biointerchange 0.1.0
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- data/.document +5 -0
- data/.rspec +1 -0
- data/.travis.yml +12 -0
- data/Gemfile +17 -0
- data/LICENSE.txt +8 -0
- data/README.md +166 -0
- data/Rakefile +50 -0
- data/VERSION +1 -0
- data/bin/biointerchange +6 -0
- data/docs/exceptions_readme.txt +13 -0
- data/examples/BovineGenomeChrX.gff3.gz +0 -0
- data/examples/gb-2007-8-3-R40.xml +243 -0
- data/examples/pubannotation.json +1 -0
- data/generators/rdfxml.rb +104 -0
- data/lib/biointerchange/core.rb +195 -0
- data/lib/biointerchange/exceptions.rb +38 -0
- data/lib/biointerchange/genomics/gff3_feature.rb +82 -0
- data/lib/biointerchange/genomics/gff3_feature_set.rb +37 -0
- data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +107 -0
- data/lib/biointerchange/genomics/gff3_reader.rb +86 -0
- data/lib/biointerchange/gff3.rb +135 -0
- data/lib/biointerchange/reader.rb +25 -0
- data/lib/biointerchange/registry.rb +29 -0
- data/lib/biointerchange/sio.rb +7124 -0
- data/lib/biointerchange/sofa.rb +1566 -0
- data/lib/biointerchange/textmining/content.rb +69 -0
- data/lib/biointerchange/textmining/document.rb +36 -0
- data/lib/biointerchange/textmining/pdfx_xml_reader.rb +161 -0
- data/lib/biointerchange/textmining/process.rb +57 -0
- data/lib/biointerchange/textmining/pubannos_json_reader.rb +72 -0
- data/lib/biointerchange/textmining/text_mining_rdf_ntriples.rb +197 -0
- data/lib/biointerchange/textmining/text_mining_reader.rb +41 -0
- data/lib/biointerchange/writer.rb +23 -0
- data/lib/biointerchange.rb +3 -0
- data/spec/exceptions_spec.rb +27 -0
- data/spec/gff3_rdfwriter_spec.rb +67 -0
- data/spec/text_mining_pdfx_xml_reader_spec.rb +89 -0
- data/spec/text_mining_pubannos_json_reader_spec.rb +71 -0
- data/spec/text_mining_rdfwriter_spec.rb +57 -0
- data/web/about.html +89 -0
- data/web/biointerchange.js +133 -0
- data/web/bootstrap/css/bootstrap-responsive.css +1040 -0
- data/web/bootstrap/css/bootstrap-responsive.min.css +9 -0
- data/web/bootstrap/css/bootstrap.css +5624 -0
- data/web/bootstrap/css/bootstrap.min.css +9 -0
- data/web/bootstrap/img/glyphicons-halflings-white.png +0 -0
- data/web/bootstrap/img/glyphicons-halflings.png +0 -0
- data/web/bootstrap/js/bootstrap.js +2027 -0
- data/web/bootstrap/js/bootstrap.min.js +6 -0
- data/web/bootstrap/js/jquery-1.8.1.min.js +2 -0
- data/web/css/rdoc-style.css +5786 -0
- data/web/css/rdoc.css +716 -0
- data/web/images/BioInterchange300.png +0 -0
- data/web/index.html +109 -0
- data/web/service/rdfizer.fcgi +68 -0
- data/web/webservices.html +123 -0
- metadata +240 -0
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module BioInterchange
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# A reader takes information from an input stream and creates an object model.
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#
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# For example, the input stream might hold text-mining data in some format. This
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# data is deserialized by the reader and turned into an object model representation,
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# i.e. an instance of a Ruby class that describes the data.
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class Reader
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# Create a new instance of a reader. Ideally you want to provide your own initialization
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# method in derived classes that takes some extra parameters for configuring/parametrizing the
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# data deserialization with +deserialize+.
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def initialize
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end
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# Reads data from the provided input stream and returns an input specific object model instance.
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#
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# +istream+:: input IO stream to deserialize
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def deserialize(istream)
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raise BioInterchange::Exceptions::ImplementationReaderError, 'You must implement this method, which reads data from an input stream and returns an object model instance.'
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end
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end
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end
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module BioInterchange
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class Registry
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def self.register_reader(uid, service)
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@@readers[uid] = service
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end
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def self.register_writer(uid, service)
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@@writers[uid] = service
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end
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def self.readers
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@@readers
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end
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def self.writers
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@@writers
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end
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private
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@@readers = {}
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@@writers = {}
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end
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end
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