Module: Bioroebe::Taxonomy::Shared

Includes:
Constants, Colours::E
Included in:
Bioroebe::Taxonomy, CheckAvailable, Interactive, IsDNA, ParseFasta
Defined in:
lib/bioroebe/taxonomy/shared.rb

Overview

include Bioroebe::Taxonomy::Shared

Constant Summary

Constants included from Constants

Constants::AA_DIR, Constants::ARRAY_PROJECT_FILES, Constants::Archaea_Taxonomy_ID, Constants::BASE, Constants::BASE_URL, Constants::BE_VERBOSE, Constants::Bacteria_Taxonomy_ID, Constants::CITATIONS, Constants::CURATED_DIR, Constants::DATA_DIR, Constants::DELNODES, Constants::DIVISION, Constants::Eukaryota_Taxonomy_ID, Constants::FILE_USE_THIS_DATABASE, Constants::GEM_DIR, Constants::GENCODE, Constants::INCOMING_DIR, Constants::INFO_DIR, Constants::LAST_INTERACTIVE_COMMAND, Constants::LOCALOME_DIR, Constants::LOCAL_MIRROR, Constants::MERGED, Constants::MODULE_PATH, Constants::NAMES, Constants::NAMES_SQL, Constants::NCBI_BASE, Constants::NODES, Constants::NODES_SQL, Constants::NT_DIR, Constants::POSTGRESQL_QUERY_SIZE, Constants::POSTGRE_LOGIN_COMMAND, Constants::PROJECT_DOC_DIR, Constants::SEQUENCES_DIR, Constants::SHARED_HOME, Constants::TAXONOMY_BROWSER, Constants::TEMP_DIR, Constants::TEST_DIR, Constants::TMP_DIR, Constants::URL1

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Constants

#info_dir?, #work_directory?

Class Method Details

.be_quiet ⇒ Object

#

Taxonomy::Shared.be_quiet

#

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# File 'lib/bioroebe/taxonomy/shared.rb', line 154

def self.be_quiet
  @be_verbose = false
end

.be_verbose? ⇒ Boolean

#

Taxonomy::Shared.be_verbose?

Whether we will be verbose or whether we will be silent.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/taxonomy/shared.rb', line 147

def self.be_verbose?
  @be_verbose
end

Instance Method Details

#be_verbose? ⇒ Boolean

#

be_verbose?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/taxonomy/shared.rb', line 161

def be_verbose?
  Taxonomy::Shared.be_verbose?
end

#cd(i = File.expand_path('~'), be_verbose = false) ⇒ Object

#

cd (cd tag, change dir tag)

This method allows for some special shortcuts, such as aa.

#

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# File 'lib/bioroebe/taxonomy/shared.rb', line 199

def cd(
    i = File.expand_path('~'),
    be_verbose = false
  )
  be_verbose = true if be_verbose == :be_verbose
  i = File.expand_path('~') if i.nil?
  i = i.to_s
  case i # case tag
  # ======================================================================= #
  # === --help
  # ======================================================================= #
  when '?',
       /^-?-?HELP$/i
    e 'You can cd to these special dirs:'
    e
    e '  '+TEMP_DIR
    e '  '+INFO_DIR
    e '  '+NT_DIR
    e '  '+LOCALOME_DIR
    e
    return
  # ======================================================================= #
  # === home
  # ======================================================================= #
  when /^HOME$/i
    i = TEMP_DIR
  # ======================================================================= #
  # === robert
  # ======================================================================= #
  when 'robert',
       '1',
       'tmp'
    i = TEMP_DIR
  # ======================================================================= #
  # === aa
  # ======================================================================= #
  when 'aa',
       'fasta'
    i = AA_DIR
  # ======================================================================= #
  # === info
  # ======================================================================= #
  when 'info','i'
    i = INFO_DIR
  # ======================================================================= #
  # === nt
  # ======================================================================= #
  when 'nt',
       'dna',
       'rna'
    i = NT_DIR
  # ======================================================================= #
  # === localome
  # ======================================================================= #
  when 'local',
       'localome',
       /^local/,'loc'
    i = LOCALOME_DIR
  end unless File.exist?(i)
  if Dir.exist? i
    if be_verbose
      e "We will now change directory to #{sdir(i)}."
    end
    Dir.chdir(i)
  else
    e "We can not change directory into #{sdir(i)}#{rev} "\
      "as this directory does not exist."
  end
end

#edit_login_file(optional_number = '') ⇒ Object

#

edit_login_file

For this we deliberately use the vim editor.

#

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# File 'lib/bioroebe/taxonomy/shared.rb', line 170

def (
    optional_number = ''
  )
  esystem "vim #{}#{optional_number.to_s}"
end

#eliminate_tabulator(i) ⇒ Object Also known as: sanitize_content

#

eliminate_tabulator

As of now, this method will remove “t” input and '|'.

#

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# File 'lib/bioroebe/taxonomy/shared.rb', line 77

def eliminate_tabulator(i)
  i.gsub(/#{TABULATOR}\|/, '')
end

#ensure_that_download_dir_exists(i = ::Bioroebe.taxonomy_download_directory?) ⇒ Object

#

ensure_that_download_dir_exists

#

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# File 'lib/bioroebe/taxonomy/shared.rb', line 282

def ensure_that_download_dir_exists(
    i = ::Bioroebe.taxonomy_download_directory?
  )
  mkdir(i) unless File.directory? i
end

#ensure_that_temp_dir_exists ⇒ Object

#

ensure_that_temp_dir_exists

#

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# File 'lib/bioroebe/taxonomy/shared.rb', line 138

def ensure_that_temp_dir_exists
  Taxonomy.ensure_that_temp_dir_exists
end

#mkdir(i) ⇒ Object

#

mkdir (mkdir tag)

Simple wrapper over creating a directory. We use the Array format.

#

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# File 'lib/bioroebe/taxonomy/shared.rb', line 190

def mkdir(i)
  ::Bioroebe.mkdir(i)
end

#readlines(i = :names) ⇒ Object

#

readlines

The readlines-wrapper uses File.foreach to iterate over the content.

Typically we can find these files at:

/root/taxonomy/names.dmp
#

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# File 'lib/bioroebe/taxonomy/shared.rb', line 100

def readlines(
    i = :names
  )
  i = i.to_sym # Keep it as a symbol.
  case i
  # ======================================================================= #
  # === :nodes
  # ======================================================================= #
  when :nodes
    if File.exist? NODES
      return File.foreach(NODES)
    else
      e 'Warning - the file at '+sfile(NODES)+' does not exist.'
      return []
    end
  # ======================================================================= #
  # === :names
  # ======================================================================= #
  when :names
    if File.exist? NAMES
      return File.foreach(NAMES)
    else
      e 'Warning - the file at '+sfile(NODES)+' does not exist.'
      return []
    end
  else
    i = i.to_s
    if File.exist? i
      return File.foreach(i)
    else
      e 'Do not know what to do with input: '+sfancy(i)
    end
  end
end

#set_pgpassword ⇒ Object Also known as: set_password

#

set_pgpassword (password tag)

Set the password for Postgresql here.

#

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# File 'lib/bioroebe/taxonomy/shared.rb', line 274

def set_pgpassword
  ::Bioroebe.set_pgpassword
end

#show_password ⇒ Object

#

show_password

This shows the password.

#

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# File 'lib/bioroebe/taxonomy/shared.rb', line 49

def show_password
  e 'The current password for the Postgresql login is:'
  e
  e "  #{sfancy(POSTGRE_PASSWORD)}"
  e
end

#show_time_now ⇒ Object Also known as: show_current_time

#

show_time_now

This will show the current time.

#

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# File 'lib/bioroebe/taxonomy/shared.rb', line 181

def show_time_now
  ::Bioroebe.show_time_now
end

#split_at(i) ⇒ Object

#

split_at

#

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# File 'lib/bioroebe/taxonomy/shared.rb', line 84

def split_at(i)
  return i.split(MAIN_DELIMITER).map(&:chomp).map() {|entry|
    eliminate_tabulator(entry)
  }
end

#split_at_tabulator(i) ⇒ Object

#

split_at_tabulator

#

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# File 'lib/bioroebe/taxonomy/shared.rb', line 68

def split_at_tabulator(i)
  i.split(FIELD_TERMINATOR) if i.is_a? String
end

#tokenize(i) ⇒ Object

#

tokenize

We will split at the given input. Input is expected to be a string.

#

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# File 'lib/bioroebe/taxonomy/shared.rb', line 61

def tokenize(i)
  i.split(TOKEN).map(&:strip)
end