aqueduct-i2b2 0.1.0

data/CHANGELOG.rdoc

@@ -0,0 +1,8 @@
+== 0.1.0
+
+* Enhancements
+  * Connects to an i2b2 server through Aqueduct interface
+
+== 0.0.0
+
+* Skeleton files to compile gem and make it available on rubygems.org

data/LICENSE

@@ -0,0 +1,112 @@
+Copyright (c) 2012 Remo Mueller
+https://github.com/remomueller
+https://rubygems.org/profiles/remomueller
+
+
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data/README.rdoc

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+= Aqueduct Wrapper - i2b2 {<img src="https://secure.travis-ci.org/remomueller/aqueduct-i2b2.png"/>}[http://travis-ci.org/remomueller/aqueduct-i2b2] {<img src="https://gemnasium.com/remomueller/aqueduct-i2b2.png" alt="Dependency Status" />}[https://gemnasium.com/remomueller/aqueduct-i2b2]
+
+Connects to an i2b2 instance using Aqueduct interface
+
+== Installation
+
+Aqueduct Wrapper - i2b2 can be installed from rubygems.org using:
+
+  gem install aqueduct-i2b2
+
+Or update your Gemfile to include:
+
+  gem 'aqueduct-i2b2'
+
+== Copyright
+
+Copyright (c) 2012 Remo Mueller. See {LICENSE}[https://github.com/remomueller/aqueduct-i2b2/blob/master/LICENSE] for further details.

data/Rakefile

@@ -0,0 +1,41 @@
+#!/usr/bin/env rake
+begin
+  require 'bundler/setup'
+rescue LoadError
+  puts 'You must `gem install bundler` and `bundle install` to run rake tasks'
+end
+begin
+  require 'rdoc/task'
+rescue LoadError
+  require 'rdoc/rdoc'
+  require 'rake/rdoctask'
+  RDoc::Task = Rake::RDocTask
+end
+
+RDoc::Task.new(:rdoc) do |rdoc|
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title    = 'AqueductI2b2'
+  rdoc.options << '--line-numbers'
+  rdoc.rdoc_files.include('CHANGELOG.rdoc')
+  rdoc.rdoc_files.include('README.rdoc')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end
+
+APP_RAKEFILE = File.expand_path("../test/dummy/Rakefile", __FILE__)
+load 'rails/tasks/engine.rake'
+
+
+
+Bundler::GemHelper.install_tasks
+
+require 'rake/testtask'
+
+Rake::TestTask.new(:test) do |t|
+  t.libs << 'lib'
+  t.libs << 'test'
+  t.pattern = 'test/**/*_test.rb'
+  t.verbose = false
+end
+
+
+task :default => :test

data/aqueduct-i2b2.gemspec

@@ -0,0 +1,31 @@
+# Compiling the Gem
+# gem build aqueduct-i2b2.gemspec
+# gem install ./aqueduct-i2b2-x.x.x.gem
+#
+# gem push aqueduct-i2b2-x.x.x.gem
+# gem list -r aqueduct-i2b2
+# gem install aqueduct-i2b2
+
+$:.push File.expand_path("../lib", __FILE__)
+
+# Maintain your gem's version:
+require "aqueduct-i2b2/version"
+
+# Describe your gem and declare its dependencies:
+Gem::Specification.new do |s|
+  s.name        = "aqueduct-i2b2"
+  s.version     = Aqueduct::I2b2::VERSION::STRING
+  s.authors     = ["Remo Mueller"]
+  s.email       = ["remosm@gmail.com"]
+  s.homepage    = "https://github.com/remomueller"
+  s.summary     = "Connect to an instance of i2b2 through Aqueduct"
+  s.description = "Connects to an instance of i2b2 through Aqueduct interface"
+
+  s.files = Dir["{app,config,db,lib}/**/*"] + ["aqueduct-i2b2.gemspec", "CHANGELOG.rdoc", "LICENSE", "Rakefile", "README.rdoc"]
+  s.test_files = Dir["test/**/*"]
+
+  s.add_dependency "rails",     "~> 3.2.1"
+  s.add_dependency "aqueduct",  "~> 0.1.0"
+
+  s.add_development_dependency "sqlite3"
+end

data/lib/aqueduct-i2b2.rb

@@ -0,0 +1,7 @@
+require "aqueduct-i2b2/version"
+require "aqueduct/wrappers/i2b2"
+
+module Aqueduct
+  module I2b2
+  end
+end

data/lib/aqueduct-i2b2/version.rb

@@ -0,0 +1,12 @@
+module Aqueduct
+  module I2b2
+    module VERSION
+      MAJOR = 0
+      MINOR = 1
+      TINY = 0
+      BUILD = nil # nil, "pre", "rc", "rc2"
+
+      STRING = [MAJOR, MINOR, TINY, BUILD].compact.join('.')
+    end
+  end
+end

data/lib/aqueduct/wrappers/i2b2.rb

@@ -0,0 +1,715 @@
+require 'aqueduct'
+
+require 'net/http'
+require 'net/https'
+require 'uri'
+
+require 'base64'
+require 'openssl'
+
+module Aqueduct
+  module Wrappers
+    class I2b2
+      include Aqueduct::Wrapper
+
+      DOMAIN = 'i2b2demo'
+
+      def external_concepts(folder = '', search_term = '')
+        search_term.blank? ? get_concepts(folder) : search_for_term(folder, search_term)
+      end
+
+      def external_concept_information(external_key = '')
+        error = ''
+        result = {}
+
+        service_url = '/i2b2/rest/OntologyService/getTermInfo'
+
+        xml = ::Builder::XmlMarkup.new
+        xml.instruct! :xml, standalone: 'yes'
+        xml.tag!("ns3:request", "xmlns:ns3" => "http://www.i2b2.org/xsd/hive/msg/1.1/",
+                                "xmlns:ns4" => "http://www.i2b2.org/xsd/cell/ont/1.1/",
+                                "xmlns:ns2" => "http://www.i2b2.org/xsd/hive/plugin/") do |req|
+          req.message_header do |mhr|
+            mhr << message_header(service_url, 'i2b2 Ontology', 1.6, 'i2b2 Hive',
+                                               'Ontology Cell', 1.6, 'i2b2 Hive')
+          end
+          req.request_header do |rqh|
+            rqh.result_waittime_ms 180000
+          end
+          req.message_body do |mgb|
+            mgb.tag!('ns4:get_term_info', "blob" => "true", "type" => "core", "synonyms" => "true", "hiddens" => "true") do |gti|
+              gti.tag!('self') do |sef|
+                sef.text! external_key
+              end
+            end
+          end
+        end
+
+        result_hash = process_concepts(send_message(xml.target!, service_url))
+        result = result_hash[:result].first unless result_hash[:result].first.blank?
+        { result: result, error: result_hash[:error] }
+      end
+
+      def count(query_concepts, conditions, tables, join_conditions, concept_to_count)
+        get_total_count(query_concepts.find_all_by_id(eval(conditions)))
+      end
+
+      def use_sql?
+        false
+      end
+
+      def concept_tables(query_concept)
+        { result: [], error: '' }
+      end
+
+      def conditions(query_concepts)
+        { conditions: "#{query_concepts.collect{|qc| qc.id}}", error: '' }
+      end
+
+      def query(sql_statement)
+        # result = [[['cname', 'cname2', 'cname3', 'cname4'],[1,2,3,4],[5,nil,7,8]],2]
+        result = [[]]
+
+        concept_list = []
+        # TODO: Replace this with query_concepts (pass in query concepts initially?)
+
+        query_concepts = QueryConcept.find_all_by_id(eval(sql_statement))
+
+
+        result_hash = get_all_covariates(query_concepts)
+
+        result = result_hash[:result]
+        error = result_hash[:error]
+
+        # THIS WORKS! (For limited ors and non complex things)
+        # query_concepts.each_with_index do |query_concept, index|
+        #   concept_list << { key: query_concept.external_key, right_operator: query_concept.right_operator, negated: query_concept.negated }
+        # end
+        #
+        # conditions = query_definition(concept_list)
+        #
+        # patient_data = run_query_get_patient_data(conditions)
+        #
+        # if patient_data.first and patient_data.first[1]
+        #   all_concepts = patient_data.first[1].keys
+        #   result[0] = ['patient_id'] + all_concepts
+        # end
+        #
+        # patient_data.each_pair do |patient_id, value_hash|
+        #   row_data = [patient_id]
+        #   all_concepts.each do |concept|
+        #     row_data << value_hash[concept][:value]
+        #   end
+        #   result << row_data
+        # end
+
+        [result, result.size]
+      end
+
+      # TODO: Update i2b2 connect to make sure the server is up and running
+      def connect
+        true
+      end
+
+      private
+
+      def current_time
+        @current_time ||= Time.now.strftime("%Y-%m-%dT%T") + Time.now.strftime("%z").gsub(/([+-]?\d\d)(\d\d)/, "#{$1}:#{$2}")
+      end
+
+      def message_header(redirect_url, sending_app_name, sending_app_version, sending_facility_name, receiving_app_name, receiving_app_version, receiving_facility_name, aat = 'AL', token_available = true)
+        @message_header ||= begin
+          xml = ::Builder::XmlMarkup.new
+          xml.proxy do |pxy|
+            pxy.redirect_url                    "#{@source.host}#{redirect_url}"
+          end
+          xml.sending_application do |sap|
+            sap.application_name                sending_app_name
+            sap.application_version             sending_app_version
+          end
+          xml.sending_facility do |sfa|
+            sfa.facility_name                   sending_facility_name
+          end
+          xml.i2b2_version_compatible           1.1
+          xml.hl7_version_compatible            2.4
+          xml.datetime_of_message               current_time
+          xml.message_control_id do |mci|
+            mci.message_num                     'iFL7f7DmuTj349bdHcDCl'
+            mci.instance_num                    0
+          end
+          xml.processing_id do |pi|
+            pi.processing_id                    'P'
+            pi.processing_mode                  'I'
+          end
+          xml.accept_acknowledgement_type       aat
+          xml.application_acknowledgement_type  'AL'
+          xml.country_code                      'US'
+          xml.project_id                        'Demo'
+          xml.receiving_application do |rap|
+            rap.application_name                receiving_app_name
+            rap.application_version             receiving_app_version
+          end
+          xml.receiving_facility do |rfa|
+            rfa.facility_name                   receiving_facility_name
+          end
+          xml.security do |sec|
+            sec.domain                          DOMAIN
+            sec.username                        @source.username
+            if token_available
+              sec.tag!('password', 'token_ms_timeout' => '1800000', 'is_token' => 'true') do |p|
+                p.text!                         session_key.to_s
+              end
+            else
+              sec.password                      @source.password
+            end
+          end
+          xml.target!
+        end
+      end
+
+      def session_key
+        @session_key ||= begin
+          service_url = '/i2b2/rest/PMService/getServices'
+
+          xml = ::Builder::XmlMarkup.new
+          xml.instruct! :xml, standalone: 'yes'
+          xml.tag!("i2b2:request", "xmlns:i2b2" => "http://www.i2b2.org/xsd/hive/msg/1.1/", "xmlns:pm" => "http://www.i2b2.org/xsd/cell/pm/1.1/") do |req|
+            req.message_header do |mhr|
+              mhr << message_header('', 'i2b2 Project Management', 1.6, 'i2b2 Hive',
+                                        'Project Management Cell', 1.6, 'i2b2 Hive', 'AL', false)
+            end
+            req.request_header do |rqh|
+              rqh.result_waittime_ms 180000
+            end
+            req.message_body do |mgb|
+              mgb.tag!('pm:get_user_configuration') do |cfg|
+                cfg.project 'undefined'
+              end
+            end
+          end
+
+          result_hash = send_message(xml.target!, service_url)
+
+          if result_hash[:error].blank?
+            # Pull out service key
+            key = result_hash[:result].scan(/<password .*?>(.*)<\/password>/).first.first
+          else
+            Rails.logger.debug "Error: #{result_hash[:error]}"
+            nil
+          end
+        end
+      end
+
+      def xmlitem(xml_string, xml_element)
+        xml_string.scan(/<#{xml_element}>(.*?)<\/#{xml_element}>/m).flatten.first.to_s
+      end
+
+      def process_concepts(result_hash, queryable = true)
+        categories = []
+
+        if result_hash[:error].blank?
+          concepts = result_hash[:result].scan(/<concept>(.*?)<\/concept>/m)
+          concepts.flatten.each do |c|
+            visual_attributes = xmlitem(c, 'visualattributes')
+
+            is_folder = ['CA', 'FA'].include?(visual_attributes[0..1])
+
+            full_folder = xmlitem(c, 'key')
+
+            categories << { tooltip:            xmlitem(c, 'tooltip'),
+                            is_folder:          is_folder,
+                            is_queryable:       queryable,
+                            key:                xmlitem(c, 'key'),
+                            level:              xmlitem(c, 'level'),
+                            name:               xmlitem(c, 'name'),
+                            visual_attributes:  visual_attributes,
+                            totalnum:           xmlitem(c, 'totalnum'),
+                            source_id:          @source.id,
+                            folder:             @source.name }
+            # c.first.gsub(/[^\w<>]/, '').inspect  # gsub(" ", "_")
+          end
+        end
+
+        { result: categories, error: result_hash[:error] }
+      end
+
+      def get_categories
+        service_url = '/i2b2/rest/OntologyService/getCategories'
+
+        xml = ::Builder::XmlMarkup.new
+        xml.instruct! :xml, standalone: 'yes'
+        xml.tag!("ns3:request", "xmlns:ns3" => "http://www.i2b2.org/xsd/hive/msg/1.1/",
+                                "xmlns:ns4" => "http://www.i2b2.org/xsd/cell/ont/1.1/",
+                                "xmlns:ns2" => "http://www.i2b2.org/xsd/hive/plugin/") do |req|
+          req.message_header do |mhr|
+            mhr << message_header(service_url, 'i2b2 Project Management', 1.6, 'i2b2 Hive',
+                                               'Project Management Cell', 1.6, 'i2b2 Hive')
+          end
+          req.request_header do |rqh|
+            rqh.result_waittime_ms 180000
+          end
+          req.message_body do |mgb|
+            mgb.tag!('ns4:get_categories', "type" => "core")
+          end
+        end
+
+        process_concepts send_message(xml.target!, service_url), false
+      end
+
+      def get_child_concepts(folder = '')
+        service_url = '/i2b2/rest/OntologyService/getChildren'
+
+        xml = ::Builder::XmlMarkup.new
+        xml.instruct! :xml, standalone: 'yes'
+        xml.tag!("ns3:request", "xmlns:ns3" => "http://www.i2b2.org/xsd/hive/msg/1.1/",
+                                "xmlns:ns4" => "http://www.i2b2.org/xsd/cell/ont/1.1/",
+                                "xmlns:ns2" => "http://www.i2b2.org/xsd/hive/plugin/") do |req|
+          req.message_header do |mhr|
+            mhr << message_header(service_url, 'i2b2 Ontology', 1.6, 'i2b2 Hive',
+                                               'Ontology Cell', 1.6, 'i2b2 Hive')
+          end
+          req.request_header do |rqh|
+            rqh.result_waittime_ms 180000
+          end
+          req.message_body do |mgb|
+            mgb.tag!('ns4:get_children', "blob" => "false", "type" => "core", "max" => "500", "synonyms" => "false", "hiddens" => "false") do |chi|
+              chi.parent folder
+            end
+          end
+        end
+
+        process_concepts send_message(xml.target!, service_url)
+      end
+
+      def get_concepts(folder = '')
+        folder.blank? ? get_categories : get_child_concepts(folder)
+      end
+
+      def items(concept_list)
+        result = ''
+
+        concept_list.each do |concept_hash|
+          item = ''
+          item << "\n\n<item>"
+          item << "\n  <hlevel>#{concept_hash[:level]}</hlevel>"
+          item << "\n  <item_name>#{concept_hash[:name]}</item_name>"
+          item << "\n  <item_key>#{concept_hash[:key]}</item_key>"
+          item << "\n  <tooltip>#{concept_hash[:tooltip]}</tooltip>"
+          item << "\n  <class>ENC</class>"
+          item << "\n  <item_icon>#{concept_hash[:visual_attributes]}</item_icon>"
+          item << "\n  <item_is_synonym>false</item_is_synonym>"
+          item << "\n</item>\n\n"
+          result << item
+        end
+
+        result
+      end
+
+      def query_definition(concept_list, query_name = Time.now.to_s)
+        panel_number = 0
+        new_panel = true
+
+        query_name = query_name.gsub(/[^\w \:+-]/, '-')
+
+        q = "<query_definition>"
+        q << "<query_name>#{query_name}</query_name>"
+        q << "<query_timing>ANY</query_timing>"
+        q << "<specificity_scale>0</specificity_scale>"
+
+        concept_list.each do |concept_item|
+          if new_panel
+            panel_number += 1
+            q += "#{'</panel>' unless panel_number == 1}<panel><panel_number>#{panel_number}</panel_number><panel_accuracy_scale>0</panel_accuracy_scale><invert>#{concept_item[:negated] ? '1' : '0'}</invert><panel_timing>ANY</panel_timing><total_item_occurrences>1</total_item_occurrences>"
+          end
+          q += items([concept_item])
+          new_panel = (concept_item[:right_operator] == 'and')
+        end
+
+        q << "</panel></query_definition>"
+        q
+      end
+
+      # This function may be necessary in certain cases (faster count for single concepts)
+      # Currently it's not called, as of initial version 2.9.0
+      def run_query_get_count(conditions)
+        result = 0
+        query_master_id = '0'
+
+        service_url = "/i2b2/rest/QueryToolService/request"
+
+        xml = ::Builder::XmlMarkup.new
+        xml.instruct! :xml, standalone: 'yes'
+        xml.tag!("ns6:request", "xmlns:ns4" => "http://www.i2b2.org/xsd/cell/crc/psm/1.1/",
+                                "xmlns:ns7" => "http://www.i2b2.org/xsd/cell/ont/1.1/",
+                                "xmlns:ns3" => "http://www.i2b2.org/xsd/cell/crc/pdo/1.1/",
+                                "xmlns:ns5" => "http://www.i2b2.org/xsd/hive/plugin/",
+                                "xmlns:ns2" => "http://www.i2b2.org/xsd/hive/pdo/1.1/",
+                                "xmlns:ns6" => "http://www.i2b2.org/xsd/hive/msg/1.1/",
+                                "xmlns:ns8" => "http://www.i2b2.org/xsd/cell/crc/psm/querydefinition/1.1/") do |req|
+          req.message_header do |mhr|
+            mhr << message_header(service_url, 'i2b2_QueryTool', 1.6, 'PHS',
+                                               'i2b2_DataRepositoryCell', 1.6, 'PHS', 'messageId')
+
+            # Message Type doesn't look like it is required...what's the purpose?
+            mhr.message_type do |mtp|
+              mtp.message_code            'Q04'
+              mtp.event_type              'EQQ'
+            end
+          end
+          req.request_header do |rqh|
+            rqh.result_waittime_ms        180000
+          end
+          req.message_body do |mgb|
+            mgb.tag!('ns4:psmheader') do |pmh|
+              pmh.user('group' => 'Demo', "login" => "demo") do |usr|
+                usr.text!                 'demo'
+              end
+              pmh.patient_set_limit       0
+              pmh.estimated_time          0
+              pmh.query_mode              'optimize_without_temp_table'
+              pmh.request_type            'CRC_QRY_runQueryInstance_fromQueryDefinition'
+            end
+            mgb.tag!('ns4:request', "xsi:type" => "ns4:query_definition_requestType", "xmlns:xsi" => "http://www.w3.org/2001/XMLSchema-instance") do |req|
+              req << conditions
+              req.result_output_list do |rol|
+                rol.result_output("priority_index" => "9", "name" => "patient_count_xml") # The only difference between this and run_query_get_patient_set
+              end
+            end
+          end
+        end
+
+        result_hash = send_message(xml.target!, service_url)
+
+        result = xmlitem(result_hash[:result], 'set_size') if result_hash[:error].blank?
+        query_master_id = xmlitem(result_hash[:result], 'result_instance_id') if result_hash[:error].blank?
+
+        {result: result, error: result_hash[:error], query_master_id: query_master_id}
+      end
+
+      def run_query_get_patient_set(conditions)
+        result = 0
+        service_url = "/i2b2/rest/QueryToolService/request"
+
+        xml = ::Builder::XmlMarkup.new
+        xml.instruct! :xml, standalone: 'yes'
+        xml.tag!("ns6:request", "xmlns:ns4" => "http://www.i2b2.org/xsd/cell/crc/psm/1.1/",
+                                "xmlns:ns7" => "http://www.i2b2.org/xsd/cell/ont/1.1/",
+                                "xmlns:ns3" => "http://www.i2b2.org/xsd/cell/crc/pdo/1.1/",
+                                "xmlns:ns5" => "http://www.i2b2.org/xsd/hive/plugin/",
+                                "xmlns:ns2" => "http://www.i2b2.org/xsd/hive/pdo/1.1/",
+                                "xmlns:ns6" => "http://www.i2b2.org/xsd/hive/msg/1.1/",
+                                "xmlns:ns8" => "http://www.i2b2.org/xsd/cell/crc/psm/querydefinition/1.1/") do |req|
+          req.message_header do |mhr|
+            mhr << message_header(service_url, 'i2b2_QueryTool', 1.6, 'PHS',
+                                               'i2b2_DataRepositoryCell', 1.6, 'PHS', 'messageId')
+
+            # Message Type doesn't look like it is required...what's the purpose?
+            mhr.message_type do |mtp|
+              mtp.message_code            'Q04'
+              mtp.event_type              'EQQ'
+            end
+          end
+          req.request_header do |rqh|
+            rqh.result_waittime_ms        180000
+          end
+          req.message_body do |mgb|
+            mgb.tag!('ns4:psmheader') do |pmh|
+              pmh.user('group' => 'Demo', "login" => "demo") do |usr|
+                usr.text!                 'demo'
+              end
+              pmh.patient_set_limit       0
+              pmh.estimated_time          0
+              pmh.query_mode              'optimize_without_temp_table'
+              pmh.request_type            'CRC_QRY_runQueryInstance_fromQueryDefinition'
+            end
+            mgb.tag!('ns4:request', "xsi:type" => "ns4:query_definition_requestType", "xmlns:xsi" => "http://www.w3.org/2001/XMLSchema-instance") do |req|
+              req << conditions
+              req.result_output_list do |rol|
+                rol.result_output("priority_index" => "9", "name" => "patientset")
+              end
+            end
+          end
+        end
+
+        result_hash = send_message(xml.target!, service_url)
+
+        result = xmlitem(result_hash[:result], 'set_size') if result_hash[:error].blank?
+        query_master_id = xmlitem(result_hash[:result], 'result_instance_id') if result_hash[:error].blank?
+
+
+        { result: result, error: result_hash[:error], query_master_id: query_master_id }
+      end
+
+      def run_pdo_request(conditions)
+
+        result_hash = run_query_get_patient_set(conditions)
+        if result_hash[:error].blank?
+          query_master_id = result_hash[:query_master_id]
+        else
+
+        end
+
+        service_url = "/i2b2/rest/QueryToolService/pdorequest"
+
+        xml = ::Builder::XmlMarkup.new
+        xml.instruct! :xml, standalone: 'yes'
+        xml.tag!("ns6:request", "xmlns:ns4" => "http://www.i2b2.org/xsd/cell/crc/psm/1.1/",
+                                "xmlns:ns7" => "http://www.i2b2.org/xsd/cell/crc/psm/querydefinition/1.1/",
+                                "xmlns:ns3" => "http://www.i2b2.org/xsd/cell/crc/pdo/1.1/",
+                                "xmlns:ns5" => "http://www.i2b2.org/xsd/hive/plugin/",
+                                "xmlns:ns2" => "http://www.i2b2.org/xsd/hive/pdo/1.1/",
+                                "xmlns:ns6" => "http://www.i2b2.org/xsd/hive/msg/1.1/") do |req|
+          req.message_header do |mhr|
+            mhr << message_header(service_url, 'i2b2_QueryTool', 1.6, 'PHS',
+                                               'i2b2_DataRepositoryCell', 1.6, 'PHS', 'messageId')
+            # Message Type doesn't look like it is required...what's the purpose?
+            mhr.message_type do |mtp|
+              mtp.message_code            'Q04'
+              mtp.event_type              'EQQ'
+            end
+          end
+          req.request_header do |rqh|
+            rqh.result_waittime_ms        180000
+          end
+          req.message_body do |mgb|
+
+            mgb.tag!('ns3:pdoheader') do |pdh|
+              pdh.patient_set_limit 0
+              pdh.estimated_time 180000
+              pdh.request_type 'getPDO_fromInputList'
+            end
+
+            mgb.tag!('ns3:request', "xmlns:xsi" => "http://www.w3.org/2001/XMLSchema-instance", "xsi:type" => "ns3:GetPDOFromInputList_requestType") do |req|
+              req.input_list do |ipl|
+                ipl.tag!('patient_list', "max" => "1000000", "min" => "0") do |pal|
+                  pal.patient_set_coll_id query_master_id
+                end
+              end
+              req.filter_list
+              req.output_option do |opo|
+                opo.tag!('patient_set', "select" => "using_input_list", "onlykeys" => "false")
+              end
+            end
+          end
+        end
+
+        result_hash = send_message(xml.target!, service_url)
+        result_hash
+      end
+
+      def run_query_get_patient_ids(conditions)
+
+        result_hash = run_pdo_request(conditions)
+
+        patient_ids = []
+
+        if result_hash[:error].blank?
+          patient_ids = result_hash[:result].scan(/<patient_id>(.*?)<\/patient_id>/).flatten
+        else
+          Rails.logger.debug result_hash[:error]
+        end
+
+        { result: patient_ids, error: result_hash[:error] }
+      end
+
+      def run_query_get_patient_data(conditions)
+        result_hash = run_pdo_request(conditions)
+        patient_data = {}
+
+        if result_hash[:error].blank?
+          # TODO: Handle case or result_hash being nil...perhaps with a to_s
+          id = result_hash[:result].scan(/<ns2:patient_set>(.*?)<\/ns2:patient_set>/m).flatten.first
+          id.scan(/<patient>(.*?)<\/patient>/m).each do |c|
+            patient_id = c.to_s.scan(/<patient_id>(.*?)<\/patient_id>/m).flatten.first
+
+            patient_data[patient_id] = {}
+
+
+
+            test2 = c.to_s.scan(/(<param .*?(<\/param>|\/>))/m).each do |pars|
+              p_string = pars.flatten.first
+              value = nil
+              unless pars[1] == "/>"
+                value = p_string.scan(/<param .*?>(.*?)<\/param>/m).flatten.first
+              end
+              column_name = p_string.scan(/column=\\"(.*?)\\"/m).flatten.first
+              display_name = p_string.scan(/column\_descriptor=\\"(.*?)\\"/m).flatten.first || column_name.to_s.capitalize #.titleize
+              patient_data[patient_id][column_name] = { value: value, display_name: display_name }
+            end
+          end
+        else
+          # TODO: Push error out to upper service
+          puts result_hash[:error]
+        end
+
+        patient_data
+      end
+
+      def get_total_count(query_concepts)
+        error = ''
+        eval_string = ''
+        patient_ids = [] # This one returns the combined evaluated expressions
+        all_patient_ids = [] # this is a partial patient ids...
+        query_concepts.each_with_index do |query_concept, index|
+          result = query_definition([{key: query_concept.external_key, right_operator: query_concept.right_operator, negated: query_concept.negated}]) # , query_concept.query.name
+          result_hash = run_query_get_patient_ids(result)
+          all_patient_ids << result_hash[:result]
+          error = result_hash[:error] unless result_hash[:error].blank?
+
+          eval_string << "("*query_concept.left_brackets unless query_concepts.size == 1
+          eval_string << result_hash[:result].to_s
+          eval_string << ")"*query_concept.right_brackets unless query_concepts.size == 1
+          if index < query_concepts.size - 1
+            case query_concept.right_operator when 'and'
+              eval_string << '&'
+            when 'or'
+              eval_string << '|'
+            else
+              return { result: 0, error: "Invalid operator '#{query_concept.right_operator}' in evaluation string.", sql_conditions: eval_string }
+            end
+          end
+        end
+
+        total_count = 0
+        begin
+          total_count = eval(eval_string).size
+          patient_ids = eval(eval_string)
+        rescue => e
+          error = "#{e}"
+        end
+
+        { result: total_count, error: error, sql_conditions: eval_string, patient_ids: patient_ids }
+      end
+
+      def get_total_query_patient_ids(query_concepts)
+        result = []
+        result_hash = get_total_count(query_concepts)
+        result = result_hash[:patient_ids] if result_hash[:error].blank?
+        result
+      end
+
+      # Access each query_concept individually and retrieve all the associated data, then trim the data based on the actual resulting patient IDs from the query.
+      def get_all_covariates(query_concepts)
+        error = ''
+        result = [[]]
+        all_patient_ids = []
+        all_concepts = []
+
+
+        query_concepts.each_with_index do |query_concept, index|
+          conditions = query_definition([{ key: query_concept.external_key, right_operator: query_concept.right_operator, negated: query_concept.negated }])
+          patient_data = run_query_get_patient_data(conditions)
+
+          if patient_data.first and patient_data.first[1] and result[0].blank?
+            all_concepts = patient_data.first[1].keys
+            result[0] = ['patient_id'] + all_concepts
+          end
+
+          patient_data.each_pair do |patient_id, value_hash|
+            row_data = [patient_id]
+
+            all_concepts.each do |concept|
+              row_data << value_hash[concept][:value]
+            end
+            result << row_data
+          end
+        end
+
+        all_patient_ids = get_total_query_patient_ids(query_concepts)
+        overall_result = [[]]
+
+        overall_result[0] = result[0]
+
+        result[1..-1].each do |row|
+          if all_patient_ids.include?(row[0])
+            overall_result << row
+            all_patient_ids.delete(row[0])
+          end
+        end
+
+        { result: overall_result, error: error }
+      end
+
+      def search_for_term(folder, term)
+        categories_hash = get_categories
+
+        return categories_hash unless categories_hash[:error].blank?
+
+        concepts = []
+        error = ''
+
+        categories = categories_hash[:result].collect{|c| c[:key].gsub(/\\\\/, '').split(/\\/).first.to_s}
+
+        categories.each do |category|
+          result_hash = search_for_term_helper(term, category)
+          concepts = (concepts | result_hash[:result]) if result_hash[:error].blank?
+          error = result_hash[:error] unless result_hash[:error].blank?
+        end
+
+        concepts = concepts.select{|c| (c[:folder] == folder or folder.blank?)}.uniq
+
+        { result: concepts, error: error }
+      end
+
+      def search_for_term_helper(term, category)
+
+        service_url = '/i2b2/rest/OntologyService/getNameInfo'
+
+        xml = ::Builder::XmlMarkup.new
+        xml.instruct! :xml, standalone: 'yes'
+        xml.tag!("ns3:request", "xmlns:ns3" => "http://www.i2b2.org/xsd/hive/msg/1.1/",
+                                "xmlns:ns4" => "http://www.i2b2.org/xsd/cell/ont/1.1/",
+                                "xmlns:ns2" => "http://www.i2b2.org/xsd/hive/plugin/") do |req|
+          req.message_header do |mhr|
+            mhr << message_header(service_url, 'i2b2 Ontology', 1.6, 'i2b2 Hive',
+                                               'Ontology Cell', 1.6, 'i2b2 Hive')
+          end
+          req.request_header do |rqh|
+            rqh.result_waittime_ms 180000
+          end
+          req.message_body do |mgb|
+            mgb.tag!('ns4:get_name_info', "blob" => "true", "type" => "core", "max" => "500", "category" => category) do |gni|
+              gni.tag!('match_str', "strategy" => "left") do |mst|
+                mst.text! term
+              end
+            end
+          end
+        end
+
+        process_concepts send_message(xml.target!, service_url)
+      end
+
+      def send_message(message, service)
+
+        url = URI.parse(@source.host + service)
+
+        use_secure = (url.scheme == 'https')
+
+        https = Net::HTTP.new(url.host, url.port)
+        https.open_timeout = 10 # Seconds
+        https.read_timeout = 30 # might need to be longer?
+        if use_secure
+          https.use_ssl = true
+          https.verify_mode = OpenSSL::SSL::VERIFY_NONE
+        end
+        headers = {'Content-Type' => 'text/xml'};
+        data = ''
+        error = ''
+        begin
+          response = https.post2(url.path, message, headers)
+          data = response.body
+
+          case response.class.name
+          when 'Net::HTTPOK'
+          else
+            error = "Error: #{response.class.name} #{data}"
+          end
+        rescue Exception => e
+          error = "Exception: #{e} #{response.class.name} #{data}"
+        end
+
+        return { result: data, error: error }
+      end
+    end
+  end
+end