renalware-core 2.0.78 → 2.0.79

data/lib/document/enum.rb

@@ -5,5 +5,9 @@ module Document
     def self.default_enums(model_name, attribute_name)
       I18n.t(attribute_name, scope: "enumerize.#{model_name.i18n_key}", cascade: true).keys
     end
+
+    def to_snomed
+      # noop
+    end
   end
 end

data/lib/renalware/configuration.rb

@@ -81,6 +81,7 @@ module Renalware
           Renalware::Letters::SummaryPart
           Renalware::Events::SummaryPart
           Renalware::Admissions::SummaryPart
+          Renalware::Admissions::ConsultSummaryPart
         )
       }
     }

data/lib/renalware/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Renalware
-  VERSION = "2.0.78"
+  VERSION = "2.0.79"
 end

data/lib/tasks/feeds/files.rake

@@ -2,22 +2,6 @@
 begin
   namespace :feeds do
     namespace :files do
-      # TODO: For some reason this is not showing up doing a rake -T
-      # Test file at = "/Users/tim/Downloads/hscorgrefdataxml_data_1.0.1_20170526000001.zip"
-      desc "Import Practices from a zip file downloaded from "\
-           "https://isd.digital.nhs.uk/trud3/user/authenticated/group/0/pack/5/subpack/341/releases " \
-           "Note: if using zsh, you must escape the brackets around the argument when calling "\
-           "e.g. "\
-           "`$ RAILS_LOG_TO_STDOUT=1 bundle exec rake app:feeds:files:import_practices\[/Users/me/x/w/z.zip\]`"
-      task :import_practices, [:absolute_zip_file_path] => [:environment] do |task, args|
-        file = Renalware::Feeds::File.build(
-          location: args.fetch(:absolute_zip_file_path),
-          file_type: :practices
-        )
-        file.save!
-        Renalware::Feeds::Files::Practices::ImportJob.perform_now(file)
-      end
-
       # TEST_ZIP_FILE_PATH = "/Users/tim/Downloads/hscorgrefdataxml_data_1.0.1_20170526000001.zip"
       desc "Import GPs"
       # Test file at "/Users/tim/Downloads/nhs_odsweekly_6.2.0_20170615000001.zip"

data/lib/tasks/hd.rake

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "benchmark"
 
 namespace :hd do

data/lib/tasks/ods.rake

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+require "nhs_api_client"
+
+namespace :ods do
+  desc "Use the NHS Organisation Data Service (ODS) API to fetch updates to practices and GPs"
+  task sync: :environment do
+    Renalware::Patients::SyncODSJob.perform_later(dry_run: ENV["dry_run"] == "true")
+  end
+end

data/spec/factories/feeds/file.rb

@@ -5,10 +5,6 @@ FactoryBot.define do
     association :file_type, factory: :feed_file_type
     accountable
 
-    trait :practices do
-      association :file_type, factory: %i(feed_file_type practices)
-    end
-
     trait :primary_care_physicians do
       association :file_type, factory: %i(feed_file_type primary_care_physicians)
     end

data/spec/factories/feeds/file_types.rb

@@ -2,15 +2,10 @@
 
 FactoryBot.define do
   factory :feed_file_type, class: "Renalware::Feeds::FileType" do
-    name { "Practices" }
-    description { "Import practices" }
+    name { "PrimaryCarePhysicians" }
+    description { "Import GPs" }
     prompt { "Where to get the file etc" }
 
-    trait :practices do
-      name { "Practices" }
-      description { "Import practices" }
-    end
-
     trait :primary_care_physicians do
       name { "GPs" }
       description { "Import GPs" }

data/spec/factories/hd/hd_session_document.rb

@@ -54,6 +54,7 @@ FactoryBot.define do
     weight { 100.0 }
     bm_stix { 1.0 }
     temperature { 36.0 }
+    respiratory_rate { 20.0 }
     blood_pressure factory: :blood_pressure, strategy: :marshal_dump
   end
 
@@ -62,6 +63,7 @@ FactoryBot.define do
     weight { 99.0 }
     bm_stix { 0.9 }
     temperature { 35.0 }
+    respiratory_rate { 25.0 }
     blood_pressure factory: :blood_pressure, strategy: :marshal_dump
   end
 

data/spec/factories/system/api_logs.rb

@@ -0,0 +1,19 @@
+# frozen_string_literal: true
+
+FactoryBot.define do
+  factory :api_log, class: "Renalware::System::APILog" do
+    identifier { "A1"}
+
+    trait :done do
+      status { Renalware::System::APILog::STATUS_DONE }
+    end
+
+    trait :working do
+      status { Renalware::System::APILog::STATUS_WORKING }
+    end
+
+    trait :error do
+      status { Renalware::System::APILog::STATUS_ERROR }
+    end
+  end
+end

data/spec/support/pathology_spec_helper.rb

@@ -25,7 +25,9 @@ module PathologySpecHelper
                                        obx_codes: ["OBX1"],
                                        requested_at: 1.year.ago,
                                        patient:,
-                                       created_at: nil)
+                                       created_at: nil,
+                                       count: 1,
+                                       result: "1.1")
     request_desc = create(:pathology_request_description, code: obr_code)
     create(
       :pathology_observation_request,
@@ -37,13 +39,15 @@ module PathologySpecHelper
     ).tap do |request|
       obx_codes.each do |obx_code|
         description = create(:pathology_observation_description, code: obx_code)
-        create(
-          :pathology_observation,
-          request: request,
-          description: description,
-          observed_at: 1.year.ago,
-          result: "1.1"
-        )
+        (1..count).each do |num|
+          create(
+            :pathology_observation,
+            request: request,
+            description: description,
+            observed_at: num.years.ago,
+            result: result
+          )
+        end
       end
     end
   end

data/vendor/assets/javascripts/renalware/double_scroll.js

@@ -0,0 +1,128 @@
+/*
+ * @name DoubleScroll
+ * @desc displays scroll bar on top and on the bottom of the div
+ * @requires jQuery
+ *
+ * @author Pawel Suwala - http://suwala.eu/
+ * @author Antoine Vianey - http://www.astek.fr/
+ * @version 0.5 (11-11-2015)
+ *
+ * Dual licensed under the MIT and GPL licenses:
+ * http://www.opensource.org/licenses/mit-license.php
+ * http://www.gnu.org/licenses/gpl.html
+ *
+ * Usage:
+ * https://github.com/avianey/jqDoubleScroll
+ */
+(function( $ ) {
+
+  jQuery.fn.doubleScroll = function(userOptions) {
+
+   // Default options
+   var options = {
+     contentElement: undefined, // Widest element, if not specified first child element will be used
+     scrollCss: {
+       'overflow-x': 'auto',
+       'overflow-y': 'hidden',
+       'height': '20px'
+     },
+     contentCss: {
+       'overflow-x': 'auto',
+       'overflow-y': 'hidden'
+     },
+     onlyIfScroll: true, // top scrollbar is not shown if the bottom one is not present
+     resetOnWindowResize: false, // recompute the top ScrollBar requirements when the window is resized
+     timeToWaitForResize: 30 // wait for the last update event (usefull when browser fire resize event constantly during ressing)
+   };
+
+   $.extend(true, options, userOptions);
+
+   // do not modify
+   // internal stuff
+   $.extend(options, {
+     topScrollBarMarkup: '<div class="doubleScroll-scroll-wrapper"><div class="doubleScroll-scroll"></div></div>',
+     topScrollBarWrapperSelector: '.doubleScroll-scroll-wrapper',
+     topScrollBarInnerSelector: '.doubleScroll-scroll'
+   });
+
+   var _showScrollBar = function($self, options) {
+
+     if (options.onlyIfScroll && $self.get(0).scrollWidth <= $self.width()) {
+       // content doesn't scroll
+       // remove any existing occurrence...
+       $self.prev(options.topScrollBarWrapperSelector).remove();
+       return;
+     }
+
+     // add div that will act as an upper scroll only if not already added to the DOM
+     var $topScrollBar = $self.prev(options.topScrollBarWrapperSelector);
+
+     if ($topScrollBar.length == 0) {
+
+       // creating the scrollbar
+       // added before in the DOM
+       $topScrollBar = $(options.topScrollBarMarkup);
+       $self.before($topScrollBar);
+
+       // apply the css
+       $topScrollBar.css(options.scrollCss);
+       $(options.topScrollBarInnerSelector).css("height", "20px");
+       $self.css(options.contentCss);
+
+       // bind upper scroll to bottom scroll
+       $topScrollBar.bind('scroll.doubleScroll', function() {
+         $self.scrollLeft($topScrollBar.scrollLeft());
+       });
+
+       // bind bottom scroll to upper scroll
+       var selfScrollHandler = function() {
+         $topScrollBar.scrollLeft($self.scrollLeft());
+       };
+       $self.bind('scroll.doubleScroll', selfScrollHandler);
+     }
+
+     // find the content element (should be the widest one)
+     var $contentElement;
+
+     if (options.contentElement !== undefined && $self.find(options.contentElement).length !== 0) {
+       $contentElement = $self.find(options.contentElement);
+     } else {
+       $contentElement = $self.find('>:first-child');
+     }
+
+     // set the width of the wrappers
+     $(options.topScrollBarInnerSelector, $topScrollBar).width($contentElement.outerWidth());
+     $topScrollBar.width($self.width());
+     $topScrollBar.scrollLeft($self.scrollLeft());
+
+   }
+
+   return this.each(function() {
+
+     var $self = $(this);
+
+     _showScrollBar($self, options);
+
+     // bind the resize handler
+     // do it once
+     if (options.resetOnWindowResize) {
+
+       var id;
+       var handler = function(e) {
+         _showScrollBar($self, options);
+       };
+
+       $(window).bind('resize.doubleScroll', function() {
+         // adding/removing/replacing the scrollbar might resize the window
+         // so the resizing flag will avoid the infinite loop here...
+         clearTimeout(id);
+         id = setTimeout(handler, options.timeToWaitForResize);
+       });
+
+     }
+
+   });
+
+ }
+
+}( jQuery ));

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.78
+  version: 2.0.79
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-05-29 00:00:00.000000000 Z
+date: 2019-06-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: active_type
@@ -987,6 +987,7 @@ files:
 - app/assets/javascripts/renalware/full_screen.js
 - app/assets/javascripts/renalware/iframe.js
 - app/assets/javascripts/renalware/keyboard_shortcuts.js
+- app/assets/javascripts/renalware/layout.js
 - app/assets/javascripts/renalware/letters.js
 - app/assets/javascripts/renalware/masonry.run.js
 - app/assets/javascripts/renalware/messaging.js
@@ -1448,13 +1449,6 @@ files:
 - app/models/renalware/feeds/files/import_job_factory.rb
 - app/models/renalware/feeds/files/practice_memberships/import_csv.rb
 - app/models/renalware/feeds/files/practice_memberships/import_job.rb
-- app/models/renalware/feeds/files/practices/convert_xml_to_csv.rb
-- app/models/renalware/feeds/files/practices/country_map.rb
-- app/models/renalware/feeds/files/practices/csv_file.rb
-- app/models/renalware/feeds/files/practices/csv_organisation.rb
-- app/models/renalware/feeds/files/practices/import_csv.rb
-- app/models/renalware/feeds/files/practices/import_job.rb
-- app/models/renalware/feeds/files/practices/xml_parser.rb
 - app/models/renalware/feeds/files/primary_care_physicians/import_csv.rb
 - app/models/renalware/feeds/files/primary_care_physicians/import_job.rb
 - app/models/renalware/feeds/files/tissue_typing/import.rb
@@ -1696,6 +1690,7 @@ files:
 - app/models/renalware/patients/ethnicity.rb
 - app/models/renalware/patients/idempotent_create_patient.rb
 - app/models/renalware/patients/language.rb
+- app/models/renalware/patients/last_successful_practice_sync_date_query.rb
 - app/models/renalware/patients/mdm_list_query.rb
 - app/models/renalware/patients/mdm_patients_query.rb
 - app/models/renalware/patients/message_param_parser.rb
@@ -1711,6 +1706,9 @@ files:
 - app/models/renalware/patients/search_form.rb
 - app/models/renalware/patients/search_query.rb
 - app/models/renalware/patients/summary.rb
+- app/models/renalware/patients/sync_gps_via_file_download_job.rb
+- app/models/renalware/patients/sync_ods_job.rb
+- app/models/renalware/patients/sync_practices_via_api.rb
 - app/models/renalware/patients/user.rb
 - app/models/renalware/patients/version.rb
 - app/models/renalware/patients/worry.rb
@@ -1779,6 +1777,7 @@ files:
 - app/models/renalware/snippets/snippet_query.rb
 - app/models/renalware/snippets/user.rb
 - app/models/renalware/system.rb
+- app/models/renalware/system/api_log.rb
 - app/models/renalware/system/country.rb
 - app/models/renalware/system/download.rb
 - app/models/renalware/system/download_query.rb
@@ -1919,6 +1918,7 @@ files:
 - app/presenters/renalware/admin/users/summary_part.rb
 - app/presenters/renalware/admissions/admission_presenter.rb
 - app/presenters/renalware/admissions/consult_presenter.rb
+- app/presenters/renalware/admissions/consult_summary_part.rb
 - app/presenters/renalware/admissions/summary_part.rb
 - app/presenters/renalware/clinical/dry_weight_presenter.rb
 - app/presenters/renalware/clinical/dry_weights_presenter.rb
@@ -2004,6 +2004,7 @@ files:
 - app/presenters/renalware/ukrdc/pathology_observation_presenter.rb
 - app/presenters/renalware/ukrdc/pathology_observation_request_presenter.rb
 - app/presenters/renalware/ukrdc/patient_presenter.rb
+- app/presenters/renalware/virology/dashboard_presenter.rb
 - app/presenters/string_presenter.rb
 - app/presenters/time_presenter.rb
 - app/presenters/true_class_presenter.rb
@@ -2018,6 +2019,7 @@ files:
 - app/validators/renalware/patients/height_validator.rb
 - app/validators/renalware/patients/primary_care_physicians/address_validator.rb
 - app/validators/renalware/patients/pulse_validator.rb
+- app/validators/renalware/patients/respiratory_rate_validator.rb
 - app/validators/renalware/patients/temperature_validator.rb
 - app/validators/renalware/patients/weight_validator.rb
 - app/values/renalware/address.rb
@@ -2077,6 +2079,7 @@ files:
 - app/views/renalware/admissions/consults/_filters.html.slim
 - app/views/renalware/admissions/consults/_filters.pdf.slim
 - app/views/renalware/admissions/consults/_form.html.slim
+- app/views/renalware/admissions/consults/_summary_part.html.slim
 - app/views/renalware/admissions/consults/_table.html.slim
 - app/views/renalware/admissions/consults/_table.pdf.slim
 - app/views/renalware/admissions/consults/edit.html.slim
@@ -2853,6 +2856,7 @@ files:
 - app/views/renalware/ukrdc/summary_mailer/export_summary.html.slim
 - app/views/renalware/ukrdc/summary_mailer/export_summary.text.erb
 - app/views/renalware/virology/dashboards/_actions.html.slim
+- app/views/renalware/virology/dashboards/_latest_hep_b_antibody_statuses.html.slim
 - app/views/renalware/virology/dashboards/show.html.slim
 - app/views/renalware/virology/profiles/_summary.html.slim
 - app/views/renalware/virology/profiles/edit.html.slim
@@ -3029,6 +3033,7 @@ files:
 - db/functions/import_gps_csv_v01.sql
 - db/functions/import_practice_memberships_csv_v01.sql
 - db/functions/import_practice_memberships_csv_v02.sql
+- db/functions/import_practice_memberships_csv_v03.sql
 - db/functions/import_practices_csv_v01.sql
 - db/functions/new_hl7_message_v01.sql
 - db/functions/preprocess_hl7_message_v01.sql
@@ -3467,6 +3472,12 @@ files:
 - db/migrate/20190513131826_add_view_count_to_system_help.rb
 - db/migrate/20190513135312_create_pathology_code_groups.rb
 - db/migrate/20190516093707_add_graft_nephectomy_on_to_tx_op_followup.rb
+- db/migrate/20190531172829_add_last_change_date_to_patient_practices.rb
+- db/migrate/20190602114659_create_system_api_logs.rb
+- db/migrate/20190603084428_add_pages_to_system_api_logs.rb
+- db/migrate/20190603135247_add_columns_to_patient_primary_care_physicians.rb
+- db/migrate/20190603143834_update_import_practice_memberships_csv.rb
+- db/migrate/20190603165812_drop_import_practices_csv_function.rb
 - db/seeds.rb
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.csv
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.rb
@@ -3638,6 +3649,7 @@ files:
 - lib/tasks/db.rake
 - lib/tasks/feeds/files.rake
 - lib/tasks/hd.rake
+- lib/tasks/ods.rake
 - lib/tasks/pathology.rake
 - lib/tasks/reporting.rake
 - lib/tasks/ukrdc.rake
@@ -3772,6 +3784,7 @@ files:
 - spec/factories/snippets/snippets.rb
 - spec/factories/snippets/users.rb
 - spec/factories/system/addresses.rb
+- spec/factories/system/api_logs.rb
 - spec/factories/system/countries.rb
 - spec/factories/system/downloads.rb
 - spec/factories/system/feedback.rb
@@ -3821,6 +3834,7 @@ files:
 - spec/support/translations.rb
 - spec/support/travel.rb
 - spec/support/webmock.rb
+- vendor/assets/javascripts/renalware/double_scroll.js
 - vendor/assets/javascripts/renalware/iframeResizer.contentWindow.js
 - vendor/assets/javascripts/renalware/iframeResizer.js
 - vendor/assets/javascripts/renalware/jquery-readyselector.js

data/app/models/renalware/feeds/files/practices/convert_xml_to_csv.rb

@@ -1,153 +0,0 @@
-# frozen_string_literal: true
-
-require_dependency "renalware/feeds"
-
-module Renalware
-  module Feeds
-    module Files
-      module Practices
-        class ConvertXmlToCsv
-          PRACTICE_ROLES = %w(RO177 RO76).freeze
-
-          def self.call(xml_path)
-            new.call(xml_path)
-          end
-
-          # Returns path to converted CSV file
-          def call(xml_path)
-            create_practice_csv_from_organisation_xml(xml_path)
-          end
-
-          private
-
-          def create_practice_csv_from_organisation_xml(xml_path)
-            file = CSVFile.new(dir: xml_path.dirname).create do |csv_writer|
-              build_practice_csv_from_organisation_xml(xml_path, csv_writer)
-            end
-            Pathname(file)
-          end
-
-          # While processing the XML using the Nokogiri Read API (wrapper by our XmlParser class)
-          # the memory footprint of the app does not rise which is the important thing here as the
-          # HSCorg XML file is around 400MB. This because we have not loaded the
-          # XML into memory (which would cause memory usage to spike over 1GB) but instead
-          # are walking over the elements. Its slower than SAX which is an alternative, as we have
-          # to inspect every Organisation in in the file even though we only want a subset of them,
-          # but its very easy to read.
-          # Currently takes around 3 minutes as a background job.
-          # Be careful when handling elements that can appear in > 1 place - e.g. Status - and
-          # check the @node.depth.
-          #
-          # There are alternative ways to parse the XML. TRUD provide an XSLT style-sheet which can
-          # extract orgs with a specific primary role (RO76 in our case) to build another XML
-          # document; they provide another XSLT for parsing the XML into CSV files. However they
-          # split the CSV files (a separate one for contact details for example), and do not not
-          # run on Mac/Linux without modification (they expect to be run on Windows).
-          #
-          # Note that the Countries in the file (with current org counts) are as follows:
-          # - ENGLAND (178568)
-          # - WALES (7013)
-          # - SCOTLAND (95)
-          # - NORTHERN IRELAND (19)
-          # - CHANNEL ISLANDS (57)
-          # - ISLE OF MAN (169)
-          #
-          # We must map the first 4 to "United Kingdom", and store e.g. Wales in address.region
-          # The others are genuine countries and left as such
-          #
-          # rubocop:disable Metrics/MethodLength, Metrics/AbcSize, Metrics/PerceivedComplexity
-          # rubocop:disable Metrics/CyclomaticComplexity
-          def build_practice_csv_from_organisation_xml(xml_path, csv_writer)
-            Rails.logger.warn "Converting XML to CSV"
-            practices_count = 0
-            regions = Hash.new(0)
-            # uk = System::Country.find_by(alpha3: "GBR")
-            countries = System::Country.all
-
-            XmlParser.new(Nokogiri::XML::Reader(open(xml_path))) do
-              org = CSVOrganisation.new
-              org.roles = []
-
-              direct_child_of_org_element = -> { @node.depth == 3 }
-
-              inside_element "Organisation" do
-                for_element "Name" do org.name = inner_xml end
-
-                for_element "Status" do
-                  # We need to check the depth of this Status element: if it is 3 we are directly
-                  # under the Organisation so that's good. Otherwise we are deeper in, probably a
-                  # role status, so ignore those.
-                  if direct_child_of_org_element.call
-                    org.active = attribute("value")&.downcase == "active"
-                  end
-                end
-
-                # Be sure not to pick up OrgId nodes under e.g. Target
-                for_element "OrgId" do
-                  if direct_child_of_org_element.call
-                    org.code = attribute("extension")
-                  end
-                end
-
-                inside_element "Contacts" do
-                  for_element "Contact" do
-                    org.telephone = attribute("value") if @node.attribute("type") == "tel"
-                  end
-                end
-                inside_element "GeoLoc" do
-                  inside_element "Location" do
-                    for_element "AddrLn1" do org.street_1 = inner_xml end
-                    for_element "AddrLn2" do org.street_2 = inner_xml end
-                    for_element "AddrLn3" do org.street_3 = inner_xml end
-                    for_element "Town" do org.city = inner_xml end
-                    for_element "County" do org.county = inner_xml end
-                    for_element "PostCode" do org.postcode = inner_xml end
-                    for_element "Country" do
-                      country_name = inner_xml
-
-                      CountryMap.new.map(country_name).tap do |mapped|
-                        org.region = mapped.region
-                        found_country = countries.find_by(name: mapped.country)
-                        if found_country.blank?
-                          Rails.logger.warn("#{country_name} not mapped")
-                          org.skip = true
-                          org.region = country_name
-                          # raise(CountryNotFoundError, country_name)
-                        else
-                          org.country_id = found_country.id
-                        end
-                      end
-                    end
-                  end
-                end
-                inside_element "Roles" do
-                  for_element "Role" do org.roles << @node.attribute("id") end
-                end
-              end
-
-              if (PRACTICE_ROLES & org.roles).any?
-                fail unless org.code&.length == 6
-
-                practices_count += 1
-                if org.skip
-                  Rails.logger.warn(
-                    "Not importing practice, probably because country country_name not found. "\
-                    "#{org}"
-                  )
-                else
-                  csv_writer << org.to_a
-                end
-              end
-            end
-            Rails.logger.warn "Found regions #{regions}"
-            Rails.logger.warn "Found #{practices_count} practices with role RO76"
-          end
-
-          class CountryNotFoundError < StandardError; end
-        end
-        # rubocop:enable Metrics/MethodLength, Metrics/AbcSize, Metrics/PerceivedComplexity
-        # rubocop:enable Metrics/CyclomaticComplexity
-      end
-    end
-  end
-end