Re-Added jobs/epha_interactions.

spec/doctors_spec.rb

@@ -81,8 +81,8 @@ def enter_search_to_field_by_name(search_text, field_name)
                  }
                            # Check map link
                               @browser.link(:text => /map.search/).click
-                              @browser.url.should match /bahnhofstr/
-                              @browser.url.should match /8753-mollis/
+                              @browser.url.should match /bahnhofstr/i
+                              @browser.url.should match /8753-mollis/i
                               @browser.back
                            # go back to search result
                               @browser.back

spec/pharmacies_spec.rb

@@ -68,7 +68,7 @@ def enter_search_to_field_by_name(search_text, field_name)
     inhalt.should match "Zaunplatz 2"
     inhalt.should match "8750 Glarus"
     @browser.link(:text => /map.search/).click
-    @browser.url.should match /8750-glarus\/zaunplatz-2/
+    @browser.url.should match /8750-glarus\/zaunplatz-2/i
     @browser.back
   # go back to search result
     @browser.back

src/model/epha_interaction.rb

@@ -26,49 +26,11 @@ module EphaInteractions
     def EphaInteractions.get
       @@epha_interactions
     end
+    def EphaInteractions.set(interactions)
+      @@epha_interactions = interactions
+    end
     CSV_FILE = File.expand_path('../../data/csv/interactions_de_utf8.csv', File.dirname(__FILE__))
     CSV_ORIGIN_URL  = 'https://download.epha.ch/data/matrix/matrix.csv'
-    def EphaInteractions.read_csv
-      @csv_file_path = CSV_FILE
-      latest = @csv_file_path.sub(/\.csv$/, '-latest.csv')
-      if File.exist?(latest) and ((Time.now-File.mtime(latest))/3600).round < 24 # less than 24 hours old
-        $stdout.puts  "#{Time.now}: EphaInteractionPlugin.update: skip as latest #{latest} #{File.exist?(latest)} is only #{((Time.now-File.mtime(latest))/3600).round} hours old"
-      else
-        FileUtils.rm_f(@csv_file_path, :verbose => true)
-        target = Mechanize.new.get(CSV_ORIGIN_URL)
-        target.save_as @csv_file_path
-        $stdout.puts  "#{Time.now}: EphaInteractionPlugin.update: #{File.expand_path(@csv_file_path)} ?  #{File.exists?(@csv_file_path)}"
-        FileUtils.cp(@csv_file_path,  latest, :preserve => true, :verbose => true) unless defined?(MiniTest)
-      end
-      if File.exists?(latest)
-        @lineno = 0
-        first_line = nil
-        File.readlines(latest).each do |line|
-          @lineno += 1
-          line = line.force_encoding('utf-8')
-          next if /ATC1.*Name1.*ATC2.*Name2/.match(line)
-          begin
-            elements = CSV.parse_line(line)
-          rescue CSV::MalformedCSVError
-            $stdout.puts "CSV::MalformedCSVError in line #{@lineno}: #{line}"
-            next
-          end
-          epha_interaction = EphaInteraction.new
-          epha_interaction.atc_code_self = elements[0]
-          epha_interaction.atc_name = elements[1]
-          epha_interaction.atc_code_other = elements[2]
-          epha_interaction.name_other = elements[3]
-          epha_interaction.info = elements[4]
-          epha_interaction.action = elements[5]
-          epha_interaction.effect = elements[6]
-          epha_interaction.measures = elements[7]
-          epha_interaction.severity = elements[8]
-          EphaInteractions.get[ [epha_interaction.atc_code_self, epha_interaction.atc_code_other  ]] = epha_interaction
-        end
-        $stdout.puts "#{Time.now}: Added #{EphaInteractions.get.size} interaction from #{latest}"; $stdout.flush
-      end
-    end
-
     def self.calculate_atc_codes(drugs)
       atc_codes = []
       if drugs and !drugs.empty?
@@ -79,7 +41,14 @@ def self.calculate_atc_codes(drugs)
       atc_codes
     end
     def EphaInteractions.get_epha_interaction(atc_code_self, atc_code_other)
-      EphaInteractions.get[ [atc_code_self, atc_code_other] ]
+      result = nil
+      @@epha_interactions.each{ | key, value |
+                                if key[0].to_s.eql?(atc_code_self) and  key[1].to_s.eql?(atc_code_other)
+                                  result = value
+                                  break
+                                end
+                              }
+      result
     end
 
     def EphaInteractions.get_interactions(my_atc_code, drugs)
@@ -114,24 +83,27 @@ def EphaInteractions.get_interactions(my_atc_code, drugs)
     end
   end
   class EphaInteraction
-    # Based on information contained in http://community.epha.ch/interactions_de_utf8.csv
+    include ODBA::Persistable
+    include Persistence
+     # Based on information contained in http://community.epha.ch/interactions_de_utf8.csv
     # ATC1  Name1 ATC2  Name2 Info  Mechanismus Effekt  Massnahmen  Grad
     # N06AB06 Sertralin M03BX02 Tizanidin Keine Interaktion Tizanidin wird über CYP1A2 metabolisiert. Sertralin beeinflusst CYP1A2 jedoch nicht.  Keine Interaktion.  Die Kombination aus Sertralin und Tizanidin hat kein bekanntes Interaktionspotential. A
     attr_accessor :atc_code_self, :atc_code_other # these two items are our unique index. They may not be changed
     attr_accessor :atc_name, :name_other, :info, :action, :effect, :measures, :severity
-    EphaInteractions.read_csv if EphaInteractions.get.size == 0
 
     def initialize
+		super
     end
 
     def init(app)
+		@pointer.append(@oid)
     end
 
     def search_terms
       terms = [
         @atc_code_self, @atc_name,
         @atc_code_other, @name_other,
-        @info ,@action, @effect,
+        @info, @action, @effect,
         @measures, @severity
       ]
       ODDB.search_terms(terms)

src/plugin/epha_interactions.rb

@@ -0,0 +1,89 @@
+#!/usr/bin/env ruby
+# encoding: utf-8
+$: << File.expand_path('../..', File.dirname(__FILE__))
+$: << File.expand_path('../../src', File.dirname(__FILE__))
+
+require 'plugin/plugin'
+require 'util/oddbconfig'
+require 'util/persistence'
+require 'drb'
+require 'model/epha_interaction'
+
+module ODDB
+  class EphaInteractionPlugin < Plugin
+    @@report = []
+
+    def debug_msg(msg)
+      if defined?(MiniTest) then $stdout.puts Time.now.to_s + ': ' + msg; $stdout.flush; return end
+      if not defined?(@checkLog) or not @checkLog
+        name = LogFile.filename('oddb/debug/', Time.now)
+        FileUtils.makedirs(File.dirname(name))
+        @checkLog = File.open(name, 'a+')
+        $stdout.puts "Opened #{name}"
+      end
+      @checkLog.puts("#{Time.now}: #{msg}")
+      @checkLog.flush
+    end
+
+    def initialize(app, options = nil)
+      super
+    end
+    def report
+      @@report.join("\n")
+    end
+
+    def update(agent=Mechanize.new, csv_file_path = ODDB::EphaInteractions::CSV_FILE)
+      @@report = []
+      latest = csv_file_path.sub(/\.csv$/, '-latest.csv')
+      if EphaInteractions.get.size > 0 and File.exist?(latest) and ((Time.now-File.mtime(latest))/3600).round < 24 # less than 24 hours old
+        msg = "EphaInteractionPlugin.update: skip #{EphaInteractions.get.size } items as latest #{latest} #{File.exist?(latest)} is only #{((Time.now-File.mtime(latest))/3600).round} hours old"
+        @@report << msg
+        debug_msg(msg)
+      else
+        FileUtils.rm_f(csv_file_path, :verbose => true)
+        target = agent.get(ODDB::EphaInteractions::CSV_ORIGIN_URL)
+		if target.is_a?(String)
+			File.open(csv_file_path, 'w+') { |file| file.write(target) }
+		else
+			target.save_as csv_file_path
+		end
+        FileUtils.cp(csv_file_path,  latest, :preserve => true, :verbose => true)
+        msg = "EphaInteractionPlugin.update latest #{latest} #{File.exists?(latest)} via #{File.expand_path(csv_file_path)} from #{ODDB::EphaInteractions::CSV_ORIGIN_URL}"
+        @@report << msg
+        debug_msg(msg)
+        @lineno = 0
+        first_line = nil
+        @app.delete_all_epha_interactions
+        File.readlines(latest).each do |line|
+          @lineno += 1
+          line = line.force_encoding('utf-8')
+          next if /ATC1.*Name1.*ATC2.*Name2/.match(line)
+          begin
+            elements = CSV.parse_line(line)
+          rescue CSV::MalformedCSVError
+            msg << "CSV::MalformedCSVError in line #{@lineno}: #{line}"
+            next
+          end
+          next if elements.size == 0 # Eg. empty line at the end
+          epha_interaction = @app.create_epha_interaction(elements[0], elements[2])
+          epha_interaction.atc_code_self = elements[0]
+          epha_interaction.atc_name = elements[1]
+          epha_interaction.atc_code_other = elements[2]
+          epha_interaction.name_other = elements[3]
+          epha_interaction.info = elements[4]
+          epha_interaction.action = elements[5]
+          epha_interaction.effect = elements[6]
+          epha_interaction.measures = elements[7]
+          epha_interaction.severity = elements[8]
+          EphaInteractions.get[ [epha_interaction.atc_code_self, epha_interaction.atc_code_other  ]] = epha_interaction
+          epha_interaction.odba_isolated_store
+        end
+        @app.odba_store
+        msg = "Added #{EphaInteractions.get.size} interactions from #{latest}";
+        @@report << msg
+        debug_msg(msg)
+      end
+      true
+    end
+  end
+end

src/util/oddbapp.rb

@@ -57,6 +57,7 @@ class OddbPrevalence
     :registrations, :slates, :users, :narcotics, :accepted_orphans,
     :commercial_forms, :rss_updates, :feedbacks, :indices_therapeutici,
     :generic_groups, :shorten_paths
+  attr_accessor  :epha_interactions_hash,  :epha_interactions
   VALID_EAN13 = /^\d{13}/
 	def initialize
 		init
@@ -73,7 +74,10 @@ def init
 		@currency_rates ||= {}
     @divisions ||= {}
 		@doctors ||= {}
-    @experiences ||= {}
+		@epha_interactions ||= []
+		@epha_interactions_hash ||= {}
+		ODDB::EphaInteractions.set(@epha_interactions_hash)
+		@experiences ||= {}
 		@fachinfos ||= {}
     @feedbacks ||= {}
 		@galenic_forms ||= []
@@ -387,6 +391,12 @@ def create_experience
     experience = ODDB::Experience.new
     @experiences.store(experience.oid, experience)
   end
+  def create_epha_interaction(atc_code_self, atc_code_other)
+    epha_interaction = ODDB::EphaInteraction.new
+    @epha_interactions_hash ||= {}
+    @epha_interactions_hash[ [atc_code_self, atc_code_other] ] = epha_interaction
+    epha_interaction
+  end
   def create_hospital(ean13)
     raise "ean13 #{ean13.to_s[0..80]} not valid" unless  ean13.to_s.match(VALID_EAN13)
     hospital = ODDB::Hospital.new(ean13)
@@ -494,6 +504,28 @@ def currencies
 	def analysis_count
 		@analysis_count ||= analysis_positions.size
 	end
+  def delete_all_epha_interactions
+	if @epha_interactions.is_a?(Array)
+		$stdout.puts "delete_all_epha_interactions for #{@epha_interactions.class} with #{@epha_interactions.size} items"
+		@epha_interactions.each do |item|
+			delete(item.pointer) if item and item.pointer
+		end
+		@epha_interactions.odba_isolated_store
+		@epha_interactions = {}
+		@epha_interactions.odba_isolated_store
+		self.odba_store
+	end
+	if  @epha_interactions_hash.is_a?(Hash)
+		$stdout.puts "delete_all_epha_interactions for @epha_interactions_hash #{@epha_interactions_hash.class} with #{@epha_interactions_hash.size} items"
+		@epha_interactions_hash.values.each do |item|
+			delete(item.pointer) if item and item.pointer
+		end
+		@epha_interactions_hash.odba_isolated_store
+		@epha_interactions_hash = {}
+		@epha_interactions_hash.odba_isolated_store
+		self.odba_store
+	end
+  end
   def delete_all_narcotics
     @narcotics.values.each do |narc|
       delete(narc.pointer)
@@ -627,10 +659,13 @@ def experience(oid)
     @experiences[oid.to_i]
   end
   def get_epha_interaction(atc_code_self, atc_code_other)
-    ODDB::EphaInteractions.get_epha_interaction(atc_code_self, atc_code_other)
+    EphaInteractions.get_epha_interaction(atc_code_self, atc_code_other)
+  end
+  def epha_interaction(oid)
+    @epha_interactions_hash[oid.to_i]
   end
   def epha_interaction_count
-    ODDB::EphaInteractions.get.size
+     @epha_interactions_hash.size
   end
   def pharmacy(ean13)
     pharmacy_by_gln(ean13)

src/util/updater.rb

@@ -15,7 +15,7 @@
 require 'plugin/dosing'
 require 'plugin/drugbank'
 require 'plugin/divisibility'
-#require 'plugin/epha_interactions'
+require 'plugin/epha_interactions'
 require 'plugin/hospitals'
 require 'plugin/lppv'
 require 'plugin/medwin'
@@ -187,6 +187,7 @@ def recipients
     end
     def run
       logfile_stats
+      update_epha_interactions
 
       # recall, hpc
       update_swissmedic_feeds

src/view/interactions/interaction_chooser.rb

@@ -119,7 +119,7 @@ def init
     ean13 = @session.user_input(:search_query)
     path = @session.request_path
     @drugs = @session.choosen_drugs
-    @interactions = ODDB::EphaInteractions.get_interactions(model.atc_class.code, @drugs)
+    @interactions = EphaInteractions.get_interactions(model.atc_class.code, @drugs)
     if @model.is_a? ODDB::Package
       nextRow = 0
       unless @hide_interaction_headers
@@ -175,7 +175,7 @@ def text_info(model, session=@session)
       span.set_attribute('class', 'print bold italic')
       list.value << span
     end
-    ODDB::EphaInteractions.get_interactions(model.atc_class.code, @session.choosen_drugs).each {
+    EphaInteractions.get_interactions(model.atc_class.code, @session.choosen_drugs).each {
       |interaction|
       headerDiv = HtmlGrid::Div.new(model, @session, self)
       headerDiv.value = []

test/data/csv/epha_interactions_de_utf8-example.csv

@@ -0,0 +1,2 @@
+"ATC1","Name1","ATC2","Name2","Info","Mechanismus","Effekt","Massnahmen","Grad"
+"C09CA01","Losartan","C07AB02","Metoprolol","Verstärkte Blutdrucksenkung","Additive Blutdrucksenkung","Eine pharmakodynamische Verstärkung der antihypertensiven Wirkung der Substanzen ist zu erwarten. AT2-Antagonisten, Betablocker und auch Thiaziddiuretika werden häufig zusammen eingesetzt","Therapeutisch häufig genutzte Kombination. Bei erwarteter additiver Blutdrucksenkung empfehlen sich Blutdruckkontrollen, insbesondere zu Beginn der Kombination. ","B"