Class: OpenBEL::Nanopub::NanopubFacets

Inherits:
Object
  • Object
show all
Includes:
Mongo, Helpers::UUIDGenerator, FacetAPI, FacetFilter
Defined in:
lib/openbel/api/nanopub/mongo_facet.rb

Constant Summary

Constants included from FacetFilter

FacetFilter::EMPTY, FacetFilter::NANOPUB_PARTS

Instance Method Summary collapse

Methods included from FacetFilter

#make_filter, #map_citation_facets, #map_experiment_context_facets, #map_metadata_facets, #map_nanopub_facets

Methods included from FacetAPI

#create_facets, #find_facets_by_filters, #remove_facets_by_filters

Constructor Details

#initialize(options = {}) ⇒ NanopubFacets

Returns a new instance of NanopubFacets.



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# File 'lib/openbel/api/nanopub/mongo_facet.rb', line 16

def initialize(options = {})
  host = options[:host]
  port = options[:port]
  db   = options[:database]
  @db  = MongoClient.new(
    host,
    port,
    :op_timeout => nil,
    :pool_size  => 30
  ).db(db)

  # Authenticate user if provided.
  username = options[:username]
  password = options[:password]
  if username && password
    auth_db = options[:authentication_database] || db
    @db.authenticate(username, password, nil, auth_db)
  end

  @nanopub             = @db[:nanopub]
  @nanopub_facet_cache = @db[:nanopub_facet_cache]

  # ensure all indexes are created and maintained
  ensure_all_indexes
end

Instance Method Details

#delete_all_facets ⇒ Object 



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# File 'lib/openbel/api/nanopub/mongo_facet.rb', line 99

def delete_all_facets
  @nanopub_facet_cache.find(
    {},
    :fields => {:_id => 0, :cache_collection => 1}
  ).each do |doc|
    cache_collection = doc['cache_collection']
    @db[cache_collection].drop()
  end

  # remove all entries in nanopub_facet_cache
  @nanopub_facet_cache.remove({})
end

#delete_facets(facets) ⇒ Object 



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# File 'lib/openbel/api/nanopub/mongo_facet.rb', line 81

def delete_facets(facets)
  # Add zero-filter to facets; clears the default search
  facets = facets.to_a
  facets.unshift([])

  # Drop facet cache collections
  @nanopub_facet_cache.find(
    {:filters => {:$in => facets}},
    :fields => {:_id => 0, :cache_collection => 1}
  ).each do |doc|
    cache_collection = doc['cache_collection']
    @db[cache_collection].drop()
  end

  # remove filter match entries in nanopub_facet_cache
  @nanopub_facet_cache.remove({:filters => {:$in => facets}})
end

#ensure_all_indexes ⇒ Object 



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# File 'lib/openbel/api/nanopub/mongo_facet.rb', line 112

def ensure_all_indexes
  @nanopub_facet_cache.ensure_index([
      [:"filters.category",   Mongo::ASCENDING],
      [:"filters.name",       Mongo::ASCENDING]
    ],
    :background => true
  )
end

#find_facets(query, filters, facet_value_limit = -1)) ⇒ Object 



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# File 'lib/openbel/api/nanopub/mongo_facet.rb', line 42

def find_facets(query, filters, facet_value_limit = -1)
  sorted_filters = sort_filters(filters)
  cache_collection = facet_cache_collection(sorted_filters)

  if no_collection?(cache_collection)
    cache_collection = "nanopub_facet_cache_#{generate_uuid}"
    create_aggr      = create_aggregation(cache_collection, query)
    @nanopub.aggregate(create_aggr[:pipeline], create_aggr[:options])
    @nanopub_facet_cache.insert({
      :filters          => sorted_filters,
      :cache_collection => cache_collection
    })
  end

  # set up field projection based on value limit
  field_projection = {
    :_id      => 0,
    :category => 1,
    :name     => 1,
    :values   => 1
  }
  if facet_value_limit > 0
    field_projection[:values] = {:$slice => facet_value_limit}
  end

  # cursor facets and apply "filter"
  @db[cache_collection].find({}, :fields => field_projection).map { |facet_doc|
    category, name     = facet_doc.values_at('category', 'name')
    facet_doc['values'].each do |value|
      value[:filter] = MultiJson.dump({
        :category => category,
        :name     => name,
        :value    => value['value']
      })
    end
    facet_doc
  }
end