Skip to content

Commit

Permalink
Most galenic_forms are now correct
Browse files Browse the repository at this point in the history
  • Loading branch information
@ngiger
ngiger committed May 6, 2015
1 parent a819eb6 commit 20f747e
Show file tree
Hide file tree
Showing 2 changed files with 258 additions and 58 deletions.
68 changes: 60 additions & 8 deletions lib/oddb2xml/compositions_syntax.rb
View file
Expand Up @@ -96,8 +96,7 @@ class CompositionParser < Parslet::Parser
rule(:words_nested) { one_word.repeat(1) >> in_parent.maybe >> space? >> one_word.repeat(0) }
# dose
# 150 U.I. hFSH et 150 U.I. hLH
rule(:dose_unit) {
(
rule(:units) {
str('cm²') |
str('g/dm²') |
str('g/l') |
Expand All @@ -118,6 +117,7 @@ class CompositionParser < Parslet::Parser
str('kJ') |
str('G') |
str('g') |
str('I.E.') |
str('l') |
str('µl') |
str('U. Ph. Eur.') |
Expand Down Expand Up @@ -146,8 +146,8 @@ class CompositionParser < Parslet::Parser
str('% m/m') |
str('% m/m') |
str('%')
).as(:unit)
}
rule(:dose_unit) { units.as(:unit) }
rule(:qty_range) { (number >> space? >> (str('+/-') | str(' - ') | str(' -') | str('-') | str('±') ) >> space? >> number).as(:qty_range) }
rule(:qty_unit) { dose_qty >> (space >> dose_unit).maybe }
rule(:dose_qty) { number.as(:qty) }
Expand Down Expand Up @@ -437,11 +437,63 @@ def tag(opts={})


rule(:prepation_separator) { str(', ') | str("\n") }
rule(:prepation_name) { (prepation_separator.absent? >> any).repeat(1) }
rule(:galenic) { prepation_name.as(:prepation_name) >> space? >>
dose.maybe >> space? >> str(',').maybe >> space? >>
(prepation_separator.absent? >> any.repeat(1) >> comma).repeat(1).maybe >>
(prepation_separator.absent? >> any).repeat(1).maybe.as(:galenic_form) >> space?

rule(:prepation_name) { ((prepation_separator|lparen).absent? >> any).repeat(1)
}
rule(:dose_with_pro) {
( match('[0-9a-zA-Z]').repeat(1) >>
str('/') >>
match('[0-9a-zA-Z\'%]').repeat(1)
).maybe
}

rule(:gal_form) {
qty_unit_silent.maybe >>
((( str("\n") # |
str(',') >> space? >> qty_unit_silent |
digits >> str('%')
).absent? >> any).repeat(1) >>
(lparen >> (rparen.absent? >> any).repeat(1) >> rparen).maybe
).as(:galenic_form) >>
space?

}

rule(:standard_galenic) {
prepation_name.as(:prepation_name) >> space? >>
prepation_separator >> space? >>
(name_without_parenthesis >> qty_unit_silent >> prepation_separator).maybe >>
(qty_unit_silent >> space?).maybe >>
(dose_with_pro >> space? >> str(',') >> space?).maybe >>
gal_form >> space?
}

rule(:qty_unit_silent) { number >> space >> units }
rule(:name_then_dose) { ((space.absent? >> any).repeat(1) >>
space >> qty_unit_silent).as(:prepation_name) >> space?.as(:galenic_form)
}

rule(:only_name) { any.repeat(1).as(:prepation_name) >> space?.as(:galenic_form)
}

rule(:name_comma_gal_form) { (space.absent? >> any).repeat(1).as(:prepation_name) >>
comma >> space >>
any.repeat(1).as(:galenic_form)
}
rule(:simple_name) { (match(["a-zA-Z0-9,%"]) | str('-') | umlaut).repeat(1) }
rule(:name_gal_form) { # e.g. Dicloabak 0,1% Augentropfen or 35 Clear-Flex 3,86 % Peritonealdialyselösung
(simple_name >> space).repeat(1).as(:prepation_name) >>
space? >>
(dose_with_pro >> space?).maybe >>
gal_form >> space?
}
rule(:galenic) {
standard_galenic |
name_comma_gal_form |
name_then_dose >> space? |
name_gal_form |
only_name >> space? |
space?
}

root :expression_comp
Expand Down
248 changes: 198 additions & 50 deletions spec/galenic_spec.rb
View file
Expand Up @@ -6,72 +6,220 @@
require 'parslet/convenience'
require 'csv'

RunAllParsingExamples = false # Takes over 3 minutes to run, all the other ones just a few seconds
GoIntoPry = true
NGoIntoPry = false
RunAllParsingExamples = false # RunAllParsingExamples /travis|localhost/i.match(hostname) != nil # takes about one minute to run

galenic_tests = {
'Acetocaustin, Lösung' => { :prepation_name=>"Acetocaustin", :galenic_form=>"Lösung" },
'3TC 150 mg, Filmtabletten' => { :prepation_name=>"3TC 150 mg", :galenic_form=>"Filmtabletten" },
'Sandostatin 0,2 mg/mL, Injektionslösung' => { :prepation_name=>"Sandostatin 0,2 mg/mL", :galenic_form=>"Injektionslösung" },
'Atorvastax-Drossapharm 20 mg' => { :prepation_name=>"Atorvastax-Drossapharm 20 mg", :galenic_form=> nil },
# 'Atorvastatin Helvepharm, 10 mg Filmtabletten' => {:prepation_name=>"Atorvastatin Helvepharm", :galenic_form=> 'Filmtabletten' },
# 'Ondansetron Labatec, 8mg/4ml concentré pour perfusion' => {:prepation_name=>"Ondansetron Labatec", :galenic_form=> 'concentré pour perfusion' },
# 'Ondansetron Labatec, 8mg/4ml, concentré pour perfusion' => {:prepation_name=>"Ondansetron Labatec", :galenic_form=> 'concentré pour perfusion' },
# 'Alustal Bäume, Injektionssuspension' => {:prepation_name=>"Alustal Bäume", :galenic_form=> 'Injektionssuspension' },
# 'Alustal 3-Bäume, Injektionssuspension' => {:prepation_name=>"Alustal 3-Bäume", :galenic_form=> 'Injektionssuspension' },
'1001 Blattgrün Dragées' => { :prepation_name=>'1001 Blattgrün ', :galenic_form=> 'Dragées' },
'Amoxicillin Streuli, Granulat zur Herstellung einer Suspension' => { :prepation_name=>'Amoxicillin Streuli', :galenic_form=> 'Granulat zur Herstellung einer Suspension', },
'3TC 150 mg, Filmtabletten' => { :prepation_name=>'3TC 150 mg', :galenic_form=>'Filmtabletten' },
'Acetocaustin, Lösung' => { :prepation_name=>'Acetocaustin', :galenic_form=>'Lösung' },
'Alustal 3-Bäume, Injektionssuspension' => {:prepation_name=>'Alustal 3-Bäume', :galenic_form=> 'Injektionssuspension' },
'Alustal Bäume, Injektionssuspension' => {:prepation_name=>'Alustal Bäume', :galenic_form=> 'Injektionssuspension' },
'Arkocaps Passiflore/Passionsblume, 300 mg, capsules'=> { :prepation_name=>'Arkocaps Passiflore/Passionsblume', :galenic_form=>'capsules' },
'Atenativ, Antithrombin III 500 I.E., Injektionspräparat' => { :prepation_name=>'Atenativ', :galenic_form=>'Injektionspräparat' },
'Atorvastatin Helvepharm, 10 mg Filmtabletten' => {:prepation_name=>'Atorvastatin Helvepharm', :galenic_form=> 'Filmtabletten' },
'Atorvastax-Drossapharm 20 mg' => {:prepation_name=> 'Atorvastax-Drossapharm 20 mg', :galenic_form=> nil},
'Co-Losartan Spirig HC 50/12,5 mg' => { :prepation_name=>'Co-Losartan Spirig HC 50/12,5 mg', :galenic_form=> nil, },
'Dicloabak 0,1% Augentropfen' => { :prepation_name=>'Dicloabak 0,1% ', :galenic_form=>'Augentropfen' },
'Kaliumchlorid 14,9 % B. Braun, Zusatzampullen'=> { :prepation_name=>'Kaliumchlorid 14,9 % B. Braun', :galenic_form=>'Zusatzampullen' },
'Ondansetron Labatec, 8mg/4ml, concentré pour perfusion' => {:prepation_name=>'Ondansetron Labatec', :galenic_form=> 'concentré pour perfusion' },
'Paronex 20, Filmtabletten'=> { :prepation_name=>'Paronex 20', :galenic_form=>'Filmtabletten' },
'Physioneal 35 Clear-Flex 3,86 % Peritonealdialyselösung' => { :prepation_name=>'Physioneal 35 Clear-Flex 3,86 % ', :galenic_form=>'Peritonealdialyselösung' },
'Sandostatin 0,2 mg/mL, Injektionslösung' => { :prepation_name=>'Sandostatin 0,2 mg/mL', :galenic_form=>'Injektionslösung' },
'Tramal 100, Injektionslösung (i.m., i.v.)' => { :prepation_name=>'Tramal 100', :galenic_form=>'Injektionslösung (i.m., i.v.)' },
'Uman Albumin Kedrion 20%' => { :prepation_name=>'Uman Albumin Kedrion 20%', :galenic_form=> nil },

}

if GoIntoPry
galenic_tests = {
'Nitroderm TTS 10' => { :prepation_name=>'Nitroderm TTS 10', :galenic_form=> nil },
'Methrexx 7.5 mg / 0.75 ml,Injektionslösung in Fertigspritzen'=> { :prepation_name=>'Methrexx', :galenic_form=> 'Injektionslösung in Fertigspritzen' },
'Phytopharma foie et bile capsules/Leber-Galle Kapseln' => { :prepation_name=>'Phytopharma', :galenic_form=> 'Kapseln' },
'Sulfure de Rhénium (186Re)-RE-186-MM-1 Cis bio International, Suspension' => { :prepation_name=>'Sulfure de Rhénium (186Re)-RE-186-MM-1 Cis bio International', :galenic_form=> 'Suspension' },
'Amoxicillin Sandoz 100mg/4ml,Granulat zur Herst.einer Suspension' => { :prepation_name=>'Amoxicillin Sandoz', :galenic_form=> 'Granulat zur Herst.einer Suspension' },

# 'Tramal 100, Injektionslösung (i.m., i.v.)' => { :prepation_name=>'Tramal 100', :galenic_form=>'Injektionslösung (i.m., i.v.)' },

describe CompositionParser do
# Fix ,Zusatzampullen
# "Kaliumchlorid 14,9 % B. Braun,Zusatzampullen"=> { :prepation_name=>"Kaliumchlorid 14,9 % B. Braun", :galenic_form=>"Zusatzampullen" },
}

def test_one_string(parser, string, expected)
res1 = parser.parse_with_debug(string)
res1.delete(:qty) if res1
res1.delete(:unit) if res1
stringified = res1 ? res1.to_s.gsub(/@\d+/, '') : nil
if res1 == nil or ! stringified.eql? expected.to_s
puts "Failed testing: #{string}"
pp res1
binding.pry
end
expect(stringified).to eq expected.to_s if expected
end

if false then describe CompositionParser do
let(:parser) { CompositionParser.new }
context "identifier parsing" do
let(:galenic_parser) { parser.galenic }
it "parses identifier" do
galenic_tests.each{
let(:qty_unit_parser) { parser.qty_unit }

galenic_tests.each{
|string, expected|
puts string
res1 = galenic_parser.parse_with_debug(string)
res1.delete(:qty) if res1
res1.delete(:unit) if res1
if res1 == nil or ! res1.to_s.gsub(/@\d+/, '').eql? expected.to_s
pp res1
binding.pry
it "parses galenic #{string}" do
test_one_string(galenic_parser, string, expected)
end
res1.should eq expected
}
end
}
end
end
else
describe CompositionParser do
context "should parse all lines in #{File.basename(AllColumn_C_Lines)}" do
let(:galenic_parser) { CompositionParser.new.galenic }
ausgabe = {}
count = 0
galenic_parser = CompositionParser.new.galenic
IO.readlines(AllColumn_C_Lines).each {
|string|
count += 1
# break if count > 100
puts string
res1 = galenic_parser.parse_with_debug(string)
ausgabe[res1[:prepation_name].to_s] = res1[:galenic_form] if res1
it "parses galenic #{string}" do
res1 = galenic_parser.parse_with_debug(string)
unless res1
pp res1
binding.pry
end
end end

if RunAllParsingExamples then describe CompositionParser do
context "should parse all lines in #{File.basename(AllColumn_C_Lines)}" do
let(:galenic_parser) { CompositionParser.new.galenic }
ausgabe = {}
count = 0
galenic_parser = CompositionParser.new.galenic
IO.readlines(AllColumn_C_Lines).each {
|string|
count += 1
# break if count > 100
puts string.strip
it "parses galenic #{string}" do
res1 = galenic_parser.parse_with_debug(string.strip)
if res1
ausgabe[res1[:prepation_name].to_s] = res1[:galenic_form] if res1
else
puts "Failed testing: #{string}"
pp res1
# binding.pry
end
}
csv_name = File.join(Oddb2xml::WorkDir, 'galenic.csv')
CSV.open(csv_name, "w+", :col_sep => ';') do |csv|
end
}
csv_name = File.join(Oddb2xml::WorkDir, 'galenic.csv')
at_exit do CSV.open(csv_name, "w+", :col_sep => ';') do |csv|
ausgabe.each do |key, value|
csv << [key, value]
end
end
end
end
end
end end

describe CompositionParser do
let(:parser) { CompositionParser.new }
context "gal_form parsing" do
let(:gal_form_parser) { parser.gal_form }

should_pass = [
', Lösung',
', 100mg Lösung',
'Lösung',
'100mg Lösung',
'Injektionslösung (i.m., i.v.)',
].each {
|id|
it "parses gal_form #{id}" do
expect(gal_form_parser).to parse(id)
end
}
should_not_pass = [
].each {
|id|
it "parses gal_form #{id}" do
expect(gal_form_parser).to_not parse(id)
end
}
end
context "name_gal_form parsing" do
let(:name_gal_form_parser) { parser.name_gal_form }

should_pass = [
'Dicloabak 0,1% Augentropfen',
'35 Clear-Flex 3,86 % Peritonealdialyselösung',
'Esmeron 100mg/10ml Injektionslösung',
].each {
|id|
it "parses name_gal_form #{id}" do
expect(name_gal_form_parser).to parse(id)
end
}
should_not_pass = [
].each {
|id|
it "parses name_gal_form #{id}" do
expect(name_gal_form_parser).to_not parse(id)
end
}
end

context "prepation_name parsing" do
let(:prepation_name_parser) { parser.prepation_name }

should_pass = [
'name',
'name more',
'name more and more',
'Dicloabak 0,1% Augentropfen',
].each {
|id|
it "parses prepation_name #{id}" do
expect(prepation_name_parser).to parse(id)
end
}
should_not_pass = [
].each {
|id|
it "parses prepation_name #{id}" do
expect(prepation_name_parser).to_not parse(id)
end
}
end
context "standard_galenic parsing" do
let(:standard_galenic_parser) { parser.standard_galenic }

should_pass = [
'Antithrombin III 500 I.E., Injektionspräparat',
'Ondansetron Labatec, 8mg/4ml, concentré pour perfusion',
].each {
|id|
it "parses standard_galenic #{id}" do
expect(standard_galenic_parser).to parse(id)
end
}
should_not_pass = [
'Dicloabak 0,1% Augentropfen',
'35 Clear-Flex 3,86 % Peritonealdialyselösung',
'Esmeron 100mg/10ml Injektionslösung',
].each {
|id|
it "parses standard_galenic #{id}" do
expect(standard_galenic_parser).to_not parse(id)
end
}
end
context "dose_with_pro parsing" do
let(:dose_with_pro_parser) { parser.dose_with_pro }

should_pass = [
'100mg/10ml',
'8mg/4ml',
].each {
|id|
it "parses dose_with_pro #{id}" do
expect(dose_with_pro_parser).to parse(id)
end
}
should_not_pass = [
'100mgx10ml',
'8mgX4ml',
].each {
|id|
it "parses dose_with_pro #{id}" do
expect(dose_with_pro_parser).to_not parse(id)
end
}
end


end

0 comments on commit 20f747e

Please sign in to comment.