rbbt-util 5.21.59 → 5.21.60

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 6af6b7d19c8318dff73f410c5e4094aeaa9466d7
-  data.tar.gz: cb78b1b85697ca27eb8716afe3b70513c4ffbe41
+  metadata.gz: 02bb66246a58680f8e703e49df480b977b2c1f6f
+  data.tar.gz: 428a2f61dbb7a216833864296f7212fbe1e1032b
 SHA512:
-  metadata.gz: 46bf19741a3c8d36219cd75fef3a103cad844dd89d4534ea8af5ec3c01fbc1d3632d07c55a1a397d5737550ad5d85961804af7ef3df19f1dee0e7ea777f4175b
-  data.tar.gz: 89ada9ba0db87dd8a2b10a2848e2d3f92c6bd2b0935177a1b50606604f7bee2a87667d6a02266842505965e79c4c3dac839a6b26bfd97eb9e1a6c21a0e02283d
+  metadata.gz: c22b4e1597fd4787667a4bc2f6a997177ea2cd93025e2b7a19720629850ddd60a1037bf7651bf570f9e2add3225c90df1375ef72fe4a2649fe4454f8ab393f83
+  data.tar.gz: edd5911b55194c38c5a2193d5937fc52911f4b18b3490bea729ad03c0f94890031083e98b9cc13a9d6beef855b354bf095f5dfe9db7852e8b06e0300d232713b

data/lib/rbbt/tsv/accessor.rb

@@ -556,18 +556,36 @@ module TSV
     end
   end
 
-  def dumper_stream(keys = nil, no_options = false)
-    TSV::Dumper.stream self do |dumper|
+  def dumper_stream(keys = nil, no_options = false, unmerge = false)
+    unmerge = false unless type == :double
+
+    options = self.options
+    options[:type] = :list if unmerge
+
+    TSV::Dumper.stream options do |dumper|
       dumper.init unless no_options
       begin
         if keys
           keys.each do |key|
-            dumper.add key, self[key]
+            if unmerge
+              Misc.zip_fields(self[key]).each do |values|
+                dumper.add key, values
+              end
+            else
+              dumper.add key, self[key]
+            end
           end
         else
           with_unnamed do
             each do |k,v|
-              dumper.add k, v
+
+              if unmerge
+                Misc.zip_fields(v).each do |values|
+                  dumper.add k, values
+                end
+              else
+                dumper.add k, v
+              end
             end
           end
         end
@@ -579,7 +597,7 @@ module TSV
     end
   end
 
-  def to_s(keys = nil, no_options = false)
+  def to_s(keys = nil, no_options = false, unmerge = false)
     if FalseClass === keys or TrueClass === keys
       no_options = keys
       keys = nil
@@ -591,7 +609,7 @@ module TSV
       end
     end
 
-    io = dumper_stream(keys, no_options)
+    io = dumper_stream(keys, no_options, unmerge)
 
     str = ''
     while block = io.read(Misc::BLOCK_SIZE)

data/lib/rbbt/tsv/excel.rb

@@ -71,7 +71,7 @@ module TSV
             cells.push v * sep2
           end
         else
-          v = remove_link(v) if remove_links
+          v = _remove_link(v) if remove_links
           cells.push v
         end
       end

data/lib/rbbt/tsv/util.rb

@@ -60,7 +60,7 @@ module TSV
 
   def self.abort_stream(file, exception = nil)
     return if file.nil?
-    if Step === file
+    if defined? Step and Step === file
       if exception
         file.exception exception 
       else

data/lib/rbbt/util/log/progress/report.rb

@@ -17,7 +17,7 @@ module Log
       end
     end
 
-    attr_accessor :history, :mean_max
+    attr_accessor :history, :mean_max, :max_history
     def thr
       count = @ticks - @last_count
       if @last_time.nil?
@@ -34,7 +34,18 @@ module Log
         @history ||= [thr]
       else
         @history << thr
-        @history.shift if @history.length > 20
+        max_history ||= case 
+                      when @ticks > 20
+                        count = @ticks - @last_count
+                        times = @max / count
+                        num = times / 20
+                        num = 2 if num < 2
+                        count * num
+                      else
+                        20
+                      end
+        max_history = 100 if max_history > 100
+        @history.shift if @history.length > max_history
       end
 
       @mean_max ||= 0

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

@@ -97,4 +97,8 @@ module Misc
     sizes = sizes.collect{|v| (v.to_f/max * 100).to_i.to_f / 100}
     url = "https://chart.googleapis.com/chart?cht=v&chs=500x300&chd=t:#{sizes * ","}&chco=FF6342,ADDE63,63C6DE,FFFFFF&chdl=#{label}"
   end
+
+  def self.in_delta?(a, b, delta = 0.0001)
+    (a.to_f - b.to_f).abs < delta
+  end
 end

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

@@ -60,6 +60,10 @@ module Misc
     first.zip(*rest)
   end
 
+  def self.choose(array, select)
+    array.zip(select).select{|e,s| s }.collect{|e,s| e }
+  end
+
   def self.field_position(fields, field, quiet = false)
     return field if Integer === field or Range === field
     raise FieldNotFoundError, "Field information missing" if fields.nil? && ! quiet

data/lib/rbbt/util/open.rb

@@ -419,12 +419,16 @@ module Open
         res = []
         while not f.eof?
           l = f.gets
-          l = Misc.fixutf8(l) 
+          l = Misc.fixutf8(l) unless options[:nofix]
           res << yield(l)
         end
         res
       else
-        Misc.fixutf8(f.read)
+        if options[:nofix]
+          f.read
+        else
+          Misc.fixutf8(f.read)
+        end
       end
     end
   end

data/share/rbbt_commands/tsv/values

@@ -40,7 +40,9 @@ end
 
 field = options[:field]
 
-TSV.traverse(tsv, :fields => [field]) do |k,v|
+fields = field.nil? ? nil : [field]
+
+TSV.traverse(tsv, :fields => fields) do |k,v|
   if options[:lines]
     puts (Array === v ? v.flatten*"\n" : v.to_s ) 
   else

data/test/rbbt/tsv/test_accessor.rb

@@ -209,4 +209,16 @@ row2    aa|aa|AA|AA    b1|b2|B1|B2    Id1|Id1|Id2|Id2
     end
   end
 
+  def test_to_s_unmerge
+    content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|A    b|B    Id1|Id2
+row2    aa|aa|AA|AA    b1|b2|B1|B2    Id1|Id1|Id2|Id2
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/)
+      assert_equal 6, CMD.cmd('grep -v "#" | cut -f 1', :in => tsv.to_s(nil, false, true)).read.split("\n").length
+    end
+  end
 end

data/test/rbbt/tsv/test_manipulate.rb

@@ -314,4 +314,5 @@ row3    a    C    Id4
 
     end
   end
+
 end

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

@@ -70,5 +70,6 @@ class TestProgress < Test::Unit::TestCase
     end
 
   end
+
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.59
+  version: 5.21.60
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-12-01 00:00:00.000000000 Z
+date: 2016-12-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -491,83 +491,83 @@ signing_key:
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/test_helper.rb
+- test/rbbt/test_workflow.rb
 - test/rbbt/resource/test_path.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/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/util/log/test_progress.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_R.rb
+- test/rbbt/util/test_log.rb
+- test/rbbt/util/test_open.rb
 - test/rbbt/util/misc/test_lock.rb
-- test/rbbt/util/misc/test_pipes.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_omics.rb
-- test/rbbt/util/misc/test_multipart_payload.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/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_doc.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/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/tsv/test_parallel.rb
-- test/rbbt/tsv/test_excel.rb
-- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_matrix.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_excel.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/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/tsv/parallel/test_through.rb
+- test/rbbt/tsv/parallel/test_traverse.rb
 - test/rbbt/test_fix_width_table.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
+- test/test_helper.rb