rbbt-util 5.27.7 → 5.27.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 72562729535554e718451adb87338503ff40a81874a9e0fed6f8eaf4e6aa0edc
+  metadata.gz: 8d3d7b4d19322b271a94d3e2fe046158857bbedf9adf79d0408b4c50d2ba9254
+  data.tar.gz: 78d6fcffe3d5efd08ec42e0493f3f7c731d31001b726ade88802460e5958354b
 SHA512:
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-  data.tar.gz: 1790b8f38f91dfbb582a394d86953156d90351a8d724fb9535a3bc72ebac5fbbfe24e88fe10cf943e2ed91ff059af68cf581bac333f5480096f85cf6e29b8018
+  metadata.gz: cc8ba1db9052fb92dc87bd037b8745f232ff20110b7e3d0da4d2e3c9f0ed90b4bdf18f68887c8a1ad1eb44f1828e9fbd614770259e73deda196047cf4f783d06
+  data.tar.gz: 3623a36d9282152a71710a71767fb829ce1258f29161451ffc1b0045c0eee152267dd62c8ca8af0e2e3de7f4ef86d9242279c3d34bbd7a3fdfa18841d857ac8a

data/lib/rbbt/tsv/attach.rb

@@ -32,7 +32,8 @@ module TSV
     done = false
     Open.write(output) do |os|
       options.delete :sep if options[:sep] == "\t"
-      os.puts TSV.header_lines(key_field, fields, options) 
+      header_lines = TSV.header_lines(key_field, fields, options) 
+      os.puts header_lines unless header_lines.empty?
 
       while line
         key, *parts = line.sub("\n",'').split(sep, -1)
@@ -212,6 +213,35 @@ module TSV
     other_filename = other.respond_to?(:filename) ? other.filename : other.inspect
     Log.low("Attaching fields:#{Misc.fingerprint fields } from #{other_filename}.")
 
+    same_key = true
+    begin
+      case
+      when (Misc.match_fields(key_field, other.key_field) and same_key)
+        Log.debug "Attachment with same key: #{other.key_field}"
+        attach_same_key other, fields
+      when (not in_namespace and self.fields.select{|f| Misc.match_fields(f, other.key_field)}.any?)
+        Log.debug "Found other key field: #{other.key_field}"
+        attach_source_key other, other.key_field, :fields => fields, :one2one => one2one
+      when (in_namespace and self.fields_in_namespace.select{|f| Misc.match_fields(f, other.key_field)}.any?)
+        Log.debug "Found other key field in #{in_namespace}: #{other.key_field}"
+        attach_source_key other, other.key_field, :fields => fields, :one2one => one2one
+      else
+        index = TSV.find_traversal(self, other, options)
+        raise FieldNotFoundError, "Cannot traverse identifiers" if index.nil?
+        Log.debug "Attachment with index: #{other.key_field}"
+        attach_index other, index, fields
+      end
+    rescue Exception
+      if same_key
+        Log.warn "Could not translate identifiers with same_key"
+        same_key = false
+        retry
+      else
+        raise $!
+      end
+    end
+    Log.debug("Attachment of fields:#{Misc.fingerprint fields } from #{other.filename.inspect} finished.")
+
     if complete
       fill = TrueClass === complete ? nil : complete
       field_length = self.fields.length 
@@ -219,6 +249,9 @@ module TSV
       other_common_pos = common_fields.collect{|f| other.fields.index f}
       this_common_pos = common_fields.collect{|f| self.fields.index f}
       missing = other.keys - self.keys
+
+      other = other.to_list if other.type == :single
+
       case type
       when :single
         missing.each do |k|
@@ -249,35 +282,6 @@ module TSV
       end
     end
 
-    same_key = true
-    begin
-      case
-      when (Misc.match_fields(key_field, other.key_field) and same_key)
-        Log.debug "Attachment with same key: #{other.key_field}"
-        attach_same_key other, fields
-      when (not in_namespace and self.fields.select{|f| Misc.match_fields(f, other.key_field)}.any?)
-        Log.debug "Found other key field: #{other.key_field}"
-        attach_source_key other, other.key_field, :fields => fields, :one2one => one2one
-      when (in_namespace and self.fields_in_namespace.select{|f| Misc.match_fields(f, other.key_field)}.any?)
-        Log.debug "Found other key field in #{in_namespace}: #{other.key_field}"
-        attach_source_key other, other.key_field, :fields => fields, :one2one => one2one
-      else
-        index = TSV.find_traversal(self, other, options)
-        raise FieldNotFoundError, "Cannot traverse identifiers" if index.nil?
-        Log.debug "Attachment with index: #{other.key_field}"
-        attach_index other, index, fields
-      end
-    rescue Exception
-      if same_key
-        Log.warn "Could not translate identifiers with same_key"
-        same_key = false
-        retry
-      else
-        raise $!
-      end
-    end
-    Log.debug("Attachment of fields:#{Misc.fingerprint fields } from #{other.filename.inspect} finished.")
-
     self
   end
 

data/lib/rbbt/tsv/attach/util.rb

@@ -4,9 +4,20 @@ module TSV
     fields = other.fields - [key_field].concat(self.fields) if fields.nil?
 
     fields = [fields].compact unless Array === fields
+
+    common_fields = self.fields & fields
+
+    fields = fields - common_fields
+
     num_fields = fields.length
 
     field_positions = fields.collect{|field| other.identify_field field}
+
+    if common_fields.any?
+      common_field_positions = common_fields.collect{|field| self.identify_field field}
+      common_field_positions_other = common_fields.collect{|field| other.identify_field field}
+    end
+
     other.with_unnamed do
       with_unnamed do
         through do |key, values|
@@ -28,6 +39,12 @@ module TSV
               new_values = field_positions.collect do |pos|
                 pos == :key ? key : other_values[pos]
               end
+
+              if common_fields.any?
+                common_field_positions.zip(common_field_positions_other).each do |p1,p2|
+                  current[p1] += other_values[p2]
+                end
+              end
             end
 
             new_values.collect!{|v| [v]}     if     type == :double and not (other.type == :double or other.type == :flat)

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

@@ -163,7 +163,7 @@ module Misc
 
   def self.fixutf8(string)
     return nil if string.nil?
-    return string if string.respond_to?(:encoding) && string.encoding == "UTF-8" && (string.respond_to?(:valid_encoding?) && string.valid_encoding?) ||
+    return string if string.respond_to?(:encoding) && string.encoding.to_s == "UTF-8" && (string.respond_to?(:valid_encoding?) && string.valid_encoding?) ||
                      (string.respond_to?(:valid_encoding) && string.valid_encoding)
 
     if string.respond_to?(:encode)

data/lib/rbbt/workflow/usage.rb

@@ -88,7 +88,7 @@ module Workflow
                           key = [workflow, task]
 
                           dep_tree[key] = workflow.dep_tree(task)
-                        end if self.task_dependencies[name.to_sym]
+                        end if name && self.task_dependencies[name.to_sym]
                         dep_tree
                       end
   end

data/test/rbbt/tsv/test_attach.rb

@@ -213,8 +213,9 @@ row2    E
 
     tsv1 = tsv2 = nil
 
-    tsv1 = Rbbt.tmp.test.test1.data.tsv :double,  :sep => /\s+/
-    tsv2 = Rbbt.tmp.test.test2.data.tsv :double,  :sep => /\s+/
+    tsv1 = Rbbt.tmp.test.test1.data.produce(true).tsv :double,  :sep => /\s+/
+    tsv2 = Rbbt.tmp.test.test2.data.produce(true).tsv :double,  :sep => /\s+/
+    Log.tsv tsv2
 
     tsv2.identifiers = Rbbt.tmp.test.test2.identifiers.produce.find #.to_s
 

data/test/rbbt/util/misc/test_format.rb

@@ -0,0 +1,10 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
+require 'rbbt/util/misc/format'
+
+class TestClass < Test::Unit::TestCase
+  def test_fixutf8
+    a = "Camión"
+    assert_equal a, Misc.fixutf8(a)
+  end
+end
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.27.7
+  version: 5.27.8
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-06-04 00:00:00.000000000 Z
+date: 2020-07-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -487,6 +487,7 @@ files:
 - test/rbbt/util/concurrency/test_threads.rb
 - test/rbbt/util/log/test_progress.rb
 - test/rbbt/util/misc/test_bgzf.rb
+- test/rbbt/util/misc/test_format.rb
 - test/rbbt/util/misc/test_lock.rb
 - test/rbbt/util/misc/test_multipart_payload.rb
 - test/rbbt/util/misc/test_omics.rb
@@ -552,6 +553,7 @@ test_files:
 - test/rbbt/util/test_colorize.rb
 - test/rbbt/util/misc/test_omics.rb
 - test/rbbt/util/misc/test_pipes.rb
+- test/rbbt/util/misc/test_format.rb
 - test/rbbt/util/misc/test_lock.rb
 - test/rbbt/util/misc/test_multipart_payload.rb
 - test/rbbt/util/misc/test_bgzf.rb