unipept 0.5.5 → 0.5.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  metadata.gz: 57edfe9cecc9210f07d56d90270b5b183be59528
-  data.tar.gz: 77fdf1c31d3528fd60ce858ece781907e5c7060e
+  metadata.gz: a5ef6c84a4836b7b55f5aedadcf694470c89608f
+  data.tar.gz: 804ec2db29552953e0769ee1ef6df9e005828b8c
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-  data.tar.gz: 45b5d0bc4f14f052f1816f7239d49fa3f9486279913b7cb0af745a339d93787e9c540ade807f22e262894b4b66208634a4ddd6225e71f8a5c4ff95afa94a81ee
+  metadata.gz: 2377ac480f2dedccb03bb6bc537a07a613e3ddd6b2b7ca59eda6fa25b0831488628fa0598ae28f2efc7d23afbf8a22b9364c0c31bea3b3b7e57fca31f635db2c
+  data.tar.gz: 7fe190b65377892f52117049a16c390415e6aea6bb9c55e283f5dc29bdd1db02fefa21d81728cd90aaab713e1b1f1a9dfc56c3efbf3bedf772f619e47a6b1f5b

data/VERSION

@@ -1 +1 @@
-0.5.5
+0.5.6

data/lib/unipept/api_runner.rb

@@ -182,7 +182,7 @@ module Unipept
     end
 
     def peptide_iterator(peptides, &block)
-      first = peptides.next
+      first = peptides.next rescue return
       if first.start_with? '>'
         # FASTA MODE ENGAGED
         fasta_header = first.chomp

data/lib/unipept/formatters.rb

@@ -25,7 +25,7 @@ module Unipept
       'csv'
     end
 
-    def header(sample_data)
+    def header(sample_data, fasta_mapper = nil)
       ""
     end
 
@@ -39,7 +39,8 @@ module Unipept
     require 'json'
     register :json
 
-    def format(data)
+    def format(data, fasta_mapper = nil)
+      # TODO: add fasta header based on fasta_mapper information
       data.to_json
     end
 
@@ -60,7 +61,6 @@ module Unipept
         else
           csv << first.keys.map(&:to_s) if first
         end
-
       end
     end
 
@@ -100,13 +100,13 @@ module Unipept
     end
 
     class ::Array
-      def to_xml( array_name = :array, item_name = :item )
-        %|<#{array_name} size="#{self.size}">|+map{|n|n.to_xml( :item )}.join+"</#{array_name}>"
+      def to_xml(array_name = :array, item_name = :item)
+        %|<#{array_name} size="#{self.size}">| + self.map{|n|n.to_xml( :item )}.join+"</#{array_name}>"
       end
     end
 
     class ::Hash
-      def to_xml( name = nil )
+      def to_xml(name = nil)
         data = to_a.map{|k,v|v.to_xml(k)}.join
         name ? "<#{name}>#{data}</#{name}>" : data
       end
@@ -114,7 +114,8 @@ module Unipept
 
     register :xml
 
-    def format(data)
+    def format(data, fasta_mapper = nil)
+      # TODO: add fasta header based on fasta_mapper information
       data.to_xml
     end
 

data/unipept.gemspec

@@ -0,0 +1,78 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+# stub: unipept 0.5.6 ruby lib
+
+Gem::Specification.new do |s|
+  s.name = "unipept"
+  s.version = "0.5.6"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib"]
+  s.authors = ["Toon Willems"]
+  s.date = "2014-06-25"
+  s.description = "CLI interface to unipept"
+  s.email = "willemstoon@gmail.com"
+  s.executables = ["unipept", "prot2pept", "peptfilter", "uniprot"]
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bin/peptfilter",
+    "bin/prot2pept",
+    "bin/unipept",
+    "bin/uniprot",
+    "lib/unipept.rb",
+    "lib/unipept/api_runner.rb",
+    "lib/unipept/batch_order.rb",
+    "lib/unipept/configuration.rb",
+    "lib/unipept/formatters.rb",
+    "test/helper.rb",
+    "test/test_unipept.rb",
+    "unipept.gemspec"
+  ]
+  s.homepage = "http://github.ugent.be/bmesuere/unipept/"
+  s.licenses = ["MIT"]
+  s.rubygems_version = "2.2.2"
+  s.summary = "CLI interface to unipept"
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 4
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<shoulda>, ["~> 3.5"])
+      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 2.0"])
+      s.add_development_dependency(%q<simplecov>, ["~> 0.8"])
+      s.add_runtime_dependency(%q<typhoeus>, ["~> 0.6"])
+      s.add_runtime_dependency(%q<cri>, ["~> 2.6"])
+    else
+      s.add_dependency(%q<shoulda>, ["~> 3.5"])
+      s.add_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_dependency(%q<bundler>, ["~> 1.0"])
+      s.add_dependency(%q<jeweler>, ["~> 2.0"])
+      s.add_dependency(%q<simplecov>, ["~> 0.8"])
+      s.add_dependency(%q<typhoeus>, ["~> 0.6"])
+      s.add_dependency(%q<cri>, ["~> 2.6"])
+    end
+  else
+    s.add_dependency(%q<shoulda>, ["~> 3.5"])
+    s.add_dependency(%q<rdoc>, ["~> 3.12"])
+    s.add_dependency(%q<bundler>, ["~> 1.0"])
+    s.add_dependency(%q<jeweler>, ["~> 2.0"])
+    s.add_dependency(%q<simplecov>, ["~> 0.8"])
+    s.add_dependency(%q<typhoeus>, ["~> 0.6"])
+    s.add_dependency(%q<cri>, ["~> 2.6"])
+  end
+end
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 0.5.5
+  version: 0.5.6
 platform: ruby
 authors:
 - Toon Willems
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-24 00:00:00.000000000 Z
+date: 2014-06-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
@@ -116,10 +116,11 @@ executables:
 - peptfilter
 - uniprot
 extensions: []
-extra_rdoc_files: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.rdoc
 files:
 - ".document"
-- ".gitignore"
 - Gemfile
 - Gemfile.lock
 - LICENSE.txt
@@ -137,6 +138,7 @@ files:
 - lib/unipept/formatters.rb
 - test/helper.rb
 - test/test_unipept.rb
+- unipept.gemspec
 homepage: http://github.ugent.be/bmesuere/unipept/
 licenses:
 - MIT

data/.gitignore

@@ -1,49 +0,0 @@
-# rcov generated
-coverage
-coverage.data
-
-# rdoc generated
-rdoc
-
-# yard generated
-doc
-.yardoc
-
-# bundler
-.bundle
-
-# jeweler generated
-pkg
-
-# Have editor/IDE/OS specific files you need to ignore? Consider using a global gitignore: 
-#
-# * Create a file at ~/.gitignore
-# * Include files you want ignored
-# * Run: git config --global core.excludesfile ~/.gitignore
-#
-# After doing this, these files will be ignored in all your git projects,
-# saving you from having to 'pollute' every project you touch with them
-#
-# Not sure what to needs to be ignored for particular editors/OSes? Here's some ideas to get you started. (Remember, remove the leading # of the line)
-#
-# For MacOS:
-#
-#.DS_Store
-
-# For TextMate
-#*.tmproj
-#tmtags
-
-# For emacs:
-#*~
-#\#*
-#.\#*
-
-# For vim:
-#*.swp
-
-# For redcar:
-#.redcar
-
-# For rubinius:
-#*.rbc