Merge pull request #512 from sparc-request/jm-deidentified-participant

JM - (SPARCFulfillment) De-identified Patient Features

app/assets/javascripts/patient_registry.js.coffee

@@ -51,4 +51,12 @@ $ ->
         type: 'DELETE'
         url: "/participants/#{participant_id}"
         data: 'protocol_id': $(this).attr('protocol_id')
-
+
+  ### De-identified Patient ###
+  $('#patient-registry-table').on 'load-success.bs.table', ->
+    $rows = $('#patient-registry-table tr')
+    $rows.each (i, item) ->
+      $this = $(item)
+      if $(item).find("td.deidentified:contains('Yes')").length
+        $this.addClass 'deidentified_patient'
+      return

app/assets/stylesheets/participants.sass

@@ -17,6 +17,10 @@
 // DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS~
 // INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR~
 // TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.~
+table#patient-registry-table tbody tr.deidentified_patient,
+table#patient-registry-modal tbody tr.deidentified_patient
+  background-color: lightgrey
+  color: black
 
 body.participants
 

app/controllers/participants_controller.rb

@@ -45,6 +45,8 @@ def index
   def find_participants(action_name)
     if action_name == "protocols_participants_in_protocol"
       @participants = Participant.by_protocol_id(@protocol.id)
+    elsif action_name == "associate_participants_to_protocol"
+      @participants = Participant.able_to_be_associated
     else
       @participants = Participant.all
     end
@@ -230,7 +232,7 @@ def find_protocols_participant
   end
 
   def participant_params
-    params.require(:participant).permit(:last_name, :first_name, :middle_initial, :mrn, :external_id,:date_of_birth, :gender, :ethnicity, :race, :address, :city, :state, :zipcode, :phone, :recruitment_source)
+    params.require(:participant).permit(:last_name, :first_name, :middle_initial, :mrn, :external_id,:date_of_birth, :gender, :ethnicity, :race, :address, :city, :state, :zipcode, :phone, :recruitment_source, :deidentified)
   end
 
   def protocols_participant_params

app/helpers/participant_helper.rb

@@ -150,6 +150,10 @@ def notes_formatter(participant)
                   button_class: 'participant_notes'})
   end
 
+  def deidentified_patient(participant)
+    participant.deidentified == false ? "No" : participant.deidentified == true ? "Yes" : "N/A"
+  end
+
   def participant_report_formatter(protocols_participant)
     icon_span = raw content_tag(:span, '', class: "glyphicon glyphicon-equalizer")
     button    = raw content_tag(:button, raw(icon_span), type: 'button', class: 'btn btn-default btn-xs report-button participant_report dropdown-toggle', id: "participant_report_#{protocols_participant.id.to_s}", 'aria-expanded' => 'false', title: 'Participant Report', 'data-title' => 'Participant Report', 'data-report_type' => 'participant_report',  'data-documentable_id' => protocols_participant.protocol_id, 'data-documentable_type' => 'Protocol', 'data-protocols_participant_id' => protocols_participant.id)

app/models/participant.rb

@@ -65,6 +65,10 @@ class Participant < ApplicationRecord
   scope :except_by_protocol_id, -> (protocol_id) {
     joins(:protocols_participants).where("protocols_participants.protocol_id != ? ", protocol_id)
   }
+  ### A participant is marked as "de-identified" and has been associated to a protocol
+  scope :deidentified_true_and_associated_to_a_protocol, -> { where(deidentified: true).joins(:protocols_participants).ids }
+
+  scope :able_to_be_associated, -> { where(id: (Participant.all.ids - deidentified_true_and_associated_to_a_protocol).uniq) }
 
   def self.title id
     participant = Participant.find id

app/views/participants/_associate_participants_to_protocol_modal.html.haml

@@ -37,6 +37,7 @@
               %th{data: {class: 'first_name truncate', align: "left", sortable: "true", field: "first_middle"}}= t(:participant)[:first_name]
               %th{data: {class: 'mrn truncate', align: "left", sortable: "true", field: "mrn"}}= t(:participant)[:mrn]
               %th{data: {class: 'date_of_birth truncate', align: "left", sortable: "true", field: "date_of_birth"}}= t(:participant)[:dob]  
+              %th{data: {class: 'deidentified truncate', align: "left", sortable: "true", field: "deidentified", visible: "true"}}= t(:participant)[:deidentified] 
               %th{data: {class: 'recruitment_source', align: "left", sortable: "true", field: "recruitment_source", visible: "false"}}= t(:participant)[:recruitment_source]
               %th{data: {class: 'phone truncate', align: "left", sortable: "true", field: "phone"}}= t(:participant)[:phone_num]
     .modal-footer

app/views/participants/_participant_form.html.haml

@@ -17,7 +17,6 @@
 -# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS~
 -# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR~
 -# TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.~
-
 .modal-dialog
   .modal-content
     = form_for participant, {remote: true, html: {class: "form-horizontal new_participant", role: "form"}} do |p|
@@ -31,6 +30,10 @@
         = render partial: 'required_fields'
         .row
           .col-md-12
+            .form-group
+              = p.label "deidentified", t(:patient)[:deidentified_patient], class: "col-sm-4 control-label"
+              .checkbox.col-sm-7
+                %label= p.check_box "deidentified"
             .form-group
               = p.label "last_name", t(:participant)[:last_name]+t(:actions)[:required], class: "col-sm-4 control-label"
               .col-sm-7= p.text_field "last_name", {class: 'form-control'}

app/views/participants/associate_participants_to_protocol.js.coffee

@@ -21,3 +21,12 @@
 $("#modal_area").html("<%= escape_javascript(render(:partial =>'participants/associate_participants_to_protocol_modal', locals: {protocol: @protocol})) %>");
 $("#modal_place").modal 'show'
 $("#patient-registry-modal").bootstrapTable()
+
+### De-identified Patient ###
+$('#patient-registry-modal').on 'load-success.bs.table', ->
+  $rows = $('#patient-registry-modal tr')
+  $rows.each (i, item) ->
+    $this = $(item)
+    if $(item).find("td.deidentified:contains('Yes')").length
+      $this.addClass 'deidentified_patient'
+    return

app/views/participants/associate_participants_to_protocol.json.jbuilder

@@ -14,6 +14,7 @@ json.rows @participants do |participant|
     json.gender participant.gender
     json.ethnicity participant.ethnicity
     json.race participant.race
+    json.deidentified deidentified_patient(participant)
     json.address truncated_formatter(participant.address)
     json.phone phoneNumberFormatter(participant)
     json.edit registry_edit_formatter(participant)

app/views/participants/index.html.haml

@@ -30,6 +30,7 @@
           %th{data: {class: 'first_name truncate', align: "left", sortable: "true", field: "first_middle"}}= t(:participant)[:first_name]
           %th{data: {class: 'mrn truncate', align: "left", sortable: "true", field: "mrn"}}= t(:participant)[:mrn]
           %th{data: {class: 'date_of_birth truncate', align: "left", sortable: "true", field: "date_of_birth"}}= t(:participant)[:dob]  
+          %th{data: {class: 'deidentified truncate', align: "left", sortable: "true", field: "deidentified", visible: "true"}}= t(:participant)[:deidentified] 
           %th{data: {class: 'recruitment_source', align: "left", sortable: "true", field: "recruitment_source", visible: "false"}}= t(:participant)[:recruitment_source]
           %th{data: {class: 'details', align: "center", field: "details"}}= t(:actions)[:details]
           %th{data: {class: 'edit', align: "center", field: "edit"}}= t(:actions)[:edit]

app/views/participants/index.json.jbuilder

@@ -14,6 +14,7 @@ json.rows @participants do |participant|
     json.gender participant.gender
     json.ethnicity participant.ethnicity
     json.race participant.race
+    json.deidentified deidentified_patient(participant)
     json.address truncated_formatter(participant.address)
     json.phone phoneNumberFormatter(participant)
     json.details registry_details_formatter(participant)

config/locales/en.yml

@@ -260,6 +260,7 @@ en:
     city: "City"
     details: "Participant Details"
     dob: "Date of Birth"
+    deidentified: "De-identified"
     ethnicity: "Ethnicity"
     first_name: "First Name"
     flash_messages:
@@ -373,6 +374,7 @@ en:
     registry: "Patient Registry"
     confirm_removal_part_1: "Are you sure you want to remove"
     confirm_removal_part_2: "from Patient Registry?"
+    deidentified_patient: "De-identified Patient"
 
   reports:
     asc: "ASC"

db/migrate/20190710135118_add_de_identified_to_participant.rb

@@ -0,0 +1,25 @@
+# Copyright © 2011-2019 MUSC Foundation for Research Development~
+# All rights reserved.~
+
+# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:~
+
+# 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.~
+
+# 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following~
+# disclaimer in the documentation and/or other materials provided with the distribution.~
+
+# 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products~
+# derived from this software without specific prior written permission.~
+
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,~
+# BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT~
+# SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL~
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS~
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR~
+# TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.~
+
+class AddDeIdentifiedToParticipant < ActiveRecord::Migration[5.2]
+  def change
+    add_column :participants, :deidentified, :boolean, default: false
+  end
+end

lib/reports/participant_report.rb

@@ -60,7 +60,8 @@ def generate(document)
         csv << ["Gender", @gender]
       end
 
-      header = [ "Participant ID" ]
+      header = ["Participant ID"]
+      header << "De-identified"
       header << "First Name"
       header << "Middle Initial"
       header << "Last Name"
@@ -80,8 +81,10 @@ def generate(document)
 
       csv << header
       participants.find_each do |participant|
+        deidentified = participant.deidentified == false ? "No" : participant.deidentified == true ? "Yes" : "N/A"
 
         data = [participant.id]
+        data << deidentified
         data << participant.first_name
         data << participant.middle_initial
         data << participant.last_name