swissparser 1.0.0 → 1.0.1

data/.gitignore

@@ -1,5 +1,6 @@
 *~
 *#
+*.rbc
 
 *.gemspec
 announcement.txt

data/CHANGELOG.rdoc

@@ -1,3 +1,13 @@
+== 1.0.1 / 2011-01-23
+
+* 1 bug fix:
+  - Handles line with a key but no content
+
+* 1 new minor feature
+  - The parser hash option can be passed to the parse method block:
+    
+    Parser = Rules.make_parser do |entries, options|
+ 
 == 1.0.0 / 2010-01-11
 
 * New release, the syntax for defining rules and parsers was simplified.

data/README.rdoc

@@ -42,7 +42,7 @@ Thanks to rvm it was successfuly tested with
 versions:
 
   * ruby-1.8.7-p302
-  * ruby-1.9.2-p0
+  * ruby-1.9.2-p136
   * jruby-1.5.2
 
 

data/Rakefile

@@ -1,3 +1,7 @@
+require 'rake/testtask'
+require 'rake/rdoctask'
+require 'cucumber/rake/task'
+
 begin
   require 'bones'
 rescue LoadError
@@ -7,8 +11,6 @@ end
 ensure_in_path 'lib'
 require 'swissparser'
 
-require 'cucumber/rake/task'
-
 task :default => :features
 
 Cucumber::Rake::Task.new(:features) do |t|
@@ -18,7 +20,9 @@ end
 
 CLOBBER << "coverage/"
 
-Bones {
+
+Bones do
+  require 'rake/rdoctask'
   name  'swissparser'
   authors  'paradigmatic'
   email  'paradigmatic@streum.org'
@@ -29,6 +33,6 @@ Bones {
   history_file 'CHANGELOG.rdoc'
   ignore_file  '.gitignore'
   rdoc.exclude ["examples/","features/"]
-}
+end
 
 # EOF

data/examples/uniprot.rb

@@ -78,8 +78,6 @@ if $0 == __FILE__
  
   proteins = Uniprot::Parser.parse_file( filename ) 
 
-  proteins.each do |e|
-    puts e.to_yaml
-  end
- 
+  puts proteins.size
+
 end

data/features/basic_parsing.feature

@@ -7,17 +7,17 @@ Background:
 AA x1
 BB y1
 CC z1
-abcd
+  abcd
 //
 AA x2
 BB y2
 CC z2
-efgh
+  efgh
 //
 AA x3
 BB y3
 CC z3
-ijkl
+  ijkl
 //
 """
 
@@ -76,4 +76,19 @@ Scenario: I can redefine rules
     And I run the parser on sample data
   Then the result evals to "%w{foo foo foo}"
 
+Scenario: I can parse a lone key
+  Given sample data:
+"""
+AA Foo
+BB
+CC Bar
+//
+"""
+    And the default rules
+    And I define a rule which adds the key to an array with "AA"
+    And I define a rule which adds the key to an array with "BB"
+    And I define a rule which adds the key to an array with "CC"
+    And I define a simple parser which returns an array
+    And I run the parser on sample data
+  Then the result evals to "[%W{AA BB CC}]"
 

data/features/step_definitions/basic_steps.rb

@@ -65,6 +65,17 @@ Given /^I define a simple parser which returns an array$/ do
   end
 end
 
+Given /^I define a rule which adds the key to an array with "([^\"]*)"$/ do |key|
+  @rules = @rules.refine do
+    with( key ) do |content| 
+      @text = [] if @text.nil?
+      @text << key
+    end
+  end
+
+end
+
+
 Given /^I run the parser on sample data$/ do
   @result = if @opt.nil?
               @parser.parse( @data )

data/lib/swissparser.rb

@@ -23,7 +23,7 @@ require 'swissparser/rules'
 
 module Swiss
 
-  VERSION = "1.0.0"
+  VERSION = "1.0.1"
 
   # Parser for a typical bioinformatic flat file, like
   # SwissProt/Uniprot, KEGG, etc.
@@ -45,7 +45,11 @@ module Swiss
     # result.
     def parse( input, opt={} )
       entries = Entries.new( @rules, input, opt )
-      @body.call( entries )
+      if @body.arity == 2
+        @body.call( entries, opt )
+      else
+        @body.call( entries )
+      end
     end
 
     # Parses a file specified by +filename+. An optional hash of

data/lib/swissparser/entries.rb

@@ -56,6 +56,12 @@ module Swiss
           if @rules.rules[key]
             entry.instance_exec( content, &@rules.rules[key] )
           end 
+        elsif line =~ /^(\S+)\s*$/
+          key = $1
+          last_key = key
+          if @rules.rules[key]
+            entry.instance_exec( "", &@rules.rules[key] )
+          end
         else
           if @rules.rules[:text][last_key]
             entry.instance_exec(  

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 1
   - 0
-  - 0
-  version: 1.0.0
+  - 1
+  version: 1.0.1
 platform: ruby
 authors: 
 - paradigmatic
@@ -14,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-12-18 00:00:00 +01:00
+date: 2011-01-23 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -62,16 +62,12 @@ extensions: []
 extra_rdoc_files: 
 - CHANGELOG.rdoc
 - README.rdoc
-- lib/swissparser.rbc
-- lib/swissparser/entries.rbc
-- lib/swissparser/rules.rbc
 files: 
 - .gitignore
 - CHANGELOG.rdoc
 - LICENSE
 - README.rdoc
 - Rakefile
-- Rakefile.compiled.rbc
 - examples/data/EColPositives_noTAT.bas
 - examples/data/kegg_enzyme_short.txt
 - examples/data/uniprot.txt
@@ -82,11 +78,8 @@ files:
 - features/step_definitions/basic_steps.rb
 - features/step_definitions/sugar_steps.rb
 - lib/swissparser.rb
-- lib/swissparser.rbc
 - lib/swissparser/entries.rb
-- lib/swissparser/entries.rbc
 - lib/swissparser/rules.rb
-- lib/swissparser/rules.rbc
 has_rdoc: true
 homepage: http://github.com/paradigmatic/SwissParser
 licenses: []

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