Class: OpenBEL::Nanopub::Nanopub

Inherits:
Object
  • Object
show all
Includes:
Mongo, API
Defined in:
lib/openbel/api/nanopub/mongo.rb

Instance Method Summary collapse

Methods included from API

#update_nanopub_by_query

Constructor Details

#initialize(options = {}) ⇒ Nanopub

Returns a new instance of Nanopub.



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# File 'lib/openbel/api/nanopub/mongo.rb', line 15

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

  @collection      = @db[:nanopub]
  @nanopub_facets = NanopubFacets.new(options)

  # ensure all indexes are created and maintained
  ensure_all_indexes
end

Instance Method Details

#count_nanopub(filters = []) ⇒ Object 



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# File 'lib/openbel/api/nanopub/mongo.rb', line 223

def count_nanopub(filters = [])
  query_hash = to_query(filters)
  @collection.count(:query => query_hash)
end

#create_nanopub(nanopub) ⇒ Object 



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# File 'lib/openbel/api/nanopub/mongo.rb', line 41

def create_nanopub(nanopub)
  # insert nanopub; acknowledge journal
  if nanopub.respond_to?(:each_pair)
    _id = @collection.insert(nanopub, :w => 1, :j => true)

    # remove nanopub_facets after insert to facets
    remove_nanopub_facets(_id)
    _id
  elsif nanopub.respond_to?(:each)
    @collection.insert(nanopub.to_a, :w => 1, :j => true)
  else
    raise "nanopub type #{nanopub.class} cannot be inserted into Mongo."
  end
end

#delete_dataset(identifier) ⇒ Object 



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# File 'lib/openbel/api/nanopub/mongo.rb', line 246

def delete_dataset(identifier)
  @collection.remove(
    { :"_dataset" => identifier },
    :j => true
  )
  @nanopub_facets.delete_all_facets
end

#delete_facets ⇒ Object 



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# File 'lib/openbel/api/nanopub/mongo.rb', line 242

def delete_facets
  @nanopub_facets.delete_all_facets
end

#delete_nanopub(value) ⇒ Object 



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# File 'lib/openbel/api/nanopub/mongo.rb', line 254

def delete_nanopub(value)
  if value.respond_to?(:each)
    value.each do |v|
      delete_nanopub_by_id(v)
    end
  else
    delete_nanopub_by_id(value)
  end
end

#delete_nanopub_by_id(value) ⇒ Object 



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# File 'lib/openbel/api/nanopub/mongo.rb', line 271

def delete_nanopub_by_id(value)
  # convert to ObjectId
  begin
    _id = to_id(value)
  rescue BSON::InvalidObjectId
    # indicate that a delete was unsuccessful
    false
  end

  # remove nanopub_facets before nanopub removal
  remove_nanopub_facets(_id)

  # remove nanopub; returns true
  @collection.remove(
    {
        :_id => _id
    },
    :j => true
  )
end

#delete_nanopub_by_query(query) ⇒ Object 



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# File 'lib/openbel/api/nanopub/mongo.rb', line 264

def delete_nanopub_by_query(query)
  @collection.remove(
    query,
    :j => true
  )
end

#ensure_all_indexes ⇒ Object 



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# File 'lib/openbel/api/nanopub/mongo.rb', line 292

def ensure_all_indexes
  @collection.ensure_index(
    { :bel_statement => Mongo::ASCENDING },
    :background => true
  )
  @collection.ensure_index(
    { :"$**" => Mongo::TEXT },
    :background => true
  )
  @collection.ensure_index(
    { :_dataset => Mongo::ASCENDING },
    :background => true
  )
  @collection.ensure_index(
    { :"experiment_context.name" => Mongo::ASCENDING },
    :background => true
  )
  @collection.ensure_index(
    { :"metadata.name" => Mongo::ASCENDING },
    :background => true
  )
end

#find_all_annotation_references ⇒ Object 



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# File 'lib/openbel/api/nanopub/mongo.rb', line 163

def find_all_annotation_references
  references = @collection.aggregate(
    [
      {
        :$project => {"references.annotations" => 1}
      },
      {
        :$unwind => "$references.annotations"
      },
      {
        :$project => {
          keyword: "$references.annotations.keyword",
          type:    "$references.annotations.type",
          domain:  "$references.annotations.domain"
        }
      },
      {
        :$group => {
          _id: "$keyword",
          type: {
            :$addToSet => "$type"
          },
          domain: {
            :$addToSet => "$domain"
          }
        }
      },
      {
        :$unwind => "$type"
      },
      {
        :$unwind => "$domain"
      },
      {
        :$project => {
          keyword: "$_id", type: "$type", domain: "$domain", _id: 0
        }
      }
    ],
    {
      allowDiskUse: true,
      cursor: {}
    }
  )

  union = []
  remap = {}
  references.each do |obj|
    annotation =
      BELParser::Expression::Model::Annotation.new(
        *obj.values_at('keyword', 'type', 'domain')
      )
    union, new_remap =
      BEL::Nanopub.union_annotation_references(union, [annotation], 'incr')
    remap.merge!(new_remap)
  end

  remap
end

#find_all_namespace_references ⇒ Object 



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# File 'lib/openbel/api/nanopub/mongo.rb', line 96

def find_all_namespace_references
  references = @collection.aggregate(
    [
      {
        :$project => {"references.namespaces" => 1}
      },
      {
        :$unwind => "$references.namespaces"
      },
      {
        :$project => {
          keyword: "$references.namespaces.keyword",
          type:    "$references.namespaces.type",
          domain:  "$references.namespaces.domain"
        }
      },
      {
        :$group => {
          _id: "$keyword",
          type: {
            :$addToSet => "$type"
          },
          domain: {
            :$addToSet => "$domain"
          }
        }
      },
      {
        :$unwind => "$type"
      },
      {
        :$unwind => "$domain"
      },
      {
        :$project => {
          keyword: "$_id", type: "$type", domain: "$domain", _id: 0
        }
      }
    ],
    {
      allowDiskUse: true,
      cursor: {}
    }
  )

  union = []
  remap = {}
  references.each do |obj|
    keyword = obj['keyword']
    type = obj['type']
    domain = obj['domain']
    uri = url = nil
    if type == :url
        url = domain
    elsif type == :uri
        uri = domain
    end
    args = [keyword, uri, url]
    namespace = BELParser::Expression::Model::Namespace.new(*args)
    union, new_remap =
      BEL::Nanopub.union_namespace_references(union, [namespace], 'incr')
    remap.merge!(new_remap)
  end

  remap
end

#find_dataset_nanopub(dataset, filters = [], offset = 0, length = 0, facet = false, facet_value_limit = -1)) ⇒ Object 



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# File 'lib/openbel/api/nanopub/mongo.rb', line 69

def find_dataset_nanopub(dataset, filters = [], offset = 0, length = 0, facet = false, facet_value_limit = -1)
  query_hash = to_query(filters)
  query_hash[:$and] ||= []
  query_hash[:$and].unshift({
    :_dataset => dataset[:identifier]
  })

  query_opts = query_options(
    query_hash,
    :skip  => offset,
    :limit => length,
    :sort  => [
      [:bel_statement, :asc]
    ]
  )

  results = {
    :cursor => @collection.find(query_hash, query_opts)
  }
  if facet
    facets_cursor = @nanopub_facets.find_facets(query_hash, filters, facet_value_limit)
    results[:facets] = facets_cursor.to_a
  end

  results
end

#find_nanopub(filters = [], offset = 0, length = 0, facet = false, facet_value_limit = -1)) ⇒ Object 



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# File 'lib/openbel/api/nanopub/mongo.rb', line 60

def find_nanopub(filters = [], offset = 0, length = 0, facet = false, facet_value_limit = -1)
  if includes_fts_search?(filters)
    text_search = get_fts_search(filters)
    nanopub_aggregate(text_search, filters, offset, length, facet, facet_value_limit)
  else
    nanopub_query(filters, offset, length, facet, facet_value_limit)
  end
end

#find_nanopub_by_id(value) ⇒ Object 



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# File 'lib/openbel/api/nanopub/mongo.rb', line 56

def find_nanopub_by_id(value)
  @collection.find_one(to_id(value))
end

#update_nanopub_by_id(value, nanopub) ⇒ Object 



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# File 'lib/openbel/api/nanopub/mongo.rb', line 228

def update_nanopub_by_id(value, nanopub)
  # add ObjectId to update
  _id = BSON::ObjectId(value)
  nanopub_h = nanopub.to_h
  nanopub_h[:_id] = _id

  # save nanopub; acknowledge journal
  @collection.save(nanopub_h, :j => true)

  # remove nanopub_facets after update to facets
  remove_nanopub_facets(_id)
  nil
end