bioroebe 0.10.80

data/lib/bioroebe/base/misc.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/base/misc.rb'
+# =========================================================================== #
+module Bioroebe
+
+class Base
+
+  require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
+
+  # ========================================================================= #
+  # === is_palindrome?
+  # ========================================================================= #
+  def is_palindrome?(i)
+    unless ::Bioroebe.respond_to?(:is_palindrome?)
+      require 'bioroebe/toplevel_methods/palindromes.rb'
+    end
+    ::Bioroebe.is_palindrome?(i)
+  end; alias is_this_sequence_a_palindrome? is_palindrome? # === is_this_sequence_a_palindrome?
+
+  require 'bioroebe/toplevel_methods/convert_global_env.rb'
+  # ========================================================================= #
+  # === convert_global_env
+  # ========================================================================= #
+  def convert_global_env(i)
+    ::Bioroebe.convert_global_env(i)
+  end
+
+  # ========================================================================= #
+  # === register_sigint
+  # ========================================================================= #
+  def register_sigint(optional_display_this_message = nil)
+    Signal.trap('SIGINT') {
+      if optional_display_this_message
+        e optional_display_this_message
+      end
+      exit
+    }
+  end
+
+  # ========================================================================= #
+  # === can_base_pair?
+  #
+  # This method will determine whether two nucleotides can base pair
+  # to one another, e. g. A=T or A=U and so forth.
+  #
+  # A boolean value will be returned.
+  # ========================================================================= #
+  def can_base_pair?(a, b)
+    _ = "#{a}#{b}" 
+    case _
+    when 'AT','TA','GC','CG','AU','UA'
+      return true
+    else
+      return false
+    end
+  end
+
+  # ========================================================================= #
+  # === directory_to_the_codon_tables?
+  #
+  # This method will return the directory to the codon-tables, a directory
+  # containing the individual .yml files.
+  # ========================================================================= #
+  def directory_to_the_codon_tables?
+    "#{project_yaml_directory?}codon_tables/"
+  end
+
+  # ========================================================================= #
+  # === write_what_into
+  #
+  # This method can be used to write into a (local) file.
+  # ========================================================================= #
+  def write_what_into(what, into)
+    ::Bioroebe.write_what_into(what, into)
+  end; alias save_file write_what_into # === save_file
+
+  # ========================================================================= #
+  # === append_what_into
+  # ========================================================================= #
+  def append_what_into(what, into)
+    ::Bioroebe.append_what_into(what, into)
+  end
+
+  # ========================================================================= #
+  # === project_yaml_directory?
+  # ========================================================================= #
+  def project_yaml_directory?
+    ::Bioroebe.project_yaml_directory?
+  end; alias yaml_directory? project_yaml_directory? # === yaml_directory?
+
+end; end

data/lib/bioroebe/base/namespace.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/base/namespace.rb'
+# =========================================================================== #
+module Bioroebe
+
+class Base # === Bioroebe::Base
+
+  # ========================================================================= #
+  # === Bioroebe::Base::NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+end; end

data/lib/bioroebe/base/prototype/README.md

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+This directory may only really include code that can be of great
+benefit to just about every subclass of the Bioroebe project,
+without (much) further restrictions.
+
+Code that is more specialized may have to go into other files.
+
+The prototype class has these important methods (but not all
+of them may be listed here).
+
+  (1) mkdir: used to create a directory.
+  (2) reset: used to initialize or rather reset the main
+             state of the object.

data/lib/bioroebe/base/prototype/e_and_ee.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/base/prototype/e_and_ee.rb'
+# =========================================================================== #
+module Bioroebe
+
+class Base
+
+  # ========================================================================= #
+  # The following two aliases may have to be changed at some later point,
+  # but for now, let's keep things simple and use a simple alias, too.
+  #
+  # The old code was like this:
+  #
+  #    def e(i = ''); ::Bioroebe.e(i)
+  #
+  # ========================================================================= #
+  alias e puts
+
+  alias ee print
+
+end; end

data/lib/bioroebe/base/prototype/misc.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/base/prototype/misc.rb'
+# =========================================================================== #
+module Bioroebe
+
+class Base
+
+  require 'bioroebe/requires/require_encoding.rb'
+  require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
+  require 'bioroebe/toplevel_methods/rds.rb'
+
+  require 'bioroebe/toplevel_methods/is_on_roebe.rb'
+  # ========================================================================= #
+  # === is_on_roebe?
+  # ========================================================================= #
+  def is_on_roebe?
+    ::Bioroebe.is_on_roebe?
+  end
+
+  # ========================================================================= #
+  # === main_encoding?
+  #
+  # The main encoding in use. Currently this is hardcoded to UTF-8.
+  # ========================================================================= #
+  def main_encoding?
+    USE_THIS_ENCODING
+  end
+
+  # ========================================================================= #
+  # === move_file
+  #
+  # This method can be used to relocate or rename a file.
+  # ========================================================================= #
+  def move_file(
+      this_file, target
+    )
+    if File.exist? this_file
+      begin
+        FileUtils.mv(this_file, target)
+      rescue Exception => error
+        pp error
+      end
+    else
+      e rev+'No file exists at `'+sfile(this_file)+'`.'
+    end
+  end; alias rename move_file # === rename
+
+  # ========================================================================= #
+  # === rds
+  #
+  # The abbreviation rds stands short for "remove double slashes".
+  # ========================================================================= #
+  def rds(i)
+    ::Bioroebe.rds(i)
+  end
+
+  # ========================================================================= #
+  # === return_pwd
+  # ========================================================================= #
+  def return_pwd
+    "#{Dir.pwd}/".squeeze('/')
+  end; alias return_working_directory return_pwd # === return_working_directory
+
+  # ========================================================================= #
+  # === mv
+  #
+  # Move/Rename a file or directory.
+  # ========================================================================= #    
+  def mv(old, new)
+    FileUtils.mv(old, new)
+  end
+
+  # ========================================================================= #
+  # === delete_file
+  # ========================================================================= #
+  def delete_file(i)
+    File.delete(i) if File.exist? i
+  end; alias remove_file delete_file # === remove_file
+       alias remove      delete_file # === remove
+
+  # ========================================================================= #
+  # === no_newlines
+  #
+  # This method will remove all newlines from a given (input) String.
+  # ========================================================================= #
+  def no_newlines(i)
+    i.delete!(N) if i
+    return i
+  end
+
+  # ========================================================================= #
+  # === no_file_exists_at
+  # ========================================================================= #
+  def no_file_exists_at(i)
+    ::Bioroebe.no_file_exists_at(i)
+  end
+
+  # ========================================================================= #
+  # === file_readlines
+  # ========================================================================= #
+  def file_readlines(i)
+    File.readlines(i, encoding: main_encoding?)
+  end; alias readlines file_readlines # === readlines
+
+end; end

data/lib/bioroebe/base/prototype/mkdir.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/base/directory.rb'
+# =========================================================================== #
+module Bioroebe
+
+class Base
+
+  require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
+
+  # ========================================================================= #
+  # === mkdir                                                     (mkdir tag)
+  # ========================================================================= #
+  def mkdir(i)
+    ::Bioroebe.mkdir(i)
+  end; alias create_directory mkdir # === create_directory
+
+end; end

data/lib/bioroebe/base/prototype/prototype.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/base/prototype/prototype.rb'
+# Bioroebe::Base
+# =========================================================================== #
+require 'bioroebe/constants/carriage_return.rb'
+require 'bioroebe/constants/files_and_directories.rb'
+require 'bioroebe/constants/newline.rb'
+require 'bioroebe/constants/tabulator.rb'
+
+require 'bioroebe/base/prototype/e_and_ee.rb'
+require 'bioroebe/base/prototype/misc.rb'
+require 'bioroebe/base/prototype/mkdir.rb'
+require 'bioroebe/base/prototype/reset.rb'
+# =========================================================================== #
+# Next, two toplevel-methods specific .rb files are required:
+# =========================================================================== #
+require 'bioroebe/toplevel_methods/rds.rb'
+require 'bioroebe/toplevel_methods/truncate.rb'

data/lib/bioroebe/base/prototype/reset.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# This reset here is just "minimal" - we try to not put too much code into
+# it.
+# =========================================================================== #
+# require 'bioroebe/base/prototype/reset.rb'
+# =========================================================================== #
+require 'bioroebe/base/namespace.rb'
+
+module Bioroebe
+
+class Base
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    # ======================================================================= #
+    # === @namespace
+    # ======================================================================= #
+    @namespace = NAMESPACE # We store the namespace here.
+  end
+
+end; end

data/lib/bioroebe/base/reset.rb

@@ -0,0 +1,11 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/base/base.rb'
+# =========================================================================== #
+# We do not have to define the method here because prototype.rb handles
+# this. This explains why this is an almost empty file here.
+# =========================================================================== #
+require 'bioroebe/base/prototype/prototype.rb'
+require 'bioroebe/base/prototype/reset.rb'

data/lib/bioroebe/biomart/LICENSE.md

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+(The MIT License)
+
+Copyright � 2009 Darren Oakley
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the 'Software'),
+to deal in the Software without restriction, including without limitation
+the rights to use, copy, modify, merge, publish, distribute, sublicense,
+and/or sell copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included
+in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS
+OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.
+
+---
+
+(Note that the MIT License here applies to the biomart component of
+bioroebe - the rest of the bioroebe code was written by me; see
+LICENCE.md in other directories.)

data/lib/bioroebe/biomart/attribute.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::Biomart::Attribute
+#
+# This class is a representation for a biomart attribute.
+# 
+# It will belong to a Biomart::Dataset.
+# =========================================================================== #
+module Bioroebe
+
+module Biomart
+
+class Attribute
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(i)
+    # ======================================================================= #
+    # === @name
+    # ======================================================================= #
+    @name         = i['internalName']
+    # ======================================================================= #
+    # === @display_name
+    # ======================================================================= #
+    @display_name = i['displayName']
+    # ======================================================================= #
+    # === @default
+    # ======================================================================= #
+    @default      = i['default'] ? true : false
+    # ======================================================================= #
+    # === @hidden
+    # ======================================================================= #
+    @hidden       = i['hideDisplay'] ? true : false
+  end
+
+  # ========================================================================= #
+  # === name?
+  # ========================================================================= #
+  def name?
+    @name
+  end; alias name name? # === name
+
+  # ========================================================================= #
+  # === display_name?
+  # ========================================================================= #
+  def display_name?
+    @display_name
+  end; alias display_name display_name? # === display_name
+
+  # ========================================================================= #
+  # === hidden?
+  #
+  # This is a convenience method to see if this attribute is hidden from 
+  # the standard MartView interface.
+  #
+  # @return [Boolean] true/false
+  # ========================================================================= #
+  def hidden?
+    @hidden
+  end; alias hidden hidden? # === hidden
+
+  # ========================================================================= #
+  # === default?
+  #
+  # This is a convenience method to see if this attribute would be enabled
+  # by default in the standard MartView interface.
+  #
+  # @return [Boolean] true/false
+  # ========================================================================= #
+  def default?
+    @default
+  end
+
+end; end; end

data/lib/bioroebe/biomart/biomart.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::Biomart::Dataset
+#
+# Class representation for a biomart database.
+#
+# Will contain many Biomart::Dataset objects, and belong to a
+# Biomart::Server.
+# =========================================================================== #
+
+# =========================================================================== #
+# Next, require the ruby files that are part of biomart.
+# =========================================================================== #
+require 'bioroebe/biomart/attribute.rb'
+require 'bioroebe/biomart/database.rb'
+require 'bioroebe/biomart/dataset.rb'
+require 'bioroebe/biomart/filter.rb'
+require 'bioroebe/biomart/server.rb'
+
+module Bioroebe
+
+module Biomart
+
+  require 'net/http'
+  require 'rexml/document' # Rexml is a part of ruby stdlib.
+  require 'csv'
+
+  begin
+    require 'builder'
+  rescue LoadError; end
+
+  # ========================================================================= #
+  # This is the base Biomart error/exception class. Rescue it if you want
+  # to catch any exceptions that this code might raise.
+  # ========================================================================= #
+  class BiomartError < StandardError # === Bioroebe::Biomart::BiomartError
+
+    # ======================================================================= #
+    # === initialize
+    # ======================================================================= #
+    def initialize(data)
+      @data = data
+      super
+    end
+
+    # ======================================================================= #
+    # === data?
+    # ======================================================================= #
+    def data?
+      @data
+    end; alias data data? # === data
+
+  end
+
+  # ========================================================================= #
+  # Error class representing HTTP errors.
+  # ========================================================================= #
+  class HTTPError      < BiomartError; end
+
+  # ========================================================================= #
+  # Error class representing biomart filter errors.  Usually raised 
+  # when a request is made for a incorrectly named (or non-existent) 
+  # filter.
+  # ========================================================================= #
+  class FilterError    < BiomartError; end
+  
+  # ========================================================================= #
+  # Error class representing biomart attribute errors.  Usually raised 
+  # when a request is made for a incorrectly named (or non-existent) 
+  # attribute.
+  # ========================================================================= #
+  class AttributeError < BiomartError; end
+
+  # ========================================================================= #
+  # Error class representing biomart dataset errors.  Usually raised 
+  # when a request is made for a incorrectly named (or non-existent) 
+  # dataset.
+  # ========================================================================= #
+  class DatasetError   < BiomartError; end
+
+  # ========================================================================= #
+  # Error class representing errors in the arguments being passed 
+  # to the api.
+  # ========================================================================= #
+  class ArgumentError < BiomartError; end
+
+  # ========================================================================= #
+  # === check_response
+  #
+  # Utility function to test the response from a http request.
+  # 
+  # Raises errors if appropriate.
+  # ========================================================================= #
+  def check_response(
+      body, code
+    )
+    # ======================================================================= #
+    # Process the response code/body to catch errors.
+    # ======================================================================= #
+    code = code.to_i if code.is_a? String
+
+    if code != 200 
+      raise HTTPError.new(code),
+            "HTTP error #{code}, please check your biomart server and URL settings."
+    else
+      if body =~ /ERROR/
+        if body =~ /Filter (.+) NOT FOUND/
+          raise FilterError.new(body),
+                "Biomart error. Filter #{$1} not found."
+        elsif body =~ /Attribute (.+) NOT FOUND/
+          raise AttributeError.new(body),
+                "Biomart error. Attribute #{$1} not found."
+        elsif body =~ /Dataset (.+) NOT FOUND/
+          raise DatasetError.new(body),
+                "Biomart error. Dataset #{$1} not found."
+        else
+          raise BiomartError.new(body), 'Biomart error.'
+        end
+      end
+    end
+  end; private :check_response
+
+  # ========================================================================= #
+  # === proxy_url
+  #
+  # Utility function to determine if we need to use a proxy.
+  #
+  # If yes, returns the proxy url, if no, we will return false.
+  # ========================================================================= #
+  def proxy_url
+    if Biomart.proxy or ENV['http_proxy'] or ENV['HTTP_PROXY']
+      proxy_uri = Biomart.proxy
+      proxy_uri ||= ENV['http_proxy']
+      proxy_uri ||= ENV['HTTP_PROXY']
+      return proxy_uri
+    else
+      return false
+    end
+  end; private :proxy_url
+
+  # ========================================================================= #
+  # === request
+  #
+  # Centralised request function for handling all of the HTTP requests 
+  # to the biomart servers.
+  # 
+  # @param [Hash] params Parameters to be passed to the request method.
+  # @return [String] The response body
+  #
+  # @example
+  #   request({
+  #     :url     => 'http://www.example.com',   # the url
+  #     :method  => 'get',                      # get/post
+  #     :query   => 'a string',                 # when using post, send this as 'query' (i.e. the biomart query xml)
+  #     :timeout => 60                          # override the default timeout
+  #   })
+  #
+  # @raise Biomart::ArgumentError Raised if a params hash is not passed (or it is empty)
+  # @raise Biomart::HTTPError Raised if a HTTP error was encountered
+  # @raise Biomart::FilterError Raised when a filter is not found
+  # @raise Biomart::AttributeError Raised when an attribute is not found
+  # @raise Biomart::DatasetError Raised when a dataset is not found
+  # @raise Biomart::BiomartError Raised for any other unhandled error
+  # ========================================================================= #
+  def request(params)
+    raise ArgumentError if !params.is_a?(Hash) || params.empty?
+
+    require 'uri'
+
+    if params[:url] =~ / /
+      params[:url].gsub!(' ','+')
+    end
+
+    uri      = URI.parse( params[:url] )
+    client   = net_http_client()
+    req      = nil
+    response = nil
+
+    case params[:method]
+    when 'post'
+      req           = Net::HTTP::Post.new(uri.path)
+      req.form_data = { 'query' => params[:query] }
+    else
+      req           = Net::HTTP::Get.new(uri.request_uri)
+    end
+
+    client.start(uri.host, uri.port) { |http|
+      if Biomart.timeout or params[:timeout]
+        http.read_timeout = params[:timeout] ? params[:timeout] : Biomart.timeout
+        http.open_timeout = params[:timeout] ? params[:timeout] : Biomart.timeout
+      end
+      response = http.request(req)
+    }
+    response_code = response.code
+    response_body = response.body
+    if defined? Encoding && response_body.encoding == Encoding::ASCII_8BIT
+      response_body = response_body.force_encoding(Encoding::UTF_8).encode
+    end
+    check_response(response_body, response_code)
+    return response_body
+  end
+
+  # ========================================================================= #
+  # Allow a proxy next.
+  # ========================================================================= #
+  class << self
+    attr_accessor :proxy  # Bioroebe::Biomart.proxy = "http://proxy.example.com/"
+    attr_accessor :timeout
+  end
+
+  # ========================================================================= #
+  # === net_http_client
+  #    
+  # Utility function to create a Net::HTTP object.
+  # ========================================================================= #
+  def net_http_client
+    client = Net::HTTP
+    if proxy_url # This is a method call.
+      proxy  = URI.parse(proxy_url)
+      client = Net::HTTP::Proxy(proxy.host, proxy.port)
+    end
+    return client
+  end; private :net_http_client
+
+end; end