bio 1.4.2 → 1.4.3

data/gemfiles/Gemfile.travis-jruby1.8

@@ -0,0 +1,7 @@
+source :rubygems
+
+gem "rake"
+
+## disabled because of build error on Travis
+#gem "libxml-ruby"
+

data/gemfiles/Gemfile.travis-jruby1.9

@@ -0,0 +1,10 @@
+source :rubygems
+
+gem "rake"
+
+## disabled because of build error on Travis
+#gem "libxml-ruby"
+
+## disabled because of "uninitialized constant XML::SaxParser" error
+#gem "soap4r-ruby1.9"
+

data/gemfiles/Gemfile.travis-ruby1.8

@@ -0,0 +1,7 @@
+source :rubygems
+
+gem "rake"
+
+gem "xmlparser"
+gem "libxml-ruby"
+

data/gemfiles/Gemfile.travis-ruby1.9

@@ -0,0 +1,10 @@
+source :rubygems
+
+gem "rake"
+
+gem "xmlparser"
+gem "libxml-ruby"
+
+## disabled because of "uninitialized constant XML::SaxParser" error
+#gem "soap4r-ruby1.9"
+

data/gemfiles/modify-Gemfile.rb

@@ -0,0 +1,28 @@
+#
+
+require 'pathname'
+
+envname_default_task = 'BIORUBY_RAKE_DEFAULT_TASK'
+
+gem_dir = Pathname.new(File.join(File.dirname(__FILE__), '..')).realpath
+
+case t = ENV[envname_default_task]
+when 'gem-test'
+  # do nothing
+else
+  $stderr.print "#{$0}: skipped: ENV[#{envname_default_task}]=#{t.inspect}\n"
+  exit(0)
+end
+
+target = ENV['BUNDLE_GEMFILE']
+unless target then
+  $stderr.puts("Error: env BUNDLE_GEMFILE is not set.")
+end
+
+File.open(target, 'a') do |w|
+  $stderr.puts "Add a line to #{target}"
+  $stderr.puts "gem 'bio', :path => '#{gem_dir}'"
+  w.puts ""
+  w.puts "gem 'bio', :path => '#{gem_dir}'"
+end
+

data/gemfiles/prepare-gemspec.rb

@@ -0,0 +1,25 @@
+#
+
+require 'pathname'
+require 'fileutils'
+
+envname_default_task = 'BIORUBY_RAKE_DEFAULT_TASK'
+
+gem_dir = Pathname.new(File.join(File.dirname(__FILE__), '..')).realpath
+
+case t = ENV[envname_default_task]
+when 'gem-test'
+  # do nothing
+else
+  $stderr.print "#{$0}: skipped: ENV[#{envname_default_task}]=#{t.inspect}\n"
+  exit(0)
+end
+
+$stderr.puts "cd #{gem_dir}"
+Dir.chdir(gem_dir)
+
+args = [ 'bioruby.gemspec', '.gemspec' ]
+
+$stderr.puts(['cp', *args].join(" "))
+FileUtils.cp(*args)
+

data/lib/bio/alignment.rb

@@ -2319,7 +2319,7 @@ module Bio
 
         # prepare temporary file
         def _prepare_tempfile(str = nil)
-          tf_in = Tempfile.open(str ? 'alignment_i' :'alignment_o')
+          tf_in = Tempfile.open(str ? 'alignment_i' : 'alignment_o')
           tf_in.print str if str
           tf_in.close(false)
           tf_in

data/lib/bio/appl/bl2seq/report.rb

@@ -4,7 +4,6 @@
 # Copyright:: Copyright (C) 2005 Naohisa Goto <ng@bioruby.org>
 # License::   The Ruby License
 #
-#  $Id:$
 #
 # Bio::Blast::Bl2seq::Report is a NCBI bl2seq (BLAST 2 sequences) output parser.
 #
@@ -15,9 +14,10 @@
 # lib/bio/appl/blast/format0.rb.
 #
 
-require 'bio/appl/blast/format0'
-
 module Bio
+
+require 'bio/appl/blast' unless const_defined?(:Blast)
+
 class Blast
 
   class Bl2seq

data/lib/bio/appl/blast/ddbj.rb

@@ -4,10 +4,7 @@
 # Copyright::  Copyright (C) 2008       Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
-# $Id:$
-#
 
-require 'bio/appl/blast/remote'
 require 'bio/io/ddbjrest'
 
 module Bio::Blast::Remote

data/lib/bio/appl/blast/format0.rb

@@ -4,8 +4,6 @@
 # Copyright::  Copyright (C) 2003-2006 GOTO Naohisa <ng@bioruby.org>
 # License::    The Ruby License
 #
-# $Id:$
-#
 # == Description
 #
 # NCBI BLAST default (-m 0 option) output parser.
@@ -19,18 +17,15 @@
 # * http://www.ncbi.nlm.nih.gov/blast/ 
 #
 
-begin
-  require 'strscan'
-rescue LoadError
-end
+require 'strscan'
 require 'singleton'
 
-#--
-#require 'bio/db'
-#++
 require 'bio/io/flatfile'
 
 module Bio
+
+  require 'bio/appl/blast' unless const_defined?(:Blast)
+
   class Blast
     module Default #:nodoc:
 
@@ -73,19 +68,6 @@ module Bio
         # Returns whole entry as a string.
         def to_s; @entry; end
 
-        #:stopdoc:
-        # prevent using StringScanner_R (in old version of strscan)
-        if !defined?(StringScanner) then
-          def initialize(*arg)
-            raise 'couldn\'t load strscan.so'
-          end #def
-        elsif StringScanner.name == 'StringScanner_R' then
-          def initialize(*arg)
-            raise 'cannot use StringScanner_R'
-          end #def
-        end
-        #:startdoc:
-
         # Defines attributes which delegate to @f0dbstat objects.
         def self.delegate_to_f0dbstat(*names)
           names.each do |x|

data/lib/bio/appl/blast/genomenet.rb

@@ -7,14 +7,12 @@
 # Copyright::  Copyright (C) 2008       Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
-# $Id:$
 #
 
 require 'net/http'
 require 'uri'
 require 'bio/command'
 require 'shellwords'
-require 'bio/appl/blast/remote'
 
 module Bio::Blast::Remote
 
@@ -58,6 +56,11 @@ module Bio::Blast::Remote
   #   tblastn  | AA    | genes-nt, genome, vgenes.nuc
   #  ----------+-------+---------------------------------------------------
   #
+  # === BLAST options
+  #
+  # Options are basically the same as those of the blastall command
+  # in NCBI BLAST. See http://www.genome.jp/tools-bin/show_man?blast2
+  #
   # == See also
   #
   # * Bio::Blast
@@ -158,7 +161,8 @@ module Bio::Blast::Remote
       host = Host
       #host = "blast.genome.jp"
       #path = "/sit-bin/nph-blast"
-      path = "/sit-bin/blast" #2005.08.12
+      #path = "/sit-bin/blast" #2005.08.12
+      path = "/tools-bin/blast" #2012.01.12
 
       options = make_command_line_options
       opt = Bio::Blast::NCBIOptions.new(options)
@@ -221,9 +225,9 @@ module Bio::Blast::Remote
           @output = result.body
           # waiting for BLAST finished
           while /Your job ID is/ =~ @output and
-              /Your result will be displayed here\<br\>/ =~ @output
-            if /This page will be reloaded automatically in\s*((\d+)\s*min\.)?\s*(\d+)\s*sec\./ =~ @output then
-              reloadtime = $2.to_i * 60 + $3.to_i
+              /Your result will be displayed here\.?\<br\>/i =~ @output
+            if /This page will be reloaded automatically in\s*((\d+)\s*min\.)?\s*((\d+)\s*sec\.)?/ =~ @output then
+              reloadtime = $2.to_i * 60 + $4.to_i
               reloadtime = 300 if reloadtime > 300
               reloadtime = 1 if reloadtime < 1
             else
@@ -238,14 +242,23 @@ module Bio::Blast::Remote
           end
         end
 
-        # workaround 2005.08.12 + 2011.01.27
-        if /\<A +HREF=\"(http\:\/\/[\-\.a-z0-9]+\.genome\.jp(\/tmp\/[^\"]+))\"\>Show all result\<\/A\>/i =~ @output.to_s then
-          @output = Bio::Command.read_uri($1)
-          txt = @output.to_s.split(/\<pre\>/)[1]
-          raise 'cannot understand response' unless txt
-          txt.sub!(/\<\/pre\>.*\z/m, '')
-          txt.sub!(/.*^ \-{20,}\s*/m, '')
-          @output = txt.gsub(/\&lt\;/, '<')
+        # workaround 2005.08.12 + 2011.01.27 + 2011.7.22
+        if /\<A +HREF=\"(http\:\/\/[\-\.a-z0-9]+\.genome\.jp)?(\/tmp\/[^\"]+)\"\>Show all result\<\/A\>/i =~ @output.to_s then
+          all_prefix = $1
+          all_path = $2
+          all_prefix = "http://#{Host}" if all_prefix.to_s.empty?
+          all_uri = all_prefix + all_path
+          @output = Bio::Command.read_uri(all_uri)
+          case all_path
+          when /\.txt\z/
+            ; # don't touch the data
+          else
+            txt = @output.to_s.split(/\<pre\>/)[1]
+            raise 'cannot understand response' unless txt
+            txt.sub!(/\<\/pre\>.*\z/m, '')
+            txt.sub!(/.*^ \-{20,}\s*/m, '')
+            @output = txt
+          end
         else
           raise 'cannot understand response'
         end
@@ -254,10 +267,14 @@ module Bio::Blast::Remote
       # for -m 0 (NCBI BLAST default) output, html tags are removed.
       if opt_m.to_i == 0 then
         #@output_bak = @output
-        txt = @output.gsub(/^\s*\<img +src\=\"\/Fig\/arrow\_top\.gif\"\>.+$\r?\n/, '')
+        txt = @output.sub!(/^\<select .*/, '')
+        #txt.gsub!(/^\s*\<img +src\=\"\/Fig\/arrow\_top\.gif\"\>.+$\r?\n/, '')
         txt.gsub!(/^.+\<\/form\>$/, '')
-        txt.gsub!(/^\<form *method\=\"POST\" name\=\"clust\_check\"\>.+$\r?\n/, '')
+        #txt.gsub!(/^\<form *method\=\"POST\" name\=\"clust\_check\"\>.+$\r?\n/, '')
+        txt.gsub!(/\<a href\=\"\/tmp[^\"]\>\&uarr\;\&nbsp\;Top\<\/a\>/, '')
         txt.gsub!(/\<[^\>\<]+\>/m, '')
+        txt.gsub!(/\&gt\;/, '>')
+        txt.gsub!(/\&lt\;/, '<')
         @output = txt
       end
 

data/lib/bio/appl/blast/ncbioptions.rb

@@ -13,10 +13,13 @@
 # It is internally used in Bio::Blast and some other classes.
 #
 
-require 'bio/appl/blast'
 require 'shellwords'
 
-class Bio::Blast
+module Bio
+
+require 'bio/appl/blast' unless const_defined?(:Blast)
+
+class Blast
 
   # A class to parse and store NCBI-tools style command-line options.
   # It is internally used in Bio::Blast and some other classes.
@@ -217,4 +220,6 @@ class Bio::Blast
 
   end #class NCBIOptions
 
-end #class Bio::Blast
+end #class Blast
+
+end #module Bio

data/lib/bio/appl/blast/remote.rb

@@ -4,12 +4,12 @@
 # Copyright::  Copyright (C) 2008  Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
-# $Id:$
-#
 
-require 'bio/appl/blast'
+module Bio
+
+require 'bio/appl/blast' unless const_defined?(:Blast)
 
-class Bio::Blast
+class Blast
 
   # Bio::Blast::Remote is a namespace for Remote Blast factory.
   module Remote
@@ -102,5 +102,6 @@ class Bio::Blast
 
   end #module Remote
 
-end #class Bio::Blast
+end #class Blast
 
+end #module Bio

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

@@ -4,16 +4,13 @@
 # Copyright::  Copyright (C) 2003 Toshiaki Katayama <k@bioruby.org>
 # License::    The Ruby License
 #
-# $Id:$
-#
 
-require 'bio/appl/blast'
-require 'bio/appl/blast/xmlparser'
-require 'bio/appl/blast/rexml'
-require 'bio/appl/blast/format8'
 require 'bio/io/flatfile'
 
 module Bio
+
+require 'bio/appl/blast' unless const_defined?(:Blast)
+
 class Blast
 
 # = Bio::Blast::Report
@@ -43,6 +40,13 @@ class Blast
 # 
 class Report
 
+  #--
+  # require lines moved here to avoid circular require
+  #++
+  require 'bio/appl/blast/xmlparser'
+  require 'bio/appl/blast/rexml'
+  require 'bio/appl/blast/format8'
+
   # for Bio::FlatFile support (only for XML data)
   DELIMITER = RS = "</BlastOutput>\n"
 

data/lib/bio/appl/blast/rpsblast.rb

@@ -4,7 +4,6 @@
 # Copyright::  Copyright (C) 2008 Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
-# $Id:$
 #
 # == Description
 #
@@ -22,10 +21,12 @@
 # * http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml
 #
 
-require 'bio/appl/blast/format0'
 require 'bio/io/flatfile'
 
 module Bio
+
+require 'bio/appl/blast' unless const_defined?(:Blast)
+
 class Blast
 
   # NCBI RPS Blast (Reversed Position Specific Blast) namespace.

data/lib/bio/appl/blast/wublast.rb

@@ -4,7 +4,6 @@
 # Copyright::  Copyright (C) 2003, 2008 Naohisa GOTO <ng@bioruby.org>
 # License::    The Ruby License
 #
-# $Id:$
 #
 # == Description
 #
@@ -21,9 +20,10 @@
 # * http://www.ebi.ac.uk/blast2/
 #
 
-require 'bio/appl/blast/format0'
-
 module Bio
+
+  require 'bio/appl/blast' unless const_defined?(:Blast)
+
   class Blast
     module WU #:nodoc:
 

data/lib/bio/command.rb

@@ -232,19 +232,37 @@ module Command
   # * (required) _cmd_: Array containing String objects
   # * (optional) _options_: Hash
   # *Returns*:: (undefined)
-  def call_command_popen(cmd, options = {})
+  def call_command_popen(cmd, options = {}, &block)
     if RUBY_VERSION >= "1.9.0" then
-      # For Ruby 1.9 or later, using command line array with options.
-      dir = options[:chdir]
-      cmd = safe_command_line_array(cmd)
-      if dir then
-        cmd = cmd + [ { :chdir => dir } ]
-      end
-      r = IO.popen(cmd, "r+") do |io|
-        yield io
+      if RUBY_ENGINE == 'jruby' then
+        _call_command_popen_jruby19(cmd, options, &block)
+      else
+        _call_command_popen_ruby19(cmd, options, &block)
       end
-      return r
+    else
+      _call_command_popen_ruby18(cmd, options, &block)
     end
+  end
+
+  # This method is internally called from the call_command method.
+  # In normal case, use call_command, and do not call this method directly.
+  #
+  # Executes the program via IO.popen.
+  # A block must be given. An IO object is passed to the block.
+  #
+  # See the document of call_command for available options.
+  #
+  # The method is written for Ruby 1.8.
+  #
+  # In Ruby 1.8, although shell unsafe characters are escaped,
+  # if inescapable characters exists, it raises RuntimeError.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _cmd_: Array containing String objects
+  # * (optional) _options_: Hash
+  # *Returns*:: (undefined)
+  def _call_command_popen_ruby18(cmd, options = {})
     # For Ruby 1.8, using command line string.
     str = make_command_line(cmd)
     # processing options
@@ -267,6 +285,66 @@ module Command
       yield io
     end
   end
+  private :_call_command_popen_ruby18
+
+  # This method is internally called from the call_command method.
+  # In normal case, use call_command, and do not call this method directly.
+  #
+  # Executes the program via IO.popen.
+  # A block must be given. An IO object is passed to the block.
+  #
+  # See the document of call_command for available options.
+  #
+  # The method can be run only on Ruby (MRI) 1.9 or later versions.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _cmd_: Array containing String objects
+  # * (optional) _options_: Hash
+  # *Returns*:: (undefined)
+  def _call_command_popen_ruby19(cmd, options = {})
+    # For Ruby 1.9 or later, using command line array with options.
+    dir = options[:chdir]
+    cmd = safe_command_line_array(cmd)
+    if dir then
+      cmd = cmd + [ { :chdir => dir } ]
+    end
+    r = IO.popen(cmd, "r+") do |io|
+      yield io
+    end
+    return r
+  end
+  private :_call_command_popen_ruby19
+
+  # This method is internally called from the call_command method.
+  # In normal case, use call_command, and do not call this method directly.
+  #
+  # Executes the program via IO.popen.
+  # A block must be given. An IO object is passed to the block.
+  #
+  # See the document of call_command for available options.
+  #
+  # The method is written for the workaround of the JRuby bugs:
+  # * {JRUBY-6195}[http://jira.codehaus.org/browse/JRUBY-6195] Process.spawn
+  #   (and related methods) ignore option hash
+  # * {JRUBY-6818}[http://jira.codehaus.org/browse/JRUBY-6818] Kernel.exec,
+  #   Process.spawn (and IO.popen etc.) raise error when program is an array
+  #   containing two strings
+  # This method may be removed after the bugs are resolved.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _cmd_: Array containing String objects
+  # * (optional) _options_: Hash
+  # *Returns*:: (undefined)
+  def _call_command_popen_jruby19(cmd, options = {}, &block)
+    if !options.empty? or cmd.size == 1 then
+      _call_command_popen_ruby18(cmd, options, &block)
+    else
+      _call_command_popen_ruby19(cmd, options, &block)
+    end
+  end
+  private :_call_command_popen_jruby19
 
   # This method is internally called from the call_command method.
   # In normal case, use call_command, and do not call this method directly.
@@ -547,33 +625,37 @@ module Command
   # BioRuby library internal use only.
   class Tmpdir
 
-    # Returns finalizer object for Tmpdir class.
-    # Internal use only. Users should not call this method directly.
-    # 
-    # Acknowledgement: The essense of the code is taken from tempfile.rb
-    # in Ruby 1.8.7.
+    # Internal use only. Users should not use this class directly.
     #
-    # ---
-    # *Arguments*:
-    # * (required) _data_: Array containing internal data
-    # *Returns*:: Proc object
-    def self.callback(data)
-      pid = $$
-      lambda {
-        path, = *data
-        if pid == $$
-          $stderr.print "removing ", path, " ..." if $DEBUG
-          if path and !path.empty? and
-              File.directory?(path) and
-              !File.symlink?(path) then
-            Bio::Command.remove_entry_secure(path)
-            $stderr.print "done\n" if $DEBUG
-          else
-            $stderr.print "skipped\n" if $DEBUG
-          end
+    # Bio::Command::Tmpdir::Remover is a class to remove temporary
+    # directory.
+    #
+    # Acknowledgement: The essense of the code is taken from tempfile.rb
+    # in Ruby trunk (svn 34413) and in Ruby 1.8.7.
+    class Remover
+      # Internal use only. Users should not call this method.
+      def initialize(data)
+        @pid = $$
+        @data = data
+      end
+
+      # Internal use only. Users should not call this method.
+      def call(*args)
+        return if @pid != $$
+
+        path, = *@data
+
+        STDERR.print "removing ", path, "..." if $DEBUG
+        if path and !path.empty? and
+            File.directory?(path) and
+            !File.symlink?(path) then
+          Bio::Command.remove_entry_secure(path)
+          $stderr.print "done\n" if $DEBUG
+        else
+          $stderr.print "skipped\n" if $DEBUG
         end
-      }
-    end
+      end
+    end #class Remover
 
     # Creates a new Tmpdir object.
     # The arguments are the same as Bio::Command.mktmpdir.
@@ -585,7 +667,7 @@ module Command
     # *Returns*:: Tmpdir object
     def initialize(prefix_suffix = nil, tmpdir = nil)
       @data = []
-      @clean_proc = self.class.callback(@data)
+      @clean_proc = Remover.new(@data)
       ObjectSpace.define_finalizer(self, @clean_proc)
       @data.push(@path = Bio::Command.mktmpdir(prefix_suffix, tmpdir).freeze)
     end