.rb', line 189

def collecting_event_graph(collecting_event, graph: nil, target: nil, collection_objects: false)
  c = collecting_event
  return nil if c.nil?

  g = initialize_graph(graph, c, target)

  if collection_objects
    c.collection_objects.each do |o|
      collection_object_graph(o, graph: g, target: c, taxon_determinations: true)
    end
  end

  c.collectors.each do |p|
    g.add(p,c)
  end

  c.georeferences.each do |r|
    g.add(r,c)
    r.georeference_authors.each do |p|
      g.add(p,r)
    end
  end

  g
end

#collection_object_graph(collection_object, graph: nil, target: nil, collecting_event: false, taxon_determinations: false, biological_associations: false, images: false) ⇒ Object

Returns Export::Graph.

Returns:

  • Export::Graph



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# File 'app/helpers/graph_helper.rb', line 292

def collection_object_graph(collection_object, graph: nil, target: nil, collecting_event: false, taxon_determinations: false, biological_associations: false, images: false)
  c = collection_object
  return nil if c.nil?

  g = initialize_graph(graph, c, target)

  collecting_event_graph(c.collecting_event, graph: g, target: c)

  if r = c.repository
    g.add(r, c)
  end

  c.biocuration_classes.each do |b|
    g.add(b, c)
  end

  c.observations.each do |o|
    g.add(o, c)
  end

  if images
    c.images.each do |i|
      image_graph(i, graph: g, target: c)
    end
  end

  if taxon_determinations
    c.taxon_determinations.each do |d|
      taxon_determination_graph(d, graph: g, target: c, taxon_names: true)
    end
  end

  if biological_associations
    c.all_biological_associations.each do |b|
      g.add_node(b.biological_association_subject)
      g.add_node(b.biological_association_object)
      g.add_node(b.biological_relationship)

      g.add_edge(b.biological_relationship, b.biological_association_subject)
      g.add_edge(b.biological_relationship, b.biological_association_object)
    end
  end

  g
end

#depiction_graph(depiction, graph: nil, target: nil) ⇒ Object 



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# File 'app/helpers/graph_helper.rb', line 130

def depiction_graph(depiction, graph: nil, target: nil)
  d = depiction
  return nil if d.nil?

  g = initialize_graph(graph, d, target)

  o = d.depiction_object
  g.add_node(o)
  g.add_edge(d, o)

  g
end

#image_graph(image, graph: nil, target: nil, depictions: false, citations: false, copyright_holders: true) ⇒ Object 



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# File 'app/helpers/graph_helper.rb', line 109

def image_graph(image, graph: nil, target: nil, depictions: false, citations: false, copyright_holders: true)
  i = image
  return nil if i.nil?

  g = initialize_graph(graph, i, target)

  if depictions
    i.depictions.each do |d|
      depiction_graph(d, graph: g, target: i)
    end
  end

  if citations
    i.citations.where(project_id: sessions_current_project_id).each do |c|
      citation_graph(c, graph: g, target: i, citation_object: true, topics: true)
    end
  end

  g
end

#initialize_graph(graph, object, target) ⇒ Object (private) 



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# File 'app/helpers/graph_helper.rb', line 375

def initialize_graph(graph, object, target)
  g = graph
  if g.nil?
    g = Export::Graph.new(object:)
  else
    g.add(object, target)
  end
  g
end

#object_graph(object) ⇒ Object 



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# File 'app/helpers/graph_helper.rb', line 20

def object_graph(object)
  return nil if object.nil?

  case object.class.base_class.name
  when 'CollectionObject'
    collection_object_graph(object, collecting_event: true, taxon_determinations: true, biological_associations: true, images: true).to_json
  when 'CollectingEvent'
    collecting_event_graph(object, collection_objects: true).to_json
  when 'TaxonName'
    taxon_name_graph(object, children: true, parents: true, otus: true, synonymy: true).to_json
  when 'Otu'
    otu_graph(object, collection_objects: true, taxon_name: true, synonymy: true, biological_associations: true, asserted_distributions: true).to_json
  when 'TaxonDetermination'
    taxon_determination_graph(object, collection_object: true, taxon_names: true).to_json
  when 'Person'
    person_graph(object).to_json
  when 'Citation'
    citation_graph(object, source: true, citation_object: true, topics: true).to_json
  when 'Source'
    source_graph(object, citations: true, authors: true, editors: true).to_json
  when 'Image'
    image_graph(object, citations: true, depictions: true).to_json
  when 'BiologicalAssociation'
    biological_association_graph(object).to_json
  else
    g = Export::Graph.new( object: )
    g.to_json
  end
end

#object_graph2(object) ⇒ Object 



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# File 'app/helpers/graph_helper.rb', line 50

def object_graph2(object)
  return nil if object.nil?

  case object.class.base_class.name
  when 'CollectionObject'
    collection_object_graph(object, collecting_event: true, taxon_determinations: true, biological_associations: true, images: true).to_json
  when 'CollectingEvent'
    collecting_event_graph(object, collection_objects: true).to_json
  when 'TaxonName'
    taxon_name_graph(object, children: true, parents: true, otus: true, synonymy: true).to_json
  when 'Otu'
    otu_graph(object, collection_objects: true, taxon_name: true, synonymy: true, biological_associations: true, asserted_distributions: true).to_json
  when 'TaxonDetermination'
    taxon_determination_graph(object, collection_object: true, taxon_names: true).to_json
  when 'Person'
    person_graph(object).to_json
  when 'Citation'
    citation_graph(object, source: true, citation_object: true, topics: true).to_json
  when 'Source'
    source_graph(object, citations: true, authors: true, editors: true).to_json
  when 'Image'
    image_graph(object, citations: true, depictions: true).to_json
  else
    g = Export::Graph.new( object: )
    g.to_json
  end
end

#objects_graph(object_scope) ⇒ Object 



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# File 'app/helpers/graph_helper.rb', line 3

def objects_graph(object_scope)
  g = initialize_graph(nil, nil, nil)

  object_scope.each do |o|

    case o.class.base_class.name
    when 'BiologicalAssociation'
      biological_association_graph(o, graph: g)
    else
      next
    end
  end

  g
end

#otu_graph(otu, graph: nil, target: nil, collection_objects: false, taxon_name: true, synonymy: false, biological_associations: true, asserted_distributions: true) ⇒ Object 



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# File 'app/helpers/graph_helper.rb', line 228

def otu_graph(otu, graph: nil, target: nil, collection_objects: false, taxon_name: true, synonymy: false, biological_associations: true, asserted_distributions: true )
  o = otu
  return nil if o.nil?
  g = initialize_graph(graph, o, target)

  if taxon_name
    taxon_name_graph(o.taxon_name, graph: g, target: o, synonymy:, parents: true)
  end

  if collection_objects
    o.collection_objects.each do |co|
      collection_object_graph(co, graph: g, target: o, collecting_event: true)
    end
  end

  if biological_associations
    o.all_biological_associations.each do |b|
      g.add_node(b.biological_association_subject)
      g.add_node(b.biological_association_object)
      g.add_node(b.biological_relationship)

      g.add_edge(b.biological_relationship, b.biological_association_subject)
      g.add_edge(b.biological_relationship, b.biological_association_object)
    end
  end

  if asserted_distributions
    o.asserted_distributions.each do |a|

      g.add_node(a)
      g.add_node(a.geographic_area)

      g.add_edge(a, a.geographic_area)
    end
  end

  g
end

#person_graph(person, graph: nil, target: nil) ⇒ Object 



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# File 'app/helpers/graph_helper.rb', line 167

def person_graph(person, graph: nil, target: nil)
  p = person
  return nil if p.nil?

  g = initialize_graph(graph, p, target)

  # TODO: Loop has_many
  [:authored_sources, :edited_sources, :human_sources].each do |m|
    p.send(m).each do |o|
      g.add(o, p)
    end
  end

  [ :collecting_events, :taxon_determinations, :authored_taxon_names, :georeferences, :collection_objects, :dwc_occurrences].each do |m|
    p.send(m).where(project_id: sessions_current_project_id).each do |o|
      g.add(o,p)
    end
  end

  g
end

#source_graph(source, graph: nil, target: nil, citations: false, authors: false, editors: false) ⇒ Object 



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# File 'app/helpers/graph_helper.rb', line 78

def source_graph(source, graph: nil, target: nil, citations: false, authors: false, editors: false)
  s = source
  return nil if s.nil?

  g = initialize_graph(graph, nil, nil)

  # We can't auto-cite, so .add can not be used
  g.add_node(s, citations: false, identifiers: true)
  g.add_edge(target, s)

  if authors && s.respond_to?(:authors)
    s.authors.each do |p|
      g.add(p, s)
    end
  end

  if editors && s.respond_to?(:editors)
    s.editors.each do |p|
      g.add(p, s)
    end
  end

  if citations
    s.citations.where(project_id: sessions_current_project_id).each do |c|
      citation_graph(c, graph: g, target: s, citation_object: true, topics: true)
    end
  end

  g
end

#taxon_determination_graph(taxon_determination, graph: nil, target: nil, collection_object: false, taxon_names: false) ⇒ Object 



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# File 'app/helpers/graph_helper.rb', line 267

def taxon_determination_graph(taxon_determination, graph: nil, target: nil, collection_object: false, taxon_names: false)
  td = taxon_determination
  return nil if td.nil?
  g = initialize_graph(graph, td, target)

  g.add(td.otu, td)

  if collection_object
    g.add(td.biological_collection_object, td)
  end

  if taxon_names
    if td.otu.taxon_name
      taxon_name_graph(td.otu.taxon_name, graph: g, target: td.otu, parents: true)
    end
  end

  td.determiners.each do |p|
    g.add(p, td)
  end

  g
end

#taxon_name_graph(taxon_name, graph: nil, target: nil, synonymy: false, children: false, otus: false, parents: false) ⇒ Object 



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# File 'app/helpers/graph_helper.rb', line 338

def taxon_name_graph(taxon_name, graph: nil, target: nil, synonymy: false, children: false, otus: false, parents: false)
  t = taxon_name
  return nil if t.nil?

  g = initialize_graph(graph, t, target)

  t.taxon_name_authors.each do |p|
    g.add(p, t)
  end

  if children
    t.children.each do |n|
      taxon_name_graph(n, target: t, graph: g)
    end
  end

  if synonymy
    t.synonyms.each do |n|
      taxon_name_graph(n, target: t, graph: g)
    end
  end

  if otus
    t.otus.each do |o|
      otu_graph(o, target: t, graph: g)
    end
  end

  if parents
    taxon_name_graph(t.parent, graph: g, target: t, parents:)
  end

  g
end