Class: ScientificNameParser
- Inherits:
-
Object
- Object
- ScientificNameParser
- Defined in:
- lib/biodiversity/parser.rb
Overview
we can use these expressions when we are ready to parse virus names class VirusParser
def initialize
@order = /^\s*[A-Z][a-z]\+virales/i
@family = /^\s*[A-Z][a-z]\+viridae|viroidae/i
@subfamily = /^\s*[A-Z][a-z]\+virinae|viroinae/i
@genus = /^\s*[A-Z][a-z]\+virus|viroid/i
@species = /^\s*[A-z0-9u0391-u03C9\[\] ]\+virus|phage|
viroid|satellite|prion[A-z0-9u0391-u03C9\[\] ]\+/ix
@parsed = nil
end
end
Constant Summary collapse
- FAILED_RESULT =
->(name) do { scientificName: { parsed: false, verbatim: name.to_s.strip, error: 'Parser error' } } end
Class Method Summary collapse
- .all(opts = {}) ⇒ Object
- .all_json ⇒ Object
- .fix_case(name_string) ⇒ Object
- .pos_json ⇒ Object
- .verbatim=(a_string) ⇒ Object
- .version ⇒ Object
Instance Method Summary collapse
-
#initialize(opts = {}) ⇒ ScientificNameParser
constructor
A new instance of ScientificNameParser.
- #parse(a_string) ⇒ Object
- #parsed ⇒ Object
- #unknown_placement?(a_string) ⇒ Boolean
- #virus?(a_string) ⇒ Boolean
Constructor Details
#initialize(opts = {}) ⇒ ScientificNameParser
Returns a new instance of ScientificNameParser.
153 154 155 156 157 158 159 160 |
# File 'lib/biodiversity/parser.rb', line 153 def initialize(opts = {}) @canonical_with_rank = !!opts[:canonical_with_rank] @verbatim = '' @clean = ScientificNameCleanParser.new @dirty = ScientificNameDirtyParser.new @canonical = ScientificNameCanonicalParser.new @parsed = nil end |
Class Method Details
.all(opts = {}) ⇒ Object
206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 |
# File 'lib/biodiversity/parser.rb', line 206 def @parsed.all(opts = {}) canonical_with_rank = !!opts[:canonical_with_rank] parsed = self.class != Hash res = { parsed: parsed, parser_version: ScientificNameParser::version} if parsed hybrid = self.hybrid rescue false res.merge!({ verbatim: @verbatim, normalized: self.value, canonical: self.canonical, hybrid: hybrid, details: self.details, parser_run: self.parser_run, positions: self.pos }) else res.merge!(self) end if (canonical_with_rank && canonical.count(' ') > 1 && res[:details][0][:infraspecies]) ScientificNameParser.add_rank_to_canonical(res) end res[:surrogate] = true if ScientificNameParser.surrogate?(res) res = {:scientificName => res} end |
.all_json ⇒ Object
237 238 239 |
# File 'lib/biodiversity/parser.rb', line 237 def @parsed.all_json self.all.to_json rescue '' end |
.fix_case(name_string) ⇒ Object
119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 |
# File 'lib/biodiversity/parser.rb', line 119 def self.fix_case(name_string) name_ary = name_string.split(/\s+/) words_num = name_ary.size res = nil if words_num == 1 res = name_ary[0].gsub(/[\(\)\{\}]/, '') if res.size > 1 res = UnicodeUtils.upcase(res[0]) + UnicodeUtils.downcase(res[1..-1]) else res = nil end else if name_ary[0].size > 1 word1 = UnicodeUtils.upcase(name_ary[0][0]) + UnicodeUtils.downcase(name_ary[0][1..-1]) else word1 = name_ary[0] end if name_ary[1].match(/^\(/) word2 = name_ary[1].gsub(/\)$/, '') + ')' word2 = word2[0] + UnicodeUtils.upcase(word2[1]) + UnicodeUtils.downcase(word2[2..-1]) else word2 = UnicodeUtils.downcase(name_ary[1]) end res = word1 + ' ' + word2 + ' ' + name_ary[2..-1].map { |w| UnicodeUtils.downcase(w) }.join(' ') res.strip! end res end |
.pos_json ⇒ Object
233 234 235 |
# File 'lib/biodiversity/parser.rb', line 233 def @parsed.pos_json self.pos.to_json rescue '' end |
.verbatim=(a_string) ⇒ Object
202 203 204 |
# File 'lib/biodiversity/parser.rb', line 202 def @parsed.verbatim=(a_string) @verbatim = a_string end |
.version ⇒ Object
115 116 117 |
# File 'lib/biodiversity/parser.rb', line 115 def self.version Biodiversity::VERSION end |
Instance Method Details
#parse(a_string) ⇒ Object
178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 |
# File 'lib/biodiversity/parser.rb', line 178 def parse(a_string) @verbatim = a_string.strip a_string = PreProcessor::clean(a_string) if virus?(a_string) @parsed = { verbatim: a_string, virus: true } elsif unknown_placement?(a_string) @parsed = { verbatim: a_string } else begin @parsed = @clean.parse(a_string) || @dirty.parse(a_string) unless @parsed index = @dirty.index || @clean.index salvage_match = a_string[0..index].split(/\s+/)[0..-2] salvage_string = salvage_match ? salvage_match.join(' ') : a_string @parsed = @dirty.parse(salvage_string) || @canonical.parse(a_string) || { verbatim: a_string } end rescue @parsed = FAILED_RESULT.(@verbatim) end end def @parsed.verbatim=(a_string) @verbatim = a_string end def @parsed.all(opts = {}) canonical_with_rank = !!opts[:canonical_with_rank] parsed = self.class != Hash res = { parsed: parsed, parser_version: ScientificNameParser::version} if parsed hybrid = self.hybrid rescue false res.merge!({ verbatim: @verbatim, normalized: self.value, canonical: self.canonical, hybrid: hybrid, details: self.details, parser_run: self.parser_run, positions: self.pos }) else res.merge!(self) end if (canonical_with_rank && canonical.count(' ') > 1 && res[:details][0][:infraspecies]) ScientificNameParser.add_rank_to_canonical(res) end res[:surrogate] = true if ScientificNameParser.surrogate?(res) res = {:scientificName => res} end def @parsed.pos_json self.pos.to_json rescue '' end def @parsed.all_json self.all.to_json rescue '' end @parsed.verbatim = @verbatim @parsed.all(canonical_with_rank: @canonical_with_rank) end |
#parsed ⇒ Object
174 175 176 |
# File 'lib/biodiversity/parser.rb', line 174 def parsed @parsed end |
#unknown_placement?(a_string) ⇒ Boolean
170 171 172 |
# File 'lib/biodiversity/parser.rb', line 170 def unknown_placement?(a_string) !!(a_string.match(/incertae\s+sedis/i) || a_string.match(/inc\.\s*sed\./i)) end |
#virus?(a_string) ⇒ Boolean
162 163 164 165 166 167 168 |
# File 'lib/biodiversity/parser.rb', line 162 def virus?(a_string) !!(a_string.match(/\sICTV\s*$/) || a_string.match(/\b(virus|viruses| phage|phages|viroid|viroids| satellite|satellites|prion|prions)\b/ix) || a_string.match(/[A-Z]?[a-z]+virus\b/)) end |