rbbt-util 5.21.110 → 5.21.111

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 76533fd3b7702e342b7d237102246b920f687fb2
-  data.tar.gz: 2c2ab122805de8b07a901e001294b56f65c49eed
+  metadata.gz: b261af4cdb9a029acc7e272d72b1bc3baa775129
+  data.tar.gz: 2f1fb775eca6be25b97b9852686f0c38e3f36ea2
 SHA512:
-  metadata.gz: d2b46293054ceca952bff6da1f9c5200f278645911b55dd8b235b634ff0170f193fac20f5797d52d946f910eec894b44bae3a79b457c3c02cc8e0d011cd85f82
-  data.tar.gz: f3f15bb7057ea0521bdcbec6290cdde7e3dcd891abe2832008a6d17f944580a6a2fc284a9c442d421501be023c347f0003b01e1838911f363302c6059057c60e
+  metadata.gz: 1801165f0f672913afe6869ece7f776f115889ec58d12c043f8687cb0e04ee821a054d14430b7335aded7c818f341ef51cfe9bdf1851410b7a21413eb92ddebd
+  data.tar.gz: 5db9691995576aa930cc8a724dc4df18b542d2c7b711a253627f5764f6467f4e4b3f00f8d328ebb9c1ca7bcf3bb0424d580ab0f346c3bc3413197da3104725a0

data/lib/rbbt/rest/client/step.rb

@@ -157,6 +157,7 @@ class WorkflowRESTClient
     end
 
     def done?
+      init_job unless @url
       @done || status.to_s == 'done'
     end
 

data/lib/rbbt/tsv/attach.rb

@@ -239,13 +239,13 @@ module TSV
     same_key = true
     begin
       case
-      when (key_field == other.key_field and same_key)
+      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.include?(other.key_field))
+      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.include?(other.key_field))
+      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

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

@@ -64,7 +64,8 @@ module TSV
     field_positions = fields.collect{|field| other.identify_field field}
     field_names     = field_positions.collect{|pos| pos == :key ? other.key_field : other.fields[pos] }
 
-    source_pos = identify_field source
+    corrected_source = all_fields.select{|f| Misc.match_fields(f, source) }.first
+    source_pos = identify_field corrected_source
 
     other.with_unnamed do
       with_unnamed do
@@ -99,6 +100,7 @@ module TSV
 
             new = Misc.zip_fields(all_new_values).each{|field_entry|
               field_entry.flatten!
+              field_entry.compact!
             }
 
             self[key] = values.concat new
@@ -229,13 +231,13 @@ module TSV
     ids.each_with_index do |list, i|
       break if i == ids.length - 1
       match = list.select{|field| 
-        ids[i + 1].select{|f| field == f}.any?
+        ids[i + 1].select{|f| Misc.match_fields(field, f) }.any?
       }
       return nil if match.empty?
       id_list << match.first
     end
 
-    if id_list.last != files.last.all_fields.first
+    if ! Misc.match_fields(id_list.last, files.last.all_fields.first)
       id_list << files.last.all_fields.first
       id_list.zip(files)
     else
@@ -258,8 +260,12 @@ module TSV
     while not path.empty?
       next_key, next_file = path.shift
 
+      next_fields = next_file.all_fields
+      corrected_next_key = next_fields.select{|f| Misc.match_fields(f, next_key)}.first
+      corrected_current_key = next_fields.select{|f| Misc.match_fields(f, current_key)}.first 
+
       if current_index.nil?
-        current_index = next_file.index(:target => next_key, :fields => [current_key], :persist => persist_input)
+        current_index = next_file.index(:target => corrected_next_key, :fields => [corrected_current_key], :persist => persist_input)
         current_index = current_index.select :key => data_file.keys
       else
         next_index = next_file.index :target => next_key, :fields => [current_key], :persist => persist_input

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

@@ -1,5 +1,18 @@
 module Misc
 
+  def self.match_fields(field1, field2)
+    return true if field1 == field2 
+    if m = field1.match(/\((.*)\)/)
+      field1 = m[1]
+    end
+
+    if m = field2.match(/\((.*)\)/)
+      field2 = m[1]
+    end
+
+    field1 == field2
+  end
+
   def self.prepare_entity(entity, field, options = {})
     return entity unless defined? Entity
     return entity unless String === entity or Array === entity

data/lib/rbbt/workflow/accessor.rb

@@ -371,7 +371,7 @@ class Step
 
     status = self.status
 
-    if done? and not (status == :done or status == :ending) and not status == :noinfo
+    if done? and not (status == :done or status == :ending or status == :producing) and not status == :noinfo
       return true 
     end
     if status == :done and not done?

data/lib/rbbt/workflow/step/run.rb

@@ -97,11 +97,12 @@ class Step
   end
 
   def checks
-    dependency_checks + input_checks
+    (dependency_checks + input_checks).uniq
   end
 
   def updated?
     return true unless done?
+
     outdated_time  = []
     outdated_dep  = []
     checks.each do |dep| 
@@ -113,8 +114,10 @@ class Step
       end
     end
 
-    outdated = outdated_time + outdated_dep
-    outdated.empty?
+    Log.low "Some newer files found: #{Misc.fingerprint outdated_time}" if outdated_time.any?
+    Log.low "Some outdated files found: #{Misc.fingerprint outdated_dep}" if outdated_dep.any?
+
+    (outdated_time + outdated_dep).empty?
   end
 
   def kill_children

data/test/rbbt/tsv/test_attach.rb

@@ -479,5 +479,57 @@ A    Id3
     assert res["row2"].include? "Id3"
     assert ! res["row2"].include?("b")
   end
+
+  def test_attached_parenthesis
+
+    content1 =<<-EOF
+#Id,ValueA,bar (ValueB)
+row1,a|aa|aaa,b
+row2,A,B
+    EOF
+
+    content2 =<<-EOF
+#foo (ValueA),OtherID
+a,Id1|Id2
+A,Id3
+    EOF
+
+    content3 =<<-EOF
+#ValueB,ValueC
+b,c
+B,C
+    EOF
+
+    content4 =<<-EOF
+#foobar (Id),ValueD
+row1,d
+row5,D
+    EOF
+
+    tsv1 = tsv2 = tsv3 = tsv4 = index = nil
+    TmpFile.with_file(content1) do |filename|
+      tsv1 = TSV.open(File.open(filename), :double, :sep => ',')
+    end
+
+    TmpFile.with_file(content2) do |filename|
+      tsv2 = TSV.open(File.open(filename), :double, :sep => ',')
+    end
+
+    TmpFile.with_file(content3) do |filename|
+      tsv3 = TSV.open(File.open(filename), :double, :sep => ',')
+    end
+
+    TmpFile.with_file(content4) do |filename|
+      tsv4 = TSV.open(File.open(filename), :double, :sep => ',')
+    end
+
+
+    assert_equal tsv1.attach(tsv2)["row1"]["OtherID"], %w(Id1 Id2)
+    assert_equal tsv1.attach(tsv2)["row2"]["OtherID"], %w(Id3)
+
+    assert_equal tsv1.attach(tsv4)["row1"]["ValueD"], %w(d)
+    assert_equal tsv4.attach(tsv1)["row1"]["bar (ValueB)"], %w(b)
+    assert_equal tsv3.attach(tsv1)["b"]["ValueD"], %w(d)
+  end
 end
 

data/test/rbbt/util/test_misc.rb

@@ -479,10 +479,10 @@ eum fugiat quo voluptas nulla pariatur?"
     assert_equal Misc.obj2md5(obj2), Misc.obj2md5(obj3)
     hash = Hash[*(0..obj1.length).zip(obj1).flatten]
 
-    Misc.benchmark(10000) do
+    Misc.benchmark(1000) do
       Misc.hash2md5(hash)
     end
-    Misc.benchmark(10000) do
+    Misc.benchmark(1000) do
       Misc.obj2md5(obj1)
     end
     Misc.profile do
@@ -564,4 +564,14 @@ eum fugiat quo voluptas nulla pariatur?"
 EOF
     assert Misc.parse_sql_values(str)[1][1] == "bb(,)b"
   end
+
+  def test_match_fields
+    f1 = "Target (Associated Gene Name)"
+    f2 = "Source (Associated Gene Name)"
+    f3 = "Associated Gene Name"
+
+    assert Misc.match_fields(f1, f2)
+    assert Misc.match_fields(f1, f3)
+    assert Misc.match_fields(f3, f1)
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.110
+  version: 5.21.111
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-11-27 00:00:00.000000000 Z
+date: 2017-12-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake