his_emr_api_lab 1.1.21 → 1.1.22

data/lib/auto12epl.rb

@@ -1,201 +0,0 @@
-#!/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

@@ -1,92 +0,0 @@
-# frozen_string_literal: true
-
-require 'cgi'
-require 'couchrest'
-
-##
-# A CouchRest wrapper for the changes API.
-#
-# 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
-
-  ##
-  # Attaches to the Changes API and streams the updates to passed block.
-  #
-  # This is a blocking call that only stops when there are no more
-  # changes to pull or is explicitly terminated by calling +choke+
-  # within the passed block.
-  def binge_changes(since: 0, limit: nil, include_docs: nil, &block)
-    catch(:choke) do
-      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?#{params}")
-      context = BingeContext.new(changes)
-      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)
-    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
-
-    def choke
-      throw :choke
-    end
-
-    def last_seq
-      @changes['last_seq']
-    end
-
-    def pending
-      @changes['pending']
-    end
-  end
-
-  def make_connection_string(protocol, username, password, host, port, database)
-    auth = username ? "#{CGI.escape(username)}:#{CGI.escape(password)}@" : ''
-
-    "#{protocol}://#{auth}#{host}:#{port}/#{database}"
-  end
-
-  def expand_route(route)
-    route = route.gsub(%r{^/+}, '')
-
-    "#{@connection_string}/#{route}"
-  end
-
-  def stringify_params(params)
-    params.reduce('') do |str_params, entry|
-      name, value = entry
-      next params unless value
-
-      param = "#{name}=#{value}"
-      str_params.empty? ? param : "#{str_params}&#{param}"
-    end
-  end
-end

data/lib/generators/lab/install/USAGE

@@ -1,9 +0,0 @@
-Description:
-    Installs the Lab engine.
-
-Example:
-    rails generate lab:install
-
-    This will create:
-        config/initializers/rswag-ui-lab.rb
-        swagger/lab/v1/swagger.yaml

data/lib/generators/lab/install/install_generator.rb

@@ -1,19 +0,0 @@
-# frozen_string_literal: true
-
-module Lab
-  class InstallGenerator < Rails::Generators::Base
-    source_root File.expand_path('templates', __dir__)
-
-    def copy_openapi_docs
-      copy_file('swagger.yaml', 'swagger/lab/v1/swagger.yaml')
-    end
-
-    def copy_rswag_initializer
-      copy_file('rswag-ui-lab.rb', 'config/initializers/rswag-ui-lab.rb')
-    end
-
-    def copy_worker
-      copy_file('start_worker.rb', 'bin/lab/start_worker.rb')
-    end
-  end
-end

data/lib/generators/lab/install/templates/rswag-ui-lab.rb

@@ -1,5 +0,0 @@
-require 'rswag/ui'
-
-Rswag::Ui.configure do |c|
-  c.swagger_endpoint '/api-docs/lab/v1/swagger.yaml', 'Lab API V1 Docs'
-end

data/lib/generators/lab/install/templates/start_worker.rb

@@ -1,32 +0,0 @@
-# frozen_string_literal: true
-
-require 'logger_multiplexor'
-
-Rails.logger = LoggerMultiplexor.new(Rails.root.join('log/lims-push.log'), $stdout)
-api = Lab::Lims::Api.new
-worker = Lab::Lims::Worker.new(api)
-
-def with_lock(lock_file)
-  File.open("log/#{lock_file}", File::RDWR | File::CREAT, 0o644) do |file|
-    unless file.flock(File::LOCK_EX | File::LOCK_NB)
-      Rails.logger.warn("Failed to start new process due to lock: #{lock_file}")
-      exit 2
-    end
-
-    file.rewind
-    file.puts("Process ##{Process.pid} started at #{Time.now}")
-
-    yield
-  end
-end
-
-case ARGV[0]&.downcase
-when 'push'
-  with_lock('lims-push.lock') { worker.push_orders }
-when 'pull'
-  with_lock('lims-pull.lock') { worker.pull_orders }
-else
-  warn 'Error: No or invalid action specified: Valid actions are push and pull'
-  warn 'USAGE: rails runner start_worker.rb push'
-  exit 1
-end