From 8677d1b7bd5b32791c440bf0de2fc4c61c98299f Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sun, 21 May 2017 07:21:44 +0000 Subject: Merge from the diet branch. * refactored ./bin/genenetwork2 and /etc/default_settings - better detection of Guix - removed unused parameters, such as GEMMA_RESULT_PATH and TEMP_TRAITS - removing some default settings, such as PYLMM_COMMAND - rename some settings, such as SQL_URI and LOG_SQL_ALCHEMY - added GUIX_JS_PATH for JS modules * Added documentation on installing binary GN2 * Updated Twitter board to latest version in Guix - it had broken * Updated many tools in the latest Guix profile --- test/lib/main_web_functionality.rb | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'test/lib/main_web_functionality.rb') diff --git a/test/lib/main_web_functionality.rb b/test/lib/main_web_functionality.rb index ec61de2d..9ae49995 100644 --- a/test/lib/main_web_functionality.rb +++ b/test/lib/main_web_functionality.rb @@ -13,16 +13,20 @@ describe MainWebFunctionality do it "Get to trait page" do page = @agent.get($host) + p page form = page.forms[1] form.buttons[0].value.must_equal "Search" # main menu is loaded # http://localhost:5003/search?species=mouse&group=BXD&type=Hippocampus+mRNA&dataset=HC_M2_0606_P&search_terms_or=&search_terms_and=MEAN%3D%2815+16%29+LRS%3D%2823+46%29&FormID=searchResult + form.fields[0].value.must_equal "searchResult" form.fields[2].value = "MEAN=(15 16) LRS=(23 46)" form.fields[3].value = "mouse" form.fields[4].value = "BXD" form.fields[5].value = "Hippocampus mRNA" form.fields[6].value = "HC_M2_0606_P" search_page = @agent.submit(form, form.buttons.first) + p "==================" + p search_page probe_link = search_page.links.find { |l| l.text =~ /1435395_s_at/ } probe_link.uri.to_s.must_equal "/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P" show_trait_page = probe_link.click -- cgit v1.2.3 From 0c600598b4f1c8a19b3bf13aa6cb197494a9c122 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 2 Apr 2018 08:49:53 +0000 Subject: Testing moved to Python --- test/lib/gntest.rb | 6 ---- test/lib/link_checker.rb | 50 ------------------------------ test/lib/main_web_functionality.rb | 62 -------------------------------------- test/lib/mapping.rb | 58 ----------------------------------- test/lib/navigation.rb | 43 -------------------------- 5 files changed, 219 deletions(-) delete mode 100644 test/lib/gntest.rb delete mode 100644 test/lib/link_checker.rb delete mode 100644 test/lib/main_web_functionality.rb delete mode 100644 test/lib/mapping.rb delete mode 100644 test/lib/navigation.rb (limited to 'test/lib/main_web_functionality.rb') diff --git a/test/lib/gntest.rb b/test/lib/gntest.rb deleted file mode 100644 index 5b21b3d5..00000000 --- a/test/lib/gntest.rb +++ /dev/null @@ -1,6 +0,0 @@ -require 'minitest/autorun' -require 'mechanize' -require 'json' - -# ---- Use some default parameters if not set -$host = "http://localhost:5003" if !$host diff --git a/test/lib/link_checker.rb b/test/lib/link_checker.rb deleted file mode 100644 index 36cb36c8..00000000 --- a/test/lib/link_checker.rb +++ /dev/null @@ -1,50 +0,0 @@ - -SKIP = "mailto:" - -class LinkChecker -end - -describe LinkChecker do - before do - @agent = Mechanize.new - @agent.agent.http.ca_file = '/etc/ssl/certs/ca-certificates.crt' - end - - it "Get to front page" do - page = @agent.get($host) - page.links.each do |link| - puts link.href - if link.href !~ /#{SKIP}/ # /static\/dbdoc\/Hippocampus/ and link.href !~ /mailto:|glossary.html|sample_r|grits.eecs.utk.edu|correlationAnnotation.html/ - # Fetch link, program will crash with exception if link is broken - linkpage = @agent.get(link.href) - puts "Link to #{link.href} is valid, response code #{linkpage.code}" - end - end - - end - - describe LinkChecker do - it "Get to trait page" do - page = @agent.get($host+'/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P') - # p page - - # Get to trait page for 1435395_s_at - # form2 = show_trait_page.forms_with("trait_page")[0] - # form2.fields[30].name.must_equal "variance:C57BL/6J" - # form2.fields[30].value.must_equal "15.287" - - # Test every link on the page to check if it's broken or not - page.links.each do |link| - puts link.href - if link.href !~ /#{SKIP}/ # /static\/dbdoc\/Hippocampus/ and link.href !~ /mailto:|glossary.html|sample_r|grits.eecs.utk.edu|correlationAnnotation.html/ - # Fetch link, program will crash with exception if link is broken - linkpage = @agent.get(link.href) - puts "Link to #{link.href} is valid, response code #{linkpage.code}" - end - end - - end - - end - -end diff --git a/test/lib/main_web_functionality.rb b/test/lib/main_web_functionality.rb deleted file mode 100644 index 9ae49995..00000000 --- a/test/lib/main_web_functionality.rb +++ /dev/null @@ -1,62 +0,0 @@ -# In these tests we navigate from the main page to search - -class MainWebFunctionality -end - -describe MainWebFunctionality do - before do - @agent = Mechanize.new - @agent.agent.http.ca_file = '/etc/ssl/certs/ca-certificates.crt' - end - - describe MainWebFunctionality do - - it "Get to trait page" do - page = @agent.get($host) - p page - form = page.forms[1] - form.buttons[0].value.must_equal "Search" # main menu is loaded - - # http://localhost:5003/search?species=mouse&group=BXD&type=Hippocampus+mRNA&dataset=HC_M2_0606_P&search_terms_or=&search_terms_and=MEAN%3D%2815+16%29+LRS%3D%2823+46%29&FormID=searchResult - form.fields[0].value.must_equal "searchResult" - form.fields[2].value = "MEAN=(15 16) LRS=(23 46)" - form.fields[3].value = "mouse" - form.fields[4].value = "BXD" - form.fields[5].value = "Hippocampus mRNA" - form.fields[6].value = "HC_M2_0606_P" - search_page = @agent.submit(form, form.buttons.first) - p "==================" - p search_page - probe_link = search_page.links.find { |l| l.text =~ /1435395_s_at/ } - probe_link.uri.to_s.must_equal "/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P" - show_trait_page = probe_link.click - # p show_trait_page - - # Get to trait page for 1435395_s_at - - form2 = show_trait_page.forms_with("trait_page")[0] - # [name: corr_dataset value: HC_M2_0606_P] - form2.fields.select { |fld| fld.name == 'corr_dataset' }.first.value.must_equal 'HC_M2_0606_P' - if $options[:database] == :small - form2.fields[30].name.must_equal "value:DBA/2J" - else - form2.fields[30].name.must_equal "variance:C57BL/6J" - end - # form2.fields[30].value.must_equal "15.287" - - # Test every link on the page to check if it's broken or not - break if not $options[:link_checker] - show_trait_page.links.each do |link| - puts link.href - if link.href !~ /static\/dbdoc\/Hippocampus/ and link.href !~ /glossary.html|sample_r|grits.eecs.utk.edu|correlationAnnotation.html/ - # Fetch link, program will crash with exception if link is broken - linkpage = @agent.get(link.href) - puts "Link to #{link.href} is valid, response code #{linkpage.code}" - end - end - - end - - end - -end diff --git a/test/lib/mapping.rb b/test/lib/mapping.rb deleted file mode 100644 index 20e5bd40..00000000 --- a/test/lib/mapping.rb +++ /dev/null @@ -1,58 +0,0 @@ -# In these tests we navigate from the main page to a specific trait then hit the different mapping tool buttons (In this case pylMM and r/qtl) followed by computing the results (marker regressions). - -require 'gntest' - -class MappingTest -end - -describe MappingTest do - before do - @agent = Mechanize.new - @agent.agent.http.ca_file = '/etc/ssl/certs/ca-certificates.crt' - end - - describe MappingTest do - it "pylmm mapping tool selection" do - url = $host+'/marker_regression' - - json = JSON::load(File.read('test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json')) - json["method"] = "pylmm" - # p json - page = @agent.post(URI.encode(url), json) - # Unpacking the page is slow - somehow - but the run is enough as a test - # form = page.forms_with("marker_regression")[0] - # form.fields.select { |fld| fld.name == 'dataset' }.first.value.must_equal 'HC_M2_0606_P' - # form.fields.select { |fld| fld.name == 'value:BXD1' }.first.value.must_equal '6.749' - end - end - - describe MappingTest do - it "R/qtl mapping tool selection" do - url = $host+'/marker_regression' # ?trait_id=1435395_s_at&dataset=HC_M2_0606_P' - - json = JSON::load(File.read('test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json')) - # p json - page = @agent.post(URI.encode(url), - json, - ({'Content-Type' => 'application/x-www-form-urlencoded'})) - form = page.forms_with("marker_regression")[0] - p form - form.fields.select { |fld| fld.name == 'dataset' }.first.value.must_equal 'HC_M2_0606_P' - form.fields.select { |fld| fld.name == 'value:BXD1' }.first.value.must_equal "15.034" - end - end - - describe MappingTest do - it "CIM mapping tool selection (using reaper)" do - url = $host+'/marker_regression' - - json = JSON::load(File.read('test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json')) - json["method"] = "reaper" - page = @agent.post(URI.encode(url), json) - form = page.forms_with("marker_regression")[0] - form.fields.select { |fld| fld.name == 'dataset' }.first.value.must_equal 'HC_M2_0606_P' - form.fields.select { |fld| fld.name == 'value:BXD1' }.first.value.must_equal "15.034" - end - end - -end diff --git a/test/lib/navigation.rb b/test/lib/navigation.rb deleted file mode 100644 index ee9f41d2..00000000 --- a/test/lib/navigation.rb +++ /dev/null @@ -1,43 +0,0 @@ -# In these tests we navigate from the main page to a specific trait then hit the different mapping tool buttons (In this case pylMM and r/qtl) followed by computing the results (marker regressions). - - -class MappingTest -end - -describe MappingTest do - before do - @agent = Mechanize.new - @agent.agent.http.ca_file = '/etc/ssl/certs/ca-certificates.crt' - end - - describe MappingTest do - it "pyLMM mapping tool selection" do - break if $options[:skip_broken] - page = @agent.get($host+'/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P') -#Navigates to http://localhost:5003/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P and clicks respective buttons. - link = page.link_with(text: 'pyLMM') - page = link.click - puts page.uri - link = page.link_with(text: 'Compute') - page = link.click - puts page.uri - probe_link.uri.to_s.must_equal "/marker_regression" - end - end - -end - -describe MappingTest do - it "R/qtl mapping tool selection" do - break if $options[:skip_broken] - page = @agent.get($host+'/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P') - link = page.link_with(text: 'R/qtl') - page = link.click - puts page.uri - form.field_with(:name => 'Methods').options[2].select - link = page.link_with(text: 'Compute') - page = link.click - puts page.uri - probe_link.uri.to_s.must_equal "/marker_regression" - end -end -- cgit v1.2.3