his_emr_api_lab 0.0.3 → 0.0.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 045fb73daab53abc457c08152c5148251a6dccb239f0c76e09f3172007e44b6e
+  metadata.gz: 7b410e215fad55950c150d2ec7a82bda3f434cca4cc287e0d4fca2a9116e9182
+  data.tar.gz: 6b3a0c75c303c2139c1f6f963875667c4606bce42d23f6a22c277412e24db960
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-  data.tar.gz: 380096a9132eb857a4a321260593640eec0d6a5b08f661e97a1ba2396619eb5984c1aca488e364930dff737ff397b07865597b9ed321c7a93101c151a8d2566f
+  metadata.gz: 4f6068aecbc02d5c3df75ac422c4d4f9baeac86c6559a1e75078ef68088b4e6702239a366fb5e5879a2925592e3440a2880668bcc50f4730c9d2051f522ac94a
+  data.tar.gz: 5e3b4d61f507f2de7847951dcdd738a50dd29ba4ae5f981ce8284f3ba11c35d6d1c337787c1b78154b96eb318fc5343d404a3827fd02c89ffc3da60eb2d617c3

data/app/controllers/lab/labels_controller.rb

@@ -2,6 +2,8 @@
 
 module Lab
   class LabelsController < ApplicationController
+    skip_before_action :authenticate
+
     def print_order_label
       order_id = params.require(:order_id)
 

data/app/services/lab/labelling_service/order_label.rb

@@ -27,7 +27,7 @@ module Lab
                                '',
                                drawer,
                                '',
-                               specimen,
+                               tests,
                                reason_for_test,
                                order.accession_number,
                                order.accession_number)
@@ -36,7 +36,7 @@ module Lab
       def reason_for_test
         return 'Unknown' unless order.reason_for_test
 
-        ConceptName.find_by_concept_id(order.reason_for_test.value_coded)&.name || 'Unknown'
+        short_concept_name(order.reason_for_test.value_coded) || 'Unknown'
       end
 
       def patient
@@ -73,6 +73,24 @@ module Lab
         ConceptName.find_by_concept_id(order.concept_id)&.name || 'Unknown'
       end
 
+      def tests
+        tests = order.tests.map do |test|
+          name = short_concept_name(test.value_coded) || 'Unknown'
+
+          next 'VL' if name.match?(/Viral load/i)
+
+          name.size > 7 ? name[0..6] : name
+        end
+
+        tests.join(', ')
+      end
+
+      def short_concept_name(concept_id)
+        ConceptName.where(concept_id: concept_id)
+                   .min_by { |concept| concept.name.size }
+                   &.name
+      end
+
       def unknown_concept
         ConceptName.find_by_name('Unknown')
       end

data/app/services/lab/lims/api.rb

@@ -29,16 +29,11 @@ module Lab
       # given block until the queue is empty or connection is terminated
       # by calling method +choke+.
       def consume_orders(from: 0, limit: 30)
-        last_seq = { value: 0 }
-
         bum.binge_changes(since: from, limit: limit, include_docs: true) do |change|
           next unless change['doc']['type']&.casecmp?('Order')
 
           yield OrderDTO.new(change['doc']), self
-          last_seq[:value] = self.last_seq
         end
-
-        last_seq[:value]
       end
 
       def create_order(order)

data/app/services/lab/lims/migrator.rb

@@ -29,6 +29,7 @@ require 'lab/lab_test'
 require 'lab/lims_order_mapping'
 require 'lab/lims_failed_import'
 
+require_relative './worker'
 require_relative '../orders_service'
 require_relative '../results_service'
 require_relative '../tests_service'
@@ -47,14 +48,16 @@ module Lab
 
         attr_reader :rejections
 
-        def consume_orders(from: nil, limit: 50_000)
+        def consume_orders(from: nil, **_kwargs)
+          limit = 50_000
+
           Parallel.each(read_orders(from, limit),
                         in_processes: MAX_THREADS,
                         finish: order_pmap_post_processor(from)) do |row|
             next unless row['doc']['type']&.casecmp?('Order')
 
-            User.current = Migrator.lab_user
-            yield OrderDTO.new(row['doc']), OpenStruct.new(last_seq: from)
+            User.current = Utils.lab_user
+            yield OrderDTO.new(row['doc']), OpenStruct.new(last_seq: (from || 0) + limit, current_seq: from)
           end
         end
 
@@ -70,7 +73,7 @@ module Lab
         private
 
         def last_seq_path
-          Rails.root.join('log/lims/migration-last-id.dat')
+          LIMS_LOG_PATH.join('migration-last-id.dat')
         end
 
         def order_pmap_post_processor(last_seq)
@@ -129,18 +132,6 @@ module Lab
         def update_last_seq(_last_seq); end
       end
 
-      def self.lab_user
-        user = User.find_by_username('lab_daemon')
-        return user if user
-
-        god_user = User.first
-
-        person = Person.create!(creator: god_user.user_id)
-        PersonName.create!(person: person, given_name: 'Lab', family_name: 'Daemon', creator: god_user.user_id)
-
-        User.create!(username: 'lab_daemon', person: person, creator: god_user.user_id)
-      end
-
       def self.save_csv(filename, rows:, headers: nil)
         CSV.open(filename, File::WRONLY | File::CREAT) do |csv|
           csv << headers if headers
@@ -148,12 +139,13 @@ module Lab
         end
       end
 
-      MIGRATION_REJECTIONS_CSV_PATH = Rails.root.join('log/lims/migration-rejections.csv')
+      MIGRATION_REJECTIONS_CSV_PATH = LIMS_LOG_PATH.join('migration-rejections.csv')
 
       def self.export_rejections(rejections)
-        headers = ['Accession number', 'NHID', 'First name', 'Last name', 'Reason']
+        headers = ['doc_id', 'Accession number', 'NHID', 'First name', 'Last name', 'Reason']
         rows = (rejections || []).map do |rejection|
           [
+            rejection.order[:_id],
             rejection.order[:tracking_number],
             rejection.order[:patient][:id],
             rejection.order[:patient][:first_name],
@@ -165,12 +157,13 @@ module Lab
         save_csv(MIGRATION_REJECTIONS_CSV_PATH, headers: headers, rows: rows)
       end
 
-      MIGRATION_FAILURES_CSV_PATH = Rails.root.join('log/lims/migration-failures.csv')
+      MIGRATION_FAILURES_CSV_PATH = LIMS_LOG_PATH.join('migration-failures.csv')
 
       def self.export_failures
-        headers = ['Accession number', 'NHID', 'Reason', 'Difference']
+        headers = ['doc_id', 'Accession number', 'NHID', 'Reason', 'Difference']
         rows = Lab::LimsFailedImport.all.map do |failure|
           [
+            failure.lims_id,
             failure.tracking_number,
             failure.patient_nhid,
             failure.reason,
@@ -181,7 +174,7 @@ module Lab
         save_csv(MIGRATION_FAILURES_CSV_PATH, headers: headers, rows: rows)
       end
 
-      MIGRATION_LOG_PATH = Rails.root.join('log/lims/migration.log')
+      MIGRATION_LOG_PATH = LIMS_LOG_PATH.join('migration.log')
 
       def self.start_migration
         log_dir = Rails.root.join('log/lims')

data/app/services/lab/lims/order_dto.rb

@@ -30,9 +30,9 @@ module Lab
 
       # Translates a LIMS specimen name to an OpenMRS concept_id
       def specimen_type_id
-        lims_specimen_name = self['sample_type']
+        lims_specimen_name = self['sample_type']&.strip&.downcase
 
-        if %w[specimen_not_collected not_assigned].include?(lims_specimen_name)
+        if %w[specimen_not_collected not_assigned not_specified].include?(lims_specimen_name)
           return ConceptName.select(:concept_id).find_by_name!('Unknown').concept_id
         end
 
@@ -53,6 +53,8 @@ module Lab
 
       # Extract requesting clinician name from LIMS
       def requesting_clinician
+        return 'Unknown' unless self['who_order_test']
+
         # TODO: Extend requesting clinician to an obs tree having extra parameters
         # like phone number and ID to closely match the lims user.
         first_name = self['who_order_test']['first_name'] || ''

data/app/services/lab/lims/order_serializer.rb

@@ -97,7 +97,9 @@ module Lab
         end
 
         def format_test_results(order)
-          order.tests.each_with_object({}) do |test, results|
+          order.tests&.each_with_object({}) do |test, results|
+            next unless test.result
+
             results[test.name] = {
               results: test.result.each_with_object({}) do |measure, measures|
                 measures[measure.indicator.name] = { result_value: "#{measure.value_modifier}#{measure.value}" }

data/app/services/lab/lims/utils.rb

@@ -39,6 +39,18 @@ module Lab
         end
       end
 
+      def self.lab_user
+        user = User.find_by_username('lab_daemon')
+        return user if user
+
+        god_user = User.first
+
+        person = Person.create!(creator: god_user.user_id)
+        PersonName.create!(person: person, given_name: 'Lab', family_name: 'Daemon', creator: god_user.user_id)
+
+        User.create!(username: 'lab_daemon', person: person, creator: god_user.user_id)
+      end
+
       def self.parse_date(str_date, fallback_date = nil)
         if str_date.blank? && fallback_date.blank?
           raise "Can't parse blank date"

data/app/services/lab/lims/worker.rb

@@ -2,12 +2,16 @@
 
 require 'cgi/util'
 
+require_relative './api'
 require_relative './exceptions'
 require_relative './order_serializer'
 require_relative './utils'
 
 module Lab
   module Lims
+    LIMS_LOG_PATH = Rails.root.join('log/lims')
+    Dir.mkdir(LIMS_LOG_PATH) unless File.exist?(LIMS_LOG_PATH)
+
     ##
     # Pull/Push orders from/to the LIMS queue (Oops meant CouchDB).
     class Worker
@@ -15,6 +19,21 @@ module Lab
 
       attr_reader :lims_api
 
+      def self.start
+        File.open(LIMS_LOG_PATH.join('worker.lock'), File::WRONLY | File::CREAT, 0o644) do |fout|
+          fout.flock(File::LOCK_EX)
+
+          User.current = Utils.lab_user
+
+          fout.write("Worker ##{Process.pid} started at #{Time.now}")
+          worker = new(Api.new)
+          worker.pull_orders
+          # TODO: Verify that names being pushed to LIMS are of the correct format (ie matching
+          # LIMS naming conventions). Enable pushing when that is done
+          # worker.push_orders
+        end
+      end
+
       def initialize(lims_api)
         @lims_api = lims_api
       end
@@ -52,8 +71,8 @@ module Lab
             lims_api.update_order(mapping.lims_id, order_dto)
             mapping.update(pushed_at: Time.now)
           else
-            order_dto = lims_api.create_order(order_dto)
-            LimsOrderMapping.create!(order: order, lims_id: order_dto['_id'], pushed_at: Time.now)
+            update = lims_api.create_order(order_dto)
+            LimsOrderMapping.create!(order: order, lims_id: update['id'], revision: update['rev'], pushed_at: Time.now)
           end
         end
 
@@ -64,7 +83,8 @@ module Lab
       # Pulls orders from the LIMS queue and writes them to the local database
       def pull_orders
         logger.info("Retrieving LIMS orders starting from #{last_seq}")
-        lims_api.consume_orders(from: last_seq) do |order_dto, context|
+
+        lims_api.consume_orders(from: last_seq, limit: 100) do |order_dto, context|
           logger.debug("Retrieved order ##{order_dto[:tracking_number]}: #{order_dto}")
 
           patient = find_patient_by_nhid(order_dto[:patient][:id])
@@ -80,6 +100,8 @@ module Lab
             save_failed_import(order_dto, 'Demographics not matching', diff)
           end
 
+          update_last_seq(context.current_seq)
+
           [:accepted, "Patient NPID, '#{order_dto[:patient][:id]}', matched"]
         rescue DuplicateNHID
           logger.warn("Failed to import order due to duplicate patient NHID: #{order_dto[:patient][:id]}")
@@ -90,8 +112,6 @@ module Lab
         rescue LimsException => e
           logger.warn("Failed to import order due to #{e.class} - #{e.message}")
           save_failed_import(order_dto, e.message)
-        ensure
-          update_last_seq(context.last_seq)
         end
       end
 
@@ -264,12 +284,12 @@ module Lab
           indicator: { concept_id: indicator.concept_id },
           value_type: value_type,
           value: value_type == 'numeric' ? value.to_f : value,
-          value_modifier: value_modifier
+          value_modifier: value_modifier.blank? ? '=' : value_modifier
         )
       end
 
       def parse_lims_result_value(value)
-        value = value['result_value']
+        value = value['result_value']&.strip
         return nil, nil, nil if value.blank?
 
         match = value&.match(/^(>|=|<|<=|>=)(.*)$/)
@@ -279,7 +299,7 @@ module Lab
       end
 
       def guess_result_datatype(result)
-        return 'numeric' if result.match?(/^[+-]?(\d+(\.\d+)|\.\d+)?$/)
+        return 'numeric' if result.strip.match?(/^[+-]?(\d+(\.\d+)|\.\d+)?$/)
 
         'text'
       end
@@ -303,7 +323,7 @@ module Lab
       end
 
       def last_seq_path
-        Rails.root.join('log/lims/last-seq.dat')
+        LIMS_LOG_PATH.join('last_seq.dat')
       end
     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/lib/couch_bum/couch_bum.rb

@@ -24,18 +24,21 @@ 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)
     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}")
@@ -46,6 +49,8 @@ class CouchBum
 
   # Context under which the callback passed to binge_changes is executed.
   class BingeContext
+    attr_accessor :current_seq
+
     def initialize(changes)
       @changes = changes
     end

data/lib/generators/lab/install/templates/swagger.yaml

@@ -175,6 +175,12 @@ paths:
         description: 'Filter by sample status: ordered, drawn'
         schema:
           type: string
+      - name: end_date
+        in: query
+        required: false
+        description: Select all results before this date
+        schema:
+          type: date
       responses:
         '200':
           description: Success
@@ -396,6 +402,32 @@ paths:
       responses:
         '204':
           description: No Content
+  "/api/v1/lab/reasons_for_test":
+    get:
+      summary: Reasons for test
+      description: Retrieve default reasons for test concept set
+      tags:
+      - Concepts
+      security:
+      - api_key: []
+      responses:
+        '200':
+          description: Success
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  type: object
+                  properties:
+                    concept_id:
+                      type: integer
+                    name:
+                      type: string
+                      example: Routine
+                  required:
+                  - concept_id
+                  - name
   "/api/v1/lab/tests/{test_id}/results":
     post:
       summary: Add results to order

data/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '0.0.3'
+  VERSION = '0.0.8'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.8
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-04-18 00:00:00.000000000 Z
+date: 2021-04-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest