renalware-core 2.0.151 → 2.0.157

data/app/views/renalware/system/view_metadata/_filters_form.html.slim

@@ -0,0 +1,19 @@
+.rounded-md.bg-orange-200.px-3.py-2.flex.items-start.shadow.mx-1.mb-5
+  i.fas.fa-info-circle.mr-2.mt-1.text-blue-500
+  | Editing filters is not possible yet
+
+table
+  thead
+    th SQL column name
+    th Filter type
+  tbody
+    - view.filters.each do |filter|
+      tr
+        td.border-0
+          code= filter.code
+        td.border-0
+          = filter.type
+          / select.m-0(name="view_metadata[filters][][1]")
+          /   option(value="")
+          /   - Renalware::System::ColumnDefinition.new.width_values.each do |val, x|
+          /     option(value=val selected=(col.width == val.to_s))=val.to_s.humanize filter[1]

data/app/views/renalware/system/view_metadata/_versions.html.slim

@@ -0,0 +1,23 @@
+/ Note we can't do vioew.versions.order(...) here
+- versions = view.versions.to_a.sort{ |a, b| b.created_at <=> a.created_at }
+.rounded-md.bg-orange-200.px-3.py-2.flex.items-start.shadow.mx-1.mb-5
+  i.fas.fa-info-circle.mr-2.mt-1.text-blue-500
+  | Restore column and filter configuration to a point in time.
+  | Unsaved column/filter changes will be lost.
+table
+  thead
+    th.col-width-date-time Last updated
+    th.col-width-small Event
+    th By
+    th
+  tbody
+    - versions.each do |version|
+      tr
+        td= l(version.created_at)
+        td= version.event
+        td= Renalware::User.find(version.whodunnit)
+        td.text-right
+          = link_to("Restore",
+                    renalware.restore_system_view_metadatum_path(view, version_at: version.created_at),
+                    data: { method: :patch },
+                    class: "button compact secondary")

data/app/views/renalware/system/view_metadata/edit.html.slim

@@ -0,0 +1,66 @@
+
+/ To remember
+/ We have klass.columns which are the actual SQL view columns
+/ We view (view metadata) columns, which is an array of hashes, each representing a column
+/ with its title. and width. Its position comes from the position inthe array.
+/
+/ Here loop through all avail columns on klass and find the matching
+/ col in view.columns. If there are columns we don't recognise (the view config is stale) they
+/ will be discarded when we save. If there are new cols we given them an empty object and it will be
+/ saved away.
+/ We need to handle validation
+/ also serialisation - see https://nandovieira.com/using-postgresql-and-jsonb-with-ruby-on-rails
+
+ruby:
+  # attribute_names = klass.columns.map(&:name) - %w(id secure_id document)
+  # view.columns = attribute_names.map do |attr|
+  #  view.columns.detect{ |col| col.code == attr } || Renalware::System::ColumnDefinition.new(code: attr)
+  # end
+
+  attribute_names = klass.columns.map(&:name) - %w(id secure_id document)
+  attribute_names = (view.columns.map(&:code) + attribute_names).uniq
+  view.columns = attribute_names.map do |attr|
+    view.columns.detect{ |col| col.code == attr } || Renalware::System::ColumnDefinition.new(code: attr)
+  end
+
+= simple_form_for(view, as: "view_metadata", method: :patch) do |f|
+  = f.input :id, as: :hidden
+  .modal
+    .modal__header
+      = render "renalware/shared/modal_close_link"
+      - title = [view.category&.humanize, view.scope&.humanize, view.title&.humanize].join(" / ")
+      h2= "Edit columns for #{title}"
+    .modal__body(style="max-height: 400px")
+      .rounded-md.bg-blue-100.px-3.py-2.flex.items-start.shadow.mx-1.mb-5
+        i.fas.fa-info-circle.mr-2.mt-1.text-blue-500
+        | Please bear in mind that changes you make will be visible by all users.
+
+      / Tabs - see also js stimulus tabs-controller
+      div(data-controller="tabs" data-tabs-active-tab="-mb-px border-l border-t border-r rounded-t")
+        ul.list-reset.flex.border-b.ml-0
+          li.-mb-px.mr-1(data-target="tabs.tab" data-action="click->tabs#change")
+            a.bg-white.inline-block.py-2.px-4.text-blue-500.hover:text-blue-700.font-semibold.no-underline(href="#") Columns
+          li.-mb-px.mr-1(data-target="tabs.tab" data-action="click->tabs#change")
+            a.bg-white.inline-block.py-2.px-4.text-blue-500.hover:text-blue-700.font-semibold.no-underline(href="#") Filters
+          li.-mb-px.mr-1(data-target="tabs.tab" data-action="click->tabs#change")
+            a.bg-white.inline-block.py-2.px-4.text-blue-500.hover:text-blue-700.font-semibold.no-underline(href="#") Previous versions
+
+        .hidden.py-4.px-4.border-l.border-b.border-r(data-target="tabs.panel")
+          = render "columns_table", view: view
+        .hidden.py-4.px-4.border-l.border-b.border-r(data-target="tabs.panel")
+          = render "filters_form", view: view
+        .hidden.py-4.px-4.border-l.border-b.border-r(data-target="tabs.panel")
+          = render "versions", view: view
+
+    .modal__footer
+      br
+      .right
+        = f.submit "Save", class: "button"
+        span= " or "
+        = link_to "Cancel",
+                "#",
+                "aria-label" => "Close",
+                  class: "reveal-modal-close"
+
+javascript:
+  initSortables();

data/app/views/renalware/transplants/mdm/_prescriptions.html.slim

@@ -6,25 +6,9 @@ article
       = render "prescription_buttons", patient: mdm.patient
 
   #prescriptions.expandable
-
-    ul.tab-strip(data-tab)
-      li.tab-title.active= link_to "Current", "#current", data: { "trigger-masonry-refresh" => true }
-      li.tab-title= link_to "Current Immunosuppressant", "#current_immunosuppressant", data: { "trigger-masonry-refresh" => true }
-      li.tab-title= link_to "Historical", "#historical", data: { "trigger-masonry-refresh" => true }
-      li.tab-title= link_to "Historical Immunosuppressant", "#historical_immunosuppressant", data: { "trigger-masonry-refresh" => true }
-
-    .tabs-content
-      #current.content.active
-        = render "renalware/mdm/prescriptions/table",
-                 prescriptions: mdm.current_prescriptions
-      #current_immunosuppressant.content
-        = render "renalware/mdm/prescriptions/table",
-                 prescriptions: mdm.current_immunosuppressant_prescriptions
-      #historical.content
-        = render "renalware/mdm/prescriptions/table",
-                 prescriptions: mdm.historical_prescriptions,
-                 show_terminated_on: true
-      #historical_immunosuppressant.content
-        = render "renalware/mdm/prescriptions/table",
-                 prescriptions: mdm.historical_immunosuppressant_prescriptions,
-                 show_terminated_on: true
+    = render Renalware::Medications::TabbedPrescriptionsListComponent.new([ \
+      { title: "Current", prescriptions: mdm.current_prescriptions, show_terminated_on: false }, \
+      { title: "Current Immunosuppressant", prescriptions: mdm.current_immunosuppressant_prescriptions, show_terminated_on: false },
+      { title: "Historical", prescriptions: mdm.historical_prescriptions },
+      { title: "Historical Immunosuppressant", prescriptions: mdm.historical_immunosuppressant_prescriptions },
+      { title: "Bone Meds", prescriptions: mdm.bone_prescriptions }])

data/app/views/renalware/users/_filters.html.slim

@@ -0,0 +1,11 @@
+.filters
+  .filters__form
+    = search_form_for user_search, url: users_path do |f|
+      .row
+        .small-9.large-4.columns
+          = f.label "Name or username contains"
+          = f.search_field :family_name_or_given_name_or_username_or_email_cont
+        .small-3.large-4.columns.actions.end
+          = f.submit t("helpers.submit.filter"), class: "button"
+          '  or
+          = link_to t("helpers.reset"), users_path

data/app/views/renalware/users/index.html.slim

@@ -0,0 +1,24 @@
+= content_for(:filters) do
+  = render "filters", user_search: user_search
+
+= within_admin_layout(title: "Users") do
+  table.all-users
+    thead
+      tr
+        th Name
+        th Position
+        th Email
+        th Role
+        th.col-width-date-time Expired at
+    tbody
+      - users.each do |user|
+        tr
+          td= user.full_name
+          td= user.professional_position
+          td= user.email
+          td
+            - user.roles.each do |role|
+              span.tag(class=role.name)= role.name.humanize
+          td= l(user.expired_at)
+
+  == pagy_foundation_nav pagy

data/config/initializers/core_extensions.rb

@@ -3,7 +3,7 @@
 require "core_extensions/i18n/handle_blank_value"
 require "core_extensions/i18n/always_cascade"
 require "core_extensions/dumb_delegator"
-require "core_extensions/active_record/sort"
+# require "core_extensions/active_record/sort"
 require "core_extensions/date"
 require "core_extensions/active_support/duration"
 require "core_extensions/scenic"
@@ -14,6 +14,6 @@ require "core_extensions/ox/element_additions"
 I18n.extend CoreExtensions::I18n::HandleBlankValue
 I18n::Backend::Simple.include(I18n::Backend::Cascade)
 I18n.extend CoreExtensions::I18n::AlwaysCascade
-ActiveRecord::Base.include(CoreExtensions::ActiveRecord::Sort)
+# ActiveRecord::Base.include(CoreExtensions::ActiveRecord::Sort)
 Date.include(CoreExtensions::Date::Constants)
 Hash.include(CoreExtensions::Hash::OpenStructConversion)

data/config/initializers/delayed_job.rb

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 
-Delayed::Worker.logger = Logger.new(Rails.root.join("log", "delayed_job.log"))
+Delayed::Worker.logger = Logger.new(Rails.root.join("log/delayed_job.log"))
 Delayed::Worker.destroy_failed_jobs = false
 Delayed::Worker.max_attempts = 10 # overridden e.g. in FeedJob
 Delayed::Worker.max_run_time = 2.hours

data/config/initializers/inflections.rb

@@ -41,6 +41,7 @@ ActiveSupport::Inflector.inflections(:en) do |inflect|
   inflect.acronym "HIV"
   inflect.acronym "HL7"
   inflect.acronym "MDM"
+  inflect.acronym "MDMs"
   inflect.acronym "NHS"
   inflect.acronym "NHS"
   inflect.acronym "ODS"

data/config/initializers/pagy.rb

@@ -7,3 +7,8 @@
 # Foundation extra: Add nav, nav_js and combo_nav_js helpers and templates for Foundation pagination
 # See https://ddnexus.github.io/pagy/extras/foundation
 require "pagy/extras/foundation"
+
+# Allow the client to request a custom number of items per page with an optional selector UI.
+# It is useful with APIs or higly user-customizable apps.
+# Usefule for testing pagination from testing by supplying eg :items => 1
+require "pagy/extras/items"

data/config/locales/renalware/clinical/allergies.en.yml

@@ -6,6 +6,7 @@ en:
           legend: Allergies
           description: Description
           recorded_at: Recorded
+          recorded_by: By
           add: Add
           delete: Delete
           edit: Edit

data/config/locales/renalware/medications/tabbed_prescriptions_list_component.yml

@@ -0,0 +1,15 @@
+en:
+  renalware:
+    medications:
+      tabbed_prescriptions_list_component:
+        title: Prescriptions
+        view_all: View All
+        drug_name: Drug
+        drug_type: Type
+        dose: Dose
+        frequency: Freq
+        route: Route
+        provider: Provider
+        administer_on_hd: Give on HD
+        terminated_on: Term on
+        started_on: Started on

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/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/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

@@ -28,6 +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/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/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