bioroebe 0.10.80

data/lib/bioroebe/www/embeddable_interface.rb

@@ -0,0 +1,686 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::EmbeddableInterface
+# =========================================================================== #
+# require 'bioroebe/www/embeddable_interface.rb'
+# include Bioroebe::EmbeddableInterface
+# =========================================================================== #
+module Bioroebe
+
+module EmbeddableInterface
+
+  require 'bioroebe/sequence/reverse_complement.rb'
+  require 'bioroebe/toplevel_methods/chunked_display.rb'
+  require 'bioroebe/toplevel_methods/is_on_roebe.rb'
+  require 'bioroebe/toplevel_methods/nucleotides.rb'
+  require 'bioroebe/toplevel_methods/shuffleseq.rb'
+  require 'bioroebe/toplevel_methods/return_source_code_of_this_method.rb'
+  require 'bioroebe/toplevel_methods/verbose.rb'
+  require 'bioroebe/utility_scripts/mirror_repeat.rb'
+  require 'bioroebe/utility_scripts/compseq/compseq.rb'
+  require 'bioroebe/aminoacids/create_random_aminoacids.rb'
+  require 'bioroebe/sequence/dna.rb'
+  require 'bioroebe/sequence/reverse_complement.rb'
+  require 'bioroebe/palindromes/palindrome_generator.rb'
+  require 'bioroebe/codons/codons.rb'
+  require 'bioroebe/blosum/blosum.rb'
+  require 'bioroebe/parsers/blosum_parser.rb'
+
+  require 'bioroebe/colours/colours.rb'
+  include Colours
+  include Colours::E
+
+  # ========================================================================= #
+  # === USE_THIS_PORT
+  # ========================================================================= #
+  if ENV['SINATRA_PORT']
+    USE_THIS_PORT = ENV['SINATRA_PORT'].to_s.dup
+  else
+    USE_THIS_PORT = '4567'
+  end
+
+  # ========================================================================= #
+  # Bioroebe.disable_colours
+  # ^^^ Unsure why were were using this. As of 21.06.2021 this is
+  #     commented out; if we re-enable it, we should explain why.
+  #     Otherwise this will probably removed in the long run.
+  # ========================================================================= #
+
+  begin
+    require 'cyberweb/toplevel_methods/misc.rb'
+  rescue LoadError; end
+
+  begin
+    require 'cyberweb/html_template/html_template.rb'
+  rescue LoadError; end
+
+  begin
+    require 'html_tags'
+    # include HtmlTags
+  rescue LoadError; end
+
+  begin
+    require 'cyberweb/sinatra/custom_extensions.rb'
+    include Cyberweb::Sinatra::CustomExtensions
+  rescue LoadError; end
+
+  # ========================================================================= #
+  # === CSS_STYLE_FOR_THE_FORMS
+  # ========================================================================= #
+  CSS_STYLE_FOR_THE_FORMS =
+    'style="margin-left:2em; margin-top:2px"'
+
+  # ========================================================================= #
+  # === ARRAY_FOR_PALINDROMES 
+  # ========================================================================= #
+  ARRAY_FOR_PALINDROMES = %w(
+    /palindromes
+  )
+
+  # ========================================================================= #
+  # === ARRAY_FOR_CHUNKED_DISPLAY
+  #
+  # List the APIs for displaying a chunked display of the DNA sequence
+  # at hand. 
+  # ========================================================================= #
+  ARRAY_FOR_CHUNKED_DISPLAY = %w(
+    /to_chunked
+    /chunked_display
+    /chunked
+  )
+
+  # ========================================================================= #
+  # === ARRAY_FOR_TO_AMINOACIDS_CONVERSION
+  # ========================================================================= #
+  ARRAY_FOR_TO_AMINOACIDS_CONVERSION = %w(
+    /to_aa /to_aminoacids
+  )
+
+  # ========================================================================= #
+  # === Bioroebe::EmbeddableInterface.routes?
+  #
+  # Define all legal routes via this Array. This Array will then be used
+  # to add more routes to any sinatra-application that needs it.
+  # ========================================================================= #
+  def self.routes?
+    [
+      'to_rna',
+      'to_rna/*',
+      'to_dna',
+      'to_dna/*',
+      'to_chunked',
+      'to_chunked/*',
+      ARRAY_FOR_PALINDROMES.first,
+      ARRAY_FOR_PALINDROMES.first+'/*'
+    ]
+  end
+
+  # ========================================================================= #
+  # === ARRAY_AVAILABLE_TOPLEVEL_ACTIONS_FOR_THE_SINATRA_INTERFACE
+  #
+  # This Array contains the actionable links for the sinatra-interface
+  # of the BioRoebe project.
+  # ========================================================================= #
+  ARRAY_AVAILABLE_TOPLEVEL_ACTIONS_FOR_THE_SINATRA_INTERFACE = %w(
+    /blosum
+    /compseq
+    /is_palindrome
+    /n_stop_codons_in_this_sequence
+    /to_aa
+    /to_chunked
+    /to_dna
+    /random_aminoacids
+    /reverse_complement
+    /mirror
+    /palindromes
+    /shuffleseq
+    /view
+  )
+
+  # ========================================================================= #
+  # === INPUT_TYPE_TEXT_AND_BR_TAG
+  # ========================================================================= #
+  INPUT_TYPE_TEXT_AND_BR_TAG =
+    '<input type="text" value="" autocomplete="off" name="user_input" '\
+    'style="border:3px solid slateblue; padding: 4px; width: 250px"><br>'
+
+  # =========================================================================== #
+  # === return_intro_for_n_stop_codons_in_this_sequence
+  # =========================================================================== #
+  def return_intro_for_n_stop_codons_in_this_sequence
+    HtmlTags.h1(
+      '(<b>6</b>) n stop codons in this sequence',
+      css_style: 'margin-left:0.25em;'
+    )
+  end
+
+  # ========================================================================= #
+  # === return_form_for_n_stop_codons_in_this_sequence
+  # ========================================================================= #
+  def return_form_for_n_stop_codons_in_this_sequence(
+      route_to_this_action = '/n_stop_codons_in_this_sequence/'
+    )
+    '<form id="'+route_to_this_action.delete('/')+'" '+
+     CSS_STYLE_FOR_THE_FORMS+' action="'+route_to_this_action+'">'+
+     INPUT_TYPE_TEXT_AND_BR_TAG+
+     return_default_submit_button+'
+     </form>'
+  end
+
+  # ========================================================================= #
+  # === erev
+  # ========================================================================= #
+  def erev(i = '')
+    ::Bioroebe.erev(i)
+  end
+
+  # =========================================================================== #
+  # === return_intro_for_reverse_complement_conversion
+  # =========================================================================== #
+  def return_intro_for_reverse_complement_conversion
+    HtmlTags.h1(
+      '(<b>5</b>) Reverse complement a DNA sequence',
+      css_style: 'margin-left:0.25em;'
+    )
+  end
+
+  # ========================================================================= #
+  # === method_reverse_complement
+  # ========================================================================= #
+  def method_reverse_complement
+    return_intro_for_reverse_complement_conversion+
+    HtmlTags.p(
+      'You can reverse complement a DNA sequence through this API.'
+    )+
+    HtmlTags.p(
+      'Simply input the nucleotide String, such as "ATGCT", '\
+      'without the "" quotes.'
+    )+
+    return_form_for_reverse_complement_action+
+    hyperlink_paragraph
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::EmbeddableInterface.localhost_to_use?
+  # ========================================================================= #
+  def self.localhost_to_use?
+    "http://localhost:#{USE_THIS_PORT}/"
+  end
+
+  # ========================================================================= #
+  # === return_form_for_reverse_complement_action
+  # ========================================================================= #
+  def return_form_for_reverse_complement_action(
+      route_to_this_action = '/reverse_complement/'
+    )
+    '<form id="reverse_complement" '+CSS_STYLE_FOR_THE_FORMS+' action="'+route_to_this_action+'">'+
+     INPUT_TYPE_TEXT_AND_BR_TAG+
+     return_default_submit_button+'
+     </form>'
+  end
+
+  # ========================================================================= #
+  # === return_sinatra_to_dna
+  #
+  # This is: http://localhost:4567/to_dna
+  # ========================================================================= #
+  def return_sinatra_to_dna
+    if Object.const_defined?(:Roebe) and Roebe.const_defined?(:Controller)
+      _ = return_intro_for_to_dna_conversion('')
+    else
+      _ = return_intro_for_to_dna_conversion
+    end
+    Cyberweb::HtmlTemplate[
+      title: 'Convert to DNA',
+      body:  _+
+      HtmlTags.p(
+        'You can "convert" a RNA sequence into DNA through this API.'
+      )+
+      HtmlTags.p(
+        'Simply input the nucleotide String, such as "ATGCT", '\
+        'without the "" quotes.'
+      )+
+      return_form_for_to_dna_action+
+      hyperlink_paragraph
+    ].to_s
+  end
+
+  # ========================================================================= #
+  # === title?
+  # ========================================================================= #
+  def title?
+    'BioRoebe Web-API'
+  end
+
+  # ========================================================================= #
+  # === return_form_for_compseq_action
+  # ========================================================================= #
+  def return_form_for_compseq_action(
+      route_to_this_action = '/compseq/'
+    )
+    '<form id="compseq" '+CSS_STYLE_FOR_THE_FORMS+' action="'+route_to_this_action+'">'+
+     INPUT_TYPE_TEXT_AND_BR_TAG+
+     return_default_submit_button+'
+     </form>'
+  end
+
+  # ========================================================================= #
+  # === return_form_for_blosum_action
+  # ========================================================================= #
+  def return_form_for_blosum_action(
+      route_to_this_action = '/blosum/'
+    )
+    '<form id="blosum" autocomplete="off" '+CSS_STYLE_FOR_THE_FORMS+' action="'+route_to_this_action+'">'+
+     INPUT_TYPE_TEXT_AND_BR_TAG+
+     return_default_submit_button+'
+     </form>'
+  end
+
+  # ========================================================================= #
+  # === return_default_submit_button
+  # ========================================================================= #
+  def return_default_submit_button
+    '<input type="submit" name="user_input_submit" value="Submit" style="3px dotted royalblue; '\
+    'color: white; background-color: olive; font-size: 1.25em; margin:3px; padding: 4px">'
+  end
+
+  # ========================================================================= #
+  # === return_form_for_to_dna_action
+  #
+  # This method will show the <form> for the DNA-input action.
+  # ========================================================================= #
+  def return_form_for_to_dna_action(
+      route_to_this_action = '/to_dna/*'
+    )
+    '<form id="to_dna" autocomplete="off" '+CSS_STYLE_FOR_THE_FORMS+
+    ' action="'+route_to_this_action+'"'+
+    ' method="post">'+
+     INPUT_TYPE_TEXT_AND_BR_TAG+
+     return_default_submit_button+'
+     </form>'
+  end
+
+  # ========================================================================= #
+  # === return_index_of_hyperlinks
+  #
+  # This method will bundle together the different indices containing the
+  # hyperlinks that will be shown on the root-directory.
+  # ========================================================================= #
+  def return_index_of_hyperlinks
+    use_this_uniform_css_style = 
+      'margin-left: 2.0em; font-weight: bold; font-size: larger'
+    result = ''.dup
+    ARRAY_AVAILABLE_TOPLEVEL_ACTIONS_FOR_THE_SINATRA_INTERFACE.each {|entry|
+      result <<
+        HtmlTags.a(
+          entry, css_style: use_this_uniform_css_style
+        )+
+        '<br>'
+    }
+    result
+  end; alias return_the_hyperlinks return_index_of_hyperlinks # === return_the_hyperlinks
+
+  # ========================================================================= #
+  # === return_sinatra_to_rna_with_arguments
+  #
+  # Usage example:
+  #
+  #   http://localhost:4567/to_rna/CAGCATCTAGTCATAGTCGATGCATGCTAGTCACA
+  #
+  # ========================================================================= #
+  def return_sinatra_to_rna_with_arguments(
+      i = web_params_as_string?
+    )
+    i = i.dup if i.frozen?
+    _ = ''.dup
+    converted = Bioroebe.to_rna(i)
+    _ << HtmlTags.bold(converted)+' ('+converted.size.to_s+' nucleotides)<br>'
+    return _
+  end
+
+  # ========================================================================= #
+  # === return_sinatra_to_dna_with_arguments
+  #
+  # Usage example:
+  #
+  #   http://localhost:4567/to_dna/UGAUCGUACUGCAUGACUGAUGGUACUGACCA
+  #
+  # ========================================================================= #
+  def return_sinatra_to_dna_with_arguments(
+      i = web_params_as_string?
+    )
+    i = i.dup if i.frozen?
+    _ = ''.dup
+    converted = Bioroebe.to_dna(i.to_s)
+    _ << HtmlTags.bold(converted)+
+         ' ('+converted.size.to_s+' nucleotides)<br>'
+    return _
+  end
+
+  # ========================================================================= #
+  # === return_sinatra_to_chunked
+  #
+  # This is: http://localhost:4567/to_chunked
+  # ========================================================================= #
+  def return_sinatra_to_chunked
+    Cyberweb::HtmlTemplate[
+      title: 'Chunked display',
+      body:  'This will display in a chunked manner..<br><br>'
+    ].to_s
+  end
+
+  # ========================================================================= #
+  # === method_shuffleseq
+  # ========================================================================= #
+  def method_shuffleseq
+    Cyberweb::HtmlTemplate[
+      title: 'Shuffleseq',
+      body:  return_intro_for_shuffleseq+
+        HtmlTags.p(
+          'You can shuffle-seq (randomize) a DNA sequence through this API.'
+        )+
+        HtmlTags.p(
+          'Simply input the nucleotide String, such as "ATGCT", '\
+          'without the "" quotes.'
+        )+
+        return_form_for_shuffleseq_action+
+        hyperlink_paragraph
+    ].to_s
+  end
+
+  # =========================================================================== #
+  # === return_intro_for_mirror_repeat_conversion
+  # =========================================================================== #
+  def return_intro_for_mirror_repeat_conversion
+    HtmlTags.h1(
+      '<b>10</b>) Mirror Repeat',
+      css_style: 'margin-left:0.25em;'
+    )
+  end
+
+  # ========================================================================= #
+  # === return_form_for_shuffleseq_action
+  # ========================================================================= #
+  def return_form_for_shuffleseq_action(
+      route_to_this_action = '/shuffleseq/'
+    )
+    '<form id="shuffleseq" '+CSS_STYLE_FOR_THE_FORMS+' action="'+route_to_this_action+'">'+
+     INPUT_TYPE_TEXT_AND_BR_TAG+
+     return_default_submit_button+'
+     </form>'
+  end
+
+  # ========================================================================= #
+  # === return_sinatra_to_chunked_with_arguments
+  #
+  # Usage example:
+  #
+  #   http://localhost:4567/to_chunked/UGAUCGUACUGCAUGACUGAUGGUACUGACCAGUACUGCAUGACUGAUGGUACUGACCAGUACUGCAUGACUGAUGGUACUGACCAGUACUGCAUGACUGAUGGUACUGACCA
+  #
+  # ========================================================================= #
+  def return_sinatra_to_chunked_with_arguments(
+      i = web_params_as_string?
+    )
+    i = i.dup if i.frozen?
+    Cyberweb::HtmlTemplate[
+      title: 'Chunked display',
+      body:  HtmlTags.pre(HtmlTags.bold(::Bioroebe.chunked_display(i)))
+    ].to_s
+  end
+
+  # =========================================================================== #
+  # === return_intro_for_to_dna_conversion
+  # =========================================================================== #
+  def return_intro_for_to_dna_conversion(
+      i = '(<b>2</b>) '
+    )
+    Cyberweb::HtmlTemplate[
+      title: 'To DNA conversion (from RNA)',
+      body: HtmlTags.h1(
+              "#{i}To DNA conversion (from RNA)",
+              css_style: 'margin-left:0.25em;'
+            )
+    ].to_s
+  end
+
+  # =========================================================================== #
+  # === return_intro_for_shuffleseq
+  # =========================================================================== #
+  def return_intro_for_shuffleseq
+    HtmlTags.h1(
+      '(<b>11</b>) Shuffleseq (randomize) a given DNA sequence',
+      css_style: 'margin-left:0.25em;'
+    )
+  end
+
+  # ========================================================================= #
+  # === return_form_for_palindromes_action
+  # ========================================================================= #
+  def return_form_for_palindromes_action(
+      route_to_this_action = '/palindromes/'
+    )
+    '<form id="palindromes" '+CSS_STYLE_FOR_THE_FORMS+' action="'+route_to_this_action+'">'+
+     INPUT_TYPE_TEXT_AND_BR_TAG+
+     return_default_submit_button+'
+     </form>'
+  end
+
+  # ========================================================================= #
+  # === method_random_aminoacids
+  # ========================================================================= #
+  def method_random_aminoacids
+    Cyberweb::HtmlTemplate[
+      title: 'Random Aminoacids',
+      body:  return_header_random_aminoacids+
+        HtmlTags.p(
+          'This entry point can be used to "create" a random sequence '\
+          'of amino acids. Simply input how many aminoacids to '\
+          'create, as a <b>number</b>.')+
+        footer
+    ].to_s
+  end
+
+  # ========================================================================= #
+  # === return_header_random_aminoacids
+  # ========================================================================= #
+  def return_header_random_aminoacids
+    HtmlTags.h1('Random aminoacids',
+      css_style: 'margin-left:0.25em;')
+  end
+
+  # ========================================================================= #
+  # === return_form_for_is_a_palindrome_action
+  # ========================================================================= #
+  def return_form_for_is_a_palindrome_action(
+      route_to_this_action = '/is_palindrome/'
+    )
+    '<form id="is_palindrome" '+CSS_STYLE_FOR_THE_FORMS+' action="'+route_to_this_action+'">'+
+     INPUT_TYPE_TEXT_AND_BR_TAG+
+     return_default_submit_button+'
+     </form>'
+  end
+
+  # ========================================================================= #
+  # === return_header_for_palindromes
+  # ========================================================================= #
+  def return_header_for_palindromes(
+      title_to_use = 'Palindromes'
+    )
+    HtmlTags.h1(
+      title_to_use,
+      css_style: 'margin-left:0.25em;'
+    )
+  end
+
+  # ========================================================================= #
+  # === not_yet_implemented
+  #
+  # This can be added as a placeholder for future changes.
+  # ========================================================================= #
+  def not_yet_implemented
+    HtmlTags.p(
+      "Not yet implemented."
+    )
+  end
+
+  # =========================================================================== #
+  # === return_intro_for_compseq
+  # =========================================================================== #
+  def return_intro_for_compseq
+    HtmlTags.h1(
+      '(<b>7</b>) Compseq a DNA sequence',
+      css_style: 'margin-left:0.25em;'
+    )
+  end
+
+  # ========================================================================= #
+  # === return_header_to_chunked_display
+  # ========================================================================= #
+  def return_header_to_chunked_display
+    HtmlTags.h1(
+      'To chunked-display',
+      css_style: 'margin-left:0.25em;'
+    )
+  end
+
+  # ========================================================================= #
+  # === return_sinatra_method_for_compseq
+  # ========================================================================= #
+  def return_sinatra_method_for_compseq
+    body = return_intro_for_compseq+
+    HtmlTags.p(
+      'You can compseq (compare sequence) a '\
+      'DNA sequence through this API.'
+    )+
+    HtmlTags.p(
+      'Simply input the nucleotide String, such as "ATGCT", '\
+      'without the "" quotes.'
+    )+
+    return_form_for_compseq_action+
+    hyperlink_paragraph
+    Cyberweb::HtmlTemplate[
+      title: title?,
+      body: body
+    ].to_s
+  end
+
+  # ========================================================================= #
+  # === return_explanation_of_how_to_use_the_aminoacid_conversion
+  # ========================================================================= #
+  def return_explanation_of_how_to_use_the_aminoacid_conversion
+    Cyberweb::HtmlTemplate[
+      title: 'To aminoacid conversion',
+      body: HtmlTags.p(
+        'This functionality requires that a DNA/RNA
+         sequence is used as input, which will then be converted
+         into the corresponding aminoacid sequence.'
+      )
+    ].to_s
+  end
+
+  # ========================================================================= #
+  # === return_form_for_to_aa_action
+  # ========================================================================= #
+  def return_form_for_to_aa_action(
+      route_to_this_action = '/to_aa/'
+    )
+    '<form id="to_aa" autocomplete="off" '+CSS_STYLE_FOR_THE_FORMS+' action="'+route_to_this_action+'">'+
+     INPUT_TYPE_TEXT_AND_BR_TAG+
+     return_default_submit_button+'
+     </form>'
+  end
+
+  # ========================================================================= #
+  # === return_paragraph_of_hyperlinks
+  # ========================================================================= #
+  def return_paragraph_of_hyperlinks
+    HtmlTags.p(
+      '<span style="font-size: larger">
+      The following <b>'+
+      ARRAY_AVAILABLE_TOPLEVEL_ACTIONS_FOR_THE_SINATRA_INTERFACE.size.to_s+
+      '</b> options are available for the '\
+      '<b>Bioroebe-sinatra interface</b>: </span>'\
+      '<br><br>'+
+      return_index_of_hyperlinks,
+      css_style: 'margin-left: 2em; '\
+                 'margin-right: 2em; '\
+                 'padding: 1.25em; '\
+                 'font-size: smaller; '\
+                 'border: 2px dotted darkblue;
+                  float: right;
+                  top: 1em;
+                 '
+    )
+  end; alias footer               return_paragraph_of_hyperlinks # === footer (footer tag)
+       alias hyperlink_paragraph  return_paragraph_of_hyperlinks # === hyperlink_paragraph
+       alias hyperlinks_paragraph return_paragraph_of_hyperlinks # === hyperlinks_paragraph
+
+  # ========================================================================= #
+  # === return_view_string
+  # ========================================================================= #
+  def return_view_string
+    body = HtmlTags.h1(
+      'Bioroebe sinatra-interface!',
+       css_style: 'margin-left:0.25em;'
+    )+
+    HtmlTags.p(
+      "The <b>following actions</b>, as links, can be used to make use "\
+      "of the Bioroebe project's www interface (through <b>sinatra</b>)."
+    )+
+    return_index_of_hyperlinks
+    Cyberweb::HtmlTemplate[
+      title: title?,
+      body: body
+    ].to_s
+  end; alias return_root_string return_view_string # === return_root_string
+
+  # ========================================================================= #
+  # === return_header_to_aminoacid_conversion
+  # ========================================================================= #
+  def return_header_to_aminoacid_conversion
+    Cyberweb::HtmlTemplate[
+      title: 'To aminoacid conversion',
+      body: HtmlTags.h1('To aminoacid conversion',
+        css_style: 'margin-left:0.25em;'
+      )
+    ].to_s
+  end
+
+  # =========================================================================== #
+  # === return_intro_for_blosum
+  # =========================================================================== #
+  def return_intro_for_blosum
+    HtmlTags.h1(
+      '(<b>16</b>) Blosum',
+      css_style: 'margin-left:0.25em;'
+    )
+  end
+
+  # ========================================================================= #
+  # === return_form_for_mirror_repeat_action
+  #
+  # This method will show the <form> for the DNA-input action.
+  # ========================================================================= #
+  def return_form_for_mirror_repeat_action(
+      route_to_this_action = '/mirror/'
+    )
+    '<form id="mirror" autocomplete="off" '+CSS_STYLE_FOR_THE_FORMS+' action="'+route_to_this_action+'">'+
+     INPUT_TYPE_TEXT_AND_BR_TAG+
+     return_default_submit_button+'
+     </form>'
+  end
+
+end
+
+# =========================================================================== #
+# === Bioroebe.embeddable_interface
+# =========================================================================== #
+def self.embeddable_interface
+  object = Object.new
+  object.extend(::Bioroebe::EmbeddableInterface)
+  return object
+end
+
+end