rbbt-util 5.21.42 → 5.21.43

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: d7e3095c61e3d45f4d025495616012edd657e844
-  data.tar.gz: f009065701ca1bb5fc077352d950a41c1448fd6f
+  metadata.gz: 10eea8e63f986c9ce28afb952ca203a7553da870
+  data.tar.gz: fb6e78a215cf9763eac45fa1cdaf5dfa6785e7d6
 SHA512:
-  metadata.gz: b6761bc6d733ef4f82e18069314df062512f53ef0f8aefdea400a6cfe63dc64939feb0570d77ff1ad1dd1edb92273024b2c240348bf11c16352b29a87953b383
-  data.tar.gz: c2e35aea73309e61fcd0d20df6e8d88b7412f7e7d513b99199e8bd9fbcb8b73d8a406d966f5505f6d52b458df5c02e697e57b3f1c717a810ba899dfe56ffe44e
+  metadata.gz: ae836057fdbf7f61c5cbfbec7f9138a933193cec13f2f091b956004f84fe8ee119b94958af79b72cb76457fe778851512418f85f74201a46208680083a8e3514
+  data.tar.gz: fb166d2973f256978e1e7cc77a611c431a9acd21a4e581acf55de1cd959353724db6a5d414842fd6983ddeac6b743d9c55a42995e833b40af5f287c8af5c8150

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

@@ -121,49 +121,93 @@ data = NULL
       EOF
     end
 
-    def self.plot(filename, data, script = nil, width = nil, height = nil, options = {})
+    def self.plot(filename, data = nil, script = nil, width = nil, height = nil, options = {}, &block)
       width ||= 200
       height ||= 200
       values = []
 
-      sources = [:plot, options[:source]].flatten.compact
+      script ||= ""
+      if block_given?
+        s = StringIO.new
+        class << s
+          def method_missing(name, *args)
+            name = name.to_s
+            if name[-1] == '='
+              arg = args.first
+              value = if String === arg
+                        arg
+                      else
+                        R.ruby2R arg
+                      end
+              add("" << name[0..-2] << "=" << value)
+            else
+              args_strs = []
+              args.each do |arg|
+                value = if String === arg
+                          arg
+                        else
+                          R.ruby2R arg
+                        end
+                args_strs << value
+              end
+              add("" << name << "(" << args_strs * ", " << ")")
+            end
+          end
 
-      data.each do |k,v|
-        v = Array === v ? v : [v]
-        next if v == "NA" or v.nil? or v.include? "NA" or v.include? nil
-        values = v
-        break
+          def add(line)
+            self.write line << "\n"
+          end
+        end
+        block.call(s)
+        s.rewind
+        script << "\n" << s.read
       end
+      sources = [:plot, options[:source]].flatten.compact
+      
+      if data
+        data.each do |k,v|
+          v = Array === v ? v : [v]
+          next if v == "NA" or v.nil? or v.include? "NA" or v.include? nil
+          values = v
+          break
+        end 
 
-      values = [values] unless Array === values
+        values = [values] unless values.nil? or Array === values
 
-      field_classes = values.collect do |v| 
-        case v
-        when FalseClass, TrueClass
-          "'logical'"
-        when Fixnum, Float
-          "'numeric'"
-        when String
-          if v.strip =~ /^[-+]?[\d\.]+$/
+        field_classes = values.collect do |v| 
+          case v
+          when FalseClass, TrueClass
+            "'logical'"
+          when Fixnum, Float
             "'numeric'"
+          when String
+            if v.strip =~ /^[-+]?[\d\.]+$/
+              "'numeric'"
+            else
+              "'character'"
+            end
+          when Symbol
+            "'factor'"
           else
-            "'character'"
+            ":NA"
           end
-        when Symbol
-          "'factor'"
-        else
-          ":NA"
         end
-      end
 
-      options[:R_open] ||= "colClasses=c('character'," + field_classes * ", " + ')' if field_classes.any?
+        options[:R_open] ||= "colClasses=c('character'," + field_classes * ", " + ')' if field_classes.any?
 
-      data.R <<-EOF, :plot, options
-png("#{ filename }", #{ width }, #{ height })
-{ #{script} }
-dev.off()
-data = NULL
-      EOF
+        data.R <<-EOF, :plot, options
+  png("#{ filename }", #{ width }, #{ height })
+  { #{script} }
+  dev.off()
+  data = NULL
+        EOF
+      else
+        R.run <<-EOF, :plot, options
+  png("#{ filename }", #{ width }, #{ height })
+  { #{script} }
+  dev.off()
+        EOF
+      end
     end
   end
 end

data/lib/rbbt/workflow/accessor.rb

@@ -350,7 +350,7 @@ class Step
   end
 
   def dirty?
-    rec_dependencies.collect{|dependency| dependency.path unless dependency.error? and not dependency.recoverable_error? }.compact.uniq.reject{|path| not Path === path or path.exists?}.any?
+    rec_dependencies.collect{|dependency| dependency.path unless dependency.error? and not dependency.recoverable_error? }.compact.uniq.reject{|path| not (Path === path) or path.exists?}.any?
   end
 
   def done?

data/lib/rbbt/workflow/step.rb

@@ -221,7 +221,11 @@ class Step
   end
 
   def clean
-    Log.medium "Cleaning step: #{path}"
+    status = " "
+    status << "dirty" if dirty?
+    status << "not running" if not done? and not running? 
+    status.strip
+    Log.medium "Cleaning step: #{path}#{status}"
     abort if not done? and running?
     Step.clean(path)
     self

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.42
+  version: 5.21.43
 platform: ruby
 authors:
 - Miguel Vazquez
@@ -487,82 +487,82 @@ signing_key:
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/rbbt/test_workflow.rb
+- test/test_helper.rb
 - test/rbbt/resource/test_path.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/simpleopt/test_setup.rb
-- test/rbbt/util/simpleopt/test_get.rb
-- test/rbbt/util/simpleopt/test_parse.rb
-- test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/association/test_item.rb
+- test/rbbt/association/test_database.rb
+- test/rbbt/association/test_open.rb
+- test/rbbt/association/test_index.rb
+- test/rbbt/association/test_util.rb
+- test/rbbt/util/test_concurrency.rb
 - test/rbbt/util/test_log.rb
+- test/rbbt/util/test_chain_methods.rb
+- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/simpleopt/test_parse.rb
+- test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/simpleopt/test_setup.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/test_semaphore.rb
+- test/rbbt/util/concurrency/test_threads.rb
+- test/rbbt/util/concurrency/processes/test_socket.rb
+- test/rbbt/util/concurrency/test_processes.rb
+- test/rbbt/util/test_tmpfile.rb
 - test/rbbt/util/test_open.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/R/test_eval.rb
+- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/util/log/test_progress.rb
+- test/rbbt/util/test_colorize.rb
+- test/rbbt/util/test_R.rb
 - test/rbbt/util/misc/test_lock.rb
-- test/rbbt/util/misc/test_multipart_payload.rb
-- test/rbbt/util/misc/test_bgzf.rb
 - test/rbbt/util/misc/test_pipes.rb
+- test/rbbt/util/misc/test_bgzf.rb
 - test/rbbt/util/misc/test_omics.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/test_R.rb
-- test/rbbt/util/log/test_progress.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/misc/test_multipart_payload.rb
 - test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/concurrency/test_processes.rb
-- test/rbbt/util/concurrency/test_threads.rb
-- test/rbbt/util/concurrency/processes/test_socket.rb
-- test/rbbt/util/test_semaphore.rb
 - test/rbbt/util/test_misc.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/R/test_model.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/test_association.rb
-- test/rbbt/knowledge_base/test_traverse.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/test_resource.rb
 - test/rbbt/test_entity.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/association/test_item.rb
-- test/rbbt/association/test_open.rb
-- test/rbbt/association/test_util.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/test_tsv.rb
 - test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/test_task.rb
-- test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_doc.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/test_persist.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/persist/test_tsv.rb
-- test/rbbt/persist/tsv/test_lmdb.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
-- test/rbbt/persist/tsv/test_sharder.rb
-- test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
-- test/rbbt/tsv/test_field_index.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/test_task.rb
+- test/rbbt/test_association.rb
+- test/rbbt/test_knowledge_base.rb
+- test/rbbt/tsv/parallel/test_traverse.rb
+- test/rbbt/tsv/parallel/test_through.rb
 - test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_matrix.rb
+- test/rbbt/tsv/test_accessor.rb
 - test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_parser.rb
 - test/rbbt/tsv/test_stream.rb
-- test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_accessor.rb
 - test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_matrix.rb
 - test/rbbt/tsv/test_attach.rb
 - test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/parallel/test_through.rb
-- test/rbbt/tsv/parallel/test_traverse.rb
+- test/rbbt/tsv/test_field_index.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_util.rb
+- test/rbbt/tsv/test_parser.rb
+- test/rbbt/test_packed_index.rb
+- test/rbbt/test_persist.rb
 - test/rbbt/test_fix_width_table.rb
-- test/test_helper.rb
+- test/rbbt/knowledge_base/test_traverse.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/test_monitor.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/test_annotations.rb
+- test/rbbt/annotations/test_util.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/persist/tsv/test_tokyocabinet.rb
+- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/persist/tsv/test_lmdb.rb
+- test/rbbt/persist/tsv/test_leveldb.rb
+- test/rbbt/persist/tsv/test_cdb.rb
+- test/rbbt/persist/tsv/test_sharder.rb
+- test/rbbt/persist/test_tsv.rb
+- test/rbbt/test_tsv.rb