RubyGems - swissparser - Versions diffs - 0.11.1 → 1.0.0 - Mend

swissparser 0.11.1 → 1.0.0

Files changed (33) hide show

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

@@ -0,0 +1,112 @@
+=begin
+Copyright (C) 2009-2010 Paradigmatic
+This file is part of SwissParser.
+SwissParser is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+SwissParser is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+You should have received a copy of the GNU General Public License
+along with SwissParser.  If not, see <http://www.gnu.org/licenses/>.
+=end
+module Swiss
+  #Parser rule set.
+  class Rules
+    DEFAULT_SEPARATOR = "//"
+    attr_reader :separator, :rules
+    #Do not initialize it directly, but use Swiss::DefaultRules#refine.
+    def initialize( separator=nil, rules={}, helpers=[] )
+      if separator.nil?
+        @separator = DEFAULT_SEPARATOR
+      else
+        @separator = separator
+      end
+      @rules = rules
+      if @rules[:text].nil?
+        @rules[:text] = {}
+      end
+      @helpers = helpers
+    end
+    # Defines a new set of rules.
+    def self.define( &proc )
+        Swiss::DefaultRules.refine &proc
+    end
+    # Extends an existing parser by allowing to redefine rules. Helper
+    # methods can be redefined too.
+    def refine( &proc )
+      new_rules = Rules.new( @separator, copy( @rules ), copy( @helpers) )
+      new_rules.instance_eval(&proc)
+      new_rules
+    end
+    # Makes a parser from a ruleset. Takes a proc argument specifying the
+    # parser behavior.
+    def make_parser( &proc )
+      Swiss::Parser.new( self, &proc )
+    end
+    # Returns an array with all the helper method blocks defined previously.
+    def get_helpers
+      @helpers
+    end
+    private
+    # Defines how to parse a line starting with +key+. The +proc+
+    # takes one argument: the rest of the line
+    def with( key, &proc )
+      @rules[key] = proc
+    end
+    def helpers( &proc )
+      @helpers << proc
+    end
+    # Defines how to parse a line without key coming *after* a
+    # specified key. The +proc+ takes one argument: the rest of the
+    # line
+    def with_text_after( key, &proc )
+      @rules[:text][key] = proc
+    end
+    # Sets the entry separator line. Default: "//"
+    def set_separator( str )
+      @separator = str
+    end
+    def copy(object)
+      case object
+        when Hash
+        hash = object
+        new_h = {}
+        hash.each { |k,v| new_h[k] = v }
+        if hash[:text]
+          new_h[:text] = copy( hash[:text] )
+        end
+        new_h
+        when Array
+        ary = object
+        new_ary = []
+        ary.each { |e| new_ary << e }
+        new_ary
+      end
+    end
+  end
+end

data/lib/swissparser/rules.rbc ADDED

@@ -0,0 +1,1699 @@
+!RBIX
+0
+x
+M
+1
+n
+n
+x
+10
+__script__
+i
+31
+45
+0
+1
+7
+2
+65
+49
+3
+2
+13
+45
+0
+4
+12
+7
+5
+12
+7
+6
+12
+65
+12
+49
+7
+4
+15
+48
+5
+15
+2
+11
+I
+6
+I
+0
+I
+0
+I
+0
+n
+p
+8
+x
+8
+Rubinius
+n
+x
+5
+Swiss
+x
+11
+open_module
+n
+x
+15
+__module_init__
+M
+1
+n
+n
+x
+5
+Swiss
+i
+32
+5
+66
+45
+0
+1
+7
+2
+1
+65
+49
+3
+3
+13
+45
+0
+4
+12
+7
+5
+12
+7
+6
+12
+65
+12
+49
+7
+4
+15
+48
+5
+11
+I
+6
+I
+0
+I
+0
+I
+0
+n
+p
+8
+x
+8
+Rubinius
+n
+x
+5
+Rules
+x
+10
+open_class
+n
+x
+14
+__class_init__
+M
+1
+n
+n
+x
+5
+Rules
+i
+175
+5
+66
+65
+7
+0
+7
+1
+64
+49
+2
+2
+15
+5
+7
+3
+7
+4
+47
+49
+5
+2
+15
+45
+6
+7
+7
+8
+7
+9
+65
+67
+48
+10
+49
+11
+4
+15
+45
+6
+12
+7
+13
+7
+14
+65
+5
+49
+15
+4
+15
+45
+6
+16
+7
+17
+7
+18
+65
+67
+48
+10
+49
+11
+4
+15
+45
+6
+19
+7
+20
+7
+21
+65
+67
+48
+10
+49
+11
+4
+15
+45
+6
+22
+7
+23
+7
+24
+65
+67
+48
+10
+49
+11
+4
+15
+5
+47
+48
+25
+15
+45
+6
+26
+7
+27
+7
+28
+65
+67
+48
+10
+49
+11
+4
+15
+45
+6
+29
+7
+30
+7
+31
+65
+67
+48
+10
+49
+11
+4
+15
+45
+6
+32
+7
+33
+7
+34
+65
+67
+48
+10
+49
+11
+4
+15
+45
+6
+35
+7
+36
+7
+37
+65
+67
+48
+10
+49
+11
+4
+15
+45
+6
+38
+7
+39
+7
+40
+65
+67
+48
+10
+49
+11
+4
+11
+I
+5
+I
+0
+I
+0
+I
+0
+n
+p
+41
+x
+17
+DEFAULT_SEPARATOR
+s
+2
+//
+x
+9
+const_set
+x
+9
+separator
+x
+5
+rules
+x
+11
+attr_reader
+x
+8
+Rubinius
+n
+x
+10
+initialize
+M
+1
+n
+n
+x
+10
+initialize
+i
+92
+23
+0
+10
+8
+1
+19
+0
+15
+23
+1
+10
+22
+44
+43
+0
+78
+49
+1
+1
+19
+1
+15
+23
+2
+10
+31
+35
+0
+19
+2
+15
+20
+0
+48
+2
+9
+44
+45
+3
+4
+38
+5
+8
+48
+20
+0
+38
+5
+15
+20
+1
+38
+6
+15
+39
+6
+7
+7
+49
+8
+1
+48
+2
+9
+85
+39
+6
+7
+7
+44
+43
+0
+78
+49
+1
+1
+13
+18
+3
+49
+9
+2
+15
+8
+86
+1
+15
+20
+2
+38
+10
+11
+I
+7
+I
+3
+I
+0
+I
+3
+n
+p
+11
+x
+4
+Hash
+x
+16
+new_from_literal
+x
+4
+nil?
+x
+17
+DEFAULT_SEPARATOR
+n
+x
+10
+@separator
+x
+6
+@rules
+x
+4
+text
+x
+2
+[]
+x
+3
+[]=
+x
+8
+@helpers
+p
+19
+I
+0
+I
+1e
+I
+1f
+I
+1f
+I
+25
+I
+20
+I
+2c
+I
+22
+I
+31
+I
+24
+I
+36
+I
+25
+I
+41
+I
+26
+I
+55
+I
+25
+I
+57
+I
+28
+I
+5c
+x
+54
+/home/falcone/prg/SwissParser/lib/swissparser/rules.rb
+p
+3
+x
+9
+separator
+x
+5
+rules
+x
+7
+helpers
+x
+17
+method_visibility
+x
+15
+add_defn_method
+n
+x
+6
+define
+M
+1
+n
+n
+x
+6
+define
+i
+26
+95
+19
+0
+15
+45
+0
+1
+43
+2
+20
+0
+13
+70
+10
+22
+44
+43
+3
+12
+49
+4
+1
+50
+5
+0
+11
+I
+4
+I
+1
+I
+0
+I
+0
+n
+p
+6
+x
+5
+Swiss
+n
+x
+12
+DefaultRules
+x
+4
+Proc
+x
+14
+__from_block__
+x
+6
+refine
+p
+5
+I
+0
+I
+2c
+I
+4
+I
+2d
+I
+1a
+x
+54
+/home/falcone/prg/SwissParser/lib/swissparser/rules.rb
+p
+1
+x
+4
+proc
+x
+13
+attach_method
+n
+x
+6
+refine
+M
+1
+n
+n
+x
+6
+refine
+i
+84
+95
+19
+0
+15
+45
+0
+1
+13
+71
+2
+47
+9
+40
+47
+48
+3
+13
+39
+4
+5
+39
+5
+47
+49
+6
+1
+5
+39
+7
+47
+49
+6
+1
+47
+49
+8
+3
+15
+8
+59
+39
+4
+5
+39
+5
+47
+49
+6
+1
+5
+39
+7
+47
+49
+6
+1
+49
+2
+3
+19
+1
+15
+20
+1
+20
+0
+13
+70
+10
+77
+44
+43
+9
+12
+49
+10
+1
+50
+11
+0
+15
+20
+1
+11
+I
+8
+I
+2
+I
+0
+I
+0
+n
+p
+12
+x
+5
+Rules
+n
+x
+3
+new
+x
+8
+allocate
+x
+10
+@separator
+x
+6
+@rules
+x
+4
+copy
+x
+8
+@helpers
+x
+10
+initialize
+x
+4
+Proc
+x
+14
+__from_block__
+x
+13
+instance_eval
+p
+9
+I
+0
+I
+32
+I
+4
+I
+33
+I
+3e
+I
+34
+I
+51
+I
+35
+I
+54
+x
+54
+/home/falcone/prg/SwissParser/lib/swissparser/rules.rb
+p
+2
+x
+4
+proc
+x
+9
+new_rules
+n
+x
+11
+make_parser
+M
+1
+n
+n
+x
+11
+make_parser
+i
+27
+95
+19
+0
+15
+45
+0
+1
+43
+2
+5
+20
+0
+13
+70
+10
+23
+44
+43
+3
+12
+49
+4
+1
+50
+5
+1
+11
+I
+5
+I
+1
+I
+0
+I
+0
+n
+p
+6
+x
+5
+Swiss
+n
+x
+6
+Parser
+x
+4
+Proc
+x
+14
+__from_block__
+x
+3
+new
+p
+5
+I
+0
+I
+3a
+I
+4
+I
+3b
+I
+1b
+x
+54
+/home/falcone/prg/SwissParser/lib/swissparser/rules.rb
+p
+1
+x
+4
+proc
+n
+x
+11
+get_helpers
+M
+1
+n
+n
+x
+11
+get_helpers
+i
+3
+39
+0
+11
+I
+1
+I
+0
+I
+0
+I
+0
+n
+p
+1
+x
+8
+@helpers
+p
+5
+I
+0
+I
+3f
+I
+0
+I
+40
+I
+3
+x
+54
+/home/falcone/prg/SwissParser/lib/swissparser/rules.rb
+p
+0
+x
+7
+private
+n
+x
+4
+with
+M
+1
+n
+n
+x
+4
+with
+i
+18
+95
+19
+1
+15
+39
+0
+20
+0
+20
+1
+13
+18
+3
+49
+1
+2
+15
+11
+I
+6
+I
+2
+I
+1
+I
+1
+n
+p
+2
+x
+6
+@rules
+x
+3
+[]=
+p
+5
+I
+0
+I
+47
+I
+4
+I
+48
+I
+12
+x
+54
+/home/falcone/prg/SwissParser/lib/swissparser/rules.rb
+p
+2
+x
+3
+key
+x
+4
+proc
+n
+x
+7
+helpers
+M
+1
+n
+n
+x
+7
+helpers
+i
+12
+95
+19
+0
+15
+39
+0
+20
+0
+49
+1
+1
+11
+I
+3
+I
+1
+I
+0
+I
+0
+n
+p
+2
+x
+8
+@helpers
+x
+2
+<<
+p
+5
+I
+0
+I
+4b
+I
+4
+I
+4c
+I
+c
+x
+54
+/home/falcone/prg/SwissParser/lib/swissparser/rules.rb
+p
+1
+x
+4
+proc
+n
+x
+15
+with_text_after
+M
+1
+n
+n
+x
+15
+with_text_after
+i
+23
+95
+19
+1
+15
+39
+0
+7
+1
+49
+2
+1
+20
+0
+20
+1
+13
+18
+3
+49
+3
+2
+15
+11
+I
+6
+I
+2
+I
+1
+I
+1
+n
+p
+4
+x
+6
+@rules
+x
+4
+text
+x
+2
+[]
+x
+3
+[]=
+p
+5
+I
+0
+I
+52
+I
+4
+I
+53
+I
+17
+x
+54
+/home/falcone/prg/SwissParser/lib/swissparser/rules.rb
+p
+2
+x
+3
+key
+x
+4
+proc
+n
+x
+13
+set_separator
+M
+1
+n
+n
+x
+13
+set_separator
+i
+5
+20
+0
+38
+0
+11
+I
+2
+I
+1
+I
+1
+I
+1
+n
+p
+1
+x
+10
+@separator
+p
+5
+I
+0
+I
+57
+I
+0
+I
+58
+I
+5
+x
+54
+/home/falcone/prg/SwissParser/lib/swissparser/rules.rb
+p
+1
+x
+3
+str
+n
+x
+4
+copy
+M
+1
+n
+n
+x
+4
+copy
+i
+112
+20
+0
+13
+45
+0
+1
+12
+49
+2
+1
+9
+76
+15
+20
+0
+19
+1
+15
+44
+43
+0
+78
+49
+3
+1
+19
+2
+15
+20
+1
+56
+4
+50
+5
+0
+15
+20
+1
+7
+6
+49
+7
+1
+9
+70
+20
+2
+7
+6
+5
+20
+1
+7
+6
+49
+7
+1
+47
+49
+8
+1
+13
+18
+3
+49
+9
+2
+15
+8
+71
+1
+15
+20
+2
+8
+111
+13
+45
+10
+11
+12
+49
+2
+1
+9
+109
+15
+20
+0
+19
+3
+15
+35
+0
+19
+4
+15
+20
+3
+56
+12
+50
+5
+0
+15
+20
+4
+8
+111
+15
+1
+11
+I
+a
+I
+5
+I
+1
+I
+1
+n
+p
+13
+x
+4
+Hash
+n
+x
+3
+===
+x
+16
+new_from_literal
+M
+1
+p
+2
+x
+9
+for_block
+t
+n
+x
+4
+copy
+i
+26
+58
+36
+37
+19
+0
+15
+37
+19
+1
+15
+15
+21
+1
+2
+20
+0
+20
+1
+13
+18
+3
+49
+0
+2
+15
+11
+I
+7
+I
+2
+I
+2
+I
+2
+n
+p
+1
+x
+3
+[]=
+p
+3
+I
+0
+I
+60
+I
+1a
+x
+54
+/home/falcone/prg/SwissParser/lib/swissparser/rules.rb
+p
+2
+x
+1
+k
+x
+1
+v
+x
+4
+each
+x
+4
+text
+x
+2
+[]
+x
+4
+copy
+x
+3
+[]=
+x
+5
+Array
+n
+M
+1
+p
+2
+x
+9
+for_block
+t
+n
+x
+4
+copy
+i
+13
+57
+19
+0
+15
+21
+1
+4
+20
+0
+49
+0
+1
+11
+I
+4
+I
+1
+I
+1
+I
+1
+n
+p
+1
+x
+2
+<<
+p
+3
+I
+0
+I
+68
+I
+d
+x
+54
+/home/falcone/prg/SwissParser/lib/swissparser/rules.rb
+p
+1
+x
+1
+e
+p
+33
+I
+0
+I
+5b
+I
+0
+I
+5c
+I
+3
+I
+5d
+I
+d
+I
+5e
+I
+12
+I
+5f
+I
+1c
+I
+60
+I
+24
+I
+61
+I
+2d
+I
+62
+I
+46
+I
+61
+I
+48
+I
+64
+I
+4d
+I
+65
+I
+57
+I
+66
+I
+5c
+I
+67
+I
+61
+I
+68
+I
+69
+I
+69
+I
+6e
+I
+5c
+I
+70
+x
+54
+/home/falcone/prg/SwissParser/lib/swissparser/rules.rb
+p
+5
+x
+6
+object
+x
+4
+hash
+x
+5
+new_h
+x
+3
+ary
+x
+7
+new_ary
+p
+27
+I
+2
+I
+19
+I
+c
+I
+1b
+I
+16
+I
+1e
+I
+25
+I
+2c
+I
+32
+I
+32
+I
+41
+I
+3a
+I
+50
+I
+3f
+I
+5f
+I
+43
+I
+64
+I
+47
+I
+73
+I
+4b
+I
+82
+I
+52
+I
+91
+I
+57
+I
+a0
+I
+5b
+I
+af
+x
+54
+/home/falcone/prg/SwissParser/lib/swissparser/rules.rb
+p
+0
+x
+13
+attach_method
+p
+3
+I
+2
+I
+17
+I
+20
+x
+54
+/home/falcone/prg/SwissParser/lib/swissparser/rules.rb
+p
+0
+x
+13
+attach_method
+p
+3
+I
+0
+I
+14
+I
+1f
+x
+54
+/home/falcone/prg/SwissParser/lib/swissparser/rules.rb
+p
+0