rbbt-util 5.21.64 → 5.21.66

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: ee390df6f2ddf89732de28343a89e5997853547f
-  data.tar.gz: ac029177dda7f0b1146c5ebadd3ef6785028f0c2
+  metadata.gz: 9ff21babc0504e17df0c48429ee4db81aebbac9a
+  data.tar.gz: 0c6ba9a55916f59bdc371510a696ec2a49582cbd
 SHA512:
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-  data.tar.gz: 3f28b826d350aee2f3bff57332f05ce33488e4eee3d4c805b823aab1f75310159180b57e58777438ff927480558ca7d3687257bdcf773633e429d9f4ea253dfc
+  metadata.gz: b34c51ad0a84893b4d809234d99e935a2d58c88fe89e04b76f9dee30c49d39f04844a7ad02dea30ac18bd98be611e226f500e2bb95248778f4689e437620a873
+  data.tar.gz: 50cb3f8b234f73a38bc406a2d328fafd2b87b83e9121e39a3885b52727c8649bcb0c456ae334f5a617343e595532d685aa567ba462942cfdc39e46c855fce68d

data/lib/rbbt/rest/client/step.rb

@@ -22,6 +22,7 @@ class WorkflowRESTClient
 
     def initialize(base_url, task = nil, base_name = nil, inputs = nil, result_type = nil, result_description = nil, is_exec = false, is_stream = false, stream_input = nil)
       @base_url, @task, @base_name, @inputs, @result_type, @result_description, @is_exec, @is_stream, @stream_input = base_url, task, base_name, inputs, result_type, result_description, is_exec, is_stream, stream_input
+      @base_url = "http://" << @base_url unless @base_url =~ /^https?:\/\//
       @mutex = Mutex.new
     end
 

data/lib/rbbt/tsv.rb

@@ -161,6 +161,8 @@ module TSV
                           data.serializer = :float
                         when (parser.cast == :to_f and (parser.type == :list or parser.type == :flat))
                           data.serializer = :float_array
+                        else
+                          data.serializer = :marshal
                         end
     end
 

data/lib/rbbt/tsv/attach.rb

@@ -192,7 +192,7 @@ module TSV
 
   
   def attach(other, options = {})
-    options      = Misc.add_defaults options, :in_namespace => false, :persist_input => true
+    options      = Misc.add_defaults options, :in_namespace => false, :persist_input => false
     fields, one2one, complete = Misc.process_options options, :fields, :one2one, :complete
     in_namespace = options[:in_namespace]
 
@@ -202,7 +202,7 @@ module TSV
       other.identifiers ||= other_identifier_file
     end
 
-    fields = other.fields - [key_field].concat(self.fields) if fields.nil?  or fields == :all 
+    fields = other.fields - [key_field].concat(self.fields) if other.fields and (fields.nil? or fields == :all)
     if in_namespace
       fields = other.fields_in_namespace - [key_field].concat(self.fields) if fields.nil?
     else

data/lib/rbbt/util/misc/annotated_module.rb

@@ -0,0 +1,58 @@
+module AnnotatedModule
+
+  def self.add_consummable_annotation(target, *annotations)
+    if annotations.length == 1 and Hash === annotations.first
+      annotations.first.each do |annotation, default|
+        target.send(:attr_accessor, annotation)
+        target.send(:define_method, "consume_#{annotation}") do
+          value = instance_variable_get("@#{annotation}") || default.dup
+          instance_variable_set("@#{annotation}", default.dup)
+          value
+        end
+      end
+    else
+      annotations.each do |annotation|
+        target.send(:attr_accessor, annotation)
+        target.send(:define_method, "consume_#{annotation}") do
+          value = instance_variable_get("@#{annotation}")
+          instance_variable_set("@#{annotation}", nil)
+        end
+      end
+    end
+  end
+
+end
+
+
+module InputModule
+  AnnotatedModule.add_consummable_annotation(self,
+    :inputs             => [],
+    :required_inputs    => [],
+    :input_types        => {},
+    :input_descriptions => {},
+    :input_defaults     => {},
+    :input_options      => {})
+
+  def input(name, type = nil, desc = nil, default = nil, options = nil)
+    name = name.to_sym
+    type = type.to_sym
+
+    @inputs             = [] if @inputs.nil?
+    @input_types        = {} if @input_types.nil?
+    @input_descriptions = {} if @input_descriptions.nil?
+    @input_defaults     = {} if @input_defaults.nil?
+    @input_options      = {} if @input_options.nil?
+    @required_inputs    = [] if @required_inputs.nil?
+
+    required = Misc.process_options options, :required if options
+    required, default = true, nil if default == :required
+    @required_inputs << name  if required
+
+    @inputs                   << name
+    @input_types[name]        = type unless type.nil?
+    @input_descriptions[name] = desc unless desc.nil?
+    @input_defaults[name]     = default unless default.nil?
+    @input_options[name]      = options unless options.nil?
+
+  end
+end

data/lib/rbbt/workflow/annotate.rb

@@ -21,35 +21,4 @@ module AnnotatedModule
     end
   end
 
-  add_consummable_annotation(self,
-    :description        => "",
-    :inputs             => [],
-    :required_inputs    => [],
-    :input_types        => {},
-    :input_descriptions => {},
-    :input_defaults     => {},
-    :input_options      => {})
-
-  def input(name, type = nil, desc = nil, default = nil, options = nil)
-    name = name.to_sym
-    type = type.to_sym
-
-    @inputs             = [] if @inputs.nil?
-    @input_types        = {} if @input_types.nil?
-    @input_descriptions = {} if @input_descriptions.nil?
-    @input_defaults     = {} if @input_defaults.nil?
-    @input_options      = {} if @input_options.nil?
-    @required_inputs    = [] if @required_inputs.nil?
-
-    required = Misc.process_options options, :required if options
-    required, default = true, nil if default == :required
-    @required_inputs << name  if required
-
-    @inputs                   << name
-    @input_types[name]        = type unless type.nil?
-    @input_descriptions[name] = desc unless desc.nil?
-    @input_defaults[name]     = default unless default.nil?
-    @input_options[name]      = options unless options.nil?
-
-  end
 end

data/lib/rbbt/workflow/definition.rb

@@ -1,8 +1,7 @@
 require 'rbbt-util'
-require 'rbbt/workflow/annotate'
+require 'rbbt/util/misc/annotated_module'
 
 module Workflow
-  include AnnotatedModule
 
   module DependencyBlock
     attr_accessor :dependency
@@ -13,11 +12,15 @@ module Workflow
     end
   end
 
+  include InputModule
   AnnotatedModule.add_consummable_annotation(self,
-                                             :result_description => "",
-                                             :result_type        => nil,
-                                             :extension          => '',
-                                             :dependencies       => [])
+    :dependencies       => [],
+    :description        => "",
+    :result_type        => nil,
+    :result_description => "",
+    :extension          => '')
+
+
   def helper(name, &block)
     helpers[name] = block
   end

data/lib/rbbt/workflow/examples.rb

@@ -32,7 +32,7 @@ module Workflow
       file = dir[input].find
       file = dir.glob(input.to_s + ".*").first if file.nil? or not file.exists?
       Log.debug "Trying #{ input }: #{file}"
-      next unless file.exists?
+      next unless file and file.exists?
 
       case input_types[input]
       when :tsv, :array, :text, :file

data/share/config.ru

@@ -70,6 +70,10 @@ load_file Rbbt.etc['app.d/preload.rb'].find_all
 #{{{ SINATRA
 load_file Rbbt.lib['sinatra.rb'].find_all
 
+Entity.entity_list_cache     = Rbbt.var.sinatra.app[app_name].find.entity_lists
+Entity.entity_map_cache      = Rbbt.var.sinatra.app[app_name].find.entity_maps
+Entity.entity_property_cache = Rbbt.var.sinatra.app[app_name].find.entity_properties
+
 #{{{ RUN
 
 Sinatra::RbbtRESTMain.add_resource_path($app_dir.www.views.find, true)

data/test/rbbt/persist/test_tsv.rb

@@ -72,4 +72,17 @@ class TestPersistTSV < Test::Unit::TestCase
     engine = "LMDB"
     run_bechmark(tsv_path, engine)
   end
+
+  def test_tsv_persist
+    content =<<-EOF
+#: :cast=:to_f
+#Key Value1 Value2
+k1 1.1 2.1
+k2 1.2 2.2
+    EOF
+    TmpFile.with_file(content) do |tsv_file|
+      tsv = TSV.open(tsv_file, :sep => " ", :persist => true, :type => :double, :merge => true)
+      iii tsv["k1"]
+    end
+  end
 end

data/test/rbbt/persist/tsv/test_tokyocabinet.rb

@@ -240,7 +240,7 @@ class TestPersistTSVTC < Test::Unit::TestCase
     end
   end
 
-  def test_fdb
+  def __test_fdb
     TmpFile.with_file do |tmp|
       repo = Persist.open_tokyocabinet(tmp, true, :list, TokyoCabinet::FDB)
       repo.write

data/test/rbbt/test_tsv.rb

@@ -350,7 +350,7 @@ b 2
     EOF
 
     TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :key_field => "Value", :grep => "#\\|2")
+      tsv = TSV.open(filename, :key_field => "Value", :grep => '2')
       assert(tsv.include?("2"))
       assert(! tsv.include?("7"))
     end

data/test/rbbt/util/test_misc.rb

@@ -444,6 +444,10 @@ eum fugiat quo voluptas nulla pariatur?"
     ppp Misc.html_tag('textarea', "hola\nadios\nagain")
   end
 
+  def test_link_title
+    ppp Misc.html_tag('a', "hola\nadios\nagain", :title => "Hola adios")
+  end
+
   def __test_lock_fd
     require 'rbbt/workflow'
     Rbbt.var.jobs.Structure.neighbour_map.glob("*")[0..1000].each do |file|

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.64
+  version: 5.21.66
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-01-11 00:00:00.000000000 Z
+date: 2017-01-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -281,6 +281,7 @@ files:
 - lib/rbbt/util/log/progress/report.rb
 - lib/rbbt/util/log/progress/util.rb
 - lib/rbbt/util/misc.rb
+- lib/rbbt/util/misc/annotated_module.rb
 - lib/rbbt/util/misc/bgzf.rb
 - lib/rbbt/util/misc/concurrent_stream.rb
 - lib/rbbt/util/misc/development.rb