Merge pull request #2336 from sparc-request/sj-incomplete_form_bug

SJ - Fixing query for incomplete responses

app/controllers/funding/services_controller.rb

@@ -70,7 +70,7 @@ def to_csv(documents)
       documents.each do |d|
         ssr = d.sub_service_requests.where(organization_id: Setting.get_value("funding_org_ids")).first
         p = ssr.protocol
-        csv << [ssr.display_id, p.primary_principal_investigator.last_name_first, p.primary_principal_investigator.try(:professional_org_lookup, 'institution'), p.short_title, d.document_file_name.humanize, d.document_updated_at.strftime('%D %l:%M %p'), PermissibleValue.get_value('status', ssr.status)]
+        csv << [ssr.display_id, p.primary_pi.last_name_first, p.primary_pi.try(:professional_org_lookup, 'institution'), p.short_title, d.document_file_name.humanize, d.document_updated_at.strftime('%D %l:%M %p'), PermissibleValue.get_value('status', ssr.status)]
       end
     end
   end

app/controllers/protocols_controller.rb

@@ -142,7 +142,7 @@ def push_to_epic
     epic_queue = EpicQueue.find params[:eq_id]
     epic_queue.update_attribute(:attempted_push, true)
     # removed 12/23/13 per request by Lane
-    #if current_user != @protocol.primary_principal_investigator then
+    #if current_user != @protocol.primary_pi then
     #  raise ArgumentError, "User is not primary PI"
     #end
 

app/controllers/surveyor/responses_controller.rb

@@ -195,33 +195,38 @@ def load_responses
           existing_responses
         else
           incomplete_responses = get_incomplete_form_responses
-          existing_responses + incomplete_responses
+          Response.includes(:survey).where(id: (incomplete_responses + existing_responses))
         end
       end
     preload_responses
   end
 
   def preload_responses
     preloader = ActiveRecord::Associations::Preloader.new
-    preloader.preload(@responses.select { |r| r.respondable_type == SubServiceRequest.name }, { respondable: { protocol: { primary_pi_role: :identity } } })
-    preloader.preload(@responses.select { |r| r.respondable_type == ServiceRequest.name }, { respondable: { protocol: { primary_pi_role: :identity } } })
+    preloader.preload(@responses.select { |r| r.respondable_type == SubServiceRequest.name }, [:question_responses, :identity, respondable: { protocol: :primary_pi } ])
+    preloader.preload(@responses.select { |r| r.respondable_type == ServiceRequest.name }, [:question_responses, :identity, respondable: { protocol: :primary_pi } ])
   end
 
   def get_incomplete_form_responses
     @filterrific.with_state.reject!(&:blank?) if @filterrific.with_state
     @filterrific.with_survey.reject!(&:blank?) if @filterrific.with_survey
 
+    state_selected  = @filterrific.with_state.try(&:any?)
+    survey_selected = @filterrific.with_survey.try(&:any?)
+
     responses = []
-    Protocol.eager_load(sub_service_requests: [:responses, :service_forms, :organization_forms]).distinct.each do |p|
-      # It should only shows those admin have access to
-      p.sub_service_requests.where(organization_id: @admin_org_ids).each do |ssr|
-        ssr.forms_to_complete.values.flatten.select do |f|
-          # Apply the State, Survey/Form, and Start/End Date filters manually
-          (@filterrific.with_state.try(&:empty?) || (@filterrific.with_state.try(&:any?) && @filterrific.with_state.include?(f.active ? 1 : 0))) &&
-          (@filterrific.with_survey.try(&:empty?) || (@filterrific.with_survey.try(&:any?) && @filterrific.with_survey.include?(f.id)))
-        end.each do |f|
-          responses << Response.new(survey: f,respondable: ssr)
-        end
+    ssrs      = SubServiceRequest.eager_load(:responses, :service_forms, :organization_forms).where(organization_id: @admin_org_ids) # It should only shows those admin have access to
+    preloader = ActiveRecord::Associations::Preloader.new
+    preloader.preload(ssrs, service_forms: :surveyable)
+    preloader.preload(ssrs, organization_forms: :surveyable)
+
+    ssrs.each do |ssr|
+      ssr.forms_to_complete.values.flatten.select do |f|
+        # Apply the State, Survey/Form, and Start/End Date filters manually
+        (!state_selected || (state_selected && @filterrific.with_state.include?(f.active ? 1 : 0))) &&
+        (!survey_selected || (@filterrific.with_survey.try(&:any?) && @filterrific.with_survey.include?(f.id)))
+      end.each do |f|
+        responses << Response.new(survey: f,respondable: ssr)
       end
     end
 

app/helpers/funding/documents_helper.rb

@@ -21,11 +21,11 @@
 module Funding::DocumentsHelper
 
   def display_pi(ssr)
-    ssr.protocol.primary_principal_investigator.last_name_first
+    ssr.protocol.primary_pi.last_name_first
   end
 
   def display_pi_institution(ssr)
-    ssr.protocol.primary_principal_investigator.try(:professional_org_lookup, 'institution')
+    ssr.protocol.primary_pi.try(:professional_org_lookup, 'institution')
   end
 
   def display_actions(ssr)

app/lib/reports/protocols.rb

@@ -60,13 +60,13 @@ def column_attrs
     attrs["IRB of Record"] = "service_request.try(:protocol).try(:human_subjects_info).try(:irb_of_record)"
     attrs["IRB Expiration Date"] = "service_request.try(:protocol).try(:human_subjects_info).try(:irb_expiration_date)"
 
-    attrs["Primary PI Last Name"]   = "service_request.try(:protocol).try(:primary_principal_investigator).try(:last_name)"
-    attrs["Primary PI First Name"]  = "service_request.try(:protocol).try(:primary_principal_investigator).try(:first_name)"
-    attrs["Primary PI Email"]       = "service_request.try(:protocol).try(:primary_principal_investigator).try(:email)"
-    attrs["Primary PI Institution"] = "service_request.try(:protocol).try(:primary_principal_investigator).try(:professional_org_lookup, 'institution')"
-    attrs["Primary PI College"]     = "service_request.try(:protocol).try(:primary_principal_investigator).try(:professional_org_lookup, 'college')"
-    attrs["Primary PI Department"]  = "service_request.try(:protocol).try(:primary_principal_investigator).try(:professional_org_lookup, 'department')"
-    attrs["Primary PI Division"]    = "service_request.try(:protocol).try(:primary_principal_investigator).try(:professional_org_lookup, 'division')"
+    attrs["Primary PI Last Name"]   = "service_request.try(:protocol).try(:primary_pi).try(:last_name)"
+    attrs["Primary PI First Name"]  = "service_request.try(:protocol).try(:primary_pi).try(:first_name)"
+    attrs["Primary PI Email"]       = "service_request.try(:protocol).try(:primary_pi).try(:email)"
+    attrs["Primary PI Institution"] = "service_request.try(:protocol).try(:primary_pi).try(:professional_org_lookup, 'institution')"
+    attrs["Primary PI College"]     = "service_request.try(:protocol).try(:primary_pi).try(:professional_org_lookup, 'college')"
+    attrs["Primary PI Department"]  = "service_request.try(:protocol).try(:primary_pi).try(:professional_org_lookup, 'department')"
+    attrs["Primary PI Division"]    = "service_request.try(:protocol).try(:primary_pi).try(:professional_org_lookup, 'division')"
 
     attrs["Primary Coordinator(s)"] = "service_request.try(:protocol).try(:coordinators).try(:map, &:full_name).try(:join, ', ')"
     attrs["Primary Coordinator Email(s)"] = "service_request.try(:protocol).try(:coordinator_emails)"
@@ -106,7 +106,7 @@ def table
 
   # Other tables to include
   def includes
-    [:organization, { service_request: { protocol: [:project_roles, :study_phases, :human_subjects_info, :investigational_products_info, primary_pi_role: { identity: { professional_organization: { parent: { parent: :parent } } } }] } }, { line_items: :service }]
+    [:organization, { service_request: { protocol: [:project_roles, :study_phases, :human_subjects_info, :investigational_products_info, primary_pi: { professional_organization: { parent: { parent: :parent } } }] } }, { line_items: :service }]
   end
 
   # Conditions

app/lib/reports/service_requests.rb

@@ -79,12 +79,12 @@ def column_attrs
       attrs["Core"] = "org_tree.select{|org| org.type == 'Core'}.first.try(:abbreviation)"
     end
 
-    attrs["Primary PI Last Name"]         = "service_request.try(:protocol).try(:primary_principal_investigator).try(:last_name)"
-    attrs["Primary PI First Name"]        = "service_request.try(:protocol).try(:primary_principal_investigator).try(:first_name)"
-    attrs["Primary PI Institution"]       = "service_request.try(:protocol).try(:primary_principal_investigator).try(:professional_org_lookup, 'institution')"
-    attrs["Primary PI College"]           = "service_request.try(:protocol).try(:primary_principal_investigator).try(:professional_org_lookup, 'college')"
-    attrs["Primary PI Department"]        = "service_request.try(:protocol).try(:primary_principal_investigator).try(:professional_org_lookup, 'department')"
-    attrs["Primary PI Division"]          = "service_request.try(:protocol).try(:primary_principal_investigator).try(:professional_org_lookup, 'division')"
+    attrs["Primary PI Last Name"]         = "service_request.try(:protocol).try(:primary_pi).try(:last_name)"
+    attrs["Primary PI First Name"]        = "service_request.try(:protocol).try(:primary_pi).try(:first_name)"
+    attrs["Primary PI Institution"]       = "service_request.try(:protocol).try(:primary_pi).try(:professional_org_lookup, 'institution')"
+    attrs["Primary PI College"]           = "service_request.try(:protocol).try(:primary_pi).try(:professional_org_lookup, 'college')"
+    attrs["Primary PI Department"]        = "service_request.try(:protocol).try(:primary_pi).try(:professional_org_lookup, 'department')"
+    attrs["Primary PI Division"]          = "service_request.try(:protocol).try(:primary_pi).try(:professional_org_lookup, 'division')"
     attrs["Primary Coordinator(s)"]       = "service_request.try(:protocol).try(:coordinators).try(:map, &:full_name).try(:join, ', ')"
     attrs["Primary Coordinator Email(s)"] = "service_request.try(:protocol).try(:coordinator_emails)"
 
@@ -129,7 +129,7 @@ def table
 
   # Other tables to include
   def includes
-    return :organization, :service_request => {:line_items => :service}
+    return :organization, service_request: { protocol: { primary_pi: { professional_organization: { parent: { parent: :parent } } } }, line_items: :service }
   end
 
   # Conditions

app/mailers/notifier.rb

@@ -191,7 +191,7 @@ def sub_service_request_deleted identity, sub_service_request, user_current
 
   def notify_for_epic_user_approval protocol
     @protocol = protocol
-    @primary_pi = @protocol.primary_principal_investigator
+    @primary_pi = @protocol.primary_pi
 
     subject = "#{@protocol.id} - Epic Rights Approval"
 
@@ -200,7 +200,7 @@ def notify_for_epic_user_approval protocol
 
   def notify_primary_pi_for_epic_user_final_review protocol
     @protocol = protocol
-    @primary_pi = @protocol.primary_principal_investigator
+    @primary_pi = @protocol.primary_pi
 
     email_to = @primary_pi.email
     subject = "#{@protocol.id} - Epic Rights User Approval"
@@ -210,7 +210,7 @@ def notify_primary_pi_for_epic_user_final_review protocol
 
   def notify_primary_pi_for_epic_user_removal(protocol, project_roles)
     @protocol       = protocol
-    @primary_pi     = @protocol.primary_principal_investigator
+    @primary_pi     = @protocol.primary_pi
     @project_roles  = project_roles
 
     subject = "#{@protocol.id} - Epic User Removal"

app/models/protocol.rb

@@ -424,10 +424,6 @@ def email_about_change_in_authorized_user(modified_roles, action)
     end
   end
 
-  def primary_principal_investigator
-    primary_pi_role.try(:identity)
-  end
-
   def billing_business_manager_email
     billing_business_manager_static_email.blank? ?  billing_managers.map(&:email).try(:join, ', ') : billing_business_manager_static_email
   end

app/models/sub_service_request.rb

@@ -410,7 +410,7 @@ def all_forms_completed?
   ##########################
   # Distributes all available surveys to primary pi and ssr requester
   def distribute_surveys
-    primary_pi = protocol.primary_principal_investigator
+    primary_pi = protocol.primary_pi
     # do nothing if we don't have any available surveys
     unless available_surveys.empty?
       SurveyNotification.service_survey(available_surveys, primary_pi, self).deliver

app/views/dashboard/protocols/show.xlsx.axlsx

@@ -156,7 +156,7 @@ end
     sheet.add_row ["SPARC #{@protocol.class.to_s} ID:",@protocol.id], style: [bold_default, default]
     sheet.add_row ["RMID:", @protocol.research_master_id], style: [bold_default, default]
     sheet.add_row ["Short Title:",@protocol.short_title], style: [bold_default, default]
-    sheet.add_row ["Primary PI Name:", @protocol.primary_principal_investigator.full_name], style: [bold_default, default]
+    sheet.add_row ["Primary PI Name:", @protocol.primary_pi.full_name], style: [bold_default, default]
     sheet.add_row ["Indirect Cost Rate:", "=Summary!B10"], style: [bold_default, percent]
 
     indirect_cost_ref = sheet.rows.last.cells.last.r
@@ -364,7 +364,7 @@ wb.insert_worksheet(0, name: "Summary") do |sheet|
   sheet.add_row ["Short Title:", @protocol.short_title], :style => [bold_default, default]
   sheet.add_row ["Protocol Title:", @protocol.title], :style => [bold_default, default]
   sheet.add_row ["Sponsor:", @protocol.sponsor_name], :style => [bold_default, default]
-  sheet.add_row ["Primary PI Name:", @protocol.primary_principal_investigator.full_name], :style => [bold_default, default]
+  sheet.add_row ["Primary PI Name:", @protocol.primary_pi.full_name], :style => [bold_default, default]
   sheet.add_row ["Business Manager:", @protocol.billing_managers.map(&:full_name).try(:join, ', ')], :style => [bold_default, default]
   sheet.add_row ["Funding Source:", @protocol.display_funding_source_value], :style => [bold_default, default]
   sheet.add_row ["Indirect Cost Rate:", @protocol.indirect_cost_rate.try(:/, 100.0) || 0.0], style: [bold_default, percent]

app/views/survey_notification/_info_table.html.haml

@@ -48,7 +48,7 @@
 
     %tr{:style => 'border: 1px solid black;'}
       %th{:style => 'border: 1px solid black; width:200px; text-align:left;'}= t(:surveyor)[:responses][:table][:headers][:primary_pi]
-      %td{:style => 'border: 1px solid black;'}= @protocol.primary_principal_investigator.full_name
+      %td{:style => 'border: 1px solid black;'}= @protocol.primary_pi.full_name
 
     %tr{:style => 'border: 1px solid black;'}
       %th{:style => 'border: 1px solid black; width:200px; text-align:left;'}= t(:surveyor)[:responses][:table][:headers][:request_owner]

app/views/surveyor/responses/index.json.jbuilder

@@ -9,7 +9,7 @@ json.(@responses) do |response|
 
   json.srid             srid == 'N/A' ? 'N/A' : link_to(srid, dashboard_protocol_path(srid.to_s.split('-').first), target: :_blank)
   json.short_title      response.try(:respondable).try(:protocol).try(:short_title) || 'N/A'
-  json.primary_pi       response.try(:respondable).try(:protocol).try(:primary_principal_investigator).try(:full_name) || 'N/A'
+  json.primary_pi       response.try(:respondable).try(:protocol).try(:primary_pi).try(:full_name) || 'N/A'
   json.title            response.survey.full_title
   json.by               response.identity.try(:full_name) || 'N/A'
   json.complete         complete_display(response)

config/environments/development.rb

@@ -33,21 +33,27 @@
   config.consider_all_requests_local       = true
   config.action_controller.perform_caching = false
 
-  # Don't care if the mailer can't send
-  config.action_mailer.raise_delivery_errors = false
-
   # Print deprecation notices to the Rails logger
   config.active_support.deprecation = :log
 
   # Expands the lines which load the assets
   config.assets.compile = true
   config.assets.debug = true
 
+  # Don't care if the mailer can't send
+  config.action_mailer.raise_delivery_errors = false
   config.action_mailer.default_url_options = { host: ENV.fetch('ROOT_URL') }
   config.action_mailer.delivery_method = :letter_opener
   config.action_mailer.perform_deliveries = true
 
-  config.log_level = :debug
+  # Print deprecation notices to the Rails logger.
+  config.active_support.deprecation = :log
+
+  # Raise an error on page load if there are pending migrations.
+  config.active_record.migration_error = :page_load
+
+  # Highlight code that triggered database queries in logs.
+  config.active_record.verbose_query_logs = true
 
   # Stuff to do on each request
   config.to_prepare do

db/schema.rb

@@ -1,23 +1,3 @@
-# Copyright © 2011-2020 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.~
-
 # This file is auto-generated from the current state of the database. Instead
 # of editing this file, please use the migrations feature of Active Record to
 # incrementally modify your database, and then regenerate this schema definition.
@@ -983,6 +963,7 @@
     t.boolean "access_empty_protocols", default: false
     t.boolean "billing_manager"
     t.boolean "allow_credit"
+    t.boolean "hold_emails", default: true
     t.index ["identity_id"], name: "index_super_users_on_identity_id"
     t.index ["organization_id"], name: "index_super_users_on_organization_id"
   end

lib/tasks/admin_turnaround_times_report.rake

@@ -59,7 +59,7 @@ namespace :data do
       if ssr.service_request.protocol && (ssr.organization_id == core.id) && (ssr.created_at.to_date > 2012-03-01)
         past_statuses = ssr.past_status_lookup
         dates = extract_status_dates(ssr)
-        pi = ssr.service_request.protocol.try(:primary_principal_investigator).try(:full_name)
+        pi = ssr.service_request.protocol.try(:primary_pi).try(:full_name)
         owner = ssr.owner_id ? Identity.find(ssr.owner_id).full_name : ""
 
         row = [ssr.service_request.protocol.id, full_ssr_id(ssr), ssr.service_request.protocol.short_title, pi, provider.abbreviation, program.abbreviation, core.abbreviation, owner, dates[0], dates[1]]

lib/tasks/billing_only_report.rake

@@ -53,7 +53,7 @@ namespace :reports do
                 research_rate = procedure.cost
                 cost = research_rate * r_qty
 
-                csv << [protocol.id, protocol.try(:primary_principal_investigator).try(:full_name), subject.name, subject.label, visit_name, visit_date, procedure.display_service_name, r_qty, research_rate, cost]
+                csv << [protocol.id, protocol.try(:primary_pi).try(:full_name), subject.name, subject.label, visit_name, visit_date, procedure.display_service_name, r_qty, research_rate, cost]
               end
             end
           end

lib/tasks/jit_report.rake

@@ -29,7 +29,7 @@ task :jit_report => :environment do
       first_submit = ssr.past_statuses.where(:status => 'submitted').first.date
       protocol = ssr.protocol
       human_subjects_info = protocol.human_subjects_info
-      csv << [first_submit.strftime('%m/%d/%y'), ssr.display_id, ssr.organization.name, protocol.primary_principal_investigator.display_name,
+      csv << [first_submit.strftime('%m/%d/%y'), ssr.display_id, ssr.organization.name, protocol.primary_pi.display_name,
         protocol.title, human_subjects_info.irb_of_record, human_subjects_info.irb_and_pro_numbers, (human_subjects_info.irb_approval_date.strftime('%m/%d/%y') rescue nil)]
     end
   end

lib/tasks/one_time_fee_report.rake

@@ -77,7 +77,7 @@ namespace :data do
         status = PermissibleValue.get_value('status', ssr.status)
         protocol_id = ssr.protocol_id
         short_title = ssr.protocol.short_title
-        pi = ssr.protocol.try(:primary_principal_investigator).try(:full_name)
+        pi = ssr.protocol.try(:primary_pi).try(:full_name)
         owner = ssr.owner_id ? Identity.find(ssr.owner_id).full_name : ""
 
         ssr.line_items.each do |li|