Merge pull request #1721 from sparc-request/jl-ui-for-protocol-merge

Jl - ui for protocol merge

app/assets/javascripts/dashboard/protocol_merges.js.coffee

@@ -0,0 +1,18 @@
+$ ->
+
+  $(document).on 'click', '#merge-button', ->
+    master_protocol_id = $('#master_protocol').val()
+    sub_protocol_id = $('#sub_protocol').val()
+
+    data =
+        'master_protocol_id'  : master_protocol_id,
+        'sub_protocol_id'     : sub_protocol_id
+
+    if confirm("Preparing to merge protocol #{master_protocol_id} and protocol #{sub_protocol_id}. Do you wish to continue?")
+      $.ajax
+          type: 'GET'
+          url: "/dashboard/protocol_merge/perform_protocol_merge"
+          data: data
+          success: ->
+            $('#master_protocol').val('')
+            $('#sub_protocol').val('')

app/controllers/dashboard/protocol_merges_controller.rb

@@ -0,0 +1,139 @@
+# Copyright © 2011-2018 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 Dashboard::ProtocolMergesController < Dashboard::BaseController
+  before_action :authorize_overlord
+  respond_to :json, :html
+
+  def show
+    @user = current_identity
+  end
+
+  def perform_protocol_merge
+    master_protocol = Protocol.where(id: params[:master_protocol_id].to_i).first
+    sub_protocol = Protocol.where(id: params[:sub_protocol_id].to_i).first
+
+    merge_srs = Dashboard::MergeSrs.new()
+    fix_ssr_ids = Dashboard::FixSsrIds.new(master_protocol)
+
+    if (master_protocol == nil) || (sub_protocol == nil)
+      flash[:alert] = 'Protocol(s) not found. Check IDs and try again.'
+    elsif (master_protocol.has_clinical_services? && sub_protocol.has_clinical_services?)
+      flash[:alert] = 'Both protocols have calendars. Only one protocol may have a calendar for merge to work.'
+    else
+      ActiveRecord::Base.transaction do
+
+        #transfer the project roles as needed
+        sub_protocol.project_roles.each do |role|
+          if role.role != 'primary-pi' && role_should_be_assigned?(role, master_protocol)
+            role.update_attributes(protocol_id: master_protocol.id)
+          end
+        end
+
+        # checking for and assigning research types, impact areas, and affiliations...
+        if has_research?(sub_protocol, 'human_subjects') && !has_research?(master_protocol, 'human_subjects')
+          sub_protocol.human_subjects_info.update_attributes(protocol_id: master_protocol.id)
+        elsif has_research?(sub_protocol, 'vertebrate_animals') && !has_research?(master_protocol, 'vertebrate_animals')
+          sub_protocol.vertebrate_animals_info.update_attributes(protocol_id: master_protocol.id)
+        elsif has_research?(sub_protocol, 'investigational_products') && !has_research?(master_protocol, 'investigational_products')
+          sub_protocol.investigational_products_info.update_attributes(protocol_id: master_protocol.id)
+        elsif has_research?(sub_protocol, 'ip_patents') && !has_research?(master_protocol, 'ip_patents')
+          sub_protocol.ip_patents_info.update_attributes(protocol_id: master_protocol.id)
+        end
+
+        sub_protocol.impact_areas.each do |area|
+          area.protocol_id = master_protocol.id
+          area.save(validate: false)
+        end
+
+        sub_protocol.affiliations.each do |affiliation|
+          affiliation.protocol_id = master_protocol.id
+          affiliation.save(validate: false)
+        end
+
+        # assigning service requests...
+        fulfillment_ssrs = []
+        sub_protocol.service_requests.each do |request|
+          request.protocol_id = master_protocol.id
+          request.save(validate: false)
+          request.sub_service_requests.each do |ssr|
+            ssr.update_attributes(protocol_id: master_protocol.id)
+            master_protocol.next_ssr_id = (master_protocol.next_ssr_id + 1)
+            master_protocol.save(validate: false)
+            if ssr.in_work_fulfillment
+              fulfillment_ssrs << ssr
+            end
+          end
+        end
+
+        #assigning arms..."
+        sub_protocol.arms.each do |arm|
+          check_arm_names(arm, master_protocol)
+          arm.protocol_id = master_protocol.id
+          arm.save(validate: false)
+        end
+
+        #assigning documents..."
+        sub_protocol.documents.each do |document|
+          document.protocol_id = master_protocol.id
+          document.save(validate: false)
+        end
+
+        #assigning_notes
+        sub_protocol.notes.each do |note|
+          note.notable_id = master_protocol.id
+          note.save(validate: false)
+        end
+
+        #delete sub protocol
+        sub_protocol.delete
+
+        #cleanup
+        merge_srs.perform_sr_merge
+        fix_ssr_ids.perform_id_fix
+      end
+      flash[:success] = 'Protocol merge successful'
+    end
+  end
+
+  private
+
+  def role_should_be_assigned?(role_to_be_assigned, protocol)
+    protocol.project_roles.each do |role|
+      if (role.role == role_to_be_assigned.role) && (role.identity_id == role_to_be_assigned.identity_id)
+        return false
+      end
+    end
+    return true
+  end
+
+  def authorize_overlord
+    unless @user.catalog_overlord?
+      render partial: 'service_requests/authorization_error',
+        locals: { error: 'You do not have access to perform a Protocol Merge',
+                  in_dashboard: false
+      }
+    end
+  end
+
+  def has_research?(protocol, research_type)
+    protocol.research_types_info.try(research_type) || false
+  end
+end

app/lib/dashboard/fix_ssr_ids.rb

@@ -0,0 +1,42 @@
+module Dashboard
+
+  class FixSsrIds
+
+    def initialize(protocol)
+      @protocol = protocol
+    end
+
+    def perform_id_fix
+      requests = @protocol.sub_service_requests.group_by(&:ssr_id)
+      if @protocol.sub_service_requests.present?
+        last_ssr_id = @protocol.sub_service_requests.sort_by(&:ssr_id).last.ssr_id.to_i
+        dup_requests_to_be_incremented = []
+
+        requests.each do |ssr_id, ssr_array|
+          if ssr_array.size > 1 # we have duplicate ssr_ids
+            ssr_array.each_with_index do |ssr, index|
+              if index > 0
+                dup_requests_to_be_incremented << ssr # place all requests with dup ids in an array to deal with later
+              end
+            end
+          end
+        end
+
+        if dup_requests_to_be_incremented.size > 0
+          dup_requests_to_be_incremented.each do |ssr|
+            ssr.ssr_id = "%04d" % (last_ssr_id + 1)
+            ssr.save(validate: false) 
+            last_ssr_id += 1
+          end
+        end
+
+        # we need to increment the protocol's next_ssr_id if we had some duplicates
+        new_last_ssr_id = @protocol.sub_service_requests.sort_by(&:ssr_id).last.ssr_id.to_i
+        if @protocol.next_ssr_id? && (@protocol.next_ssr_id <= new_last_ssr_id)
+          @protocol.next_ssr_id = new_last_ssr_id + 1
+          @protocol.save(validate: false)
+        end
+      end
+    end
+  end
+end

app/lib/dashboard/merge_srs.rb

@@ -0,0 +1,100 @@
+module Dashboard
+
+  class MergeSrs
+
+    def perform_sr_merge
+      ServiceRequest.skip_callback(:save, :after, :set_original_submitted_date)
+
+      protocols = Protocol.joins(:service_requests).group('protocols.id').having('count(protocol_id) >= 2').to_a
+      protocols.each do |protocol|
+
+        # Merge remaining service requests into service request with most recently
+        # updated status
+        recent_service_request = protocol.service_requests.preload(:audits).distinct.map do |sr|
+          last_status_change = sr.audits.reverse.find { |a| a.audited_changes["status"] }
+          if last_status_change
+            [sr, last_status_change.created_at]
+          end
+        end.compact.sort do |l, r|
+          l[1] <=> r[1]
+        end
+
+        recent_service_request = if recent_service_request.empty?
+          # If audit trail runs out, use most recently updated ServiceRequest
+          protocol.service_requests.order(:updated_at).last
+        else
+          recent_service_request.last[0]
+        end
+
+        # And the latest submitted_at date
+        latest_submitted_at = protocol.service_requests.
+          order(:submitted_at).
+          where.not(submitted_at: nil).
+          pluck(:submitted_at).
+          last
+
+        if latest_submitted_at
+          recent_service_request.submitted_at = latest_submitted_at
+          recent_service_request.audit_comment = 'merge_srs'
+          recent_service_request.save(validate: false)
+        end
+
+        # Keep the earliest original_submitted_date among service requests
+        earliest_original_submitted_date = protocol.service_requests.
+          order(:original_submitted_date).
+          where.not(original_submitted_date: nil).
+          pluck(:original_submitted_date).
+          first
+
+        if earliest_original_submitted_date
+          recent_service_request.original_submitted_date = earliest_original_submitted_date
+          recent_service_request.audit_comment = 'merge_srs'
+          recent_service_request.save(validate: false)
+        end
+
+        # Move all SSR's, LineItems and ServiceRequest Notes under this recent_service_request
+        protocol.sub_service_requests.where.not(service_request_id: recent_service_request.id).each do |ssr|
+          ssr.service_request_id = recent_service_request.id
+          ssr.audit_comment = 'merge_srs'
+          ssr.save(validate: false)
+        end
+        line_items = LineItem.joins(:service_request).where(service_requests: { protocol_id: protocol.id }).where.not(service_request_id: recent_service_request.id)
+        line_items.each do |li|
+          li.service_request_id = recent_service_request.id
+          li.audit_comment = 'merge_srs'
+          li.save(validate: false)
+        end
+
+        protocol.service_requests.where.not(id: recent_service_request.id).each do |sr|
+          sr.notes.each do |note|
+            note.notable_id = recent_service_request.id
+            note.audit_comment = 'merge_srs'
+            note.save(validate: false)
+          end
+        end
+
+        delete_empty_srs(protocol)
+      end
+    end
+
+    private
+
+    def delete_empty_srs(protocol)
+      protocol.service_requests.includes(:sub_service_requests).where(sub_service_requests: { id: nil }).each do |sr|
+        begin
+          sr.destroy
+          sr.audits.last.update(comment: 'merge_srs')
+        rescue
+          # Probably a funky Note body...
+          sr.notes.each do |note|
+            note.notable_id = nil
+            note.audit_comment = 'merge_srs'
+            note.save(validate: false)
+          end
+          sr.reload.destroy
+          sr.audits.last.update(comment: 'merge_srs')
+        end
+      end
+    end
+  end
+end

app/views/dashboard/protocol_merges/_merge_tool.html.haml

@@ -0,0 +1,19 @@
+#protocol-merges-container
+  %h1{style: 'text-align:center;'}
+    Protocol Merge Tool
+  %p &nbsp
+  %p &nbsp
+  %p &nbsp
+  %p
+    = label_tag 'master_protocol', 'Enter the id of the Master Protocol:' 
+    = text_field_tag 'master_protocol', nil, style: 'margin-left:207px'
+  %p &nbsp
+  %p &nbsp
+  %p
+    = label_tag 'sub_protocol', 'Enter the id of the Protocol to be merged into the Master Protocol:' 
+    = text_field_tag 'sub_protocol'
+  %p &nbsp
+  %p &nbsp
+  %p{style: 'text-align:center;'}
+    %button.btn.btn-info.navbar-btn#merge-button{ type: 'button', title: "Perform Protocol Merge"}
+      = "Perform Protocol Merge"

app/views/dashboard/protocol_merges/perform_protocol_merge.js.coffee

@@ -0,0 +1 @@
+$("#flashes_container").html("<%= j render 'shared/flash' %>")

app/views/dashboard/protocol_merges/show.html.haml

@@ -0,0 +1,26 @@
+-# Copyright © 2011-2018 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.
+
+= render 'dashboard/protocol_merges/merge_tool.html.haml'
+
+:javascript
+  $(document).ready( function() {
+    Sparc.protocol.ready();
+  })

app/views/layouts/dashboard/_dashboard_header.html.haml

@@ -35,6 +35,8 @@
           %li
             %button.btn.btn-info.navbar-btn#epic-queue-btn{ type: 'button', title: t(:dashboard)[:navbar][:tooltips][:epic_queue], data: { toggle: 'tooltip', placement: 'bottom', delay: '{"show":"500"}'} }
               = t(:dashboard)[:navbar][:epic_queue]
+        - if current_user.catalog_overlord?
+          = link_to "Protocol Merge", dashboard_protocol_merge_path, :class => ' header_button btn btn-primary btn-md', style: 'margin-top:7px;'
         - if @show_messages
           %li
             %button.btn.btn-danger.navbar-btn#messages-btn{ type: 'button', title: t(:dashboard)[:navbar][:tooltips][:messages], data: { toggle: 'tooltip', placement: 'bottom', delay: '{"show":"500"}'} }

config/routes.rb

@@ -257,6 +257,10 @@
     resources :epic_queues, only: [:index, :destroy]
     resources :epic_queue_records, only: [:index]
 
+    resource :protocol_merge do
+      get :perform_protocol_merge
+    end
+
     resources :fulfillments
 
     resources :line_items do