renalware-core 2.0.148 → 2.0.155

data/config/locales/renalware/navigation/renal.en.yml

@@ -18,6 +18,7 @@ en:
         studies: Clinical Studies
         renal_registry_checks: Renal Registry Checks
         hospital_units: Dialysis Units
+        users: Users
       mdms:
         menu_title: MDMs
         hd: HD

data/config/locales/renalware/nhs_number.en.yml

@@ -0,0 +1,6 @@
+en:
+  activerecord:
+    errors:
+      messages:
+        nhs_number_invalid_checkdigit: "is invalid - please check"
+        nhs_number_not_numeric: "is invalid -  must be 10 digits"

data/config/locales/renalware/patients/side_menu.en.yml

@@ -26,6 +26,7 @@ en:
           demographics: Demographics
           clinical_summary: Clinical Summary
           inpatient_admissions: Inpatient Admissions (%{count})
+          messages: Messages
           proms: PROMS
         modalities:
           heading: Modalities

data/config/locales/renalware/pd/adequacy_result.en.yml

@@ -0,0 +1,9 @@
+en:
+  activerecord:
+    attributes:
+      renalware/pd/adequacy_result:
+        dial_24_vol_in: Dial 24 vol in (ml)
+        dial_24_vol_out: Dial 24 vol out (ml)
+        urine_24_vol: Urine 24 vol (ml)
+        height: Height (m)
+        weight: Weight (kg)

data/config/locales/renalware/pd/dashboard.en.yml

@@ -8,6 +8,9 @@ en:
             add_capd_regime: CAPD Regime
             add_apd_regime: APD Regime
             add_pet_adequacy: PET Adequacy
+            add_unified_pet_adequacy: PET & Adequacy
+            add_pet: PET
+            add_adequacy: Adequacy
             add_exit_site_infection: Exit Site Infection
             add_peritonitis_episode: Peritonitis Episode
             add_pd_assessment: PD Assessment

data/config/locales/renalware/pd/pet_result.en.yml

@@ -0,0 +1,23 @@
+en:
+  activerecord:
+    attributes:
+      renalware/pd/pet_result:
+        net_uf: PET_netUF
+        d_pcr: PET_D_Pcr
+        dextrose_concentration: Dextrose
+        dextrose_concentration_id: Dextrose
+        volume_in: Volume in (ml)
+        volume_out: Volume out (ml)
+        infusion_time: Infusion time (min)
+        drain_time: Drain time (min)
+        overnight_dextrose_concentration: Overnight dextrose
+        overnight_dextrose_concentration_id: Overnight dextrose
+        overnight_volume_in: Overnight vol in (ml)
+        overnight_volume_out: Overnight vol out (ml)
+        overnight_dwell_time: Overnight dwell time (min)
+
+  enumerize:
+    renalware/pd/pet_result:
+      pet_type:
+        fast: Fast
+        full: Full

data/config/locales/renalware/renal/registry.en.yml

@@ -8,3 +8,4 @@ en:
           comorbidities_at_esrf: Comorbidities
           first_seen_on: Date first seen
           cause_of_death: Cause of death
+          esrf: ESRF

data/config/permissions.yml

@@ -7,6 +7,7 @@ super_admin:
   - Renalware::HD::Dialyser
   - Renalware::HD::CannulationType
   - Renalware::System::Download
+  - Renalware::Pathology::ObservationDescription
 admin:
   - Renalware::User
   - Renalware::BagType

data/config/routes.rb

@@ -28,6 +28,7 @@ Renalware::Engine.routes.draw do
   draw :snippets
   draw :system
   draw :transplants
+  draw :users
   draw :virology
 
   # Last

data/config/routes/messaging.rb

@@ -2,7 +2,7 @@
 
 namespace :messaging do
   namespace :internal do
-    resources :messages, only: [:new, :create] do
+    resources :messages, only: [:new, :create, :index] do
       resources :receipts, only: [] do
         patch :mark_as_read, on: :member
       end
@@ -14,3 +14,11 @@ namespace :messaging do
     end
   end
 end
+
+resources :patients, only: [] do
+  namespace :messaging do
+    namespace :internal do
+      resources :messages, only: :index
+    end
+  end
+end

data/config/routes/pathology.rb

@@ -2,6 +2,7 @@
 
 resources :patients, only: [] do
   namespace :pathology do
+    resources :charts, only: [:show]
     get "observations/current",
         to: "current_observation_results#index",
         as: "current_observations"
@@ -11,6 +12,11 @@ resources :patients, only: [] do
     get "observations/historical",
         to: "historical_observation_results#index",
         as: "historical_observations"
+    scope constraints: { format: :json, date: /\d{4}-\d{2}-\d{2}/ } do
+      get "observations/nearest/code_group/:code_group_id/date/:date",
+          to: "nearest_observation_results#index",
+          as: "nearest_observations"
+    end
     resources :observation_requests, only: [:index, :show]
     resources :patient_rules
     get "descriptions/:description_id/observations",
@@ -22,6 +28,7 @@ end
 
 namespace :pathology do
   resources :code_groups
+  resources :observation_descriptions, except: :destroy
   namespace :requests do
     # NOTE: This needs to be POST since the params may exceed url char limit in GET
     post "requests/new", to: "requests#new", as: "new_request"

data/config/routes/patients.rb

@@ -1,6 +1,7 @@
 # frozen_string_literal: true
 
 namespace :patients do
+  get "mdms/:scope", to: "mdms#show", as: :mdms
   resources :primary_care_physicians
   resources :practices, only: [] do
     collection do

data/config/routes/pd.rb

@@ -15,6 +15,9 @@ resources :patients, only: [] do
     resources :peritonitis_episodes, only: [:new, :create, :show, :edit, :update]
     resources :exit_site_infections, only: [:new, :create, :show, :edit, :update]
     resources :pet_adequacy_results, except: [:destroy]
+    resources :unified_pet_adequacies, only: [:new, :create]
+    resources :pet_results
+    resources :adequacy_results
     resources :assessments, except: [:index, :destroy]
     resources :training_sessions, except: [:index, :destroy]
     resource :mdm, only: :show, controller: "mdm"
@@ -22,6 +25,8 @@ resources :patients, only: [] do
 end
 
 namespace :pd do
+  resources :pet_completions, only: :index
+  resources :adequacy_completions, only: :index
   resources :bag_types, except: [:show]
   resources :infection_organisms
   resources :mdm_patients, only: :index

data/config/routes/renal.rb

@@ -12,6 +12,7 @@ namespace :renal do
     collection do
       get :patients
       get :deaths
+      get :missing_esrf
     end
   end
 end

data/config/routes/system.rb

@@ -5,6 +5,9 @@ namespace :system do
   resources :user_feedback, except: :destroy, controller: "user_feedback"
   resources :messages
   resources :downloads
+  resources :view_metadata, only: [:edit, :update] do
+    patch :restore, on: :member
+  end
 end
 
 match "/404", to: "system/errors#not_found", via: :all
@@ -25,7 +28,8 @@ devise_for :users,
 
 # An ajax-polled route which will cause the users browser to redirect to the login page
 #  when their session expires
-get "/session_timed_out" => "session_timeout#has_user_timed_out", as: "session_timed_out"
+get "/check_session_expired" => "session_timeout#check_session_expired", as: "check_session_expired"
+get "/keep_session_alive" => "session_timeout#keep_session_alive", as: "keep_session_alive"
 
 super_admin_constraint = lambda do |request|
   current_user = request.env["warden"].user || Renalware::NullUser.new

data/config/routes/users.rb

@@ -0,0 +1,3 @@
+# frozen_string_literal: true
+
+resources :users, only: :index

data/db/functions/convert_to_float_with_explicit_return_v01.sql

@@ -0,0 +1,18 @@
+-- Note there is already a convert_to_float function but that remains untouched - this version
+-- has different arguments so is a new (overlaoded) function.
+CREATE OR REPLACE FUNCTION renalware.convert_to_float(v_input text, default_value_if_cannot_be_coerced float)
+RETURNS float AS $$
+DECLARE v_float_value float DEFAULT NULL;
+BEGIN
+    BEGIN
+        v_float_value := v_input::float;
+    EXCEPTION WHEN OTHERS THEN
+        RETURN default_value_if_cannot_be_coerced;
+    END;
+RETURN v_float_value;
+END;
+$$ LANGUAGE plpgsql;
+
+COMMENT ON FUNCTION renalware.convert_to_float(text, float) IS
+'Tries to coerce v_input into a float (double precision) and it it cannot,
+returns default_value_if_cannot_be_coerced';

data/db/functions/generate_secure_id_v01.sql

@@ -9,7 +9,7 @@ CREATE OR REPLACE FUNCTION generate_secure_id(length integer default 24)
   */
   RETURNS text AS
   $body$
-  SELECT string_agg (substr('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789',
+  SELECT string_agg (substr('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ9999999999',
                      ceil (random() * 62)::integer,
                      1), '')
   FROM   generate_series(1, length)

data/db/functions/update_current_observation_set_from_trigger_v05.sql

@@ -0,0 +1,92 @@
+set SEARCH_PATH=renalware,public;
+
+CREATE OR REPLACE FUNCTION update_current_observation_set_from_trigger() RETURNS TRIGGER AS $body$
+-- TC 14/12/2017 v02
+-- This function is called by a trigger when a row is inserted or updated in
+-- pathology_observations. Its purpose is to keep current_observation_sets up to date
+-- with the latest observations for any patient.
+-- The current_observation_sets table maintains a jsonb hash into which we insert or replace
+-- the observation, keyed by OBX code.
+-- e.g.  .. {"HGB": { "result": 123.1, "observed_at": '2017-12-12-01:01:01'}, ..
+DECLARE
+  a_patient_id bigint;
+  a_code text;
+  current_observed_at timestamp;
+  current_result text;
+  new_observed_at timestamp;
+BEGIN
+  -- RAISE NOTICE 'TRIGGER called on %',TG_TABLE_NAME ;
+
+  /*
+  If inserting or updating, we _could_ assume the last observation to be inserted is
+  the most 'recent' one (with the latest observed_at date).
+  However the order of incoming messages is not guaranteed, so we have two options:
+  1. Refresh the entire current_observation_set for the patient
+  2. Check the current observed_at date in the jsonb and only update if we have a more
+     recent one
+  We have gone for 2.
+  */
+
+  IF (TG_OP = 'INSERT' OR TG_OP = 'UPDATE') AND (NEW.result != '') THEN
+
+    -- Note we could re-generate the entire current pathology for the patient using
+    --  select refresh_current_observation_set(a_patient_id);
+    -- which is safer but uses more resources, so avoiding this for now.
+
+    -- Find and store patient_id into local variable
+    select request.patient_id into a_patient_id
+      from pathology_observation_requests request
+      where request.id = NEW.request_id;
+
+    -- Find and store the obx code into local variable
+    select description.code into a_code
+      from pathology_observation_descriptions description
+      where description.id = NEW.description_id;
+
+    -- Important! Create the observation_set if it doesn't exist yet
+    -- ignore the error if the row already exists
+    insert into pathology_current_observation_sets (patient_id)
+    values (a_patient_id)
+    ON CONFLICT DO NOTHING;
+
+    -- We are going to compare the current and new observed_at dates
+    -- so need to cast them  to a timestamp
+    select cast(New.observed_at as timestamp) into new_observed_at;
+
+    -- Get the most recent date and value for this observation
+    -- and store to variables.
+    select
+    cast(values -> a_code ->> 'observed_at' as timestamp),
+    values -> a_code ->> 'result'
+    into current_observed_at, current_result from
+    pathology_current_observation_sets
+    where patient_id = a_patient_id;
+
+    -- Output some info to help us debug. This can be removed later.
+    -- RAISE NOTICE '  Request id % Patient id % Code %', NEW.request_id, a_patient_id, a_code;
+    -- RAISE NOTICE '  Last %: % at %', a_code, current_result, current_observed_at;
+    -- RAISE NOTICE '  New  %: % at %', a_code, NEW.result, new_observed_at;
+
+    IF current_observed_at IS NULL OR new_observed_at >= current_observed_at THEN
+      -- The new pathology_observation row contain a more recent result that the old one.
+      -- (note there may not be an old one if the patient has neve had this obs before).
+
+      -- RAISE NOTICE '  Updating pathology_current_observation_sets..';
+
+      -- Update the values jsonb column with the new hash for this code, e.g.
+      -- .. {"HGB": { "result": 123.1, "observed_at": '2017-12-12-01:01:01'}, ..
+            -- Note the `set values` below actually reads in the jsonb, updates it,
+            -- and wites the whole thing back.
+      update pathology_current_observation_sets
+        set updated_at = CURRENT_TIMESTAMP,
+          values = jsonb_set(
+          values,
+          ('{'||a_code||'}')::text[], -- defined in the fn path::text[]
+          jsonb_build_object('result', NEW.result, 'observed_at', new_observed_at),
+          true)
+        where patient_id = a_patient_id;
+    END IF;
+  END IF;
+  RETURN NULL ;
+END $body$ LANGUAGE plpgsql VOLATILE COST 100;
+-- End function

data/db/functions/update_pathology_observations_nresult_from_trigger_v01.sql

@@ -0,0 +1,13 @@
+CREATE OR REPLACE FUNCTION update_pathology_observations_nresult_from_trigger() RETURNS TRIGGER AS $body$
+DECLARE
+BEGIN
+  IF (TG_OP = 'INSERT' OR TG_OP = 'UPDATE') THEN
+    NEW.nresult = convert_to_float(NEW.result, NULL);
+  END IF;
+  RETURN NEW ;
+END $body$ LANGUAGE plpgsql;
+
+COMMENT ON FUNCTION update_pathology_observations_nresult_from_trigger() IS
+'Tries to coerce the result column into the nresult column as a float.
+Sets nresult to NULL if result is eg text and cannot be coerced.
+nresult is a performance optimisation useful for instance in graphing';

data/db/migrate/20200122182018_update_patient_current_modalities.rb

@@ -0,0 +1,7 @@
+class UpdatePatientCurrentModalities < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      update_view :patient_current_modalities, version: 2, revert_to_version: 1
+    end
+  end
+end

data/db/migrate/20200122182036_create_transplant_mdm_patients.rb

@@ -0,0 +1,7 @@
+class CreateTransplantMDMPatients < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_view :transplant_mdm_patients
+    end
+  end
+end

data/db/migrate/20200122190909_create_view_metadata.rb

@@ -0,0 +1,44 @@
+class CreateViewMetadata < ActiveRecord::Migration[5.2]
+  def change
+    enable_extension "hstore"
+    within_renalware_schema do
+      create_table(
+        :system_view_metadata,
+        comment: "Holds descriptive and layout data to help us construct "\
+                 "data-driven parts of the Renalware UI e.g. MDMs"
+      ) do |t|
+        t.text :schema_name, null: false
+        t.text :view_name, null: false
+        t.text :slug, comment: "May be used in urls - must be lower case with no spaces"
+        t.text :category, comment: "e.g. MDM"
+        t.text :scope, comment: "e.g. PD"
+        t.text :parent_name
+        t.references(
+          :parent,
+          index: true,
+          foreign_key: { to_table: :system_view_metadata },
+          comment: "Self-join in case a view should have children"
+        )
+        t.text :title, comment: "A label that may appear in the UI"
+        t.jsonb(
+          :columns,
+          comment: "Array of column_names. If empty, all cols displayed. "\
+                   "Array order is the display order",
+          null: false,
+          default: []
+        )
+        t.jsonb(
+          :filters,
+          null: false,
+          default: [],
+          comment: "Array of filter definition for generating filters. " \
+                   "Must be the name of a column in the SQL view. "
+        )
+        t.integer :position, null: false, default: 0
+        t.text :description, comment: "A description of the SQL view's function"
+        t.timestamps null: false
+      end
+      add_index :system_view_metadata, %i(category scope slug), unique: true
+    end
+  end
+end

data/db/migrate/20200131133223_create_hd_mdm_patients.rb

@@ -0,0 +1,7 @@
+class CreateHDMDMPatients < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_view :hd_mdm_patients
+    end
+  end
+end

data/db/migrate/20200205185151_add_columns_to_system_view_metadata.rb

@@ -0,0 +1,13 @@
+class AddColumnsToSystemViewMetadata < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_enum :system_view_display_type, %w(tabular)
+      create_enum :system_view_category, %w(mdm report)
+      remove_column :system_view_metadata, :category, :string
+      change_table :system_view_metadata do |t|
+        t.enum :display_type, enum_name: :system_view_display_type, default: :tabular, null: false
+        t.enum :category, enum_name: :system_view_category, default: :mdm, null: false
+      end
+    end
+  end
+end

data/db/migrate/20200219113324_create_supportive_care_mdm_patients_view.rb

@@ -0,0 +1,7 @@
+class CreateSupportiveCareMDMPatientsView < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_view :supportive_care_mdm_patients
+    end
+  end
+end

data/db/migrate/20200226145010_add_unique_indexes.rb

@@ -0,0 +1,47 @@
+class AddUniqueIndexes < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      # Allow only one un-terminated transplant_registration_status per patient
+      # Removed this for now as the way we update the terminated_on in the model
+      # prevents us from enforcing this constraint atm.
+      # remove_index :transplant_registration_statuses, :registration_id
+      # add_index(
+      #   :transplant_registration_statuses,
+      #   :registration_id,
+      #   unique: true,
+      #   where: "terminated_on is null"
+      # )
+
+      # Allow only one current modality_modalities per patient
+      # Removed until we have had a change to housekeep the duplicates
+      # add_index(
+      #   :modality_modalities,
+      #   :patient_id,
+      #   unique: true,
+      #   where: "ended_on is null",
+      #   name: :index_modality_modalities_on_patient_id_current
+      # )
+
+      # Removed this for now as prevents adding new profiles. Need to address holistically in
+      # a separate PR
+      # # An access profile must have a start date
+      # change_column_null :access_profiles, :started_on, false
+      # # Allow only on unterminated access profile per patient
+      # add_index(
+      #   :access_profiles,
+      #   :patient_id,
+      #   unique: true,
+      #   where: "terminated_on is null",
+      #   name: :index_access_profiles_on_patient_id_current
+      # )
+
+      # Allow only one transplant_registration per patient
+      remove_index :transplant_registrations, :patient_id
+      add_index :transplant_registrations, :patient_id, unique: true
+
+      # Allow only one renal_profile per patient
+      remove_index :renal_profiles, :patient_id
+      add_index :renal_profiles, :patient_id, unique: true
+    end
+  end
+end