Add tests

.gitlab-ci.yml

+default:
+  image: docker:24.0.5
+  services:
+    - docker:24.0.5-dind
+  before_script:
+    - docker info
+
+variables:
+  DOCKER_TLS_CERTDIR: "/certs"
+
+stages:
+  - build
+  - test
+
+
+
+build-job:
+  stage: build
+  script:
+    - apt install ruby
+    - gem install bundler
+    - sudo -u nobody -g nogroup bundle install
+    - apt install git
+    - git clone https://github.com/touzet/pampa.git
+    - docker build -t pampa:web .
+    - docker run -dtp 80:80 pampa:web
+
+
+
+test-home:
+  stage: test
+  script:
+    - ruby tests/test_home.rb
+    
+test-form:
+  stage: test
+  script:
+    - ruby tests/test_form.rb
+    
+test-help:
+  stage: test
+  script:
+    - ruby tests/test_help.rb
+    
+test-analysis:
+  stage: test
+  script:
+    - ruby tests/test_analysis.rb
+    
+

tests/test_analysis.rb

+# -- Packages --
+require 'rubygems'
+# require 'webdrivers'
+require 'watir'
+require 'test/unit'
+require 'open-uri'
+require 'email_address'
+
+
+puts "=========================================================================="
+puts "                        Testing PAMPA Web"
+puts "=========================================================================="
+
+$browsers = [
+    "Watir::Browser.new :chrome, options: {args: ['--no-sandbox']}",
+    "Watir::Browser.new :firefox, options: {args: ['--no-sandbox']}",
+    "Watir::Browser.new :edge, options: {args: ['--no-sandbox']}"
+    ]
+$form_url = "http://localhost/pampa/form.php"
+
+
+
+class PampaWebAnalyseTest < Test::Unit::TestCase
+
+    def test_01_result_page
+        puts "* result - Launch page result (1/4)"
+        $browsers.each do |br_string|
+            puts br_string
+            br = eval(br_string)
+            br.goto $form_url
+
+            # launch analysis
+            e = br.button(id: 'example_1')
+            assert(e.present?)
+            e.click
+            e = br.button(id: 'run')
+            assert(e.present?)
+            e.click
+            br.wait_until {|b| b.url != $form_url}
+
+            # check content
+            e = br.url
+            assert(/http:\/\/localhost\/pampa\/result\/[A-Za-z0-9_]+\/results\.php/ =~ e)
+            e = br.h2
+            assert(e.present? && (e.text.include? "Results for job"))
+            es = br.elements(css: '#result_pampa td')
+            assert(es.size == 80)
+            assert(es[1].text == "Castor canadensis" && es[14].text == "8.09E-10")
+            e = br.h3
+            assert(e.present? && e.text == "Download")
+            es = br.elements(css: "h3 + ul li")
+            assert(es.size == 4)
+
+            br.close
+        end
+    end
+
+    def test_02_result_links
+        puts "* result - Buttons and links result (2/4)"
+        $browsers.each do |br_string|
+            puts br_string
+            br = eval(br_string)
+            br.goto $form_url
+
+            # launch analysis
+            e = br.button(id: 'example_1')
+            assert(e.present?)
+            e.click
+            e = br.button(id: 'run')
+            assert(e.present?)
+            e.click
+            br.wait_until {|b| b.url != $form_url}
+
+            # check links
+            br.div(id: 'center').as.each do |link|
+                if link.href.start_with?("http")  # web links
+                    status_code = URI.open(link.href).status[0]
+                    assert(status_code=='200')
+                elsif link.href.start_with?("mailto:")
+                    email = link.href[7..-1]
+                    assert(EmailAddress.valid? email)
+                else 
+                    puts '- "' + link.href + '" not tested'
+                end
+            end
+            br.close
+        end
+    end
+
+    def test_03_details_simple_page
+        puts "* result - Launch page details simple (3/4)"
+        $browsers.each do |br_string|
+            puts br_string
+            br = eval(br_string)
+            br.goto $form_url
+
+            # launch analysis
+            e = br.button(id: 'example_1')
+            assert(e.present?)
+            e.click
+            e = br.button(id: 'run')
+            assert(e.present?)
+            e.click
+            br.wait_until {|b| b.url != $form_url}
+
+            # launch details page
+            e = br.elements(css: '#result_pampa td')[1]
+            assert(e.present?)
+            e.click
+            Watir::Wait.until { br.windows.size == 2 }
+            handles = br.windows.map(&:handle)
+            window = br.window(handle: handles[1])
+            window.use
+
+            # check content
+            e = br.url
+            assert(/http:\/\/localhost\/pampa\/result\/[A-Za-z0-9_]+\/details_Castor-TOF\.php/ =~ e)
+            e = br.h2
+            e.text  # ODD Avoid firefox from crashing
+            assert(e.present? && (/Results for job [A-Za-z0-9_]+( \([A-Za-z0-9_]+\))?\nMass spectrum Castor-TOF\.csv/ =~ e.text))
+            assert(br.text.include? "Taxonomic group : Castor canadensis (species)")
+            es = br.tds
+            assert(es.size == 56 && es[1].text == "1177.59461")
+            e = br.div(css: '[data-root-id]')
+            assert(e.present?)
+
+            br.close
+        end
+    end
+
+    def test_04_details_multiple_page
+        puts "* result - Launch page details multiple (4/4)"
+        $browsers.each do |br_string|
+            puts br_string
+            br = eval(br_string)
+            br.goto $form_url
+
+            # launch analysis
+            e = br.button(id: 'example_1')
+            assert(e.present?)
+            e.click
+            e = br.button(id: 'run')
+            assert(e.present?)
+            e.click
+            br.wait_until {|b| b.url != $form_url}
+
+            # launch details page
+            e = br.elements(css: '#result_pampa td')[56]
+            assert(e.present?)
+            e.click
+            Watir::Wait.until { br.windows.size == 2 }
+            handles = br.windows.map(&:handle)
+            window = br.window(handle: handles[1])
+            window.use
+
+            # check content
+            e = br.url
+            assert(/http:\/\/localhost\/pampa\/result\/[A-Za-z0-9_]+\/details_Whale-TOF\.php/ =~ e)
+            e = br.h2
+            e.text  # Need to call `element.text` before assert to prevent firefox from crashing
+            assert(e.present? && (/Results for job [A-Za-z0-9_]+( \([A-Za-z0-9_]+\))?\nMass spectrum Whale-TOF\.csv/ =~ e.text))
+            assert(br.text.include? "Taxonomic group : Globicephala melas (species), with P-value 6.32E-16")
+            es = br.tds
+            assert(es.size == 234)
+            assert(es[176].text == "652")
+            assert(br.text.include? "GPSGEPGTAGSPGTPGPQGLLGAPGFLGLPGSR")
+            es = br.divs(css: '[data-root-id]')
+            assert(es.size == 3)
+
+            br.close
+        end
+    end
+
+end

tests/test_form.rb

+# -- Packages --
+require 'rubygems'
+# require 'webdrivers'
+require 'watir'
+require 'test/unit'
+require 'open-uri'
+require 'email_address'
+
+
+puts "=========================================================================="
+puts "                        Testing PAMPA Web"
+puts "=========================================================================="
+
+$browsers = [
+    "Watir::Browser.new :chrome, options: {args: ['--no-sandbox']}",
+    "Watir::Browser.new :firefox, options: {args: ['--no-sandbox']}",
+    "Watir::Browser.new :edge, options: {args: ['--no-sandbox']}"
+    ]
+$form_url = "http://localhost/pampa/form.php"
+
+
+
+class PampaWebFormTest < Test::Unit::TestCase
+
+    def test_01_launch_page
+        puts "* pampa/form.php - Launch page (1/5)"
+        $browsers.each do |br_string|
+            puts br_string
+            br = eval(br_string)
+            br.goto $form_url
+
+            # check text
+            e = br.element(id: 'title')
+            assert(e.present? && (e.text == "Pampa"))
+            e = br.element(class: 'onglet_left')
+            assert(e.present? && e.text == "Pampa")
+            assert(br.text.include? "Mass spectra")
+            assert(br.table(class: 'pampa_choice').present?)
+            assert(br.button(id: 'run').present?)
+            br.close
+        end
+    end
+
+    def test_02_buttons_links
+        puts "* pampa/form.php - Buttons and links (2/5)"
+        $browsers.each do |br_string|
+            puts br_string
+            br = eval(br_string)
+            br.goto $form_url
+
+            # check links
+            br.div(id: 'center').as.each do |link|
+                if link.href.start_with?("http")  # web links
+                    status_code = URI.open(link.href).status[0]
+                    assert(status_code=='200')
+                elsif link.href.start_with?("mailto:")
+                    email = link.href[7..-1]
+                    assert(EmailAddress.valid? email)
+                else 
+                    puts '- "' + link.href + '" not tested'
+                end
+            end
+            br.close
+        end
+    end
+
+    def test_03_display
+        puts "* pampa/form.php - Normal display (3/5)"
+        $browsers.each do |br_string|
+            puts br_string
+            br = eval(br_string)
+            br.goto $form_url
+
+            # check options
+            e = br.checkbox(name: 'spectra_example_1')
+            assert(e.exists? && !(e.set?))
+            e = br.radio(name: 'error_margin_selection', value: 'MALDI_TOF')
+            assert(e.exists? && e.set?)
+            e = br.radio(id: 'reference_source_default')
+            assert(e.exists? && !(e.set?))
+            e = br.radio(id: 'reference_source_user')
+            assert(e.exists? && !(e.set?))
+            e = br.checkbox(name: 'taxonomic_group_selection', value: 'mammals')
+            assert(e.exists? && e.set?)
+            e = br.checkbox(name: 'ptm_deamidation', value: 'deamidation')
+            assert(e.exists? && e.set?)
+            e = br.radio(name: 'nearoptimal_selection', value: 'optimal')
+            assert(e.exists? && e.set?)
+
+            # check hidden elements
+            e = br.tr(id: 'spectra_input')
+            assert(e.present?)
+            e = br.tr(id: 'spectra_example')
+            assert(e.exists? && !(e.visible?))
+            e = br.div(id: 'block_reference_source_default')
+            assert(e.exists? && !(e.visible?))
+            e = br.div(id: 'block_reference_source_user')
+            assert(e.exists? && !(e.visible?))
+            e = br.div(id: 'block_results')
+            assert(e.exists? && !(e.visible?))
+
+            br.close
+        end
+    end
+
+    def test_04_interactions
+        puts "* pampa/form.php - Js interactions (4/5)"
+        $browsers.each do |br_string|
+            puts br_string
+            br = eval(br_string)
+            br.goto $form_url
+
+            # check basic mode
+            e = br.radio(id: 'reference_source_default')
+            assert(e.exists?)
+            e.click
+            e = br.div(id: 'block_reference_source_default')
+            assert(e.present?)
+            e = br.div(id: 'block_reference_source_user')
+            assert(e.exists? && !(e.visible?))
+            e = br.div(id: 'block_results')
+            assert(e.present?)
+
+            # check reset button
+            e = br.button(id: "reset")
+            assert(e.present?)
+            e.click
+            e = br.tr(id: 'spectra_input')
+            assert(e.present?)
+            e = br.tr(id: 'spectra_example')
+            assert(e.exists? && !(e.visible?))
+            e = br.checkbox(name: 'spectra_example_1')
+            assert(e.exists? && !(e.set?))
+            e = br.radio(name: 'error_margin_selection', value: 'MALDI_TOF')
+            assert(e.present? && e.set?)
+            e = br.radio(id: 'reference_source_default')
+            assert(e.present? && !(e.set?))
+            e = br.radio(id: 'reference_source_user')
+            assert(e.present? && !(e.set?))
+            e = br.checkbox(name: 'taxonomic_group_selection', value: 'mammals')
+            assert(e.exists? && e.set?)
+            e = br.checkbox(name: 'ptm_deamidation', value: 'deamidation')
+            assert(e.exists? && e.set?)
+            e = br.radio(name: 'nearoptimal_selection', value: 'optimal')
+            assert(e.exists? && e.set?)
+            e = br.div(id: 'block_reference_source_default')
+            assert(e.exists? && !(e.visible?))
+            e = br.div(id: 'block_reference_source_user')
+            assert(e.exists? && !(e.visible?))
+            e = br.div(id: 'block_results')
+            assert(e.exists? && !(e.visible?))
+
+            # check advanced mode
+            e = br.radio(id: 'reference_source_user')
+            assert(e.exists?)
+            e.click
+            e = br.div(id: 'block_reference_source_default')
+            assert(e.exists? && !(e.visible?))
+            e = br.div(id: 'block_reference_source_user')
+            assert(e.present?)
+            e = br.div(id: 'block_results')
+            assert(e.present?)
+
+            br.close
+        end
+    end
+
+    def test_05_example
+        puts "* pampa/form.php - Example (5/5)"
+        $browsers.each do |br_string|
+            puts br_string
+            br = eval(br_string)
+            br.goto $form_url
+
+            # example button effect (form)
+            e = br.button(id: 'example_1')
+            assert(e.present?)
+            e.click
+            # visibility
+            e = br.checkbox(name: 'spectra_example_1')
+            assert(e.exists? && !e.visible? && e.set?)
+            e = br.button(id: 'back_to_normal')
+            assert(e.present?)
+            e = br.tr(id: 'spectra_input')
+            assert(e.exists? && !(e.visible?))
+            e = br.radio(name: 'error_margin_selection', value: 'MALDI_TOF')
+            assert(e.present? && e.set?)
+            e = br.radio(id: 'reference_source_default')
+            assert(e.present? && e.set?)
+            e = br.div(id: 'block_reference_source_default')
+            assert(e.present?)
+            e = br.div(id: 'block_reference_source_user')
+            assert(e.exists? && !(e.visible?))
+            e = br.div(id: 'block_results')
+            assert(e.present?)
+            # parameters
+            e = br.text_field(name: 'job_name')
+            assert(e.present? && e.value == "example_1")
+            e = br.checkbox(name: 'taxonomic_group_selection', value: 'mammals')
+            assert(e.exists? && e.set?)
+            es = br.inputs(css: '[list="taxonomic_node_list"]')
+            assert(es.size == 1)
+            e = es[0]
+            assert(e.present? && e.value == "")
+            e = br.checkbox(name: 'ptm_deamidation', value: 'deamidation')
+            assert(e.exists? && e.set?)
+            e = br.radio(name: 'nearoptimal_selection', value: 'optimal')
+            assert(e.exists? && e.set?)
+
+            # custom upload after example
+            br.button(id: 'back_to_normal').click
+            e = br.tr(id: 'spectra_input')
+            assert(e.present?)
+            e = br.tr(id: 'spectra_example')
+            assert(e.exists? && !(e.visible?))
+            e = br.checkbox(name: 'spectra_example_1')
+            assert(e.exists? && !(e.set?))
+            e = br.text_field(name: 'job_name')
+            assert(e.present? && e.value != "example_1")
+
+            br.close
+        end
+    end
+
+end

tests/test_help.rb

+# -- Packages --
+require 'rubygems'
+# require 'webdrivers'
+require 'watir'
+require 'test/unit'
+require 'open-uri'
+require 'email_address'
+
+
+puts "=========================================================================="
+puts "                        Testing PAMPA Web"
+puts "=========================================================================="
+
+$browsers = [
+    "Watir::Browser.new :chrome, options: {args: ['--no-sandbox']}",
+    "Watir::Browser.new :firefox, options: {args: ['--no-sandbox']}",
+    "Watir::Browser.new :edge, options: {args: ['--no-sandbox']}"
+    ]
+$help_url = "http://localhost/pampa/help.php"
+
+
+
+class PampaWebHelpTest < Test::Unit::TestCase
+
+    def test_01_launch_page
+        puts "* pampa/help.php - Launch page (1/2)"
+        $browsers.each do |br_string|
+            puts br_string
+            br = eval(br_string)
+            br.goto $help_url
+
+            # check text
+            e = br.element(id: 'title')
+            assert(e.present? && (e.text == "Pampa"))
+            e = br.element(class: 'onglet_right')
+            assert(e.present? && e.text == "Help")
+            assert(br.text.include? "Peptide markers are organized within peptide tables")
+            assert(br.element(id: 'PTM_description').present?)
+            br.close
+        end
+    end
+
+    def test_02_buttons_links
+        puts "* pampa/help.php - Buttons and links (2/2)"
+        $browsers.each do |br_string|
+            puts br_string
+            br = eval(br_string)
+            br.goto $help_url
+
+            # check links
+            br.div(id: 'center').as.each do |link|
+                if link.href.start_with?("http")  # web links
+                    status_code = URI.open(link.href).status[0]
+                    assert(status_code=='200')
+                elsif link.href.start_with?("mailto:")
+                    email = link.href[7..-1]
+                    assert(EmailAddress.valid? email)
+                else 
+                    puts '- "' + link.href + '" not tested'
+                end
+            end
+            br.close
+        end
+    end
+
+end

tests/test_home.rb

+# -- Packages --
+require 'rubygems'
+# require 'webdrivers'
+require 'watir'
+require 'test/unit'
+require 'open-uri'
+require 'email_address'
+
+
+puts "=========================================================================="
+puts "                        Testing PAMPA Web"
+puts "=========================================================================="
+
+$browsers = [
+    "Watir::Browser.new :chrome, options: {args: ['--no-sandbox']}",
+    "Watir::Browser.new :firefox, options: {args: ['--no-sandbox']}",
+    "Watir::Browser.new :edge, options: {args: ['--no-sandbox']}"
+    ]
+$home_url = "http://localhost/pampa/"
+
+
+
+class PampaWebHomeTest < Test::Unit::TestCase
+
+    def test_01_launch_page
+        puts "* pampa - Launch page (1/2)"
+        $browsers.each do |br_string|
+            puts br_string
+            br = eval(br_string)
+            br.goto $home_url
+
+            # check text
+            e = br.element(id: 'title')
+            assert(e.present? && (e.text == "Pampa"))
+            e = br.element(class: 'onglet_left')
+            assert(e.present? && e.text == "Pampa")
+            assert(br.text.include? "PAMPA is available in two versions.")
+
+            br.close
+        end
+    end
+
+    def test_02_buttons_links
+        puts "* pampa - Buttons and links (2/2)"
+        $browsers.each do |br_string|
+            puts br_string
+            br = eval(br_string)
+            br.goto $home_url
+
+            # check links
+            br.div(id: 'center').as.each do |link|
+                assert(link.href != "")
+                if link.href.start_with?("http")  # web links
+                    status_code = URI.open(link.href).status[0]
+                    assert(status_code=='200')
+                elsif link.href.start_with?("mailto:")  # mails
+                    email = link.href[7..-1]
+                    assert(EmailAddress.valid? email)
+                else 
+                    puts '- "' + link.href + '" not tested'
+                end
+            end
+            br.close
+        end
+    end
+
+end
+