rbbt-util 4.3.0 → 4.4.0

data/README.rdoc

@@ -4,7 +4,8 @@
 
     :script
 
-    bash < <(curl -s https://rvm.beginrescueend.com/install/rvm)
+    curl -L https://get.rvm.io | bash -s stable --ruby
+
     cd
     cat .bash_profile > tmp.bash_profile
     echo '[[ -s "$HOME/.rvm/scripts/rvm" ]] && . "$HOME/.rvm/scripts/rvm"' >> tmp.bash_profile
@@ -42,7 +43,7 @@
 
     :script
     
-    gem install rbbt-util rbbt-sources rbbt-text rbbt-phgx
+    gem install rbbt-util rbbt-sources rbbt-text rbbt-phgx rbbt-entities rbbt-views
 
 3.bis - Or install github repos and make ruby use them
 
@@ -50,10 +51,13 @@
 
     cd
     cd git/
-    git clone git://github.com/mikisvaz/rbbt-util.git
-    git clone git://github.com/mikisvaz/rbbt-sources.git
-    git clone git://github.com/mikisvaz/rbbt-text.git
-    git clone git://github.com/mikisvaz/rbbt-phgx.git
+    git clone git@github.com:mikisvaz/rbbt-util.git
+    git clone git@github.com:mikisvaz/rbbt-sources.git
+    git clone git@github.com:mikisvaz/rbbt-text.git
+    git clone git@github.com:mikisvaz/rbbt-phgx.git
+    git clone git@github.com:mikisvaz/rbbt-entities.git
+    git clone git@github.com:mikisvaz/rbbt-dm.git
+    git clone git@github.com:mikisvaz/rbbt-views.git
     alias druby="env RBBT_LOG=0 ruby $(for d in $HOME/git/rbbt-*;do echo -n "-I$d/lib ";done)"
     alias drake="env RBBT_LOG=0 rake $(for d in $HOME/git/rbbt-*;do echo -n "-I$d/lib ";done)"
 
@@ -67,6 +71,7 @@
     
     :script
 
+    mkdir -p ~/.rbbt/etc
     mkdir -p ~/git/workflows
     echo "~/git/workflows/" > ~/.rbbt/etc/workflow_dir
 

data/bin/rbbt_exec.rb

@@ -12,9 +12,17 @@ code = case
          Open.read(code_file)
        end
 
-data = eval code
+begin
+  data = eval code
+rescue Exception
+  puts "#:rbbt_exec Error"
+  puts $!.message
+  puts $!.backtrace * "\n"
+  exit(-1)
+end
 
 data = data.to_s(:sort, true) if TSV === data
+data = data * "\n" if Array === data
 
 case
 when (output.nil? or output == '-')

data/lib/rbbt/annotations.rb

@@ -7,6 +7,7 @@ module Annotated
   attr_accessor :context
   attr_accessor :container
   attr_accessor :container_index
+  attr_accessor :id
 
   def self.extended(base)
     base.annotation_types ||= []
@@ -29,12 +30,12 @@ module Annotated
   end
 
   def id
-    Misc.hash2md5 info.merge :self => self
+    @id ||= self.respond_to?(:annotation_id) ? annotation_id : Misc.hash2md5(info.merge(:self => self))
   end
 
   def self.load(object, info)
     annotation_types = info[:annotation_types] || []
-    annotation_types = annotation_types.split("+") if String === annotation_types
+    annotation_types = annotation_types.split("|") if String === annotation_types
 
     return object if annotation_types.nil? or annotation_types.empty?
 
@@ -43,6 +44,7 @@ module Annotated
       mod.setup(object, *info.values_at(*mod.all_annotations))
     end
 
+    object.id = info[:entity_id] if info.include? :entity_id
     object
   end
 
@@ -61,13 +63,15 @@ module Annotated
         when field == "JSON"
           info.to_json
         when field == "annotation_types"
-          annotation_types.collect{|t| t.to_s} * "+"
+          annotation_types.collect{|t| t.to_s} * "|"
         when field == "literal"
           (Array === self ? "Array:" << self * "|" : self).gsub(/\n|\t/, ' ')
         when info.include?(field.to_sym)
-          info.delete(field.to_sym)
+          res = info.delete(field.to_sym)
+          Array === res ? "Array:" << res * "|" : res
         when self.respond_to?(field)
-          self.send(field)
+          res = self.send(field)
+          Array === res ? "Array:"<< res * "|" : res
         end
       end
 
@@ -89,7 +93,7 @@ module Annotated
 
     object = object["Array:".length..-1].split("|") if object =~ /^Array:/
 
-    if Array === values
+    if Array === values.first
       Misc.zip_fields(values).collect do |list|
         fields.each_with_index do |field,i|
           if field == "JSON"
@@ -116,6 +120,19 @@ module Annotated
     self.load(object, info)
   end
 
+  def self.json(annotations, literal = false)
+    annotations = [annotations] unless Array === annotations
+    hash = {}
+    annotations.each do |annotation|
+      if literal
+        hash[annotation.id] = annotation.info.merge(:literal => annotation)
+      else
+        hash[annotation.id] = annotation.info
+      end
+    end
+    hash.to_json
+  end
+
   def self.tsv(annotations, *fields)
     return nil if annotations.nil?
     fields = case
@@ -124,8 +141,15 @@ module Annotated
                fields << :annotation_types
              when (fields == [:literal] and not annotations.empty?)
                fields << :literal
+             when (fields == [:all] and Annotated === annotations)
+               fields = [:annotation_types] + annotations.annotations 
+               fields << :literal
              when (fields == [:all] and not annotations.empty?)
-               fields = [:annotation_types] + (Annotated === annotations ? annotations.annotations : annotations.compact.first.annotations)
+               raise "Input array must be annotated or its elements must be" if not Annotated === annotations.compact.first and not Array === annotations.compact.first
+               raise "Input array must be annotated or its elements must be. No duble arrays of singly annotated entities." if not Annotated === annotations.compact.first and Array === annotations.compact.first
+               fields = [:annotation_types] + (Annotated === annotations ? 
+                                               annotations.annotations : 
+                                               annotations.compact.first.annotations)
                fields << :literal
              when annotations.empty?
                [:annotation_types, :literal]
@@ -137,7 +161,7 @@ module Annotated
 
     case
     when (Annotated === annotations and not (AnnotatedArray === annotations and annotations.double_array))
-      tsv = TSV.setup({}, :key_field => "Single", :fields => fields, :type => :list, :unnamed => true)
+      tsv = TSV.setup({}, :key_field => "List", :fields => fields, :type => :list, :unnamed => true)
       tsv[annotations.id] = annotations.tsv_values(*fields)
     when Array === annotations 
       tsv = TSV.setup({}, :key_field => "ID", :fields => fields, :type => :list, :unnamed => true)
@@ -158,7 +182,7 @@ module Annotated
       end
 
       case tsv.key_field 
-      when "Single"
+      when "List"
         annotated_entities.first
       else
         annotated_entities
@@ -251,6 +275,7 @@ module Annotation
 
     inputs = Misc.positional2hash(all_annotations, *values)
     inputs.each do |name, value|
+      value = value.split("|") if String === value and value.index "|"
       object.send(name.to_s + '=', value)
     end
 
@@ -282,9 +307,11 @@ module AnnotatedArray
     annotation_types.each do |mod|
       mod.setup(value, *info.values_at(*mod.all_annotations))
     end
-    value.context = self.context
-    value.container = self
-    value.container_index = pos
+    if Annotated === value
+      value.context = self.context
+      value.container = self
+      value.container_index = pos
+    end
     value
   end
 
@@ -295,9 +322,11 @@ module AnnotatedArray
       annotation_types.each do |mod|
         mod.setup(value, info)
       end
-      value.context = self.context
-      value.container = self
-      value.container_index = i
+      if Annotated === value
+        value.context = self.context
+        value.container = self
+        value.container_index = i
+      end
       i += 1
       yield value
     end
@@ -319,18 +348,25 @@ module AnnotatedArray
     res
   end
 
-  def annotated_array_select
+  def annotated_array_select(method = nil, *args)
     res = []
-    annotated_array_each do |value|
-      res << value if yield(value)
+    if method
+      res = self.zip(self.send(method, *args)).select{|e,result| result}.collect{|element,r| element}
+    else
+      annotated_array_each do |value|
+        res << value if yield(value)
+      end
     end
 
     annotation_types.each do |mod|
       mod.setup(res, *info.values_at(*mod.annotations))
     end
+
     res.context = self.context
     res.container = self.container
 
+    res.extend AnnotatedArray if AnnotatedArray === self
+
     res
   end
 
@@ -346,16 +382,23 @@ module AnnotatedArray
     res.context = self.context
     res.container = self.container
 
+    res.extend AnnotatedArray if AnnotatedArray === self
+
     res
   end
 
   def annotated_array_subset(list)
     value = (self & list)
+
     annotation_types.each do |mod|
       mod.setup(value, *info.values_at(*mod.all_annotations))
     end
+
     value.context = self.context
     value.container = self.container
+
+    value.extend AnnotatedArray if AnnotatedArray === self
+
     value
   end
 
@@ -369,6 +412,8 @@ module AnnotatedArray
     value.context = self.context
     value.container = self.container
 
+    value.extend AnnotatedArray if AnnotatedArray === self
+
     value
   end
 
@@ -382,6 +427,8 @@ module AnnotatedArray
     value.context = self.context
     value.container = self.container
 
+    value.extend AnnotatedArray if AnnotatedArray === self
+
     value
   end
  
@@ -395,6 +442,8 @@ module AnnotatedArray
     value.context = self.context
     value.container = self.container
 
+    value.extend AnnotatedArray if AnnotatedArray === self
+
     value
   end
 
@@ -408,6 +457,8 @@ module AnnotatedArray
     value.context = self.context
     value.container = self.container
 
+    value.extend AnnotatedArray if AnnotatedArray === self
+
     value
   end
 
@@ -421,6 +472,8 @@ module AnnotatedArray
     value.context = self.context
     value.container = self.container
 
+    value.extend AnnotatedArray if AnnotatedArray === self
+
     value
   end
 
@@ -434,18 +487,19 @@ module AnnotatedArray
     value.context = self.context
     value.container = self.container
 
+    value.extend AnnotatedArray if AnnotatedArray === self
+
     value
   end
 
-  def annotated_array_sort
-    value = self.annotated_array_clean_sort
+  def annotated_array_sort(&block)
+    value = self.collect.sort(&block).collect{|value| value.respond_to?(:clean_annotations) ? value.clean_annotations.dup : value.dup }
 
     annotation_types.each do |mod|
       mod.setup(value, *info.values_at(*mod.annotations))
     end
 
-    value.context = self.context
-    value.container = self.container
+    value.extend AnnotatedArray if AnnotatedArray === self
 
     value
   end
@@ -466,6 +520,8 @@ module AnnotatedArray
       value << e if method.shift
     end
 
+    value.extend AnnotatedArray if AnnotatedArray === self
+
     value
   end
 

data/lib/rbbt/persist.rb

@@ -1,5 +1,3 @@
-require 'digest/md5'
-
 require 'rbbt/util/misc'
 require 'rbbt/util/open'
 
@@ -91,6 +89,11 @@ module Persist
       FixWidthTable.get(path) 
     when :string, :text
       Open.read(path)
+    when :binary
+      f = File.open(path, 'rb')
+      res = f.read
+      f.close
+      res
     when :array
       res = Open.read(path).split("\n", -1)
       res.pop
@@ -128,11 +131,16 @@ module Persist
       Open.write(path, Annotated.tsv(content, :all).to_s)
     when :string, :text
       Open.write(path, content)
+    when :binary
+      f = File.open(path, 'wb')
+      f.puts content
+      f.close
+      content
     when :array
-      if content.any?
-        Open.write(path, content * "\n" + "\n")
-      else
+      if content.empty?
         Open.write(path, "")
+      else
+        Open.write(path, content * "\n" + "\n")
       end
     when :marshal_tsv
       Open.write(path, Marshal.dump(content.dup))
@@ -185,7 +193,7 @@ module Persist
           []
         when (keys.length == 1 and keys.first =~ /:SINGLE$/)
           key = keys.first
-          values = repo.write_and_close do
+          values = repo.read_and_close do
             repo[key]
           end
           Annotated.load_tsv_values(key, values, "literal", "annotation_types", "JSON")

data/lib/rbbt/persist/tsv.rb

@@ -83,15 +83,21 @@ module Persist
 
         def write_and_close
           write if @closed or not write?
-          res = yield
-          close
+          res = begin
+                  yield
+                ensure
+                  close
+                end
           res
         end
 
         def read_and_close
           read if @closed or write?
-          res = yield
-          close
+          res = begin
+                  yield
+                ensure
+                  close
+                end
           res
         end
 

data/lib/rbbt/resource.rb

@@ -7,6 +7,7 @@ require 'rbbt/resource/rake'
 module Resource
   extend ChainMethods
   self.chain_prefix = :resource
+
   def self.extended(base)
     setup_chains(base)
     if not base.respond_to? :pkgdir

data/lib/rbbt/resource/path.rb

@@ -36,6 +36,10 @@ module Path
     Path.setup File.dirname(self), @pkgdir, @resource
   end
 
+  def glob(pattern = '*')
+    Dir.glob(File.join(self, pattern))
+  end
+
   def path_get_brackets(name)
     join name
   end
@@ -128,8 +132,8 @@ module Path
     Open.read(self.produce.find)
   end
 
-  def open
-    Open.open(self.produce.find)
+  def open(options = {})
+    Open.open(self.produce.find, options)
   end
 
   def to_s
@@ -191,4 +195,41 @@ module Path
       [identifier_file_path]
     end
   end
+
+  def set_extension(new_extension = nil)
+    new_path = self.sub(/\.[^\.\/]+$/, "." << new_extension.to_s)
+    Path.setup new_path, @pkgdir, @resource
+  end
+
+  def doc_file(relative_to = 'lib')
+    if located?
+      lib_dir = Path.caller_lib_dir(self, relative_to)
+      relative_file = File.join( 'doc', self.sub(lib_dir,''))
+      Path.setup File.join(lib_dir, relative_file) , @pkgdir, @resource
+    else
+      Path.setup File.join('doc', self) , @pkgdir, @resource
+    end
+  end
+
+  def source_for_doc_file(relative_to = 'lib')
+    if located?
+      lib_dir = Path.caller_lib_dir(Path.caller_lib_dir(self, 'doc'), relative_to)
+      relative_file = self.sub(/(.*\/)doc\//, '\1').sub(lib_dir + "/",'')
+      file = File.join(lib_dir, relative_file)
+
+      if not File.exists?(file)
+        file= Dir.glob(file.sub(/\.[^\.\/]+$/, '.*')).first
+      end
+
+      Path.setup file, @pkgdir, @resource
+    else
+      relative_file = self.sub(/^doc\//, '\1')
+
+      if not File.exists?(relative_file)
+        relative_file = Dir.glob(relative_file.sub(/\.[^\.\/]+$/, '.*')).first
+      end
+
+      Path.setup relative_file , @pkgdir, @resource
+    end
+  end
 end