module SequenceServer
  # Module to contain methods for generating sequence retrieval links.
  module Links
    require 'erb'

    # Provide a method to URL encode _query parameters_. See [1].
    include ERB::Util
    #
    alias_method :encode, :url_encode

    NCBI_ID_PATTERN = /gi\|(\d+)\|/

    # Your custom method should have following pattern:
    #
    # Input
    # -----
    # sequence_id: Array of sequence ids
    #
    # Return
    # ------
    # The return value should be a Hash:
    #
    # {
    #   # Required. Display title.
    #   :title => "title",
    #
    #   # Required. Generated url.
    #   :url => url,
    #
    #   # Optional. Left-right order in which the link should appear.
    #   :order => num,
    #
    #   # Optional. Classes, if any, to apply to the link.
    #   :class => "class1 class2",
    #
    #   # Optional. Class name of a FontAwesome icon to use.
    #   :icon => "fa-icon-class"
    # }
    #
    # If no url could be generated, return nil.
    #
    # Helper methods
    # --------------
    #
    # Following helper methods are available to help with link generation.
    #
    #   encode:
    #     URL encode query params.
    #
    #     Don't use this function to encode the entire URL. Only params.
    #
    #     e.g:
    #         sequence_id = encode sequence_id
    #         url = "http://www.ncbi.nlm.nih.gov/nucleotide/#{sequence_id}"
    #
    #   querydb:
    #     Returns an array of databases that were used for BLASTing.
    #
    #   which_blastdb:
    #     Returns the database from which the given hit came from.
    #
    #     e.g:
    #
    #         hit_database = which_blastdb sequence_id
    #
    # Examples:
    # ---------
    # See methods provided by default for an example implementation.

    def sequence_viewer(sequence_id)
      sequence_id  = encode sequence_id
      database_ids = encode querydb.map(&:id).join(' ')
      url = "get_sequence/?sequence_ids=#{sequence_id}" \
            "&database_ids=#{database_ids}"

      {
        :order => 0,
        :url   => url,
        :title => 'Sequence',
        :class => 'view-sequence',
        :icon  => 'fa-eye'
      }
    end

    def fasta_download(sequence_id)
      sequence_id  = encode sequence_id
      database_ids = encode querydb.map(&:id).join(' ')
      url = "get_sequence/?sequence_ids=#{sequence_id}" \
            "&database_ids=#{database_ids}&download=fasta"

      {
        :order => 1,
        :title => 'FASTA',
        :url   => url,
        :icon  => 'fa-download'
      }
    end

    def ncbi(sequence_id)
      return nil unless sequence_id.match(NCBI_ID_PATTERN)
      ncbi_id = Regexp.last_match[1]
      ncbi_id = encode ncbi_id
      url = "http://www.ncbi.nlm.nih.gov/#{querydb.first.typ}/#{ncbi_id}"
      {
        :order => 2,
        :title => 'View on NCBI',
        :url   => url,
        :icon  => 'fa-external-link'
      }
    end
  end
end

# [1]: https://stackoverflow.com/questions/2824126/whats-the-difference-between-uri-escape-and-cgi-escape