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-rw-r--r--test/lib/gntest.rb6
-rw-r--r--test/lib/link_checker.rb50
-rw-r--r--test/lib/main_web_functionality.rb58
-rw-r--r--test/lib/mapping.rb58
-rw-r--r--test/lib/navigation.rb43
5 files changed, 0 insertions, 215 deletions
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 ec61de2d..00000000
--- a/test/lib/main_web_functionality.rb
+++ /dev/null
@@ -1,58 +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)
- 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[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)
- 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
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 04:51:46 +0000