renalware-core 2.0.0.pre.beta12 → 2.0.0.pre.rc1

data/app/models/renalware/drugs/classification.rb

@@ -0,0 +1,11 @@
+require_dependency "renalware/drugs"
+
+module Renalware
+  module Drugs
+    class Classification < ApplicationRecord
+      self.table_name = "drug_types_drugs" # a relic from migrating from habtm
+      belongs_to :drug
+      belongs_to :drug_type, class_name: "Type"
+    end
+  end
+end

data/app/models/renalware/drugs/drug.rb

@@ -5,9 +5,9 @@ module Renalware
     class Drug < ApplicationRecord
       acts_as_paranoid
 
-      has_and_belongs_to_many :drug_types,
-                              class_name: "Type",
-                              association_foreign_key: :drug_type_id
+      has_many :classifications, dependent: :destroy
+      has_many :drug_types, through: :classifications
+
       scope :ordered, -> { order(:name) }
 
       validates :name, presence: true

data/app/models/renalware/drugs/type.rb

@@ -5,7 +5,8 @@ module Renalware
     class Type < ApplicationRecord
       self.table_name = "drug_types"
 
-      has_and_belongs_to_many :drugs, foreign_key: :drug_type_id
+      has_many :classifications, foreign_key: :drug_type_id, dependent: :destroy
+      has_many :drugs, through: :classifications
 
       include OrderedSetScope
 

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

@@ -3,10 +3,12 @@ module Renalware
     class MDMPatientsQuery
       include ModalityScopes
       MODALITY_NAMES = "HD".freeze
+      DEFAULT_SEARCH_PREDICATE = "hgb_date".freeze
       attr_reader :q, :relation
 
       def initialize(relation: HD::Patient.all, q:)
-        @q = q
+        @q = q || {}
+        @q[:s] = DEFAULT_SEARCH_PREDICATE if @q[:s].blank?
         @relation = relation
       end
 
@@ -19,17 +21,10 @@ module Renalware
           relation
             .includes(:hd_profile)
             .extending(ModalityScopes)
-            .extending(Scopes)
+            .extending(PatientPathologyScopes)
             .with_current_key_pathology
             .with_current_modality_matching(MODALITY_NAMES)
             .search(q)
-          # .order("pathology_current_key_observations.hgb_result asc")
-        end
-      end
-
-      module Scopes
-        def with_current_key_pathology
-          eager_load(:current_key_observation_set) # .joins(:current_key_observation)
         end
       end
     end

data/app/models/renalware/hd/session/closed.rb

@@ -26,21 +26,28 @@ module Renalware
 
       class SessionDocument < ::Renalware::HD::SessionDocument
         class Info < Renalware::HD::SessionDocument::Info
+          # rubocop:disable Rails/Validation
           validates_presence_of attribute_set.map(&:name)
+          # rubocop:enable Rails/Validation
         end
         attribute :info, Info
 
         class Observations < Renalware::HD::SessionDocument::Observations
-          validates_presence_of :pulse, :blood_pressure, :weight_measured, :temperature_measured
-          validates_presence_of :weight, if: ->{ weight_measured&.yes? }
-          validates_presence_of :temperature, if: ->{ temperature_measured&.yes? }
+          validates :pulse, presence: true
+          validates :blood_pressure, presence: true
+          validates :weight_measured, presence: true
+          validates :temperature_measured, presence: true
+          validates :weight, presence: { if: ->{ weight_measured&.yes? } }
+          validates :temperature, presence: { if: ->{ temperature_measured&.yes? } }
           validates :blood_pressure, "renalware/patients/blood_pressure_presence" => true
         end
         attribute :observations_before, Observations
         attribute :observations_after, Observations
 
         class Dialysis < Renalware::HD::SessionDocument::Dialysis
+          # rubocop:disable Rails/Validation
           validates_presence_of attribute_set.map(&:name)
+          # rubocop:enable Rails/Validation
         end
         attribute :dialysis, Dialysis
 

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

@@ -8,7 +8,8 @@ module Renalware
       include Accountable
       include ExplicitStateModel
 
-      validates_presence_of :type # Prevent instances of this of this base from being saved
+      # Prevent instances of this of this base class from being saved
+      validates :type, presence: true
 
       has_states :open, :closed, :dna
 

data/app/models/renalware/hd/sessions/auditable_session_collection.rb

@@ -35,13 +35,6 @@ module Renalware
           number_of_sessions_with_dialysis_minutes_shortfall_gt_5_pct
         ).freeze
 
-        def to_h
-          AUDITABLE_ATTRIBUTES.each_with_object({}) do |sym, hash|
-            hash[sym] = public_send(sym)
-            hash
-          end
-        end
-
         def initialize(sessions)
           @sessions = Array(sessions).map do |session|
             Renalware::HD::Sessions::AuditableSession.new(session)
@@ -49,6 +42,13 @@ module Renalware
           super(@sessions)
         end
 
+        def to_h
+          AUDITABLE_ATTRIBUTES.each_with_object({}) do |sym, hash|
+            hash[sym] = public_send(sym)
+            hash
+          end
+        end
+
         def number_of_missed_sessions
           sessions.count(&:dna?)
         end

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

@@ -7,7 +7,7 @@ module Renalware
 
       belongs_to :letter
 
-      validates_presence_of :content
+      validates :content, presence: true
     end
   end
 end

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

@@ -3,7 +3,7 @@ require_dependency "renalware/letters"
 module Renalware
   module Letters
     class Description < ApplicationRecord
-      validates_presence_of :text
+      validates :text, presence: true
 
       has_many :letters
     end

data/app/models/renalware/letters/event/clinic_visit.rb

@@ -21,6 +21,10 @@ module Renalware
         "Clinic Visit"
       end
 
+      def clinical?
+        true
+      end
+
       def to_link
         lambda { |patient, event = self|
           link_to(

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

@@ -16,6 +16,7 @@ module Renalware
         include_primary_care_physician_as_default_main_recipient
         assign_default_ccs
         build_salutation
+        letter.pathology_timestamp = Time.zone.now
         letter
       end
 

data/app/models/renalware/letters/part/allergies.rb

@@ -6,7 +6,7 @@ module Renalware
     class Part::Allergies < SimpleDelegator
       attr_reader :allergy_status
 
-      def initialize(patient, _event = Event::Unknown.new)
+      def initialize(patient, _letter, _event = Event::Unknown.new)
         patient = ::Renalware::Clinical.cast_patient(patient.__getobj__)
         @allergy_status = patient.allergy_status
         super(patient.allergies)

data/app/models/renalware/letters/part/prescriptions.rb

@@ -6,7 +6,7 @@ module Renalware
     class Part::Prescriptions < DumbDelegator
       include ::PresenterHelper
 
-      def initialize(patient, _event = Event::Unknown.new)
+      def initialize(patient, _letter, _event = Event::Unknown.new)
         @patient = patient
         super(prescriptions)
       end

data/app/models/renalware/letters/part/problems.rb

@@ -3,7 +3,7 @@ require "renalware/letters/part"
 module Renalware
   module Letters
     class Part::Problems < DumbDelegator
-      def initialize(patient, _event = Event::Unknown.new)
+      def initialize(patient, _letter, _event = Event::Unknown.new)
         @patient = patient
         super(patient.problems.includes(:notes))
       end

data/app/models/renalware/letters/part/recent_pathology_results.rb

@@ -1,5 +1,7 @@
 require "renalware/letters/part"
 
+# When rendered, the template in `to_partial_path` will be used, and our Part object here will be
+# available in the partial as `recent_pathology_results`.
 module Renalware
   module Letters
     class Part::RecentPathologyResults < Part
@@ -16,19 +18,19 @@ module Renalware
       end
 
       def find_recent_pathology_results
-        presenter = Pathology::CurrentObservationResults::Presenter.new
-        descriptions = Letters::RelevantObservationDescription.all
-        query = Pathology::CurrentObservationsForDescriptionsQuery.new(
-          patient: @patient,
-          descriptions: descriptions
-        )
-
-        # Only select display result with a value
-        results = query.call.reject{ |result| result.result.blank? }
+        check_letter
+        range = Time.zone.at(1)..letter.pathology_timestamp
+        Renalware::Pathology::CurrentObservationsForDescriptionsQuery.new(
+          patient: patient,
+          descriptions: Renalware::Letters::RelevantObservationDescription.all
+        ).call.where(observed_at: range).reject{ |obs| obs.id.nil? }
+      end
 
-        # Removes the header from the results, this will be unnecessary when
-        # a custom Presenter is implemented
-        presenter.present(results)[1..-1]
+      def check_letter
+        if letter.pathology_timestamp.blank?
+          raise ArgumentError,
+                "letter.pathology_timestamp cannot be nil when rendering letter pathology!"
+        end
       end
     end
   end

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

@@ -3,10 +3,11 @@ require "renalware/letters/part"
 module Renalware
   module Letters
     class Part
-      attr_reader :patient, :event
+      attr_reader :patient, :letter, :event
 
-      def initialize(patient, event)
+      def initialize(patient, letter, event)
         @patient = patient
+        @letter = letter
         @event = event
       end
     end

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

@@ -16,7 +16,7 @@ module Renalware
                                     allow_destroy: true,
                                     reject_if: :patient_or_primary_care_physician?
 
-      validates_presence_of :addressee_id, if: :contact?
+      validates :addressee_id, presence: { if: :contact? }
 
       delegate :primary_care_physician?, :patient?, :contact?, to: :person_role
 

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

@@ -6,7 +6,9 @@ module Renalware
       belongs_to :user
       belongs_to :letter
 
-      validates_presence_of :user, :letter, :signed_at
+      validates :user, presence: true
+      validates :letter, presence: true
+      validates :signed_at, presence: true
 
       def to_s
         name = user.full_name

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

@@ -32,13 +32,12 @@ module Renalware
       def call
         # Note:
         #
-        #   CurrentObservation.where(patient: @patient, description_name: @descriptions.map(&:name))
+        #   CurrentObservation.where(patient: patient, description_name: descriptions.map(&:name))
         #
         # is potentially a replacement for the SQL below, but it does not return
         # null values. We'd need a bit of SQL to join again onto pathology_observation_descriptions
         # and fill the missing observations with NULLs in order to keep the output of this query
         # the same.
-
         Observation
           .includes(:description)
           .select(<<-SQL)
@@ -58,10 +57,14 @@ module Renalware
           .order("pathology_observation_descriptions.id")
           .ordered
           .where(["pathology_observation_requests.patient_id = ? OR " \
-                  "pathology_observation_requests.patient_id IS NULL", @patient.id])
-          .where(pathology_observation_descriptions: { id: @descriptions })
+                  "pathology_observation_requests.patient_id IS NULL", patient.id])
+          .where(pathology_observation_descriptions: { id: descriptions })
       end
       # rubocop:enable Metrics/MethodLength
+
+      private
+
+      attr_reader :patient, :descriptions
     end
   end
 end

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

@@ -1,9 +1,8 @@
 require_dependency "renalware/pathology"
 
+# Responsible for finding Observations for the specified descriptions.
 module Renalware
   module Pathology
-    # Responsible for finding Observations for the specified descriptions.
-    #
     class ObservationsForDescriptionsQuery
       def initialize(relation: Observation.all, descriptions: ObservationDescription.all)
         @relation = relation

data/app/models/renalware/patients/bookmark.rb

@@ -10,7 +10,7 @@ module Renalware
 
       validates :patient, presence: true
       validates :user, presence: true
-      validates_uniqueness_of :user_id, scope: [:patient_id, :deleted_at]
+      validates :user_id, uniqueness: { scope: [:patient_id, :deleted_at] }
 
       scope :ordered, -> { order(urgent: :desc, updated_at: :asc) }
     end

data/app/models/renalware/patients/patient_hospital_identifiers.rb

@@ -18,10 +18,6 @@ module Renalware
       delegate :to_s, to: :first
       alias_method :to_sym, :name
 
-      def initialize(patient)
-        @patient = patient
-      end
-
       Identifier = Struct.new(:name, :id) do
         def to_s
           return "" unless id
@@ -29,6 +25,10 @@ module Renalware
         end
       end
 
+      def initialize(patient)
+        @patient = patient
+      end
+
       def first
         @first ||= Identifier.new(*all.first)
       end

data/app/models/renalware/patients/practice.rb

@@ -8,9 +8,9 @@ module Renalware
 
       accepts_nested_attributes_for :address, allow_destroy: true
 
-      validates_presence_of :name
-      validates_presence_of :address
-      validates_presence_of :code
+      validates :name, presence: true
+      validates :address, presence: true
+      validates :code, presence: true
     end
   end
 end

data/app/models/renalware/patients/primary_care_physician.rb

@@ -18,8 +18,8 @@ module Renalware
 
       validates_with PrimaryCarePhysicians::AddressValidator
       validates :email, email: true, allow_blank: true
-      validates_uniqueness_of :code
-      validates_presence_of :practitioner_type
+      validates :code, uniqueness: true
+      validates :practitioner_type, presence: true
 
       scope :ordered, -> { order(family_name: :asc) }
 

data/app/models/renalware/renal/low_clearance/mdm_patients_query.rb

@@ -0,0 +1,63 @@
+require_dependency "renalware/renal"
+
+module Renalware
+  module Renal
+    module LowClearance
+      class MDMPatientsQuery
+        include ModalityScopes
+        DEFAULT_SEARCH_PREDICATE = "ure_date ASC".freeze
+        attr_reader :query, :relation, :named_filter
+
+        def initialize(relation: Patient.all, query: nil, named_filter: nil)
+          @query = query || {}
+          @named_filter = named_filter || :none
+          @query[:s] = DEFAULT_SEARCH_PREDICATE if @query[:s].blank?
+          @relation = relation
+        end
+
+        def call
+          search.result
+        end
+
+        def search
+          @search ||= begin
+            relation
+              .extending(PatientPathologyScopes)
+              .extending(ModalityScopes)
+              .extending(NamedFilterScopes)
+              .with_current_key_pathology
+              .with_current_modality_of_class(LowClearance::ModalityDescription)
+              .public_send(named_filter.to_s)
+              .search(query)
+          end
+        end
+
+        module NamedFilterScopes
+          def none
+            self # NOOP
+          end
+
+          def on_worryboard
+            joins("RIGHT OUTER JOIN patient_worries ON patient_worries.patient_id = patients.id")
+          end
+
+          def tx_candidates
+            self
+          end
+
+          def urea
+            where("pathology_current_key_observation_sets.ure_result::float >= 30")
+          end
+
+          def hgb_low
+            where("pathology_current_key_observation_sets.hgb_result::float < 100")
+          end
+
+          def hgb_high
+            where("pathology_current_key_observation_sets.hgb_result::float > 130")
+          end
+        end
+      end
+    end
+  end
+end

data/app/models/renalware/renal/low_clearance/modality_description.rb

@@ -0,0 +1,13 @@
+require_dependency "renalware/renal"
+
+module Renalware
+  module Renal
+    module LowClearance
+      class ModalityDescription < Modalities::Description
+        def to_sym
+          :low_clearance
+        end
+      end
+    end
+  end
+end

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

@@ -7,6 +7,8 @@ module Renalware
       include Document::Base
       extend Enumerize
 
+      has_paper_trail class_name: "Renalware::Renal::Version"
+
       belongs_to :patient, touch: true
       belongs_to :prd_description
       has_one :address_at_diagnosis, as: :addressable, class_name: "Address"

data/app/models/renalware/renal/registry/preflight_checks/deaths_query.rb

@@ -36,7 +36,7 @@ module Renalware
             @search ||= relation.ransack(query_params)
           end
 
-          def self.missing_data_for(patient)
+          def self.missing_data_for(_patient)
             [
               :cause_of_death
             ]

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

@@ -0,0 +1,9 @@
+require_dependency "renalware/accesses"
+
+module Renalware
+  module Renal
+    class Version < PaperTrail::Version
+      self.table_name = :renal_versions
+    end
+  end
+end

data/app/models/renalware/renal.rb

@@ -9,5 +9,9 @@ module Renalware
     def self.cast_patient(patient)
       ActiveType.cast(patient, ::Renalware::Renal::Patient)
     end
+
+    module LowClearance
+      MDM_FILTERS = %w(urea hgb_low hgb_high on_worryboard).freeze # tx_candidates
+    end
   end
 end

data/app/models/renalware/role.rb

@@ -1,10 +1,11 @@
 module Renalware
   class Role < ApplicationRecord
-    ROLES = %i(devops super_admin admin clinician read_only).freeze
+    ROLES = %i(devops super_admin admin clinical read_only).freeze
 
-    has_and_belongs_to_many :users, join_table: :roles_users
+    has_many :roles_users, dependent: :destroy
+    has_many :users, through: :roles_users
 
-    validates_uniqueness_of :name
+    validates :name, uniqueness: true
 
     def self.fetch(ids)
       return none if Array.wrap(ids).empty?

data/app/models/renalware/roles_user.rb

@@ -0,0 +1,6 @@
+module Renalware
+  class RolesUser < ApplicationRecord
+    belongs_to :role
+    belongs_to :user
+  end
+end

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

@@ -0,0 +1,16 @@
+require_dependency "renalware/system"
+
+module Renalware
+  module System
+    class UserFeedback < ApplicationRecord
+      extend Enumerize
+      validates :author, presence: true
+      validates :category, presence: true
+      validates :comment, presence: true
+
+      belongs_to :author, class_name: "User"
+
+      enumerize :category, in: %i(general bug missing_feature), default: :general
+    end
+  end
+end

data/app/models/renalware/transplants/donor_modality_description.rb

@@ -3,6 +3,9 @@ require_dependency "renalware/transplants"
 module Renalware
   module Transplants
     class DonorModalityDescription < Modalities::Description
+      def to_sym
+        :transplant
+      end
     end
   end
 end

data/app/models/renalware/transplants/recipient_modality_description.rb

@@ -3,6 +3,9 @@ require_dependency "renalware/transplants"
 module Renalware
   module Transplants
     class RecipientModalityDescription < Modalities::Description
+      def to_sym
+        :transplant
+      end
     end
   end
 end

data/app/models/renalware/user.rb

@@ -3,18 +3,21 @@ module Renalware
     include Deviseable
     include Personable
 
-    has_and_belongs_to_many :roles, join_table: :roles_users
+    has_many :roles_users, dependent: :destroy
+    has_many :roles, through: :roles_users
 
     validates :username, presence: true, uniqueness: true
-    validates_presence_of :given_name
-    validates_presence_of :family_name
+    validates :given_name, presence: true
+    validates :family_name, presence: true
     validate :approval_with_roles, on: :update
-    validates_presence_of :professional_position,
-                          on: :update,
-                          unless: :skip_validation
-    validates_presence_of :signature,
-                          on: :update,
-                          unless: :skip_validation
+    validates :professional_position, presence: {
+      on: :update,
+      unless: :skip_validation
+    }
+    validates :signature, presence: {
+      on: :update,
+      unless: :skip_validation
+    }
 
     scope :unapproved, -> { where(approved: [nil, false]) }
     scope :inactive, lambda {
@@ -38,9 +41,11 @@ module Renalware
       %i(unapproved inactive)
     end
 
+    # rubocop:disable Naming/PredicateName
     def has_role?(name)
       role_names.include?(name.to_s)
     end
+    # rubocop:enable Naming/PredicateName
 
     def role_names
       @role_names ||= roles.pluck(:name)

data/app/models/renalware.rb

@@ -1,10 +1,7 @@
 module Renalware
-  def self.table_name_prefix
-    # 'renalware_' # TODO: eventually, prefix the tables
-    ""
-  end
-
+  # :nocov
   def self.use_relative_model_naming?
     true
   end
+  # :nocov
 end

data/app/policies/renalware/base_policy.rb

@@ -70,7 +70,7 @@ module Renalware
     end
 
     def has_write_privileges?
-      user_is_super_admin? || user_is_admin? || user_is_clinician?
+      user_is_super_admin? || user_is_admin? || user_is_clinical?
     end
 
     def has_any_role?

data/app/policies/renalware/system/user_feedback_policy.rb

@@ -0,0 +1,8 @@
+require_dependency "renalware/snippets"
+
+module Renalware
+  module System
+    class UserFeedbackPolicy < BasePolicy
+    end
+  end
+end