bio 1.2.1 → 1.3.0

data/lib/bio/appl/paml/yn00/report.rb

@@ -0,0 +1,32 @@
+#
+# = bio/appl/paml/baseml/report.rb - parser class for PAML program yn00
+#
+# Copyright::  Copyright (C) 2008
+#              Naohisa Goto <ng@bioruby.org>
+#
+# License::    The Ruby License
+#
+# == Description
+#
+# This file contains Bio::PAML::Yn00::Report, a parser class for a result
+# of yn00.
+#
+# == References
+#
+# * http://abacus.gene.ucl.ac.uk/software/paml.html
+#
+
+require 'bio/appl/paml/yn00'
+
+module Bio::PAML
+  class Yn00
+
+    # UNDER CONSTRUCTION.
+    #
+    # Bio::PAML::Yn00::Report is a parser class for a yn00 result.
+    #
+    class Report < Bio::PAML::Common::Report
+    end #class Report
+
+  end #class Yn00
+end #module Bio::PAML

data/lib/bio/appl/psort.rb

@@ -7,7 +7,7 @@ module Bio
 #               Mitsuteru C. Nakao <n@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: psort.rb,v 1.13 2007/04/05 23:35:39 trevor Exp $
+# $Id:$
 #
 
 require 'bio/appl/psort/report'
@@ -111,7 +111,7 @@ require 'uri'
         begin
           result = nil
           Bio::Command.start_http(@uri.host) {|http|
-            result, = http.post(@uri.path, data)
+            result = http.post(@uri.path, data)
           }
           @report = result.body
           output = parse_report(@report)

data/lib/bio/appl/pts1.rb

@@ -8,7 +8,7 @@ module Bio
 #               Mitsuteru C. Nakao <n@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: pts1.rb,v 1.5 2007/04/05 23:35:39 trevor Exp $
+# $Id:$
 #
 
 require 'uri'
@@ -116,7 +116,7 @@ class PTS1
   #  serv.function #=> "METAZOA-specific"
   # 
   def function(func = nil)
-    return @function.keys.to_s if func == nil
+    return @function.keys.join('') if func == nil
 
     if FUNCTION.values.include?(func)
       @function = Hash[*FUNCTION.find {|x| x[1] == func}]
@@ -146,12 +146,12 @@ class PTS1
   def exec(query)
     seq = set_sequence_in_fastaformat(query)
     
-    @form_data = {'function' => @function.values.to_s,
+    @form_data = {'function' => @function.values.join(''),
                   'sequence' => seq.seq,
                   'name'     => seq.definition }
     @uri = URI.parse(["http:/", @host, @cgi_path].join('/'))
 
-    result, = Bio::Command.post_form(@uri, @form_data)
+    result = Bio::Command.post_form(@uri, @form_data)
     @output = Report.new(result.body)
     
     return @output
@@ -229,7 +229,7 @@ class PTS1
     private
 
     def parse
-      @output.each do |line|
+      @output.each_line do |line|
         case line
         when /Name<\/td><td>(\S.+)<\/td><\/tr>/
           @entry_id = $1

data/lib/bio/appl/tmhmm/report.rb

@@ -5,7 +5,7 @@
 #              Mitsuteru C. Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: report.rb,v 1.8 2007/04/05 23:35:40 trevor Exp $
+#  $Id:$
 #
 # == Description
 #
@@ -14,6 +14,8 @@
 # == References
 #
 
+require 'enumerator'
+
 module Bio
 
   # = TMHMM class for http://www.cbs.dtu.dk/services/TMHMM/
@@ -81,6 +83,13 @@ module Bio
 
       #
       def initialize(entry = nil)
+        begin
+          str = entry.to_str
+        rescue NoMethodError
+        end
+        if str then
+          entry = str.enum_for(:each_line)
+        end
         parse_header(entry)
         @tmhs = parse_tmhs(entry)
       end

data/lib/bio/command.rb

@@ -1,18 +1,21 @@
 #
 # = bio/command.rb - general methods for external command execution
 #
-# Copyright::	Copyright (C) 2003-2006
+# Copyright::	Copyright (C) 2003-2008
 # 		Naohisa Goto <ng@bioruby.org>,
 #		Toshiaki Katayama <k@bioruby.org>
 # License::	The Ruby License
 #
-#  $Id: command.rb,v 1.17 2007/04/05 23:35:39 trevor Exp $
+#  $Id:$
 #
 
 require 'open3'
 require 'uri'
 require 'open-uri'
+require 'cgi'
 require 'net/http'
+require 'tmpdir'
+require 'fileutils'
 
 module Bio
 
@@ -32,6 +35,10 @@ module Command
   module_function
 
   # Escape special characters in command line string for cmd.exe on Windows.
+  # ---
+  # *Arguments*:
+  # * (required) _str_: String
+  # *Returns*:: String object
   def escape_shell_windows(str)
     str = str.to_s
     raise 'cannot escape control characters' if UNESCAPABLE_CHARS =~ str
@@ -43,6 +50,10 @@ module Command
   end
 
   # Escape special characters in command line string for UNIX shells.
+  # ---
+  # *Arguments*:
+  # * (required) _str_: String
+  # *Returns*:: String object
   def escape_shell_unix(str)
     str = str.to_s
     raise 'cannot escape control characters' if UNESCAPABLE_CHARS =~ str
@@ -50,6 +61,10 @@ module Command
   end
 
   # Escape special characters in command line string.
+  # ---
+  # *Arguments*:
+  # * (required) _str_: String
+  # *Returns*:: String object
   def escape_shell(str)
     case RUBY_PLATFORM
     when /mswin32|bccwin32/
@@ -60,6 +75,10 @@ module Command
   end
 
   # Generate command line string with special characters escaped.
+  # ---
+  # *Arguments*:
+  # * (required) _ary_: Array containing String objects
+  # *Returns*:: String object
   def make_command_line(ary)
     case RUBY_PLATFORM
     when /mswin32|bccwin32/
@@ -71,32 +90,92 @@ module Command
 
   # Generate command line string with special characters escaped
   # for cmd.exe on Windows.
+  # ---
+  # *Arguments*:
+  # * (required) _ary_: Array containing String objects
+  # *Returns*:: String object
   def make_command_line_windows(ary)
     ary.collect { |str| escape_shell_windows(str) }.join(" ")
   end
 
   # Generate command line string with special characters escaped
   # for UNIX shells.
+  # ---
+  # *Arguments*:
+  # * (required) _ary_: Array containing String objects
+  # *Returns*:: String object
   def make_command_line_unix(ary)
     ary.collect { |str| escape_shell_unix(str) }.join(" ")
   end
 
+  # Returns an Array of command-line command and arguments
+  # that can be safely passed to Kernel.exec etc.
+  # If the given array is already safe (or empty), returns the given array.
+  # ---
+  # *Arguments*:
+  # * (required) _ary_: Array
+  # *Returns*:: Array
+  def safe_command_line_array(ary)
+    ary = ary.to_ary
+    return ary if ary.size >= 2 or ary.empty?
+    if ary.size != 1 then
+      raise 'Bug: assersion of ary.size == 1 failed'
+    end
+    arg0 = ary[0]
+    begin
+      arg0 = arg0.to_ary
+    rescue NoMethodError
+      arg0 = [ arg0, arg0 ]
+    end
+    [ arg0 ]
+  end
+
   # Executes the program.  Automatically select popen for Windows
   # environment and fork for the others.
   # A block must be given. An IO object is passed to the block.
-  def call_command(cmd, &block)
+  #
+  # Available options:
+  #   :chdir => "path" : changes working directory to the specified path.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _cmd_: Array containing String objects
+  # * (optional) _options_: Hash
+  # *Returns*:: (undefined)
+  def call_command(cmd, options = {}, &block) #:yields: io
     case RUBY_PLATFORM
     when /mswin32|bccwin32/
-      call_command_popen(cmd, &block)
+      call_command_popen(cmd, options, &block)
     else
-      call_command_fork(cmd, &block)
+      call_command_fork(cmd, options, &block)
     end
   end
 
   # Executes the program via IO.popen for OS which doesn't support fork.
   # A block must be given. An IO object is passed to the block.
-  def call_command_popen(cmd)
+  # ---
+  # *Arguments*:
+  # * (required) _cmd_: Array containing String objects
+  # * (optional) _options_: Hash
+  # *Returns*:: (undefined)
+  def call_command_popen(cmd, options = {})
     str = make_command_line(cmd)
+    # processing options
+    if dir = options[:chdir] then
+      case RUBY_PLATFORM
+      when /mswin32|bccwin32/
+        # Unix-like dir separator is changed to Windows dir separator
+        # by using String#gsub.
+        dirstr = dir.gsub(/\//, "\\")
+        chdirstr = make_command_line([ 'cd', '/D', dirstr ])
+        str = chdirstr + ' && ' + str
+      else
+        # UNIX shell
+        chdirstr = make_command_line([ 'cd', dir ])
+        str = chdirstr + ' && ' + str
+      end
+    end
+    # call command by using IO.popen
     IO.popen(str, "w+") do |io|
       io.sync = true
       yield io
@@ -108,13 +187,28 @@ module Command
   #
   # From the view point of security, this method is recommended
   # rather than call_command_popen.
-  def call_command_fork(cmd)
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _cmd_: Array containing String objects
+  # * (optional) _options_: Hash
+  # *Returns*:: (undefined)
+  def call_command_fork(cmd, options = {})
+    dir = options[:chdir]
+    cmd = safe_command_line_array(cmd)
     IO.popen("-", "r+") do |io|
       if io then
         # parent
         yield io
       else
         # child
+        # chdir to options[:chdir] if available
+        begin
+          Dir.chdir(dir) if dir
+        rescue Exception
+          Process.exit!(1)
+        end
+        # executing the command
         begin
           Kernel.exec(*cmd)
         rescue Errno::ENOENT, Errno::EACCES
@@ -130,8 +224,13 @@ module Command
   # A block must be given. IO objects are passed to the block.
   #
   # You would use this method only when you really need to get stderr.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _cmd_: Array containing String objects
+  # *Returns*:: (undefined)
   def call_command_open3(cmd)
-    cmd = cmd.collect { |x| x.to_s }
+    cmd = safe_command_line_array(cmd)
     Open3.popen3(*cmd) do |pin, pout, perr|
       yield pin, pout, perr
     end
@@ -142,12 +241,22 @@ module Command
   # standard output as a string.
   # 
   # Automatically select popen for Windows environment and fork for the others.
-  def query_command(cmd, query = nil)
+  #
+  # Available options:
+  #   :chdir => "path" : changes working directory to the specified path.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _cmd_: Array containing String objects
+  # * (optional) _query_: String
+  # * (optional) _options_: Hash
+  # *Returns*:: String or nil
+  def query_command(cmd, query = nil, options = {})
     case RUBY_PLATFORM
     when /mswin32|bccwin32/
-      query_command_popen(cmd, query)
+      query_command_popen(cmd, query, options)
     else
-      query_command_fork(cmd, query)
+      query_command_fork(cmd, query, options)
     end
   end
 
@@ -156,14 +265,22 @@ module Command
   # standard output as a string.
   #
   # IO.popen is used for OS which doesn't support fork.
-  def query_command_popen(cmd, query = nil)
-    str = make_command_line(cmd)
-    IO.popen(str, "w+") do |io|
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _cmd_: Array containing String objects
+  # * (optional) _query_: String
+  # * (optional) _options_: Hash
+  # *Returns*:: String or nil
+  def query_command_popen(cmd, query = nil, options = {})
+    ret = nil
+    call_command_popen(cmd, options) do |io|
       io.sync = true
       io.print query if query
       io.close_write
-      io.read
+      ret = io.read
     end
+    ret
   end
 
   # Executes the program with the query (String) given to the standard input,
@@ -173,37 +290,39 @@ module Command
   # Fork (by using IO.popen("-")) and exec is used to execute the program.
   #
   # From the view point of security, this method is recommended
-  # rather than query_popen.
-  def query_command_fork(cmd, query = nil)
-    IO.popen("-", "r+") do |io|
-      if io then
-        # parent
-        io.sync = true
-        io.print query if query
-        io.close_write
-        io.read
-      else
-        # child
-        begin
-          Kernel.exec(*cmd)
-        rescue Errno::ENOENT, Errno::EACCES
-          Process.exit!(127)
-        rescue Exception
-        end
-        Process.exit!(1)
-      end
+  # rather than query_command_popen.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _cmd_: Array containing String objects
+  # * (optional) _query_: String
+  # * (optional) _options_: Hash
+  # *Returns*:: String or nil
+  def query_command_fork(cmd, query = nil, options = {})
+    ret = nil
+    call_command_fork(cmd, options) do |io|
+      io.sync = true
+      io.print query if query
+      io.close_write
+      ret = io.read
     end
+    ret
   end
 
   # Executes the program via Open3.popen3 with the query (String) given
   # to the stain, waits the program termination, and
   # returns the data from stdout and stderr as an array of the strings.
   #
-  # From the view point of security, this method is recommended
-  # rather than exec_local_popen.
+  # You would use this method only when you really need to get stderr.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _cmd_: Array containing String objects
+  # * (optional) _query_: String
+  # *Returns*:: Array containing 2 objects: output string (or nil) and stderr string (or nil)
   def query_command_open3(cmd, query = nil)
     errorlog = nil
-    cmd = cmd.collect { |x| x.to_s }
+    cmd = safe_command_line_array(cmd)
     Open3.popen3(*cmd) do |pin, pout, perr|
       perr.sync = true
       t = Thread.start { errorlog = perr.read }
@@ -218,7 +337,78 @@ module Command
     end
   end
 
-  # Same as OpenURI.open_uri(uri).read.
+  # Same as FileUtils.remove_entry_secure after Ruby 1.8.3.
+  # In Ruby 1.8.2 or previous version, it only shows warning message
+  # and does nothing.
+  #
+  # It is strongly recommended using Ruby 1.8.5 or later.
+  # ---
+  # *Arguments*:
+  # * (required) _path_: String
+  # * (optional) _force_: boolean
+  def remove_entry_secure(path, force = false)
+    begin
+      FileUtils.remove_entry_secure(path, force)
+    rescue NoMethodError
+      warn "The temporary file or directory is not removed because of the lack of FileUtils.remove_entry_secure. Use Ruby 1.8.3 or later (1.8.5 or later is strongly recommended): #{path}"
+      nil
+    end
+  end
+
+  # Backport of Dir.mktmpdir in Ruby 1.9.
+  #
+  # Same as Dir.mktmpdir(prefix_suffix) in Ruby 1.9 except that
+  # prefix must be a String, nil, or omitted.
+  #
+  # ---
+  # *Arguments*:
+  # * (optional) _prefix_: String
+  # 
+  def mktmpdir(prefix = 'd', tmpdir = nil, &block)
+    prefix = prefix.to_str
+    begin
+      Dir.mktmpdir(prefix, tmpdir, &block)
+    rescue NoMethodError
+      suffix = ''
+      # backported from Ruby 1.9.0.
+      # ***** Below is excerpted from Ruby 1.9.0's lib/tmpdir.rb ****
+      # ***** Be careful about copyright. ****
+      tmpdir ||= Dir.tmpdir
+      t = Time.now.strftime("%Y%m%d")
+      n = nil
+      begin
+        path = "#{tmpdir}/#{prefix}#{t}-#{$$}-#{rand(0x100000000).to_s(36)}"
+        path << "-#{n}" if n
+        path << suffix
+        Dir.mkdir(path, 0700)
+      rescue Errno::EEXIST
+        n ||= 0
+        n += 1
+        retry
+      end
+
+      if block_given?
+        begin
+          yield path
+        ensure
+          remove_entry_secure path
+        end
+      else
+        path
+      end
+      # ***** Above is excerpted from Ruby 1.9.0's lib/tmpdir.rb ****
+    end
+  end
+
+  # Same as OpenURI.open_uri(uri).read
+  # and 
+  # it uses proxy if an environment variable (same as OpenURI.open_uri)
+  # is set.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _uri_: URI object or String
+  # *Returns*:: String
   def read_uri(uri)
     OpenURI.open_uri(uri).read
   end
@@ -229,6 +419,11 @@ module Command
   # it uses proxy if an environment variable (same as OpenURI.open_uri)
   # is set.
   #
+  # ---
+  # *Arguments*:
+  # * (required) _address_: String containing host name or IP address
+  # * (optional) _port_: port (sanme as Net::HTTP::start)
+  # *Returns*:: (same as Net::HTTP::start except for proxy support)
   def start_http(address, port = 80, &block)
     uri = URI.parse("http://#{address}:#{port}")
     # Note: URI#find_proxy is an unofficial method defined in open-uri.rb.
@@ -248,6 +443,11 @@ module Command
   # it uses proxy if an environment variable (same as OpenURI.open_uri)
   # is set.
   #
+  # ---
+  # *Arguments*:
+  # * (required) _address_: String containing host name or IP address
+  # * (optional) _port_: port (sanme as Net::HTTP::start)
+  # *Returns*:: (same as Net::HTTP.new except for proxy support)
   def new_http(address, port = 80)
     uri = URI.parse("http://#{address}:#{port}")
     # Note: URI#find_proxy is an unofficial method defined in open-uri.rb.
@@ -260,6 +460,36 @@ module Command
     end
   end
 
+  # Same as:
+  #  http = Net::HTTP.new(...); http.post_form(path, params)
+  # and 
+  # it uses proxy if an environment variable (same as OpenURI.open_uri)
+  # is set.
+  # In addition, +header+ can be set.
+  # (Note that Content-Type and Content-Length are automatically
+  # set by default.)
+  # +uri+ must be a URI object, +params+ must be a hash, and
+  # +header+ must be a hash.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _http_: Net::HTTP object or compatible object
+  # * (required) _path_: String
+  # * (optional) _params_: Hash containing parameters
+  # * (optional) _header_: Hash containing header strings
+  # *Returns*:: (same as Net::HTTP::post_form)
+  def http_post_form(http, path, params = nil, header = {})
+    data = make_cgi_params(params)
+
+    hash = {
+      'Content-Type'   => 'application/x-www-form-urlencoded',
+      'Content-Length' => data.length.to_s
+    }
+    hash.update(header)
+
+    http.post(path, data, hash)
+  end
+
   # Same as:
   # Net::HTTP.post_form(uri, params)
   # and 
@@ -271,6 +501,12 @@ module Command
   # +uri+ must be a URI object, +params+ must be a hash, and
   # +header+ must be a hash.
   #
+  # ---
+  # *Arguments*:
+  # * (required) _uri_: URI object or String
+  # * (optional) _params_: Hash containing parameters
+  # * (optional) _header_: Hash containing header strings
+  # *Returns*:: (same as Net::HTTP::post_form)
   def post_form(uri, params = nil, header = {})
     unless uri.is_a?(URI)
       uri = URI.parse(uri)
@@ -289,6 +525,13 @@ module Command
     end
   end
 
+  # Builds parameter string for from Hash of parameters for
+  # application/x-www-form-urlencoded.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _params_: Hash containing parameters
+  # *Returns*:: String
   def make_cgi_params(params)
     data = ""
     case params
@@ -310,7 +553,12 @@ module Command
         end.join('&')
       when String
         data = params.map do |str|
-          URI.escape(str.strip)
+          key, val = str.split(/\=/, 2)
+          if val then
+            make_cgi_params_key_value(key, val)
+          else
+            CGI.escape(str)
+          end
         end.join('&')
       end
     when String
@@ -319,15 +567,23 @@ module Command
     return data
   end
 
+  # Builds parameter string for from a key string and a value (or values)
+  # for application/x-www-form-urlencoded.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _key_: String
+  # * (required) _value_: String or Array containing String
+  # *Returns*:: String
   def make_cgi_params_key_value(key, value)
     result = []
     case value
     when Array
       value.each do |val|
-        result << [key, val].map {|x| URI.escape(x.to_s) }.join('=')
+        result << [key, val].map {|x| CGI.escape(x.to_s) }.join('=')
       end
     else
-      result << [key, value].map {|x| URI.escape(x.to_s) }.join('=')
+      result << [key, value].map {|x| CGI.escape(x.to_s) }.join('=')
     end
     return result
   end