rbbt-util 5.17.75 → 5.17.76

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: a505c667ea3b1aca300361a1709050429f59c657
-  data.tar.gz: ba08caef992d51ae80fdcbac82748b54d2d8c8dd
+  metadata.gz: e7c82572a3836b322f205a0244a4f29440ecaa94
+  data.tar.gz: 38e3e52b6284fd289652ab74e0ce40c72af08744
 SHA512:
-  metadata.gz: 6208d475f7f0c0d7068b3f0ff17ccc4cc73b07b35b69e246958562f8570683b52b39c3377c0c2f9d47eb52ef2df26bf72d94b07fc9f1d5fddee3cdf41c16c04f
-  data.tar.gz: ab176c569aa2412155057a411f71ce3b37ac3b6fd222410e384f1e9a279fc525b3569c7365b80e432e7c46ed68b7382ff0a2bb6ae92dd6b9901d32cde292370c
+  metadata.gz: 4103bd134db485801a2357481671267df121661602bd2e5bdfa420d85adba2feb1a685bfae7aac5aa49ce3867b6ad4ef164b22abe642bacd59ce0273793cf012
+  data.tar.gz: 4199d15dffe1e0c61438233f806ed90856a81d22d3a1be00f6621b243de301c7a72cee07dca042970ec68a666eba188dbf0d9ec5422bd93011d1497f2d770172

data/lib/rbbt/entity.rb

@@ -68,7 +68,7 @@ module Entity
     @entity_property_cache = dir
   end
 
-  attr_accessor :all_formats
+  attr_accessor :all_formats, :all_properties
   def self.extended(base)
     base.extend Annotation
     Entity.formats[base.to_s] = base
@@ -122,6 +122,10 @@ module Entity
         }
       end
 
+      def all_properties
+        annotation_types.select{|m| Entity === m}.collect{|e| e.all_properties}.flatten.uniq
+      end
+
       def self.property(name, &block)
         case
         when (Hash === name and name.size == 1)
@@ -174,8 +178,9 @@ module Entity
           end
         else 
           raise "Type not undestood in property: #{ type }"
-
         end
+        @all_properties ||= []
+        @all_properties << name
       end
 
       def self.persist(method_name, type = nil, options = {})

data/lib/rbbt/util/R/plot.rb

@@ -36,7 +36,11 @@ module R
             ":NA"
           end
         end
-        options[:R_open] ||= "colClasses=c('character'," + field_classes * ", " + ')'
+        if field_classes.any?
+          options[:R_open] ||= "colClasses=c('character'," + field_classes * ", " + ')'
+        else
+          options[:R_open] ||= "colClasses=c('character')"
+        end
 
         TmpFile.with_file nil, true, :extension => 'svg' do |tmpfile|
           data.R <<-EOF, sources, options

data/lib/rbbt/workflow/step/run.rb

@@ -292,7 +292,7 @@ class Step
         raise "Error in job: #{status}"
       end
     end
-    clean if dirty? 
+    clean if dirty? or not running?
     run(true) unless started?
     join unless done?
     self
@@ -424,6 +424,7 @@ class Step
   def abort
     _abort
     log(:aborted, "Job aborted") unless aborted? or error?
+    self
   end
 
   def join_stream

data/share/Rlib/util.R

@@ -447,3 +447,45 @@ rbbt.model.inpute <- function(data, formula, ...){
 #    data$Prediction = NULL
     data
 }
+
+rbbt.tsv.melt <- function(tsv, key_field = 'ID'){
+    tsv[key_field] = rownames(tsv)
+    return(melt(tsv))
+}
+
+rbbt.ranks <- function(x){
+    l = sum(!is.na(x))
+    i = sort(x, index.return=T, na.last=NA)$ix 
+    vv = rep(NA,length(x))
+
+    c = 1
+    for (pos in i){
+        vv[pos] = c / l
+        c = c + 1
+    }
+    return(vv)
+}
+
+rbbt.ranks <- function(x){
+    x = as.numeric(x)
+    missing = is.na(x)
+    l = sum(!missing)
+    x.fixed = x[!missing]
+    x.i = sort(x.fixed, index.return=T, na.last=NA)$ix 
+
+    vv = rep(NA,length(x))
+
+    c = 1
+    for (pos in x.i){
+        vv[pos] = c / l
+        c = c + 1
+    }
+
+    vv.complete = rep(NA,length(x))
+    vv.complete[!missing] = vv
+    return(vv.complete)
+}
+
+rbbt.default_code <- function(organism){
+    return(organism + "/feb2014")
+}

data/test/rbbt/test_entity.rb

@@ -182,4 +182,9 @@ class TestEntity < Test::Unit::TestCase
     assert ! string.clean_annotations.respond_to?(:reverse_text_single)
 
   end
+
+  def test_all_properties
+    puts ReversableString.setup("TEST").all_properties
+    puts ReversableString.all_properties
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.75
+  version: 5.17.76
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-09-08 00:00:00.000000000 Z
+date: 2015-09-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake