study_engine 0.0.2

data/app/views/study_engine/mailer/assessment_recorded_notification.erb

@@ -0,0 +1,8 @@
+This email confirms that a <%= @study_name %> assessment has been recorded for a study participant. Assessment details are located below:
+
+Study ID: <%= @assessment.study_id %>
+Assessment: <%= @assessment.event %>
+Domains: <%= domains_and_group_summary(@assessment) %>
+Date and time: <%= @assessment.assessment_updated_at %>
+Method applied: <%= @assessment.method_applied %>
+Coordinator: <%= @assessment.coordinator_email %>

data/app/views/study_engine/mailer/assessment_url_notification.erb

@@ -0,0 +1,6 @@
+This email confirms your request for a URL that will provide access to an assessment for a study participant. Details pertaining to your request are located below:
+
+Study ID: <%= @assessment.study_id %>
+Assessment: <%= @assessment.event %>
+URL: <%= assessment_url(@assessment) %>
+Date and time requested: <%= @assessment.created_at %>

data/config/routes.rb

@@ -0,0 +1,15 @@
+StudyEngine::Engine.routes.draw do
+  namespace :admin do
+    root to: "assessments#index"
+    resources :assessments do
+      resource :notes
+    end
+  end
+
+  resources :assessments do
+    get :timeout, on: :member
+    post :notification, on: :member
+  end
+  root to: "assessments#index"
+end
+

data/db/migrate/20160422185859_create_tables.rb

@@ -0,0 +1,52 @@
+class CreateTables < ActiveRecord::Migration
+  def change
+    create_table "study_engine_answers" do |t|
+      t.integer  "result_id",          limit: 4
+      t.string   "question_context",   limit: 255
+      t.string   "response_title",     limit: 255
+      t.string   "response_id",        limit: 255
+      t.datetime "created_at",                     null: false
+      t.datetime "updated_at",                     null: false
+      t.string   "question_id",        limit: 255
+      t.string   "question_title",     limit: 255
+      t.string   "question_promis_id", limit: 255
+      t.string   "response_promis_id", limit: 255
+      t.string   "response_before",    limit: 255
+    end
+
+    create_table "study_engine_assessments" do |t|
+      t.text     "finished_cat_assessment_ids", limit: 65535
+      t.datetime "created_at",                                null: false
+      t.datetime "updated_at",                                null: false
+      t.string   "study_id",                    limit: 255
+      t.string   "event",                       limit: 255
+      t.integer  "group_index",                 limit: 4
+      t.string   "method_applied",              limit: 255
+      t.integer  "coordinator_id",              limit: 4
+      t.datetime "assessment_updated_at",                     null: false
+      t.text     "notes",                       limit: 65535
+      t.datetime "completed_at"
+    end
+
+    create_table "study_engine_results" do |t|
+      t.integer  "assessment_id",  limit: 4
+      t.string   "bank_id",        limit: 255
+      t.boolean  "finished",                                            default: false
+      t.decimal  "theta",                      precision: 10, scale: 5
+      t.decimal  "standard_error",             precision: 10, scale: 5
+      t.datetime "created_at",                                                          null: false
+      t.datetime "updated_at",                                                          null: false
+    end
+
+    add_index "study_engine_results", ["assessment_id"], name: "index_study_engine_results_on_assessment_id", using: :btree
+    add_index "study_engine_results", ["bank_id"], name: "index_results_on_cat_assessment_id", using: :btree
+
+    create_table "study_engine_study_ids" do |t|
+      t.string   "study_id_study", limit: 255
+      t.string   "study_id_site",  limit: 255
+      t.string   "study_id_id",    limit: 255
+      t.datetime "created_at"
+      t.datetime "updated_at"
+    end
+  end
+end

data/lib/study_engine.rb

@@ -0,0 +1,5 @@
+require "study_engine/config"
+require "study_engine/engine" if defined?(Rails)
+
+module StudyEngine
+end

data/lib/study_engine/config.rb

@@ -0,0 +1,37 @@
+require "active_support/core_ext/module/attribute_accessors"
+require "cat_engine/config"
+
+module StudyEngine
+  def self.configure
+    yield self
+  end
+
+  mattr_accessor(:study_name) { "" }
+  mattr_accessor(:study_url) { "" }
+  mattr_accessor(:notification_email) { "" }
+  mattr_accessor(:welcome_content) { "" }
+
+  mattr_accessor(:groups) { Hash.new }
+  mattr_accessor(:banks) { [] }
+  mattr_accessor(:bank_finder) { Proc.new { banks } }
+  mattr_accessor(:events) { ["Baseline", "6 month", "12 month"] }
+  mattr_accessor(:enabled_application_methods) {
+    [
+      "In-person",
+      "By phone",
+      "By URL",
+      "By mail",
+      "Paper form",
+    ]
+  }
+
+  mattr_accessor(:redcap_token) { "" }
+
+  class << self
+    delegate :cat_path, :cat_path=,
+      :cat_engine_source_path, :cat_engine_source_path=,
+      :cat_engine_executable_path, :cat_engine_executable_path=,
+      to: CatEngine
+  end
+end
+

data/lib/study_engine/cucumber.rb

@@ -0,0 +1,96 @@
+Given "the assessment timeout interval is set to $count seconds" do |count|
+  @original_assessment_timeout_interval = StudyEngine::Assessment.timeout_interval
+  StudyEngine::Assessment.timeout_interval = count.to_i
+end
+
+After do
+  if defined?(@original_assessment_timeout_interval)
+    StudyEngine::Assessment.timeout_interval = @original_assessment_timeout_interval
+  end
+end
+
+Given "the following study ids exist:" do |table|
+  table.raw.each do |row|
+    StudyEngine::StudyID::Bank.find_or_create_from_full_study_id row.first
+  end
+end
+
+Given "the following assessment results exist:" do |table|
+  table.hashes.each do |attributes|
+    study_id = attributes["study_id"]
+    baseline = attributes["baseline"]
+    three_month  = attributes["3 month"]
+    six_month  = attributes["6 month"]
+    twelve_month = attributes["12 month"]
+
+    create_stub_assessment study_id, "Baseline", baseline if baseline.present?
+    create_stub_assessment study_id, "3 month",  three_month if three_month.present?
+    create_stub_assessment study_id, "6 month",  six_month if six_month.present?
+    create_stub_assessment study_id, "12 month", twelve_month if twelve_month.present?
+  end
+end
+
+def create_stub_assessment study_id, event, time
+  assessment = StudyEngine::Assessment.create!({
+    study_id: study_id,
+    event: event,
+    method_applied: "In-person",
+  })
+  assessment.results.each do |result|
+    result.update_attribute :finished, true
+  end
+  assessment.update({
+    created_at: time,
+    assessment_updated_at: time,
+    completed_at: time,
+  })
+  assessment
+end
+
+When /^I choose "(.+?)" and "(.+?)" for the question pair$/ do |before, after|
+  within all(".paired-bank")[0] do
+    choose before
+  end
+  within all(".paired-bank")[1] do
+    choose after
+  end
+end
+
+When /^I should see the progress bar at (\d+%)$/ do |percent|
+  begin
+    find(".percentage", text: percent)
+  rescue Capybara::ElementNotFound
+    find(".percentage").text.should == percent
+  end
+end
+
+Then 'I should see the "Start Assessment" form' do
+  page.should have_css("form input[value='Start Assessment']")
+end
+
+Then "I should see the following assessment results:" do |table|
+  assessments = all(".results-table tr").map do |row|
+    row.all("th,td").map(&:text)
+  end
+  table.diff! assessments
+end
+
+Then "I should see that notes are present" do
+  find("label.note.-saved")
+end
+
+Then 'I should download a csv named "$filename" with the following contents:' do |filename, table|
+  page.response_headers['Content-Disposition'].should include("filename=\"#{filename}\"")
+  page.execute_script """
+    window.xhrDownload = function(url) {
+      var xhr = new XMLHttpRequest();
+      xhr.open('GET', url, false);
+      xhr.send(null);
+      return xhr.responseText;
+    };
+  """
+  csv = page.evaluate_script("xhrDownload('#{@last_path}');")
+  csv_table = CSV.parse(csv)
+  table.diff! csv_table
+end
+

data/lib/study_engine/engine.rb

@@ -0,0 +1,7 @@
+require "csv_builder"
+
+module StudyEngine
+  class Engine < ::Rails::Engine
+    isolate_namespace StudyEngine
+  end
+end

data/lib/study_engine/version.rb

@@ -0,0 +1,3 @@
+module StudyEngine
+  VERSION = "0.0.2"
+end

data/lib/tasks/study_engine_tasks.rake

@@ -0,0 +1,10 @@
+namespace :study_engine do
+  desc "compile the CAT Engine"
+  task :compile_cat_engine => "cat_engine:compile_cat_engine"
+
+  desc "sync study ids from REDCap"
+  task :sync_study_ids => :environment do
+    StudyEngine::StudyID::Sync.call
+  end
+end
+

data/spec/ar_helper.rb

@@ -0,0 +1,30 @@
+require "spec_helper"
+require "active_record"
+require "database_cleaner"
+require "byebug"
+
+ActiveRecord::Base.establish_connection adapter: "sqlite3", database: ":memory:"
+
+# sqlite3 hates our mysql indexes
+ActiveRecord::Migration.class_eval do
+  def add_index *; end
+end
+
+DatabaseCleaner.strategy = :transaction
+silence_stream(STDOUT) do
+  load "spec/schema.rb"
+end
+
+RSpec.configure do |config|
+  config.before(:each) do
+    DatabaseCleaner.start
+  end
+
+  config.after(:each) do
+    DatabaseCleaner.clean
+  end
+end
+
+# silence deprecation warning
+I18n.enforce_available_locales = true
+

data/spec/models/study_engine/answer_spec.rb

@@ -0,0 +1,28 @@
+require "ar_helper"
+require "study_engine/answer"
+
+module StudyEngine
+  describe Answer do
+    its(:result) { should be_nil }
+
+    describe "#response" do
+      it "returns a value object" do
+        subject.response_id = "OMG"
+        subject.response_promis_id = "1"
+        subject.response_title = "WTF"
+        subject.response.should == CatEngine::Response.new(id: "OMG", promis_id: "1", title: "WTF")
+      end
+    end
+
+    describe "#question" do
+      it "returns a value object" do
+        subject.question_id = "OMG"
+        subject.question_promis_id = "123"
+        subject.question_context = "WTF"
+        subject.question_title = "BBQ"
+        subject.question.should == CatEngine::Question.new(id: "OMG", promis_id: "123", context: "WTF", title: "BBQ", responses: [])
+      end
+    end
+  end
+end
+

data/spec/models/study_engine/assessment_spec.rb

@@ -0,0 +1,250 @@
+require "ar_helper"
+require "study_engine/assessment"
+require "study_engine/config"
+require "study_engine/result" # FIXME
+
+module StudyEngine
+  describe Assessment do
+    let(:ids) { %w(Alpha Bravo Charlie Delta Echos) }
+
+    before { StudyEngine.banks = ids }
+
+    context "new" do
+      its(:stream_id) { should be_nil }
+      its(:study_id) { should be_nil }
+      its(:event) { should be_nil }
+      its(:percent_complete) { should == 0 }
+
+      its(:group_index) { should be_nil }
+      its(:group_index_name) { should == "" }
+
+      describe "#results" do
+        it "pads the list with unpersisted results for each cat assessment" do
+          results = subject.results.map do |result|
+            [result.bank_id, result.persisted?]
+          end
+
+          results.should == [
+            ["Alpha", false],
+            ["Bravo", false],
+            ["Charlie", false],
+            ["Delta", false],
+            ["Echos", false],
+          ]
+        end
+      end
+
+      describe "#results_summary" do
+        it "is a string of how many banks are completed" do
+          subject.results_summary.should == "0/5"
+        end
+      end
+
+      # straight up comparison fails
+      its(:"current_result.bank_id") { should == "Alpha" }
+
+      describe "#current_question" do
+        it "delegates to current_result" do
+          question = double
+          result = double(current_question: question)
+          subject.stub current_result: result
+
+          subject.current_question.should == question
+        end
+      end
+
+
+      describe "#save_answer" do
+        it "delegates to current_result" do
+          result = double
+          answer = double
+          subject.stub(current_result: result)
+
+          result.should_receive(:save_answer).with(answer)
+
+          # make valid
+          subject.study_id = "OUT-BBB-1234"
+          subject.event = "Baseline"
+          subject.save_answer answer
+
+          subject.should be_persisted
+        end
+      end
+
+      it { should_not be_complete }
+      it { should be_incomplete }
+    end
+
+    context "in progress" do
+      before do
+        subject.study_id = "OUT-BBB-1234"
+        subject.event = "Baseline" # make valid
+        subject.save!
+
+        subject.results[0].update_attribute :finished, true
+        subject.results[1].update_attribute :finished, true
+      end
+
+      its(:stream_id) { should == StudyID.new("STR-BBB-1001") }
+      its(:study_id) { should == StudyID.new("OUT-BBB-1234") }
+
+      its(:percent_complete) { should == 40 }
+
+      its(:group_index) { should be_nil }
+
+      # straight up comparison fails
+      its(:"current_result.bank_id") { should == "Charlie" }
+
+      describe "#results" do
+        it "pads the list with unpersisted results for each cat assessment" do
+
+          results = subject.results.map do |result|
+            [result.bank_id, result.persisted?]
+          end
+
+          results.should == [
+            ["Alpha", true],
+            ["Bravo", true],
+            ["Charlie", false],
+            ["Delta", false],
+            ["Echos", false],
+          ]
+        end
+      end
+
+      it { should_not be_complete }
+      it { should be_incomplete }
+    end
+
+    context "complete" do
+      before do
+        subject.study_id = "OUT-BBB-1234"
+        subject.event = "Baseline" # make valid
+
+        subject.save!
+        subject.results.each do |result|
+          result.update_attribute :finished, true
+        end
+      end
+
+      describe "#results" do
+        it "pads the list with unpersisted results for each cat assessment" do
+          results = subject.results.map do |result|
+            [result.bank_id, result.persisted?]
+          end
+
+          results.should == [
+            ["Alpha", true],
+            ["Bravo", true],
+            ["Charlie", true],
+            ["Delta", true],
+            ["Echos", true],
+          ]
+        end
+      end
+
+      its(:percent_complete) { should == 100 }
+
+      its(:group_index) { should be_nil }
+      its(:current_result) { should be_nil }
+
+      describe "#current_question" do
+        it "raises an error" do
+          lambda { subject.current_question }.should raise_exception(StandardError)
+        end
+      end
+
+      describe "#history=" do
+        it "raises an error" do
+          lambda { subject.history = double }.should raise_exception(StandardError)
+        end
+      end
+
+      it { should be_complete }
+      it { should_not be_incomplete }
+    end
+
+    describe "#study_id=" do
+      it "assigns the parts" do
+        subject.study_id = "FIX-BBB-0000"
+        subject.study_id.study.should == "FIX"
+        subject.study_id.site.should == "BBB"
+        subject.study_id.id.should == "0000"
+        subject.study_id.should == StudyID.new("FIX-BBB-0000")
+      end
+    end
+
+    describe "groups" do
+      def create_assessment attributes = {}
+        attributes.reverse_merge! event: "12 month"
+        described_class.new(attributes).tap do |assessment|
+          assessment.save(validate: false)
+        end
+      end
+
+      before do
+        StudyEngine.groups = { "12 month" => %w(A B C) }
+      end
+
+      describe "#group_index" do
+        it "is 0 when there is one twelve month assessment" do
+          create_assessment.group_index.should == 0
+        end
+
+        it "is 1 when there are two twelve month assessments" do
+          create_assessment
+          create_assessment.group_index.should == 1
+        end
+
+        it "is 2 when there are three twelve month assessments" do
+          2.times { create_assessment }
+          create_assessment.group_index.should == 2
+        end
+
+        it "is 0 when there are four twelve month assessments" do
+          3.times { create_assessment }
+          create_assessment.group_index.should == 0
+        end
+
+        it "is nil when subject is not a twelve month assessment" do
+          assessment = create_assessment(event: "baseline")
+          assessment.group_index.should be_nil
+        end
+
+        it "doesnt change after subsequent assessments are added" do
+          assessment = create_assessment
+          assessment.group_index.should == 0
+          create_assessment
+          assessment.group_index.should == 0
+        end
+
+        it "retains previous group index if restarted" do
+          a1 = create_assessment study_id: "ABC-DEF-1234"
+          a2 = create_assessment study_id: "ABC-DEF-1234"
+          a2.group_index.should == a1.group_index
+        end
+      end
+
+      describe "#group_index_name" do
+        it "is A when group_index is 0" do
+          assessment = create_assessment
+          assessment.group_index = 0
+          assessment.group_index_name.should == "A"
+        end
+
+        it "is B when group_index is 1" do
+          assessment = create_assessment
+          assessment.group_index = 1
+          assessment.group_index_name.should == "B"
+        end
+
+        it "is C when group_index is 2" do
+          assessment = create_assessment
+          assessment.group_index = 2
+          assessment.group_index_name.should == "C"
+        end
+      end
+    end
+  end
+end
+