diff options
Diffstat (limited to 'test')
| -rw-r--r-- | test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json | 142 | ||||
| -rw-r--r-- | test/lib/gntest.rb | 5 | ||||
| -rw-r--r-- | test/lib/mapping.rb | 70 |
3 files changed, 185 insertions, 32 deletions
diff --git a/test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json b/test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json new file mode 100644 index 00000000..15428553 --- /dev/null +++ b/test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json @@ -0,0 +1,142 @@ +{ + "temp_uuid" : "unknown", +"maf" : "0.01", +"control_marker" : "mCV24506226", +"dataset" : "HC_M2_0606_P", + "do_control" : "false", + "maf" : "0.01", + "manhattan_plot" : "False", + "mapmethod_rqtl_geno" : "em", + "mapmodel_rqtl_geno" : "normal", + "method" : "rqtl_geno", + "num_bootstrap" : "2000", + "num_perm" : "", + "pair_scan" : "false", + "suggestive" : "0", + "trait_id" : "1433387_at", + "value:129S1/SvImJ" : "6.920", + "value:A/J" : "7.437", + "value:AKR/J" : "7.550", + "value:B6D2F1" : "7.742", + "value:BALB/cByJ" : "6.613", + "value:BALB/cJ" : "6.664", + "value:BXD1" : "6.749", + "value:BXD100" : "x", + "value:BXD101" : "x", + "value:BXD102" : "x", + "value:BXD103" : "x", + "value:BXD11" : "7.398", + "value:BXD12" : "7.073", + "value:BXD13" : "8.191", + "value:BXD14" : "x", + "value:BXD15" : "7.406", + "value:BXD16" : "6.890", + "value:BXD18" : "x", + "value:BXD19" : "6.980", + "value:BXD2" : "7.248", + "value:BXD20" : "7.554", + "value:BXD21" : "7.316", + "value:BXD22" : "7.327", + "value:BXD23" : "7.605", + "value:BXD24" : "7.306", + "value:BXD24a" : "x", + "value:BXD25" : "x", + "value:BXD27" : "7.800", + "value:BXD28" : "7.023", + "value:BXD29" : "7.518", + "value:BXD30" : "x", + "value:BXD31" : "7.301", + "value:BXD32" : "7.161", + "value:BXD33" : "7.140", + "value:BXD34" : "8.180", + "value:BXD35" : "x", + "value:BXD36" : "x", + "value:BXD37" : "x", + "value:BXD38" : "7.350", + "value:BXD39" : "6.976", + "value:BXD40" : "7.411", + "value:BXD41" : "x", + "value:BXD42" : "7.050", + "value:BXD43" : "6.866", + "value:BXD44" : "7.246", + "value:BXD45" : "7.576", + "value:BXD48" : "7.108", + "value:BXD48a" : "7.192", + "value:BXD49" : "x", + "value:BXD5" : "6.771", + "value:BXD50" : "7.528", + "value:BXD51" : "7.408", + "value:BXD52" : "x", + "value:BXD53" : "x", + "value:BXD54" : "x", + "value:BXD55" : "6.720", + "value:BXD56" : "x", + "value:BXD59" : "x", + "value:BXD6" : "7.372", + "value:BXD60" : "7.178", + "value:BXD61" : "7.198", + "value:BXD62" : "7.618", + "value:BXD63" : "7.076", + "value:BXD64" : "6.576", + "value:BXD65" : "7.046", + "value:BXD65a" : "7.046", + "value:BXD65b" : "7.385", + "value:BXD66" : "7.108", + "value:BXD67" : "7.342", + "value:BXD68" : "7.668", + "value:BXD69" : "7.310", + "value:BXD70" : "7.278", + "value:BXD71" : "x", + "value:BXD72" : "x", + "value:BXD73" : "7.342", + "value:BXD73a" : "7.841", + "value:BXD74" : "7.298", + "value:BXD75" : "7.133", + "value:BXD76" : "7.448", + "value:BXD77" : "7.014", + "value:BXD78" : "x", + "value:BXD79" : "7.916", + "value:BXD8" : "7.148", + "value:BXD81" : "x", + "value:BXD83" : "7.322", + "value:BXD84" : "7.298", + "value:BXD85" : "7.243", + "value:BXD86" : "7.719", + "value:BXD87" : "7.145", + "value:BXD88" : "x", + "value:BXD89" : "7.162", + "value:BXD9" : "6.708", + "value:BXD90" : "7.497", + "value:BXD91" : "x", + "value:BXD93" : "7.558", + "value:BXD94" : "6.817", + "value:BXD95" : "x", + "value:BXD98" : "7.753", + "value:BXD99" : "8.076", + "value:C3H/HeJ" : "7.536", + "value:C57BL/6ByJ" : "6.940", + "value:C57BL/6J" : "7.309", + "value:CAST/EiJ" : "8.796", + "value:CXB1" : "6.430", + "value:CXB10" : "6.958", + "value:CXB11" : "6.182", + "value:CXB12" : "6.432", + "value:CXB13" : "6.388", + "value:CXB2" : "7.687", + "value:CXB3" : "6.312", + "value:CXB4" : "6.453", + "value:CXB5" : "6.959", + "value:CXB6" : "7.022", + "value:CXB7" : "6.334", + "value:CXB8" : "6.790", + "value:CXB9" : "6.545", + "value:D2B6F1" : "7.615", + "value:DBA/2J" : "7.816", + "value:KK/HlJ" : "8.035", + "value:LG/J" : "7.594", + "value:NOD/ShiLtJ" : "8.220", + "value:NZO/HlLtJ" : "7.629", + "value:PWD/PhJ" : "6.320", + "value:PWK/PhJ" : "7.235", + "value:WSB/EiJ" : "7.650" +} diff --git a/test/lib/gntest.rb b/test/lib/gntest.rb new file mode 100644 index 00000000..865ef51d --- /dev/null +++ b/test/lib/gntest.rb @@ -0,0 +1,5 @@ +require 'minitest/autorun' +require 'mechanize' + +# ---- Use some default parameters if not set +$host = "http://localhost:5003" if !$host diff --git a/test/lib/mapping.rb b/test/lib/mapping.rb index 08b6b5da..4c8ff632 100644 --- a/test/lib/mapping.rb +++ b/test/lib/mapping.rb @@ -1,5 +1,6 @@ # 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 @@ -11,41 +12,46 @@ describe MappingTest do end describe MappingTest do - it "pyLMM mapping tool selection" do - url = $host+'/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P' - page = @agent.get(url) - # get the form - # form = @agent.page.form_with(:name => "my-form") - # get the button you want from the form - # page.forms.each do |form| - # p form - # end - # button = page.button_with(:value => "pylmm_compute") - # submit the form using that button - # agent.submit(form, button) - # 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" + 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 - 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 -end - -describe MappingTest do + 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" + 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] + 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 "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 '6.749' + end + end + end |