renalware-core 2.0.0.pre.rc1 → 2.0.0.pre.rc3

data/app/presenters/renalware/pathology/patient_presenter.rb

@@ -3,10 +3,6 @@ require "renalware/hd"
 module Renalware
   module Pathology
     class PatientPresenter < SimpleDelegator
-      delegate :hgb_result,
-               :hgb_observed_at,
-               to: :current_key_observation_set
-
       def initialize(patient)
         super(Pathology.cast_patient(patient.__getobj__))
       end

data/app/presenters/renalware/renal/clinical_summary_presenter.rb

@@ -11,7 +11,7 @@ module Renalware
       def current_prescriptions
         @current_prescriptions ||= begin
           prescriptions = @patient.prescriptions
-                                  .includes(drug: [:drug_types])
+                                  .includes(drug: [:drug_types, :classifications])
                                   .includes(:medication_route)
                                   .current
                                   .ordered

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

@@ -0,0 +1,19 @@
+.filters
+  .filters__form
+    = search_form_for user_search, url: admin_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_cont
+        .small-3.large-4.columns.actions.end
+          = f.submit t("helpers.submit.filter"), class: "button"
+          span= " or "
+          = link_to t("helpers.reset"), admin_users_path
+
+dl.sub-nav
+  dd(class=("active" if params[:q].nil?))
+    = link_to "All", admin_users_path(q: nil)
+  dd(class=("active" if params.fetch(:q, {})[:unapproved]))
+    = link_to "Unapproved", admin_unapproved_users_path
+  dd(class=("active" if params.fetch(:q, {})[:inactive]))
+    = link_to "Inactive", admin_inactive_users_path

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

@@ -1,22 +1,19 @@
 = within_admin_layout(title: "Users") do
 
-  dl.sub-nav
-    dd(class=("active" if params[:q].nil?))
-      = link_to "All", admin_users_path(q: nil)
-    dd(class=("active" if params.fetch(:q, {})[:unapproved]))
-      = link_to "Unapproved", admin_unapproved_users_path
-    dd(class=("active" if params.fetch(:q, {})[:inactive]))
-      = link_to "Inactive", admin_inactive_users_path
+  = render "filters", user_search: user_search
 
   table
     thead
       th.col-width-tiny
       th.col-width-tiny ID
-      th.col-width-medium User
-      th.col-width-small Login
-      th Email
+      th.col-width-medium= 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 Added
+      th.col-width-date-time= sort_link(user_search, :created_at, "Added")
       th.col-width-tiny Approved
 
     tbody
@@ -29,6 +26,6 @@
           td= user.email
           td= user.telephone
           td= l user.created_at
-          td= user.approved?
+          td= yes_no(user.approved?)
 
   = paginate users

data/app/views/renalware/admissions/consults/_filters.html.slim

@@ -5,8 +5,8 @@
       method: :get do |f|
     .row
       .columns.medium-4.large-3
-        = f.input :hospital_unit_id_eq,
-                  collection: Renalware::Hospitals::Unit.pluck(:name, :id),
+        = f.input :consult_site_id_eq,
+                  collection: Renalware::Admissions::ConsultSite.pluck(:name, :id),
                   label: "Site"
       .columns.medium-3.large-2
         = f.input :requires_aki_nurse_eq,

data/app/views/renalware/admissions/consults/_form.html.slim

@@ -1,34 +1,3 @@
-= content_for(:javascript)
-  javascript:
-    $(document).ready(function() {
-      function replaceOptionsInWardDropdown(data) {
-        var $select = $('#admissions_consult_hospital_ward_id');
-        $select.html("<option />");
-        if (data != undefined) {
-          $.each(data, function(index, hash) {
-            $select.append($('<option />', { value: hash["id"], text: hash["name"] }));
-          });
-        }
-      };
-
-      $(document).on('change', '#admissions_consult_hospital_unit_id', function(evt) {
-        var wardsUrl = $("option:selected", this).data("wards-url");
-        if (wardsUrl == undefined) {
-          replaceOptionsInWardDropdown(undefined);
-        } else {
-          var jqxhr = $.getJSON(wardsUrl)
-            .done(function(data) {
-              replaceOptionsInWardDropdown(data);
-            })
-            .fail(function(error, a, b) {
-              console.log( "error", a, b);
-            })
-        }
-        return true;
-      })
-    });
-
-= render "renalware/shared/errors", model: consult
 = simple_form_for(consult,
                   html: { autocomplete: "off" },
                   wrapper: :horizontal_form) do |f|
@@ -48,31 +17,22 @@
                       placeholder: "Search by patient name or hospital/NHS no." }\
             }
 
-  / Because simple form doesn't easily allow to add data attributes to select options
-  / (without us wrapping a rails f.select and thus loosing a bunch of formatting and support for
-  / .error classes etc.), we use a custom select_container input which allows us to build a custom
-  / options collection and pass it in.
-  / Credit to https://stackoverflow.com/questions/17554748/how-do-i-add-html-attributes-to-select-
-  / options-with-simple-form-rails#answer-34827962
-  ruby:
-    options_html = capture do
-      Renalware::Hospitals::Unit.select(:id, :unit_code).all.map do |unit|
-        concat(content_tag(:option,
-                           value: unit.id,
-                           selected: unit.id == consult.hospital_unit_id,
-                           "data-wards-url" => hospitals_unit_wards_url(unit, format: :json)) { unit.unit_code })
-      end
-    end
-
-  = f.input :hospital_unit_id,
-            as: :select_container,
-            options_html: options_html,
+  = f.input :consult_site_id,
+            collection: Renalware::Admissions::ConsultSite.all,
             include_blank: true,
-            wrapper: :horizontal_medium
+            wrapper: :horizontal_medium,
+            include_blank: "Select local site (or enter other site below)",
+            label: "Site"
 
   = f.association :hospital_ward,
-                 collection: Renalware::Hospitals::Ward.where(hospital_unit_id: consult.hospital_unit_id),
-                 wrapper: :horizontal_medium
+                  as: :grouped_select,
+                  group_method: :wards,
+                  collection: Renalware::Hospitals::Unit.includes(wards: [:hospital_unit]),
+                  label_method: ->(s){ "#{s.to_s} (#{s.hospital_unit.unit_code})" },
+                  wrapper: :horizontal_medium,
+                  include_blank: "Select local ward (or enter other ward below)"
+
+  = f.input :other_site_or_ward, wrapper: :horizontal_medium
   = f.input :started_on, as: :date_picker, wrapper: :horizontal_datepicker
   = f.input :consult_type, wrapper: :horizontal_medium
   = f.input :decided_on, as: :date_picker, wrapper: :horizontal_datepicker

data/app/views/renalware/admissions/consults/_table.html.slim

@@ -2,7 +2,7 @@
   table
     thead
       tr
-        th.col-width-medium Site/Ward
+        th.col-width-large Location
         th.at-least.col-width-medium Patient
         th.col-width-nhs-no NHS No.
         th.col-width-reference-no Hosp Nos.
@@ -18,7 +18,7 @@
       - consults.each do |consult|
         - uid = "consult-#{consult.id}"
         tr
-          td= consult.unit_and_ward
+          td= consult.location
           td= consult.patient_name
           td= consult.patient_nhs_number
           td= consult.patient_hospital_identifiers
@@ -43,7 +43,7 @@
 
                 = dropdown_btn_item(icon: "fa-edit",
                                     url: edit_admissions_consult_path(consult),
-                                    title: "Edit",
+                                    title: "View/Edit",
                                     enabled: policy(consult).edit?)
 
                 = dropdown_btn_item(icon: "fa-trash",

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

@@ -1,2 +1,2 @@
-= within_admin_layout(title: dashboard.title) do
+= within_admin_layout(title: composed_dashboard_title(current_user.full_name), page_title: "Dashboard") do
   = render "content", dashboard: dashboard

data/app/views/renalware/hd/mdm_patients/_patient.html.slim

@@ -16,6 +16,6 @@ tr
   td= patient.dialysing_at_unit
   td= transplant_patient.current_registration_status
   td= patient.transport_summary
-  td= pathology_patient.hgb_result
-  td= l(pathology_patient.hgb_observed_at&.to_date)
+  td= patient.current_observation_set.hgb_result
+  td= l(patient.current_observation_set.hgb_observed_at)
   td.actions= link_to t(".view"), view_proc.call(patient)

data/app/views/renalware/letters/letters/_pathology.html.slim

@@ -2,7 +2,8 @@ ruby:
   new_pathology_timestamp = Time.zone.now
   diff = Renalware::Pathology::ObservationsDiff.new(
     patient: letter.patient,
-    between_dates: [letter.pathology_timestamp, new_pathology_timestamp],
+    observation_set_a: letter.pathology_snapshot,
+    observation_set_b: letter.patient.current_observation_set&.values,
     descriptions: Renalware::Letters::RelevantObservationDescription.all
   )
 
@@ -22,5 +23,4 @@ ruby:
                 as: :inline_radio_buttons,
                 label: "Include pathology updates below"
 
-
     = diff.to_html

data/app/views/renalware/letters/parts/_recent_pathology_results.html.slim

@@ -2,8 +2,8 @@
   h3 Recent Investigations
 
   - if recent_pathology_results.any?
-    - recent_pathology_results.each do |observation|
-      span #{l(observation.observed_at&.to_date)}: #{observation.description.code} #{observation.result};
-      |  
+     - recent_pathology_results.each do |code, observation|
+        span #{l(observation[:observed_at]&.to_date)}: #{code} #{observation[:result]};
+        |  
   - else
     p None

data/app/views/renalware/mdm_patients/_patient.html.slim

@@ -5,12 +5,12 @@ tr
   td= patient.sex.code
   td= patient.age
   td= patient.modality_description&.name
-  td= patient.hgb_result
-  td= l(patient.hgb_observed_at&.to_date)
-  td= patient.ure_result
-  td= l(patient.ure_observed_at&.to_date)
-  td= patient.cre_result
-  td= l(patient.cre_observed_at&.to_date)
-  td= patient.mdrd_result
+  td= patient.current_observation_set.hgb_result
+  td= l(patient.current_observation_set.hgb_observed_at)
+  td= patient.current_observation_set.ure_result
+  td= l(patient.current_observation_set.ure_observed_at)
+  td= patient.current_observation_set.cre_result
+  td= l(patient.current_observation_set.cre_observed_at)
+  td= patient.current_observation_set.mdrd_result
   td= l(patient.esrf_date)
   td.actions= link_to t(".view"), view_proc.call(patient)

data/app/views/renalware/pathology/current_observation_results/index.html.slim

@@ -1,3 +1,14 @@
 = within_patient_layout title: "Current Pathology Results",
                         navigation_partial: "renalware/pathology/navigation" do
-  = table.render(rows)
+  table.current-observations
+    thead
+      tr
+        td.col-width-date Date
+        td.col-width-small Result
+        td Description
+    tbody
+      - observation_set.each_observation do |observation|
+        tr
+          td= l(observation.observed_at&.to_date)
+          td= observation.result
+          th= observation.description

data/app/views/renalware/pathology/observations/_diff.html.slim

@@ -1,22 +1,28 @@
 / Use by Pathology::ObservationsDiff renderer
-table.table.pathology-observation-diff
-  thead
-    tr
-      th.col-width-tiny(rowspan=2) Code
-      th.col-width-medium(colspan=2) Used
-      th.col-width-medium(colspan=2) Newer
-    tr
-      th.col-width-tiny Result
-      th.col-width-datetime Date
-      th.col-width-tiny Result
-      th.col-width-datetime Date
+.row
+  - diff.to_h.to_a.in_groups_of(11, false) do |group|
+    .columns.medium-6.large-4.end
+      table.table.pathology-observation-diff.columns
+        thead
+          tr
+            th.col-width-tiny(rowspan=2) Code
+            th.col-width-medium(colspan=2) Currently Used
+            th.col-width-medium(colspan=2) Newer
+          tr
+            th.col-width-tiny Result
+            th.col-width-datetime Date
+            th.col-width-tiny Result
+            th.col-width-datetime Date
 
-  tbody
-    - diffs.each do |code, arr|
-      tr
-        th= code
-        td
-          b= arr[0]&.result
-        td= l(arr[0]&.observed_at)
-        td= arr[1]&.result
-        td= l(arr[1]&.observed_at)
+        tbody
+          - group.each do |arr|
+            - if arr.present?
+              - code = arr[0]
+              - curr = arr[1][0]
+              - poss = arr[1][1]
+              tr
+                th= code
+                th= curr&.result
+                td.col-width-date= l(curr&.observed_at&.to_date)
+                td= poss&.result
+                td.col-width-date= l(poss&.observed_at&.to_date)

data/config/initializers/core_extensions.rb

@@ -5,9 +5,11 @@ require "core_extensions/active_record/sort"
 require "core_extensions/date"
 require "core_extensions/active_support/duration"
 require "core_extensions/scenic"
+require "core_extensions/hash"
 
 I18n.extend CoreExtensions::I18n::HandleBlankValue
 I18n::Backend::Simple.send(:include, I18n::Backend::Cascade)
 I18n.extend CoreExtensions::I18n::AlwaysCascade
 ActiveRecord::Base.send(:include, CoreExtensions::ActiveRecord::Sort)
 Date.include CoreExtensions::Date::Constants
+Hash.send(:include, CoreExtensions::Hash::OpenStructConversion)

data/config/locales/renalware/admissions/consults.en.yml

@@ -10,6 +10,15 @@ en:
         hospital_ward: Ward
         consult_type: Type
         contact_number: Bleep/Ext
+        other_site_or_ward: Other site or ward
+    errors:
+      models:
+        renalware/admissions/consult:
+          attributes:
+            other_site_or_ward:
+              blank: Please enter a location, or choose a Site or Ward above
+      renalware/admissions/consult:
+        other_site_or_ward:
   enumerize:
     renalware/admissions/consult:
       transfer_priority:

data/config/locales/renalware/dashboard/dashboard.yml

@@ -2,7 +2,7 @@ en:
   renalware:
     dashboard:
       dashboards:
-        title: "%{name}'s Dashboard"
+        title: "Dashboard / "
         content:
           letters:
             in_progress:

data/config/locales/renalware/patient.yml

@@ -22,7 +22,6 @@ en:
         alcohol:
         smoking:
 
-
   enumerize:
     renalware/patient:
       allergy_status:

data/db/migrate/20171204112150_create_consult_sites.rb

@@ -0,0 +1,14 @@
+class CreateConsultSites < ActiveRecord::Migration[5.1]
+  def change
+    create_table :admission_consult_sites do |t|
+      t.string :name, index: :unique
+    end
+
+    remove_column :admission_consults, :hospital_unit_id
+    add_column :admission_consults, :other_site_or_ward, :string
+    add_reference :admission_consults,
+                  :consult_site,
+                  references: :admission_consult_sites,
+                  index: true
+  end
+end

data/db/migrate/20171211161400_create_pathology_current_table.rb

@@ -0,0 +1,19 @@
+# The pathology_current_observation_sets table has a values hash (jsonb)
+# of the most recent pathology.
+#
+# You can refresh the content of this table with the following query:
+#   select refresh_current_observation_set(id) from patients;
+
+class CreatePathologyCurrentTable < ActiveRecord::Migration[5.1]
+  def change
+    create_table :pathology_current_observation_sets do |t|
+      t.references :patient, null: false, foreign_key: true, index: { unique: true }
+      t.jsonb :values, index: { using: :gin }, default: {}
+
+      t.datetime :created_at, null: false, default: -> { 'CURRENT_TIMESTAMP' }
+      t.datetime :updated_at, null: false, default: -> { 'CURRENT_TIMESTAMP' }
+    end
+
+    drop_view :pathology_current_key_observation_sets, revert_to_version: 2
+  end
+end

data/db/migrate/20171213111513_create_fn_to_refresh_current_obs.rb

@@ -0,0 +1,50 @@
+class CreateFnToRefreshCurrentObs < ActiveRecord::Migration[5.1]
+  def up
+    sql = <<-SQL
+      CREATE OR REPLACE FUNCTION refresh_current_observation_set(a_patient_id integer)
+        -- Function to update the pathology_current_observation_set for a patient.
+        -- It stores the most recent results into the jsonb hash on that table.
+        -- To run for all patients, use
+        --   select refresh_current_observation_set(id) from patients;
+        --
+          RETURNS integer
+          LANGUAGE 'plpgsql'
+          as $$
+        BEGIN
+        with current_patient_obs as(
+            select
+              DISTINCT ON (p.id, obxd.id)
+        p.id as patient_id,
+              obxd.code,
+              json_build_object('result',(obx.result),'observed_at',obx.observed_at) as value
+              from patients p
+              inner join pathology_observation_requests obr on obr.patient_id = p.id
+              inner join pathology_observations obx on obx.request_id = obr.id
+              inner join pathology_observation_descriptions obxd on obx.description_id = obxd.id
+              where p.id = a_patient_id
+              order by p.id, obxd.id, obx.observed_at desc
+          ),
+          current_patient_obs_as_jsonb as (
+            select patient_id,
+              jsonb_object_agg(code, value) as values,
+              CURRENT_TIMESTAMP,
+              CuRRENT_TIMESTAMP
+              from current_patient_obs
+              group by patient_id order by patient_id
+          )
+          insert into pathology_current_observation_sets (patient_id, values, created_at, updated_at)
+            select * from current_patient_obs_as_jsonb
+            ON conflict (patient_id)
+            DO UPDATE
+            SET values = excluded.values, updated_at = excluded.updated_at;
+        RETURN a_patient_id;
+      END
+      $$;
+    SQL
+    ActiveRecord::Base.connection.execute(sql)
+  end
+
+  def down
+    ActiveRecord::Base.connection.execute("drop function if exists refresh_current_observation_set(integer)")
+  end
+end