Merge branch 'release-1.0.0'

.tool-versions

@@ -0,0 +1,2 @@
+ruby 2.3.1
+bundler 1.17.3

CHANGELOG.md

@@ -0,0 +1,7 @@
+# 1.0.0
+
+Site has been released for a long time, but starting at 1.0.0 for the purposes of adding a change log
+
+- use date_discovery for date filtering instead of created_at
+- rake task to fix non-breaking spaces and  character in database
+- process strings during import to prevent the above issue

Gemfile

@@ -35,6 +35,7 @@ gem 'slack-notifier', '~> 1.5.1'
 # Authentication and Authorization
 gem 'cancancan', '~> 1.10'
 gem 'devise', '~> 4.2.0'
+gem 'bcrypt', '~> 3.1.17' # Required on Ubuntu 20+
 
 # Background jobs
 gem 'redis', '~> 3.3.1'
@@ -76,3 +77,5 @@ end
 gem 'web-console', '~> 2.0', group: :development
 gem 'byebug', group: [:development, :test]
 gem 'annotate', '~> 2.7.1'
+
+gem "activerecord-session_store", "~> 1.1"

Gemfile.lock

@@ -37,6 +37,12 @@ GEM
       activemodel (= 4.2.6)
       activesupport (= 4.2.6)
       arel (~> 6.0)
+    activerecord-session_store (1.1.3)
+      actionpack (>= 4.0)
+      activerecord (>= 4.0)
+      multi_json (~> 1.11, >= 1.11.2)
+      rack (>= 1.5.2, < 3)
+      railties (>= 4.0)
     activesupport (4.2.6)
       i18n (~> 0.7)
       json (~> 1.7, >= 1.7.7)
@@ -53,7 +59,7 @@ GEM
       rack
       thread_safe
     arel (6.0.3)
-    bcrypt (3.1.11)
+    bcrypt (3.1.18)
     binding_of_caller (0.7.2)
       debug_inspector (>= 0.0.1)
     browserify-rails (3.1.0)
@@ -150,6 +156,7 @@ GEM
     minitest (5.9.0)
     mocha (1.1.0)
       metaclass (~> 0.0.1)
+    multi_json (1.15.0)
     net-scp (1.2.1)
       net-ssh (>= 2.6.5)
     net-ssh (3.2.0)
@@ -255,8 +262,10 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
+  activerecord-session_store (~> 1.1)
   annotate (~> 2.7.1)
   appsignal (~> 1.1.9)
+  bcrypt (~> 3.1.17)
   browserify-rails (~> 3.1.0)
   byebug
   cancancan (~> 1.10)
@@ -297,4 +306,4 @@ DEPENDENCIES
   yard (~> 0.8.7.6)
 
 BUNDLED WITH
-   1.12.5
+   1.17.3

app/controllers/bulk_uploads_controller.rb

@@ -1,50 +1,87 @@
+# frozen_string_literal: true
+
 class BulkUploadsController < ApplicationController
   before_action :authenticate_user!
   load_and_authorize_resource
 
-  def show
-  end
+  def show; end
 
   def index
     @bulk_uploads = BulkUpload.includes(:reports).order(:created_at).page(params[:page])
   end
 
-  def new
-  end
+  def new; end
 
   def edit
-    @bulk_upload = BulkUpload.find(params[:id]) or raise_404
+    (@bulk_upload = BulkUpload.find(params[:id])) || raise_404
   end
 
   def update
-    redirect_to(:back) and return if params[:file].nil?
+    redirect_to(:back) && return if params[:file].nil?
 
     result = CsvImporter.import(params[:file].path)
-    @bulk_upload = BulkUpload.find(params[:id]) or raise_404
+    (@bulk_upload = BulkUpload.find(params[:id])) || raise_404
     @bulk_upload.update(result)
 
     if result[:successful]
-      redirect_to @bulk_upload, flash: {success: t("bulk_uploads.upload_successful")}
+      redirect_to @bulk_upload, flash: { success: t('bulk_uploads.upload_successful') }
     else
-      redirect_to @bulk_upload, flash: {error: t("bulk_uploads.upload_error")}
+      redirect_to @bulk_upload, flash: { error: t('bulk_uploads.upload_error') }
     end
   end
 
   def create
-    redirect_to(:back) and return if params[:file].nil?
+    redirect_to(:back) && return unless params[:files].present?
 
-    result = CsvImporter.import(params[:file].path)
-    if result[:successful]
-      redirect_to BulkUpload.create(result), flash: {success: t("bulk_uploads.upload_successful")}
-    else
-      redirect_to BulkUpload.create(result), flash: {error: t("bulk_uploads.upload_error")}
+    results = [] # store of all this BulkUpload's reports (successful and not)
+    blocking_files = [] # store of this BulkUpload's invalid files ( { filename:, error_messages: } )
+
+    ActiveRecord::Base.transaction do
+      params[:files].each do |file|
+        import = CsvImporter.import file.path
+        results << import
+
+        next if import[:successful]
+
+        blocking_files.push({
+                              filename: file.original_filename,
+                              error_messages: import[:happy_accidents].map { |hash| hash[:message] }.uniq
+                            })
+      end
+
+      raise ActiveRecord::Rollback unless blocking_files.empty?
+
+      # Only reached if no files are 'blocking'
+      results.each { |_result| BulkUpload.create results }
+      return redirect_to bulk_uploads_path, flash: { success: t('bulk_uploads.upload_successful') }
     end
+
+    error_message = generate_bulk_upload_error_message(blocking_files)
+
+    redirect_to bulk_uploads_path, flash: { error: error_message }
   end
 
   def destroy
-    bulk_upload = BulkUpload.find(params[:id]) or raise_404
+    (bulk_upload = BulkUpload.find(params[:id])) || raise_404
     bulk_upload.destroy
 
-    redirect_to action: :index, notice: "That bulk upload has been successfully deleted from the system. Thank you!"
+    redirect_to action: :index, notice: 'That bulk upload has been successfully deleted from the system. Thank you!'
+  end
+
+  private
+
+  def generate_bulk_upload_error_message(blocking_files)
+    error_message = t('bulk_uploads.upload_error')
+    tab = "&nbsp;" * 4
+
+
+    blocking_files.each do |file|
+      error_message += [
+        file[:filename],
+        file[:error_messages].map { |message| tab + message }.flatten
+      ].join("<br>")
+    end
+
+    error_message
   end
 end

app/controllers/reports_controller.rb

@@ -91,6 +91,12 @@ def lock
 
   def search
     @countries = CountryUtilities.all_countries
+
+    # Find date of earliest record, to limit the date range filters.
+    report_dates = Report.pluck("data -> 'answers' -> 'date_of_discovery' -> 'selected'").compact
+    report_years = report_dates.map { |report_date| report_date.split('/').last }
+
+    @earliest_report_year = report_years.present? ? report_years.uniq.min.to_i : 1950
   end
 
   def export
@@ -117,6 +123,12 @@ def validate
   def thank_you
   end
 
+  def destroy
+    Report.find(params['id']).destroy
+    flash[:success] = "The report with ID #{params['id']} has been successfully deleted from the system."
+    redirect_to action: :index
+  end
+
   private
     def report_params
       {data: params.require(:report)[:data]}

app/helpers/application_helper.rb

@@ -32,4 +32,16 @@ def current_controller?(url)
   def display_or_default(data, default="N/A")
     data.present? ? data : default
   end
+
+  # Bulk Upload index errors should persist so users can see the errors in their bulk upload
+  def flash_should_persist?
+    return false unless controller_name == 'bulk_uploads' && action_name == 'index'
+    return false unless flash.present?
+
+    begin
+      flash.any? { |key, val| key == 'error' }
+    rescue
+      false
+    end
+  end
 end

app/models/bulk_upload.rb

@@ -10,5 +10,5 @@
 #
 
 class BulkUpload < ActiveRecord::Base
-  has_many :reports
+  has_many :reports, dependent: :destroy
 end

app/models/report.rb

@@ -26,6 +26,8 @@ class Report < ActiveRecord::Base
   belongs_to :bulk_upload
   has_many :validations, dependent: :destroy
   has_many :images, dependent: :destroy
+
+  validates :user_id, presence: true
 
   def user_name
     "#{user&.first_name} #{user&.last_name}".strip
@@ -43,8 +45,9 @@ def can_be_validated?
     state&.downcase == "submitted"
   end
 
+  # Rescue required because of invalid dates in database.
   CONVERSIONS = {
-    "date_of_discovery" => lambda { |value| Date.strptime(value, "%d/%m/%Y") }
+    "date_of_discovery" => lambda { |value| Date.strptime(value, "%d/%m/%Y") rescue nil }
   }
 
   def answer_to question, page=nil, tab_index=0
@@ -88,7 +91,7 @@ def self.search(params)
       query = self
       query = SearchBuilder.by_report_id(query, params)
       query = SearchBuilder.by_country_of_discovery(query, params)
-      query = SearchBuilder.by_date_created_range(query, params)
+      query = SearchBuilder.by_date_of_discovery_range(query, params)
       query = SearchBuilder.by_agencies(query, params)
       query = SearchBuilder.by_genus(query, params)
       query = SearchBuilder.by_users(query, params)

app/views/bulk_uploads/new.html.erb

@@ -14,7 +14,7 @@
 
 <%= form_tag bulk_uploads_path, multipart: true do %>
   <fieldset class="form__group">
-    <%= file_field_tag "file", required: true %>
+    <%= file_field_tag "files[]", multiple: true, required: true %>
   </fieldset>
 
   <%= submit_tag "Upload file", class: "button button-primary" %>

app/views/layouts/_flash_notification.html.erb

@@ -1,6 +1,8 @@
 <% flash.each do |key, value| %>
-  <div class="alert alert-<%= key %>">
+  <div class="alert alert-<%= key %> <%= 'js-stay' if flash_should_persist? %>"
+  <% unless flash_should_persist? %>
     <p class="alert__close"><i class="fa fa-close"></i> Close</p>
+  <% end %>
     <h4 class="alert__title">
       <i class="fa fa-<%= alert_key_to_fa_icon(key) %>"></i> <%= key.titleize %>!
     </h4>

app/views/reports/_table.html.erb

@@ -31,12 +31,18 @@
                   <a href="<%= report_summary_path(report.id) %>">View</a>
                 <% end %>
               <% end %>
+
               <% if can? :update, report %>
                 <a href="<%= edit_report_path(report.id) %>">Edit</a>
               <% end %>
+
               <% if can?(:validate, report) && report.can_be_validated? %>
                 <a href="<%= validate_report_path(report.id) %>">Validate</a>
               <% end %>
+
+              <% if can?(:destroy, report) %>
+                <%= link_to 'Delete', "/reports/#{report.id}", method: :delete %>
+              <% end %>
             </td>
           </tr>
       <% end %>

app/views/reports/index.html.erb

@@ -11,11 +11,11 @@
 
 <% if current_user.is_role?(:provider) %>
   <h2>My reports</h2>
-  <%= render partial: "table", locals: {reports: @user_reports, table: "user"}  %>
+  <%= render partial: "table", locals: { reports: @user_reports, table: "user" }  %>
 
   <h2>Agency reports</h2>
-  <%= render partial: "table", locals: {reports: @agency_reports, table: "agency"}  %>
+  <%= render partial: "table", locals: { reports: @agency_reports, table: "agency" }  %>
 <% else %>
-  <%= render partial: "table", locals: {reports: @reports}  %>
+  <%= render partial: "table", locals: { reports: @reports}  %>
 <% end %>
 

app/views/reports/search.html.erb

@@ -29,14 +29,14 @@
 
     <%= label_tag :from_date, 'Date of discovery (from)' %>
     <div class="form__field">
-      <%= date_select :from_date, params[:from_date], include_blank: true, order: [:day, :month, :year], default: nil %>
+      <%= date_select :from_date, params[:from_date], include_blank: true, start_year: @earliest_report_year, order: [:day, :month, :year], default: nil %>
     </div>
   </div>
 
   <div class="form__group">
     <%= label_tag :to_date, 'Date of discovery (to)' %>
     <div class="form__field">
-      <%= date_select :to_date, params[:to_date], include_blank: true, order: [:day, :month, :year], default: nil %>
+      <%= date_select :to_date, params[:to_date], include_blank: true, start_year: @earliest_report_year, order: [:day, :month, :year], default: nil %>
     </div>
   </div>