bonnie_bundler 2.2.0 → 3.0.0

data/LICENSE.txt

@@ -0,0 +1,201 @@
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data/README.md

@@ -2,3 +2,15 @@ bonnie_bundler
 ==============
 
 Gem for creating and managing bonnie bundles
+
+## License
+
+Copyright 2014 The MITRE Corporation
+
+Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
+
+```
+http://www.apache.org/licenses/LICENSE-2.0
+```
+
+Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

data/bonnie-bundler.gemspec

@@ -7,23 +7,23 @@ Gem::Specification.new do |s|
   s.email = "pophealth-talk@googlegroups.com"
   s.homepage = "http://github.com/projecttacoma/bonnie_bundler"
   s.authors = ["The MITRE Corporation"]
-  s.version = '2.2.0'
+  s.version = '3.0.0'
   s.license = 'Apache-2.0'
 
-  s.add_dependency 'health-data-standards', '~> 4.0'
+  s.add_dependency 'health-data-standards', '~> 4.3.2'
   s.add_dependency 'quality-measure-engine', '~> 3.2'
   s.add_dependency 'hquery-patient-api', '~> 1.1'
   s.add_dependency 'simplexml_parser', '~> 1.0'
   s.add_dependency 'hqmf2js', '~> 1.4'
 
-  s.add_dependency 'rails', '~> 4.2'
+  s.add_dependency 'rails', '>= 4.2', '< 6.0'
   s.add_dependency 'mongoid', '~> 5.0'
   s.add_dependency 'rubyzip', '~> 1.2', '>= 1.2.1'
   s.add_dependency 'zip-zip', '~> 0.3'
   s.add_dependency 'diffy', '~> 3.0.0'
 
   # needed for parsing value sets (we need to use roo rather than rubyxl because the value sets are in xls rather than xlsx)
-  s.add_dependency 'roo', '~> 1.13'
+  s.add_dependency 'roo', '~> 2.7'
 
   s.files = s.files = `git ls-files`.split("\n")
 end

data/lib/bonnie_bundler.rb

@@ -14,7 +14,6 @@ require_relative 'models/measure.rb'
 require_relative 'models/cql_measure.rb'
 require_relative 'measures/loading/exceptions.rb'
 require_relative 'measures/loading/loader.rb'
-require_relative 'measures/loading/base_loader_definition.rb'
 require_relative 'measures/loading/cql_loader.rb'
 require_relative 'measures/loading/value_set_loader.rb'
 require_relative 'measures/logic_extractor.rb'

data/lib/measures/elm_parser.rb

@@ -2,6 +2,7 @@ module CqlElm
   class Parser
     #Fields are combined with the refId to find elm node that corrosponds to the current annotation node.
     @fields = ['expression', 'operand', 'suchThat']
+    @html_hash = {"&amp;": '&', "&quot;": '"', "&lt;": '<', "&gt;": '>', "&apos;": "'"}
     @previousNoTrailingSpaceNotPeriod = false
     
     def self.parse(elm_xml)
@@ -47,9 +48,14 @@ module CqlElm
         else
           if (/^define/ =~ child.to_html)
             define_name = child.to_html.split("\"")[1]
+            # Modify special characters back in the the define_name
+            @html_hash.each { |k,v| define_name.gsub!(k.to_s, v) }
           end
+          clause_text = child.to_html.gsub(/\t/, "  ")
+          # Modify special characters back in the clause text
+          @html_hash.each { |k,v| clause_text.gsub!(k.to_s, v) }
           clause = {
-            text: child.to_html.gsub(/\t/, "  ")
+            text: clause_text
           }
           clause[:ref_id] = child['r'] unless child['r'].nil?
           ret[:children] << clause

data/lib/measures/loading/cql_loader.rb

@@ -1,62 +1,93 @@
 module Measures
   # Utility class for loading CQL measure definitions into the database from the MAT export zip
-  class CqlLoader < BaseLoaderDefinition
+  class CqlLoader
+    # Returns true if ths uploaded measure zip file is a composite measure
+    def self.composite_measure?(measure_dir)
+      # Look through all xml files at current directory level and find QDM 
+      files = Dir.glob("#{measure_dir}/**.xml").select 
+      begin
+        # Iterate over all files passed in, extract file to temporary directory.
+        files.each do |xml_file|
+          if xml_file && xml_file.size > 0
+            # Open up xml file and read contents.
+            doc = Nokogiri::XML.parse(File.read(xml_file))
+            # Check if root node in xml file matches either the HQMF file or ELM file.
+            if doc.root.name == 'QualityMeasureDocument' # Root node for HQMF XML
+              # Xpath to determine if it is a composite or not
+              doc.root.add_namespace_definition('cda', 'urn:hl7-org:v3')
+              return !doc.at_xpath('//cda:measureAttribute[cda:code[@code="MSRTYPE"]][cda:value[@code="COMPOSITE"]]').nil?
+            end
+          end
+        end     
+      rescue Exception => e
+        raise MeasureLoadingException.new "Error Checking MAT Export: #{e.message}"
+      end
+      false
+    end
 
+    # Verifies that the zip file contains a valid measure
+    # Works for both regular & composite measures
     def self.mat_cql_export?(zip_file)
-      # Open the zip file and iterate over each of the files.
-      Zip::ZipFile.open(zip_file.path) do |zip_file|
-        # Check for CQL, HQMF, ELM and Human Readable
-        cql_entry = zip_file.glob(File.join('**','**.cql')).select {|x| !x.name.starts_with?('__MACOSX') }.first
-        elm_json = zip_file.glob(File.join('**','**.json')).select {|x| !x.name.starts_with?('__MACOSX') }.first
-        human_readable_entry = zip_file.glob(File.join('**','**.html')).select { |x| !x.name.starts_with?('__MACOSX') }.first
-
-        # Grab all xml files in the zip.
-        zip_xml_files = zip_file.glob(File.join('**','**.xml')).select {|x| !x.name.starts_with?('__MACOSX') }
+      # Extract contents of zip file while retaining the directory structure
+      original = Dir.pwd
+      Dir.mktmpdir do |tmp_dir|
+        current_directory = unzip_measure_contents(zip_file, tmp_dir)
+        # Check if measure contents are valid
+        return valid_measure_contents?(current_directory, true)
+      end
+    end
 
-        if zip_xml_files.count > 0
-          xml_files_hash = extract_xml_files(zip_file, zip_xml_files)
-          !cql_entry.nil? && !elm_json.nil? && !human_readable_entry.nil? && !xml_files_hash[:HQMF_XML].nil? && !xml_files_hash[:ELM_XML].nil?
-        else
-          false
+    # Returns the base directory of the measure
+    def self.unzip_measure_contents(zip_file, tmp_dir)
+      Zip::ZipFile.open(zip_file.path) do |zip_file|
+        zip_file.each do |f|
+          f_path = File.join(tmp_dir, f.name)
+          FileUtils.mkdir_p(File.dirname(f_path))
+          f.extract(f_path)
+        end
+      end
+      current_directory = tmp_dir
+      # Detect if the zip file contents were stored into a single directory
+      if Dir.glob("#{current_directory}/*").count < 3
+        # If there is a single folder containing the zip file contents, step into it (ignore __MACOSX file if it exists)
+        Dir.glob("#{current_directory}/*").select.each do |file|
+          if !file.end_with?('__MACOSX') && File.directory?(file)
+            current_directory = file
+            break
+          end
         end
       end
+      return current_directory
     end
 
-    def self.load_mat_cql_exports(user, zip_file, out_dir, measure_details, vsac_options, vsac_ticket_granting_ticket)
-      measure = nil
-      cql = nil
-      hqmf_path = nil
-      # Grabs the cql file contents, the elm_xml contents, elm_json contents and the hqmf file path
-      files = get_files_from_zip(zip_file, out_dir)
-
-      # Load hqmf into HQMF Parser
-      hqmf_model = Measures::Loader.parse_hqmf_model(files[:HQMF_XML_PATH])
-
-      # Get main measure from hqmf parser
-      main_cql_library = hqmf_model.cql_measure_library
-
-      cql_artifacts = process_cql(files, main_cql_library, user, vsac_options, vsac_ticket_granting_ticket, hqmf_model.hqmf_set_id)
-
-      # Create CQL Measure
-      hqmf_model.backfill_patient_characteristics_with_codes(cql_artifacts[:all_codes_and_code_names])
-      json = hqmf_model.to_json
-      json.convert_keys_to_strings
-
-      # Set the code list ids of data criteria and source data criteria that use direct reference codes to GUIDS.
-      json['source_data_criteria'], json['data_criteria'] = set_data_criteria_code_list_ids(json, cql_artifacts)
+    # Verifies contents of the given measure are valid (works for regular, composite and component measures)
+    def self.valid_measure_contents?(measure_dir, check_components = false)
+      # If composite measure given, check components
+      if check_components
+        Dir.glob("#{measure_dir}/*").each do |file|
+          if File.directory?(file)
+            if !valid_measure_contents?(file)
+              return false
+            end
+          end
+        end
+      end
 
-      # Create CQL Measure
-      measure = Measures::Loader.load_hqmf_cql_model_json(json, user, cql_artifacts[:all_value_set_oids], main_cql_library, cql_artifacts[:cql_definition_dependency_structure],
-                                                          cql_artifacts[:elms], cql_artifacts[:elm_annotations], files[:CQL], nil, cql_artifacts[:value_set_oid_version_objects])
-      measure['episode_of_care'] = measure_details['episode_of_care']
-      measure['type'] = measure_details['type']
-      measure['calculate_sdes'] = measure_details['calculate_sdes']
+      # Grab all cql, elm & human readable docs from measure
+      cql_entry = Dir.glob(File.join(measure_dir,'**.cql')).select {|x| !File.basename(x).starts_with?('__MACOSX') }.first
+      elm_json = Dir.glob(File.join(measure_dir,'**.json')).select {|x| !File.basename(x).starts_with?('__MACOSX') }.first
+      human_readable_entry = Dir.glob(File.join(measure_dir,'**.html')).select {|x| !File.basename(x).starts_with?('__MACOSX') }.first
 
-      # Create, associate and save the measure package.
-      measure.package = CqlMeasurePackage.new(file: BSON::Binary.new(zip_file.read()))
-      measure.package.save
+      # Grab all xml files in the measure.
+      xml_files = Dir.glob(File.join(measure_dir,'**.xml')).select {|x| !File.basename(x).starts_with?('__MACOSX') }
 
-      measure
+      # Find key value pair for HQMF and ELM xml files.
+      if xml_files.count > 0
+        xml_files_hash = retrieve_elm_and_hqmf(xml_files)
+        !cql_entry.nil? && !elm_json.nil? && !human_readable_entry.nil? && !xml_files_hash[:HQMF_XML].nil? && !xml_files_hash[:ELM_XML].nil?
+      else
+        false
+      end
     end
 
     def self.set_data_criteria_code_list_ids(json, cql_artifacts)
@@ -84,28 +115,175 @@ module Measures
       return json['source_data_criteria'], json['data_criteria']
     end
 
-    def self.load(file, user, measure_details, vsac_options, vsac_ticket_granting_ticket)
+    # Returns an array of measures
+    # Single measure returned into the array if it is a non-composite measure
+    def self.extract_measures(measure_zip, current_user, measure_details, vsac_options, vsac_ticket_granting_ticket)
       measure = nil
-      Dir.mktmpdir do |dir|
-        measure = load_mat_cql_exports(user, file, dir, measure_details, vsac_options, vsac_ticket_granting_ticket)
+      component_measures = []
+      # Unzip measure contents while retaining the directory structure
+      Dir.mktmpdir do |tmp_dir|
+        current_directory = unzip_measure_contents(measure_zip, tmp_dir)
+        if !valid_measure_contents?(current_directory, true)
+          raise MeasureLoadingException.new("Zip file was not a MAT package.")
+        end
+        component_elms = {}
+        component_elms[:ELM_JSON] = []
+
+        # If it is a composite measure, load in each of the components
+        # Components must be loaded first so their elms can be passed onto the composite
+        if composite_measure?(current_directory)
+          component_measures = create_component_measures(current_directory, current_user, measure_details, vsac_options, vsac_ticket_granting_ticket)
+          component_measures.each do |component_measure|
+            component_elms[:ELM_JSON].push(*component_measure.elm)
+          end
+        end
+
+        # Load in regular/composite measure measure
+        begin
+          measure = create_measure(current_directory, current_user, measure_details, vsac_options, vsac_ticket_granting_ticket, component_elms)
+        rescue => e
+          component_measures.each { |component| component.delete }
+          raise e
+        end
+
+        # Create, associate and save the measure package.
+        measure_package = CqlMeasurePackage.new(file: BSON::Binary.new(measure_zip.read()))
+        measure.package = measure_package
+        measure.package.save 
+
+        component_measures.each do |component_measure|
+          # Update the components' hqmf_set_id, formatted as follows:
+          #   <composite_hqmf_set_id>&<component_hqmf_set_id>
+          component_measure.hqmf_set_id = measure.hqmf_set_id + '&' + component_measure.hqmf_set_id
+          component_measure.component = true;
+          # Associate the component with the composite
+          measure.component_hqmf_set_ids.push(component_measure.hqmf_set_id)
+        end
+      end # End of temporary directory usage 
+
+      # Put measure (and component measures) into an array to return
+      measures = component_measures << measure
+      return measures
+    end
+
+    # Creates a composite's component measures 
+    def self.create_component_measures(current_directory, current_user, measure_details, vsac_options, vsac_ticket_granting_ticket)
+      component_measures = []
+      Dir.glob("#{current_directory}/*").sort.each do |file|
+        if File.directory?(file)
+          component_measures << create_measure(file, current_user, measure_details, vsac_options, vsac_ticket_granting_ticket)
+        end
       end
+      component_measures
+    end
+
+    # Creates and returns a measure 
+    def self.create_measure(measure_dir, user, measure_details, vsac_options, vsac_ticket_granting_ticket, component_elms=nil)
+      measure = nil
+
+      # Grabs the cql file contents, the elm_xml contents, elm_json contents and the hqmf file path
+      files = get_files_from_directory(measure_dir)
+
+      # Load hqmf into HQMF Parser
+      hqmf_model = Measures::Loader.parse_hqmf_model(files[:HQMF_XML_PATH])
+
+      # Get main measure from hqmf parser
+      main_cql_library = hqmf_model.cql_measure_library
+
+      cql_artifacts = process_cql(files, main_cql_library, user, vsac_options, vsac_ticket_granting_ticket, hqmf_model.hqmf_set_id, component_elms)
+
+      # Create CQL Measure
+      hqmf_model.backfill_patient_characteristics_with_codes(cql_artifacts[:all_codes_and_code_names])
+      json = hqmf_model.to_json
+      json.convert_keys_to_strings
+
+      # Set the code list ids of data criteria and source data criteria that use direct reference codes to GUIDS.
+      json['source_data_criteria'], json['data_criteria'] = set_data_criteria_code_list_ids(json, cql_artifacts)
+
+      # Create CQL Measure
+      measure_details["composite"] = composite_measure?(measure_dir)
+      measure = Measures::Loader.load_hqmf_cql_model_json(json, user, cql_artifacts[:all_value_set_oids], main_cql_library, cql_artifacts[:cql_definition_dependency_structure],
+                                                          cql_artifacts[:elms], cql_artifacts[:elm_annotations], files[:CQL], measure_details, cql_artifacts[:value_set_oid_version_objects])
       measure
     end
 
+    def self.get_files_from_directory(dir)
+      cql_paths = Dir.glob(File.join("#{dir}/**.cql")).sort
+      xml_paths = Dir.glob(File.join("#{dir}/**.xml")).sort
+      elm_json_paths = Dir.glob(File.join("#{dir}/**.json")).sort
+      
+      begin
+        cql_contents = []
+        cql_paths.each do |cql_path|
+          cql_contents << open(cql_path).read
+        end
+
+        elm_json = []
+        elm_json_paths.each do |elm_json_path|
+          elm_json << open(elm_json_path).read
+        end
+        
+        xml_file_hash = retrieve_elm_and_hqmf(xml_paths)
+        elm_xml_paths = xml_file_hash[:ELM_XML]
+        elm_xml = []
+        elm_xml_paths.each do |elm_xml_path|
+          elm_xml << open(elm_xml_path).read
+        end
+
+        files = { :HQMF_XML_PATH => xml_file_hash[:HQMF_XML],
+                  :ELM_JSON => elm_json,
+                  :CQL => cql_contents,
+                  :ELM_XML => elm_xml }
+        return files
+      rescue Exception => e
+        raise MeasureLoadingException.new "Error Parsing Measure Logic: #{e.message}"
+      end
+    end
+
+    # Takes in array of xml files and returns hash with keys HQMF_XML and ELM_XML
+    def self.retrieve_elm_and_hqmf(files)
+      file_paths_hash = {}
+      file_paths_hash[:ELM_XML] = []
+      begin
+        files.each do |xml_file_path|
+          if xml_file_path && xml_file_path.size > 0
+            # Open up xml file and read contents.
+            doc = Nokogiri::XML.parse(File.read(xml_file_path))
+            # Check if root node in xml file matches either the HQMF file or ELM file.
+            if doc.root.name == 'QualityMeasureDocument' # Root node for HQMF XML
+              file_paths_hash[:HQMF_XML] = xml_file_path
+            elsif doc.root.name == 'library' # Root node for ELM XML
+              file_paths_hash[:ELM_XML] << xml_file_path
+            end
+          end
+        end     
+      rescue Exception => e
+        raise MeasureLoadingException.new "Error Checking MAT Export: #{e.message}"
+      end
+      file_paths_hash
+    end
+
     # Manages all of the CQL processing that is not related to the HQMF.
-    def self.process_cql(files, main_cql_library, user, vsac_options, vsac_ticket_granting_ticket, measure_id=nil)
+    def self.process_cql(files, main_cql_library, user, vsac_options, vsac_ticket_granting_ticket, measure_id=nil, component_elms=nil)
       elm_strings = files[:ELM_JSON]
       # Removes 'urn:oid:' from ELM for Bonnie and Parse the JSON
       elm_strings.each { |elm_string| elm_string.gsub! 'urn:oid:', '' }
       elms = elm_strings.map{ |elm| JSON.parse(elm, :max_nesting=>1000)}
       elm_annotations = parse_elm_annotations(files[:ELM_XML])
 
+      if (!component_elms.nil?)
+        elms.push(*component_elms[:ELM_JSON]) 
+      end
       # Hash of define statements to which define statements they use.
       cql_definition_dependency_structure = populate_cql_definition_dependency_structure(main_cql_library, elms)
-      # Go back for the library statements
-      cql_definition_dependency_structure = populate_used_library_dependencies(cql_definition_dependency_structure, main_cql_library, elms)
-      # Add unused libraries to structure and set the value to empty hash
-      cql_definition_dependency_structure = populate_unused_included_libraries(cql_definition_dependency_structure, elms)
+      begin
+        # Go back for the library statements
+        cql_definition_dependency_structure = populate_used_library_dependencies(cql_definition_dependency_structure, main_cql_library, elms)
+        # Add unused libraries to structure and set the value to empty hash
+        cql_definition_dependency_structure = populate_unused_included_libraries(cql_definition_dependency_structure, elms)
+      rescue => e
+        raise MeasureLoadingException.new("Measure package missing a library or component.")
+      end
 
       # fix up statement names in cql_statement_dependencies to not use periods <<WRAP 1>>
       # this is matched with an UNWRAP in MeasuresController in the bonnie project
@@ -177,7 +355,7 @@ module Measures
                        :all_codes_and_code_names => all_codes_and_code_names}
     end
 
-    # returns a list of objects that include the valueset oids and their versions
+    # Returns a list of objects that include the valueset oids and their versions
     def self.get_value_set_oid_version_objects(value_sets, single_code_references)
       # [LDC] need to make this an array of objects instead of a hash because Mongo is
       # dumb and *let's you* have dots in keys on object creation but *doesn't let you*
@@ -268,50 +446,6 @@ module Measures
       return single_code_references, all_codes_and_code_names
     end
 
-    # Opens the zip and grabs the cql file contents, the ELM contents (XML and JSON) and hqmf_path.
-    def self.get_files_from_zip(zip_file, out_dir)
-      Zip::ZipFile.open(zip_file.path) do |file|
-        cql_entries = file.glob(File.join('**','**.cql')).select {|x| !x.name.starts_with?('__MACOSX') }
-        zip_xml_files = file.glob(File.join('**','**.xml')).select {|x| !x.name.starts_with?('__MACOSX') }
-        elm_json_entries = file.glob(File.join('**','**.json')).select {|x| !x.name.starts_with?('__MACOSX') }
-        
-        begin
-          cql_paths = []
-          cql_entries.each do |cql_file|
-            cql_paths << extract(file, cql_file, out_dir) if cql_file.size > 0
-          end
-          cql_contents = []
-          cql_paths.each do |cql_path|
-            cql_contents << open(cql_path).read
-          end
-
-          elm_json_paths = []
-          elm_json_entries.each do |json_file|
-            elm_json_paths << extract(file, json_file, out_dir) if json_file.size > 0
-          end
-          elm_json = []
-          elm_json_paths.each do |elm_json_path|
-            elm_json << open(elm_json_path).read
-          end
-          
-          xml_file_paths = extract_xml_files(file, zip_xml_files, out_dir)
-          elm_xml_paths = xml_file_paths[:ELM_XML]
-          elm_xml = []
-          elm_xml_paths.each do |elm_xml_path|
-            elm_xml << open(elm_xml_path).read
-          end
-
-          files = { :HQMF_XML_PATH => xml_file_paths[:HQMF_XML],
-                    :ELM_JSON => elm_json,
-                    :CQL => cql_contents,
-                    :ELM_XML => elm_xml }
-          return files
-        rescue Exception => e
-          raise MeasureLoadingException.new "Error Parsing Measure Logic: #{e.message}"
-        end
-      end
-    end
-
     private
     def self.parse_elm_annotations(xmls)
       elm_annotations = {}