rbbt-util 5.5.2 → 5.5.3

checksums.yaml

@@ -1,15 +1,15 @@
 ---
 !binary "U0hBMQ==":
   metadata.gz: !binary |-
-    NTE0ZTY1ZWVjMjZjMzBlMTQzNjNlMzlmYjY1NzBjNDFjZTc1NzExMA==
+    YTZhNzI1NTUwMDE2ZWY3NTVkY2UyMWM3OTFlNTFjZmZkZmY5YmNkZQ==
   data.tar.gz: !binary |-
-    OWM2NGYwNDA0ODA4Y2FiNGQzMzE4ZjUwZDBiYTdiYmM2ZGVhYTc0ZQ==
+    ZGQyYjgxYjg4MzgxZTk3Y2QwNTdhOWEwODUzMzk0ODJlZWY0MGMxMQ==
 !binary "U0hBNTEy":
   metadata.gz: !binary |-
-    ODg1YTYxNGE5NWZkY2YyYmUzYmQ5ODlkZjQ0ZDgzZGZlNzA1YzZmNGU0NDZm
-    YzM2OGI3Y2RiOGMwNTI0ZDAyOWFiOTRjYmY5ODVmMjJkZjBlYTVkMWI2NTJj
-    ZGUyOGE4YWVmMjQyMzg2OGU2YzhjNjU3MDc5YTcwN2VjNDQwY2M=
+    YzkxYmJmYzQwMTAxMmIyMmJkZWZlZjY3ZDdiOWFkOTdmZGUwMDc1Zjc1ODE5
+    YjMzYmNhM2YxMzg4YjllZTAwNDZjYTc2ZmVhNDZiMzQ2YjI2MTFkNTUzODZh
+    YzZkYjg4NWU4ZWEwZDM2NDE3NGZhYzIxYmJkZTZiNDAzMzQ3ODM=
   data.tar.gz: !binary |-
-    NTk5NDg5OWZhYzU4ZDA3ODJlZjJmZDU2MTk5ZmJiNzJmNThhZWZhNmMxOWFj
-    YTY4MWI3Yjg5NmVmZWFkYTc5Mjk0OGI1YWQ3ZDc4NzJjNzIxZGE3ZTBkMjU2
-    ODM4ZGIwNDhhMThlNzRhNDQ2M2E1Y2QxNjg4YTkyZWZmYjU1NmI=
+    NmI5MzRjNjFjYzcwOThhZTc2Njg2MmViZmFlNWNlOTFiYWI4N2NjM2E3MzBi
+    MjY0ZWVhMzY4ZmMxNTI5ZjE4OTFiMTA2Mzg3YzFlNmJkZTU4NjE1MmYwZjdh
+    NjhhNGU4NTdmNzFkOTA2OGUzNzUyMjc5ZTU0ZjA4NzUxZTc2Yjg=

data/bin/rbbt_Rutil.rb

@@ -1,4 +1,6 @@
 #!/usr/bin/env ruby
 require 'rbbt-util'
+require 'rbbt/util/R'
+
+STDOUT.write File.join(R::LIB_DIR, "util.R")
 
-STDOUT.write Rbbt.share.lib.R["util.R"].find

data/etc/app.d/base.rb

@@ -0,0 +1,34 @@
+#{{{ MODULES AND HELPERS
+register Sinatra::RbbtRESTMain
+register Sinatra::RbbtRESTEntity
+register Sinatra::RbbtRESTWorkflow
+register Sinatra::RbbtRESTFileServer
+register Sinatra::RbbtRESTKnowledgeBase
+helpers Sinatra::RbbtMiscHelpers
+
+#{{{ SESSIONS
+use Rack::Session::Cookie, :key => 'rack.session',
+  :path => '/',
+  :expire_after => 2592000,
+  :secret => 'StudyExplorer secret!!'
+
+
+#{{{ DIRECTORIES
+local_var = Rbbt.var.find
+set :cache_dir           , local_var.sinatra.cache.find
+set :file_dir            , local_var.sinatra.files.find
+set :permalink_dir       , local_var.sinatra.permalink.find
+set :favourites_dir      , local_var.sinatra.favourites.find
+set :favourite_lists_dir , local_var.sinatra.favourite_lists
+set :favourite_maps_dir  , local_var.sinatra.favourite_maps
+
+#{{{ WORKFLOWS
+
+if Rbbt.etc.workflows.find.exists?
+ Rbbt.etc.workflows.find.read.split("\n").each do |workflow|
+  Workflow.require_workflow workflow
+  add_workflow Kernel.const_get(workflow), true
+ end
+end
+
+

data/etc/app.d/entities.rb

@@ -0,0 +1,40 @@
+Rbbt.etc.requires.read.split("\n").each do |file|
+  next if file.empty?
+  Log.debug("requiring #{ file }")
+  require file
+end if Rbbt.etc.requires.exists?
+
+
+Entity.entity_list_cache = Rbbt.var.find.sinatra.entity_lists
+Entity.entity_map_cache = Rbbt.var.find.sinatra.entity_maps
+Entity.entity_property_cache = Rbbt.var.find.sinatra.entity_properties
+
+Rbbt.etc.entities.read.split("\n").each do |name|
+  next if name.empty?
+  mod = Kernel.const_get name
+  Log.debug("Including Entity::REST for #{ name }")
+  mod.module_eval do
+    include Entity::REST
+  end
+end if Rbbt.etc.entities.exists?
+
+$annotation_repo = Rbbt.var.find(:lib).sinatra.annotation_repo.find
+Rbbt.etc.persit_properties.yaml.each do |name,list|
+  next if name.empty?
+  mod = Kernel.const_get name
+  mod.module_eval do
+   list.each do |elem|
+     prop, type, repo = elem.split(",").collect{|e| e.strip}
+
+     Log.debug("Persist #{name} #{prop}: #{[type, repo].compact * ", "}")
+     if repo == 'repo'
+      options = {:annotation_repo => $annotation_repo}
+     else
+      options = {}
+     end
+     persist prop, type, options
+   end
+  end
+end if Rbbt.etc.persit_properties.exists?
+
+

data/etc/app.d/finder.rb

@@ -0,0 +1,10 @@
+#{{{ FINDER
+finder = Finder.new
+if ENV['RBBT_FINDER']
+  finder.add_instance(KEGG.pathways, :grep => '^hsa\|^#', :fields => ["Pathway Name"], :namespace => "Hsa/jun2011", :fix => Proc.new{|l| l.sub(/ - Homo sapiens.*/,'')})
+  finder.add_instance(Organism.lexicon("Hsa/jun2011"), :persist => true, :namespace => "Hsa/jun2011", :grep => '^LRG_', :invert_grep => true)
+end
+set :finder, finder
+Log.debug("Finder started with: #{finder.instances.length} instances")
+
+

data/etc/app.d/init.rb

@@ -0,0 +1,11 @@
+require 'zurb-foundation'
+require 'modular-scale'
+
+require 'rbbt'
+require 'rbbt/rest/main'
+require 'rbbt/rest/entity'
+require 'rbbt/rest/workflow'
+require 'rbbt/rest/file_server'
+require 'rbbt/rest/helpers'
+
+YAML::ENGINE.yamler = 'syck' if defined? YAML::ENGINE and YAML::ENGINE.respond_to? :yamler

data/etc/app.d/resources.rb

@@ -0,0 +1,9 @@
+EntityRESTHelpers.entity_resources.unshift Rbbt.www.views.find
+RbbtRESTHelpers.template_resources.unshift Rbbt.www.views.find
+RbbtRESTHelpers.add_sass_load_path "#{Gem.loaded_specs['compass'].full_gem_path}/frameworks/compass/stylesheets"
+RbbtRESTHelpers.add_sass_load_path "#{Gem.loaded_specs['zurb-foundation'].full_gem_path}/scss/" 
+RbbtRESTHelpers.add_sass_load_path "#{Gem.loaded_specs['modular-scale'].full_gem_path}/stylesheets/" 
+RbbtRESTHelpers.javascript_resources << Path.setup("#{Gem.loaded_specs['zurb-foundation'].full_gem_path}/js/foundation")
+RbbtRESTHelpers.javascript_resources << Path.setup("#{Gem.loaded_specs['zurb-foundation'].full_gem_path}/js/vendor")
+
+

data/lib/rbbt.rb

@@ -4,9 +4,3 @@ module Rbbt
   extend Resource
   pkgdir = 'rbbt'
 end
-
-#Open.cachedir        = Rbbt.var.cache["open-remote"].find :user
-#TmpFile.tmpdir       = Rbbt.tmp.find :user
-#FileCache.cachedir   = Rbbt.var.cache.filecache.find :user
-#Persist.cachedir     = Rbbt.var.cache.persistence.find :user
-

data/lib/rbbt/annotations/util.rb

@@ -2,7 +2,14 @@ require 'json'
 
 module Annotated
 
-  def self.load(object, info)
+  def self.flatten(array)
+    return array if array.nil?  or array.empty?
+    return array.flatten if AnnotatedArray === array
+    return array if array.compact.collect{|e| e.info }.uniq.length > 1
+    array.compact.first.annotate(array.flatten).tap{|a| a.extend AnnotatedArray }
+  end
+
+  def self.load_entity(object, info)
     annotation_types = info.delete(:annotation_types) || info.delete("annotation_types") || []
     annotation_types = annotation_types.split("|") if String === annotation_types
 
@@ -34,9 +41,23 @@ module Annotated
     end
   end
 
+  def self.load_info(fields, values)
+    info = {}
+    fields.each_with_index do |field,i|
+      next if field == "literal"
+      if field == "JSON"
+        JSON.parse(values[i]).each do |key, value|
+          info[key.to_sym] = value
+        end
+      else
+        info[field.to_sym] = resolve_array(values[i])
+      end
+    end
+    info
+  end
+
   def self.load_tsv_values(id, values, *fields)
     fields = fields.flatten
-    info = {}
     literal_pos = fields.index "literal"
 
     object = case
@@ -49,36 +70,18 @@ module Annotated
     object = resolve_array(object)
 
     if Array === values.first
-      Misc.zip_fields(values).collect do |list|
-        fields.each_with_index do |field,i|
-          next if field == "literal"
-          if field == "JSON"
-            JSON.parse(list[i]).each do |key, value|
-              info[key.to_sym] = value
-            end
-          else
-            info[field.to_sym] = resolve_array(list[i])
-          end
-        end
+      Misc.zip_fields(values).collect do |v|
+        info = load_info(fields, v)
       end
     else
-      fields.each_with_index do |field,i|
-        next if field == "literal"
-        if field == "JSON"
-          JSON.parse(values[i]).each do |key, value|
-            info[key.to_sym] = value
-          end
-        else
-          info[field.to_sym] = resolve_array(values[i])
-        end
-      end
+      info = load_info(fields, values)
     end
 
-    self.load(object, info)
+    self.load_entity(object, info)
 
     object
   end
- 
+
   def self.load_tsv(tsv)
     tsv.with_unnamed do
       annotated_entities = tsv.collect do |id, values|
@@ -104,7 +107,7 @@ module Annotated
                fields = AnnotatedArray === annotations ? annotations.annotations : annotations.compact.first.annotations
                fields << :annotation_types
 
-             when (fields == [:literal] and not annotations.empty?)
+             when (fields == [:literal] and not annotations.compact.empty?)
                fields << :literal
 
              when (fields == [:all] and Annotated === annotations)
@@ -112,9 +115,9 @@ module Annotated
                fields << :annotated_array if AnnotatedArray === annotations
                fields << :literal
 
-             when (fields == [:all] and not annotations.empty?)
+             when (fields == [:all] and not annotations.compact.empty?)
                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
+               raise "Input array must be annotated or its elements must be. No double 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)

data/lib/rbbt/entity.rb

@@ -97,7 +97,6 @@ module Entity
           define_method ary_name, &block 
           
           define_method name do |*args|
-            #ary_name = "_ary_" << __method__.to_s
             case
             when Array === self
               self.send(ary_name, *args)

data/lib/rbbt/resource/path.rb

@@ -55,6 +55,7 @@ module Path
   end
 
   SEARCH_PATHS = {
+    :current => File.join(File.expand_path('.'), "{TOPLEVEL}", "{SUBPATH}"),
     :user    => File.join(ENV['HOME'], ".{PKGDIR}", "{TOPLEVEL}", "{SUBPATH}"),
     :global  => File.join('/', "{TOPLEVEL}", "{PKGDIR}", "{SUBPATH}"),
     :local   => File.join('/usr/local', "{TOPLEVEL}", "{PKGDIR}", "{SUBPATH}"),
@@ -81,7 +82,7 @@ module Path
 
     path = nil
     if where.nil?
-      %w(user local global lib).each do |w| 
+      %w(current user local global lib).each do |w| 
         w = w.to_sym
         next unless search_paths.include? w
         path = find(w, caller_lib, search_paths)

data/lib/rbbt/util/R.rb

@@ -3,7 +3,7 @@ require 'rbbt/tsv'
 
 module R
 
-  LIB_DIR = File.join(File.expand_path(File.dirname(__FILE__)),'../../../share/lib/R')
+  LIB_DIR = File.join(File.expand_path(File.dirname(__FILE__)),'../../../share/Rlib')
   UTIL    = File.join(LIB_DIR, 'util.R')
 
   def self.run(command, options = {})
@@ -37,12 +37,12 @@ source('#{UTIL}');
 
   def self.interactive(script, options = {})
     TmpFile.with_file do |init_file|
-        Open.write(init_file) do |file|
-          file.puts "# Loading basic rbbt environment"
-          file.puts "library(utils);\n"
-          file.puts "source('#{R::UTIL}');\n"
-          file.puts 
-          file.puts script
+        Open.write(init_file) do |f|
+          f.puts "# Loading basic rbbt environment"
+          f.puts "library(utils);\n"
+          f.puts "source('#{R::UTIL}');\n"
+          f.puts 
+          f.puts script
         end
         CMD.cmd("env R_PROFILE='#{init_file}' xterm \"$RHOME/bin/R\"")
     end
@@ -97,6 +97,7 @@ if (! is.null(data)){ rbbt.tsv.write('#{f}', data); }
 
   def R_interactive(pre_script = nil)
     TmpFile.with_file do |f|
+      Log.debug{"R Script:\n" << pre_script }
       TmpFile.with_file(pre_script) do |script_file|
         Open.write(f, self.to_s)
         script = "data_file = '#{f}';\n"

data/lib/rbbt/util/misc.rb

@@ -21,10 +21,11 @@ end
 module Misc
   class FieldNotFoundError < StandardError;end
 
+
   def self.correct_icgc_mutation(pos, ref, mut_str)
     mut = mut_str
     mut = '-' * (mut_str.length - 1) if mut =~/^-[ACGT]/
-    mut = "+" << mut if ref == '-'
+      mut = "+" << mut if ref == '-'
     [pos, [mut]]
   end
 
@@ -1123,7 +1124,7 @@ end
     mod
   end
 
-  def self.string2hash(string)
+  def self.string2hash_old(string)
 
     options = {}
     string.split(/#/).each do |str|
@@ -1133,37 +1134,112 @@ end
         option, value = str, true
       end
 
-    option = option.sub(":",'').to_sym if option.chars.first == ':'
-    value  = value.sub(":",'').to_sym if String === value and value.chars.first == ':'
+      option = option.sub(":",'').to_sym if option.chars.first == ':'
+      value  = value.sub(":",'').to_sym if String === value and value.chars.first == ':'
 
-    if value == true
-      options[option] = option.to_s.chars.first != '!' 
-    else
-      options[option] = Thread.start do
-        $SAFE = 0;
-        case 
-        when value =~ /^(?:true|T)$/i
-          true
-        when value =~ /^(?:false|F)$/i
-          false
-        when Symbol === value
-          value
-        when (String === value and value =~ /^\/(.*)\/$/)
-          Regexp.new /#{$1}/
-        else
-          begin
-            Kernel.const_get value
-          rescue
-            begin  
-              raise if value =~ /[a-z]/ and defined? value
-              eval(value) 
-            rescue Exception
-              value 
+      if value == true
+        options[option] = option.to_s.chars.first != '!' 
+      else
+        options[option] = Thread.start do
+          $SAFE = 0;
+          case 
+          when value =~ /^(?:true|T)$/i
+            true
+          when value =~ /^(?:false|F)$/i
+            false
+          when Symbol === value
+            value
+          when (String === value and value =~ /^\/(.*)\/$/)
+            Regexp.new /#{$1}/
+          else
+            begin
+              Kernel.const_get value
+            rescue
+              begin  
+                raise if value =~ /[a-z]/ and defined? value
+                eval(value) 
+              rescue Exception
+                value 
+              end
             end
           end
-        end
-      end.value
+        end.value
+      end
     end
+
+    options
+  end
+
+  def self.string2hash(string)
+    options = {}
+
+    string.split('#').each do |str|
+      key, sep, value = str.partition "="
+
+      key = key[1..-1].to_sym if key[0] == ":"
+
+      options[key] = true and next if value.empty?
+      options[key] = value[1..-1].to_sym and next if value[0] == ":"
+      options[key] = Regexp.new(/#{value[1..-2]}/) and next if value[0] == "/" and value[-1] == "/"
+      options[key] = value[1..-2] and next if value =~ /^['"].*['"]$/
+      options[key] = value.to_i and next if value =~ /^\d+$/
+      options[key] = value.to_f and next if value =~ /^\d*\.\d+$/
+      options[key] = true and next if value == "true"
+      options[key] = false and next if value == "false"
+      options[key] = value and next 
+
+      options[key] = begin
+                       saved_safe = $SAFE
+                       $SAFE = 0
+                       eval(value)
+                     rescue Exception
+                       value
+                     ensure
+                       $SAFE = saved_safe
+                     end
+    end
+
+    return options
+
+    options = {}
+    string.split(/#/).each do |str|
+      if str.match(/(.*)=(.*)/)
+        option, value = $1, $2
+      else
+        option, value = str, true
+      end
+
+      option = option.sub(":",'').to_sym if option.chars.first == ':'
+      value  = value.sub(":",'').to_sym if String === value and value.chars.first == ':'
+
+      if value == true
+        options[option] = option.to_s.chars.first != '!' 
+      else
+        options[option] = Thread.start do
+          $SAFE = 0;
+          case 
+          when value =~ /^(?:true|T)$/i
+            true
+          when value =~ /^(?:false|F)$/i
+            false
+          when Symbol === value
+            value
+          when (String === value and value =~ /^\/(.*)\/$/)
+            Regexp.new /#{$1}/
+          else
+            begin
+              Kernel.const_get value
+            rescue
+              begin  
+                raise if value =~ /[a-z]/ and defined? value
+                eval(value) 
+              rescue Exception
+                value 
+              end
+            end
+          end
+        end.value
+      end
     end
 
     options

data/share/rbbt_commands/app/start

@@ -17,5 +17,10 @@ Misc.in_dir(app_dir) do
   require 'rack'
   ENV["RBBT_FINDER"] = "true" if options.include?(:finder)
   ENV["RACK_ENV"] = options[:environment] if options.include?(:environment)
-  Rack::Server.start(options.merge(:config => 'config.ru'))
+
+  if File.exists? 'config.ru'
+    Rack::Server.start(options.merge(:config => 'config.ru'))
+  else
+    Rack::Server.start(options.merge(:config => Rbbt.share['config.ru'].find))
+  end
 end

data/test/rbbt/test_annotations.rb

@@ -70,7 +70,7 @@ class TestAnnotations < Test::Unit::TestCase
     annotation_str = "Annotation String"
     info = {:annotation_str => annotation_str, :annotation_types => [AnnotatedString]}
 
-    Annotated.load(str, info)
+    Annotated.load_entity(str, info)
     assert_equal annotation_str, str.annotation_str
   end
 

data/test/rbbt/util/test_R.rb

@@ -2,7 +2,7 @@ require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helpe
 require 'rbbt/util/R'
 
 class TestR < Test::Unit::TestCase
-  def _test_sum
+  def test_sum
     assert_equal "6", R.run('cat(3+3)').read.split(/\n/).last
   end
 

data/test/rbbt/util/test_misc.rb

@@ -81,9 +81,16 @@ class TestMisc < Test::Unit::TestCase
     assert_equal(true, Misc.string2hash("true")["true"])
     assert_equal(1, Misc.string2hash("a=1")["a"])
     assert_equal('b', Misc.string2hash("a=b")["a"])
-    assert_equal('d', Misc.string2hash("a=b#c=d#:h=j")["c"])
-    assert_equal('j', Misc.string2hash("a=b#c=d#:h=j")[:h])
+    assert_equal('d', Misc.string2hash("a=b#c=d#:h='j'")["c"])
+    assert_equal('j', Misc.string2hash("a=b#c=d#:h='j'")[:h])
     assert_equal(:j, Misc.string2hash("a=b#c=d#:h=:j")[:h])
+
+    Misc.benchmark(1000) do
+      Misc.string2hash_old("a=b#c=d#:h=:j#test='1'#:num=1#:sep=/#/")
+    end
+    Misc.benchmark(1000) do
+      Misc.string2hash("a=b#c=d#:h=:j#test='1'#:num=1#:sep=/#/")
+    end
   end
   
   def test_named_array
@@ -121,9 +128,6 @@ class TestMisc < Test::Unit::TestCase
     hash = {:a => true}
     assert_equal hash, Misc.string2hash(Misc.hash2string(hash))
 
-    hash = {:a => Misc}
-    assert_equal hash, Misc.string2hash(Misc.hash2string(hash))
- 
     hash = {:a => :b}
     assert_equal hash, Misc.string2hash(Misc.hash2string(hash))
  

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.5.2
+  version: 5.5.3
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-10-22 00:00:00.000000000 Z
+date: 2013-10-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -84,6 +84,11 @@ extra_rdoc_files:
 - README.rdoc
 files:
 - LICENSE
+- etc/app.d/base.rb
+- etc/app.d/entities.rb
+- etc/app.d/finder.rb
+- etc/app.d/init.rb
+- etc/app.d/resources.rb
 - lib/rbbt-util.rb
 - lib/rbbt.rb
 - lib/rbbt/annotations.rb
@@ -138,8 +143,8 @@ files:
 - lib/rbbt/workflow/step.rb
 - lib/rbbt/workflow/task.rb
 - lib/rbbt/workflow/usage.rb
+- share/Rlib/util.R
 - share/install/software/lib/install_helpers
-- share/lib/R/util.R
 - share/rbbt_commands/app/start
 - share/rbbt_commands/conf/web_user/add
 - share/rbbt_commands/conf/web_user/list