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: { id: GnUUID.uuid(name), parsed: false, verbatim: name, error: "Parser internal error" } } end
Class Method Summary collapse
- .add_rank_to_canonical(parsed) ⇒ Object
- .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.
- #noparse?(a_string) ⇒ Boolean
- #parse(a_string) ⇒ Object
- #parsed ⇒ Object
- #virus?(a_string) ⇒ Boolean
Constructor Details
#initialize(opts = {}) ⇒ ScientificNameParser
Returns a new instance of ScientificNameParser.
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# File 'lib/biodiversity/parser.rb', line 170 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
.add_rank_to_canonical(parsed) ⇒ Object
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# File 'lib/biodiversity/parser.rb', line 118 def self.add_rank_to_canonical(parsed) return parsed if parsed[:scientificName][:hybrid] name = parsed[:scientificName] parts = name[:canonical].split(" ") name_ary = parts[0..1] name[:details][0][:infraspecies].each do |data| infrasp = data[:string] rank = data[:rank] name_ary << (rank && rank != "n/a" ? "#{rank} #{infrasp}" : infrasp) end parsed[:scientificName][:canonical] = name_ary.join(" ") parsed end |
.all(opts = {}) ⇒ Object
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# File 'lib/biodiversity/parser.rb', line 228 def @parsed.all(opts = {}) canonical_with_rank = !!opts[:canonical_with_rank] parsed = self.class != Hash res = { id: @id, 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 res[:surrogate] = true if ScientificNameParser.surrogate?(res) res = {:scientificName => res} if (canonical_with_rank && canonical.count(" ") > 1 && res[:scientificName][:details][0][:infraspecies]) ScientificNameParser.add_rank_to_canonical(res) end res end |
.all_json ⇒ Object
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# File 'lib/biodiversity/parser.rb', line 261 def @parsed.all_json self.all.to_json rescue "" end |
.fix_case(name_string) ⇒ Object
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# File 'lib/biodiversity/parser.rb', line 136 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
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# File 'lib/biodiversity/parser.rb', line 257 def @parsed.pos_json self.pos.to_json rescue "" end |
.verbatim=(a_string) ⇒ Object
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# File 'lib/biodiversity/parser.rb', line 223 def @parsed.verbatim=(a_string) @verbatim = a_string @id = GnUUID.uuid(@verbatim) end |
.version ⇒ Object
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# File 'lib/biodiversity/parser.rb', line 132 def self.version Biodiversity::VERSION end |
Instance Method Details
#noparse?(a_string) ⇒ Boolean
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# File 'lib/biodiversity/parser.rb', line 188 def noparse?(a_string) incertae_sedis = a_string.match(/incertae\s+sedis/i) || a_string.match(/inc\.\s*sed\./i) rna = a_string.match(/[^A-Z]RNA[^A-Z]*/) incertae_sedis || rna end |
#parse(a_string) ⇒ Object
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# File 'lib/biodiversity/parser.rb', line 199 def parse(a_string) @verbatim = a_string a_string = PreProcessor::clean(a_string) if virus?(a_string) @parsed = { verbatim: @verbatim, virus: true } elsif noparse?(a_string) @parsed = { verbatim: @verbatim } 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: @verbatim } end rescue @parsed = FAILED_RESULT.(@verbatim) end end def @parsed.verbatim=(a_string) @verbatim = a_string @id = GnUUID.uuid(@verbatim) end def @parsed.all(opts = {}) canonical_with_rank = !!opts[:canonical_with_rank] parsed = self.class != Hash res = { id: @id, 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 res[:surrogate] = true if ScientificNameParser.surrogate?(res) res = {:scientificName => res} if (canonical_with_rank && canonical.count(" ") > 1 && res[:scientificName][:details][0][:infraspecies]) ScientificNameParser.add_rank_to_canonical(res) end 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
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# File 'lib/biodiversity/parser.rb', line 195 def parsed @parsed end |
#virus?(a_string) ⇒ Boolean
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# File 'lib/biodiversity/parser.rb', line 179 def virus?(a_string) !!(a_string.match(/\sICTV\s*$/) || a_string.match(/\b(virus|viruses|particle|particles| phage|phages|viroid|viroids|virophage| prion|prions|NPV)\b/ix) || a_string.match(/[A-Z]?[a-z]+virus\b/) || a_string.match(/\b[A-Za-z]*(satellite[s]?|NPV)\b/)) end |