Skip to content

Commit

Permalink
Fix import swissmedic by companies
Browse files Browse the repository at this point in the history
  • Loading branch information
@ngiger
ngiger committed Jul 16, 2013
1 parent 013a801 commit a296e4d
Show file tree
Hide file tree
Showing 4 changed files with 869 additions and 70 deletions.
4 changes: 2 additions & 2 deletions jobs/update_textinfo_swissmedicinfo
View file
Expand Up @@ -29,8 +29,8 @@ module ODDB
m = /xml_file=(\w.+)/.match(arg)
opts[:xml_file] = m[1]
opts[:download] = false
elsif arg =~ /^\d{5}$/
opts[:iksnrs] << arg
elsif arg =~ /^\d{3,5}$/
opts[:iksnrs] << sprintf('%05d', arg.to_i)
else arg =~ /^\w*$/
opts[:companies] << arg if arg.size > 0
end
Expand Down
124 changes: 79 additions & 45 deletions src/plugin/text_info.rb
View file
Expand Up @@ -426,7 +426,6 @@ def eventtarget string
end

def TextInfoPlugin::get_iksnrs_from_string(string)
puts "get_iksnrs_from_string: #{string}"
iksnrs = []
src = string.gsub(/[^0-9,\s]/, "")
if(matches = src.strip.scan(/\d{5}|\d{2}\s*\d{3}|\d\s*{5}/))
Expand Down Expand Up @@ -916,7 +915,9 @@ def textinfo_swissmedicinfo_index
end
index
end
def textinfo_swissmedicinfo_company_index(company)
def textinfo_swissmedicinfo_company_index(company, target)
ids = []
match_iksnr = /Zulassungsnummer\s*([\d’]+.........)/
setup_default_agent
url = 'http://www.swissmedicinfo.ch/?Lang=DE'
# accept form
Expand All @@ -936,30 +937,66 @@ def textinfo_swissmedicinfo_company_index(company)
form3['__EVENTTARGET'] = "ctl00$MainContent$ucCompanySearchResult1$GVCompanies"
form3['__EVENTARGUMENT'] = 'Select$0'
page3 = form3.submit
dump_file = File.join(ODDB.config.data_dir, 'html', "#{company}_index.html")
File.open(dump_file, 'w') { |fh| fh.puts(Nokogiri::Slop(page3.body).text) }

nrPatInfo = /Patienteninformationen\s*\((\d*)/i.match(page3.body)
unless nrPatInfo
puts Nokogiri::Slop(page3.body).text
puts "Could not find any Patienteninformationen for #{company}"
return []
if target.eql?(:fi) or target.eql?(:both)
nrFachInfo = /Fachinformationen\s*\((\d*)/i.match(page3.body)
unless nrFachInfo
puts Nokogiri::Slop(page3.body).text
puts "Could not find any Fachinformationen for #{company}"
return []
end
nrInfos = nrFachInfo[1].to_i
0.upto(nrInfos-1) {
|counter|
form4 = page3.form_with(:id => 'ctl01')
form4['__EVENTTARGET'] = "ctl00$MainContent$ucSearchResult1$ucResultGridFI$GVMonographies"
form4['__EVENTARGUMENT'] = "Select$#{counter}"
page4 = form4.submit
iksnr = match_iksnr.match(Nokogiri::Slop(page4.body).text)
unless iksnr
puts "textinfo_swissmedicinfo_company_index counter nrFachInfo #{counter}/#{nrInfos} no iksnr in #{Nokogiri::Slop(page4.body).text}"
next
end
id = iksnr[1].gsub(/[^\d,]/,'').to_i
if id < 100 or id > 100000
puts "#{company}: counter #{counter}: Found bad iksnr #{id} in #{iksnr[0]}"
end
ids << sprintf("%05d", id)
puts "textinfo_swissmedicinfo_company_index counter nrFachInfo #{counter}/#{nrInfos} adding #{sprintf("%05d", id)}"
}
end
ids = []
0.upto(nrPatInfo[1].to_i-1) {
|counter|
form4 = page3.form_with(:id => 'ctl01')
form4['__EVENTTARGET'] = "ctl00$MainContent$ucSearchResult1$ucResultGridPI$GVMonographies"
form4['__EVENTARGUMENT'] = "Select$#{counter}"
page4 = form4.submit
match_iksnr_strict = /Zulassungsnummer([\d’ ]+)/
match_iksnr = /Zulassungsnummer([\d’]+.........)/
iksnr = match_iksnr.match(Nokogiri::Slop(page4.body).text)
next unless iksnr
id = iksnr[1].gsub(/[^\d,]/,'').to_i
if id < 100 or id > 100000
puts "#{company}: counter #{counter}: Found bad iksnr #{id} in #{iksnr[0]}"
end
ids << id
}
puts "textinfo_swissmedicinfo_company_index #{company} #{target.inspect} fachinfo #{ids.sort.uniq.join(',')}. Used #{dump_file}"
if target.eql?(:fi) or target.eql?(:both)
nrPatInfo = /Patienteninformationen\s*\((\d*)/i.match(page3.body)
unless nrPatInfo
puts Nokogiri::Slop(page3.body).text
puts "Could not find any Patienteninformationen for #{company}"
return []
end
nrInfos = nrPatInfo[1].to_i
0.upto(nrInfos-1) {
|counter|
puts "textinfo_swissmedicinfo_company_index counter nrPatInfo #{counter}"
form4 = page3.form_with(:id => 'ctl01')
form4['__EVENTTARGET'] = "ctl00$MainContent$ucSearchResult1$ucResultGridPI$GVMonographies"
form4['__EVENTARGUMENT'] = "Select$#{counter}"
page4 = form4.submit
iksnr = match_iksnr.match(Nokogiri::Slop(page4.body).text)
unless iksnr
puts "textinfo_swissmedicinfo_company_index counter nrPatInfo #{counter}/#{nrInfos} no iksnr in #{Nokogiri::Slop(page4.body).text}"
next
end
id = iksnr[1].gsub(/[^\d,]/,'').to_i
if id < 100 or id > 100000
puts "#{company}: counter #{counter}: Found bad iksnr #{id} in #{iksnr[0]}"
end
ids << sprintf("%05d", id)
puts "textinfo_swissmedicinfo_company_index counter nrPatInfo #{counter}/#{nrInfos} adding #{sprintf("%05d", id)}"
}
end
puts "textinfo_swissmedicinfo_company_index #{company} #{target.inspect} patinfo #{ids.sort.uniq.join(',')}"
ids.sort.uniq
end

Expand Down Expand Up @@ -1026,29 +1063,24 @@ def match(node_set, name)
def extract_matched_name(iksnr, type, lang)
name = nil
return name unless @doc
path = "//medicalInformation[@type='#{type[0].downcase + 'i'}' and @lang='#{lang.to_s}']/content[match(., \"#{iksnr}\")]"
path = "//medicalInformation[@type='#{type[0].downcase + 'i'}' and @lang='#{lang.to_s}']/authNrs"
match = @doc.xpath(path, Class.new do
def match(node_set, iksnr)
expr = /#{iksnr[0..1]}(.|\s)?#{iksnr[2..4]}\s?/
found_node = catch(:found) do
node_set.find_all do |node|
html = Nokogiri::HTML(node.text)
pos = (html.text =~ /Zulassungsnummer|Num.ro\s*d.autorisation/).to_i
unless pos == 0
src = html.text[pos..-1]
throw :found, node if src =~ expr
end
false
end
nil
node_set.find_all do |node|
pp node
node.text =~ /#{iksnr}/
end
found_node ? [found_node] : []
end
end.new).first
if match and title = match.parent.at('./title')
name = title.text
end
name
end.new).each{
|x|
if /#{iksnr}/.match(x.text)
name = x.parent.at('./title').text
puts "extract_matched_name #{iksnr} #{type} #{lang} path is #{path} returns #{name}"
return name
end
}
puts "extract_matched_name could not find #{iksnr}"
return name
end
def extract_image(name, type, lang, dist)
if File.exists?(dist)
Expand Down Expand Up @@ -1191,7 +1223,7 @@ def swissmedicinfo_xml(xml_file = File.join(ODDB.config.data_dir, 'xml', 'AipsDo
if @options[:xml_file]
xml_file = @options[:xml_file]
end
Nokogiri::XML(File.open(xml_file,'r').read)
@doc = Nokogiri::XML(File.open(xml_file,'r').read)
end
def import_swissmedicinfo_by_index(index, target)
title,keys = title_and_keys_by(target)
Expand All @@ -1203,11 +1235,13 @@ def import_swissmedicinfo_by_index(index, target)
@doc = nil
end
def import_swissmedicinfo_by_iksnrs(iksnrs, target)
puts "import_swissmedicinfo_by_iksnrs #{iksnrs.inspect} target #{target}"
title,keys = title_and_keys_by(target)
@updated,@skipped,@invalid,@notfound = report_sections_by(title)
@doc = swissmedicinfo_xml
iksnrs.each do |iksnr|
names = Hash.new{|h,k| h[k] = {} }
puts "import_swissmedicinfo_by_iksnrs iksnr #{iksnr.inspect} #{names.inspect}"
[:de, :fr].each do |lang|
keys.each_pair do |typ, type|
names[lang][typ] = [extract_matched_name(iksnr, type, lang)]
Expand All @@ -1221,7 +1255,7 @@ def import_swissmedicinfo_by_iksnrs(iksnrs, target)
def import_swissmedicinfo_by_companies(companies, target)
iksnrs = []
companies.each do |company|
iksnrs += textinfo_swissmedicinfo_company_index(company)
iksnrs += textinfo_swissmedicinfo_company_index(company, target)
end
import_swissmedicinfo_by_iksnrs(iksnrs, target)
end
Expand Down

0 comments on commit a296e4d

Please sign in to comment.