rbbt-util 5.27.13 → 5.28.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 99b1ad9e8d9403c7f77e22b16497456324c340b08122b765033530f713e35c3c
-  data.tar.gz: 2d33590e395b9ca715e1c16d509d0a62a1ebeab2315b700ff4377a08803c89af
+  metadata.gz: fae2c7a6c6a64059a77fd43d0edf3c6b3a5835cea870b58ddf07a8e24deec18c
+  data.tar.gz: d92b6fbda894fd77dd5e69b391a1087e3401864f20a7422f92443fd01cc6b03b
 SHA512:
-  metadata.gz: '097ce6c8c16c17441f5a8748ba4ab33afecf6d22d4d54c7ce53475cd642407ae5013346ba482f7fa9375176ab6790febfe030e9f7959ba7b928b5d3762382237'
-  data.tar.gz: 2fb616d7d66fc2eb979c9911921faecf163f51dd3323ac127265bcaefd0e8a4e3aab9ef41cc9bdf8bd351d44d4ef2cc388c692d5dc9a2d1b811155f21e3f0889
+  metadata.gz: 1d3e95466731e2b8f1af738d6d689b81145d462a3b2cc6b755533f1b7bccd413bc76e2af80f053e8685afe527a582905271b2661f132b271a53491b60f024005
+  data.tar.gz: ca684d7817e67d324ae6767c8b802e2065855915cc541db5f65b070ef47d7862e98b0acc4e991cef38bd65e97ac1224bdcd03e1e4cc1211e937023bd1757e4a8

data/lib/rbbt/annotations/util.rb

@@ -74,7 +74,7 @@ module Annotated
 
     object = case
              when literal_pos
-               values[literal_pos]
+               values[literal_pos].tap{|o| o.force_encoding(Encoding.default_external)}
              else
                id.dup
              end
@@ -119,7 +119,7 @@ module Annotated
                fields = AnnotatedArray === annotations ? annotations.annotations : annotations.compact.first.annotations
                fields << :annotation_types
 
-             when (fields == [:literal] and not annotations.compact.empty?)
+             when (fields == [:literal] and ! annotations.compact.empty?)
                fields << :literal
 
              when (fields == [:all] && Annotated === annotations)

data/lib/rbbt/resource/path.rb

@@ -13,7 +13,7 @@ module Path
     string.resource = resource
     string.search_paths = search_paths
     string.search_order = search_order
-    string.libdir = libdir || Path.caller_lib_dir
+    string.libdir = libdir || Path.caller_lib_dir 
     string
   end
 
@@ -52,11 +52,11 @@ module Path
   def join(name)
     raise "Invalid path: #{ self }" if self.nil?
     new = if self.empty?
-            self.annotate name.to_s.dup
+            self.annotate name.to_s.dup.chomp
           else
-            self.annotate File.join(self, name.to_s)
+            self.annotate File.join(self, name.to_s.chomp)
           end
-    new.original = File.join(self.original, name.to_s) if self.original
+    new.original = File.join(self.original, name.to_s.chomp) if self.original
     new
   end
 

data/lib/rbbt/resource/util.rb

@@ -1,6 +1,6 @@
 module Path
 
-  def self.caller_lib_dir(file = nil, relative_to = 'lib')
+  def self.caller_lib_dir(file = nil, relative_to = ['lib', 'bin'])
     file = caller.reject{|l| 
       l =~ /rbbt\/(?:resource\.rb|workflow\.rb)/ or
       l =~ /rbbt\/resource\/path\.rb/ or
@@ -9,13 +9,14 @@ module Path
       l =~ /progress-monitor\.rb/ 
     }.first.sub(/\.rb[^\w].*/,'.rb') if file.nil?
 
+    relative_to = [relative_to] unless Array === relative_to
     file = File.expand_path(file)
-    return Path.setup(file) if File.exist? File.join(file, relative_to)
+    return Path.setup(file) if relative_to.select{|d| File.exist? File.join(file, d)}.any?
 
     while file != '/'
       dir = File.dirname file
 
-      return dir if File.exist? File.join(dir, relative_to)
+      return dir if relative_to.select{|d| File.exist? File.join(dir, d)}.any?
 
       file = File.dirname file
     end

data/share/workflow_config.ru

@@ -43,7 +43,11 @@ etc_dir = Rbbt.etc
 load_file etc_dir['app.d/pre.rb'].find 
 
 app.get '/' do
-  redirect to(File.join('/', wf.to_s))
+  begin
+    template_render('main', params, 'main', :cache_type => :asynchronous)
+  rescue TemplateMissing
+    redirect to(File.join('/', wf.to_s))
+  end
 end
 
 #{{{ BASE

data/test/rbbt/test_resource.rb

@@ -69,11 +69,11 @@ class TestTSV < Test::Unit::TestCase
   end
 
   def test_libdir
-    assert File.exist? TestResource[].share.Rlib["util.R"].find :lib
-    assert File.exist? TestResource[].share.Rlib["util.R"].find 
+    assert File.exist?(TestResource[].share.Rlib["util.R"].find(:lib))
+    assert File.exist?(TestResource[].share.Rlib["util.R"].find)
   end
 
-  def test_server
+  def __test_server
     require 'rbbt/sources/organism'
     TmpFile.with_file :extension => 'gz' do |tmp|
       Organism.get_from_server("Hsa/b37/known_sites/dbsnp_138.vcf.gz", tmp, 'http://rbbt.bsc.es')

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.27.13
+  version: 5.28.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-07-16 00:00:00.000000000 Z
+date: 2020-07-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake