renalware-core 2.0.28 → 2.0.30

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: b58bef85d36bdb2af561a3229a51aac0bb690b3498cab8804076fdc4a5a5d149
+  metadata.gz: b29e1fc4d6a1bb7e86fdcf56f18246fd8e39119376366f7017838cedfd4b087f
+  data.tar.gz: d5cd02cdd2dcb4b42cd8c5d0ecc32f7dfce445e45a00adee57556b49adba4ad1
 SHA512:
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-  data.tar.gz: 776a1be9ade866026a0ed0cc7956eeb7983194c6da7a57b192a74ca16b15721865fdfda5d1442826a0673b09e27caa60922550854352f5c05c239cbfd4f1cf52
+  metadata.gz: 529f354080faf23959520fbf19b5db5da08e2bbf9cacab2d76f35964c807e43ad509ca2f7259942ca336fff48489224b39ceb4db9d23c789604455d6020114a1
+  data.tar.gz: a5f9c60d939e1c7afde8800f06da5d9d65b61e373d34530a5e2f6cdd2354f2cc86c9d1455193d7dc7a45531204b845cb6f64d11363fabf94c4ca609da166a8cd

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

@@ -49,8 +49,7 @@ article.clinical-allergies {
   }
 }
 
-.clinical-header,
-.research-study-participation-alerts {
+.clinical-header {
   background-color: $table-border-colour;
   padding: 0em .2em .2em .6em;
 
@@ -125,25 +124,17 @@ article.clinical-allergies {
   }
 }
 
-.research-study-participation-alerts {
-  .lozenge {
-    ul {
-      li {
-        background-color: $nhs-pink;
-        color: $white;
-      }
-    }
-  }
-}
-
 .patient-alerts {
-  @media pring {
+  color: $white;
+
+  @media print {
     display: none;
   }
 
   &.lozenge {
     ul {
       margin: 0;
+      //font-size: 0.9rem;
 
       li {
         background-color: $nhs-orange;
@@ -157,29 +148,33 @@ article.clinical-allergies {
           background-color: darken($nhs-orange, 5);
         }
 
-        &:hover,
-        span:hover {
-          color: white
-        }
-
         &.urgent {
           background-color: $nhs-red;
 
           &:hover {
-            background-color: darken($nhs-red, 5);
+            background-color: darken($nhs-red, 7);
           }
         }
 
         &.research-study-participant {
-          background-color: $nhs-green;
+          background-color: darken($nhs-green, 3);
+          color: $white;
 
           &:hover {
             background-color: darken($nhs-green, 5);
           }
 
           a {
+            color: $white;;
+            border-bottom: 1px dotted $white
+          }
+
+          .date {
+            border-left: 1px solid $mid-grey;
+          }
+
+          span {
             color: $white;
-            border-bottom: 1px dotted $light-grey;
           }
         }
 
@@ -187,7 +182,8 @@ article.clinical-allergies {
           padding: 0 .4rem;
         }
 
-        .body {
+        .body,
+        .external_application_link {
           padding-left: 0;
         }
 
@@ -196,7 +192,6 @@ article.clinical-allergies {
         .actions {
           font-style: italic;
           border-left: 1px solid $winter-sky;
-          color: $light-grey;
           white-space: nowrap;
 
           .fa {

data/app/controllers/renalware/research/studies_controller.rb

@@ -66,7 +66,10 @@ module Renalware
       def study_params
         params
           .require(:research_study)
-          .permit(:code, :description, :leader, :notes, :started_on, :terminated_on)
+          .permit(
+            :code, :description, :leader, :notes, :started_on, :terminated_on,
+            :application_url
+          )
       end
     end
   end

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

@@ -75,7 +75,7 @@ module Renalware
           session = session.becomes!(Session::Closed)
           session.profile = patient.hd_profile
           session.signed_off_at = Time.zone.now
-          session.dry_weight = Renalware::Clinical::DryWeight.for_patient(patient).first
+          session.dry_weight = most_recent_dry_weight
           session
         end
 
@@ -83,6 +83,13 @@ module Renalware
           session_type.constantize
         end
 
+        def most_recent_dry_weight
+          Renalware::Clinical::DryWeight
+            .for_patient(patient)
+            .order(assessed_on: :desc)
+            .first
+        end
+
         def lookup_access_type_abbreviation(session)
           return unless session.document&.respond_to?(:info)
           access_type = Accesses::Type.find_by(name: session.document.info.access_type)

data/app/models/renalware/research/study_participant.rb

@@ -9,6 +9,7 @@ module Renalware
       acts_as_paranoid
       validates :participant_id, presence: true, uniqueness: { scope: :study }
       validates :study, presence: true
+      validates :external_id, uniqueness: true # added by a trigger
       belongs_to :study, touch: true
       belongs_to :patient,
                  class_name: "Renalware::Patient",
@@ -18,6 +19,11 @@ module Renalware
       def to_s
         patient&.to_s
       end
+
+      def external_application_participant_url
+        return if study.application_url.blank?
+        study.application_url.gsub("{external_id}", external_id.to_s)
+      end
     end
   end
 end

data/app/views/renalware/research/_alert.html.slim

@@ -2,5 +2,13 @@ li.patient-alert.research-study-participant
   i.fa.fa-warning
   span.title= link_to(participation.study.code, research_study_participants_path(participation.study))
   span.body participant
-  span.date= l(participation.joined_on)
 
+  / A Study might have a url linking to an external study application. In this case show the link
+  / in the alert.
+  - if participation.external_application_participant_url.present?
+    span.external_application_link
+      = link_to(participation.external_application_participant_url, target: "_blank") do
+        i.fa.fa-external-link
+        |  Launch application
+
+  span.date= l(participation.joined_on)

data/app/views/renalware/research/studies/_form.html.slim

@@ -2,6 +2,15 @@
   = f.input :code, wrapper: :horizontal_small
   = f.input :description, wrapper: :horizontal_large
   = f.input :leader, wrapper: :horizontal_small
+  = f.input :application_url,
+            wrapper: :horizontal_medium,
+            hint: "If there is an an external application associated with this study " \
+                  "you can enter it here and, for participanting patients, the link " \
+                  "will appear at the top of patient pages.<br/>" \
+                  "Use the format https://my-research-app/participants/{external_id}<br/> if you " \
+                  "The {external_id} placeholder will be replaced with " \
+                  "research_study_particpant_external_id".html_safe,
+            placeholder: "e.g. https://my-research-app/participants/{external_id}"
   = f.input :started_on, as: :date_picker, wrapper: :horizontal_datepicker
   = f.input :terminated_on, as: :date_picker, wrapper: :horizontal_datepicker
   = f.input :notes, as: :text, wrapper: :horizontal_large, input_html: { rows: 6 }

data/app/views/renalware/research/study_participants/_table.html.slim

@@ -9,6 +9,7 @@
         th.col-width-reference-no Hosp no
         th.col-width-tiny Age
         th Sex
+        th External ID
         th.col-width-small
     tbody
       - participants.each do |participant|
@@ -20,6 +21,7 @@
           td= participant.patient.hospital_identifiers
           td= participant.patient.age
           td= participant.patient.sex
+          td= participant.external_id
           td
             = link_to "Delete",
                       research_study_participant_path(study, participant),

data/db/functions/pseudo_encrypt_v01.sql

@@ -0,0 +1,28 @@
+/*
+See https://wiki.postgresql.org/wiki/Pseudo_encrypt
+Encrypt an id eg 101 and generate a unique integer eg
+  select pseudo_encrypt(101); # => 1064847687
+pseudo_encrypt will always return the same number for any input integer.
+Useful creating a psuedo-random id that is guaranteed to be unique.
+Could be used in conjunction with a sequence
+*/
+CREATE OR REPLACE FUNCTION renalware.pseudo_encrypt(VALUE int) returns int AS $$
+DECLARE
+l1 int;
+l2 int;
+r1 int;
+r2 int;
+i int:=0;
+BEGIN
+ l1:= (VALUE >> 16) & 65535;
+ r1:= VALUE & 65535;
+ WHILE i < 3 LOOP
+   l2 := r1;
+   r2 := l1 # ((((1366 * r1 + 150889) % 714025) / 714025.0) * 32767)::int;
+   l1 := l2;
+   r1 := r2;
+   i := i + 1;
+ END LOOP;
+ RETURN ((r1 << 16) + l1);
+END;
+$$ LANGUAGE plpgsql strict immutable;

data/db/functions/update_research_study_participants_from_trigger_v01.sql

@@ -0,0 +1,22 @@
+set SEARCH_PATH=renalware,public;
+CREATE OR REPLACE FUNCTION renalware.update_research_study_participants_from_trigger() RETURNS TRIGGER AS $body$
+/*
+TC 05/06/2018
+After a participant is added to a study, assign them an external_id, to be used when sending this
+data for example to an external study application.
+We use pseudo_encrypt() to generate a random id which is guaranteed to be unique as it is based
+on the id. Its not the most secure however as, without a secret, the id can be reverse engineered
+if our pseudo_encrypt sql function open source (which it is). If this is deemed to be a problem
+(our intention at this point is rudimentary obfuscation), a hospital can override replace this
+function with a more secure one.
+An alternative to using a trigger is to use an after_ or before_save hook in Rails. The trigger
+approach is chosen as, unlike a traditional Rails app, some direct data manipulation can be expected
+in Renalware, even if that is just during migration.
+*/
+BEGIN
+  IF (TG_OP = 'INSERT') THEN
+    NEW.external_id = renalware.pseudo_encrypt(NEW.id::integer);
+    RETURN NEW;
+  END IF;
+  RETURN NULL;
+END $body$ LANGUAGE plpgsql VOLATILE COST 100;

data/db/migrate/20180605114332_create_pseudo_encrypt_function.rb

@@ -0,0 +1,9 @@
+class CreatePseudoEncryptFunction < ActiveRecord::Migration[5.1]
+  def up
+    load_function "pseudo_encrypt_v01.sql"
+  end
+
+  def down
+    connection.execute("DROP FUNCTION renalware.pseudo_encrypt(int);")
+  end
+end

data/db/migrate/20180605141806_add_external_id_to_research_study_participants.rb

@@ -0,0 +1,40 @@
+class AddExternalIdToResearchStudyParticipants < ActiveRecord::Migration[5.1]
+  def change
+    # The external_id is for obfuscating the participant id using a random integer.
+    # It is used e.g. when passing to an external research application
+    add_column(
+      :research_study_participants,
+      :external_id,
+      :integer,
+      null: true
+    )
+
+    reversible do |direction|
+      direction.up do
+        # Create a function the trigger will call..
+        load_function("update_research_study_participants_from_trigger_v01.sql")
+
+        # .. and the trigger when a row is inserted
+        load_trigger("update_research_study_participants_trigger_v01.sql")
+
+        # Populate the just-created external_id column with the correct value that the trigger
+        # would otherwise create if it were added in the future.
+        connection.execute(
+          "UPDATE renalware.research_study_participants SET external_id = renalware.pseudo_encrypt(id::integer) where external_id is NULL;"
+        )
+      end
+      direction.down do
+        connection.execute("
+          DROP TRIGGER IF EXISTS update_research_study_participants_trigger ON renalware.research_study_participants;
+          DROP FUNCTION IF EXISTS update_research_study_participants_from_trigger();
+        ")
+      end
+    end
+
+    # Now we have created and populated the external_id we need to add a unique index.
+    # external_id is guaranteed to be unique because the generating function (called by the
+    # trigger when a row is inserted) is based on the id.
+    # See db/functions/update_research_study_participants_from_trigger_v01
+    add_index :research_study_participants, :external_id, unique: true
+  end
+end

data/db/migrate/20180605175211_add_application_url_to_research_studies.rb

@@ -0,0 +1,5 @@
+class AddApplicationUrlToResearchStudies < ActiveRecord::Migration[5.1]
+  def change
+    add_column :research_studies, :application_url, :string, null: true
+  end
+end

data/db/triggers/update_research_study_participants_trigger_v01.sql

@@ -0,0 +1,6 @@
+-- Create the trigger which will call out function every time a row in pathology_observations
+-- is inserted or updated
+DROP TRIGGER IF EXISTS update_research_study_participants_trigger ON renalware.research_study_participants;
+CREATE TRIGGER update_research_study_participants_trigger
+  BEFORE INSERT ON renalware.research_study_participants FOR EACH ROW
+  EXECUTE PROCEDURE renalware.update_research_study_participants_from_trigger();

data/lib/core_extensions/active_record/migration_helpers.rb

@@ -23,18 +23,35 @@ module CoreExtensions
         load_sql_file(DatabaseObjectPaths.triggers, filename)
       end
 
-      def load_sql_file(path, filename)
-        connection.execute(File.read(path.join(filename)))
+      def load_sql_file(paths, filename)
+        found = false
+        paths.each do |path|
+          file_path = path.join(filename)
+          if File.exist?(file_path)
+            connection.execute(File.read(file_path))
+            found = true
+          end
+        end
+        unless found
+          raise "Cannot file #{filename} in #{paths.join(', ')}"
+        end
       end
 
+      # Make sure to look in the host Rails app as well as in the engine
       class DatabaseObjectPaths
         class << self
           def triggers
-            Renalware::Engine.root.join("db", "triggers")
+            [
+              Rails.root.join("db", "triggers"),
+              Renalware::Engine.root.join("db", "triggers")
+            ]
           end
 
           def functions
-            Renalware::Engine.root.join("db", "functions")
+            [
+              Rails.root.join("db", "functions"),
+              Renalware::Engine.root.join("db", "functions")
+            ]
           end
         end
       end

data/lib/renalware/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Renalware
-  VERSION = "2.0.28"
+  VERSION = "2.0.30"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: renalware-core
 version: !ruby/object:Gem::Version
-  version: 2.0.28
+  version: 2.0.30
 platform: ruby
 authors:
 - Airslie
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-05-31 00:00:00.000000000 Z
+date: 2018-06-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: active_type
@@ -2878,12 +2878,14 @@ files:
 - db/functions/import_practices_csv_v01.sql
 - db/functions/preprocess_hl7_message_v01.sql
 - db/functions/preprocess_hl7_message_v02.sql
+- db/functions/pseudo_encrypt_v01.sql
 - db/functions/refresh_all_matierialized_views_v01.sql
 - db/functions/refresh_current_observation_set_v01.sql
 - db/functions/update_current_observation_set_from_trigger_v01.sql
 - db/functions/update_current_observation_set_from_trigger_v02.sql
 - db/functions/update_current_observation_set_from_trigger_v03.sql
 - db/functions/update_current_observation_set_from_trigger_v04.sql
+- db/functions/update_research_study_participants_from_trigger_v01.sql
 - db/migrate/20141004150240_create_ethnicities.rb
 - db/migrate/20141010170329_create_death_causes.rb
 - db/migrate/20141020170329_create_patients.rb
@@ -3262,6 +3264,9 @@ files:
 - db/migrate/20180511171835_create_unique_indexes_on_obr_obr_codes.rb
 - db/migrate/20180514151627_create_system_messages.rb
 - db/migrate/20180516111411_create_view_patient_current_modalities.rb
+- db/migrate/20180605114332_create_pseudo_encrypt_function.rb
+- db/migrate/20180605141806_add_external_id_to_research_study_participants.rb
+- db/migrate/20180605175211_add_application_url_to_research_studies.rb
 - db/seeds.rb
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.csv
 - db/seeds/default/accesses/access_pd_catheter_insertion_techniques.rb
@@ -3346,6 +3351,7 @@ files:
 - db/static.obsolete/medication_routes.yml
 - db/triggers/feed_messages_preprocessing_trigger_v01.sql
 - db/triggers/update_current_observation_set_trigger_v01.sql
+- db/triggers/update_research_study_participants_trigger_v01.sql
 - db/views/medication_current_prescriptions_v01.sql
 - db/views/pathology_current_key_observation_sets_v01.sql
 - db/views/pathology_current_key_observation_sets_v02.sql