bel 0.2.0 → 0.2.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 40b40949e19877e45095c94afb6c86384683d3ec
+  metadata.gz: 3f744cb7280ca000b3f0d88c83e997cbaf05f654
+  data.tar.gz: e49304e421acd5e906fcf4022c91b9156ccc4b90
 SHA512:
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-  data.tar.gz: ea570c12d61203e0fb486c9535a471d29977d71c2b3984a240ca4258abbabfccc9fe44594e42e066bc828751fd10d4d567a49c6c90b4cf83c4e1328463f71f15
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+  data.tar.gz: 1e42739d9092c3f1a92e6b3b64cdcc028f5f9582ca60aabfe388ace26fd70b34d5c86db421d83b93af17dfd7421531e8116ff035ba1fd144f9e883aa6bbddc4f

data/bin/bel_upgrade

@@ -0,0 +1,153 @@
+#!/usr/bin/env ruby
+# bel_upgrade: Upgrade BEL content to a new set of resources.
+#
+# From BEL file
+# usage: ruby bel_upgrade -b file.bel -c file.json
+#
+# From standard in
+# usage: echo "<BEL DOCUMENT STRING>" | ruby bel_upgrade -c file.json
+
+require 'bel'
+require 'json'
+require 'optparse'
+require 'set'
+require 'open-uri'
+
+# setup and parse options
+options = {}
+OptionParser.new do |opts|
+  opts.banner = "Usage: upgrade-namespaces.rb [options] [.bel file]"
+  opts.on('-b', '--bel FILE', 'BEL file to upgrade.  STDIN (standard in) can also be used for BEL content.') do |bel|
+    options['bel'] = bel
+  end
+  opts.on("-c", "--changelog [FILE | URI]", "Change log JSON") do |change_log|
+    options['change_log'] = change_log
+  end
+end.parse!
+
+# option guards
+unless options['bel'] or not STDIN.tty?
+  $stderr.puts "No bel content provided.  Either use --bel option or STDIN (standard in).  Use -h / --help for details." 
+  exit 1
+end
+unless options['change_log']
+  $stderr.puts "Missing --changelog option. Use -h / --help for details."
+  exit 1
+end
+if not File.exists? options['change_log']
+  begin
+    open(options['change_log']) do |f|
+      unless f.content_type == 'application/json'
+        $stderr.puts "Expected application/json content type, actual: #{f.content_type}"
+        exit 1
+      end
+    end
+  rescue OpenURI::HTTPError => e
+    $stderr.puts "Cannot read URI for change_log, #{options['change_log']}, status: #{e}"
+    exit 1
+  end
+end
+if options['bel'] and not File.exists? options['bel']
+  $stderr.puts "No file for bel, #{options['bel']}"
+  exit 1
+end
+
+# read bel content
+content = (STDIN.tty?) ? File.open(options['bel']).read : $stdin.read
+
+# read change log
+changelog = nil
+if File.exists? options['change_log']
+  File.open(options['change_log']) do |f|
+    changelog = JSON.parse(f.read)
+  end
+else
+  open(options['change_log']) do |file|
+    changelog = JSON.parse(file.read)
+  end
+end
+
+unless changelog
+  $stderr.puts "Cannot retrieve change_log #{options['change_log']}"
+end
+
+class Main
+
+  EvidenceMatcher = Regexp.compile(/SET Evidence = ([0-9a-zA-Z]+)/)
+  attr_reader :ttl
+
+  def initialize(content, change_log)
+    @change_log = change_log
+    @keywords_seen = Set.new
+    parser = BEL::Script::Parser.new
+    parser.add_observer self
+    parser.parse(content)
+  end
+  def update(obj)
+    # redefine namespace based on change log's `redefine` block
+    if obj.is_a? BEL::Script::NamespaceDefinition
+      if @change_log.has_key? 'redefine'
+        redefine = @change_log['redefine']
+        if redefine.has_key? obj.prefix
+          entry = redefine[obj.prefix]
+          obj.prefix = entry['new_keyword']
+          obj.value = entry['new_url']
+        end
+      end
+
+      # deduplicate namespaces for output purposes
+      if @keywords_seen.include? obj.prefix
+        return
+      end
+      @keywords_seen.add(obj.prefix)
+    end
+
+    if obj.is_a? BEL::Script::Annotation
+      if obj.name == 'Evidence'
+        ev = obj.to_s
+        ev.gsub!(EvidenceMatcher, 'SET Evidence = "\1"')
+        puts ev
+        return
+      end
+    end
+
+    if obj.is_a? BEL::Script::Parameter
+      if @change_log.has_key? obj.ns
+        clog_ns = @change_log[obj.ns]
+        if clog_ns.has_key? obj.value
+          replacement = clog_ns[obj.value]
+          if replacement == 'unresolved' or replacement == 'withdrawn'
+            $stderr.puts "no replacement value for #{obj.ns} '#{obj.value}' - value '#{replacement}'"
+            return
+          end
+          obj.value = replacement
+        end
+      end
+      # redefine param namespace based on change log's `redefine` block
+      if @change_log.has_key? 'redefine'
+        redefine = @change_log['redefine']
+        if redefine.has_key? obj.ns
+          obj.ns = redefine[obj.ns]['new_keyword']
+        end
+      end
+      return
+    end
+
+    if obj.is_a? BEL::Script::Term
+      return # do not print (part of statement)
+    end
+
+    puts obj.to_s
+  end
+
+  private
+
+  def error_file(file_name)
+    $stderr.puts "#{file_name} is not readable"
+    exit 1
+  end
+end
+
+Main.new(content, changelog)
+# vim: ts=2 sw=2:
+# encoding: utf-8

data/lib/bel.rb

@@ -1,6 +1,7 @@
-# vim: ts=2 sw=2:
 module BEL
   autoload :Language,  "#{File.dirname(__FILE__)}/bel/language"
   autoload :Namespace, "#{File.dirname(__FILE__)}/bel/namespace"
   autoload :Script,    "#{File.dirname(__FILE__)}/bel/script"
 end
+# vim: ts=2 sw=2:
+# encoding: utf-8

data/lib/bel/language.rb

@@ -1,5 +1,3 @@
-# vim: ts=2 sw=2:
-
 module BEL
   module Language
     class Signature
@@ -574,3 +572,5 @@ module BEL
     end
   end
 end
+# vim: ts=2 sw=2:
+# encoding: utf-8

data/lib/bel/namespace.rb

@@ -1,4 +1,3 @@
-# vim: ts=2 sw=2:
 require 'open-uri'
 require_relative './language' 
 
@@ -104,3 +103,5 @@ module BEL
     ]
   end
 end
+# vim: ts=2 sw=2:
+# encoding: utf-8

data/lib/bel/parse_objects.rb

@@ -1,4 +1,3 @@
-# vim: ts=2 sw=2:
 require 'singleton'
 
 module BEL
@@ -112,3 +111,5 @@ module BEL
     private
   end
 end
+# vim: ts=2 sw=2:
+# encoding: utf-8

data/lib/bel/script.rb

@@ -1,5 +1,4 @@
 
-# vim: ts=2 sw=2:
 =begin
 
 class << self
@@ -186841,3 +186840,5 @@ if __FILE__ == $0
   parser.add_observer(DefaultObserver.new)
   parser.parse(content) 
 end
+# vim: ts=2 sw=2:
+# encoding: utf-8

metadata

@@ -1,120 +1,123 @@
 --- !ruby/object:Gem::Specification
 name: bel
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.2.1
 platform: ruby
 authors:
 - Anthony Bargnesi
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
 date: 2014-01-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: 10.1.0
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 10.1.0
-  prerelease: false
+        version: '10.1'
   type: :development
-- !ruby/object:Gem::Dependency
-  name: rspec
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.14.0
+        version: '10.1'
+- !ruby/object:Gem::Dependency
+  name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.14.0
-  prerelease: false
+        version: '2.14'
   type: :development
-- !ruby/object:Gem::Dependency
-  name: yard
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.8.7.0
+        version: '2.14'
+- !ruby/object:Gem::Dependency
+  name: yard
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.8.7.0
-  prerelease: false
+        version: '0.8'
   type: :development
-- !ruby/object:Gem::Dependency
-  name: rdoc
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 4.0.0
+        version: '0.8'
+- !ruby/object:Gem::Dependency
+  name: rdoc
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 4.0.0
-  prerelease: false
+        version: '4.0'
   type: :development
-- !ruby/object:Gem::Dependency
-  name: bundler
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.3.0
+        version: '4.0'
+- !ruby/object:Gem::Dependency
+  name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.3.0
-  prerelease: false
+        version: '1.3'
   type: :development
-description: The BEL gem allows the reading, writing, and processing of BEL (Biological Expression Language) with a natural DSL.
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+description: The BEL gem allows the reading, writing, and processing of BEL (Biological
+  Expression Language) with a natural DSL.
 email: abargnesi@selventa.com
-executables: []
+executables:
+- bel_upgrade
 extensions: []
 extra_rdoc_files: []
 files:
+- LICENSE
+- bin/bel_upgrade
 - lib/bel.rb
-- lib/bel/parse_objects.rb
-- lib/bel/namespace.rb
 - lib/bel/language.rb
+- lib/bel/namespace.rb
+- lib/bel/parse_objects.rb
 - lib/bel/script.rb
-- LICENSE
 homepage: https://github.com/OpenBEL/bel.rb
 licenses:
 - Apache-2.0
 metadata: {}
-post_install_message:
+post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project:
-rubygems_version: 2.1.9
-signing_key:
+rubyforge_project: 
+rubygems_version: 2.2.0
+signing_key: 
 specification_version: 4
 summary: Process BEL with ruby.
 test_files: []
-has_rdoc:
+has_rdoc: