bel 1.0.0 → 1.0.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/VERSION

@@ -1 +1 @@
-1.0.0
+1.0.1

data/bin/bel_validate.rb

@@ -0,0 +1,85 @@
+#!/usr/bin/env ruby
+# bel_validate: Show parsed objects from XBEL file or stdin content for debugging purposes.
+#
+# From file
+# usage: bel_validate -f file.xbel
+#
+# From standard in
+# usage: echo "<BEL DOCUMENT STRING>" | bel_validate
+
+$:.unshift(File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
+require 'bel'
+require 'optparse'
+
+# additive String helpers
+class String
+  def rjust_relative(distance, string)
+    rjust(distance - string.size + size)
+  end
+end
+
+# setup and parse options
+options = {}
+OptionParser.new do |opts|
+  opts.banner = "Usage: bel_validate [options] [.xbel file]"
+  opts.on('-x', '--xbel FILE', 'XBEL file to parse.  STDIN (standard in) can also be used for XBEL content.') do |xbel|
+    options[:xbel] = xbel
+  end
+end.parse!
+
+if options[:xbel] and not File.exists? options[:xbel]
+  $stderr.puts "No file for xbel, #{options[:xbel]}"
+  exit 1
+end
+
+# read xbel content
+content =
+if options[:xbel]
+  File.open(options[:xbel], :external_encoding => 'UTF-8')
+else
+  $stdin
+end
+
+#namespaces = ... # bel2_validate
+
+class Main
+
+  def initialize(content)
+    BEL.nanopub(content, :xbel).each do |obj|
+      spec = BELParser::Language.specification obj.metadata.bel_version
+      namespaces = obj.references.namespaces.each.map do |ns|
+      end
+      stmt_str = obj.bel_statement.to_s
+      namespaces = {}
+      BELParser::Expression::Validator
+        .new(spec, namespaces, BELParser::Resource.default_uri_reader, BELParser::Resource.default_url_reader)
+        .each(StringIO.new stmt_str) do |(line_number, line, ast, results)|
+        puts "#{line_number}: #{line}"
+        puts "  AST Type: #{ast.type}"
+      
+        puts "  Syntax results:"
+        
+        results.syntax_results.each do |res|
+          puts "    #{res}"
+        end
+
+        puts "  Semantics results:" 
+        results.semantics_results.each do |res|
+          if res.is_a?(BELParser::Language::Semantics::SignatureMappingSuccess)
+            puts "    Matched signature: #{res.signature.string_form}"
+          end
+          if res.is_a?(BELParser::Language::Semantics::SignatureMappingWarning)
+            puts "    Failed signature: #{res.signature.string_form}"
+            res.results.select(&:failure?).each do |warning|
+              puts "      #{warning}"
+            end
+          end
+        end 
+      end        
+    end
+  end
+
+  end
+Main.new(content)
+# vim: ts=2 sw=2:
+# encoding: utf-8

metadata

@@ -1,76 +1,76 @@
 --- !ruby/object:Gem::Specification
 name: bel
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.0.1
 platform: ruby
 authors:
 - Anthony Bargnesi
 - Natalie Catlett
 - Nick Bargnesi
 - William Hayes
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
 date: 2016-06-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: bel_parser
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 1.0.0
-  type: :runtime
+  name: bel_parser
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 1.0.0
 - !ruby/object:Gem::Dependency
-  name: rdf
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 2.0.0
-  type: :runtime
+  name: rdf
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 2.0.0
 - !ruby/object:Gem::Dependency
-  name: rdf-vocab
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 2.0.0
-  type: :runtime
+  name: rdf-vocab
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 2.0.0
 - !ruby/object:Gem::Dependency
-  name: ffi
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.9.8
-  type: :runtime
+  name: ffi
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.9.8
-description: " The BEL gem allows the reading, writing, and processing of BEL (Biological
-  Expression Language) with a natural DSL. "
+description: " The BEL gem allows the reading, writing, and processing of BEL (Biological\
+  \ Expression Language) with a natural DSL. "
 email:
 - abargnesi@selventa.com
 - ncatlett@selventa.com
@@ -82,6 +82,7 @@ executables:
 - bel_parse.rb
 - bel
 - bel2rdf.rb
+- bel_validate.rb
 - bel_compare.rb
 - bel_rdfschema.rb
 extensions:
@@ -103,6 +104,7 @@ files:
 - bin/bel_rdfschema.rb
 - bin/bel_summarize.rb
 - bin/bel_upgrade.rb
+- bin/bel_validate.rb
 - ext/mri/bel-ast.c
 - ext/mri/bel-ast.h
 - ext/mri/bel-node-stack.c
@@ -247,7 +249,7 @@ homepage: https://github.com/OpenBEL/bel.rb
 licenses:
 - Apache-2.0
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options:
 - "--title"
 - BEL Ruby Documentation
@@ -283,10 +285,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.5.1
-signing_key: 
+rubyforge_project:
+rubygems_version: 2.6.4
+signing_key:
 specification_version: 4
 summary: Process BEL with ruby.
 test_files: []
-has_rdoc: