swissparser 0.7.0 → 0.8.0

data/.gitignore

@@ -0,0 +1,8 @@
+*~
+*#
+
+*.gemspec
+announcement.txt
+
+doc/
+pkg/

data/{History.txt → CHANGELOG.rdoc}

@@ -1,3 +1,9 @@
+== 0.8.0 / 2009-11-14
+
+* 1 new feature:
+  - helper methods are now defined with the helper method. When the
+  parser is extended they can be overriden in a one per one basis.
+
 == 0.7.0 / 2009-11-14
 
 * *Important* *change*: SwissParser is now required with:

data/README.rdoc

@@ -0,0 +1,57 @@
+= SwissParser
+   by Paradigmatic
+   http://github.com/paradigmatic/SwissParser
+
+== DESCRIPTION:
+
+Simple DSL to define parser for flat files formats common in biofinformatics.
+
+== FEATURES:
+
+SwissParser is currently under fast development. However, the code base should
+be stable enough to be used for bioinformatics research.
+
+* Defines parsers with a clear and compact declarative syntax.
+* The whole parsing workflow is configurable.
+* The user can create new parsers by extending existing parsers.
+* Parser have access to global parameters and user defined helper methods.
+
+== USAGE:
+
+See tutorials: http://wiki.github.com/paradigmatic/SwissParser 
+
+
+== REQUIREMENTS:
+
+Only pure standard ruby. Tested with version 1.8.7 only but should work with JRuby and others.
+
+If you want to participate in SwissParser developpement, you will need the gem *bones*.
+
+== INSTALL:
+
+SwissParser is available as a gem through gemcutter. If you still use
+rubyforge, you will need to change the sources as explained here:
+http://gemcutter.org/pages/gem_docs
+
+Then you can simply install SwissParser with:
+
+  gem install swissparser
+
+and start defining parsers by requiring it:
+
+  require 'swissparser'
+
+Alternatively, you can download the whole source tree or just the
+swissparser.rb file using the github site:
+
+http://github.com/paradigmatic/SwissParser
+
+Finally, if you want to participate in the development or use the edge
+version you can clone the project with git:
+
+  $ git clone git://github.com/paradigmatic/SwissParser
+ 
+== LICENSE:
+
+Distributed under GPLv3. See the included LICENSE file for details.
+

data/Rakefile

@@ -16,6 +16,8 @@ Bones {
   email  'paradigmatic@streum.org'
   url  'http://github.com/paradigmatic/SwissParser'
   version  Swiss::VERSION
+  readme_file 'README.rdoc'
+  history_file 'CHANGELOG.rdoc'
   ignore_file  '.gitignore'
   rdoc.exclude ["examples/data"]
 }

data/examples/kegg_demo.rb

@@ -35,17 +35,13 @@ enzyme_parser = Swiss::Parser.define do
   end
 
 
-  helpers do
-    
-    def parse_gene_ids( string, entry )
-      string.split(" ").each do |item|
-        if item =~ /(\d+)\(\w+\)/
-          entry[:genes] << $1
-        end
+  helper :parse_gene_ids do |string, entry|
+    string.split(" ").each do |item|
+      if item =~ /(\d+)\(\w+\)/
+        entry[:genes] << $1
       end
     end
   end
-    
   
   rules do
 

data/lib/swissparser.rb

@@ -19,7 +19,7 @@ along with SwissParser.  If not, see <http://www.gnu.org/licenses/>.
 
 module Swiss
 
-  VERSION = "0.7.0"
+  VERSION = "0.8.0"
 
   # This class defines parsing rules. Its methods
   # are accessible within the +rules+ section of
@@ -112,7 +112,7 @@ module Swiss
         @separator = DEFAULT_SEPARATOR
         @actions = {}
         @actions[:text] = {}
-        @helpers = lambda {}
+        @helpers = {}
       elsif args.size == 7
         actions,separator,before,the_begin,the_end,after,helpers = *args
         @actions = actions.clone
@@ -162,10 +162,13 @@ module Swiss
       @after = proc
     end
 
-    # Helpers methods accessible to rules and actions can be
-    # defined using this method.
-    def helpers(&proc)
-      @helpers = proc
+    # Define an helper method accessible to rules and actions.
+    # This method tales two argument:
+    # * A symbol which will be the method name
+    # * A block which is the method implementation. The block can take parameters.
+    # The helper method can then be called as a regular method.
+    def helper(name, &proc)
+      @helpers[name] = proc
     end
 
     # Defines parsing rules inside a parser definition. The ParsingRules
@@ -211,7 +214,11 @@ module Swiss
     # it returns an array containing _entry_ objects.
     def parse_file( filename, params={} )
       @ctx = ParsingContext.new( params )
-      @ctx.instance_exec( &@helpers )
+      helperModule = Module.new
+      @helpers.each do |name, proc|
+        helperModule.send( :define_method, name, proc )
+      end
+      @ctx.extend( helperModule )
       container = @ctx.instance_exec( &@before )
       File.open( filename, 'r' ) do |file|
         entry = @ctx.instance_exec( &@begin )

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: swissparser
 version: !ruby/object:Gem::Version 
-  version: 0.7.0
+  version: 0.8.0
 platform: ruby
 authors: 
 - paradigmatic
@@ -29,12 +29,13 @@ executables: []
 extensions: []
 
 extra_rdoc_files: 
-- History.txt
-- README.txt
+- CHANGELOG.rdoc
+- README.rdoc
 files: 
-- History.txt
+- .gitignore
+- CHANGELOG.rdoc
 - LICENSE
-- README.txt
+- README.rdoc
 - Rakefile
 - examples/data/EColPositives_noTAT.bas
 - examples/data/kegg_enzyme_short.txt
@@ -52,7 +53,7 @@ licenses: []
 post_install_message: 
 rdoc_options: 
 - --main
-- README.txt
+- README.rdoc
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 

data/README.txt

@@ -1,32 +0,0 @@
-= SwissParser
-   by Paradigmatic
-   http://github.com/paradigmatic/SwissParser
-
-== DESCRIPTION:
-
-Simple DSL to define parser for flat files formats common in biofinformatics.
-
-== FEATURES:
-
-* Defines parsers with a declarative syntax.
-* The whole parsing workflow is configurable.
-* The user can create new parsers by extending existing parsers.
-
-== SYNOPSIS:
-
-  See examples
-
-== REQUIREMENTS:
-
-Only prue standard ruby. Tested with version 1.8.7 only but should work with JRuby and others.
-
-If you want to participate in SwissParser developpement, you will need the gem *bones*.
-
-== INSTALL:
-
-Soon available as a gem...
-
-== LICENSE:
-
-Distributed under GPLv3. See included LICENSE file.
-