swissparser 0.11.0 → 0.11.1

data/CHANGELOG.rdoc

@@ -1,3 +1,8 @@
+== 0.11.1 / 2009-11-17
+
+* 1 bug fix:
+  - Corrected skip_entry! issue.
+
 == 0.11.0 / 2009-11-16
 
 * 1 new feature:

data/benchmarks/whole_uniprot.txt

@@ -0,0 +1,7 @@
+$ time ruby tutorial_1.rb uniprot_sprot.dat 
+Parsed: 512205
+real 3313.672   user 3239.700   sys 66.360      pcpu 99.77
+
+$ time ruby bioruby.rb uniprot_sprot.dat 
+512205
+real 1054.322   user 998.170    sys 55.580      pcpu 99.94

data/features/parsing_context.feature

@@ -8,7 +8,7 @@ Feature: Sharing context
      YY b1
      c1
      //
-     XX a1
+     XX a2
      YY b2
      c2
      //
@@ -40,9 +40,9 @@ Feature: Sharing context
   Scenario: Skipping entries
     Given a simple parser
     When I extend it
-      And set with("XX") to skip the entry
+      And I set it to skip entries with("XX") containing "a1"
       And I run the extended parser on data
-    Then the result should contain '0' entries
+    Then the result should contain '1' entries
 
 
 

data/features/step_definitions/extra.rb

@@ -37,11 +37,20 @@ When /^the after action returns @foo$/ do
 end
 
 When /^set with\("([^\"]*)"\) to skip the entry$/ do |key|
-  @ext_parser = @ext_parser.extend do 
-    rules do
-      with(key) { skip_entry! }
-    end
-  end 
+  
 end
 
 
+
+
+When /^I set it to skip entries with\("([^\"]*)"\) containing "([^\"]*)"$/ do |key, val|
+ @ext_parser = @ext_parser.extend do 
+    rules do
+      with(key) do |c,e|
+        if c.include?(val)
+          skip_entry!
+        end
+      end
+    end
+  end
+end

data/lib/swissparser.rb

@@ -23,7 +23,7 @@ require 'swissparser/parsing_rules'
 
 module Swiss
 
-  VERSION = "0.11.0"
+  VERSION = "0.11.1"
 
 
   # Parser for a typical bioinformatic flat file.
@@ -164,7 +164,7 @@ module Swiss
       entry = @ctx.instance_exec( &@begin )
       data.each_line do |line|
         if @ctx.should_skip?
-          if line == @separator
+          if line.include? @separator
             state = :end
             entry = init_entry
           end
@@ -211,7 +211,7 @@ module Swiss
     
     def parse_line( line, holder )
       line.chomp!
-      if line == @separator
+      if line.include? @separator
         :end
       elsif line =~ /^(\S+)\s+(.*)$/
         key,value = $1,$2

data/lib/swissparser/parsing_context.rb

@@ -5,26 +5,26 @@ module Swiss
   class ParsingContext
 
     def initialize(parameters)
-      @params = parameters
-      @skip = false
+      @params__ = parameters
+      @skip__ = false
     end   
 
     # Retrieves a parsing parameter by key. Returns nil if 
     # there is no parameter with the provided key.
     def param( key ) 
-      @params[key]
+      @params__[key]
     end
 
     def skip_entry!()
-      @skip = true
+      @skip__ = true
     end
 
     def should_skip?()
-      @skip
+      @skip__
     end
 
     def reset_skip()
-      @skip = false
+      @skip__ = false
     end
 
 
@@ -35,7 +35,7 @@ module Swiss
 
     #Method instance_exec exists since version 1.9
     if RUBY_VERSION < "1.9"
-      #Used to execute rules and action using the ParsingContext as context
+      #Used to execuxte rules and action using the ParsingContext as context
       #Stolen from http://eigenclass.org/hiki/bounded+space+instance_exec
       def instance_exec(*args, &block)
         begin

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: swissparser
 version: !ruby/object:Gem::Version 
-  version: 0.11.0
+  version: 0.11.1
 platform: ruby
 authors: 
 - paradigmatic
@@ -41,12 +41,13 @@ extensions: []
 extra_rdoc_files: 
 - CHANGELOG.rdoc
 - README.rdoc
+- benchmarks/whole_uniprot.txt
 files: 
-- .gitignore
 - CHANGELOG.rdoc
 - LICENSE
 - README.rdoc
 - Rakefile
+- benchmarks/whole_uniprot.txt
 - examples/data/EColPositives_noTAT.bas
 - examples/data/kegg_enzyme_short.txt
 - examples/data/uniprot.txt

data/.gitignore

@@ -1,9 +0,0 @@
-*~
-*#
-
-*.gemspec
-announcement.txt
-
-coverage/
-doc/
-pkg/