Project upload tests

Gemfile

@@ -6,13 +6,13 @@ gem 'jquery-rails'
 gem 'jquery-ui-rails'
 gem 'rake'
 
-
 # gem 'quality-measure-engine', :git => 'https://github.com/pophealth/quality-measure-engine.git', :branch => 'master'
 
 # gem 'quality-measure-engine', :path => '../quality-measure-engine'
 
 gem 'quality-measure-engine', '3.1.2'
-gem 'health-data-standards', "3.5.3"
+#gem 'health-data-standards', "3.5.3"
+gem 'health-data-standards',:git => 'https://github.com/ESRogs/health-data-standards.git', :branch => 'master'
 
 # gem 'health-data-standards',:git => 'https://github.com/projectcypress/health-data-standards.git', :branch => 'master'
 

app/models/calculated_product_test.rb

@@ -1,4 +1,4 @@
-
+require 'zip/zip'
 class CalculatedProductTest < ProductTest
 
   aasm :column => :state do
@@ -20,6 +20,46 @@ class CalculatedProductTest < ProductTest
   #after the test is created generate the population
   after_create :gen_pop
 
+  def initialize(args = nil)
+    if args != nil
+      if args.has_key?("test_zip")
+        test_zip = args["test_zip"]
+        @uploaded_patient_xml_strings = get_file_contents_from_zip(test_zip)
+        # ROGTODO: should the patient strings be passed as part of agrs to super?
+        measure_ids = get_measure_ids_from_patient_xml_string(@uploaded_patient_xml_strings[0])
+        @uploaded_patient_xml_strings.each do |ps|
+          patient_measure_ids = get_measure_ids_from_patient_xml_string(ps)
+          patient_measure_ids.each { |pmi| raise "Patients have different measure ids!" unless measure_ids.include?(pmi) }
+        end
+        # ROGTODO: don't hardcode effective_date
+        return super({"name"=>args["name"], "product_id"=>args["product_id"], "effective_date"=>"1388534399", "measure_ids"=>measure_ids})
+      end
+    end
+    super(args)
+  end
+
+  def get_file_contents_from_zip(test_zip)
+    data = test_zip.open.read
+    content_strings = []
+    Zip::ZipFile.open(test_zip.path()) do |zipfile|
+      zipfile.each do |entry|
+        cs = entry.get_input_stream.read
+        content_strings.push(cs)
+      end
+    end
+    content_strings
+  end
+
+  def get_measure_ids_from_patient_xml_string(patient_xml_string)
+    doc = Nokogiri::XML(patient_xml_string)
+    # ROGTODO: handle other formats?
+    doc.root.add_namespace_definition('cda', 'urn:hl7-org:v3')
+    nodes = doc.xpath("/cda:ClinicalDocument/cda:component/cda:structuredBody/cda:component/cda:section/cda:entry/cda:organizer/cda:templateId[@root='2.16.840.1.113883.10.20.24.3.97']")
+    measure_ids = []
+    nodes.each { |node| measure_ids << node.next_element["extension"] }
+    measure_ids
+  end
+
   def gen_pop
     self.generate_population
   end
@@ -31,25 +71,40 @@ def calculate_expected_results
   end
 
   def generate_records
-    min_set = PatientPopulation.min_coverage(self.measure_ids, self.bundle)
-    p_ids = min_set[:minimal_set]
-    overflow = min_set[:overflow]
-    all = p_ids + overflow
-    randomization_ids = all
-    while p_ids.length < 5 && overflow.length != 0
+    if @uploaded_patient_xml_strings != nil
+      @uploaded_patient_xml_strings.each do |ps|
+        pr = HealthDataStandards::Import::BulkRecordImporter.import_and_return_unsaved_record(ps)
+        pr["test_id"] = self.id
+        pr.save
+      end
+      # ROGTODO: need to do the medical_record_assigner part?
+    else
+      min_set = PatientPopulation.min_coverage(self.measure_ids, self.bundle)
+      p_ids = min_set[:minimal_set]
+      print "minimal ids:\n"
+      print p_ids.length.to_s() + "\n"
+      p_ids.each { |pid| print pid + "\n" }
+      print "\n"
+      overflow = min_set[:overflow]
+      print "overflow length: " + overflow.length.to_s() + "\n"
+      all = p_ids + overflow
+      randomization_ids = all
+      while p_ids.length < 5 && overflow.length != 0
         p_ids << overflow.sample
-    end
-    #randomly pick a number of other patients to give to the vendor
+      end
+      #randomly pick a number of other patients to give to the vendor
 
-    # do this synchronously because it does not take long
-    # p_ids = Record.where(:test_id=>nil, :type=>"ep").collect{|p| p.medical_record_number}
-    pcj = Cypress::PopulationCloneJob.new({'patient_ids' =>p_ids, 'test_id' => self.id, "randomize_names"=> true, "randomization_ids" => randomization_ids})
-    pcj.perform
+      # do this synchronously because it does not take long
+      # p_ids = Record.where(:test_id=>nil, :type=>"ep").collect{|p| p.medical_record_number}
+      pcj = Cypress::PopulationCloneJob.new({'patient_ids' =>p_ids, 'test_id' => self.id, "randomize_names"=> true, "randomization_ids" => randomization_ids})
+      pcj.perform
 
-    self.records.each do |r|
-      r.medical_record_assigner = "Cypress" if r.medical_record_assigner.nil?
-      r.save!
+      self.records.each do |r|
+        r.medical_record_assigner = "Cypress" if r.medical_record_assigner.nil?
+        r.save!
+      end
     end
+
     #now calculate the expected results
     self.calculate
   end