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

checksums.yaml

@@ -1,7 +1,7 @@
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data/app/assets/stylesheets/renalware/modules/_dashboard.scss

@@ -1,10 +1,19 @@
 .dashboard-content {
   margin-top: 10px;
 
-  p.empty-section {
+  h3 {
+    font-size: 1.1rem;
+    font-weight: bold;
+  }
+
+  p {
     padding-left: 0;
-    color: $dashboard-muted-color;
-    clear: both;
+
+    &.empty-section {
+      padding-left: 0;
+      color: $dashboard-muted-color;
+      clear: both;
+    }
   }
 }
 

data/app/assets/stylesheets/renalware/modules/_letters.scss

@@ -1,9 +1,3 @@
-// When the letter summary part is included in the clinical summary, make it 12 cols wide.
-.page--clinical_summaries {
-  .summary-part--letters {
-    @include grid-column(12);
-  }
-}
 
 table.contacts tbody td{
   vertical-align: top;

data/app/assets/stylesheets/renalware/modules/_pathology.scss

@@ -23,6 +23,11 @@ table#observations {
     border: 1px solid #ddd;
     font-size: 0.8rem;
   }
+
+  &.transposed {
+    tr { display: block; float: left; }
+    th, td { display: block; }
+  }
 }
 
 .current-observations {

data/app/assets/stylesheets/renalware/modules/_patients.scss

@@ -377,3 +377,27 @@ form {
     }
   }
 }
+
+.page--clinical_summaries {
+  .summary-part--letters {
+    @include grid-column(12);
+  }
+
+  .summary-part--problems,
+  .summary-part--prescriptions {
+    @include grid-column(12);
+
+    @media #{$large-up} {
+      @include grid-column(6);
+    }
+  }
+
+  .summary-part--events,
+  .summary-part--admissions {
+    @include grid-column(12);
+
+    @media #{$xxlarge-up} {
+      @include grid-column(6);
+    }
+  }
+}

data/app/assets/stylesheets/renalware/modules/_users.scss

@@ -0,0 +1,36 @@
+.admin-users {
+  td.approved {
+    text-align: center;
+    color: $nhs-light-green;
+
+    .unapproved {
+      color: $nhs-red;
+      font-weight: bold;
+    }
+  }
+
+  .tag {
+    color: $white;
+    padding: .05rem .5rem .15rem .5rem;
+    border: none;
+    margin: .1rem .3rem .2rem 0;
+    border-radius: .3rem;
+    background-color: $mid-grey;
+
+    &.devops {
+
+    }
+
+    &.clinical {
+      background-color: $nhs-green;
+    }
+
+    &.admin {
+      background-color: $nhs-blue;
+    }
+
+    &.super_admin {
+      background-color: $nhs-red;
+    }
+  }
+}

data/app/controllers/renalware/admin/cache_controller.rb

@@ -0,0 +1,17 @@
+require_dependency "renalware/admin"
+
+module Renalware
+  module Admin
+    class CacheController < BaseController
+      def show
+        authorize [:renalware, :admin, :cache], :show?
+      end
+
+      def destroy
+        authorize [:renalware, :admin, :cache], :destroy?
+        Rails.cache.clear
+        redirect_to admin_cache_path, notice: "Cache successfully cleared"
+      end
+    end
+  end
+end

data/app/controllers/renalware/admin/users_controller.rb

@@ -6,6 +6,7 @@ module Renalware
       query = params.fetch(:q, {})
       query[:s] ||= "family_name"
       search = User
+        .includes(:roles)
         .where.not(username: :systemuser)
         .search(query)
       users = search.result(distinct: true).page(page).per(per_page)

data/app/controllers/renalware/api/token_authenticated_api_controller.rb

@@ -0,0 +1,25 @@
+#
+# From https://gist.github.com/josevalim/fb706b1e933ef01e4fb6
+#
+module Renalware
+  module API
+    class TokenAuthenticatedApiController < ApplicationController
+      before_action :authenticate_user_from_token!
+      before_action :authenticate_user! # fallback
+
+      private
+
+      def authenticate_user_from_token!
+        username = params[:username].presence
+        user = username && User.find_by(username: username)
+
+        # Notice how we use Devise.secure_compare to compare the token
+        # in the database with the token given in the params, mitigating
+        # timing attacks.
+        if user && Devise.secure_compare(user.authentication_token, params[:token])
+          sign_in user, store: false
+        end
+      end
+    end
+  end
+end

data/app/controllers/renalware/api/v1/patients/patients_controller.rb

@@ -0,0 +1,17 @@
+require_dependency "renalware/patients"
+require_dependency "renalware/api"
+
+module Renalware
+  module API
+    module V1
+      module Patients
+        class PatientsController < TokenAuthenticatedApiController
+          def show
+            patient = Patient.find_by!(local_patient_id: params[:id])
+            render locals: { patient: patient }
+          end
+        end
+      end
+    end
+  end
+end

data/app/controllers/renalware/concerns/devise_controller_methods.rb

@@ -37,6 +37,7 @@ module Renalware
         devise_parameter_sanitizer.permit(:sign_in, keys: [:username, :password, :remember_me])
       end
 
+      # rubocop:disable Metrics/MethodLength
       def configure_account_update_parameters
         devise_parameter_sanitizer.permit(
           :account_update,
@@ -49,10 +50,12 @@ module Renalware
             :password_confirmation,
             :current_password,
             :professional_position,
-            :signature
+            :signature,
+            :with_extended_validation
           ]
         )
       end
+      # rubocop:enable Metrics/MethodLength
     end
   end
 end

data/app/controllers/renalware/devise/sessions_controller.rb

@@ -17,35 +17,6 @@ module Renalware
       max_duration_has_passed ? dashboard_path : super
     end
 
-    # Important note: Since Devise 4.4.0 the gem's SessionsController#create will do an implicit
-    # check to see if the resource (User signing-in) is valid (or rather, I think it checks for the
-    # presence of anything in resource.errors). If the user is not valid it now
-    # skips the redirect to the path specified in .after_sign_in_path_for.
-    # The result for us was that the user _could_ log on, but they stayed on the login screen
-    # (the appearance of the menu indicated they were in fact logged in). The redirect was not
-    # happening because the user was invalid (ie there were validation errors and
-    # user.valid? == false).
-    # The reason for the validation errors is that we have some conditional validation in User;
-    # for instance only validate #signature during an update, not on
-    # a create - after all #signature is something they set up later in their 'profile'.
-    # So what we have to do here is stop Devise from thinking the user in invalid by skipping
-    # validations.
-    # See https://github.com/plataformatec/devise/issues/4742#issuecomment-355154023
-    # Note that ideally we should move signature, professional position etc to a Profile model
-    # and then we could remove the conditional validation.
-    def create
-      super do |resource|
-        # This first line clears any existing errors that prevent Devise redirecting on successful
-        # login. It does not negate any password validations however. Its just a workaround to get
-        # the redirect to work.
-        resource.errors.clear
-        # This second line means resource.valid? returns true ie conditional on: :update validations
-        # are skipped. This line is not necessary (clearing the error above actually solves the
-        # problem) but does no harm and is belt and braces.
-        resource.skip_validation = true
-      end
-    end
-
     private
 
     def last_sign_in_at

data/app/controllers/renalware/pathology/historical_observation_results_controller.rb

@@ -3,19 +3,17 @@ require_dependency "renalware/pathology"
 module Renalware
   module Pathology
     class HistoricalObservationResultsController < Pathology::BaseController
+      include Renalware::Concerns::Pageable
       before_action :load_patient
 
       def index
-        table_view = HistoricalObservationResults::HTMLTableView.new(view_context)
-        presenter = HistoricalObservationResults::Presenter.new
-        service = ViewObservationResults.new(@patient.observations, presenter)
-        service.call(params)
-
-        render :index, locals: {
-          rows: presenter.view_model,
-          paginator: presenter.paginator,
-          table: table_view
-        }
+        observations_table = CreateObservationsGroupedByDateTable.new(
+          patient: patient,
+          observation_descriptions: RelevantObservationDescription.all,
+          page: page || 1,
+          per_page: 25
+        ).call
+        render :index, locals: { table: observations_table }
       end
     end
   end

data/app/controllers/renalware/pathology/recent_observation_results_controller.rb

@@ -3,19 +3,17 @@ require_dependency "renalware/pathology"
 module Renalware
   module Pathology
     class RecentObservationResultsController < Pathology::BaseController
+      include Renalware::Concerns::Pageable
       before_action :load_patient
 
       def index
-        table_view = RecentObservationResults::HTMLTableView.new(view_context)
-        presenter = RecentObservationResults::Presenter.new
-        service = ViewObservationResults.new(@patient.observations, presenter)
-        service.call(params)
-
-        render :index, locals: {
-          rows: presenter.view_model,
-          paginator: presenter.paginator,
-          table: table_view
-        }
+        observations_table = CreateObservationsGroupedByDateTable.new(
+          patient: patient,
+          observation_descriptions: RelevantObservationDescription.all,
+          page: page || 1,
+          per_page: per_page || 100
+        ).call
+        render :index, locals: { table: observations_table }
       end
     end
   end

data/app/controllers/renalware/renal/aki_alerts_controller.rb

@@ -37,7 +37,12 @@ module Renalware
       end
 
       def aki_alert_params
-        params.require(:renal_aki_alert).permit(:notes, :action_id, :hotlist, :hospital_ward_id)
+        params
+          .require(:renal_aki_alert)
+          .permit(
+            :notes, :action_id, :hotlist, :hospital_ward_id,
+            :max_cre, :cre_date, :max_aki, :aki_date
+          )
       end
     end
   end

data/app/controllers/renalware/reporting/audits_controller.rb

@@ -7,7 +7,7 @@ module Renalware
 
       def index
         authorize Audit, :index?
-        render locals: { audits: present(Audit.all, AuditPresenter) }
+        render locals: { audits: present(Audit.enabled, AuditPresenter) }
       end
 
       def show

data/app/controllers/renalware/system/errors_controller.rb

@@ -13,7 +13,9 @@ module Renalware
 
       def generate_test_internal_server_error
         raise "This is an intentionally raised error - please ignore it. " \
-              "It is used only to test system integration"
+              "It is used only to test system integration. " \
+              "The rest of this messages is padding to test that the title is truncated to 256 " \
+              "characters#{'.' * 100}"
       end
     end
   end

data/app/controllers/renalware/transplants/wait_lists_controller.rb

@@ -6,19 +6,28 @@ module Renalware
       include Renalware::Concerns::Pageable
 
       def show
-        query = Registrations::WaitListQuery.new(quick_filter: params[:filter], q: params[:q])
         registrations = query.call.page(page).per(per_page || 50)
         authorize registrations
         render locals: {
           path_params: path_params,
           registrations: registrations,
-          q: query.search }
+          q: query.search
+        }
       end
 
       private
 
+      def query
+        @query ||= begin
+          Registrations::WaitListQuery.new(
+            named_filter: params[:named_filter],
+            q: params[:q]
+          )
+        end
+      end
+
       def path_params
-        params.permit([:controller, :action, :filter])
+        params.permit([:controller, :action, :named_filter])
       end
     end
   end

data/app/models/renalware/admin.rb

@@ -0,0 +1,4 @@
+module Renalware
+  module Admin
+  end
+end

data/app/models/renalware/api.rb

@@ -0,0 +1,6 @@
+module Renalware
+  module API
+    module V1
+    end
+  end
+end

data/app/models/renalware/clinics/current_observations.rb

@@ -3,6 +3,7 @@ require "attr_extras"
 
 module Renalware
   module Clinics
+    # TODO: Move this to a view?
     class CurrentObservations
       NULL_DATE = nil
       pattr_initialize :patient

data/app/models/renalware/events/event_query.rb

@@ -8,7 +8,7 @@ module Renalware
       def initialize(patient:, query: {})
         @query = query
         @patient = patient
-        @query[:s] = "created_at DESC" if @query[:s].blank?
+        @query[:s] = "datetime DESC" if @query[:s].blank?
       end
 
       def call

data/app/models/renalware/feeds/hl7_message.rb

@@ -51,6 +51,7 @@ module Renalware
       end
 
       class Observation < SimpleDelegator
+        attr_reader :cancelled
         alias_attribute :date_time, :observation_date
         alias_attribute :value, :observation_value
 
@@ -60,7 +61,21 @@ module Renalware
 
         # TODO: Implement comment extraction
         def comment
-          ""
+          @comment || ""
+        end
+
+        # Some messages may come through with result text like
+        #   ##TEST CANCELLED## Insufficient specimen received
+        # in which case replace with something more concise.
+        # We could save the actual message somewhere
+        def observation_value
+          if super.upcase.at("CANCELLED")
+            @comment = super
+            @cancelled = true
+            ""
+          else
+            super
+          end
         end
 
         # Because some units of measurement, such as 10^12/L for WBC, contain a caret, the caret

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

@@ -4,7 +4,7 @@ module Renalware
       include ModalityScopes
       include PatientPathologyScopes
       MODALITY_NAMES = "HD".freeze
-      DEFAULT_SEARCH_PREDICATE = "hgb_date".freeze
+      DEFAULT_SEARCH_PREDICATE = "hgb_date desc".freeze
       attr_reader :q, :relation
 
       def initialize(relation: HD::Patient.all, q:)

data/app/models/renalware/letters/pdf_letter_cache.rb

@@ -36,8 +36,12 @@ module Renalware
       end
 
       # Note the letter must be a LetterPresenter which has a #to_html method
+      # The to_html method should (and does on the LetterPrsenter class) render the complete
+      # html including surrounding layout with inline css and images. This way if the layout changes
+      # or the image is changed for example, the cache for the pdf is no longer valid and a new
+      # key and cache entry will be created.
       def self.cache_key_for(letter)
-        "#{letter.id}-#{Digest::MD5.hexdigest(letter.to_html)}"
+        "letter:pdf:#{letter.id}:#{Digest::MD5.hexdigest(letter.to_html)}"
       end
     end
   end

data/app/models/renalware/medications/prescription.rb

@@ -47,6 +47,7 @@ module Renalware
       scope :ordered, -> { includes(:drug).order("drugs.name") }
       scope :with_medication_route, -> { includes(:medication_route) }
       scope :with_drugs, -> { includes(drug: :drug_types) }
+      scope :with_classifications, -> { includes(drug: :classifications) }
       scope :with_termination, -> { includes(termination: [:created_by]) }
       scope :current, lambda { |date = Date.current|
         eager_load(:termination)

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

@@ -0,0 +1,39 @@
+require_dependency "renalware/pathology"
+
+module Renalware
+  module Pathology
+    class CreateObservationsGroupedByDateTable
+      attr_reader :patient, :observation_descriptions, :options
+
+      def initialize(patient:, observation_descriptions:, **options)
+        @patient = patient
+        @observation_descriptions = observation_descriptions
+        @options = options
+      end
+
+      def call
+        if observation_descriptions.blank?
+          raise(ArgumentError, "No observation_descriptions supplied")
+        end
+        create_observations_table
+      end
+
+      private
+
+      def fetch_grouped_observations
+        ObservationsGroupedByDateQuery.new(
+          patient: patient,
+          observation_descriptions: observation_descriptions,
+          **options
+        )
+      end
+
+      def create_observations_table
+        ObservationsGroupedByDateTable.new(
+          relation: fetch_grouped_observations,
+          observation_descriptions: observation_descriptions
+        )
+      end
+    end
+  end
+end

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

@@ -7,7 +7,7 @@ module Renalware
       belongs_to :description, class_name: "ObservationDescription"
 
       validates :description, presence: true
-      validates :result, presence: true
+      validates :result, presence: true, unless: ->(obs) { obs.cancelled? }
       validates :observed_at, presence: true
 
       scope :ordered, -> { order(observed_at: :desc) }

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

@@ -0,0 +1,12 @@
+require_dependency "renalware/pathology"
+
+module Renalware
+  module Pathology
+    # Backed by a view, returns pathology results grouped by the day the observation
+    # was made. Please check if this is used in code - it may not be,
+    # However the underlying view is a useful way of investigating a patient's results
+    # so please do not remove the view.
+    class ObservationDigest < ApplicationRecord
+    end
+  end
+end

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

@@ -76,7 +76,8 @@ module Renalware
             description_id: observation_description.id,
             observed_at: parse_time(observation.date_time),
             result: observation.value,
-            comment: observation.comment
+            comment: observation.comment,
+            cancelled: observation.cancelled
           }
         end.compact
       end

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

@@ -0,0 +1,91 @@
+require_dependency "renalware/pathology"
+require "attr_extras"
+
+module Renalware
+  module Pathology
+    # A custom relation-like object, implementing a kaminiari-like pagination interface.
+    # Its a query object but means to be used like a relation. If passed into a view you can
+    # do = paginate(relation).
+    # See ObservationsGroupedByDateTable for intended usage.
+    #
+    # .all() returns a jsonb hash of OBX results for each day a patient had an observation.
+    # Only returns observations whose code matches observation_descriptions
+    #
+    # Example usage:
+    #   observation_descriptions = ..
+    #   rows = ObservationsGroupedByDateQuery.new(
+    #     patient: patient,
+    #     observation_descriptions: observation_descriptions,
+    #     per_page: 50,
+    #     page: 1
+    #   )
+    #
+    # Example output:
+    #   patient_id  observation_date  observations
+    #   ------------------------------------------
+    #   1           2018-02-02        {"CYA": "14"}
+    #   1           2016-06-15        {"CMVDNA": "0.10"}
+    #   1           2016-03-15        {"NA": "137", "TP": "74", "ALB": "48", "ALP": "71", ...
+    #   1           2016-02-29        {"NA": "136", "TP": "78", "ALB": "47", "ALP": "71", ...
+    #
+    #
+    class ObservationsGroupedByDateQuery
+      attr_reader :patient, :observation_descriptions, :page, :limit
+      alias :current_page :page
+      alias :limit_value :limit
+
+      def initialize(patient:, observation_descriptions:, page: 1, per_page: 50)
+        @patient = patient
+        @observation_descriptions = observation_descriptions
+        @page = Integer(page)
+        @limit = Integer(per_page)
+      end
+
+      def total_pages
+        result = conn.execute(to_count_sql)
+        total = result.getvalue(0, 0)
+        (total.to_f / limit).ceil
+      end
+
+      def offset
+        (page - 1) * limit
+      end
+
+      def all
+        conn.execute(to_paginated_sql)
+      end
+
+      private
+
+      def to_sql
+        <<-SQL.squish
+          select obs_req.patient_id, cast(observed_at as date) as observed_on,
+          jsonb_object_agg(obs_desc.code, obs.result) results
+          from pathology_observations obs
+          inner join pathology_observation_requests obs_req on obs.request_id = obs_req.id
+          inner join pathology_observation_descriptions obs_desc on obs.description_id = obs_desc.id
+          where patient_id = #{conn.quote(patient.id)}
+          and obs.description_id in (#{observation_description_ids})
+          group by patient_id, observed_on
+          order by patient_id asc, observed_on desc
+        SQL
+      end
+
+      def to_count_sql
+        "select count(*) from (#{to_sql}) as query"
+      end
+
+      def to_paginated_sql
+        to_sql + " limit #{limit} offset #{offset}"
+      end
+
+      def conn
+        ActiveRecord::Base.connection
+      end
+
+      def observation_description_ids
+        observation_descriptions.map(&:id).join(",")
+      end
+    end
+  end
+end