rbbt-util 5.26.12 → 5.26.13

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 5a26934f329b7164d590e5e56b3c652395aed839642f30143c6f73cb42b4de12
-  data.tar.gz: ec812f3cd06f25081bfdcd0bff71a8382a8813d69ecb91ecf84a7df5c4d01899
+  metadata.gz: '078d0e5f58ba3c4bffecee8dc71be5040d628548988dce67027cbfe232709f5a'
+  data.tar.gz: 4003e46456bb1b9d295b7d5af5c11c60cc64026a204a8f8eec48f258f2043999
 SHA512:
-  metadata.gz: 1da22127c3b3674fd0c96d43d86355b1c79d9dcb75a7f6b82ed22f147530f6cef618b425cc556dcbe7ddd810e5c1ef05d44bef86c978f51ff29613ad8a0f33cd
-  data.tar.gz: c79ba4273b3c50625976d6a07cb9545bdd7a5e42380cab89cbe12f0ab28cd452238e61c937e16e558889f78e6f35f77b083413a389d7a44cd02e56b212880e35
+  metadata.gz: 4084802c7d8e72c953b917bb2dad8ee55918ea26285da8ab89bd22b6675c32d7e70b11eab4df072d45dbbaed460f7f375814b2e1dc679501e34fd42232407ee7
+  data.tar.gz: bfe0152f5d9cde983ae27f722ab0e695a5e38b72a6d0f27430eaf837962dab66e91f2f0157bde3dbaf06bc224bae072a7577a6abc0d273970b537c20578d604e

data/lib/rbbt/association/database.rb

@@ -113,7 +113,6 @@ module Association
   def self.open_stream(stream, options = {})
     fields, persist, data = Misc.process_options options, :fields, :persist, :data
 
-
     parser = TSV::Parser.new stream, options.merge(:fields => nil, :key_field => nil)
     options = options.merge(parser.options)
     options = Misc.add_defaults options, :type => :double, :merge => true
@@ -124,6 +123,8 @@ module Association
 
     parser.key_field = source_pos
     parser.fields = field_pos
+    parser.field_positions = field_pos
+    parser.key_position = source_pos
 
     #case parser.type
     #when :single
@@ -160,9 +161,10 @@ module Association
     data ||= {}
     tsv = nil
     TmpFile.with_file do |tmpfile|
-      tmp_data = Persist.open_database(tmpfile, true, :double, "HDB")
+      tmp_data = Persist.open_database(tmpfile, true, open_options[:type], "HDB")
 
       tsv = TSV.parse parser.stream, tmp_data, open_options
+      tsv = tsv.to_double
       tsv.key_field = source_header
       tsv.fields = field_headers
 

data/lib/rbbt/association/util.rb

@@ -152,7 +152,8 @@ module Association
       target_format = process_formats(specs[:target][1] || specs[:target][0], format) || target_format unless target_format
     end
 
-    Log.low "Headers -- #{[source_pos, field_pos, source_header, field_headers, source_format, target_format]}"
-    [source_pos, field_pos, source_header, field_headers, source_format, target_format]
+    res = [source_pos, field_pos, source_header, field_headers, source_format, target_format]
+    Log.low "Headers -- #{res}"
+    res
   end
 end

data/lib/rbbt/tsv/parser.rb

@@ -356,7 +356,6 @@ module TSV
       key_field = Misc.process_options options, :key_field
       fields    = Misc.process_options options, :fields
 
-
       if (key_field.nil? or key_field == 0 or key_field == :key) and
         (fields.nil? or fields == @fields or (not @fields.nil? and fields == (1..@fields.length).to_a))
 

data/lib/rbbt/workflow/definition.rb

@@ -18,7 +18,7 @@ module Workflow
     :description        => "",
     :result_type        => nil,
     :result_description => "",
-    :extension          => '')
+    :extension          => nil)
 
 
   def helper(name, &block)
@@ -108,7 +108,20 @@ module Workflow
       :extension          => consume_extension,
       :input_options      => consume_input_options
     }
-    
+
+    task_info[:extension] = case task_info[:result_type].to_s
+                            when "tsv"
+                              "tsv"
+                            when "yaml"
+                              "yaml"
+                            when "marshal"
+                              "marshal"
+                            when "json"
+                              "json"
+                            else
+                              nil
+                            end if task_info[:extension].nil?
+
     task = Task.setup(task_info, &block)
 
     last_task = task

data/share/Rlib/util.R

@@ -757,7 +757,7 @@ rbbt.install.bioc <-function(pkg){
 rbbt.install.biocManager <-function(pkg, ...){
     cat("Try BiocManager install:", pkg, "\n")
     res = FALSE
-    tryCatch({ BiocManager::install(pkg, ...) }, error = function(e){ warning(paste("Could not install BiocManager ", pkg, "\n")); res = FALSE })
+    tryCatch({ BiocManager::install(pkg, ...); res = TRUE }, error = function(e){ warning(paste("Could not install BiocManager ", pkg, "\n")); res = FALSE })
     return(res)
 }
 
@@ -782,8 +782,8 @@ rbbt.require <- function(pkg, ...){
     for (pkg in new.packages){ 
         if (!rbbt.install.github(pkg, ...)){
             if (!rbbt.install.CRAN(pkg, ...)){
+              if (!rbbt.install.biocManager(pkg, ...)){
                 if (!rbbt.install.bioc(pkg, ...)){
-                    if (!rbbt.install.biocManager(pkg, ...)){
                         stop("Error!", pkg)
                     }
                 }

data/test/rbbt/association/test_database.rb

@@ -59,7 +59,8 @@ TP53 NFKB1|GLI1 activation|activation true|true
   end
 
   def test_gene_ages
-    assert Association.database('/home/mvazquezg/git/workflows/genomics/share/gene_ages', :source => "FamilyAge", :merge => true, :target => "Ensembl Gene ID", :persist => false).values.first.length > 1
+    file = datafile_test('gene_ages')
+    assert Association.database(file, :source => "FamilyAge", :merge => true, :target => "Ensembl Gene ID", :persist => false).values.first.length > 1
   end
 
   def __test_reorder_multiple_mismatch

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.12
+  version: 5.26.13
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-05-28 00:00:00.000000000 Z
+date: 2019-05-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake