rbbt-util 5.27.13 → 5.28.0

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checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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  SHA256:
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- data.tar.gz: 2d33590e395b9ca715e1c16d509d0a62a1ebeab2315b700ff4377a08803c89af
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+ metadata.gz: fae2c7a6c6a64059a77fd43d0edf3c6b3a5835cea870b58ddf07a8e24deec18c
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+ data.tar.gz: d92b6fbda894fd77dd5e69b391a1087e3401864f20a7422f92443fd01cc6b03b
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  SHA512:
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+ metadata.gz: 1d3e95466731e2b8f1af738d6d689b81145d462a3b2cc6b755533f1b7bccd413bc76e2af80f053e8685afe527a582905271b2661f132b271a53491b60f024005
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+ data.tar.gz: ca684d7817e67d324ae6767c8b802e2065855915cc541db5f65b070ef47d7862e98b0acc4e991cef38bd65e97ac1224bdcd03e1e4cc1211e937023bd1757e4a8
@@ -74,7 +74,7 @@ module Annotated
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  object = case
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  when literal_pos
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- values[literal_pos]
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+ values[literal_pos].tap{|o| o.force_encoding(Encoding.default_external)}
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  else
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  id.dup
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  end
@@ -119,7 +119,7 @@ module Annotated
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  fields = AnnotatedArray === annotations ? annotations.annotations : annotations.compact.first.annotations
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  fields << :annotation_types
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- when (fields == [:literal] and not annotations.compact.empty?)
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+ when (fields == [:literal] and ! annotations.compact.empty?)
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  fields << :literal
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  when (fields == [:all] && Annotated === annotations)
@@ -13,7 +13,7 @@ module Path
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  string.resource = resource
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  string.search_paths = search_paths
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  string.search_order = search_order
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- string.libdir = libdir || Path.caller_lib_dir
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+ string.libdir = libdir || Path.caller_lib_dir
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  string
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  end
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@@ -52,11 +52,11 @@ module Path
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  def join(name)
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  raise "Invalid path: #{ self }" if self.nil?
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  new = if self.empty?
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- self.annotate name.to_s.dup
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+ self.annotate name.to_s.dup.chomp
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  else
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- self.annotate File.join(self, name.to_s)
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+ self.annotate File.join(self, name.to_s.chomp)
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  end
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- new.original = File.join(self.original, name.to_s) if self.original
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+ new.original = File.join(self.original, name.to_s.chomp) if self.original
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  new
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  end
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@@ -1,6 +1,6 @@
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  module Path
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- def self.caller_lib_dir(file = nil, relative_to = 'lib')
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+ def self.caller_lib_dir(file = nil, relative_to = ['lib', 'bin'])
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  file = caller.reject{|l|
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  l =~ /rbbt\/(?:resource\.rb|workflow\.rb)/ or
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  l =~ /rbbt\/resource\/path\.rb/ or
@@ -9,13 +9,14 @@ module Path
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  l =~ /progress-monitor\.rb/
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  }.first.sub(/\.rb[^\w].*/,'.rb') if file.nil?
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+ relative_to = [relative_to] unless Array === relative_to
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  file = File.expand_path(file)
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- return Path.setup(file) if File.exist? File.join(file, relative_to)
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+ return Path.setup(file) if relative_to.select{|d| File.exist? File.join(file, d)}.any?
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  while file != '/'
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  dir = File.dirname file
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- return dir if File.exist? File.join(dir, relative_to)
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+ return dir if relative_to.select{|d| File.exist? File.join(dir, d)}.any?
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  file = File.dirname file
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  end
@@ -43,7 +43,11 @@ etc_dir = Rbbt.etc
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  load_file etc_dir['app.d/pre.rb'].find
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  app.get '/' do
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- redirect to(File.join('/', wf.to_s))
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+ begin
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+ template_render('main', params, 'main', :cache_type => :asynchronous)
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+ rescue TemplateMissing
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+ redirect to(File.join('/', wf.to_s))
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+ end
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  end
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  #{{{ BASE
@@ -69,11 +69,11 @@ class TestTSV < Test::Unit::TestCase
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  end
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  def test_libdir
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- assert File.exist? TestResource[].share.Rlib["util.R"].find :lib
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- assert File.exist? TestResource[].share.Rlib["util.R"].find
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+ assert File.exist?(TestResource[].share.Rlib["util.R"].find(:lib))
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+ assert File.exist?(TestResource[].share.Rlib["util.R"].find)
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  end
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- def test_server
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+ def __test_server
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  require 'rbbt/sources/organism'
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  TmpFile.with_file :extension => 'gz' do |tmp|
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  Organism.get_from_server("Hsa/b37/known_sites/dbsnp_138.vcf.gz", tmp, 'http://rbbt.bsc.es')
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: rbbt-util
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  version: !ruby/object:Gem::Version
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- version: 5.27.13
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+ version: 5.28.0
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  platform: ruby
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  authors:
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  - Miguel Vazquez
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2020-07-16 00:00:00.000000000 Z
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+ date: 2020-07-23 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rake