oddb2xml 2.6.9 → 2.7.4
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- checksums.yaml +5 -5
- data/.github/workflows/ruby.yml +40 -0
- data/.standard.yml +2 -0
- data/Elexis_Artikelstamm_v5.xsd +0 -3
- data/Gemfile +3 -3
- data/History.txt +28 -0
- data/README.md +3 -3
- data/Rakefile +24 -23
- data/bin/check_artikelstamm +11 -11
- data/bin/compare_v5 +23 -23
- data/bin/oddb2xml +14 -13
- data/lib/oddb2xml.rb +1 -1
- data/lib/oddb2xml/builder.rb +1075 -1048
- data/lib/oddb2xml/calc.rb +232 -233
- data/lib/oddb2xml/chapter_70_hack.rb +38 -32
- data/lib/oddb2xml/cli.rb +252 -235
- data/lib/oddb2xml/compare.rb +70 -59
- data/lib/oddb2xml/compositions_syntax.rb +448 -430
- data/lib/oddb2xml/compressor.rb +20 -20
- data/lib/oddb2xml/downloader.rb +156 -128
- data/lib/oddb2xml/extractor.rb +295 -302
- data/lib/oddb2xml/options.rb +34 -35
- data/lib/oddb2xml/parslet_compositions.rb +263 -269
- data/lib/oddb2xml/semantic_check.rb +39 -33
- data/lib/oddb2xml/util.rb +166 -164
- data/lib/oddb2xml/version.rb +1 -1
- data/lib/oddb2xml/xml_definitions.rb +32 -33
- data/oddb2xml.gemspec +32 -31
- data/spec/artikelstamm_spec.rb +116 -135
- data/spec/builder_spec.rb +495 -524
- data/spec/calc_spec.rb +552 -593
- data/spec/check_artikelstamm_spec.rb +26 -26
- data/spec/cli_spec.rb +173 -174
- data/spec/compare_spec.rb +9 -11
- data/spec/composition_syntax_spec.rb +390 -409
- data/spec/compressor_spec.rb +48 -48
- data/spec/data/refdata_NonPharma.xml +0 -3
- data/spec/data/refdata_Pharma.xml +0 -26
- data/spec/data/transfer.dat +1 -0
- data/spec/data/varia_De.htm +2 -2
- data/spec/data_helper.rb +47 -49
- data/spec/downloader_spec.rb +251 -260
- data/spec/extractor_spec.rb +172 -164
- data/spec/galenic_spec.rb +233 -256
- data/spec/options_spec.rb +116 -119
- data/spec/parslet_spec.rb +833 -861
- data/spec/spec_helper.rb +153 -153
- data/test_options.rb +39 -42
- data/tools/win_fetch_cacerts.rb +2 -3
- metadata +48 -5
- data/.travis.yml +0 -29
data/lib/oddb2xml/options.rb
CHANGED
@@ -1,61 +1,60 @@
|
|
1
|
-
|
2
|
-
require
|
3
|
-
require 'oddb2xml/version'
|
1
|
+
require "optimist"
|
2
|
+
require "oddb2xml/version"
|
4
3
|
|
5
4
|
module Oddb2xml
|
6
5
|
module Options
|
7
|
-
def self.parse(args =ARGV)
|
6
|
+
def self.parse(args = ARGV)
|
8
7
|
if args.is_a?(String)
|
9
|
-
args = args.split(
|
8
|
+
args = args.split(" ")
|
10
9
|
end
|
11
10
|
|
12
|
-
@opts = Optimist
|
13
|
-
version "
|
11
|
+
@opts = Optimist.options(args) do
|
12
|
+
version "#{$0} ver.#{Oddb2xml::VERSION}"
|
14
13
|
banner <<-EOS
|
15
14
|
#{File.expand_path($0)} version #{Oddb2xml::VERSION}
|
16
15
|
Usage:
|
17
16
|
oddb2xml [option]
|
18
17
|
produced files are found under data
|
19
|
-
EOS
|
20
|
-
opt :append,
|
18
|
+
EOS
|
19
|
+
opt :append, "Additional target nonpharma", default: false
|
21
20
|
opt :artikelstamm, "Create Artikelstamm Version 3 and 5 for Elexis >= 3.1"
|
22
|
-
opt :compress_ext,
|
23
|
-
opt :extended,
|
21
|
+
opt :compress_ext, "format F. {tar.gz|zip}", type: :string, default: nil, short: "c"
|
22
|
+
opt :extended, "pharma, non-pharma plus prices and non-pharma from zurrose.
|
24
23
|
Products without EAN-Code will also be listed.
|
25
24
|
File oddb_calc.xml will also be generated"
|
26
|
-
opt :format,
|
27
|
-
If F is given, -o option is ignored.", :
|
28
|
-
opt :include,
|
29
|
-
'xml' format includes always ean14 records.", :
|
30
|
-
opt :increment,
|
25
|
+
opt :format, "File format F, default is xml. {xml|dat}
|
26
|
+
If F is given, -o option is ignored.", type: :string, default: "xml"
|
27
|
+
opt :include, "Include target option for ean14 for 'dat' format.
|
28
|
+
'xml' format includes always ean14 records.", short: "i"
|
29
|
+
opt :increment, "Increment price by x percent. Forces -f dat -p zurrose.
|
31
30
|
create additional field price_resellerpub as
|
32
31
|
price_extfactory incremented by x percent (rounded to the next 0.05 francs)
|
33
32
|
in oddb_article.xml. In generated zurrose_transfer.dat PRPU is set to this price
|
34
|
-
Forces -f dat -p zurrose.", :
|
35
|
-
opt :fi,
|
36
|
-
opt :price,
|
37
|
-
opt :tag_suffix,
|
38
|
-
If S is given, it is also used as prefix of filename.", :
|
39
|
-
opt :context,
|
40
|
-
opt :calc,
|
33
|
+
Forces -f dat -p zurrose.", type: :int, default: nil, short: "I"
|
34
|
+
opt :fi, "Optional fachinfo output.", short: "o"
|
35
|
+
opt :price, "Price source (transfer.dat) from ZurRose", default: nil
|
36
|
+
opt :tag_suffix, "XML tag suffix S. Default is none. [A-z0-9]
|
37
|
+
If S is given, it is also used as prefix of filename.", type: :string, short: "t"
|
38
|
+
opt :context, "{product|address}. product is default.", default: "product", type: :string, short: "x"
|
39
|
+
opt :calc, "create only oddb_calc.xml with GTIN, name and galenic information"
|
41
40
|
|
42
41
|
opt :skip_download, "skips downloading files it the file is already under downloads.
|
43
42
|
Downloaded files are saved under downloads"
|
44
|
-
opt :log,
|
45
|
-
opt :use_ra11zip,
|
46
|
-
|
43
|
+
opt :log, "log important actions", short: :none
|
44
|
+
opt :use_ra11zip, "Use the ra11.zip (a zipped transfer.dat from Galexis)",
|
45
|
+
default: File.exist?("ra11.zip") ? "ra11.zip" : nil, type: :string
|
47
46
|
end
|
48
|
-
|
47
|
+
|
49
48
|
@opts[:percent] = @opts[:increment]
|
50
|
-
if @opts[:increment]
|
49
|
+
if @opts[:increment]
|
51
50
|
@opts[:nonpharma] = true
|
52
51
|
@opts[:price] = :zurrose
|
53
52
|
end
|
54
|
-
@opts[:ean14]
|
53
|
+
@opts[:ean14] = @opts[:increment]
|
55
54
|
@opts.delete(:increment)
|
56
55
|
@opts[:nonpharma] = @opts[:append]
|
57
56
|
@opts.delete(:append)
|
58
|
-
if @opts[:extended]
|
57
|
+
if @opts[:extended]
|
59
58
|
@opts[:nonpharma] = true
|
60
59
|
@opts[:price] = :zurrose
|
61
60
|
@opts[:calc] = true
|
@@ -63,22 +62,22 @@ EOS
|
|
63
62
|
if @opts[:artikelstamm]
|
64
63
|
@opts[:extended] = true
|
65
64
|
@opts[:price] = :zurrose
|
66
|
-
end
|
65
|
+
end
|
67
66
|
@opts[:price] = :zurrose if @opts[:price].is_a?(TrueClass)
|
68
|
-
@opts[:price]
|
67
|
+
@opts[:price] = @opts[:price].to_sym if @opts[:price]
|
69
68
|
@opts[:ean14] = @opts[:include]
|
70
69
|
@opts[:format] = @opts[:format].to_sym if @opts[:format]
|
71
70
|
@opts.delete(:include)
|
72
71
|
@opts.delete(:help)
|
73
72
|
@opts.delete(:version)
|
74
73
|
|
75
|
-
@opts[:address]
|
76
|
-
@opts[:address]
|
74
|
+
@opts[:address] = false
|
75
|
+
@opts[:address] = true if /^addr(ess)*$/i.match?(@opts[:context])
|
77
76
|
@opts.delete(:context)
|
78
77
|
|
79
78
|
@opts.delete(:price) unless @opts[:price]
|
80
79
|
|
81
|
-
@opts.each{|k,v| @opts.delete(k) if /_given$/.match(k.to_s)}
|
80
|
+
@opts.each { |k, v| @opts.delete(k) if /_given$/.match?(k.to_s) }
|
82
81
|
end
|
83
82
|
end
|
84
83
|
end
|
@@ -1,79 +1,74 @@
|
|
1
|
-
# encoding: utf-8
|
2
|
-
|
3
1
|
# This file is shared since oddb2xml 2.0.0 (lib/oddb2xml/parse_compositions.rb)
|
4
2
|
# with oddb.org src/plugin/parse_compositions.rb
|
5
3
|
#
|
6
4
|
# It allows an easy parsing of the column P Zusammensetzung of the swissmedic packages.xlsx file
|
7
5
|
#
|
8
6
|
|
9
|
-
require
|
10
|
-
require
|
11
|
-
require
|
12
|
-
include Parslet
|
7
|
+
require "parslet"
|
8
|
+
require "parslet/convenience"
|
9
|
+
require "oddb2xml/compositions_syntax"
|
13
10
|
VERBOSE_MESSAGES ||= false
|
14
11
|
|
15
12
|
module ParseUtil
|
13
|
+
include Parslet
|
16
14
|
# this class is responsible to patch errors in swissmedic entries after
|
17
15
|
# oddb.org detected them, as it takes sometimes a few days (or more) till they get corrected
|
18
16
|
# Reports the number of occurrences of each entry
|
19
17
|
@@saved_parsed ||= {}
|
20
|
-
@@nr_saved_parsed_used
|
18
|
+
@@nr_saved_parsed_used ||= 0
|
21
19
|
|
22
20
|
class HandleSwissmedicErrors
|
23
|
-
|
24
21
|
attr_accessor :nrParsingErrors
|
25
|
-
class ErrorEntry
|
22
|
+
class ErrorEntry < Struct.new("ErrorEntry", :pattern, :replacement, :nr_occurrences)
|
26
23
|
end
|
27
24
|
|
28
25
|
def reset_errors
|
29
26
|
@errors = []
|
30
|
-
@
|
31
|
-
@
|
27
|
+
@nr_lines = 0
|
28
|
+
@nr_parsing_errors = 0
|
32
29
|
end
|
33
30
|
|
34
31
|
# error_entries should be a hash of pattern, replacement
|
35
32
|
def initialize(error_entries)
|
36
33
|
reset_errors
|
37
|
-
error_entries.each{ |pattern, replacement| @errors << ErrorEntry.new(pattern, replacement, 0) }
|
34
|
+
error_entries.each { |pattern, replacement| @errors << ErrorEntry.new(pattern, replacement, 0) }
|
38
35
|
end
|
39
36
|
|
40
37
|
def report
|
41
|
-
s = ["Report of changed compositions in #{@
|
42
|
-
@errors.each {
|
43
|
-
|
44
|
-
s << " replaced #{entry.nr_occurrences} times '#{entry.pattern}' by '#{entry.replacement}'"
|
38
|
+
s = ["Report of changed compositions in #{@nr_lines} lines. Had #{@nr_parsing_errors} parsing errors"]
|
39
|
+
@errors.each { |entry|
|
40
|
+
s << " replaced #{entry.nr_occurrences} times '#{entry.pattern}' by '#{entry.replacement}'"
|
45
41
|
}
|
46
42
|
s
|
47
43
|
end
|
48
44
|
|
49
45
|
def apply_fixes(string)
|
50
46
|
result = string.clone
|
51
|
-
@errors.each{
|
52
|
-
|entry|
|
47
|
+
@errors.each { |entry|
|
53
48
|
intermediate = result.clone
|
54
|
-
result = result.gsub(entry.pattern,
|
49
|
+
result = result.gsub(entry.pattern, entry.replacement)
|
55
50
|
unless result.eql?(intermediate)
|
56
|
-
|
57
|
-
|
51
|
+
entry.nr_occurrences += 1
|
52
|
+
puts "#{File.basename(__FILE__)}:#{__LINE__}: fixed \nbefore: #{intermediate}\nafter: #{result}" if $VERBOSE
|
58
53
|
end
|
59
54
|
}
|
60
|
-
@
|
55
|
+
@nr_lines += 1
|
61
56
|
result
|
62
57
|
end
|
63
58
|
# hepar sulfuris D6 2,2 mg hypericum perforatum D2 0,66 mg where itlacks a comma and should be hepar sulfuris D6 2,2 mg, hypericum perforatum D2 0,66 mg
|
64
59
|
end
|
65
60
|
|
66
|
-
def
|
67
|
-
string.split(/\s+/u).collect { |word| word.capitalize }.join(
|
61
|
+
def self.capitalize(string)
|
62
|
+
string.split(/\s+/u).collect { |word| word.capitalize }.join(" ").strip
|
68
63
|
end
|
69
64
|
|
70
|
-
def
|
65
|
+
def self.nr_saved_parsed_used
|
71
66
|
@@nr_saved_parsed_used
|
72
67
|
end
|
73
68
|
|
74
|
-
def
|
75
|
-
active_agents = active_agents_string ? active_agents_string.
|
76
|
-
key = [
|
69
|
+
def self.parse_compositions(composition_text, active_agents_string = "")
|
70
|
+
active_agents = active_agents_string ? active_agents_string.delete("[").downcase.split(/,\s+/) : []
|
71
|
+
key = [composition_text, active_agents]
|
77
72
|
saved_value = @@saved_parsed[key]
|
78
73
|
if saved_value
|
79
74
|
@@nr_saved_parsed_used += 1
|
@@ -81,20 +76,22 @@ module ParseUtil
|
|
81
76
|
end
|
82
77
|
comps = []
|
83
78
|
lines = composition_text.gsub(/\r\n?/u, "\n").split(/\n/u)
|
84
|
-
lines.select do
|
85
|
-
|
86
|
-
composition = ParseComposition.from_string(line)
|
79
|
+
lines.select do |line|
|
80
|
+
composition = ParseComposition.from_string(line)
|
87
81
|
if composition.is_a?(ParseComposition)
|
88
|
-
composition.substances.each do
|
89
|
-
|
90
|
-
|
91
|
-
|
92
|
-
|
93
|
-
|
94
|
-
|
95
|
-
|
96
|
-
|
97
|
-
|
82
|
+
composition.substances.each do |substance_item|
|
83
|
+
active_substance_name = substance_item.name.downcase.sub(/^cum\s/, "")
|
84
|
+
substance_item.is_active_agent = !active_agents.find { |x|
|
85
|
+
/#{x.downcase
|
86
|
+
.gsub('(', '\(')
|
87
|
+
.gsub(')', '\)')
|
88
|
+
.gsub('[', '\[')
|
89
|
+
.gsub(']', '\]')
|
90
|
+
}($|\s)/
|
91
|
+
.match(active_substance_name)
|
92
|
+
}.nil?
|
93
|
+
substance_item.is_active_agent = true if substance_item.chemical_substance && active_agents.find { |x| x.downcase.eql?(substance_item.chemical_substance.name.downcase) }
|
94
|
+
end
|
98
95
|
comps << composition
|
99
96
|
end
|
100
97
|
end
|
@@ -103,202 +100,194 @@ module ParseUtil
|
|
103
100
|
comps
|
104
101
|
rescue => error
|
105
102
|
puts "error #{error}"
|
106
|
-
|
103
|
+
# binding.pry
|
107
104
|
end
|
108
|
-
|
109
105
|
end
|
110
106
|
|
111
|
-
class IntLit
|
112
|
-
def eval
|
107
|
+
class IntLit < Struct.new(:int)
|
108
|
+
def eval
|
109
|
+
int.to_i
|
110
|
+
end
|
113
111
|
end
|
114
|
-
|
115
|
-
|
112
|
+
|
113
|
+
class QtyLit < Struct.new(:qty)
|
114
|
+
def eval
|
115
|
+
qty.to_i
|
116
|
+
end
|
116
117
|
end
|
117
118
|
|
118
119
|
class CompositionTransformer < Parslet::Transform
|
119
120
|
@@more_info = nil
|
120
|
-
def
|
121
|
+
def self.get_ratio(parse_info)
|
121
122
|
if parse_info[:ratio]
|
122
|
-
if parse_info[:ratio].to_s.length > 0
|
123
|
-
parse_info[:ratio].to_s.sub(/^,\s+/,
|
124
|
-
else
|
125
|
-
nil
|
123
|
+
if (parse_info[:ratio].to_s.length > 0) && (parse_info[:ratio].to_s != ", ")
|
124
|
+
parse_info[:ratio].to_s.sub(/^,\s+/, "").sub(/,\s+$/, "")
|
126
125
|
end
|
127
|
-
else
|
128
|
-
nil
|
129
126
|
end
|
130
127
|
end
|
131
128
|
|
132
|
-
def
|
133
|
-
return unless /^E \d\d\d/.match(substance.name)
|
129
|
+
def self.check_e_substance(substance)
|
130
|
+
return unless /^E \d\d\d/.match?(substance.name)
|
134
131
|
unless substance.more_info
|
135
132
|
case substance.name[2]
|
136
133
|
when "1"
|
137
|
-
substance.more_info =
|
134
|
+
substance.more_info = "color."
|
138
135
|
when "2"
|
139
|
-
substance.more_info =
|
140
|
-
else
|
136
|
+
substance.more_info = "conserv."
|
141
137
|
end
|
142
138
|
substance.more_info ||= @@more_info
|
143
139
|
end
|
144
140
|
@@more_info = substance.more_info
|
145
141
|
end
|
146
142
|
|
147
|
-
def
|
148
|
-
@@more_info
|
149
|
-
@@excipiens
|
150
|
-
@@excipiens.dose
|
143
|
+
def self.add_excipiens(info)
|
144
|
+
@@more_info = nil
|
145
|
+
@@excipiens = ParseSubstance.new(info[:excipiens_description] || "Excipiens")
|
146
|
+
@@excipiens.dose = info[:dose] if info[:dose]
|
151
147
|
@@excipiens.more_info = CompositionTransformer.get_ratio(info)
|
152
|
-
@@excipiens.cdose
|
148
|
+
@@excipiens.cdose = info[:dose_corresp] if info[:dose_corresp]
|
153
149
|
@@excipiens.more_info = info[:more_info] if info[:more_info]
|
154
150
|
end
|
155
151
|
|
156
|
-
rule(:
|
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|
-
|
158
|
-
|
159
|
-
puts "#{File.basename(__FILE__)}:#{__LINE__}: dictionary #{dictionary}" if VERBOSE_MESSAGES
|
160
|
-
@@corresp = dictionary[:corresp].to_s
|
152
|
+
rule(corresp: simple(:corresp)) { |dictionary|
|
153
|
+
puts "#{File.basename(__FILE__)}:#{__LINE__}: dictionary #{dictionary}" if VERBOSE_MESSAGES
|
154
|
+
@@corresp = dictionary[:corresp].to_s
|
161
155
|
}
|
162
|
-
rule(
|
163
|
-
|
164
|
-
|
165
|
-
|
166
|
-
|
167
|
-
|
168
|
-
|
169
|
-
@@substances << substance
|
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|
-
substance
|
156
|
+
rule(substance_name: simple(:substance_name),
|
157
|
+
dose: simple(:dose)) { |dictionary|
|
158
|
+
puts "#{File.basename(__FILE__)}:#{__LINE__}: dictionary #{dictionary}" if VERBOSE_MESSAGES
|
159
|
+
dose = dictionary[:dose].is_a?(ParseDose) ? dictionary[:dose] : nil
|
160
|
+
substance = ParseSubstance.new(dictionary[:substance_name], dose)
|
161
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+
@@substances << substance
|
162
|
+
substance
|
171
163
|
}
|
172
164
|
|
173
|
-
rule(
|
174
|
-
|
175
|
-
|
176
|
-
puts "#{File.basename(__FILE__)}:#{__LINE__}: dictionary #{dictionary}" if VERBOSE_MESSAGES
|
177
|
-
@@corresp = dictionary[:more_info].to_s.strip.sub(/:$/, '')
|
165
|
+
rule(more_info: simple(:more_info)) { |dictionary|
|
166
|
+
puts "#{File.basename(__FILE__)}:#{__LINE__}: dictionary #{dictionary}" if VERBOSE_MESSAGES
|
167
|
+
@@corresp = dictionary[:more_info].to_s.strip.sub(/:$/, "")
|
178
168
|
}
|
179
|
-
rule(
|
180
|
-
|
181
|
-
|
182
|
-
|
183
|
-
|
184
|
-
|
185
|
-
|
186
|
-
|
187
|
-
|
188
|
-
|
189
|
-
@@substances << substance
|
190
|
-
substance
|
169
|
+
rule(more_info: simple(:more_info),
|
170
|
+
substance_name: simple(:substance_name),
|
171
|
+
dose: simple(:dose)) { |dictionary|
|
172
|
+
puts "#{File.basename(__FILE__)}:#{__LINE__}: dictionary #{dictionary}" if VERBOSE_MESSAGES
|
173
|
+
dose = dictionary[:dose].is_a?(ParseDose) ? dictionary[:dose] : nil
|
174
|
+
substance = ParseSubstance.new(dictionary[:substance_name].to_s, dose)
|
175
|
+
substance.more_info = dictionary[:more_info].to_s.strip.sub(/:$/, "") if dictionary[:more_info] && (dictionary[:more_info].to_s.length > 0)
|
176
|
+
CompositionTransformer.check_e_substance(substance)
|
177
|
+
@@substances << substance
|
178
|
+
substance
|
191
179
|
}
|
192
180
|
|
193
|
-
rule(:
|
194
|
-
:
|
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|
-
:
|
196
|
-
|
197
|
-
|
198
|
-
|
199
|
-
|
200
|
-
|
201
|
-
|
202
|
-
substance
|
181
|
+
rule(lebensmittel_zusatz: simple(:lebensmittel_zusatz),
|
182
|
+
more_info: simple(:more_info),
|
183
|
+
digits: simple(:digits)) { |dictionary|
|
184
|
+
puts "#{File.basename(__FILE__)}:#{__LINE__}: dictionary #{dictionary}" if VERBOSE_MESSAGES
|
185
|
+
substance = ParseSubstance.new("#{dictionary[:lebensmittel_zusatz]} #{dictionary[:digits]}")
|
186
|
+
substance.more_info = dictionary[:more_info].to_s.strip.sub(/:$/, "") if dictionary[:more_info] && (dictionary[:more_info].to_s.length > 0)
|
187
|
+
CompositionTransformer.check_e_substance(substance)
|
188
|
+
@@substances << substance
|
189
|
+
substance
|
203
190
|
}
|
204
|
-
rule(:
|
205
|
-
|
206
|
-
|
207
|
-
|
208
|
-
|
209
|
-
|
210
|
-
|
211
|
-
|
212
|
-
|
213
|
-
|
214
|
-
|
215
|
-
|
216
|
-
end
|
217
|
-
nil
|
191
|
+
rule(excipiens: subtree(:excipiens)) { |dictionary|
|
192
|
+
puts "#{File.basename(__FILE__)}:#{__LINE__}: dictionary #{dictionary}" if VERBOSE_MESSAGES
|
193
|
+
info = dictionary[:excipiens].is_a?(Hash) ? dictionary[:excipiens] : dictionary[:excipiens].first
|
194
|
+
if info[:excipiens_description] ||
|
195
|
+
info[:dose] ||
|
196
|
+
info[:dose_corresp] ||
|
197
|
+
info[:more_info] ||
|
198
|
+
CompositionTransformer.get_ratio(dictionary)
|
199
|
+
CompositionTransformer.add_excipiens(info)
|
200
|
+
info
|
201
|
+
end
|
202
|
+
nil
|
218
203
|
}
|
219
|
-
rule(:
|
220
|
-
|
221
|
-
|
222
|
-
|
223
|
-
|
224
|
-
|
225
|
-
|
226
|
-
|
227
|
-
|
228
|
-
:
|
229
|
-
|
230
|
-
|
231
|
-
|
232
|
-
|
233
|
-
|
234
|
-
|
235
|
-
|
236
|
-
|
237
|
-
|
238
|
-
|
239
|
-
|
240
|
-
|
241
|
-
|
242
|
-
|
243
|
-
|
244
|
-
|
245
|
-
|
246
|
-
|
247
|
-
|
248
|
-
|
249
|
-
dictionary[:substance].salts << dictionary[:substance_ut].last
|
250
|
-
@@substances -= dictionary[:substance_ut]
|
251
|
-
end
|
252
|
-
dictionary[:substance]
|
204
|
+
rule(composition: subtree(:composition)) { |dictionary|
|
205
|
+
puts "#{File.basename(__FILE__)}:#{__LINE__}: dictionary #{dictionary}" if VERBOSE_MESSAGES
|
206
|
+
info = dictionary[:composition].is_a?(Hash) ? dictionary[:composition] : dictionary[:composition].first
|
207
|
+
CompositionTransformer.add_excipiens(info) if info.is_a?(Hash)
|
208
|
+
info
|
209
|
+
}
|
210
|
+
rule(substance: simple(:substance),
|
211
|
+
chemical_substance: simple(:chemical_substance),
|
212
|
+
substance_ut: sequence(:substance_ut),
|
213
|
+
ratio: simple(:ratio)) { |dictionary|
|
214
|
+
puts "#{File.basename(__FILE__)}:#{__LINE__}: dictionary #{dictionary}" if VERBOSE_MESSAGES
|
215
|
+
ratio = CompositionTransformer.get_ratio(dictionary)
|
216
|
+
if ratio && (ratio.length > 0)
|
217
|
+
if dictionary[:substance].more_info
|
218
|
+
dictionary[:substance].more_info += " " + ratio.strip
|
219
|
+
else
|
220
|
+
dictionary[:substance].more_info = ratio.strip
|
221
|
+
end
|
222
|
+
end
|
223
|
+
if dictionary[:chemical_substance]
|
224
|
+
dictionary[:substance].chemical_substance = dictionary[:chemical_substance]
|
225
|
+
@@substances -= [dictionary[:chemical_substance]]
|
226
|
+
end
|
227
|
+
if dictionary[:substance_ut].size > 0
|
228
|
+
dictionary[:substance].salts += dictionary[:substance_ut].last.salts
|
229
|
+
dictionary[:substance_ut].last.salts = []
|
230
|
+
dictionary[:substance].salts << dictionary[:substance_ut].last
|
231
|
+
@@substances -= dictionary[:substance_ut]
|
232
|
+
end
|
233
|
+
dictionary[:substance]
|
253
234
|
}
|
254
235
|
|
255
|
-
rule(:
|
256
|
-
rule(:
|
257
|
-
|
236
|
+
rule(int: simple(:int)) { IntLit.new(int) }
|
237
|
+
rule(number: simple(:nb)) {
|
238
|
+
/[eE.]/.match?(nb) ? Float(nb) : Integer(nb)
|
258
239
|
}
|
259
240
|
rule(
|
260
|
-
:
|
261
|
-
:
|
262
|
-
|
263
|
-
|
241
|
+
qty_range: simple(:qty_range),
|
242
|
+
unit: simple(:unit)
|
243
|
+
) {
|
244
|
+
ParseDose.new(qty_range, unit)
|
245
|
+
}
|
264
246
|
rule(
|
265
|
-
:
|
266
|
-
|
267
|
-
|
247
|
+
qty_range: simple(:qty_range)
|
248
|
+
) {
|
249
|
+
ParseDose.new(qty_range)
|
250
|
+
}
|
268
251
|
rule(
|
269
|
-
:
|
270
|
-
:
|
271
|
-
|
272
|
-
|
252
|
+
qty: simple(:qty),
|
253
|
+
unit: simple(:unit)
|
254
|
+
) {
|
255
|
+
ParseDose.new(qty, unit)
|
256
|
+
}
|
273
257
|
rule(
|
274
|
-
:
|
258
|
+
unit: simple(:unit)
|
259
|
+
) { ParseDose.new(nil, unit) }
|
275
260
|
rule(
|
276
|
-
:
|
261
|
+
qty: simple(:qty)
|
262
|
+
) { ParseDose.new(qty, nil) }
|
277
263
|
rule(
|
278
|
-
:
|
279
|
-
:
|
280
|
-
:
|
281
|
-
)
|
264
|
+
qty: simple(:qty),
|
265
|
+
unit: simple(:unit),
|
266
|
+
dose_right: simple(:dose_right)
|
267
|
+
) {
|
282
268
|
dose = ParseDose.new(qty, unit)
|
283
|
-
dose.unit = dose.unit.to_s +
|
269
|
+
dose.unit = dose.unit.to_s + " et " + ParseDose.new(dose_right).to_s
|
284
270
|
dose
|
285
271
|
}
|
286
272
|
|
287
273
|
@@substances ||= []
|
288
|
-
@@excipiens
|
289
|
-
def
|
290
|
-
@@more_info
|
274
|
+
@@excipiens = nil
|
275
|
+
def self.clear_substances
|
276
|
+
@@more_info = nil
|
291
277
|
@@substances = []
|
292
|
-
@@excipiens
|
293
|
-
@@corresp
|
278
|
+
@@excipiens = nil
|
279
|
+
@@corresp = nil
|
294
280
|
end
|
295
|
-
|
281
|
+
|
282
|
+
def self.substances
|
296
283
|
@@substances.clone
|
297
284
|
end
|
298
|
-
|
285
|
+
|
286
|
+
def self.excipiens
|
299
287
|
@@excipiens ? @@excipiens.clone : nil
|
300
288
|
end
|
301
|
-
|
289
|
+
|
290
|
+
def self.corresp
|
302
291
|
@@corresp ? @@corresp.clone : nil
|
303
292
|
end
|
304
293
|
end
|
@@ -306,29 +295,31 @@ end
|
|
306
295
|
class ParseDose
|
307
296
|
attr_reader :qty, :qty_range
|
308
297
|
attr_accessor :unit
|
309
|
-
def initialize(qty=nil, unit=nil)
|
298
|
+
def initialize(qty = nil, unit = nil)
|
310
299
|
puts "ParseDose.new from #{qty.inspect} #{unit.inspect} #{unit.inspect}" if VERBOSE_MESSAGES
|
311
|
-
if qty
|
312
|
-
string = qty.to_s.
|
313
|
-
if string.index(
|
300
|
+
if qty && (qty.is_a?(String) || qty.is_a?(Parslet::Slice))
|
301
|
+
string = qty.to_s.delete("'")
|
302
|
+
if string.index("-") && (string.index("-") > 0)
|
314
303
|
@qty_range = string
|
315
304
|
elsif string.index(/\^|\*|\//)
|
316
|
-
@qty
|
305
|
+
@qty = string
|
317
306
|
else
|
318
|
-
@qty
|
307
|
+
@qty = string.index(".") ? string.to_f : string.to_i
|
319
308
|
end
|
320
309
|
elsif qty
|
321
|
-
@qty
|
310
|
+
@qty = qty.eval
|
322
311
|
else
|
323
312
|
@qty = 1
|
324
313
|
end
|
325
314
|
@unit = unit ? unit.to_s : nil
|
326
315
|
end
|
316
|
+
|
327
317
|
def eval
|
328
318
|
self
|
329
319
|
end
|
320
|
+
|
330
321
|
def to_s
|
331
|
-
return @unit unless @qty
|
322
|
+
return @unit unless @qty || @qty_range
|
332
323
|
res = "#{@qty}#{@qty_range}"
|
333
324
|
res = "#{res} #{@unit}" if @unit
|
334
325
|
res
|
@@ -336,32 +327,36 @@ class ParseDose
|
|
336
327
|
end
|
337
328
|
|
338
329
|
class ParseSubstance
|
339
|
-
attr_accessor
|
340
|
-
attr_accessor
|
341
|
-
|
330
|
+
attr_accessor :name, :chemical_substance, :chemical_qty, :chemical_unit, :is_active_agent, :dose, :cdose, :is_excipiens
|
331
|
+
attr_accessor :description, :more_info, :salts
|
332
|
+
attr_writer :unit, :qty
|
333
|
+
def initialize(name, dose = nil)
|
342
334
|
puts "ParseSubstance.new from #{name.inspect} #{dose.inspect}" if VERBOSE_MESSAGES
|
343
335
|
@name = ParseUtil.capitalize(name.to_s)
|
344
|
-
@name.sub!(/\baqua\b/i,
|
345
|
-
@name.sub!(/\bDER\b/i,
|
346
|
-
@name.sub!(/\bad pulverem\b/i,
|
347
|
-
@name.sub!(/\bad iniectabilia\b/i,
|
348
|
-
@name.sub!(/\bad suspensionem\b/i,
|
349
|
-
@name.sub!(/\bad solutionem\b/i,
|
350
|
-
@name.sub!(/\bpro compresso\b/i,
|
351
|
-
@name.sub!(/\bpro\b/i,
|
352
|
-
@name.sub!(/ Q\.S\. /i,
|
353
|
-
@name.sub!(/\s+\bpro$/i,
|
336
|
+
@name.sub!(/\baqua\b/i, "aqua")
|
337
|
+
@name.sub!(/\bDER\b/i, "DER")
|
338
|
+
@name.sub!(/\bad pulverem\b/i, "ad pulverem")
|
339
|
+
@name.sub!(/\bad iniectabilia\b/i, "ad iniectabilia")
|
340
|
+
@name.sub!(/\bad suspensionem\b/i, "ad suspensionem")
|
341
|
+
@name.sub!(/\bad solutionem\b/i, "ad solutionem")
|
342
|
+
@name.sub!(/\bpro compresso\b/i, "pro compresso")
|
343
|
+
@name.sub!(/\bpro\b/i, "pro")
|
344
|
+
@name.sub!(/ Q\.S\. /i, " q.s. ")
|
345
|
+
@name.sub!(/\s+\bpro$/i, "")
|
354
346
|
@dose = dose if dose
|
355
347
|
@salts = []
|
356
348
|
end
|
349
|
+
|
357
350
|
def qty
|
358
|
-
return @dose.qty_range if @dose
|
351
|
+
return @dose.qty_range if @dose&.qty_range
|
359
352
|
@dose ? @dose.qty : @qty
|
360
353
|
end
|
354
|
+
|
361
355
|
def unit
|
362
356
|
return @unit if @unit
|
363
357
|
@dose ? @dose.unit : @unit
|
364
358
|
end
|
359
|
+
|
365
360
|
def to_string
|
366
361
|
s = "#{@name}:"
|
367
362
|
s = " #{@qty}" if @qty
|
@@ -372,51 +367,54 @@ class ParseSubstance
|
|
372
367
|
end
|
373
368
|
|
374
369
|
class ParseComposition
|
375
|
-
attr_accessor
|
376
|
-
|
377
|
-
|
378
|
-
|
379
|
-
|
380
|
-
|
381
|
-
|
382
|
-
|
383
|
-
|
384
|
-
|
385
|
-
|
386
|
-
|
387
|
-
|
388
|
-
|
389
|
-
|
390
|
-
|
391
|
-
|
392
|
-
|
393
|
-
|
370
|
+
attr_accessor :source, :label, :label_description, :substances, :galenic_form, :route_of_administration,
|
371
|
+
:corresp, :excipiens
|
372
|
+
|
373
|
+
ERRORS_TO_FIX = {
|
374
|
+
/(\d+)\s+-\s*(\d+)/ => '\1-\2',
|
375
|
+
"o.1" => "0.1",
|
376
|
+
/\s+(mg|g) DER:/ => ' \1, DER:',
|
377
|
+
" mind. " => " min. ",
|
378
|
+
" streptococci pyogen. " => " streptococci pyogen ",
|
379
|
+
" ut excipiens" => ", excipiens",
|
380
|
+
" Corresp. " => " corresp. ",
|
381
|
+
",," => ",",
|
382
|
+
"avena elatior,dactylis glomerata" => "avena elatior, dactylis glomerata",
|
383
|
+
" color.: corresp. " => " corresp.",
|
384
|
+
/ U\.: (excipiens) / => ' U. \1 ',
|
385
|
+
/ U\.: (alnus|betula|betula|betulae) / => ' U., \1 ',
|
386
|
+
/^(acari allergeni extractum (\(acarus siro\)|).+\s+U\.:)/ => 'A): \1',
|
387
|
+
"Solvens: alprostadilum" => "alprostadilum"
|
388
|
+
}
|
389
|
+
@@error_handler = ParseUtil::HandleSwissmedicErrors.new(ERRORS_TO_FIX)
|
394
390
|
|
395
391
|
def initialize(source)
|
396
392
|
@substances ||= []
|
397
393
|
puts "ParseComposition.new from #{source.inspect} @substances #{@substances.inspect}" if VERBOSE_MESSAGES
|
398
394
|
@source = source.to_s
|
399
395
|
end
|
400
|
-
|
401
|
-
|
396
|
+
|
397
|
+
def self.reset
|
398
|
+
@@error_handler = ParseUtil::HandleSwissmedicErrors.new(ERRORS_TO_FIX)
|
402
399
|
end
|
403
|
-
|
404
|
-
|
400
|
+
|
401
|
+
def self.report
|
402
|
+
@@error_handler.report
|
405
403
|
end
|
406
|
-
|
407
|
-
|
408
|
-
|
404
|
+
|
405
|
+
def self.from_string(string)
|
406
|
+
return nil if string.nil? || string.eql?(".") || string.eql?("")
|
407
|
+
stripped = string.gsub(/^"|["\n]+$/, "")
|
409
408
|
return nil unless stripped
|
410
|
-
if /(U\.I\.|U\.)$/.match(stripped)
|
411
|
-
|
409
|
+
cleaned = if /(U\.I\.|U\.)$/.match?(stripped)
|
410
|
+
stripped
|
412
411
|
else
|
413
|
-
|
412
|
+
stripped.sub(/\.+$/, "")
|
414
413
|
end
|
415
|
-
value = nil
|
416
414
|
puts "ParseComposition.from_string #{string}" if VERBOSE_MESSAGES # /ng-tr/.match(Socket.gethostbyname(Socket.gethostname).first)
|
417
415
|
|
418
|
-
cleaned = @@
|
419
|
-
puts "ParseComposition.new cleaned #{cleaned}" if VERBOSE_MESSAGES
|
416
|
+
cleaned = @@error_handler.apply_fixes(cleaned)
|
417
|
+
puts "ParseComposition.new cleaned #{cleaned}" if VERBOSE_MESSAGES && !cleaned.eql?(stripped)
|
420
418
|
CompositionTransformer.clear_substances
|
421
419
|
result = ParseComposition.new(cleaned)
|
422
420
|
parser = CompositionParser.new
|
@@ -430,8 +428,8 @@ class ParseComposition
|
|
430
428
|
ast = transf.apply(parser.parse(cleaned))
|
431
429
|
end
|
432
430
|
rescue Parslet::ParseFailed => error
|
433
|
-
@@
|
434
|
-
puts "#{File.basename(__FILE__)}:#{__LINE__}: failed parsing ==> #{cleaned}"
|
431
|
+
@@error_handler.nrParsingErrors += 1
|
432
|
+
puts "#{File.basename(__FILE__)}:#{__LINE__}: failed parsing ==> #{cleaned} #{error}"
|
435
433
|
return nil
|
436
434
|
end
|
437
435
|
result.source = string
|
@@ -441,50 +439,46 @@ class ParseComposition
|
|
441
439
|
result.substances = CompositionTransformer.substances
|
442
440
|
result.excipiens = CompositionTransformer.excipiens
|
443
441
|
result.corresp = CompositionTransformer.corresp if CompositionTransformer.corresp
|
444
|
-
if result
|
445
|
-
pro_qty = "/#{result.excipiens.qty} #{result.excipiens.unit}".sub(/\/1\s+/,
|
446
|
-
result.substances.each {
|
447
|
-
|
448
|
-
|
449
|
-
|
450
|
-
substance.dose.unit = "#{substance.dose.unit}#{pro_qty}" if substance.unit and not substance.unit.eql?(result.excipiens.unit)
|
442
|
+
if result&.excipiens&.unit
|
443
|
+
pro_qty = "/#{result.excipiens.qty} #{result.excipiens.unit}".sub(/\/1\s+/, "/")
|
444
|
+
result.substances.each { |substance|
|
445
|
+
next unless substance.is_a?(ParseSubstance)
|
446
|
+
substance.chemical_substance.unit = "#{substance.chemical_substance.unit}#{pro_qty}" if substance.chemical_substance
|
447
|
+
substance.dose.unit = "#{substance.dose.unit}#{pro_qty}" if substance.unit && !substance.unit.eql?(result.excipiens.unit)
|
451
448
|
}
|
452
449
|
end
|
453
|
-
if ast.is_a?(Array)
|
450
|
+
if ast.is_a?(Array) && ast.first.is_a?(Hash)
|
454
451
|
label = ast.first[:label].to_s if ast.first[:label]
|
455
452
|
label_description = ast.first[:label_description].to_s if ast.first[:label_description]
|
456
|
-
elsif ast
|
457
|
-
label = ast[:label].to_s if
|
453
|
+
elsif ast&.is_a?(Hash)
|
454
|
+
label = ast[:label].to_s if ast[:label]
|
458
455
|
label_description = ast[:label_description].to_s if ast[:label_description]
|
459
456
|
end
|
460
457
|
if label
|
461
|
-
if label
|
462
|
-
result.label
|
458
|
+
if label && !/((A|B|C|D|E|I|II|III|IV|\)+)\s+et\s+(A|B|C|D|E|I|II|III|IV|\))+)/.match(label)
|
459
|
+
result.label = label
|
463
460
|
end
|
464
|
-
result.label_description = label_description.gsub(/:+$/,
|
461
|
+
result.label_description = label_description.gsub(/:+$/, "").strip if label_description
|
465
462
|
end
|
466
|
-
result.corresp = ast[:corresp].to_s.sub(/:\s+/,
|
467
|
-
|
463
|
+
result.corresp = ast[:corresp].to_s.sub(/:\s+/, "") if !result.corresp && ast.is_a?(Hash) && ast[:corresp]
|
464
|
+
result
|
468
465
|
end
|
469
466
|
end
|
470
467
|
|
471
468
|
class GalenicFormTransformer < CompositionTransformer
|
472
|
-
|
473
|
-
|
474
|
-
|
475
|
-
|
476
|
-
|
477
|
-
|
478
|
-
name = dictionary[:preparation_name] ? dictionary[:preparation_name].to_s : nil
|
479
|
-
form = dictionary[:galenic_form] ? dictionary[:galenic_form].to_s : nil
|
480
|
-
# name, form
|
469
|
+
rule(preparation_name: simple(:preparation_name),
|
470
|
+
galenic_form: simple(:preparation_name)) { |dictionary|
|
471
|
+
puts "#{File.basename(__FILE__)}:#{__LINE__}: dictionary #{dictionary}" if VERBOSE_MESSAGES
|
472
|
+
dictionary[:preparation_name] ? dictionary[:preparation_name].to_s : nil
|
473
|
+
dictionary[:galenic_form] ? dictionary[:galenic_form].to_s : nil
|
474
|
+
# name, form
|
481
475
|
}
|
482
476
|
end
|
483
477
|
|
484
478
|
class ParseGalenicForm
|
485
|
-
def
|
486
|
-
return nil if string
|
487
|
-
stripped = string.gsub(/^"|["\n]+$/,
|
479
|
+
def self.from_string(string)
|
480
|
+
return nil if string.nil?
|
481
|
+
stripped = string.gsub(/^"|["\n]+$/, "")
|
488
482
|
return nil unless stripped
|
489
483
|
puts "ParseGalenicForm.from_string #{string}" if VERBOSE_MESSAGES # /ng-tr/.match(Socket.gethostbyname(Socket.gethostname).first)
|
490
484
|
|
@@ -499,13 +493,13 @@ class ParseGalenicForm
|
|
499
493
|
ast = transf.apply(parser.parse(string))
|
500
494
|
end
|
501
495
|
rescue Parslet::ParseFailed => error
|
502
|
-
@@
|
503
|
-
puts "#{File.basename(__FILE__)}:#{__LINE__}: failed parsing ==> #{string}"
|
496
|
+
@@error_handler.nrParsingErrors += 1
|
497
|
+
puts "#{File.basename(__FILE__)}:#{__LINE__}: failed parsing ==> #{string} #{error}"
|
504
498
|
return nil
|
505
499
|
end
|
506
500
|
return [] unless ast
|
507
|
-
form = ast[:galenic_form] ? ast[:galenic_form].to_s.sub(/^\/\s+/,
|
501
|
+
form = ast[:galenic_form] ? ast[:galenic_form].to_s.sub(/^\/\s+/, "") : nil
|
508
502
|
name = ast[:prepation_name] ? ast[:prepation_name].to_s.strip : nil
|
509
|
-
|
503
|
+
[name, form]
|
510
504
|
end
|
511
505
|
end
|