his_emr_api_lab 0.0.15 → 1.0.4

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 5a67e4211a1d0b61d6f8a51357ee2a9fb898bd1c7973d2fc224039451f0a00d1
+  metadata.gz: 6142a8351eea3dc6cc2dde34b014948bd95c5d4398355ddc29d2aa0ddff8c095
+  data.tar.gz: ca4493c370000ab13cae02629c8cc3ea840f9bf03a70dee35a3f8bc3574e12e3
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+  metadata.gz: b18abf5a9f7e00c213ff41bea37c924f7c5abafbfefd5f63727c76093d26e057391ddb047e4a2583fbfdb9d98bd05895387cc6b26aacfe54df4a290cb804f9b9
+  data.tar.gz: e7e23b2a1eb5d387855e7acc7e1bd60dcdfca08938245693a07833a6fc43314e1127a9108eaaf8e1536fa3e16acaaa74ecf104d107b3fb71a98ad9b0c4b8a875

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

@@ -45,10 +45,11 @@ module Lab
           paths = [
             "#{ENV['HOME']}/apps/nlims_controller/config/#{filename}",
             "/var/www/nlims_controller/config/#{filename}",
-            Rails.root.parent.join("nlims_controller/config/#{filename}"),
-            Rails.root.join('config/lims-couch.yml')
+            Rails.root.parent.join("nlims_controller/config/#{filename}")
           ]
 
+          paths = [Rails.root.join('config/lims-couchdb.yml'), *paths] if filename == 'couchdb.yml'
+
           paths.each do |path|
             Rails.logger.debug("Looking for LIMS couchdb config at: #{path}")
             return path if File.exist?(path)

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

@@ -83,9 +83,9 @@ module Lab
 
       # Translates a LIMS sample priority to a concept_id
       def reason_for_test
-        return unknown_concept.concept_id unless self['sample_priority']
+        return unknown_concept.concept_id unless self['priority']
 
-        ConceptName.find_by_name!(self['sample_priority']).concept_id
+        ConceptName.find_by_name!(self['priority']).concept_id
       end
 
       def lab_program

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

@@ -18,14 +18,16 @@ module Lab
             tracking_number: serialized_order.accession_number,
             sending_facility: current_facility_name,
             receiving_facility: serialized_order.target_lab,
-            tests: serialized_order.tests.collect(&:name),
+            tests: serialized_order.tests.map { |test| format_test_name(test.name) },
             patient: format_patient(serialized_order.patient_id),
             order_location: format_order_location(serialized_order.encounter_id),
             sample_type: format_sample_type(serialized_order.specimen.name),
             sample_status: format_sample_status(serialized_order.specimen.name),
             sample_statuses: format_sample_status_trail(order),
+            test_statuses: format_test_status_trail(order),
+            who_order_test: format_orderer(order),
             districy: current_district, # yes districy [sic]...
-            priority: serialized_order.reason_for_test.name,
+            priority: format_sample_priority(serialized_order.reason_for_test.name),
             date_created: serialized_order.order_date,
             test_results: format_test_results(serialized_order),
             type: 'Order'
@@ -67,7 +69,7 @@ module Lab
         end
 
         def format_sample_type(name)
-          name.casecmp?('Unknown') ? 'not_specified' : name
+          name.casecmp?('Unknown') ? 'not_specified' : name.titleize
         end
 
         def format_sample_status(name)
@@ -75,9 +77,7 @@ module Lab
         end
 
         def format_sample_status_trail(order)
-          if order.concept_id == ConceptName.find_by_name!('Unknown').concept_id
-            return []
-          end
+          return [] if order.concept_id == ConceptName.find_by_name!('Unknown').concept_id
 
           user = User.find(order.discontinued_by || order.creator)
           drawn_by = PersonName.find_by_person_id(user.user_id)
@@ -96,13 +96,39 @@ module Lab
           ]
         end
 
+        def format_test_status_trail(order)
+          order.tests.each_with_object({}) do |test, trail|
+            test_name = format_test_name(ConceptName.find_by_concept_id!(test.value_coded).name)
+
+            current_test_trail = trail[test_name] = {}
+
+            current_test_trail[test.obs_datetime.strftime('%Y%m%d%H%M%S')] = {
+              status: 'Drawn',
+              updated_by: find_user(test.creator)
+            }
+
+            next unless test.result
+
+            current_test_trail[test.obs_datetime.strftime('%Y%m%d%H%M%S')] = {
+              status: 'Verified',
+              updated_by: find_user(test.result.creator)
+            }
+          end
+        end
+
+        def format_orderer(order)
+          find_user(order.creator)
+        end
+
         def format_test_results(order)
           order.tests&.each_with_object({}) do |test, results|
             next unless test.result
 
-            results[test.name] = {
+            results[format_test_name(test.name)] = {
               results: test.result.each_with_object({}) do |measure, measures|
-                measures[measure.indicator.name] = { result_value: "#{measure.value_modifier}#{measure.value}" }
+                measures[format_test_name(measure.indicator.name)] = {
+                  result_value: "#{measure.value_modifier}#{measure.value}"
+                }
               end,
               result_date: test.result.first&.date,
               result_entered_by: {}
@@ -110,6 +136,20 @@ module Lab
           end
         end
 
+        def format_test_name(test_name)
+          return 'Viral Load' if test_name.casecmp?('HIV Viral load')
+
+          return 'TB' if test_name.casecmp?('TB Program')
+
+          test_name.titleize
+        end
+
+        def format_sample_priority(priority)
+          return 'Routine' if priority&.casecmp?('Medical examination, routine')
+
+          priority&.titleize
+        end
+
         def current_health_center
           health_center = Location.current_health_center
           raise 'Current health center not set' unless health_center
@@ -134,6 +174,20 @@ module Lab
         def current_facility_name
           current_health_center.name
         end
+
+        def find_user(user_id)
+          user = User.find(user_id)
+          person_name = PersonName.find_by(person_id: user.person_id)
+          phone_number = PersonAttribute.find_by(type: PersonAttributeType.where(name: 'Cell phone number'),
+                                                 person_id: user.person_id)
+
+          {
+            first_name: person_name&.given_name,
+            last_name: person_name&.family_name,
+            phone_number: phone_number&.value,
+            id: user.username
+          }
+        end
       end
     end
   end

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

@@ -26,11 +26,11 @@ module Lab
           User.current = Utils.lab_user
 
           fout.write("Worker ##{Process.pid} started at #{Time.now}")
-          worker = new(CouchDbApi.new)
+          worker = new(Api::CouchDbApi.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
+          worker.push_orders
         end
       end
 
@@ -209,7 +209,7 @@ module Lab
         raise MissingAccessionNumber if order_dto[:tracking_number].blank?
 
         logger.info("Importing LIMS order ##{order_dto[:tracking_number]}")
-        mapping = LimsOrderMapping.find_by(lims_id: order_dto[:_id])
+        mapping = find_order_mapping_by_lims_id(order_dto[:_id])
 
         ActiveRecord::Base.transaction do
           if mapping
@@ -221,7 +221,6 @@ module Lab
                                               order_id: order['id'],
                                               pulled_at: Time.now,
                                               revision: order_dto['_rev'])
-            byebug unless mapping.errors.empty?
           end
 
           order
@@ -313,7 +312,7 @@ module Lab
       end
 
       def guess_result_datatype(result)
-        return 'numeric' if result.strip.match?(/^[+-]?(\d+(\.\d+)|\.\d+)?$/)
+        return 'numeric' if result.strip.match?(/^[+-]?((\d+(\.\d+)?)|\.\d+)$/)
 
         'text'
       end
@@ -339,6 +338,16 @@ module Lab
       def last_seq_path
         LIMS_LOG_PATH.join('last_seq.dat')
       end
+
+      def find_order_mapping_by_lims_id(lims_id)
+        mapping = Lab::LimsOrderMapping.find_by(lims_id: lims_id)
+        return nil unless mapping
+
+        return mapping if Lab::LabOrder.where(order_id: mapping.order_id).exists?
+
+        mapping.destroy
+        nil
+      end
     end
   end
 end

data/db/migrate/20210610095024_fix_numeric_results_value_type.rb

@@ -0,0 +1,20 @@
+class FixNumericResultsValueType < ActiveRecord::Migration[5.2]
+  def up
+    results = Lab::LabResult.all.includes(:children)
+
+    ActiveRecord::Base.connection.transaction do
+      results.each do |result|
+        result.children.each do |measure|
+          next unless measure.value_text&.match?(/^[+-]?((\d+(\.\d+)?)|\.\d+)$/)
+
+          puts "Updating result value type for result measure ##{measure.obs_id}"
+          measure.value_numeric = measure.value_text
+          measure.value_text = nil
+          measure.save!
+        end
+      end
+    end
+  end
+
+  def down; end
+end

data/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '0.0.15'
+  VERSION = '1.0.4'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 0.0.15
+  version: 1.0.4
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-05-21 00:00:00.000000000 Z
+date: 2021-06-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest
@@ -270,6 +270,7 @@ 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
+- db/migrate/20210610095024_fix_numeric_results_value_type.rb
 - lib/auto12epl.rb
 - lib/couch_bum/couch_bum.rb
 - lib/generators/lab/install/USAGE