rbbt-util 5.34.17 → 5.34.20

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 60845114700c0dc2ce3c016fd4264f2de5aa01a18f90f13a7d534c6379a575c8
+  metadata.gz: 4109d61e49c9573bc85f7c2b8358b1dbd0bdd032dd0376f01c39f3d1e15e2c46
+  data.tar.gz: 478773feffcb9b316244ac01a28ed975a08ea21093743db33f11afc0d29a85cb
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+  metadata.gz: 3090d957c156550db02ba305451af8f09aae6b076038e0390003cb6eac060045a61a41f2a1d81dbcdc6278fb1fc0373a188103a0c9748f2f6974862b7361f254
+  data.tar.gz: 3d6f359bd83c0f10a7f31f6b5d20573ce4d7ed621b4742bbbd9f9ef8169e480e4a61b60d2f7cb21a2009f3d4cab79a0890331cee489363627900453b06a7ae4d

data/lib/rbbt/association/item.rb

@@ -136,7 +136,8 @@ module AssociationItem
   end
 
   property :filter => :array do |*args,&block|
-    keys = tsv.with_unnamed do tsv.select(*args,&block).keys end
+    block = args.pop if Proc === args.last
+    keys = tsv.with_unnamed do tsv.select(*args, &block).keys end
     keys = self.annotate keys
     keys
   end

data/lib/rbbt/entity.rb

@@ -158,23 +158,23 @@ module Entity
         when :single, :single2array
           single_name = "_single_" << name
           define_method single_name, &block 
-          define_method name do |*args|
+          define_method name do |*args, &block|
             if Array === self
               res = self.collect{|e| e.send(single_name, *args)}
               res.first.annotate(res) if Annotated === res.first && type == :single2array
               res
             else
-              self.send(single_name, *args)
+              self.send(single_name, *args, &block)
             end
           end
         when :array, :array2single
           ary_name = "_ary_" << name
           define_method ary_name, &block 
 
-          define_method name do |*args|
+          define_method name do |*args, &block|
             case
             when Array === self
-              self.send(ary_name, *args)
+              self.send(ary_name, *args, &block)
             when (Array === self.container and not self.container_index.nil? and self.container.respond_to? ary_name)
               cache_code = Misc.hash2md5({:name => ary_name, :args => args})
               res = (self.container._ary_property_cache[cache_code] ||=  self.container.send(name, *args))
@@ -184,7 +184,7 @@ module Entity
                 res[self.container_index]
               end
             else
-              res = self.make_list.send(ary_name, *args)
+              res = self.make_list.send(ary_name, *args, &block)
               Hash === res ? res[self] : res[0]
             end
           end

data/lib/rbbt/hpc/batch.rb

@@ -372,8 +372,7 @@ function batch_sync_contain_dir(){
 
         prepare_environment +=<<-EOF
 # Load singularity modules
-module load intel/2018.1
-module load singularity
+command -v singularity &> /dev/null || module load singularity
 mkdir -p "#{singularity_opt_dir}"
         EOF
 

data/lib/rbbt/knowledge_base/entity.rb

@@ -23,7 +23,7 @@ class KnowledgeBase
     entity_options = self.entity_options
     IndiferentHash.setup entity_options if entity_options and not IndiferentHash === entity_options
     options = entity_options[type.to_s] || entity_options[Entity.formats[type.to_s].to_s] || {}
-    options[:format] = @format[type] if @format.include? :type
+    options[:format] = @format[type] if Hash === @format && @format.include?(type)
     namespace = self.namespace
     namespace = db_namespace(database_name) if namespace.nil? and database_name
     options = {:organism => namespace}.merge(options)

data/lib/rbbt/resource/path.rb

@@ -354,7 +354,7 @@ module Path
 
   def yaml
     self.open do |f|
-      YAML.load f
+      YAML.unsafe_load f
     end
   end
 

data/lib/rbbt/resource.rb

@@ -71,6 +71,10 @@ module Resource
     end
   end
 
+  def claims
+    resources.keys.collect{|path| path.sub(subdir, '').sub(/^\//,'') }
+  end
+
   attr_accessor :server_missing_resource_cache
   def get_from_server(path, final_path, remote_server = nil)
     remote_server ||= self.remote_server

data/test/rbbt/util/log/test_progress.rb

@@ -87,5 +87,25 @@ class TestProgress < Test::Unit::TestCase
     end
   end
 
+  def test_file
+    size = 10000
+
+    TmpFile.with_file do |file|
+
+      Log::ProgressBar.with_bar(size, :desc => "Bar 1", :file => file) do |bar|
+        bar.init
+        nums = []
+        100.times do
+          nums << rand(size)
+        end
+        nums.sort.each do |num|
+          bar.pos num
+          sleep 0.1
+        end
+        bar.tick
+      end
+    end
+  end
+
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.34.17
+  version: 5.34.20
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-10-10 00:00:00.000000000 Z
+date: 2022-11-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake