Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing

7 files changed, 21 insertions, 222 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 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
diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 256bf6ef..64553ed8 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -4,6 +4,8 @@ import requests
 from lxml.html import parse
 from requests.exceptions import ConnectionError
 
+DO_FAIL=False  # fail on error
+
 def is_root_link(link):
     pattern = re.compile("^/$")
     return pattern.match(link)
@@ -25,24 +27,34 @@ def get_links(doc):
               , doc.cssselect("a")))
 
 def verify_link(link):
+    if link[0] == "#":
+        # local link on page
+        return
+    print("verifying "+link)
     try:
-        result = requests.get(link, timeout=20)
+        result = requests.get(link, timeout=20, verify=False)
         if result.status_code == 200:
             print(link+" ==> OK")
+        elif result.status_code == 307:
+            print(link+" ==> REDIRECT")
         else:
             print("ERROR: link `"+link+"` failed with status "
                   , result.status_code)
+            if DO_FAIL:
+                raise Exception("Failed verify")
     except ConnectionError as ex:
         print("ERROR: ", link, ex)
+        if DO_FAIL:
+            raise ex
 
 def check_page(host, start_url):
     print("")
-    print("Checking links in page `"+start_url+"`")
+    print("Checking links host "+host+" in page `"+start_url+"`")
     doc = parse(start_url).getroot()
     links = get_links(doc)
     internal_links = filter(is_internal_link, links)
     external_links = filter(lambda x: not is_internal_link(x), links)
-    external_links.append("http://somenon-existentsite.brr")
+    # external_links.append("http://somenon-existentsite.brr")
     for link in internal_links:
         verify_link(host+link)
 
diff --git a/test/requests/test-website.py b/test/requests/test-website.py
index 2bef6eb1..118c9df1 100755
--- a/test/requests/test-website.py
+++ b/test/requests/test-website.py
@@ -8,12 +8,16 @@ import argparse
 from link_checker import check_links
 from mapping_tests import check_mapping
 from main_web_functionality import check_main_web_functionality
+import link_checker
+import sys
 
 print("Mechanical Rob firing up...")
 
 def run_all(args_obj, parser):
     print("")
     print("Running all tests.")
+    print(args_obj)
+    link_checker.DO_FAIL = args_obj.fail
     check_main_web_functionality(args_obj, parser)
     check_links(args_obj, parser)
     check_mapping(args_obj, parser)
@@ -32,6 +36,8 @@ This is Mechanical-Rob - an automated web server tester for
 """
 parser = argparse.ArgumentParser(description=desc)
 
+parser.add_argument("--fail", help="Fail and stop on any error", action="store_true")
+
 parser.add_argument("-d", "--database", metavar="DB", type=str
                     , default="db_webqtl_s"
                     , help="Use database (default db_webqtl_s)")