Hi,

I am having problems with integrating sequenceserver (v. 1.14) that I am using on apache server with my own jbrowse on the same apache server. I did all (it seems so at least) what is written here .

Still - no links! Obviously, I am missing something basic here and will be very glad for your help!!!! I am not an expert (to say the least) in ruby. Here is my links.rb file -

Hope I will find my mistake here... THANKS!

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+)\|/
    UNIPROT_ID_PATTERN = /sp\|(\w+)\|/
    require 'json'
    # Link generators return a Hash like below.
    #
    # {
    #   # 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.
    #
    #   whichdb:
    #     Returns the database from which the given hit came from.
    #
    #     e.g:
    #
    #         hit_database = whichdb
    #
    # Examples:
    # ---------
    # See methods provided by default for an example implementation.

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

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

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

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

    def ncbi
      return nil unless 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.type}/#{ncbi_id}"
      {
        :order => 2,
        :title => 'NCBI',
        :url   => url,
        :icon  => 'fa-external-link'
      }
    end

    def uniprot
      return nil unless id.match(UNIPROT_ID_PATTERN)
      uniprot_id = Regexp.last_match[1]
      uniprot_id = encode uniprot_id
      url = "http://www.uniprot.org/uniprot/#{uniprot_id}"
      {
        :order => 2,
        :title => 'Uniprot',
        :url   => url,
        :icon  => 'fa-external-link'
      }
    end

    def jbrowse
           qstart = hsps.map(&:qstart).min
           sstart = hsps.map(&:sstart).min
           qend = hsps.map(&:qend).max
           send = hsps.map(&:send).max
           first_hit_start = hsps.map(&:sstart).at(0)
           first_hit_end = hsps.map(&:send).at(0)
           my_features = ERB::Util.url_encode(JSON.generate([{
               :seq_id => accession,
               :start => sstart,
               :end => send,
               :type => "match",
               :subfeatures =>  hsps.map {
                 |hsp| {
                   :start => hsp.send < hsp.sstart ? hsp.send : hsp.sstart,
                   :end => hsp.send < hsp.sstart ? hsp.sstart : hsp.send,
                   :type => "match_part"
                 } 
               }
           }]))
           my_track = ERB::Util.url_encode(JSON.generate([
                {
                   :label => "BLAST",
                   :key => "BLAST hits",
                   :type => "JBrowse/View/Track/CanvasFeatures",
                   :store => "url",
                   :glyph => "JBrowse/View/FeatureGlyph/Segments"
                }
           ]))
           url = "<http://http://mysite/pomegranate/>" \
                        "?loc=#{accession}:#{first_hit_start-500}..#{first_hit_start+500}" \
                        "&addFeatures=#{my_features}" \
                        "&addTracks=#{my_track}" \
                        "&tracks=BLAST" \
                        "&highlight=#{accession}:#{first_hit_start}..#{first_hit_end}"
           {
             :order => 2,
             :title => 'JBrowse',
             :url   => url,
             :icon  => 'fa-external-link'
           }
    end
  end
end

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