rbbt-util 5.21.68 → 5.21.69

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 7a3ebc764edda4f545ebecab158bafd4d2d115ea
+  metadata.gz: 399599687a33ccd54d3e3072a1293d167e39af90
+  data.tar.gz: a615f143621c1d9b81346ca23b8ee432fc6a67fc
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+  metadata.gz: '029a96a494c99358d38858cdb772e78314d6e923248589a2145e6b3e1d52dec61eb66429890d7ede8224be097c41c53c0a6d4ffbae23d3263f8ba9c250997a89'
+  data.tar.gz: 4b05254ba442351affed8db14ae7b462b06f6f92d310adf9e9336cd04e33dc626e3ed3d86c8bfb84544d81ef764e1ec5abe743fb971843df9a04fb8362d76bd4

data/lib/rbbt/association/database.rb

@@ -30,36 +30,50 @@ module Association
     target_field = tsv.fields.first
     namespace = tsv.namespace
 
-    if source_final_format and source_field != source_final_format 
-      Log.debug("Changing source format from #{tsv.key_field} to #{source_final_format}")
+    data = Misc.process_options options, :data
 
-      identifier_files = tsv.identifier_files.dup
-      identifier_files = [Organism.identifiers("NAMESPACE")] if identifier_files.empty?
-      identifier_files.concat Entity.identifier_files(source_final_format) if defined? Entity
-      identifier_files.uniq!
-      identifier_files.collect!{|f| f.annotate(f.gsub(/\bNAMESPACE\b/, namespace))} if namespace
-      identifier_files.reject!{|f| f.match(/\bNAMESPACE\b/)}
+    data ||= {}
+    TmpFile.with_file do |tmpfile1|
+      TmpFile.with_file do |tmpfile2|
+        tmp_data1 = Persist.open_database(tmpfile1, true, :double, "HDB")
+        tmp_data2 = Persist.open_database(tmpfile2, true, :double, "HDB")
+
+        if source_final_format and source_field != source_final_format 
+          Log.debug("Changing source format from #{tsv.key_field} to #{source_final_format}")
+
+          identifier_files = tsv.identifier_files.dup
+          identifier_files = [Organism.identifiers("NAMESPACE")] if identifier_files.empty?
+          identifier_files.concat Entity.identifier_files(source_final_format) if defined? Entity
+          identifier_files.uniq!
+          identifier_files.collect!{|f| f.annotate(f.gsub(/\bNAMESPACE\b/, namespace))} if namespace
+          identifier_files.reject!{|f| f.match(/\bNAMESPACE\b/)}
+
+          tsv = TSV.translate(tsv, source_field, source_final_format, options.merge(:identifier_files => identifier_files, :persist_data => tmp_data1))
+        end
 
-      tsv = TSV.translate(tsv, source_field, source_final_format, options.merge(:identifier_files => identifier_files))
-    end
+        # Translate target 
+        if target_final_format and target_field != target_final_format
+          Log.debug("Changing target format from #{target_field} to #{target_final_format}")
+          old_key_field = tsv.key_field 
+          tsv.key_field = "MASK"
 
-    # Translate target 
-    if target_final_format and target_field != target_final_format
-      Log.debug("Changing target format from #{target_field} to #{target_final_format}")
-      old_key_field = tsv.key_field 
-      tsv.key_field = "MASK"
+          identifier_files = tsv.identifier_files.dup 
+          identifier_files.concat Entity.identifier_files(target_final_format) if defined? Entity
+          identifier_files.uniq!
+          identifier_files.collect!{|f| f.annotate(f.gsub(/\bNAMESPACE\b/, namespace))} if namespace
+          identifier_files.reject!{|f| f.match(/\bNAMESPACE\b/)}
 
-      identifier_files = tsv.identifier_files.dup 
-      identifier_files.concat Entity.identifier_files(target_final_format) if defined? Entity
-      identifier_files.uniq!
-      identifier_files.collect!{|f| f.annotate(f.gsub(/\bNAMESPACE\b/, namespace))} if namespace
-      identifier_files.reject!{|f| f.match(/\bNAMESPACE\b/)}
+          tsv = TSV.translate(tsv, target_field, target_final_format, options.merge(:identifier_files => identifier_files, :persist_data => tmp_data2))
+          tsv.key_field = old_key_field
+        end
 
-      tsv = TSV.translate(tsv, target_field, target_final_format, options.merge(:identifier_files => identifier_files))
-      tsv.key_field = old_key_field
-    end
+        tsv.through do |k,v|
+          data[k] = v
+        end
 
-    tsv
+        tsv.annotate data
+      end
+    end
   end
 
   def self.reorder_tsv(tsv, options = {})
@@ -84,7 +98,7 @@ module Association
       tsv.fields = field_headers
 
       if source_format or target_format
-        tsv = translate tsv, source_format, target_format, :persist => true, :persist_data => data
+        tsv = translate tsv, source_format, target_format, :persist => true, :data => data
       else
         tsv.through do |k,v|
           data[k] = v
@@ -152,7 +166,7 @@ module Association
       tsv.fields = field_headers
 
       if source_format or target_format
-        tsv = translate tsv, source_format, target_format, :persist => true, :persist_data => data, :data => data
+        tsv = translate tsv, source_format, target_format, :persist => true, :data => data
       else
         tsv.through do |k,v|
           data[k] = v

data/lib/rbbt/association/index.rb

@@ -7,11 +7,11 @@ module Association
     options = options.nil? ? {} : options.dup
     persist_options = persist_options.nil? ?  Misc.pull_keys(options, :persist)  : persist_options.dup 
 
-    persist_options = Misc.add_defaults persist_options.dup, :persist => true
+    persist_options = Misc.add_defaults persist_options.dup, :persist => true, :dir => Rbbt.var.associations
     persist = persist_options[:persist]
 
     file = version_file(file, options[:namespace]) if options[:namespace] and String === file
-    Persist.persist_tsv(file, "Association Index", options, persist_options.merge(:engine => "BDB")) do |data|
+    Persist.persist_tsv(file, nil, options, persist_options.merge(:engine => "BDB", :prefix => "Association Index")) do |data|
       options = Misc.add_defaults options.dup, :monitor => "Building index for #{Misc.fingerprint file}"
       recycle = options[:recycle]
       undirected = options[:undirected]

data/lib/rbbt/association/open.rb

@@ -13,12 +13,12 @@ module Association
 
     options = Misc.add_defaults options, :zipped => true, :merge => true, :monitor => {:desc => "Opening database #{Misc.fingerprint file}"}
     options[:zipped] = false unless options[:merge]
-    persist_options = Misc.add_defaults persist_options, :persist => true, :dir => Rbbt.var.associations
+    persist_options = Misc.add_defaults persist_options.dup, :persist => true, :dir => Rbbt.var.associations
     persist = persist_options[:persist]
 
     file = version_file(file, options[:namespace]) if options[:namespace] and String === file
 
-    data = Persist.persist_tsv(file, "Association Database", options, persist_options) do |data|
+    data = Persist.persist_tsv(file, nil, options, persist_options.merge(:prefix => "Association Database")) do |data|
       file = file.call if Proc === file
 
       options = options.dup

data/lib/rbbt/association/util.rb

@@ -57,7 +57,7 @@ module Association
 
     if source_specs.first and not all_fields.include? source_specs.first and defined? Entity and (_format = Entity.formats[source_specs.first.to_s])
       _source = all_fields.select{|f| Entity.formats[f.to_s] == _format }.first
-      raise "Source not found #{source_specs}. Options: #{Misc.fingerprint all_fields}" if _target.nil?
+      raise "Source not found #{source_specs}. Options: #{Misc.fingerprint all_fields}" if _source.nil?
       source_specs[0] = _source
     end
 

data/lib/rbbt/tsv/serializers.rb

@@ -57,7 +57,11 @@ module TSV
 
   class StringDoubleArraySerializer
     def self.dump(array)
-      array.collect{|a| a.collect{|a| a.to_s} * "|"} * "\t"
+      begin
+      array.collect{|a| a.collect{|a| a.to_s } * "|"} * "\t"
+      rescue Encoding::CompatibilityError
+        array.collect{|a| a.collect{|a| a.to_s.force_encoding('UTF-8')} * "|"} * "\t"
+      end
     end
 
     def self.load(string)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.68
+  version: 5.21.69
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-01-31 00:00:00.000000000 Z
+date: 2017-02-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake