renalware-core 2.0.0.pre.rc10 → 2.0.0.pre.rc11

data/app/models/renalware/pathology/observations_grouped_by_date_table.rb

@@ -0,0 +1,59 @@
+require_dependency "renalware/pathology"
+require "attr_extras"
+
+module Renalware
+  module Pathology
+    # A helper class wrapping a custom relation object which has aggregated a
+    # patient's pathology results by date of observation using raw SQL + PGResult.
+    # Note we implement the required interface for kaminari pagination (we delegate to the
+    # underlying relation to achieve this).
+    #
+    # This class exists to make the underlying PGResult set (wrapped in a custom relation-like
+    # object) easier to consume.
+    #
+    # Example usage:
+    # (ruby)
+    # codes = %i(HGB PLT WBC)
+    # rows = ObservationsGroupedByDateQuery.new(patient_id: 1, codes: codes)
+    # table = ObservationsGroupedByDateTable.new(rows: rows, codes: %i(HGB PLT WBC))
+    # (html)
+    # table
+    #   tr
+    #     td Date
+    #     - table.codes do |code|
+    #       td= code
+    #   tbody
+    #     tr
+    #       - table.each_row do |row|
+    #         td= l(row.observed_on)
+    #         - table.codes.each do |code|
+    #           td= row.result_for(code)
+    #
+    # = paginate(table)
+    #
+    class ObservationsGroupedByDateTable
+      attr_reader_initialize [:observation_descriptions!, :relation!]
+      delegate :current_page, :total_pages, :limit_value, to: :relation
+
+      def rows
+        @rows ||= relation.all.map(&:with_indifferent_access).map { |row| Row.new(row) }
+      end
+
+      class Row
+        pattr_initialize :row
+
+        def observed_on
+          Date.parse(row[:observed_on])
+        end
+
+        def result_for(code)
+          results[code&.to_sym]
+        end
+
+        def results
+          @results = JSON.parse(row[:results]).with_indifferent_access
+        end
+      end
+    end
+  end
+end

data/app/models/renalware/pd/mdm_patients_query.rb

@@ -4,10 +4,12 @@ module Renalware
       include ModalityScopes
       include PatientPathologyScopes
       MODALITY_NAMES = "PD".freeze
+      DEFAULT_SEARCH_PREDICATE = "hgb_date desc".freeze
       attr_reader :q, :relation
 
       def initialize(relation: PD::Patient.all, q:)
-        @q = q
+        @q = q || {}
+        @q[:s] = DEFAULT_SEARCH_PREDICATE if @q[:s].blank?
         @relation = relation
       end
 

data/app/models/renalware/renal/aki_alert.rb

@@ -9,6 +9,7 @@ module Renalware
       belongs_to :action, class_name: "Renal::AKIAlertAction"
       belongs_to :hospital_ward, class_name: "Hospitals::Ward"
       validates :patient, presence: true
+      validates :max_aki, inclusion: 1..3, allow_nil: true
       alias_attribute :decided_by, :updated_by
     end
   end

data/app/models/renalware/reporting/audit.rb

@@ -6,6 +6,8 @@ module Renalware
       validates :name, presence: true
       validates :view_name, presence: true
 
+      scope :enabled, ->{ where(enabled: true) }
+
       def self.available_audit_materialized_views
         result = connection.execute("SELECT oid::regclass::text FROM pg_class
                                      WHERE  relkind in ('m', 'v') and relname like 'reporting_%';")

data/app/models/renalware/system/update_user.rb

@@ -21,7 +21,6 @@ module Renalware
 
       def update!(params)
         User.transaction do
-          user.skip_validation = true
           approve if can_approve?(params)
           unexpire if can_unexpire?(params)
           authorise(params)

data/app/models/renalware/transplants/registrations/wait_list_query.rb

@@ -1,22 +1,24 @@
+require_dependency "renalware/transplants"
+
 module Renalware
   module Transplants
     module Registrations
       class WaitListQuery
-        def initialize(quick_filter:, q: nil)
-          @quick_filter = quick_filter.to_sym
-          @q = q || {}
+        def initialize(named_filter:, q: nil)
+          @named_filter = named_filter&.to_sym || :active
+          @q = (q || ActionController::Parameters.new).permit(:s, :q)
         end
 
         def call
           search
             .result
             .extending(Scopes)
-            .apply_filter(@quick_filter)
+            .apply_filter(named_filter)
         end
 
         def search
           @search ||= begin
-            query = query_for_filter(@quick_filter).merge(@q)
+            query = query_for_filter(named_filter).merge(q)
             QueryableRegistration
               .includes(patient: [current_modality: :description])
               .search(query).tap do |s|
@@ -42,6 +44,8 @@ module Renalware
 
         private
 
+        attr_reader :q, :named_filter
+
         def query_for_filter(filter)
           case filter
           when :active

data/app/models/renalware/transplants.rb

@@ -1,5 +1,7 @@
 module Renalware
   module Transplants
+    WAITLIST_FILTERS = %w(active suspended active_and_suspended working_up status_mismatch).freeze
+
     def self.table_name_prefix
       "transplant_"
     end

data/app/models/renalware/user.rb

@@ -1,3 +1,5 @@
+require "devise"
+
 module Renalware
   class User < ApplicationRecord
     include Deviseable
@@ -12,11 +14,11 @@ module Renalware
     validate :approval_with_roles, on: :update
     validates :professional_position, presence: {
       on: :update,
-      unless: :skip_validation
+      if: ->(user){ user.with_extended_validation }
     }
     validates :signature, presence: {
       on: :update,
-      unless: :skip_validation
+      if: ->(user){ user.with_extended_validation }
     }
 
     scope :unapproved, -> { where(approved: [nil, false]) }
@@ -25,13 +27,16 @@ module Renalware
     }
     scope :author, -> { where.not(signature: nil) }
     scope :ordered, -> { order(:family_name, :given_name) }
+    scope :excluding_system_user, -> { where.not(username: SystemUser.username) }
+    scope :with_no_role, lambda {
+      left_joins(:roles)
+        .distinct("roles_users.user_id")
+        .where("roles_users.user_id is null")
+    }
 
-    # Non-persistent attribute to signify we want to bypassing the :update validations
-    attr_writer :skip_validation
-
-    def skip_validation
-      @skip_validation || reset_password_token
-    end
+    # Non-persistent attribute to signify we want to use extended validation.
+    # We need to refactor this by ising a form object for updating a user.
+    attr_accessor :with_extended_validation
 
     def self.policy_class
       UserPolicy
@@ -59,8 +64,21 @@ module Renalware
       signed
     end
 
+    def generate_new_authentication_token!
+      build_authentication_token.tap do |token|
+        update_column(:authentication_token, token)
+      end
+    end
+
     private
 
+    def build_authentication_token
+      loop do
+        token = ::Devise.friendly_token
+        break token unless User.find_by(authentication_token: token)
+      end
+    end
+
     def approval_with_roles
       if approved? && roles.empty?
         errors.add(:approved, "approved users must have a role")

data/app/policies/renalware/admin/cache_policy.rb

@@ -0,0 +1,15 @@
+require_dependency "renalware/admin"
+
+module Renalware
+  module Admin
+    class CachePolicy < BasePolicy
+      def show?
+        user_is_super_admin?
+      end
+
+      def destroy
+        user_is_super_admin?
+      end
+    end
+  end
+end

data/app/presenters/renalware/admin/users/summary_part.rb

@@ -0,0 +1,23 @@
+module Renalware
+  module Admin
+    module Users
+      class SummaryPart < Renalware::SummaryPart
+        def to_partial_path
+          "renalware/admin/users/summary_part"
+        end
+
+        def users_needing_approval_count
+          @users_needing_approval_count ||= User.unapproved.count
+        end
+
+        def users_needing_approval_title
+          [
+            users_needing_approval_count,
+            "user".pluralize(users_needing_approval_count),
+            "awaiting approval"
+          ].join(" ")
+        end
+      end
+    end
+  end
+end

data/app/presenters/renalware/events/summary_part.rb

@@ -3,8 +3,8 @@ require_dependency "renalware/events"
 module Renalware
   module Events
     class SummaryPart < Renalware::SummaryPart
-      def current_events
-        @current_events ||= begin
+      def recent_events
+        @recent_events ||= begin
           Events::Event.includes([:created_by, :event_type])
                        .for_patient(patient)
                        .limit(Renalware.config.clinical_summary_max_events_to_display)
@@ -12,20 +12,27 @@ module Renalware
         end
       end
 
-      def current_events_count
+      def recent_events_count
         title_friendly_collection_count(
-          actual: current_events.size,
+          actual: recent_events.size,
           total: patient.summary.events_count
         )
       end
 
+      # AR::Relation#cache_key here will issue:
+      #   SELECT COUNT(*) AS "size", MAX("events"."updated_at") AS timestamp
+      #   FROM "events" WHERE "events"."patient_id" = 1
+      # and use size and timestamp in the cache key.
+      # We purposefully don't use the recent_events relation here as it has includes and a limit
+      # and apart from being slower, using LIMIT in cache_key sql has been known to produce
+      # inconsistent results.
+      def cache_key
+        Events::Event.for_patient(patient).cache_key
+      end
+
       def to_partial_path
         "renalware/events/events/summary_part"
       end
-
-      # def cache_key
-      #   Events::Event.for_patient(patient).maximum(:updated_at)
-      # end
     end
   end
 end

data/app/presenters/renalware/hd/mdm_presenter.rb

@@ -14,7 +14,7 @@ module Renalware
         @sessions ||= begin
           sessions = Sessions::LatestPatientSessionsQuery
                        .new(patient: patient)
-                       .call(max_sessions: 6)
+                       .call(max_sessions: 6).includes(:patient, :hospital_unit)
           CollectionPresenter.new(sessions, SessionPresenter, view_context)
         end
       end

data/app/presenters/renalware/letters/summary_part.rb

@@ -19,9 +19,9 @@ module Renalware
         "renalware/letters/summary_part"
       end
 
-      # def cache_key
-      #   letters_patient.letters.maximum(:updated_at)
-      # end
+      def cache_key
+        letters_patient.letters.cache_key
+      end
 
       private
 
@@ -41,7 +41,7 @@ module Renalware
       end
 
       def letters_patient
-        Renalware::Letters.cast_patient(patient)
+        @letters_patient ||= Renalware::Letters.cast_patient(patient)
       end
     end
   end

data/app/presenters/renalware/mdm_presenter.rb

@@ -1,3 +1,4 @@
+# rubocop:disable Metrics/ClassLength
 require_dependency "renalware/clinics"
 
 module Renalware
@@ -14,11 +15,12 @@ module Renalware
     end
 
     def pathology_for_codes(codes = nil)
-      presenter = Pathology::HistoricalObservationResults::Presenter.new
-      options = {}
-      options[:descriptions] = pathology_descriptions_for_codes(codes) if Array(codes).any?
-      Pathology::ViewObservationResults.new(pathology_patient.observations, presenter, options).call
-      OpenStruct.new(table: pathology_table_view, rows: presenter.view_model)
+      Pathology::CreateObservationsGroupedByDateTable.new(
+        patient: patient,
+        observation_descriptions: pathology_descriptions_for_codes(codes),
+        page: 1,
+        per_page: 10
+      ).call
     end
 
     def clinic_visits(limit: 6)
@@ -89,9 +91,11 @@ module Renalware
       @current_problems ||= patient.problems.current.limit(6).with_created_by.ordered
     end
 
+    # rubocop:disable Lint/UnusedMethodArgument
     def events_of_type(type: nil)
       Events::Event.for_patient(patient).includes([:created_by, :event_type]).limit(6).ordered
     end
+    # rubocop:enable Lint/UnusedMethodArgument
     alias_method :events, :events_of_type
 
     def letters
@@ -111,16 +115,20 @@ module Renalware
     private
 
     def pathology_descriptions_for_codes(codes)
-      Pathology::ObservationDescription.for(Array(codes))
+      if codes.nil?
+        Pathology::RelevantObservationDescription.all
+      else
+        Pathology::ObservationDescription.for(Array(codes))
+      end
     end
 
     def pathology_patient
       Renalware::Pathology.cast_patient(patient)
     end
 
-    def pathology_table_view
-      Pathology::HistoricalObservationResults::HTMLTableView.new(view_context)
-    end
+    # def pathology_table_view
+    #   Pathology::HistoricalObservationResults::HTMLTableView.new(view_context)
+    # end
 
     def execute_prescriptions_query(relation)
       query = Medications::PrescriptionsQuery.new(relation: relation)
@@ -128,6 +136,7 @@ module Renalware
            .with_created_by
            .with_medication_route
            .with_drugs
+           .with_classifications
            .with_termination
            .eager_load(drug: [:drug_types])
            .map { |prescrip| Medications::PrescriptionPresenter.new(prescrip) }

data/app/presenters/renalware/pathology/historical_observation_results/html_table_view.rb

@@ -43,7 +43,21 @@ module Renalware
       end
 
       def format_body_cell(cell)
-        content_tag(:td, cell, class: cell.html_class)
+        if cell.respond_to?(:cancelled?)
+          if cell.cancelled?
+            # content = cell.cancelled ? "CANCL" : cell.to_s
+            content_tag(:td, class: cell.html_class, style: "text-align: center") do
+              tooltip_with_block(label: cell.comment) do
+                content_tag(:i, "", class: "fa fa-warning centre")
+              end
+            end
+          else
+            content_tag(:td, cell, class: cell.html_class)
+          end
+        else
+          # A date?
+          content_tag(:td, cell, class: cell.html_class)
+        end
       end
     end
   end

data/app/presenters/renalware/problems/summary_part.rb

@@ -3,13 +3,11 @@ require_dependency "renalware/problems"
 module Renalware
   module Problems
     class SummaryPart < Renalware::SummaryPart
-      def current_problems
-        @current_problems ||= patient.problems.current.ordered
-      end
+      delegate :cache_key, to: :problems
 
-      # def cache_key
-      #   current_problems.maximum(:updated_at)
-      # end
+      def problems
+        @problems ||= patient.problems.ordered
+      end
 
       def to_partial_path
         "renalware/problems/problems/summary_part"

data/app/presenters/renalware/summary_part.rb

@@ -5,6 +5,7 @@ module Renalware
   # reporting dashboards or summary pages. The Clinical Summary for instance comprises an array
   # of various SummaryParts
   class SummaryPart
+    DATE_FORMAT = "%Y%m%d%H%M%S%L".freeze
     rattr_initialize :patient
     attr_implement :to_partial_path
 
@@ -13,16 +14,16 @@ module Renalware
       nil
     end
 
-    def cache?
-      cache_key.present?
-    end
-
     def render?
       true
     end
 
     protected
 
+    def date_formatted_for_cache(date)
+      date&.strftime(DATE_FORMAT)
+    end
+
     def title_friendly_collection_count(actual:, total:)
       if total > actual
         "#{actual} of #{total}"

data/app/views/renalware/admin/cache/show.html.slim

@@ -0,0 +1,20 @@
+= within_admin_layout(title: "Cache") do
+  .panel
+    p
+      | The cache (backed by Redis) stores some queries and html fragments in order to make
+      |  the rendering of pages faster and less resource intensive. Cached elements are invalidated
+      |  when the underlying database data changes (but it only examines the updated_at column and
+      |  count of records, in order to catch edits, inserts and deletions) or the html template
+      |  changes (changes are only reflected after am app restart in this latter case).
+    p
+      | There are certain cases where you might need to clear the cache:
+    ol
+      li
+        | You have changed the underlying database data directly in SQL without also updating the
+        |  updated_at column.
+
+  = link_to "Clear the Application Cache",
+            admin_cache_path,
+            method: :delete,
+            data: { confirm: "Are you sure you want to clear the application cache?\n" },
+            class: "button alert"

data/app/views/renalware/admin/feeds/files/index.html.slim

@@ -1,5 +1,4 @@
 = within_admin_layout(title: "File Imports") do
-
   .row
     .small-12.columns.panel
       .row

data/app/views/renalware/admin/users/_summary_part.html.slim

@@ -0,0 +1,3 @@
+section.admin--users
+  h2 Admin
+  = link_to summary_part.users_needing_approval_title, admin_users_path(q: { unapproved: true })

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

@@ -2,19 +2,25 @@
 
   = render "filters", user_search: user_search
 
-  table
+  table.admin-users
     thead
       th.col-width-tiny
       th.col-width-tiny ID
-      th.col-width-medium= sort_link(user_search,
+      th.col-width-large= sort_link(user_search,
                                      :family_name,
                                      [:family_name, :given_name],
                                      "User")
       th.col-width-small= sort_link(user_search, :username, "Login")
       th= sort_link(user_search, :email, "Email")
-      th Telephone #
-      th.col-width-date-time= sort_link(user_search, :created_at, "Added")
-      th.col-width-tiny Approved
+      th.col-width-medium Role
+      th.col-width-tiny= sort_link(user_search, :approved, "Approved")
+      th.col-width-date= sort_link(user_search, :expired_at, "Expired On")
+      th.col-width-date-time.show-for-large-up= sort_link(user_search, :current_sign_in_at, "Current sign in")
+      th.col-width-date-time.show-for-large-up= sort_link(user_search, :last_sign_in_at, "Last sign in")
+      th.col-width-date-time.show-for-large-up= sort_link(user_search, :last_activity_at, "Last activity")
+      th.col-width-medium.show-for-xlarge-up Telephone #
+      th.col-width-date-time.show-for-xlarge-up= sort_link(user_search, :created_at, "Added")
+
 
     tbody
       - users.each do |user|
@@ -24,8 +30,19 @@
           td= user.to_s
           td= user.username
           td= user.email
-          td= user.telephone
-          td= l user.created_at
-          td= yes_no(user.approved?)
+          td
+            - user.roles.each do |role|
+              span.tag(class=role.name)= role.name.humanize
+          td.approved
+            - if user.approved?
+              i.fa.fa-check-square-o
+            - else
+              i.unapproved.fa.fa-square-o
+          td.expired= l(user.expired_at&.to_date)
+          td.show-for-large-up= l(user.current_sign_in_at)
+          td.show-for-large-up= l(user.last_sign_in_at)
+          td.show-for-large-up= l(user.last_activity_at)
+          td.show-for-xlarge-up= user.telephone
+          td.show-for-xlarge-up= l(user.created_at)
 
   = paginate users

data/app/views/renalware/admissions/_summary_part.html.slim

@@ -1,14 +1,13 @@
-.columns.large-12.xlarge-6
-  #admissions
-    article
-      header
-        h2= "Admissions (#{summary_part.admissions_count})"
+#admissions.summary-part--admissions
+  article
+    header
+      h2= "Admissions (#{summary_part.admissions_count})"
 
-        ul
-          li= link_to admissions_admissions_path(query: { term: summary_part.patient_nhs_number }),
-                      class: "button" do
-            | View All
+      ul
+        li= link_to admissions_admissions_path(query: { term: summary_part.patient_nhs_number }),
+                    class: "button" do
+          | View All
 
-      = render "renalware/admissions/admissions/table",
-               admissions: summary_part.admissions,
-               compact: true
+    = render "renalware/admissions/admissions/table",
+             admissions: summary_part.admissions,
+             compact: true

data/app/views/renalware/api/v1/patients/patients/show.json.jbuilder

@@ -0,0 +1,17 @@
+json.nhs_number patient.nhs_number
+json.secure_id patient.secure_id
+json.legacy_patient_id patient.legacy_patient_id
+json.local_patient_id patient.local_patient_id
+json.local_patient_id_2 patient.local_patient_id_2
+json.local_patient_id_3 patient.local_patient_id_3
+json.local_patient_id_4 patient.local_patient_id_4
+json.local_patient_id_5 patient.local_patient_id_5
+json.title patient.title
+json.given_name patient.given_name
+json.family_name patient.family_name
+json.born_on patient.born_on&.to_s
+json.died_on patient.died_on&.to_s
+json.sex patient.sex&.code
+json.ethnicity patient.ethnicity&.code
+json.medications_url api_v1_patient_medications_prescriptions_url(patient_id: patient)
+json.hd_profile_url api_v1_patient_hd_current_profile_url(patient_id: patient)

data/app/views/renalware/dashboard/dashboards/_content.html.slim

@@ -32,3 +32,6 @@
                receipts: dashboard.unread_electronic_ccs
     - else
       p.empty-section= t(".electronic_ccs.none")
+
+  - if current_user_is_admin?
+    = render Renalware::Admin::Users::SummaryPart.new(nil)

data/app/views/renalware/devise/registrations/edit.html.slim

@@ -10,6 +10,8 @@
 
       = custom_devise_error_messages!
 
+      = f.hidden_field :with_extended_validation
+
       .field.large-8.small-6
         = f.label :email
         = f.email_field :email, autofocus: true

data/app/views/renalware/events/events/_summary_part.html.slim

@@ -1,9 +1,8 @@
-.columns.large-12.xlarge-6
-  span
-  #events
+- cache(summary_part) do
+  #events.summary-part--events
     article
       header
-        h2= link_to "Events (#{summary_part.current_events_count})",
+        h2= link_to "Events (#{summary_part.recent_events_count})",
                     patient_events_path(summary_part.patient)
 
         ul
@@ -12,4 +11,4 @@
           li= link_to patient_events_path(summary_part.patient), class: "button" do
             | View All
 
-      = render "renalware/events/events/table", events: summary_part.current_events
+      = render "renalware/events/events/table", events: summary_part.recent_events