rbbt-util 5.4.1 → 5.5.0

data/lib/rbbt/tsv/parser.rb

@@ -18,6 +18,7 @@ module TSV
 
       line = stream.gets
       raise "Empty content" if line.nil?
+      line = Misc.fixutf8 line
       line.chomp!
 
       # Process options line
@@ -33,7 +34,7 @@ module TSV
 
       # Process fields line
 
-      if line and line =~ /^#{@header_hash}/
+      if line and Misc.fixutf8(line) =~ /^#{@header_hash}/
         line.chomp!
         @fields = line.split(@sep)
         @key_field = @fields.shift

data/lib/rbbt/tsv/util.rb

@@ -69,6 +69,8 @@ module TSV
       pos ||= :key if key_field == field
       Log.medium "Field #{ field } was not found. Options: #{fields * ", "}" if pos.nil?
       pos
+    when key_field == field
+      :key
     else
       raise "No fields specified in TSV.identify_field" if fields.nil?
       Log.medium "Field #{ field } was not found. Options: (#{key_field}), #{fields * ", "}"

data/lib/rbbt/util/cmd.rb

@@ -1,4 +1,3 @@
-require 'rbbt/util/misc'
 require 'rbbt/util/log'
 require 'stringio'
 
@@ -99,7 +98,7 @@ module CMD
   end
 
   def self.cmd(cmd, options = {}, &block)
-    options = Misc.add_defaults options, :stderr => Log::DEBUG
+    options[:stderr] ||= Log::DEBUG
     in_content = options.delete(:in)
     stderr     = options.delete(:stderr)
     pipe       = options.delete(:pipe)

data/lib/rbbt/util/log.rb

@@ -17,54 +17,48 @@ module Log
     @logfile = nil
   end
 
-  #def self.severity=(severity)
-  #  @severity = severity
-  #end
-
-  #def self.severity
-  #  @severity
-  #end
-
   SEVERITY_COLOR = ["0;37m", "0;32m", "0;33m", "0;31m","0;37m", "0;32m", "0;33m"].collect{|e| "\033[#{e}"}
 
-  def self.log(message, severity = MEDIUM)
-    message ||= ""
+  def self.log(message = nil, severity = MEDIUM, &block)
+    message ||= block
     severity_color = SEVERITY_COLOR[severity]
     font_color = {false => "\033[0;37m", true => "\033[0m"}[severity >= INFO]
 
-    if severity >= self.severity and not message.empty?
-      str = "\033[0;37m#{Time.now.strftime("[%m/%d/%y-%H:%M:%S]")}#{severity_color}[#{severity.to_s}]\033[0m:#{font_color} " <<  message.strip  << "\033[0m"
-      STDERR.puts str
-      logfile.puts str unless logfile.nil?
-    end
+    return if severity < self.severity
+    message = message.call if Proc === message
+    return if message.nil? or message.empty?
+
+    str = "\033[0;37m#{Time.now.strftime("[%m/%d/%y-%H:%M:%S]")}#{severity_color}[#{severity.to_s}]\033[0m:#{font_color} " <<  message.strip  << "\033[0m"
+    STDERR.puts str
+    logfile.puts str unless logfile.nil?
   end
 
-  def self.debug(message)
-    log(message, DEBUG)
+  def self.debug(message = nil, &block)
+    log(message, DEBUG, &block)
   end
 
-  def self.low(message)
-    log(message, LOW)
+  def self.low(message = nil, &block)
+    log(message, LOW, &block)
   end
 
-  def self.medium(message)
-    log(message, MEDIUM)
+  def self.medium(message = nil, &block)
+    log(message, MEDIUM, &block)
   end
 
-  def self.high(message)
-    log(message, HIGH)
+  def self.high(message = nil, &block)
+    log(message, HIGH, &block)
   end
 
-  def self.info(message)
-    log(message, INFO)
+  def self.info(message = nil, &block)
+    log(message, INFO, &block)
   end
 
-  def self.warn(message)
-    log(message, WARN)
+  def self.warn(message = nil, &block)
+    log(message, WARN, &block)
   end
 
-  def self.error(message)
-    log(message, ERROR)
+  def self.error(message = nil, &block)
+    log(message, ERROR, &block)
   end
 
 
@@ -84,16 +78,26 @@ module Log
   end
 end
 
-def ddd(message, file = $stdout)
-  Log.debug "DEVEL: " << caller.first
-  Log.debug ""
-  Log.debug "=> " << message.inspect
-  Log.debug ""
-end
-
 def ppp(message)
-  puts "PRINT: " << caller.first
+  stack = caller
+  puts "#{Log::SEVERITY_COLOR[1]}PRINT:#{Log::SEVERITY_COLOR[0]} " << stack.first
   puts ""
-  puts "=> " << message.inspect
+  puts "=> " << message
   puts ""
 end
+
+def ddd(message, file = $stdout)
+  stack = caller
+  Log.debug{"#{Log::SEVERITY_COLOR[1]}DEVEL:#{Log::SEVERITY_COLOR[0]} " << stack.first}
+  Log.debug{""}
+  Log.debug{"=> " << message.inspect}
+  Log.debug{""}
+end
+
+def fff(object)
+  stack = caller
+  Log.debug{"#{Log::SEVERITY_COLOR[1]}FINGERPRINT:#{Log::SEVERITY_COLOR[0]} " << stack.first}
+  Log.debug{""}
+  Log.debug{require 'rbbt/util/misc'; "=> " << Misc.fingerprint(object) }
+  Log.debug{""}
+end

data/lib/rbbt/util/misc.rb

@@ -1,9 +1,5 @@
 require 'lockfile'
-require 'rbbt/util/chain_methods'
-require 'rbbt/resource/path'
-require 'rbbt/annotations'
 require 'net/smtp'
-require 'narray'
 require 'digest/md5'
 
 class Hash
@@ -16,6 +12,12 @@ class Hash
   end
 end
 
+module LaterString
+  def to_s
+    yield
+  end
+end
+
 module Misc
   class FieldNotFoundError < StandardError;end
 
@@ -201,10 +203,48 @@ module Misc
     filename
   end
 
+  def self.fingerprint(obj)
+    case obj
+    when nil
+      "nil"
+    when Symbol
+      ":" << obj.to_s
+    when String
+      if obj.length > 100
+        "'" << obj[0..20-1] << "<...#{obj.length}...>" << obj[-10..-1] << " " << "'"
+      else 
+        "'" << obj << "'"
+      end
+    when Array
+      if (length = obj.length) > 10
+        "[#{length}-" <<  (obj.values_at(0,1, length / 2, -2, -1).collect{|e| fingerprint(e)} * ",") << "]"
+      else
+        "[" << (obj.collect{|e| fingerprint(e) } * ",") << "]"
+      end
+    when TSV
+      obj.with_unnamed do
+        "TSV:{"<< fingerprint(obj.all_fields|| []).inspect << "," << fingerprint(obj.keys).inspect << "}"
+      end
+    when Hash
+      if obj.length > 10
+        "H:{"<< fingerprint(obj.keys) << "," << fingerprint(obj.values) << "}"
+      else
+        new = "{"
+        obj.each do |k,v|
+          new << k.to_s << '=>' << fingerprint(v) << ' '
+        end
+        new << "}"
+      end
+    else
+      obj.to_s
+    end
+  end
+
+
   def self.remove_long_items(obj)
     case
     when TSV === obj
-      remove_long_items(obj.fields + obj.keys.sort)
+      remove_long_items((obj.all_fields || []) + obj.keys.sort)
     when (Array === obj and obj.length > ARRAY_MAX_LENGTH)
       remove_long_items(obj[0..ARRAY_MAX_LENGTH-2] << "TRUNCATED at #{ ARRAY_MAX_LENGTH } (#{obj.length})")
     when (Hash === obj and obj.length > ARRAY_MAX_LENGTH)
@@ -310,7 +350,6 @@ module Misc
   def self.send_email(from, to, subject, message, options = {})
     IndiferentHash.setup(options)
     options = Misc.add_defaults options, :from_alias => nil, :to_alias => nil, :server => 'localhost', :port => 25, :user => nil, :pass => nil, :auth => :login
-    IndiferentHash.setup(options)
 
     server, port, user, pass, from_alias, to_alias, auth = Misc.process_options options, :server, :port, :user, :pass, :from_alias, :to_alias, :auth
 
@@ -406,6 +445,7 @@ end
   }
 
   def self.fast_align(reference, sequence)
+    require 'narray'
     init_gap = -1
     gap = -2
     diff = -2
@@ -486,11 +526,35 @@ end
   end
 
   def self.is_filename?(string)
-    return true if Path === string
+    return true if string.respond_to? :exists
     return true if String === string and string.length < 265 and File.exists? string
     return false
   end
 
+  def self.sorted_array_hits(a1, a2)
+    e1, e2 = a1.shift, a2.shift
+    counter = 0
+    match = []
+    while true
+      break if e1.nil? or e2.nil?
+      case e1 <=> e2
+      when 0
+        match << counter
+        e1, e2 = a1.shift, a2.shift
+        counter += 1
+      when -1
+        while not e1.nil? and e1 < e2
+          e1 = a1.shift 
+          counter += 1
+        end
+      when 1
+        e2 = a2.shift
+        e2 = a2.shift while not e2.nil? and e2 < e1
+      end
+    end
+    match
+  end
+
   def self.intersect_sorted_arrays(a1, a2)
     e1, e2 = a1.shift, a2.shift
     intersect = []
@@ -542,6 +606,33 @@ end
     new
   end
 
+  def self.binary_include?(array, elem)
+    upper = array.size - 1
+    lower = 0
+
+    return -1 if upper < lower
+
+    while(upper >= lower) do
+      idx = lower + (upper - lower) / 2
+      value = array[idx]
+
+      case elem <=> value
+      when 0
+        return true
+      when -1
+        upper = idx - 1
+      when 1
+        lower = idx + 1
+      else
+        raise "Cannot compare #{[elem.inspect, value.inspect] * " with "}"
+      end
+    end
+
+    return false
+  end
+
+
+
   def self.array2hash(array, default = nil)
     hash = {}
     array.each do |key, value|
@@ -748,10 +839,11 @@ end
 
   def self.html_tag(tag, content = nil, params = {})
     attr_str = hash_to_html_tag_attributes(params)
+    attr_str = " " << attr_str if String === attr_str and attr_str != ""
     html = if content.nil?
-      "<#{ tag } #{attr_str} />"
+      "<#{ tag }#{attr_str}/>"
     else
-      "<#{ tag } #{attr_str} >#{ content }</#{ tag }>"
+      "<#{ tag }#{attr_str}>#{ content }</#{ tag }>"
     end
 
     html
@@ -982,7 +1074,7 @@ end
 
       end
 
-      str << "_" << hash2md5(v.info) if Annotated === v
+      str << "_" << hash2md5(v.info) if defined? Annotated and Annotated === v
     end
     hash.unnamed = unnamed if hash.respond_to? :unnamed
 
@@ -1099,7 +1191,7 @@ end
     chunks
   end
 
-  # Divides the array into +num+ chunks of the same size by placing one
+  # Divides the array into chunks of +num+ same size by placing one
   # element in each chunk iteratively.
   def self.ordered_divide(array, num)
     last = array.length - 1
@@ -1120,6 +1212,7 @@ end
 
   def self.snake_case(string)
     return nil if string.nil?
+    string = string.to_s if Symbol === string
     string.
       gsub(/([A-Z]{2,})([A-Z][a-z])/,'\1_\2').
       gsub(/([a-z])([A-Z])/,'\1_\2').
@@ -1187,54 +1280,49 @@ class RBBTError < StandardError
 end
 
 module IndiferentHash
-  extend ChainMethods
-  self.chain_prefix = :indiferent
-
-  def indiferent_get_brackets(key)
-    case 
-    when (Symbol === key and indiferent_clean_include? key)
-      indiferent_clean_get_brackets(key)
-    when (Symbol === key and indiferent_clean_include? key.to_s)
-      indiferent_clean_get_brackets(key.to_s)
-    when (String === key and indiferent_clean_include? key)
-      indiferent_clean_get_brackets(key)
-    when (String === key and indiferent_clean_include? key.to_sym)
-      indiferent_clean_get_brackets(key.to_sym)
+
+  def self.setup(hash)
+    hash.extend IndiferentHash 
+  end
+
+  def [](key)
+    res = super(key) and return res
+
+    case key
+    when Symbol, Module
+      super(key.to_s)
+    when String
+      super(key.to_sym)
     else
-      indiferent_clean_get_brackets(key) 
+      super(key)
     end
   end
 
-  def indiferent_values_at(*key_list)
-    res = []
-    key_list.each{|key| res << indiferent_get_brackets(key)}
-    res
+  def values_at(*key_list)
+    key_list.inject([]){|acc,key| acc << self[key]}
   end
 
-  def indiferent_include?(key)
-    case
-    when Symbol === key
-      indiferent_clean_include?(key) or indiferent_clean_include?(key.to_s) 
-    when String === key
-      indiferent_clean_include?(key) or indiferent_clean_include?(key.to_sym) 
+  def include?(key)
+    case key
+    when Symbol, Module
+      super(key) || super(key.to_s)
+    when String
+      super(key) || super(key.to_sym)
     else
-      indiferent_clean_include?(key)
+      super(key)
     end
   end
 
-  def indiferent_delete(value)
-    if indiferent_clean_include? value.to_s
-      indiferent_clean_delete(value.to_s) 
+  def delete(key)
+    case key
+    when Symbol, Module
+      super(key) || super(key.to_s)
+    when String
+      super(key) || super(key.to_sym)
     else
-      indiferent_clean_delete(value.to_sym) 
+      super(key)
     end
   end
-
-  def self.setup(hash)
-    return hash if IndiferentHash === hash
-    hash.extend IndiferentHash unless IndiferentHash === hash
-    hash
-  end
 end
 
 module PDF2Text

data/lib/rbbt/util/open.rb

@@ -1,6 +1,6 @@
 require 'rbbt/util/cmd'
-require 'rbbt/util/misc'
 require 'rbbt/util/tmpfile'
+require 'rbbt/util/misc'
 
 require 'zlib'
 
@@ -19,6 +19,8 @@ module Open
                              File.exists?(Rbbt.etc.repository_dirs.find) ? 
                                File.read(Rbbt.etc.repository_dirs.find).split("\n") :
                                []
+                           rescue
+                             []
                            end
     end
 
@@ -393,11 +395,6 @@ module Open
       end
     when String === content
       file_write(file, content, mode)
-      #File.open(file, mode) do |f|
-      #  f.flock(File::LOCK_EX)
-      #  f.write content 
-      #  f.flock(File::LOCK_UN)
-      #end
     else
       begin
         File.open(file, mode) do |f| 
@@ -415,14 +412,3 @@ module Open
     end
   end
 end
-
-if __FILE__ == $0
-  require 'benchmark'
-  require 'progress-monitor'
-
-  file = '/home/mvazquezg/rbbt/data/dbs/entrez/gene_info'
-  puts Benchmark.measure {
-    #Open.open(file).read.split(/\n/).each do |l| l end
-    Open.read(file) do |l| l end
-  }
-end