his_emr_api_lab 0.0.4 → 0.0.9

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: a13aafea421131fd8d95c1175fedbdfc921c72772b6e3ca9196a9a189f69a5c0
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+  data.tar.gz: c8730aa9b485c346096238cb7837fc09b2ffe735ef2104990336ca49d6c40902205f7bc9676966210d19ddbd253ee32a67947ce427c3ad8d7ecccb173c40d612

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/migrator.rb

@@ -142,9 +142,10 @@ module Lab
       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],
@@ -159,9 +160,10 @@ module Lab
       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,

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'] || ''
@@ -67,6 +69,10 @@ module Lab
       end
 
       def start_date
+        if self['date_created'].blank?
+          raise LimsException, 'Order missing created date'
+        end
+
         Utils.parse_date(self['date_created'])
       end
 

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

@@ -28,7 +28,9 @@ module Lab
           fout.write("Worker ##{Process.pid} started at #{Time.now}")
           worker = new(Api.new)
           worker.pull_orders
-          worker.push_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
 
@@ -282,12 +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(/^(>|=|<|<=|>=)(.*)$/)
@@ -297,7 +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

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/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 = '0.0.4'
+  VERSION = '0.0.9'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 0.0.4
+  version: 0.0.9
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-04-20 00:00:00.000000000 Z
+date: 2021-04-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest