1. remove cruft. 2. js string fix. 3. add kaminari to gemfile -- this…

… will replace will_paginate

JS fix, cleanup.

Clean up vestiges of 'protect_simple_description', which was removed. Add tests and solidify models (add associations, etc.).

abstract 'Internet ID' to configurable string. Cleanup, readme.

Don't introduce Kaminari -- will_paginate is in maintenance mode, but elastic-search rails still uses it internally so stick with it for now. Change a couple uses of 'paginate()' on ES-backed models to 'page()' from the elasticsearch-rails interface.

Dockerfile

@@ -8,7 +8,7 @@ RUN apt-get update -qq && apt-get install -y \
 RUN mkdir /app
 WORKDIR /app
 COPY Gemfile /app/Gemfile
-#COPY Gemfile.lock /app/Gemfile.lock
+COPY Gemfile.lock /app/Gemfile.lock
 RUN bundle install
 COPY . /app
 

Gemfile.lock

@@ -218,7 +218,7 @@ GEM
     multi_xml (0.6.0)
     multipart-post (2.3.0)
     mutex_m (0.1.2)
-    net-imap (0.4.2)
+    net-imap (0.4.3)
       date
       net-protocol
     net-ldap (0.18.0)
@@ -282,7 +282,7 @@ GEM
       rake (>= 12.2)
       thor (~> 1.0, >= 1.2.2)
       zeitwerk (~> 2.6)
-    rake (13.0.6)
+    rake (13.1.0)
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)

README.md

@@ -10,6 +10,10 @@ Contact the StudyFinder team at studyfinder@umn.edu if you:
 - Have any questions about StudyFinder, or
 - Want to learn more about updates or enhancements of the tool.
 
+## Upgrade notes for 2.1
+
+The main page carousel/video feature was an accessibility and usability issue, and has been replaced with a three-wide panel of "featured studies". These can be configured in the admin panel, where the carousel configuration formerly was.
+
 ## Development
 
 The easiest way to get started with a development environment is to use `docker-compose`:

app/assets/javascripts/views/modals.js

@@ -89,7 +89,7 @@ $('#contact-study-team-modal').on('show.bs.modal', function (event) {
   var trialId = button.data('trial-id');
   var modal = $(this);
   // pass some trial attributes from the search results into the modal
-  modal.find('.study-email').text(studyEmail).attr('href', 'mailto:' + studyEmail + "?bcc=sfinder+study-team-emails@umn.edu");
+  modal.find('.study-email').text(studyEmail).attr('href', 'mailto:' + studyEmail + "?bcc=" + STUDY_CONTACT_BCC);
   modal.find('#contact-study-team-modal-submit').data('trial_id', trialId).data('button', button);
 
   if(window.studyTeamWidget !== undefined) {

app/controllers/admin/trials_controller.rb

@@ -76,12 +76,12 @@ def recent_as
 
   def index
     if params[:q].blank?
-      @trials = Trial.includes(:trial_interventions, :conditions).paginate(page: params[:page]).where(visible: true)
+      @trials = Trial.includes(:trial_interventions, :conditions).page(page_param).where(visible: true)
       if SystemInfo.trial_approval
         @trials = @trials.where(approved: true)
       end
     else
-      @trials = Trial.includes(:trial_interventions, :conditions).match_all_admin({ q: params[:q].downcase }).page(params[:page]).records
+      @trials = Trial.includes(:trial_interventions, :conditions).match_all_admin({ q: params[:q].downcase }).page(page_param).records
     end
 
     add_breadcrumb 'Trials Administration'
@@ -114,9 +114,9 @@ def update
 
   def all_under_review
     if params[:q].blank?
-      @trials = Trial.includes(:trial_locations).paginate(page: params[:page]).where(approved: false).where(visible: true).order(created_at: :desc)
+      @trials = Trial.includes(:trial_locations).page(page_param).where(approved: false).where(visible: true).order(created_at: :desc)
     else
-      @trials = Trial.includes(:trial_locations).match_all_under_review_admin({ q: params[:q].downcase }).page(params[:page]).records
+      @trials = Trial.includes(:trial_locations).match_all_under_review_admin({ q: params[:q].downcase }).page(page_param).records
     end
 
     add_breadcrumb 'Trials Administration', :admin_trials_path

app/controllers/application_controller.rb

@@ -40,6 +40,10 @@ def authorize_researcher
   end
   helper_method :authorize_researcher
 
+  def page_param
+    params[:page].to_i > 0 ? params[:page].to_i : 1
+  end
+
   private
     def system
       @system_info = SystemInfo.current

app/helpers/application_helper.rb

@@ -40,7 +40,10 @@ def highlight(record, key)
     else
       record['_source'][key]
     end
-
   end
 
+  def username_string
+    ENV['username_string']
+  end
+
 end

app/lib/modules/ldap.rb

@@ -5,14 +5,14 @@ class Ldap
 
     ###################
     # 1. Authenicate with our departmental LDAP account
-    # 2. If successful, look up the user by x500 in LDAP
+    # 2. If successful, look up the user by username in LDAP
     # 3. If found, authenticate with their LDAP username string and the password they entered into our login form
     # 4. If successful, check if the user exists in Study Finder
     # 5. If not found, create them
     # 6. If found, log them into the Study Finder
     ###################
 
-    def authenticate(x500, password)
+    def authenticate(username, password)
       # initialize our return hash with some defaults
       _return = Hash.new
       _return[:ldap_user] = nil
@@ -35,7 +35,7 @@ def authenticate(x500, password)
       if departmental_ldap.bind
 
         # now search for the user logging in
-        filter = Net::LDAP::Filter.eq( "uid", x500 ) # is this correct?
+        filter = Net::LDAP::Filter.eq( "uid", username ) # is this correct?
         user_search = departmental_ldap.search( base: ENV['base'], filter: filter ).first
 
         # departmental_ldap.search( :base => ENV['base'], :filter => filter ) do |entry|

app/models/subgroup.rb

@@ -1,6 +1,9 @@
 class Subgroup < ApplicationRecord
   self.table_name = 'study_finder_subgroups'
+
   belongs_to :group, optional: true
+  has_many :trial_subgroups
+  has_many :trials, through: :trial_subgroups
 
   validates_presence_of :name
 

app/models/system_info.rb

@@ -38,4 +38,12 @@ def self.ga_version
     self.first.try(:google_analytics_version)
   end
 
+  def self.default_email
+    self.first.try(:default_email)
+  end
+
+  def self.study_contact_bcc
+    self.first.try(:study_contact_bcc)
+  end
+
 end

app/models/trial.rb

@@ -564,11 +564,10 @@ def self.filters(search)
       end
 
       if search.has_key?('category')
-        ret << { term: { category_ids: search[:category] } }
+        ret << { term: { category_ids: search['category'] } }
       end
-
       if search.has_key?('subcat')
-        ret << { term: { subcategory_ids: search[:subcat] } }
+        ret << { term: { subcategory_ids: search['subcat'] } }
       end
 
       if (search.has_key?('gender')) and (search[:gender] == 'Male' or search[:gender] == 'Female')
@@ -603,11 +602,11 @@ def self.range_filters(search)
     end
 
     if search.has_key?('adults')
-      ret << { range: { max_age: { gte: 19 } } }
+      ret << { range: { max_age: { gte: 18 } } }
     end
 
     if search.has_key?('seniors')
-      ret << { range: { max_age: { gte: 66 } } }
+      ret << { range: { max_age: { gte: 65 } } }
     end
 
     ret

app/views/admin/approvals/index.html.erb

@@ -11,7 +11,7 @@
 
   <table class="table table-bordered table-trials">
     <tr>
-      <th>Internet ID</th>
+      <th><%= username_string %></th>
       <th>Trial System ID</th>
       <th>Trial Brief Title</th>
       <th>Date</th>

app/views/admin/system/edit.html.erb

@@ -33,7 +33,7 @@
           <i>An address to be BCCd when a user sends a message to a study team contact address. This may be used by staff to collect and monitor contact requests.</i>
         </small>
 
-        <!-- <%= f.input :secret_key, hint: 'Secret key will be required by researchers to add or update trials.' %> -->
+        <%= f.input :secret_key, hint: 'Secret key will be required by researchers to add or update trials.' %>
         <label>Display "Healthy Volunteers" Filter</label>
         <small>
           <i>Turning on will enable the Healthy Volunteer filter for studies.</i>
@@ -179,10 +179,12 @@
     if(window.localStorage.getItem('utm_source')) {
       campaignElement.value = window.localStorage.getItem('utm_source');
     }
-    var formElement = document.getElementById('edit_study_finder_system_info_1');
+    var formElement = document.getElementById('edit_system_info_1');
     formElement.addEventListener('submit', function (evt) {
       evt.preventDefault();
       window.localStorage.setItem('utm_source', campaignElement.value);
       this.submit();
     }, false);
+  });
+
 </script>

app/views/admin/users/index.html.erb

@@ -3,7 +3,7 @@
     <h3 class="float-left">Users</h3>
     <div class="float-right header-button"><%= link_to 'Add User', new_admin_user_path, class: 'btn btn-school'%></div>  
   </div>
-  <p class="description">This section is where the administrator can add/edit other admin users within StudyFinder.  To add a new user click the "Add User" button above.  You will need their unique email and internet_id.  Once a user has been added, they will be able to access the entire admininstration area, so only grant these privileges to administrative staff.</p>
+  <p class="description">This section is where the administrator can add/edit other admin users within StudyFinder.  To add a new user click the "Add User" button above.  You will need their unique email and <%= username_string %>.  Once a user has been added, they will be able to access the entire admininstration area, so only grant these privileges to administrative staff.</p>
 
   <table class="table table-bordered table-trials">
     <tr>

app/views/layouts/application.html.erb

@@ -15,6 +15,8 @@
 </head>
 <body>
   <script>
+    const DEFAULT_EMAIL = '<%= SystemInfo.default_email %>';
+    const STUDY_CONTACT_BCC = '<%= SystemInfo.study_contact_bcc %>';
     const GA_VERSION = <%= SystemInfo.ga_version %>;
   </script>
   <div class="container main-content">

app/views/sessions/new.html.erb

@@ -5,7 +5,7 @@
 
     <%= simple_form_for @user, url: sessions_path do |f| %>
       <div class="form-inputs">
-        <%= f.input :internet_id, required: false, autofocus: true, label: 'Internet ID' %>
+        <%= f.input :internet_id, required: false, autofocus: true, label: username_string %>
         <%= f.input :password, required: false %>
       </div>
 

app/views/shared/_flash.html.erb

@@ -1,7 +1,7 @@
 <% flash.each do |type, message| %>
   <% unless message.empty? %>
   <div class="alert <%= bootstrap_class_for(type) %> fade show">
-    <i class="fa <%= bootstrap_icon_for(type) %>"></i>
+    <i class="fa-solid <%= bootstrap_icon_for(type) %>"></i>
     <% if message.kind_of? Array %>
       <ul>
         <% message.each do |m| %>

app/views/studies/index.html.erb

@@ -51,7 +51,7 @@
   <hr/>
 
   <% if @trials.empty? %>
-    <div class="alert"><i class="fa fa-warning"></i> There were no trials that matched your search for <strong><%= @search_query %></strong></div>
+    <div class="alert"><i class="fa-solid fa-warning"></i> There were no trials that matched your search for <strong><%= @search_query %></strong></div>
   <% end %>
 
   <% @trials.each_with_index do |t, i| %>

app/views/themed/_home_lower_right.html.erb

@@ -1,15 +1,12 @@
 <h2 class="mt-3">Join a national registry!</h2>
-  <div class="row5">
-    <div class="col-md-12">
-      <%= link_to "https://researchmatch.org?rm=<%= @system_info.research_match_campaign" do %>
-      <%= image_tag "rsm-large.jpg", class: 'img-fluid', style: 'width: 50%;' %>
-      <% end %>
-    </div>
-    <div >
-
-<!--           <a href="https://researchmatch.org?rm=<%= @system_info.research_match_campaign %>" target:"_blank">
-        <h3 class="hyperlink-header">ResearchMatch</h3>
-      </a> -->
-      <p>ResearchMatch.org connects volunteers with research studies across the country. Volunteers of any age, race, ethnicity, or health status are invited to join. Log on, register, and receive emails when studies might be a good fit for you.</p>
-    </div>
-  </div>
+<div class="row5">
+  <div class="col-md-12">
+    <%= link_to "https://researchmatch.org?rm=<%= @system_info.research_match_campaign" do %>
+    <%= image_tag "rsm-large.jpg", class: 'img-fluid', style: 'width: 50%;' %>
+    <% end %>
+  </div>
+  <div >
+
+    <p>ResearchMatch.org connects volunteers with research studies across the country. Volunteers of any age, race, ethnicity, or health status are invited to join. Log on, register, and receive emails when studies might be a good fit for you.</p>
+  </div>
+</div>

config/application.example.yml

@@ -7,4 +7,5 @@ departmental_pw: 'PASSWORD'
 theme: 'umn'
 ELASTICSEARCH_URL: 'elastic.umn.edu'
 wkhtmltopdf_binary_path: 'PATH'
-DEFAULT_URL_HOST: 'yourstudyfinder.example.com' # Used in email links/URLs
+DEFAULT_URL_HOST: 'yourstudyfinder.example.com' # Used in email links/URLs
+username_string: 'Internet ID' # What a login 'username' is called at your institution. Appears in various templates.

config/application.rb

@@ -8,15 +8,6 @@
 
 module StudyFinder
   class Application < Rails::Application
-    # Initialize configuration defaults for originally generated Rails version.
-    #config.load_defaults 5.0
-
-    # Configuration for the application, engines, and railties goes here.
-    #
-    # These settings can be overridden in specific environments using the files
-    # in config/environments, which are processed later.
-    #
-    # config.time_zone = "Central Time (US & Canada)"
-    # config.eager_load_paths << Rails.root.join("extras")
+    config.load_defaults 7.0
   end
 end

config/deploy.rb

@@ -2,8 +2,8 @@
 lock "3.17.1"
 
 set :application, "study_finder"
-set :repo_url, "https://github.umn.edu/hst/study_finder_umn.git"
-set :deploy_to, "/var/www/webapps/study_finder"
+set :repo_url, "https://your-repo.com/study_finder_umn.git"
+set :deploy_to, "/your/deploy/dir/study_finder"
 set :default_env, { path: "/opt/ruby31/bin:$PATH" }
 set :passenger_restart_with_touch, true
 set :branch, ENV.fetch("GIT_BRANCH", "master").sub(/^origin\//, "")

config/deploy/production.rb

@@ -1 +1 @@
-server "walleye0.ahc.umn.edu", user: "webcluster2", roles: %w{app db web}
+server "prod-server", user: "deploy-user", roles: %w{app db web}

config/deploy/staging.rb

@@ -1 +1 @@
-server "goldfish0.ahc.umn.edu", user: "webcluster2", roles: %w{app db web}
+server "staging-server", user: "deploy-user", roles: %w{app db web}

config/initializers/assets.rb

@@ -1,7 +1,7 @@
 # Be sure to restart your server when you modify this file.
 
 # Version of your assets, change this if you want to expire all your assets.
-Rails.application.config.assets.version = '1.7'
+Rails.application.config.assets.version = '2.1'
 
 # Add additional assets to the asset load path.
 # Rails.application.config.assets.paths << Emoji.images_path

db/schema.rb

@@ -165,7 +165,6 @@
     t.boolean "trial_approval", default: false, null: false
     t.boolean "alert_on_empty_system_id", default: false, null: false
     t.string "study_contact_bcc"
-    t.boolean "protect_simple_description", default: false, null: false
     t.boolean "healthy_volunteers_filter", default: true, null: false
     t.boolean "gender_filter", default: true, null: false
     t.integer "google_analytics_version"

db/seeds.rb

@@ -17,7 +17,7 @@
     <p>To help potential participants better navigate and connect with University research opportunities, we encourage you to periodically review your studies and update the description and contact information, as appropriate.</p><p>Please also be aware that people may email you via StudyFinder to inquire about a study. We urge you to work directly with these potential participants, and to contact the StudyFinder team with any questions.</p><h3>How to update your study</h3><p>You can update select study information on this website or directly in the source data (<a href=\"http://clinicaltrials.gov\">ClinicalTrials.gov</a> and/or OnCore).</p><p>To update your study on StudyFinder: </p>
     <ul>
       <li>Click on the maroon  \"Look up/Edit Study Information\" button toward the bottom of this page.</li>
-      <li>Log in using your x500.</li>
+      <li>Log in using your Internet ID.</li>
       <li>Look up your study information by entering the System ID, which is either Study NCT ID from <a href=\"http://clinicaltrials.gov\">ClinicalTrials.gov</a>, or Protocol ID from OnCore.</li>
       <li>Ensure the primary contact is a suitable person for potential participants to reach out to via email.</li>
       <li>Save your changes by entering the secret key, and clicking the \"Update Trial\" button at the bottom of the page.</li>
@@ -102,7 +102,7 @@
 # Trials
 # ============================================
 
-# Rake::Task['studyfinder:ctgov:load'].invoke
+Rake::Task['studyfinder:ctgov:load'].invoke
 
 # ============================================
 # Trial attribute settings