his_emr_api_lab 0.0.2 → 0.0.3

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_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
 
   ##
@@ -29,7 +33,13 @@ class CouchBum
   end
 
   def couch_rest(method, route, *args, **kwargs)
-    CouchRest.send(method, expand_route(route), *args, **kwargs)
+    url = expand_route(route)
+
+    logger.debug("CouchBum: Executing #{method} #{url}")
+    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

data/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '0.0.2'
+  VERSION = '0.0.3'
 end

data/lib/tasks/loaders/data/tests.csv

@@ -35,6 +35,7 @@ Blood,"Liver Function Tests","2019-11-19 14:05:31"
 Blood,"Renal Function Test","2019-11-19 14:05:31"
 Blood,Lipogram,"2019-11-19 14:05:31"
 Blood,FBC,"2019-11-19 14:05:31"
+Blood,"FBS","2021-04-11 00:00:00"
 Blood,Electrolytes,"2019-11-19 14:05:31"
 Blood,Enzymes,"2019-11-19 14:05:31"
 Blood,Glucose,"2019-11-19 14:05:31"
@@ -42,6 +43,22 @@ Blood,"Prothrombin Time","2019-11-19 14:05:31"
 Blood,APTT,"2019-11-19 14:05:31"
 Blood,INR,"2019-11-19 14:05:31"
 Blood,ESR,"2019-11-19 14:05:31"
+Blood,"D/Coombs","2021-04-11 00:00:00"
+Blood,"creat","2021-04-11 00:00:00"
+Blood,"Widal","2021-04-11 00:00:00"
+Blood,"AAFB (3rd)","2021-04-11 00:00:00"
+Blood,"Urine micro","2021-04-11 00:00:00"
+Blood,"AAFB (1st)","2021-04-11 00:00:00"
+Blood,ASOT,"2021-04-11 00:00:00"
+Blood,"Blood C/S","2021-04-11 00:00:00"
+Blood,"Cryptococcal Ag","2021-04-11 00:00:00"
+Blood,"I/Ink","2021-04-11 00:00:00"
+Blood,"Prot& Sugar","2021-04-11 00:00:00"
+Blood,C_S,"2021-04-11 00:00:00"
+Blood,hep,"2021-04-11 00:00:00"
+Blood,"Cryptococcal Antigen","2021-04-11 00:00:00"
+Blood,Resistance,"2021-04-11 00:00:00"
+Blood,Sickle,"2021-04-11 00:00:00"
 Blood,"Sickling Test","2019-11-19 14:05:31"
 Blood,"Manual Differential & Cell Morphology","2019-11-19 14:05:31"
 Blood,"Pancreatic Function Test","2019-11-19 14:05:31"
@@ -69,8 +86,12 @@ Blood,HbA1c,"2019-11-19 14:05:31"
 Blood,Microalbumin,"2019-11-19 14:05:31"
 Blood,Microprotein,"2019-11-19 14:05:31"
 Blood,"Von Willebrand Factor","2019-11-19 14:05:31"
+Blood,"HIV_viral_load","2021-04-13 00:00:00"
+Blood,"Viral laod","2021-04-11 00:00:00"
 Blood,"Viral Load","2019-11-19 14:05:31"
 Blood,"Urine Lam","2019-11-19 14:05:31"
+Blood,"Protein and Sugar","2021-04-16"
+Blood,"White cell count","2021-04-16"
 Blood,Urea,"2019-11-19 14:05:31"
 Blood,Creatinine,"2019-11-19 14:05:31"
 Blood,ALT,"2019-11-19 14:05:31"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.0.3
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-04-07 00:00:00.000000000 Z
+date: 2021-04-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest
@@ -24,6 +24,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 2.0.0
+- !ruby/object:Gem::Dependency
+  name: parallel
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.20.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.20.1
 - !ruby/object:Gem::Dependency
   name: rails
   requirement: !ruby/object:Gem::Requirement
@@ -211,6 +225,7 @@ files:
 - README.md
 - Rakefile
 - app/controllers/lab/application_controller.rb
+- app/controllers/lab/labels_controller.rb
 - app/controllers/lab/orders_controller.rb
 - app/controllers/lab/reasons_for_test_controller.rb
 - app/controllers/lab/results_controller.rb
@@ -233,8 +248,11 @@ files:
 - app/serializers/lab/test_serializer.rb
 - app/services/lab/accession_number_service.rb
 - app/services/lab/concepts_service.rb
+- app/services/lab/labelling_service/order_label.rb
 - app/services/lab/lims/api.rb
 - app/services/lab/lims/config.rb
+- app/services/lab/lims/exceptions.rb
+- app/services/lab/lims/migrator.rb
 - app/services/lab/lims/order_dto.rb
 - app/services/lab/lims/order_serializer.rb
 - app/services/lab/lims/utils.rb
@@ -250,6 +268,7 @@ files:
 - db/migrate/20210323080140_change_lims_id_to_string_in_lims_order_mapping.rb
 - db/migrate/20210326195504_add_order_revision_to_lims_order_mapping.rb
 - db/migrate/20210407071728_create_lab_lims_failed_imports.rb
+- lib/auto12epl.rb
 - lib/couch_bum/couch_bum.rb
 - lib/generators/lab/install/USAGE
 - lib/generators/lab/install/install_generator.rb