renalware-core 2.0.149 → 2.0.156

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

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

data/db/migrate/20200421082715_add_body_surface_area_to_clinic_visits.rb

@@ -0,0 +1,8 @@
+class AddBodySurfaceAreaToClinicVisits < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      add_column :clinic_visits, :body_surface_area, :decimal, precision: 8, scale: 2
+      add_column :clinic_visits, :total_body_water, :decimal, precision: 8, scale: 2
+    end
+  end
+end

data/db/migrate/20200421132911_create_pd_pet_dextrose_concentrations.rb

@@ -0,0 +1,13 @@
+class CreatePDPETDextroseConcentrations < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_table :pd_pet_dextrose_concentrations do |t|
+        t.string :name, null: false, index: { unique: true }
+        t.float :value, null: false, index: { unique: true }
+        t.boolean :hidden, null: false, default: false
+        t.integer :position, null: false, default: 0
+        t.timestamps null: false
+      end
+    end
+  end
+end

data/db/migrate/20200421143546_create_pet_results.rb

@@ -0,0 +1,66 @@
+class CreatePETResults < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_enum :pd_pet_type, %w(full fast)
+
+      create_table :pd_pet_results do |t|
+        t.references :patient, null: false, foreign_key: true
+
+        # The first set are inputs when seeing the patient
+        t.date :performed_on, null: false
+        t.enum :test_type, enum_name: :pd_pet_type, null: false
+        t.integer :volume_in
+        t.integer :volume_out
+        t.references(
+          :dextrose_concentration,
+          foreign_key: { to_table: :pd_pet_dextrose_concentrations },
+          index: true,
+          null: true
+        )
+        t.integer :infusion_time
+        t.integer :drain_time
+        t.integer :overnight_volume_in
+        t.integer :overnight_volume_out
+        t.references(
+          :overnight_dextrose_concentration,
+          foreign_key: { to_table: :pd_pet_dextrose_concentrations },
+          index: true,
+          null: true
+        )
+        t.integer :overnight_dwell_time
+
+        # This set is manually or automatically added pathology after the fact
+        # Refers to dialysate samples
+        [0, 2, 4, 6].each do |hr|
+          t.float :"sample_#{hr}hr_time"
+          t.float :"sample_#{hr}hr_urea"
+          t.float :"sample_#{hr}hr_creatinine"
+          t.float :"sample_#{hr}hr_glc"
+          t.float :"sample_#{hr}hr_sodium"
+          t.float :"sample_#{hr}hr_protein"
+        end
+
+        # Blood results back from the lab
+        t.float :serum_time
+        t.float :serum_urea
+        t.float :serum_creatinine
+        t.float :plasma_glc
+        t.float :serum_ab
+        t.float :serum_na
+
+        # This set is for calculated fields
+        t.integer :net_uf
+        t.float :d_pcr
+        t.boolean :complete, default: false, null: false, indeex: true
+
+        t.datetime :deleted_at, index: true
+        t.references :created_by, index: true, null: false
+        t.references :updated_by, index: true, null: false
+        t.timestamps null: false
+      end
+
+      add_foreign_key :pd_pet_results, :users, column: :created_by_id
+      add_foreign_key :pd_pet_results, :users, column: :updated_by_id
+    end
+  end
+end

data/db/migrate/20200427123229_create_adequacy_results.rb

@@ -0,0 +1,54 @@
+class CreateAdequacyResults < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_table :pd_adequacy_results do |t|
+        t.references :patient, null: false, foreign_key: true
+
+        # The first set are inputs after seeing the patient
+        t.date :performed_on, null: false
+        t.integer :dial_24_vol_in
+        t.integer :dial_24_vol_out
+        t.boolean :dial_24_missing, null: false, default: false
+        t.integer :urine_24_vol
+        t.boolean :urine_24_missing, null: false, default: false
+
+        # Blood results back from the lab
+        t.float :serum_urea
+        t.float :serum_creatinine
+        t.float :plasma_glc
+        t.float :serum_ab
+
+        # Dialysate results back from the lab
+        t.float :dialysate_urea
+        t.float :dialysate_creatinine
+        t.float :dialysate_glu
+        t.float :dialysate_na
+        t.float :dialysate_protein
+
+        # Urine results back from the lab
+        t.float :urine_urea
+        t.float :urine_creatinine
+        t.float :urine_na
+        t.float :urine_k
+
+        # Calculations
+        t.float :total_creatinine_clearance
+        t.float :pertitoneal_creatinine_clearance
+        t.float :renal_creatinine_clearance
+        t.float :total_ktv
+        t.float :pertitoneal_ktv
+        t.float :renal_ktv
+        t.float :dietry_protein_intake
+        t.boolean :complete, default: false, null: false, indeex: true
+
+        t.datetime :deleted_at, index: true
+        t.references :created_by, index: true, null: false
+        t.references :updated_by, index: true, null: false
+        t.timestamps null: false
+      end
+
+      add_foreign_key :pd_adequacy_results, :users, column: :created_by_id
+      add_foreign_key :pd_adequacy_results, :users, column: :updated_by_id
+    end
+  end
+end