ACS-1689-import-measures-rake

Gemfile.lock

@@ -1,24 +1,26 @@
 GIT
   remote: https://github.com/projecttacoma/simplexml_parser.git
-  revision: 0ea6c4cf9c5cb70c848ee7beaf30779b9ea77f15
+  revision: 9f83211e2407f0d933afbd1648c57f500b7527af
   branch: master
   specs:
-    simplexml_parser (1.0.0)
+    simplexml_parser (1.1.0)
+      health-data-standards (~> 4.3.4)
+      tilt (~> 1.4)
 
 PATH
   remote: .
   specs:
     health-data-standards (4.0.3)
-      activesupport (~> 4.2.0)
+      activesupport (< 6.0)
       builder (~> 3.1)
       erubis (~> 2.7.0)
       highline (~> 1.7.0)
       log4r (~> 1.1.10)
       memoist (~> 0.9.1)
-      mongoid (~> 5.0.0)
-      mongoid-tree (~> 2.0.0)
-      nokogiri (~> 1.8.2)
-      protected_attributes (~> 1.0.5)
+      mongoid (~> 7.0.0)
+      mongoid-tree (~> 2.1.1)
+      nokogiri (>= 1.10.5)
+      protected_attributes_continued (~> 1.5.0)
       rest-client (~> 1.8.0)
       rubyzip (~> 1.2.1)
       uuid (~> 2.3.7)
@@ -27,104 +29,104 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    activemodel (4.2.6)
-      activesupport (= 4.2.6)
-      builder (~> 3.1)
-    activesupport (4.2.6)
-      i18n (~> 0.7)
-      json (~> 1.7, >= 1.7.7)
+    activemodel (5.2.4)
+      activesupport (= 5.2.4)
+    activesupport (5.2.4)
+      concurrent-ruby (~> 1.0, >= 1.0.2)
+      i18n (>= 0.7, < 2)
       minitest (~> 5.1)
-      thread_safe (~> 0.3, >= 0.3.4)
       tzinfo (~> 1.1)
-    addressable (2.4.0)
+    addressable (2.7.0)
+      public_suffix (>= 2.0.2, < 5.0)
     ansi (1.5.0)
-    awesome_print (1.7.0)
-    bson (4.2.2)
-    builder (3.2.2)
-    bundler-audit (0.6.0)
-      bundler (~> 1.2)
+    awesome_print (1.8.0)
+    bson (4.7.0)
+    builder (3.2.4)
+    bundler-audit (0.6.1)
+      bundler (>= 1.2.0, < 3)
       thor (~> 0.18)
     byebug (6.0.2)
     cane (2.3.0)
       parallel
+    concurrent-ruby (1.1.5)
     crack (0.4.3)
       safe_yaml (~> 1.0.0)
-    docile (1.1.5)
-    domain_name (0.5.20170404)
+    docile (1.3.2)
+    domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
     erubis (2.7.0)
     factory_girl (4.1.0)
       activesupport (>= 3.0.0)
-    hashdiff (0.3.0)
-    highline (1.7.8)
+    hashdiff (1.0.0)
+    highline (1.7.10)
     http-cookie (1.0.3)
       domain_name (~> 0.5)
-    i18n (0.7.0)
-    json (1.8.6)
+    i18n (1.7.0)
+      concurrent-ruby (~> 1.0)
+    json (2.3.0)
     log4r (1.1.10)
     log_switch (1.0.0)
-    macaddr (1.7.1)
-      systemu (~> 2.6.2)
+    macaddr (1.7.2)
+      systemu (~> 2.6.5)
     memoist (0.9.3)
     mime-types (2.99.3)
-    mini_portile2 (2.3.0)
-    minitest (5.9.0)
-    minitest-reporters (1.1.9)
+    mini_portile2 (2.4.0)
+    minitest (5.13.0)
+    minitest-reporters (1.4.2)
       ansi
       builder
       minitest (>= 5.0)
       ruby-progressbar
-    mongo (2.4.3)
-      bson (>= 4.2.1, < 5.0.0)
-    mongoid (5.0.2)
-      activemodel (~> 4.0)
-      mongo (~> 2.1)
-      origin (~> 2.1)
-      tzinfo (>= 0.3.37)
-    mongoid-tree (2.0.1)
-      mongoid (>= 4.0, < 6.0)
+    mongo (2.11.2)
+      bson (>= 4.6.0, < 5.0.0)
+    mongoid (7.0.5)
+      activemodel (>= 5.1, < 6.1)
+      mongo (>= 2.5.1, < 3.0.0)
+    mongoid-tree (2.1.1)
+      mongoid (>= 4.0, < 8)
     netrc (0.11.0)
-    nokogiri (1.8.2)
-      mini_portile2 (~> 2.3.0)
-    origin (2.3.1)
-    parallel (1.9.0)
-    protected_attributes (1.0.9)
-      activemodel (>= 4.0.1, < 5.0)
-    rake (11.2.2)
+    nokogiri (1.10.7)
+      mini_portile2 (~> 2.4.0)
+    parallel (1.19.1)
+    protected_attributes_continued (1.5.0)
+      activemodel (>= 5.0)
+    public_suffix (4.0.1)
+    rake (13.0.1)
     rest-client (1.8.0)
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 3.0)
       netrc (~> 0.7)
-    ruby-progressbar (1.8.1)
-    rubyzip (1.2.2)
-    safe_yaml (1.0.4)
-    simplecov (0.11.2)
-      docile (~> 1.1.0)
-      json (~> 1.8)
+    ruby-progressbar (1.10.1)
+    rubyzip (1.2.4)
+    safe_yaml (1.0.5)
+    simplecov (0.17.1)
+      docile (~> 1.1)
+      json (>= 1.8, < 3)
       simplecov-html (~> 0.10.0)
-    simplecov-html (0.10.0)
+    simplecov-html (0.10.2)
     systemu (2.6.5)
     tailor (1.1.5)
       log_switch (>= 0.3.0)
       term-ansicolor (>= 1.0.5)
       text-table (>= 1.2.2)
-    term-ansicolor (1.3.2)
+    term-ansicolor (1.7.1)
       tins (~> 1.0)
     text-table (1.2.4)
-    thor (0.20.0)
-    thread_safe (0.3.5)
-    tins (1.10.2)
-    tzinfo (1.2.2)
+    thor (0.20.3)
+    thread_safe (0.3.6)
+    tilt (1.4.1)
+    tins (1.22.2)
+    tzinfo (1.2.5)
       thread_safe (~> 0.1)
     unf (0.1.4)
       unf_ext
-    unf_ext (0.0.7.4)
-    uuid (2.3.8)
+    unf_ext (0.0.7.6)
+    uuid (2.3.9)
       macaddr (~> 1.0)
-    webmock (2.1.0)
+    webmock (3.7.6)
       addressable (>= 2.3.6)
       crack (>= 0.3.2)
-      hashdiff
+      hashdiff (>= 0.4.0, < 2.0.0)
     zip-zip (0.3)
       rubyzip (>= 1.0.0)
 
@@ -147,4 +149,4 @@ DEPENDENCIES
   webmock
 
 BUNDLED WITH
-   1.16.1
+   1.17.3

README.md

@@ -1,3 +1,11 @@
+Q-Centrix has two versions of ECQM:
+    1. [ECQM-API](https://github.com/q-centrix/ecqm-api) - original repo; from 2015
+    2. [ECQM-API-V2](https://github.com/q-centrix/ecqm-api-v2) - created 2019
+
+Both Q-Centrix ECQM repositories rely on this repo, health-data-standards, to run calculations. The main branch for each repo:
+    1. ECQM-API uses branch 'acs-1691-to-mongoid7'
+    2. ECQM-API-V2 uses branch 'r5'
+
 This is a project to generate and consume HITSP C32, QRDA Category I, and QRDA Category III.
 
 In addition this project also contains libraries for parsing HQMF documents and for dealing with NLM valuesets.

health-data-standards.gemspec

@@ -13,14 +13,14 @@ Gem::Specification.new do |s|
 
   s.add_dependency 'rest-client', '~>1.8.0'
   s.add_dependency 'erubis', '~> 2.7.0'
-  s.add_dependency 'mongoid', '~> 5.0.0'
-  s.add_dependency 'mongoid-tree', '~> 2.0.0'
-  s.add_dependency 'activesupport', '~> 4.2.0'
+  s.add_dependency 'mongoid', '~> 7.0.0'
+  s.add_dependency 'mongoid-tree', '~> 2.1.1'
+  s.add_dependency 'activesupport', '< 6.0'
 
-  s.add_dependency 'protected_attributes', '~> 1.0.5'
+  s.add_dependency 'protected_attributes_continued', '~> 1.5.0'
   s.add_dependency 'uuid', '~> 2.3.7'
   s.add_dependency 'builder', '~> 3.1'
-  s.add_dependency 'nokogiri', '~> 1.8.2'
+  s.add_dependency 'nokogiri', '>= 1.10.5'
   s.add_dependency 'highline', "~> 1.7.0"
 
   s.add_dependency 'rubyzip', '~> 1.2.1'

lib/health-data-standards.rb

@@ -9,7 +9,7 @@
 require 'ostruct'
 require 'log4r'
 require 'memoist'
-require 'protected_attributes'
+require 'protected_attributes_continued'
 
 # Freedom patches
 require_relative 'health-data-standards/ext/symbol'
@@ -34,63 +34,65 @@
 require_relative 'health-data-standards/import/provider_import_utils'
 require_relative 'health-data-standards/import/hdata/metadata_importer'
 
-require_relative 'health-data-standards/models/thing_with_codes'
-require_relative 'health-data-standards/models/result_value'
-require_relative 'health-data-standards/models/coded_result_value'
-require_relative 'health-data-standards/models/physical_quantity_result_value'
-require_relative 'health-data-standards/models/cda_identifier'
-require_relative 'health-data-standards/models/reference'
-require_relative 'health-data-standards/models/entry'
-require_relative 'health-data-standards/models/allergy'
-require_relative 'health-data-standards/models/encounter'
-require_relative 'health-data-standards/models/condition'
-require_relative 'health-data-standards/models/communication'
-require_relative 'health-data-standards/models/immunization'
-require_relative 'health-data-standards/models/fulfillment_history'
-require_relative 'health-data-standards/models/order_information'
-require_relative 'health-data-standards/models/medication'
-require_relative 'health-data-standards/models/procedure'
-require_relative 'health-data-standards/models/lab_result'
-require_relative 'health-data-standards/models/family_history'
-require_relative 'health-data-standards/models/functional_status'
-require_relative 'health-data-standards/models/care_experience'
-require_relative 'health-data-standards/models/medical_equipment'
-require_relative 'health-data-standards/models/record'
-require_relative 'health-data-standards/models/personable'
-require_relative 'health-data-standards/models/provider'
-require_relative 'health-data-standards/models/provider_performance'
-require_relative 'health-data-standards/models/support'
-require_relative 'health-data-standards/models/vital_sign'
-require_relative 'health-data-standards/models/insurance_provider'
-require_relative 'health-data-standards/models/guarantor'
-require_relative 'health-data-standards/models/person'
-require_relative 'health-data-standards/models/organization'
-require_relative 'health-data-standards/models/address'
-require_relative 'health-data-standards/models/telecom'
-require_relative 'health-data-standards/models/transfer'
+# require_relative 'health-data-standards/models/thing_with_codes'
+# require_relative 'health-data-standards/models/result_value'
+# require_relative 'health-data-standards/models/coded_result_value'
+# require_relative 'health-data-standards/models/physical_quantity_result_value'
+# require_relative 'health-data-standards/models/cda_identifier'
+# require_relative 'health-data-standards/models/reference'
+# require_relative 'health-data-standards/models/entry'
+# require_relative 'health-data-standards/models/allergy'
+# require_relative 'health-data-standards/models/encounter'
+# require_relative 'health-data-standards/models/condition'
+# require_relative 'health-data-standards/models/communication'
+# require_relative 'health-data-standards/models/immunization'
+# require_relative 'health-data-standards/models/fulfillment_history'
+# require_relative 'health-data-standards/models/order_information'
+# require_relative 'health-data-standards/models/medication'
+# require_relative 'health-data-standards/models/procedure'
+# require_relative 'health-data-standards/models/lab_result'
+# require_relative 'health-data-standards/models/family_history'
+# require_relative 'health-data-standards/models/functional_status'
+# require_relative 'health-data-standards/models/care_experience'
+# require_relative 'health-data-standards/models/medical_equipment'
+# require_relative 'health-data-standards/models/record'
+# require_relative 'health-data-standards/models/personable'
+# require_relative 'health-data-standards/models/provider'
+# require_relative 'health-data-standards/models/provider_performance'
+# require_relative 'health-data-standards/models/support'
+# require_relative 'health-data-standards/models/vital_sign'
+# require_relative 'health-data-standards/models/insurance_provider'
+# require_relative 'health-data-standards/models/guarantor'
+# require_relative 'health-data-standards/models/person'
+# require_relative 'health-data-standards/models/organization'
+# require_relative 'health-data-standards/models/address'
+# require_relative 'health-data-standards/models/telecom'
+# require_relative 'health-data-standards/models/transfer'
 require_relative 'health-data-standards/models/svs/value_set'
 require_relative 'health-data-standards/models/svs/concept'
-require_relative 'health-data-standards/models/admission_source'
-require_relative 'health-data-standards/models/facility'
-require_relative 'health-data-standards/models/component'
-require_relative 'health-data-standards/models/metadata/base'
-require_relative 'health-data-standards/models/metadata/author'
-require_relative 'health-data-standards/models/metadata/change_info'
-require_relative 'health-data-standards/models/metadata/link_info'
-require_relative 'health-data-standards/models/metadata/pedigree'
-require_relative 'health-data-standards/models/provider_preference'
-require_relative 'health-data-standards/models/patient_preference'
-require_relative 'health-data-standards/models/care_goal'
-require_relative 'health-data-standards/models/encounter_principal_diagnosis'
-require_relative 'health-data-standards/models/assessment'
-require_relative 'health-data-standards/models/adverse_event'
+# require_relative 'health-data-standards/models/admission_source'
+# require_relative 'health-data-standards/models/facility'
+# require_relative 'health-data-standards/models/component'
+# require_relative 'health-data-standards/models/metadata/base'
+# require_relative 'health-data-standards/models/metadata/author'
+# require_relative 'health-data-standards/models/metadata/change_info'
+# require_relative 'health-data-standards/models/metadata/link_info'
+# require_relative 'health-data-standards/models/metadata/pedigree'
+# require_relative 'health-data-standards/models/provider_preference'
+# require_relative 'health-data-standards/models/patient_preference'
+# require_relative 'health-data-standards/models/care_goal'
+# require_relative 'health-data-standards/models/encounter_principal_diagnosis'
+# require_relative 'health-data-standards/models/assessment'
+# require_relative 'health-data-standards/models/adverse_event'
 
 require_relative 'health-data-standards/models/qrda/id'
 require_relative 'health-data-standards/models/qrda/device'
 require_relative 'health-data-standards/models/qrda/person'
 require_relative 'health-data-standards/models/qrda/organization'
+require_relative 'health-data-standards/models/qrda/information_recipient'
 require_relative 'health-data-standards/models/qrda/custodian'
 require_relative 'health-data-standards/models/qrda/legal_authenticator'
+require_relative 'health-data-standards/models/qrda/participant'
 require_relative 'health-data-standards/models/qrda/author'
 require_relative 'health-data-standards/models/qrda/header'
 

lib/health-data-standards/export/cat_3.rb

@@ -15,6 +15,7 @@ def export(measures, header, effective_date, start_date, end_date, qrda3_version
         measures.each do |measure|
           results[measure['hqmf_id']] = HealthDataStandards::CQM::QueryCache.aggregate_measure(measure['hqmf_id'], effective_date, filter, test_id)
         end
+
         @rendering_context.render(:template => 'show', 
                                   :locals => {:measures => measures, :start_date => start_date, 
                                               :end_date => end_date,
@@ -23,4 +24,4 @@ def export(measures, header, effective_date, start_date, end_date, qrda3_version
       end
     end
   end
-end
+end