rbbt-util 5.26.86 → 5.26.87

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 5267bbf2d76c3a1ec0920fa5ecb03acf711ae541198d220055afae0965fa9630
+  metadata.gz: 658585f6a78ccc8f2a4579b1b512a9470030edbd1e724addb2b5f1ef3b71c218
+  data.tar.gz: cb64eb69d269a924b585745f6fa4be0aad88c4ed62a9510e9a85ddc3f243caf3
 SHA512:
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-  data.tar.gz: 7cc7b7c0207712ff2541d9ced370131c431359f28de3f9aaee4d1ce840f59506c6e05776021f04fe47d8fe461362f7fbfa867cc2982afe760dc451178342ab08
+  metadata.gz: 58458df66b0881d89894db3c526dd21b5490de6e0e55c403ef44c09827b36c3da90509d3158d8cc5438a1d3f235a6f0650eb470d0b79c3919e216879341d87aa
+  data.tar.gz: c5e2964e08101856061dd68103b2a970518d1542c163cb17d2c4f0bbe40b92a3cf225ec0859d2b97d2138d6cdf08ada9f69020555c11acafbe6bcd2bbcdb809b

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

@@ -10,7 +10,7 @@ module TSV
     other.with_unnamed do
       with_unnamed do
         through do |key, values|
-          self[key] = [] if self[key].nil?
+          self[key] = [] unless self.include? key
           current = self[key]
           current = [current] unless Array === current
           if other.include? key

data/share/rbbt_commands/tsv/attach

@@ -15,6 +15,7 @@ Use - to read from STDIN
 
 -f--fields* Fields to attach (all if not specified)
 -i--identifiers* Identifier file
+-c--complete Complete TSV with keys new in other files
 -h--help Print this help
 
 EOF
@@ -30,6 +31,7 @@ end
 file1, *rest = ARGV
 fields = options[:fields]
 identifiers = options[:identifiers] 
+complete = options[:complete] 
 
 if identifiers.nil?
   require 'rbbt/sources/organism'
@@ -44,7 +46,7 @@ tsv = tsv.to_double if tsv.type == :flat
 rest.each do |file2|
   file_fields = TSV.parse_header(file2).all_fields - tsv.all_fields
   these_fields = fields ? fields & file_fields : nil
-  tsv = tsv.attach file2, :fields => these_fields, :identifiers => identifiers
+  tsv = tsv.attach file2, :fields => these_fields, :identifiers => identifiers, :complete => complete
 end
 
 puts tsv.to_s

data/share/rbbt_commands/tsv/get

@@ -14,6 +14,7 @@ Use - to read from STDIN
 -tch--tokyocabinet File is a tokyocabinet hash database
 -tcb--tokyocabinet_bd File is a tokyocabinet B database
 -f--fields* Fields to extract
+-hh--header_hash* Change the character used to mark the header line (defaults to #)
 -k--key_field* Use this field as key
 -h--help Print this help
 -l--lines Separate in lines
@@ -45,7 +46,7 @@ fields = options[:fields]
 key_field = options[:key_field]
 fields = fields.split(/[,|]/, -1) unless fields.nil?
 
-parser = TSV::Parser.new tsv, :key_field => key_field,  :fields => fields, :type => options[:type]
+parser = TSV::Parser.new tsv, :key_field => key_field,  :fields => fields, :type => options[:type], :header_hash => options[:header_hash]
 fields ||= parser.fields
 
 TSV.traverse(parser) do |k,v|

data/test/rbbt/tsv/test_attach.rb

@@ -531,5 +531,41 @@ row5,D
     assert_equal tsv4.attach(tsv1)["row1"]["bar (ValueB)"], %w(b)
     assert_equal tsv3.attach(tsv1)["b"]["ValueD"], %w(d)
   end
+
+  def test_attach_single_nils
+    content1 =<<-EOF
+#Id,ValueA
+row1,
+row2,AA
+    EOF
+    content2 =<<-EOF
+#Id,ValueB
+row1,B
+row2,BB
+    EOF
+    content3 =<<-EOF
+#Id,ValueC
+row1,
+row2,CC
+    EOF
+
+    tsv1 = tsv2 = tsv3 = tsv4 = index = nil
+    TmpFile.with_file(content1) do |filename|
+      tsv1 = TSV.open(File.open(filename), :double, :sep => ',', :type => :single)
+      tsv1.keys.each{|k| tsv1[k] = nil if tsv1[k] == ""}
+    end
+
+    TmpFile.with_file(content2) do |filename|
+      tsv2 = TSV.open(File.open(filename), :double, :sep => ',', :type => :single)
+      tsv2.keys.each{|k| tsv2[k] = nil if tsv2[k] == ""}
+    end
+
+    TmpFile.with_file(content3) do |filename|
+      tsv3 = TSV.open(File.open(filename), :double, :sep => ',', :type => :single)
+      tsv3.keys.each{|k| tsv3[k] = nil if tsv3[k] == ""}
+    end
+
+    assert_equal tsv1.attach(tsv2, :complete => true).attach(tsv3, :complete => true)["row1"], [nil, "B", nil]
+  end
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.86
+  version: 5.26.87
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-11-13 00:00:00.000000000 Z
+date: 2019-11-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -531,91 +531,91 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.6
+rubygems_version: 3.0.4
 signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/rbbt/test_entity.rb
-- test/rbbt/workflow/test_doc.rb
-- test/rbbt/workflow/test_step.rb
-- test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/test_task.rb
-- test/rbbt/resource/test_path.rb
-- 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_lock.rb
-- test/rbbt/util/misc/test_multipart_payload.rb
-- test/rbbt/util/misc/test_bgzf.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/R/test_plot.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/util/R/test_model.rb
+- test/test_helper.rb
+- test/rbbt/test_annotations.rb
+- test/rbbt/association/test_database.rb
+- test/rbbt/association/test_item.rb
+- test/rbbt/association/test_index.rb
+- test/rbbt/association/test_open.rb
+- test/rbbt/association/test_util.rb
+- test/rbbt/test_association.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/knowledge_base/test_traverse.rb
 - test/rbbt/util/test_config.rb
-- test/rbbt/util/test_log.rb
-- test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/util/log/test_progress.rb
-- test/rbbt/util/test_tmpfile.rb
 - test/rbbt/util/test_R.rb
-- test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/test_tmpfile.rb
+- test/rbbt/util/test_filecache.rb
 - test/rbbt/util/test_misc.rb
-- test/rbbt/util/test_open.rb
-- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/log/test_progress.rb
+- test/rbbt/util/misc/test_multipart_payload.rb
+- test/rbbt/util/misc/test_pipes.rb
+- test/rbbt/util/misc/test_bgzf.rb
+- test/rbbt/util/misc/test_lock.rb
+- test/rbbt/util/misc/test_omics.rb
+- test/rbbt/util/test_semaphore.rb
+- test/rbbt/util/simpleopt/test_get.rb
 - test/rbbt/util/simpleopt/test_parse.rb
 - test/rbbt/util/simpleopt/test_setup.rb
-- test/rbbt/util/simpleopt/test_get.rb
-- test/rbbt/util/test_python.rb
-- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/test_open.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_log.rb
+- test/rbbt/util/test_colorize.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/test_concurrency.rb
+- test/rbbt/util/R/test_eval.rb
+- test/rbbt/util/R/test_plot.rb
+- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/test_simpleopt.rb
 - test/rbbt/util/test_chain_methods.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_attach.rb
-- test/rbbt/tsv/test_filter.rb
+- test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/util/test_python.rb
+- test/rbbt/tsv/test_index.rb
 - test/rbbt/tsv/test_parser.rb
-- test/rbbt/tsv/test_accessor.rb
-- test/rbbt/tsv/test_matrix.rb
 - test/rbbt/tsv/test_field_index.rb
-- test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_stream.rb
+- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_change_id.rb
 - test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/test_excel.rb
 - test/rbbt/tsv/parallel/test_through.rb
 - test/rbbt/tsv/parallel/test_traverse.rb
-- test/rbbt/tsv/test_stream.rb
-- test/rbbt/test_association.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/association/test_item.rb
-- test/rbbt/association/test_open.rb
-- test/rbbt/association/test_util.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_matrix.rb
+- test/rbbt/tsv/test_util.rb
+- test/rbbt/tsv/test_attach.rb
+- test/rbbt/tsv/test_excel.rb
+- test/rbbt/test_monitor.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/annotations/test_util.rb
+- test/rbbt/test_packed_index.rb
+- test/rbbt/workflow/test_task.rb
+- test/rbbt/workflow/test_doc.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/step/test_dependencies.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/test_entity.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/test_persist.rb
+- test/rbbt/persist/tsv/test_tokyocabinet.rb
 - test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_lmdb.rb
-- test/rbbt/persist/tsv/test_sharder.rb
 - test/rbbt/persist/tsv/test_leveldb.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
+- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/persist/tsv/test_sharder.rb
+- test/rbbt/persist/tsv/test_lmdb.rb
 - test/rbbt/persist/test_tsv.rb
 - test/rbbt/test_tsv.rb
-- test/rbbt/test_annotations.rb
 - test/rbbt/test_fix_width_table.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/test_persist.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_traverse.rb
-- test/test_helper.rb
+- test/rbbt/test_knowledge_base.rb
+- test/rbbt/resource/test_path.rb