rbbt-util 5.19.32 → 5.19.34

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: cf020e8c4f0769534aa863d6643190f45cc2f9b6
+  metadata.gz: 891d8471ba86780e53a5363adac579490a665f05
+  data.tar.gz: f80a9947a157c9aaa5b8de42f2119004afe391b1
 SHA512:
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+  data.tar.gz: e49d24357ed693a1cedfe88ae3b9c43d92f28080de7cacf627bc6c5aa2bd3d0c072c07c74a30b9a10f7e7c7f6a46b88771f1e3e40d3967cbe5ce2a25f3c7938a

data/etc/app.d/entities.rb

@@ -1,11 +1,3 @@
-
-#{{{ Require files
-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.sinatra.find.entity_lists
 Entity.entity_map_cache      = Rbbt.var.sinatra.find.entity_maps
 Entity.entity_property_cache = Rbbt.var.sinatra.find.entity_properties

data/etc/app.d/requires.rb

@@ -0,0 +1,7 @@
+#{{{ Require files
+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?
+

data/lib/rbbt/association/item.rb

@@ -108,8 +108,17 @@ module AssociationItem
     fields = [self.source_type, self.target_type].concat info_fields
     type = [self.source_type, self.target_type] * "~"
     tsv = TSV.setup({}, :key_field => type, :fields => fields, :type => :list, :namespace => self.namespace)
-    self.each do |match|
-      tsv[match] = [match.source, match.target].concat match.info.values_at(*info_fields)
+    index = index(database)
+    index.with_unnamed do
+      index.chunked_values_at(self).each_with_index do |v,i|
+        p = self[i]
+        source, _sep, target = p.partition("~")
+        if info_fields.empty?
+          tsv[p] = [source, target]
+        else
+          tsv[p] = [source, target].concat v 
+        end
+      end
     end
     tsv.entity_options = {:organism => namespace}
     knowledge_base.entity_options.each do |type,options|
@@ -119,8 +128,8 @@ module AssociationItem
   end
 
   property :filter => :array do |*args,&block|
-    keys = tsv.select(*args,&block).keys
-    keys = self.annotate Annotated.purge(keys)
+    keys = tsv.with_unnamed do tsv.select(*args,&block).keys end
+    keys = self.annotate keys
     keys
   end
 

data/lib/rbbt/tsv/manipulate.rb

@@ -359,7 +359,7 @@ module TSV
     new.entity_options = entity_options
     new.entity_templates = entity_templates
     
-   case
+    case
     when (method.nil? and block_given?)
       through do |key, values|
         new[key] = values if invert ^ (yield key, values)

data/lib/rbbt/tsv/serializers.rb

@@ -36,7 +36,8 @@ module TSV
     end
 
     def self.load(string)
-      return [] if string.nil?
+      return nil if string.nil? or string == 'nil'
+      return [] if string.empty?
       string.split("\t", -1)
     end
   end

data/share/config.ru

@@ -43,6 +43,9 @@ load_file Rbbt.etc['app.d/resources.rb'].find
 #{{{ KNOWLEDGEBASE
 load_file Rbbt.etc['app.d/knowledge_bases.rb'].find
 
+#{{{ REQUIRES
+load_file Rbbt.etc['app.d/requires.rb'].find
+
 #{{{ ENTITIES
 load_file Rbbt.etc['app.d/entities.rb'].find
 

data/share/rbbt_commands/workflow/knowledge_base

@@ -10,7 +10,7 @@ Access workflow knowledge_base
 
 $ rbbt workflow knowledge_base <workflow> [<database>] [<action>] [<options>]
 
-Access workflow knowledge base
+Access workflow knowledge base. Allowed actions are: list_databases, summary, and subset
 
 -h--help Show this help:
 -s--source_entities* Source entities
@@ -78,4 +78,6 @@ when :subset
       end
     end
   end
+else
+  raise ParameterException, "Action not understood: #{ action }"
 end

data/share/rbbt_commands/workflow/server

@@ -14,8 +14,6 @@ require 'rbbt/rest/knowledge_base'
 require 'rbbt/rest/helpers'
 require 'rbbt/rest/web_tool'
 
-#options = SOPT.get "-e--environment*:-p--port*:-s--server*:-b--bind*:-e--environment*:-R--RServe_session*:--finder:--views*:-w--workflows*"
-
 options = SOPT.setup <<EOF
 Start an rbbt app
 
@@ -69,6 +67,10 @@ app.use Rack::Deflater
 
 load Rbbt.etc['app.d/resources.rb'].find
 
+load Rbbt.etc['app.d/requires.rb'].find
+
+load Rbbt.etc['app.d/entities.rb'].find
+
 app.class_eval do
   eval Rbbt.etc['app.d/finder.rb'].read
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.19.32
+  version: 5.19.34
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-04-15 00:00:00.000000000 Z
+date: 2016-04-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -163,6 +163,7 @@ files:
 - etc/app.d/grid_system.rb
 - etc/app.d/init.rb
 - etc/app.d/knowledge_bases.rb
+- etc/app.d/requires.rb
 - etc/app.d/resources.rb
 - etc/app.d/workflows.rb
 - lib/rbbt-util.rb