rbbt-util 5.27.13 → 5.28.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/rbbt/annotations/util.rb +2 -2
- data/lib/rbbt/resource/path.rb +4 -4
- data/lib/rbbt/resource/util.rb +4 -3
- data/share/workflow_config.ru +5 -1
- data/test/rbbt/test_resource.rb +3 -3
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA256:
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-
metadata.gz:
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-
data.tar.gz:
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+
metadata.gz: fae2c7a6c6a64059a77fd43d0edf3c6b3a5835cea870b58ddf07a8e24deec18c
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4
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data.tar.gz: d92b6fbda894fd77dd5e69b391a1087e3401864f20a7422f92443fd01cc6b03b
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 1d3e95466731e2b8f1af738d6d689b81145d462a3b2cc6b755533f1b7bccd413bc76e2af80f053e8685afe527a582905271b2661f132b271a53491b60f024005
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7
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+
data.tar.gz: ca684d7817e67d324ae6767c8b802e2065855915cc541db5f65b070ef47d7862e98b0acc4e991cef38bd65e97ac1224bdcd03e1e4cc1211e937023bd1757e4a8
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@@ -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
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@@ -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
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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)
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data/lib/rbbt/resource/path.rb
CHANGED
@@ -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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data/lib/rbbt/resource/util.rb
CHANGED
@@ -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
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@@ -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,
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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,
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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
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data/share/workflow_config.ru
CHANGED
@@ -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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-
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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
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data/test/rbbt/test_resource.rb
CHANGED
@@ -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?
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assert File.exist?
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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
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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')
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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.
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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-
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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
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