his_emr_api_lab 0.0.2 → 0.0.7

data/app/services/lab/metadata.rb

@@ -18,6 +18,6 @@ module Lab
     ORDER_TYPE_NAME = 'Lab'
 
     # Programs
-    LAB_PROGRAM_NAME = 'Lab Program'
+    LAB_PROGRAM_NAME = 'Laboratory Program'
   end
 end

data/app/services/lab/orders_search_service.rb

@@ -5,44 +5,54 @@ module Lab
   module OrdersSearchService
     class << self
       def find_orders(filters)
-        date = filters.delete(:date)
-        status = filters.delete(:status)
+        extra_filters = pop_filters(filters, :date, :end_date, :status)
 
         orders = Lab::LabOrder.prefetch_relationships
                               .where(filters)
                               .order(start_date: :desc)
 
-        orders = filter_orders_by_date(orders, date) if date
-        orders = filter_orders_by_status(orders, status) if status
+        orders = filter_orders_by_status(orders, pop_filters(extra_filters, :status))
+        orders = filter_orders_by_date(orders, extra_filters)
 
         orders.map { |order| Lab::LabOrderSerializer.serialize_order(order) }
       end
 
-      def filter_orders_by_date(orders, date)
-        orders.where('start_date < DATE(?)', date.to_date + 1.day)
-      end
+      def filter_orders_by_date(orders, date: nil, end_date: nil)
+        date = date&.to_date
+        end_date = end_date&.to_date
 
-      def filter_orders_by_status(orders, status)
-        case status.downcase
-        when 'ordered' then orders.where(concept_id: unknown_concept_id)
-        when 'drawn' then orders.where.not(concept_id: unknown_concept_id)
+        if date && end_date
+          return orders.where('start_date BETWEEN ? AND ?', date, end_date + 1.day)
         end
-      end
 
-      def unknown_concept_id
-        ConceptName.find_by_name!('Unknown').concept_id
+        if date
+          return orders.where('start_date BETWEEN ? AND ?', date, date + 1.day)
+        end
+
+        return orders.where('start_date < ?', end_date + 1.day) if end_date
+
+        orders
       end
 
-      def filter_orders_by_status(orders, status)
-        case status.downcase
+      def filter_orders_by_status(orders, status: nil)
+        case status&.downcase
         when 'ordered' then orders.where(concept_id: unknown_concept_id)
         when 'drawn' then orders.where.not(concept_id: unknown_concept_id)
+        else orders
         end
       end
 
       def unknown_concept_id
         ConceptName.find_by_name!('Unknown').concept_id
       end
+
+      def pop_filters(params, *filters)
+        filters.each_with_object({}) do |filter, popped_params|
+          next unless params.key?(filter)
+
+          popped_params[filter.to_sym] = params.delete(filter)
+        end
+      end
     end
   end
 end

data/app/services/lab/orders_service.rb

@@ -27,7 +27,7 @@ module Lab
       #       },
       #       program_id: { type: :integer, required: false },
       #       patient_id: { type: :integer, required: false }
-      #       specimen_type_id: { type: :object, properties: { concept_id: :integer }, required: %i[concept_id] },
+      #       specimen: { type: :object, properties: { concept_id: :integer }, required: %i[concept_id] },
       #       test_type_ids: {
       #         type: :array,
       #         items: {
@@ -71,11 +71,15 @@ module Lab
         end
 
         order = Lab::LabOrder.find(order_id)
-        unless order.concept_id == unknown_concept_id
+        unless order.concept_id == unknown_concept_id || params[:force_update]&.to_s&.casecmp?('true')
           raise ::UnprocessableEntityError
         end
 
-        order.update!(concept_id: specimen_id)
+        order.update!(concept_id: specimen_id,
+                      discontinued: true,
+                      discontinued_by: User.current.user_id,
+                      discontinued_date: params[:date]&.to_date || Date.today,
+                      discontinued_reason_non_coded: 'Sample drawn/updated')
         Lab::LabOrderSerializer.serialize_order(order)
       end
 
@@ -87,10 +91,7 @@ module Lab
         order.reason_for_test&.void(reason)
         order.target_lab&.void(reason)
 
-        order.tests.each do |test|
-          test.result&.void(reason)
-          test.void(reason)
-        end
+        order.tests.each { |test| test.void(reason) }
 
         order.void(reason)
       end
@@ -119,7 +120,7 @@ module Lab
           program_id: program_id,
           type: EncounterType.find_by_name!(Lab::Metadata::ENCOUNTER_TYPE_NAME),
           encounter_datetime: order_params[:date] || Date.today,
-          provider_id: order_params[:provider_id] || User.current&.user_id
+          provider_id: order_params[:provider_id] || User.current.person.person_id
         )
       end
 

data/app/services/lab/results_service.rb

@@ -3,14 +3,26 @@
 module Lab
   module ResultsService
     class << self
+      ##
+      # Attach results to a test
+      #
+      # Params:
+      #   test_id: The tests id (maps to obs_id of the test's observation in OpenMRS)
+      #   params: A hash comprising the following fields
+      #     - encounter_id: Encounter to create result under (can be ommitted but provider_id has to specified)
+      #     - provider_id: Specify a provider for an encounter the result is going to be created under
+      #     - date: Retrospective date when the result was received (can be ommitted, defaults to today)
+      #     - measures: An array of measures. A measure is an object of the following structure
+      #         - indicator: An object that has a concept_id field (concept_id of the indicator)
+      #         - value_type: An enum that's limited to 'numeric', 'boolean', 'text', and 'coded'
       def create_results(test_id, params)
         ActiveRecord::Base.transaction do
           test = Lab::LabTest.find(test_id)
           encounter = find_encounter(test, encounter_id: params[:encounter_id],
-                                           date: params[:date],
+                                           date: params[:date]&.to_date,
                                            provider_id: params[:provider_id])
 
-          results_obs = create_results_obs(encounter, test, params[:date])
+          results_obs = create_results_obs(encounter, test, params[:date], params[:comments])
           params[:measures].map { |measure| add_measure_to_results(results_obs, measure, params[:date]) }
 
           Lab::ResultSerializer.serialize(results_obs)
@@ -32,23 +44,41 @@ module Lab
       end
 
       # Creates the parent observation for results to which the different measures are attached
-      def create_results_obs(encounter, test, date)
+      def create_results_obs(encounter, test, date, comments = nil)
+        void_existing_results_obs(encounter, test)
+
         Lab::LabResult.create!(
           person_id: encounter.patient_id,
           encounter_id: encounter.encounter_id,
-          concept_id: ConceptName.find_by_name!(Lab::Metadata::TEST_RESULT_CONCEPT_NAME).concept_id,
+          concept_id: test_result_concept.concept_id,
           order_id: test.order_id,
           obs_group_id: test.obs_id,
-          obs_datetime: date&.to_datetime || DateTime.now
+          obs_datetime: date&.to_datetime || DateTime.now,
+          comments: comments
         )
       end
 
+      def void_existing_results_obs(encounter, test)
+        result = Lab::LabResult.find_by(person_id: encounter.patient_id,
+                                        concept_id: test_result_concept.concept_id,
+                                        obs_group_id: test.obs_id)
+        return unless result
+
+        result.measures.map { |child_obs| child_obs.void("Updated/overwritten by #{User.current.username}") }
+        result.void("Updated/overwritten by #{User.current.username}")
+      end
+
+      def test_result_concept
+        ConceptName.find_by_name!(Lab::Metadata::TEST_RESULT_CONCEPT_NAME)
+      end
+
       def add_measure_to_results(results_obs, params, date)
         validate_measure_params(params)
 
         Observation.create!(
           person_id: results_obs.person_id,
           encounter_id: results_obs.encounter_id,
+          order_id: results_obs.order_id,
           concept_id: params[:indicator][:concept_id],
           obs_group_id: results_obs.obs_id,
           obs_datetime: date&.to_datetime || DateTime.now,
@@ -57,7 +87,9 @@ module Lab
       end
 
       def validate_measure_params(params)
-        raise InvalidParameterError, 'measures.value is required' if params[:value].blank?
+        if params[:value].blank?
+          raise InvalidParameterError, 'measures.value is required'
+        end
 
         if params[:indicator]&.[](:concept_id).blank?
           raise InvalidParameterError, 'measures.indicator.concept_id is required'

data/config/routes.rb

@@ -6,6 +6,8 @@ Lab::Engine.routes.draw do
     resources :results, only: %i[index create destroy]
   end
 
+  get 'api/v1/lab/labels/order', to: 'labels#print_order_label'
+
   # Metadata
   # TODO: Move the following to namespace /concepts
   resources :specimen_types, only: %i[index], path: 'api/v1/lab/specimen_types'

data/lib/auto12epl.rb

@@ -0,0 +1,201 @@
+#!/usr/bin/ruby
+# Jeremy Espino MD MS
+# 28-JAN-2016
+
+
+class Float
+  # function to round down a float to an integer value
+  def round_down n=0
+    n < 1 ? self.to_i.to_f : (self - 0.5 / 10**n).round(n)
+  end
+end
+
+# Generates EPL code that conforms to the Auto12-A standard for specimen labeling
+class Auto12Epl
+
+  attr_accessor :element_font
+  attr_accessor :barcode_human_font
+
+  DPI = 203
+  LABEL_WIDTH_IN = 2.0
+  LABEL_HEIGHT_IN = 0.5
+
+  # font constants
+  FONT_X_DOTS = [8, 10, 12, 14, 32]
+  FONT_Y_DOTS = [12, 16, 20, 24, 24]
+  FONT_PAD_DOTS = 2
+
+  # element heights
+  HEIGHT_MARGIN = 0.031
+  HEIGHT_ELEMENT = 0.1
+  HEIGHT_ELEMENT_SPACE = 0.01
+  HEIGHT_PID = 0.1
+  HEIGHT_BARCODE = 0.200
+  HEIGHT_BARCODE_HUMAN = 0.050
+
+  # element widths
+  WIDTH_ELEMENT = 1.94
+  WIDTH_BARCODE = 1.395
+  WIDTH_BARCODE_HUMAN = 1.688
+
+  # margins
+  L_MARGIN = 0.031
+  L_MARGIN_BARCODE = 0.25
+
+  # stat locations
+  L_MARGIN_BARCODE_W_STAT = 0.200
+  L_MARGIN_W_STAT = 0.150
+  STAT_WIDTH_ELEMENT = 1.78
+  STAT_WIDTH_BARCODE = 1.150
+  STAT_WIDTH_BARCODE_HUMAN = 1.400
+
+  # constants for generated EPL code
+  BARCODE_TYPE = '1A'
+  BARCODE_NARROW_WIDTH = '2'
+  BARCODE_WIDE_WIDTH = '2'
+  BARCODE_ROTATION = '0'
+  BARCODE_IS_HUMAN_READABLE = 'N'
+  ASCII_HORZ_MULT = 1
+  ASCII_VERT_MULT = 1
+
+
+  def initialize(element_font = 1, barcode_human_font = 1)
+    @element_font = element_font
+    @barcode_human_font = barcode_human_font
+  end
+
+  # Calculate the number of characters that will fit in a given length
+  def max_characters(font, length)
+
+    dots_per_char = FONT_X_DOTS.at(font-1) + FONT_PAD_DOTS
+
+    num_char = ( (length * DPI)  / dots_per_char).round_down
+
+    num_char.to_int
+  end
+
+  # Use basic truncation rule to truncate the name element i.e., if > maxCharacters cutoff and trail with +
+  def truncate_name(last_name, first_name, middle_initial, is_stat)
+    if is_stat
+      name_max_characters = max_characters(@element_font, STAT_WIDTH_ELEMENT)
+    else
+      name_max_characters = max_characters(@element_font, WIDTH_ELEMENT)
+    end
+
+    if concatName(last_name, first_name, middle_initial).length > name_max_characters
+      # truncate last?
+      if last_name.length > 12
+        last_name = last_name[0..11] + '+'
+      end
+
+      # truncate first?
+      if concatName(last_name, first_name, middle_initial).length  > name_max_characters && first_name.length > 7
+        first_name = first_name[0..7] + '+'
+      end
+    end
+
+    concatName(last_name, first_name, middle_initial)
+
+  end
+
+  def concatName(last_name, first_name, middle_initial)
+    last_name + ', ' + first_name + (middle_initial == nil ? '' : ' ' + middle_initial)
+  end
+
+  # The main function to generate the EPL
+  def generate_epl(last_name, first_name, middle_initial, pid, dob, age, gender, col_date_time, col_name, tests, stat, acc_num, schema_track)
+
+    # format text and set margin
+    if stat == nil
+      name_text = truncate_name(last_name, first_name, middle_initial, false)
+      pid_dob_age_gender_text = full_justify(pid, dob + ' ' + age + ' ' + gender, @element_font, WIDTH_ELEMENT)
+      l_margin = L_MARGIN
+      l_margin_barcode = L_MARGIN_BARCODE
+    else
+      name_text = truncate_name(last_name, first_name, middle_initial, true)
+      pid_dob_age_gender_text = full_justify(pid, dob + ' ' + age + ' ' + gender, @element_font, STAT_WIDTH_ELEMENT)
+      stat_element_text = pad_stat_w_space(stat)
+      l_margin = L_MARGIN_W_STAT
+      l_margin_barcode = L_MARGIN_BARCODE_W_STAT
+    end
+    barcode_human_text = "#{acc_num} * #{schema_track.gsub(/\-/i, '')}"
+    collector_element_text = "Col: #{col_date_time} #{col_name}"
+    tests_element_text = tests
+
+    # generate EPL statements
+    name_element = generate_ascii_element(to_dots(l_margin), to_dots(HEIGHT_MARGIN), 0, @element_font, false, name_text)
+    pid_dob_age_gender_element = generate_ascii_element(to_dots(l_margin), to_dots(HEIGHT_MARGIN + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE), 0, @element_font, false, pid_dob_age_gender_text)
+    barcode_human_element = generate_ascii_element(to_dots(l_margin_barcode), to_dots(HEIGHT_MARGIN + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE + HEIGHT_BARCODE), 0, @barcode_human_font, false, barcode_human_text)
+    collector_element = generate_ascii_element(to_dots(l_margin), to_dots(HEIGHT_MARGIN + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE + HEIGHT_BARCODE + HEIGHT_BARCODE_HUMAN + HEIGHT_ELEMENT_SPACE), 0, @element_font, false, collector_element_text)
+    tests_element = generate_ascii_element(to_dots(l_margin), to_dots(HEIGHT_MARGIN + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE + HEIGHT_BARCODE + HEIGHT_BARCODE_HUMAN + HEIGHT_ELEMENT_SPACE + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE), 0, @element_font, false, tests_element_text)
+    barcode_element = generate_barcode_element(to_dots(l_margin_barcode), to_dots(HEIGHT_MARGIN + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE + HEIGHT_ELEMENT + HEIGHT_ELEMENT_SPACE), to_dots(HEIGHT_BARCODE)-4, schema_track)
+    stat_element = generate_ascii_element(to_dots(L_MARGIN)+FONT_Y_DOTS.at(@element_font - 1)+FONT_PAD_DOTS, to_dots(HEIGHT_MARGIN), 1, @element_font, true, stat_element_text)
+
+    # combine EPL statements
+    if stat == nil
+      "\nN\nR216,0\nZT\nS1\n#{name_element}\n#{pid_dob_age_gender_element}\n#{barcode_element}\n#{barcode_human_element}\n#{collector_element}\n#{tests_element}\nP3\n"
+    else
+      "\nN\nR216,0\nZT\nS1\n#{name_element}\n#{pid_dob_age_gender_element}\n#{barcode_element}\n#{barcode_human_element}\n#{collector_element}\n#{tests_element}\n#{stat_element}\nP3\n"
+    end
+
+  end
+
+  # Add spaces before and after the stat text so that black bars appear across the left edge of label
+  def pad_stat_w_space(stat)
+    num_char = max_characters(@element_font, LABEL_HEIGHT_IN)
+    spaces_needed = (num_char - stat.length) / 1
+    space = ''
+    spaces_needed.times do
+      space = space + ' '
+    end
+    space + stat + space
+  end
+
+  # Add spaces between the NPID and the dob/age/gender so that line is fully justified
+  def full_justify(pid, dag, font, length)
+    max_char = max_characters(font, length)
+    spaces_needed = max_char - pid.length - dag.length
+    space = ''
+    spaces_needed.times do
+      space = space + ' '
+    end
+    pid + space + dag
+  end
+
+  # convert inches to number of dots using DPI
+  def to_dots(inches)
+    (inches * DPI).round
+  end
+
+  # generate ascii EPL
+  def generate_ascii_element(x, y, rotation, font, is_reverse, text)
+    "A#{x.to_s},#{y.to_s},#{rotation.to_s},#{font.to_s},#{ASCII_HORZ_MULT},#{ASCII_VERT_MULT},#{is_reverse ? 'R' : 'N'},\"#{text}\""
+  end
+
+  # generate barcode EPL
+  def generate_barcode_element(x, y, height, schema_track)
+    schema_track = schema_track.gsub("-", "").strip
+    "B#{x.to_s},#{y.to_s},#{BARCODE_ROTATION},#{BARCODE_TYPE},#{BARCODE_NARROW_WIDTH},#{BARCODE_WIDE_WIDTH},#{height.to_s},#{BARCODE_IS_HUMAN_READABLE},\"#{schema_track}\""
+  end
+
+end
+
+if __FILE__ == $0
+
+  auto = Auto12Epl.new
+
+  puts auto.generate_epl("Banda", "Mary", "U", "Q23-HGF", "12-SEP-1997", "19y", "F", "01-JAN-2016 14:21", "byGD", "CHEM7,Ca,Mg", nil, "KCH-16-00001234", "1600001234")
+  puts "\n"
+  puts auto.generate_epl("Banda", "Mary", "U", "Q23-HGF", "12-SEP-1997", "19y", "F", "01-JAN-2016 14:21", "byGD", "CHEM7,Ca,Mg", "STAT CHEM", "KCH-16-00001234", "1600001234")
+  puts "\n"
+  puts auto.generate_epl("Bandajustrightlas", "Mary", "U", "Q23-HGF", "12-SEP-1997", "19y", "F", "01-JAN-2016 14:21", "byGD", "CHEM7,Ca,Mg", "STAT CHEM", "KCH-16-00001234", "1600001234")
+  puts "\n"
+  puts auto.generate_epl("Bandasuperlonglastnamethatwonfit", "Marysuperlonglastnamethatwonfit", "U", "Q23-HGF", "12-SEP-1997", "19y", "F", "01-JAN-2016 14:21", "byGD", "CHEM7,Ca,Mg", "STAT CHEM", "KCH-16-00001234", "1600001234")
+  puts "\n"
+  puts auto.generate_epl("Bandasuperlonglastnamethatwonfit", "Mary", "U", "Q23-HGF", "12-SEP-1997", "19y", "F", "01-JAN-2016 14:21", "byGD", "CHEM7,Ca,Mg", "STAT CHEM", "KCH-16-00001234", "1600001234")
+  puts "\n"
+  puts auto.generate_epl("Banda", "Marysuperlonglastnamethatwonfit", "U", "Q23-HGF", "12-SEP-1997", "19y", "F", "01-JAN-2016 14:21", "byGD", "CHEM7,Ca,Mg", "STAT CHEM", "KCH-16-00001234", "1600001234")
+
+
+
+end

data/lib/couch_bum/couch_bum.rb

@@ -8,8 +8,12 @@ require 'couchrest'
 #
 # See: https://github.com/couchrest/couchrest
 class CouchBum
+  cattr_accessor :logger
+
   def initialize(database:, protocol: 'http', host: 'localhost', port: 5984, username: nil, password: nil)
     @connection_string = make_connection_string(protocol, username, password, host, port, database)
+
+    CouchBum.logger ||= Logger.new(STDOUT)
   end
 
   ##
@@ -20,22 +24,33 @@ class CouchBum
   # within the passed block.
   def binge_changes(since: 0, limit: nil, include_docs: nil, &block)
     catch(:choke) do
-      extra_params = stringify_params(limit: limit, include_docs: include_docs)
+      logger.debug("Binging #{limit} changes from '#{since}'")
+      params = stringify_params(limit: limit, include_docs: include_docs)
+      params = "since=#{since}&#{params}" unless since.blank?
 
-      changes = couch_rest(:get, "_changes?since=#{since}&#{extra_params}")
+      changes = couch_rest(:get, "_changes?#{params}")
       context = BingeContext.new(changes)
-      changes['results'].each { |change| context.instance_exec(change, &block) }
+      changes['results'].each do |change|
+        context.current_seq = change['seq']
+        context.instance_exec(change, &block)
+      end
     end
   end
 
   def couch_rest(method, route, *args, **kwargs)
-    CouchRest.send(method, expand_route(route), *args, **kwargs)
+    url = expand_route(route)
+    CouchRest.send(method, url, *args, **kwargs)
+  rescue CouchRest::Exception => e
+    logger.error("Failed to communicate with CouchDB: Status: #{e.http_code} - #{e.http_body}")
+    raise e
   end
 
   private
 
   # Context under which the callback passed to binge_changes is executed.
   class BingeContext
+    attr_accessor :current_seq
+
     def initialize(changes)
       @changes = changes
     end