swissparser 0.11.1 → 1.0.0
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- data/.gitignore +9 -0
- data/CHANGELOG.rdoc +9 -0
- data/README.rdoc +28 -17
- data/Rakefile +2 -2
- data/Rakefile.compiled.rbc +622 -0
- data/examples/kegg_demo.rb +39 -63
- data/examples/uniprot.rb +85 -0
- data/features/basic_parsing.feature +79 -30
- data/features/extra.feature +52 -0
- data/features/step_definitions/basic_steps.rb +84 -0
- data/features/step_definitions/sugar_steps.rb +71 -0
- data/lib/swissparser.rb +39 -194
- data/lib/swissparser.rbc +928 -0
- data/lib/swissparser/entries.rb +137 -0
- data/lib/swissparser/entries.rbc +2360 -0
- data/lib/swissparser/rules.rb +112 -0
- data/lib/swissparser/rules.rbc +1699 -0
- metadata +55 -32
- data/benchmarks/whole_uniprot.txt +0 -7
- data/examples/parse_from_uri.rb +0 -88
- data/examples/signal_demo.rb +0 -100
- data/examples/tutorial_1.rb +0 -88
- data/examples/tutorial_2.rb +0 -65
- data/examples/uniprot_param_demo.rb +0 -85
- data/features/parser_extension.feature +0 -83
- data/features/parsing_context.feature +0 -48
- data/features/polite.feature +0 -16
- data/features/step_definitions/core.rb +0 -71
- data/features/step_definitions/definitions.rb +0 -68
- data/features/step_definitions/extra.rb +0 -56
- data/lib/swiss_parser.rb +0 -13
- data/lib/swissparser/parsing_context.rb +0 -60
- data/lib/swissparser/parsing_rules.rb +0 -39
data/.gitignore
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data/CHANGELOG.rdoc
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== 1.0.0 / 2010-01-11
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* New release, the syntax for defining rules and parsers was simplified.
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ATTENTION: this version is not backward compatible !
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== 0.90.0 / 2009-12-30
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* Complete rewrite to simplify parser definition.
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== 0.11.1 / 2009-11-17
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* 1 bug fix:
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== DESCRIPTION:
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Simple DSL to define parser for flat files formats common in
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Simple DSL to define parser for flat files formats common in
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biofinformatics, such as Swissprot, Uniprot, KEGG, TREMBL, etc.
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SwissParser API was changed in its version 1.0.0 to simplify parser
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definition. The code was tested on entire Uniprot and KEGG releases
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and functional testing guarantees that existing features will not
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break after an update.
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=== Compatibility with 0.x versions
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The 1.x versions represent an API change which is *not* *backward*
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*compatible*. However, the rules definitions and helper need small
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changes. A wiki page will soon give instructions for updating your
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parsers.
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== FEATURES:
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* Defines parsers with a clear and compact declarative syntax.
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* The whole parsing workflow is configurable.
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* Able to parse remote files accessible from a web or an FTP server.
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* Users can create new parsers by extending existing parsers.
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*
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* Parser rules have access to user defined helper methods.
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== USAGE:
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See
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See:
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* tutorials: http://wiki.github.com/paradigmatic/SwissParser
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* examples: http://github.com/paradigmatic/SwissParser/tree/master/examples/
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== REQUIREMENTS:
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SwissParser uses only pure standard ruby.
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Thanks to
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Thanks to rvm it was successfuly tested with
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versions:
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* 1.
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* 1.
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* jruby-bin-1.3.1
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* ruby-1.8.7-p302
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* ruby-1.9.2-p0
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* jruby-1.5.2
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If you want to participate in SwissParser developpement, you will need the gem *bones*.
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No other gems are required to use it. However, if you want to
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participate in SwissParser developpement, you will need the gem
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*bones*, *rspec* and *cucumber*.
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rubyforge, you will need to change the sources as explained here:
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http://gemcutter.org/pages/gem_docs
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== INSTALL:
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Then you can simply install SwissParser with:
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gem install swissparser
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and start
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and start parsers definitions by requiring it:
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require 'swissparser'
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data/Rakefile
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task :default => :features
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Cucumber::Rake::Task.new(:features) do |t|
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t.cucumber_opts = "--format pretty"
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t.rcov = true
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t.cucumber_opts = "--format pretty --tags ~@skip"
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#t.rcov = true
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end
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CLOBBER << "coverage/"
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===
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http://github.com/paradigmatic/SwissParser
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development_dependencies=
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