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Reworked parsing of parenthesis in names
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@ngiger
ngiger committed Apr 15, 2015
1 parent ea2d19b commit b1cd540
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Showing 2 changed files with 49 additions and 40 deletions.
42 changes: 25 additions & 17 deletions lib/oddb2xml/parslet_compositions.rb
View file
Expand Up @@ -14,9 +14,9 @@
class DoseParser < Parslet::Parser

# Single character rules
rule(:lparen) { str('(') >> space? }
rule(:rparen) { str(')') >> space? }
rule(:comma) { str(',') >> space? }
rule(:lparen) { str('(') }
rule(:rparen) { str(')') }
rule(:comma) { str(',') }

rule(:space) { match('\s').repeat(1) }
rule(:space?) { space.maybe }
Expand All @@ -35,16 +35,21 @@ class DoseParser < Parslet::Parser
).maybe
)
}
rule(:radio_isotop) { match['a-zA-Z'].repeat(1) >> str('(') >> digits >> str('-') >> match['a-zA-Z'].repeat(1-3) >> str(')') >>
rule(:radio_isotop) { match['a-zA-Z'].repeat(1) >> lparen >> digits >> str('-') >> match['a-zA-Z'].repeat(1-3) >> rparen >>
((space? >> match['a-zA-Z']).repeat(1)).repeat(0)
} # e.g. Xenonum (133-Xe) or yttrii(90-Y) chloridum zum Kalibrierungszeitpunkt
rule(:identifier) { (match['a-zA-Zéàèèçïöäüâ'] | digit >> str('-')) >> match['0-9a-zA-Z\-éàèèçïöäüâ\'\/\.:%'].repeat(0) }
# handle stuff like acidum 9,11-linolicum specially
rule(:identifier_with_comma) { match['0-9a-zA-Z'] >> match['0-9a-zA-Z,\-'].repeat(1) }
# handle stuff like acidum 9,11-linolicum specially. it must contain at least one a-z
rule(:identifier_with_comma) { match['0-9,\-'].repeat(0) >> match['a-zA-Z'].repeat(1) >> match['0-9a-zA-Z,\-\(\)'].repeat(0) }
rule(:one_word) { match(['a-zA-Zé,']).repeat(1) >> match(['0-9a-zA-Z\-éàèèçïöäüâ\'\/\.:%']).repeat(0) >> space? }
rule(:in_parent) { lparen >> one_word.repeat(1) >> rparen }
rule(:words_nested) { one_word.repeat(1) >> in_parent.maybe >> space? >> one_word.repeat(0) }
rule(:name_with_parenthesis) {
(match('[a-zA-Z]') >> ((match('[0-9]') >> space >> match('[a-zA-Z]')).maybe >>match('[a-zA-Z_\- \(\)]')).repeat) >> space?
}
# dose
# retinoli palmitas 7900 U.I.
# 25
rule(:dose_unit) { (
str('% V/V') |
str('µg') |
Expand All @@ -57,8 +62,8 @@ class DoseParser < Parslet::Parser
str('l') |
str('µl') |
str('ml') |
str('U.I') |
str('U.I.') |
# str('U.I') |
str('U.') |
str('Mia. U.') |
str('%')
Expand Down Expand Up @@ -109,19 +114,21 @@ class SubstanceParser < DoseParser

# Grammar parts
rule(:farbstoff) { ((str('antiox.:') | str('color.:')) >> space).maybe >> (str('E').as(:farbstoff) >> space >> digits.as(:digits) >> match['(a-z)'].repeat(0,3)) } # Match Wirkstoffe like E 270
# rule(:name_simple_part) { ((identifier_with_comma) >> space?).repeat(1) }
rule(:name_simple_part) { ((identifier_with_comma | identifier) >> space?).repeat(1) }
rule(:substance_in_parenthesis) { (name_complex_part >> space?).repeat(1) >> (comma >> (name_simple_part >> space?).repeat(0)).repeat(0) }
rule(:name_complex_part) { identifier |
str('>') |
digit.repeat >> space >> dose_unit.absent? >> any.repeat | # match stuff like typus 1 inactivatum
str('(') >> substance_in_parenthesis >> str(')') >> digit.repeat(0,1) >> str('-like:').maybe # Match name_with_parenthesis like (D-Antigen)
# str('>') |
# digit.repeat >> space >> dose_unit.absent? >> any.repeat | # match stuff like typus 1 inactivatum
space? >> lparen >> substance_in_parenthesis >> space? >> rparen >> digit.repeat(0,1) >> str('-like:').maybe # Match name_with_parenthesis like (D-Antigen)
}
rule(:der) { (str('DER:') >> space >> (digit >> match['\.-']).maybe >> digit >> str(':') >> digit).as(:der) } # DER: 1:4 or DER: 3.5:1 or DER: 6-8:1
rule(:substance_name) { (name_simple_part >> (space? >> name_complex_part).repeat(0)).as(:substance_name) }
# rule(:substance_name) { (name_simple_part >> (space? >> name_complex_part).repeat(0)).as(:substance_name) }
rule(:substance_name) { words_nested | identifier_with_comma }
rule(:substance) { farbstoff |
((name_simple_part | radio_isotop | substance_name).as(:substance_name) >>
((radio_isotop | substance_name).as(:substance_name) >>
(space? >> dose.maybe.as(:dose))).as(:substance) >>
(space >> str('ad solutionem pro') >> space >> dose.as(:ad_solutionem)).maybe
(space >> str('ad solutionem pro').maybe >> space? >> dose.as(:ad_solutionem)).maybe
}
rule(:excipiens) { (str('excipiens') >> space? >>
(str('pro compresso').as(:pro_compresso)).maybe |
Expand All @@ -132,6 +139,7 @@ class SubstanceParser < DoseParser
) |
((
((str('ad emulsionem').as(:ad_emulsionem) |
str('aqua q.s. ad suspensionem pro').as(:ad_suspensionem) |
str('ad solutionem pro').as(:ad_solutionem_pro) |
str('pro dosi') |
str('corresp.') # | (space >> name_simple_part)
Expand Down Expand Up @@ -160,8 +168,10 @@ class SubstanceParser < DoseParser

#rule(:one_substance) { (str(',') >> space).maybe >> (excipiens) } # Sometimes it is handy for debugging to be able to debug just one the different variants
rule(:one_substance) { (str(',') >> space).maybe >> (der | excipiens | histamin | named_substance | substance_residui | substance_conserv | substance_et | substance_ut | substance_corresp | substance ) }
rule(:one_substance) { (str(',') >> space).maybe >> (excipiens | substance ) }
rule(:all_substances) { one_substance.repeat(1)}
# rule(:one_substance) { (str(',') >> space).maybe >> ( substance | excipiens) }
rule(:one_substance) { ( excipiens | substance ) >> (str(',') >> space).maybe }
rule(:one_substance) { ( substance ) >> (str(',') >> space).maybe }
rule(:all_substances) { one_substance.repeat(1) }
root :all_substances
end

Expand Down Expand Up @@ -193,7 +203,6 @@ def SubstanceTransformer.add_substance(substance)
) {
|dictionary|
puts "#{__LINE__}: dictionary #{dictionary}"
# binding.pry
ParseSubstance.new(dictionary[:substance_name].to_s.sub(/^excipiens /i, ''), dictionary[:dose])
}
rule(:substance_name => simple(:substance_name),
Expand Down Expand Up @@ -437,7 +446,6 @@ def ParseComposition.from_string(string)
result.source = string
result.label = ast[:label].to_s if ast[:label]
result.label_description = ast[:label_description].to_s if ast[:label_description]
binding.pry
if ast.is_a?(Parslet::Slice)
else
ast.find_all{|x| x.is_a?(ParseSubstance)}.each{ |x| result.substances << x }
Expand Down
47 changes: 24 additions & 23 deletions spec/parslet_spec.rb
View file
Expand Up @@ -10,7 +10,7 @@
require 'parslet/rig/rspec'

RunAllCompositionsTests = false # takes over a minute!
RunAllTests = false
RunAllTests = true
RunFailingSpec = false
RunMostImportantParserTests = true
RunExcipiensTest = true
Expand Down Expand Up @@ -274,27 +274,36 @@ def run_substance_tests(hash_string_to_name)
# run_substance_tests(tests) if RunAllTests
# run_substance_tests( { "acari allergeni extractum 50'000 U.:" => 'Acari Allergeni Extractum', })
if RunMostImportantParserTests
context "should return correct substance for 'pyrazinamidum 500 mg'" do
string = "pyrazinamidum 500 mg"
substance = ParseSubstance.from_string(string)
specify { expect(substance.name).to eq 'Pyrazinamidum' }
specify { expect(substance.qty).to eq 500.0 }
specify { expect(substance.unit).to eq 'mg' }
context "should parse a complex composition" do
source = 'globulina equina (immunisé avec coeur) 8 mg'
source = 'globulina equina (immunisé avec coeur, tissu pulmonaire, reins de porcins) 8 mg'
composition = ParseSubstance.from_string(source)
end

context "should return correct substance for 9,11-linolicum " do
string = "acidum 9,11-linolicum"
string = "acidum 9,11-linolicum 3.25 mg"
substance = ParseSubstance.from_string(string)
substance = nil; composition = nil
[ "9,11-linolicum",
# "9,11-linolicum 3.25 mg"
].each {
|string|
substance = ParseSubstance.from_string(string)
specify { expect(substance.name).to eq '9,11-linolicum' }
specify { expect(substance.chemical_substance).to eq nil }
composition = ParseComposition.from_string(string)
}

composition = ParseComposition.from_string(string)
specify { expect(substance.to_s.eql?(composition.substances.first.to_s)).to eq true }
specify { expect(substance.name).to eq 'Acidum 9,11-linolicum' }
specify { expect(substance.qty).to eq 3.25}
specify { expect(substance.unit).to eq 'mg' }
specify { expect(substance.chemical_substance).to eq nil }
end if TryRun

context "should return correct substance for 'pyrazinamidum 500 mg'" do
string = "pyrazinamidum 500 mg"
substance = ParseSubstance.from_string(string)
specify { expect(substance.name).to eq 'Pyrazinamidum' }
specify { expect(substance.qty).to eq 500.0 }
specify { expect(substance.unit).to eq 'mg' }
end

context "should return correct substance for 'Xenonum(133-xe) 74 -740 Mb'" do
string = "Xenonum(133-Xe) 74 -740 MBq"
substance = ParseSubstance.from_string(string)
Expand Down Expand Up @@ -334,8 +343,6 @@ def run_substance_tests(hash_string_to_name)
pp substance

composition = ParseComposition.from_string(string)
pp composition
binding.pry
specify { expect(substance.name).to eq 'Calcii Lactas Pentahydricus' }
specify { expect(substance.qty).to eq 25.0}
specify { expect(substance.unit).to eq 'mg' }
Expand Down Expand Up @@ -408,15 +415,10 @@ def run_substance_tests(hash_string_to_name)
specify { expect(substance.unit).to eq 'ml' }
end

context "should parse a complex composition" do
source = 'globulina equina (immunisé avec coeur, tissu pulmonaire, reins de porcins) 8 mg'
composition = ParseSubstance.from_string(source)
end
end
context "should return correct substance for 'toxoidum pertussis 25 µg et haemagglutininum filamentosum 25 µg'" do
string = "toxoidum pertussis 25 µg et haemagglutininum filamentosum 15 µg"
substance = ParseSubstance.from_string(string)
pp substance; binding.pry
specify { expect(substance.name).to eq 'Toxoidum Pertussis' }
specify { expect(substance.qty).to eq 25.0}
specify { expect(substance.unit).to eq 'µg' }
Expand All @@ -430,7 +432,6 @@ def run_substance_tests(hash_string_to_name)
context "should return correct substance for corresp with two et substances" do
string = "viperis antitoxinum equis F(ab')2 corresp. Vipera aspis > 1000 LD50 mus et Vipera berus > 500 LD50 mus et Vipera ammodytes > 1000 LD50 mus"
substance = ParseSubstance.from_string(string)
pp substance; binding.pry
specify { expect(substance.name).to eq 'Toxoidum Pertussis' }
specify { expect(substance.qty).to eq 25.0}
specify { expect(substance.unit).to eq 'µg' }
Expand All @@ -450,7 +451,7 @@ def run_substance_tests(hash_string_to_name)
"I) DTPa-IPV-Komponente (Suspension): toxoidum diphtheriae 30 U.I., toxoidum pertussis 25 µg et haemagglutininum filamentosum 25 µg"
composition = ParseComposition.from_string(source)
pp composition
binding.pry
# binding.pry
specify { expect(composition.source).to eq source }

specify { expect(composition.label).to eq 'I' }
Expand Down

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