renalware-core 2.0.152 → 2.0.158

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

@@ -1,10 +1,6 @@
 class AddUniqueIndexes < ActiveRecord::Migration[5.2]
   def change
     within_renalware_schema do
-      # Allow only one transplant_registration per patient
-      remove_index :transplant_registrations, :patient_id
-      add_index :transplant_registrations, :patient_id, unique: true
-
       # 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.
@@ -17,13 +13,14 @@ class AddUniqueIndexes < ActiveRecord::Migration[5.2]
       # )
 
       # Allow only one current modality_modalities per patient
-      add_index(
-        :modality_modalities,
-        :patient_id,
-        unique: true,
-        where: "ended_on is null",
-        name: :index_modality_modalities_on_patient_id_current
-      )
+      # 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
@@ -38,6 +35,10 @@ class AddUniqueIndexes < ActiveRecord::Migration[5.2]
       #   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

data/db/migrate/20200622120232_add_limits_to_path_obs_descriptions.rb

@@ -0,0 +1,18 @@
+class AddLimitsToPathObsDescriptions < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      add_column(
+        :pathology_observation_descriptions,
+        :lower_threshold,
+        :float,
+        comment: "Value below which a result can be seen as abnormal"
+      )
+      add_column(
+        :pathology_observation_descriptions,
+        :upper_threshold,
+        :float,
+        comment: "Value above which a result can be seen as abnormal"
+      )
+    end
+  end
+end

data/db/migrate/20200626081248_overload_convert_to_float_function.rb

@@ -0,0 +1,13 @@
+class OverloadConvertToFloatFunction < ActiveRecord::Migration[5.2]
+  def up
+    within_renalware_schema do
+      load_function("convert_to_float_with_explicit_return_v01.sql")
+    end
+  end
+
+  def down
+    within_renalware_schema do
+      connection.execute("DROP FUNCTION renalware.convert_to_float(text, float)")
+    end
+  end
+end

data/db/migrate/20200626090256_add_nresult_to_pathology_observations.rb

@@ -0,0 +1,29 @@
+class AddNresultToPathologyObservations < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      add_column(
+        :pathology_observations,
+        :nresult,
+        :float,
+        index: false,
+        null: true,
+        comment: "The result column cast to a float, for ease of using graphing and claculations."\
+                 "Will be null if the result has a text value that cannot be coreced into a number"
+      )
+
+      reversible do |direction|
+        direction.up do
+          load_function("update_pathology_observations_nresult_from_trigger_v01.sql")
+          load_trigger("update_pathology_observations_nresult_trigger_v01.sql")
+        end
+        direction.down do
+          connection.execute(
+            "DROP TRIGGER IF EXISTS update_pathology_observations_nresult_trigger "\
+            "ON pathology_observations; "\
+            "DROP FUNCTION IF EXISTS update_pathology_observations_nresult_from_trigger();"
+          )
+        end
+      end
+    end
+  end
+end

data/db/migrate/20200628094228_add_prescriber_to_users.rb

@@ -0,0 +1,14 @@
+class AddPrescriberToUsers < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      add_column(
+        :users,
+        :prescriber,
+        :boolean,
+        null: false,
+        default: false,
+        comment: "A user can only add or terminate a prescription if this is set to true"
+      )
+    end
+  end
+end

data/db/migrate/20200812074223_add_public_flag_to_messages.rb

@@ -0,0 +1,18 @@
+class AddPublicFlagToMessages < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      add_column(
+        :messaging_messages,
+        :public,
+        :boolean,
+        null: false,
+        default: false,
+        comment: "If true, the message will be displayed on a patient's clinical summary and " \
+                 "their messages page. If false (ie private), the message can only be viewed " \
+                 "by the sender (in their sent messages) and by the recipients. " \
+                 "New messages once this migration is run will always have public=true. "\
+                 "Historical messages will remain private."
+      )
+    end
+  end
+end

data/db/migrate/20200815150303_create_system_versions.rb

@@ -0,0 +1,16 @@
+class CreateSystemVersions < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_table :system_versions do |t|
+        t.string   :item_type, null: false
+        t.integer  :item_id,   null: false
+        t.string   :event,     null: false
+        t.string   :whodunnit
+        t.jsonb    :object
+        t.jsonb    :object_changes
+        t.datetime :created_at
+      end
+      add_index :system_versions, [:item_type, :item_id]
+    end
+  end
+end

data/db/migrate/20200817085618_create_pd_mdm_patients.rb

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

data/db/migrate/20200817103930_create_low_clearance_mdm_patients.rb

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

data/db/migrate/20201001144512_update_fn_update_current_obs_set_triggerv05.rb

@@ -0,0 +1,13 @@
+class UpdateFnUpdateCurrentObsSetTriggerv05 < ActiveRecord::Migration[5.2]
+  def up
+    within_renalware_schema do
+      load_function("update_current_observation_set_from_trigger_v05.sql")
+    end
+  end
+
+  def down
+    within_renalware_schema do
+      load_function("update_current_observation_set_from_trigger_v04.sql")
+    end
+  end
+end

data/db/migrate/20201001145452_add_position_to_letter_descriptions.rb

@@ -0,0 +1,5 @@
+class AddPositionToLetterDescriptions < ActiveRecord::Migration[5.2]
+  def change
+    add_column :letter_descriptions, :position, :integer, default: 0, null: false, index: true
+  end
+end

data/db/migrate/20201009090959_make_drug_types_unique.rb

@@ -0,0 +1,8 @@
+class MakeDrugTypesUnique < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      add_index(:drug_types, :code, unique: true)
+      add_index(:drug_types, :name, unique: true)
+    end
+  end
+end

data/db/migrate/20201012160414_add_suggested_measurement_unit_to_pathology_observation_descriptions.rb

@@ -0,0 +1,18 @@
+class AddSuggestedMeasurementUnitToPathologyObservationDescriptions < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      add_column(
+        :pathology_observation_descriptions,
+        :suggested_measurement_unit_id,
+        :integer,
+        null: true
+      )
+
+      add_foreign_key(
+        :pathology_observation_descriptions,
+        :pathology_measurement_units,
+        column: :suggested_measurement_unit_id
+      )
+    end
+  end
+end

data/db/migrate/20201012171428_create_ukrdc_measurement_units.rb

@@ -0,0 +1,18 @@
+class CreateUKRDCMeasurementUnits < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      create_table :ukrdc_measurement_units do |t|
+        t.string :name, null: false, index: :unique
+        t.string :description, null: true
+        t.timestamps null: false
+      end
+
+      add_reference(
+        :pathology_measurement_units,
+        :ukrdc_measurement_unit,
+        index: { name: "index_pathology_measurement_units_ukrdc_mu" },
+        null: true
+      )
+    end
+  end
+end

data/db/migrate/20201015160542_add_position_to_drug_types.rb

@@ -0,0 +1,31 @@
+class AddPositionToDrugTypes < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      add_column(
+        :drug_types,
+        :position,
+        :integer,
+        default: 0,
+        null: false,
+        index: true,
+        comment: "Controls display order"
+      )
+      add_column(
+        :drug_types,
+        :weighting,
+        :integer,
+        null: false,
+        default: 0,
+        comment: "More important drug types have a higher value so their colour trumps other "\
+                 "types a drug might have."
+      )
+      add_column(
+        :drug_types,
+        :colour,
+        :string,
+        null: true,
+        comment: "A CSS colour e.f. '#A12A12'"
+      )
+    end
+  end
+end

data/db/migrate/20201020155510_add_bmi_to_clinic_visits.rb

@@ -0,0 +1,31 @@
+class AddBMIToClinicVisits < ActiveRecord::Migration[5.2]
+  def change
+    within_renalware_schema do
+      add_column(
+        :clinic_visits,
+        :bmi,
+        :decimal,
+        precision: 10,
+        scale: 1,
+        null: true,
+        comment: "Body Mass Index calculated using a before_save when the clinic visit is updated"
+      )
+
+      reversible do |direction|
+        direction.up do
+          # Update the bmi for existing clinic visits, but restrict to avoid generating a
+          # non-sense value in case height or weight were entered incorrectly.
+          # NB: height is in metres and weight in kg
+          connection.execute(
+            "update renalware.clinic_visits "\
+            "set bmi = round(((weight / height)::decimal / height::decimal), 1) "\
+            "where height > 0 and height < 3 and weight > 0 and weight < 500;"
+          )
+        end
+        direction.down do
+          # noop
+        end
+      end
+    end
+  end
+end

data/db/migrate/20201020164524_update_pd_mdm_patients_view.rb

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

data/db/migrate/20201020170921_update_hd_mdm_patients_view.rb

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

data/db/migrate/20201020171139_update_low_clearance_mdm_patients_view.rb

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