class PubliSciServer

# File lib/publisci/helpers.rb, line 14
def self.configure_server(opts)
  set :port, opts[:port].to_i if opts[:port]
  set :bind, opts[:bind] if opts[:bind]
  if opts[:type]
    if opts[:type] == "fourstore"
      uri = opts[:uri] || 'http://localhost:80802'
      set :repository, RDF::FourStore::Repository.new(uri.dup)
    else
      set :repository, RDF::Repository.new
    end
  else
    set :repository, RDF::Repository.new
  end
end

# File lib/publisci/helpers.rb, line 123
def clear_repository
  repo = settings.repository
  if repo.is_a? RDF::FourStore::Repository
  passwd = settings.sudo_pass
  raise "need sudo password set to clear 4store" unless passwd
  `echo #{passwd} | sudo -S killall 4s-backend`
  `echo #{passwd} | sudo -S killall 4s-httpd`
  `echo #{passwd} | sudo -S 4s-backend-setup test`
  `echo #{passwd} | sudo -S 4s-backend test`
  `echo #{passwd} | sudo -S 4s-httpd -U test`

  else
    repo.clear
  end
end

# File lib/publisci/helpers.rb, line 42
def content_for(data,fallback=:to_html,format=(params[:format] || request.accept))
  if params[:format]
    format = CONTENT_TYPES[format]
  else
    format = format.first
  end
  if CONTENT_TYPES.values.include? format
    content_type format #, :charset => 'utf-8'
  end

  case format.to_s
  when 'text/xml'
    data.to_xml
  when 'application/json'
    data.to_json
  else
    if data.respond_to? fallback
      data.send(fallback)
    else
      data.to_s
    end
  end
end

# File lib/publisci/helpers.rb, line 94
def content_response(html_resp,content=:no_content)
  if !CONTENT_TYPES.keys.include?(params[:format].to_s) and request.accept? 'text/html'
    if html_resp.is_a? Symbol
      haml html_resp
    else
      html_resp
    end
  else
    content
  end
end

# File lib/publisci/helpers.rb, line 106
def create_repository(type,uri)
  if type == "in_memory"
    flash[:notice] = "#{type} repository created!"
    RDF::Repository.new
  elsif type == "4store"
    unless RDF::URI(uri).valid?
      flash[:notice] = "Need a valid URI for a FourStore repository"
      nil
    end

    flash[:notice] = "#{type} repository created!"
    RDF::FourStore::Repository.new(uri)
  else
    raise "UnkownTypeForSomeReason?: #{type}"
  end
end

# File lib/publisci/helpers.rb, line 139
    def default_prefixes
      <<-EOF
PREFIX qb:    <http://purl.org/linked-data/cube#>
PREFIX rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs:  <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl:   <http://www.w3.org/2002/07/owl#>
PREFIX skos:  <http://www.w3.org/2004/02/skos/core#>

      EOF
    end

# File lib/publisci/helpers.rb, line 159
    def example_dsl
      <<-EOF
data do
  object "https://raw.github.com/wstrinz/bioruby-publisci/master/spec/csv/bacon.csv"

  object "https://raw.github.com/wstrinz/bioruby-publisci/master/resources/weather.numeric.arff"
end
      EOF
    end

# File lib/publisci/helpers.rb, line 150
    def example_query
      default_prefixes +
      <<-EOF
SELECT * WHERE {
  ?s ?p ?o
} LIMIT 10
      EOF
    end

# File lib/publisci/helpers.rb, line 9
def format_ttl(str)
  #TODO make this actually work right
  str.gsub("\n","\n<br>").gsub('<br>     ','<br>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ').gsub('<br>   ','<br>&nbsp; &nbsp; &nbsp; ')
end

# File lib/publisci/helpers.rb, line 5
def h(str)
  CGI::escapeHTML(str.to_s)
end

# File lib/publisci/helpers.rb, line 180
def import_rdf(input,type)
  if input.is_a?(File) || input.is_a?(Tempfile)
    f = Tempfile.new(['',".#{type}"])
    begin
      f.write(input.read)
      f.close
      oldsize = settings.repository.size
      settings.repository.load(f.path, format: type)
    ensure
      f.unlink
    end
    "#{settings.repository.size - oldsize} triples imported"
  else
    oldsize = settings.repository.size
    read = RDF::Reader.for(type.to_sym)
    read = read.new(input)
    settings.repository << read
    "#{settings.repository.size - oldsize} triples imported"
  end
end

# File lib/publisci/helpers.rb, line 169
def load_dsl(script)
  ev = PubliSci::DSL::Instance.new
  begin
    ev.instance_eval(script)
  rescue Exception => e
    raise "Caught error in eval #{e} #{e.backtrace}"
  end

  import_rdf(ev.instance_eval("generate_n3"),:ttl)
end

# File lib/publisci/helpers.rb, line 29
    def print_usage
      str = puts <<-EOF
Bio-PubliSci Server Interface

Description: Start the server and point your browser to localhost:4567

Usage: bio-publisci-server [options]

      EOF
    end

# File lib/publisci/helpers.rb, line 201
def query_repository(query,format_result = true)
  repo = settings.repository
  if repo.is_a? RDF::FourStore::Repository
    sols = SPARQL::Client.new("#{settings.repository.uri}/sparql/").query(query)
  elsif repo.is_a? RDF::Repository
    sols = SPARQL::Client.new(settings.repository).query(query)
  else
    raise "Unrecognized Repository: #{settings.repository.class}"
  end

 sols

end

# File lib/publisci/helpers.rb, line 66
def rdf_content_for(data,fallback=:to_html,format=(params[:format] || request.accept))
  if params[:format]
    format = CONTENT_TYPES[format]
  else
    format = format.first
  end
  if CONTENT_TYPES.values.include? format
    content_type format #, :charset => 'utf-8'
  end

  case format.to_s
  when 'text/xml'
    data.to_rdfxml
  when 'application/rdf+xml'
    data.to_rdfxml
  when 'application/json'
    data.dump(:jsonld, :standard_prefixes => true)
  when 'text/n3'
    data.to_ttl
  else
    if data.respond_to? fallback
      data.send(fallback)
    else
      data.to_s
    end
  end
end