his_emr_api_lab 0.0.15 → 1.0.0

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: bd7ca74bdf0af442d3a4c6f9a1f9e0a73d4d61571f1e39ae6ce5352246cd801d
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+  data.tar.gz: 9c68ca05bb1accaac6942c37f2399ae5ef5f94bde87cbd30811f35e394a9b2a43e2671f266173839156b980c3030051fc5e9fc4103c3b8f41a7dcd84e5324e35

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_serializer.rb

@@ -24,6 +24,8 @@ module Lab
             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,
             date_created: serialized_order.order_date,
@@ -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)
@@ -96,6 +96,31 @@ module Lab
           ]
         end
 
+        def format_test_status_trail(order)
+          order.tests.each_with_object({}) do |test, trail|
+            test_name = ConceptName.find_by_concept_id!(test.value_coded).name
+            test_name = 'Viral load' if test_name.casecmp?('HIV Viral Load')
+
+            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
@@ -134,6 +159,20 @@ 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
 

data/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '0.0.15'
+  VERSION = '1.0.0'
 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: 1.0.0
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-05-21 00:00:00.000000000 Z
+date: 2021-06-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest