medreg 0.1

data/lib/medreg/resilient_loop.rb

@@ -0,0 +1,94 @@
+#!/usr/bin/env ruby
+# encoding: utf-8
+
+require 'timeout'
+require 'medreg'
+
+module Medreg
+  #
+  # ResilientLoop is a helper class for running long lasting jobs like imports
+  # It has the following characterstics
+  # * Possible to restart a failed job at the failing id
+  # * Retry an import after a timeout (e.g. of 10 seconds) 
+  #
+  # -------------
+  # requirements:
+  # -------------
+  # Needed is state-id (e.g. an EAN13 code) which allows to distingish whether
+  # a loop item was already processed or not
+  #
+  # ---------------
+  # implementation:
+  # ---------------
+  # the state is saved in a text file
+  # 
+  ExampleUsage = %(
+      r_loop = ResilientLoop.new(LoopName)
+      loop_entries.each{
+        |entry|
+          next if r_loop.must_skip?(entry)
+          r_loop.try_run(entry, TimeoutValue) { /* do your work */ }
+      }
+      r_loop.finished
+)
+  class ResilientLoop
+    attr_reader :state_file, :nr_skipped, :state_id
+    attr_writer :nr_retries
+    
+    def initialize(loopname, state_id = nil)
+      @loopname   = loopname
+      @state_id   = state_id
+      @nr_skipped = 0
+      @nr_retries = 3
+      get_state
+    end
+
+    def must_skip?(id)
+      return false unless @state_id
+      if id 
+        clear_state if id.to_s.eql?(@state_id.to_s)
+        @nr_skipped += 1        
+        return true
+      else
+        return false
+      end
+    end
+
+    def try_run(state, timeout_in_secs = 10, &block)
+      idx = 0
+      while idx < @nr_retries
+        idx += 1
+        begin
+          status = timeout(timeout_in_secs) do
+            block.call
+            save_state(state)
+            return
+          end
+        rescue Timeout::Error
+          raise Timeout::Error if @nr_retries == idx
+        end
+      end
+    end
+
+    def finished
+      clear_state
+    end
+private 
+    def get_state
+      @state_file = File.join(LOG_PATH, @loopname + '.state')
+      if File.exists?(@state_file)
+        content = IO.read(@state_file)
+        eval("@state_id = #{content}")
+      else
+        @state_id = nil
+      end
+    end
+    def save_state(state)
+      File.open(@state_file, 'w+') { |f| f.write(state)}
+    end
+    def clear_state
+      @state_id = nil
+      FileUtils.rm_f(@state_file)
+    end
+  end
+end

data/lib/medreg/version.rb

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+#!/usr/bin/env ruby
+
+module Medreg
+    VERSION = '0.1'
+end

data/medreg.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'medreg/version'
+
+Gem::Specification.new do |spec|
+  spec.name        = "medreg"
+  spec.version     =  Medreg::VERSION
+  spec.author      = "Niklaus Giger, Zeno R.R. Davatz"
+  spec.email       = "ngiger@ywesee.com, zdavatz@ywesee.com"
+  spec.description = "Personen und Betriebe Adressen für die Schweiz."
+  spec.summary     = "Helper module for ch.oddb.org"
+  spec.homepage    = "https://github.com/zdavatz/medreg"
+  spec.license       = "GPL-v2"
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_dependency 'mechanize'
+  spec.add_dependency 'rubyXL', '3.3.1'
+
+  spec.add_development_dependency "bundler"
+  spec.add_development_dependency "rake"
+  spec.add_development_dependency "flexmock"
+  spec.add_development_dependency "simplecov"
+  spec.add_development_dependency "minitest" if /^1\./.match(RUBY_VERSION)
+end
+

data/test/suite.rb

@@ -0,0 +1,11 @@
+#!/usr/bin/env ruby
+# encoding: utf-8
+
+$: << File.expand_path(File.dirname(__FILE__))
+# require 'minitest'
+require 'simplecov'
+SimpleCov.start
+
+Dir.foreach(File.dirname(__FILE__)) { |file|
+	require file if /^test_.*\.rb$/o.match(file)
+}

data/test/test_company.rb

@@ -0,0 +1,112 @@
+#!/usr/bin/env ruby
+# encoding: utf-8
+# TestCompanyPlugin -- oddb.org -- 11.05.2012 -- yasaka@ywesee.com
+# TestCompanyPlugin -- oddb.org -- 23.03.2011 -- mhatakeyama@ywesee.com
+
+$: << File.expand_path('..', File.dirname(__FILE__))
+$: << File.expand_path("../../src", File.dirname(__FILE__))
+
+gem 'minitest'
+require 'minitest/autorun'
+require 'flexmock'
+require 'medreg/company'
+require 'tempfile'
+
+module Medreg
+class TestCompanyPlugin <Minitest::Test
+  include FlexMock::TestCase
+  Test_Companies_XLSX = File.expand_path(File.join(__FILE__, '../data/companies_20141014.xlsx'))
+  def setup
+    @config  = flexmock('config',
+             :empty_ids => nil,
+             :pointer   => 'pointer'
+            )
+    @config  = flexmock('config')
+    @company = flexmock('company', :pointer => 'pointer',
+                        :ean13= => 'ean13',
+                        :name= => 'name',
+                        :addresses= => 'addresses',
+                        :business_area= => 'business_area',
+                        :odba_isolated_store => 'odba_isolated_store',
+                        :oid => 'oid',
+                        :narcotics= => 'narcotics',
+                        :odba_store => 'odba_store',
+                       )
+    @app     = flexmock('appX',
+              :config => @config,
+              :create_company => @company,
+              :companies => [@company],
+              :company_by_gln => nil,
+              :company_by_origin => @company,
+              :update           => 'update',
+            )
+    @plugin = Medreg::Company.new(@app)
+    flexmock(@plugin, :get_latest_file => [true, Test_Companies_XLSX])
+    $stderr.puts "Test_Companies_XLSX #{Test_Companies_XLSX}"
+  end
+
+  def test_update_7601002026444
+    @plugin = Medreg::Company.new(@app, [7601001396371])
+    flexmock(@plugin, :get_latest_file => [true, Test_Companies_XLSX])
+    flexmock(@plugin, :get_company_data => {})
+    flexmock(@plugin, :puts => nil)
+    startTime = Time.now
+    csv_file = Medreg::Companies_YAML
+    FileUtils.rm_f(csv_file) if File.exists?(csv_file)
+    created, updated, deleted, skipped = @plugin.update
+    diffTime = (Time.now - startTime).to_i
+    # $stdout.puts "result: created #{created} deleted #{deleted} skipped #{skipped} in #{diffTime} seconds"
+    assert_equal(1, created)
+    assert_equal(0, updated)
+    assert_equal(0, deleted)
+    assert_equal(0, skipped)
+    assert_equal(1, Medreg::Company.all_companies.size)
+    assert(File.exists?(csv_file), "file #{csv_file} must be created")
+    linden = Medreg::Company.all_companies.first
+    addresses = linden[:addresses]
+    assert_equal(1, addresses.size)
+    first_address = addresses.first
+    assert_equal(ODDB::Address2, first_address.class)
+    assert_equal(nil, first_address.fon)
+    assert_equal('5102 Rupperswil', first_address.location)
+    assert_equal('öffentliche Apotheke', linden[:ba_type])
+    assert_equal('5102', first_address.plz)
+    assert_equal('Rupperswil', first_address.city)
+    assert_equal('4', first_address.number)
+    assert_equal('Mitteldorf', first_address.street)
+    assert_equal(nil, first_address.additional_lines)
+    assert_equal('AB Lindenapotheke AG', first_address.name)
+    inhalt = IO.read(csv_file)
+    assert(inhalt.index('6011 Verzeichnis a/b/c BetmVV-EDI') > 0, 'must find btm')
+#	7601001396371	AB Lindenapotheke AG		Mitteldorf	4	5102	Rupperswil	Aargau	Schweiz	öffentliche Apotheke	6011 Verzeichnis a/b/c BetmVV-EDI
+  end
+  def test_update_all
+    @plugin = Medreg::Company.new(@app)
+    flexmock(@plugin, :get_latest_file => [true, Test_Companies_XLSX])
+    flexmock(@plugin, :get_company_data => {})
+    flexmock(@plugin, :puts => nil)
+    startTime = Time.now
+    csv_file = Medreg::Companies_YAML
+    FileUtils.rm_f(csv_file) if File.exists?(csv_file)
+    created, updated, deleted, skipped = @plugin.update
+    diffTime = (Time.now - startTime).to_i
+    # $stdout.puts "result: created #{created} deleted #{deleted} skipped #{skipped} in #{diffTime} seconds"
+    assert_equal(3, created)
+    assert_equal(0, updated)
+    assert_equal(0, deleted)
+    assert_equal(1, skipped)
+    assert(File.exists?(csv_file), "file #{csv_file} must be created")
+  end
+
+  def test_get_latest_file
+    current  = File.expand_path(File.join(__FILE__, "../../../data/xls/companies_#{Time.now.strftime('%Y.%m.%d')}.xlsx"))
+    FileUtils.rm_f(current) if File.exists?(current)
+    @plugin = Medreg::Company.new(@app)
+    res = @plugin.get_latest_file
+    assert(res[0], 'needs_update must be true')
+    assert(res[1].match(/latest/), 'filename must match latest')
+    assert(File.exists?(res[1]), 'companies_latest.xls must exist')
+    assert(File.size(Test_Companies_XLSX) <File.size(res[1]))
+  end
+end
+end

data/test/test_person.rb

@@ -0,0 +1,154 @@
+#!/usr/bin/env ruby
+# encoding: utf-8
+
+$: << File.expand_path('..', File.dirname(__FILE__))
+$: << File.expand_path("../../src", File.dirname(__FILE__))
+
+gem 'minitest'
+require 'minitest/autorun'
+require 'flexmock'
+require 'medreg/person'
+require 'tempfile'
+require 'ostruct'
+
+Minitest::Test.i_suck_and_my_tests_are_order_dependent!()
+
+class TestPerson <Minitest::Test
+  include FlexMock::TestCase
+  RunTestTakingLong = false
+  Test_Personen_XLSX = File.expand_path(File.join(__FILE__, '../../data/xlsx/Personen_20141014.xlsx'))
+  def setup
+    @config = flexmock('config')
+    @doctor = flexmock('doctor', :pointer => 'pointer', :oid => 'oid')
+    @app    = flexmock('app',
+              :config => @config,
+             :doctors => [@doctor],
+             :create_doctor => @doctor,
+             :doctor_by_gln => nil,
+             :doctor_by_origin => @doctor,
+             :update           => 'update'
+            )
+    @plugin = Medreg::Person.new(@app)
+    flexmock(@plugin, :get_latest=> Test_Personen_XLSX)
+  end
+
+  SomeTestCases = {
+    7601000010735 => OpenStruct.new(:family_name => 'Cevey',        :first_name => 'Philippe Marc', :authority  => 'Waadt'),
+    7601000813282 => OpenStruct.new(:family_name => 'ABANTO PAYER', :first_name => 'Dora Carmela',  :authority  => 'Waadt'),
+  }
+
+  # Anita Hensel 7601000972620
+  def test_aaa_zuest # name starts with aaa we want this test to be run as first
+    {  7601000254207 => OpenStruct.new(:family_name => 'Züst', :first_name => 'Peter', :authority  => 'Glarus')}.each do
+      |gln, info|
+      @plugin = Medreg::Person.new(@app, [gln])
+      flexmock(@plugin, :get_latest_file => [ true, Test_Personen_XLSX ] )
+      flexmock(@plugin, :get_doctor_data => {})
+      assert(File.exists?(Test_Personen_XLSX))
+      startTime = Time.now
+      csv_file = ODDB::Doctors::Personen_YAML
+      FileUtils.rm_f(csv_file) if File.exists?(csv_file)
+      created, updated, deleted, skipped = @plugin.update
+      diffTime = (Time.now - startTime).to_i
+      assert_equal(0, deleted)
+      assert_equal(0, skipped)
+      assert_equal(1, created)
+      assert_equal(0, updated)
+      assert_equal(1, Medreg::Person.all_doctors.size)
+      zuest = Medreg::Person.all_doctors.first[1] # a hash
+      assert_equal(true, zuest[:may_dispense_narcotics])
+      assert_equal(true, zuest[:may_sell_drugs])
+      assert_equal(nil, zuest[:remark_sell_drugs])
+      assert_equal(nil, zuest[:exam])
+      assert_equal('Züst', zuest[:name])
+      assert_equal('Peter', zuest[:firstname])
+      assert_equal(["Allgemeine Innere Medizin, 2003, Schweiz"], zuest[:specialities])
+      assert_equal(3, zuest[:capabilities].size)
+      [ "Sportmedizin, 2004, Schweiz",
+        "Praxislabor, 2002, Schweiz",
+        "Sachkunde für dosisintensives Röntgen, 2004, Schweiz",
+      ].each {
+        |cap|
+          assert(zuest[:capabilities].index(cap), "Muss Erfahrung #{cap} fuer Züst finden")
+      }
+      addresses = zuest[:addresses]
+      assert_equal(1, addresses.size)
+      first_address = addresses.first
+       assert_equal(ODDB::Address2, first_address.class)
+      assert_equal(1, first_address.fon.size)
+      assert_equal(['Bahnhofstr. 3'], first_address.additional_lines)
+      assert_equal('8753 Mollis', first_address.location)
+      assert_equal('at_praxis', first_address.type)
+      assert_equal('055 6122353', first_address.fon.first)
+      assert_equal('Praxis Dr. med. Peter Züst', first_address.name)
+      assert_equal('8753', first_address.plz)
+      assert_equal('Mollis', first_address.city)
+      assert_equal('Bahnhofstr.', first_address.street)
+      assert_equal('3', first_address.number)
+    end
+  end
+  def test_parse
+    SomeTestCases.each{
+      |gln, info|
+      info.gln = gln
+      root = File.expand_path(File.join(__FILE__, "../.."))
+      @plugin = Medreg::Person.new(@app, [gln])
+      html_file = "#{root}/data/html/medreg/#{gln}.html"
+      assert(File.exist?(html_file), "File \#{html_file} must exist")
+      doc_hash = @plugin.parse_details(Nokogiri::HTML(File.read(html_file)),
+                                      gln,
+                                      info,
+                                      )
+      assert(doc_hash.is_a?(Hash), 'doc_hash must be a Hash')
+      assert(doc_hash[:addresses], 'doc_hash must have addresses')
+      assert(doc_hash[:addresses].size > 0, 'doc_hash must have at least one address')
+    }
+  end
+
+  def test_update_single
+    SomeTestCases.each{
+      |gln, info|
+      @plugin = Medreg::Person.new(@app, [gln])
+      flexmock(@plugin, :get_latest_file => [ true, Test_Personen_XLSX ] )
+      flexmock(@plugin, :get_doctor_data => {})
+      assert(File.exists?(Test_Personen_XLSX))
+      startTime = Time.now
+      csv_file = ODDB::Doctors::Personen_YAML
+      FileUtils.rm_f(csv_file) if File.exists?(csv_file)
+      created, updated, deleted, skipped = @plugin.update
+      diffTime = (Time.now - startTime).to_i
+      assert_equal(0, deleted)
+      assert_equal(0, skipped)
+      assert_equal(1, created)
+      assert_equal(0, updated)
+      assert(File.exists?(csv_file), "file #{csv_file} must be created")
+      expected = "Doctors update \n\nNumber of doctors: 1\nSkipped doctors: 0\nNew doctors: 1\nUpdated doctors: 0\nDeleted doctors: 0\n"
+      assert_equal(expected, @plugin.report)
+    }
+  end
+
+  def test_update_some_glns
+    glns_ids_to_search = [7601000078261, 7601000813282, 7601000254207, 7601000186874, 7601000201522, 7601000295958,
+                          7601000010735, 7601000268969, 7601000019080, 7601000239730 ]
+    @plugin = Medreg::Person.new(@app, glns_ids_to_search)
+
+    flexmock(@plugin, :get_latest_file => [ true, Test_Personen_XLSX ] )
+    flexmock(@plugin, :get_doctor_data => {})
+    assert(File.exists?(Test_Personen_XLSX))
+    startTime = Time.now
+    csv_file = ODDB::Doctors::Personen_YAML
+    FileUtils.rm_f(csv_file) if File.exists?(csv_file)
+    created, updated, deleted, skipped = @plugin.update
+    diffTime = (Time.now - startTime).to_i
+    assert_equal(0, deleted)
+    assert_equal(0, skipped)
+    assert_equal(0, updated)
+    assert_equal(glns_ids_to_search.size - 1 , created) # we have one gln_id mentioned twice
+    assert(File.exists?(csv_file), "file #{csv_file} must be created")
+  end if RunTestTakingLong
+
+  def test_zzz_get_latest_file # name starts with zzz we want this test to be run as last one (takes longest)
+    @plugin = Medreg::Person.new(@app, [7601000813282])
+    needs_update, latest = @plugin.get_latest_file
+  end if RunTestTakingLong
+end

data/test/test_run.rb

@@ -0,0 +1,20 @@
+#!/usr/bin/env ruby
+# TestArray -- odba -- 30.01.2007 -- hwyss@ywesee.com
+
+$: << File.dirname(__FILE__)
+$: << File.expand_path('../lib', File.dirname(__FILE__))
+
+require 'minitest/autorun'
+require 'flexmock'
+require 'medreg/medreg'
+
+module ODBA
+  class TestArray < Minitest::Test
+    include FlexMock::TestCase
+    def setup
+    end
+    def test_company_importer
+      assert Medreg.run('company')
+    end
+  end
+end

metadata

@@ -0,0 +1,182 @@
+--- !ruby/object:Gem::Specification
+name: medreg
+version: !ruby/object:Gem::Version
+  version: '0.1'
+  prerelease: 
+platform: ruby
+authors:
+- Niklaus Giger, Zeno R.R. Davatz
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-12-10 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: mechanize
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rubyXL
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 3.3.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 3.3.1
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: flexmock
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Personen und Betriebe Adressen für die Schweiz.
+email: ngiger@ywesee.com, zdavatz@ywesee.com
+executables:
+- medreg
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- .travis.yml
+- Gemfile
+- History.txt
+- LICENSE
+- README.textile
+- Rakefile
+- bin/medreg
+- lib/medreg.rb
+- lib/medreg/address.rb
+- lib/medreg/ba_type.rb
+- lib/medreg/company.rb
+- lib/medreg/company_importer.rb
+- lib/medreg/medreg.rb
+- lib/medreg/person.rb
+- lib/medreg/person_importer.rb
+- lib/medreg/resilient_loop.rb
+- lib/medreg/version.rb
+- medreg.gemspec
+- test/data/companies_20141014.xlsx
+- test/suite.rb
+- test/test_company.rb
+- test/test_person.rb
+- test/test_run.rb
+homepage: https://github.com/zdavatz/medreg
+licenses:
+- GPL-v2
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.25
+signing_key: 
+specification_version: 3
+summary: Helper module for ch.oddb.org
+test_files: []