Tests: Mapping tests pass now

2 files changed, 246 insertions, 143 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
index 15428553..195c16e4 100644
--- 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
@@ -1,142 +1,245 @@
 {
     "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"
-}
+    "control_marker": "NES13033186",
+ "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": "1435395_s_at",
+ "value:129S1/SvImJ": "15.468",
+ "value:A/J": "15.230",
+ "value:AKR/J": "15.798",
+ "value:B6D2F1": "15.575",
+ "value:BALB/cByJ": "15.138",
+ "value:BALB/cJ": "15.222",
+ "value:BXD1": "15.034",
+ "value:BXD100": "x",
+ "value:BXD101": "x",
+ "value:BXD102": "x",
+ "value:BXD104": "x",
+ "value:BXD105": "x",
+ "value:BXD106": "x",
+ "value:BXD107": "x",
+ "value:BXD108": "x",
+ "value:BXD109": "x",
+ "value:BXD11": "15.364",
+ "value:BXD110": "x",
+ "value:BXD111": "x",
+ "value:BXD112": "x",
+ "value:BXD113": "x",
+ "value:BXD114": "x",
+ "value:BXD115": "x",
+ "value:BXD116": "x",
+ "value:BXD117": "x",
+ "value:BXD119": "x",
+ "value:BXD12": "14.992",
+ "value:BXD120": "x",
+ "value:BXD121": "x",
+ "value:BXD122": "x",
+ "value:BXD123": "x",
+ "value:BXD124": "x",
+ "value:BXD125": "x",
+ "value:BXD126": "x",
+ "value:BXD127": "x",
+ "value:BXD128": "x",
+ "value:BXD128a": "x",
+ "value:BXD13": "15.290",
+ "value:BXD130": "x",
+ "value:BXD131": "x",
+ "value:BXD132": "x",
+ "value:BXD133": "x",
+ "value:BXD134": "x",
+ "value:BXD135": "x",
+ "value:BXD136": "x",
+ "value:BXD137": "x",
+ "value:BXD138": "x",
+ "value:BXD139": "x",
+  "value:BXD14": "x",
+ "value:BXD141": "x",
+ "value:BXD142": "x",
+ "value:BXD144": "x",
+ "value:BXD145": "x",
+ "value:BXD146": "x",
+ "value:BXD147": "x",
+ "value:BXD148": "x",
+ "value:BXD149": "x",
+ "value:BXD15": "15.188",
+ "value:BXD150": "x",
+ "value:BXD151": "x",
+ "value:BXD152": "x",
+ "value:BXD153": "x",
+ "value:BXD154": "x",
+ "value:BXD155": "x",
+ "value:BXD156": "x",
+ "value:BXD157": "x",
+ "value:BXD16": "15.340",
+ "value:BXD160": "x",
+ "value:BXD161": "x",
+ "value:BXD162": "x",
+ "value:BXD165": "x",
+ "value:BXD168": "x",
+ "value:BXD169": "x",
+ "value:BXD170": "x",
+ "value:BXD171": "x",
+ "value:BXD172": "x",
+ "value:BXD173": "x",
+ "value:BXD174": "x",
+ "value:BXD175": "x",
+ "value:BXD176": "x",
+ "value:BXD177": "x",
+ "value:BXD178": "x",
+ "value:BXD18": "x",
+ "value:BXD180": "x",
+ "value:BXD181": "x",
+ "value:BXD183": "x",
+ "value:BXD184": "x",
+ "value:BXD186": "x",
+ "value:BXD187": "x",
+ "value:BXD188": "x",
+ "value:BXD189": "x",
+ "value:BXD19": "15.144",
+ "value:BXD190": "x",
+ "value:BXD191": "x",
+ "value:BXD192": "x",
+ "value:BXD193": "x",
+ "value:BXD194": "x",
+ "value:BXD195": "x",
+ "value:BXD196": "x",
+ "value:BXD197": "x",
+ "value:BXD198": "x",
+ "value:BXD199": "x",
+ "value:BXD2": "15.538",
+ "value:BXD20": "15.194",
+ "value:BXD200": "x",
+ "value:BXD201": "x",
+ "value:BXD202": "x",
+ "value:BXD203": "x",
+ "value:BXD204": "x",
+ "value:BXD205": "x",
+ "value:BXD206": "x",
+ "value:BXD207": "x",
+ "value:BXD208": "x",
+ "value:BXD209": "x",
+ "value:BXD21": "15.088",
+ "value:BXD210": "x",
+ "value:BXD211": "x",
+ "value:BXD212": "x",
+ "value:BXD213": "x",
+ "value:BXD214": "x",
+ "value:BXD215": "x",
+ "value:BXD216": "x",
+ "value:BXD217": "x",
+ "value:BXD218": "x",
+ "value:BXD219": "x",
+ "value:BXD22": "15.499",
+ "value:BXD220": "x",
+ "value:BXD23": "14.988",
+ "value:BXD24": "15.562",
+ "value:BXD24a": "x",
+ "value:BXD25": "x",
+ "value:BXD27": "15.598",
+ "value:BXD28": "15.510",
+ "value:BXD29": "15.041",
+ "value:BXD30": "x",
+ "value:BXD31": "14.834",
+ "value:BXD32": "15.245",
+ "value:BXD33": "15.466",
+ "value:BXD34": "15.302",
+ "value:BXD35": "x",
+ "value:BXD36": "x",
+ "value:BXD37": "x",
+ "value:BXD38": "15.131",
+ "value:BXD39": "15.430",
+ "value:BXD40": "15.488",
+ "value:BXD41": "x",
+ "value:BXD42": "14.878",
+ "value:BXD43": "15.542",
+ "value:BXD44": "15.417",
+ "value:BXD45": "14.910",
+ "value:BXD48": "15.487",
+ "value:BXD48a": "15.328",
+ "value:BXD49": "x",
+ "value:BXD5": "15.622",
+ "value:BXD50": "15.435",
+ "value:BXD51": "15.183",
+ "value:BXD52": "x",
+ "value:BXD53": "x",
+ "value:BXD54": "x",
+ "value:BXD55": "14.928",
+ "value:BXD56": "x",
+ "value:BXD59": "x",
+ "value:BXD6": "15.366",
+ "value:BXD60": "15.502",
+ "value:BXD61": "15.622",
+ "value:BXD62": "15.198",
+ "value:BXD63": "15.238",
+ "value:BXD64": "15.572",
+ "value:BXD65": "15.485",
+ "value:BXD65a": "15.284",
+ "value:BXD65b": "15.318",
+ "value:BXD66": "15.406",
+ "value:BXD67": "15.509",
+ "value:BXD68": "15.552",
+ "value:BXD69": "15.667",
+ "value:BXD70": "15.104",
+ "value:BXD71": "x",
+ "value:BXD72": "x",
+ "value:BXD73": "15.210",
+ "value:BXD73a": "15.223",
+ "value:BXD73b": "x",
+ "value:BXD74": "15.666",
+ "value:BXD75": "15.554",
+ "value:BXD76": "15.234",
+ "value:BXD77": "15.613",
+ "value:BXD78": "x",
+ "value:BXD79": "15.124",
+ "value:BXD8": "15.548",
+ "value:BXD81": "x",
+ "value:BXD83": "15.512",
+ "value:BXD84": "15.426",
+ "value:BXD85": "15.252",
+ "value:BXD86": "15.457",
+ "value:BXD87": "15.320",
+ "value:BXD88": "x",
+ "value:BXD89": "15.316",
+ "value:BXD9": "15.669",
+ "value:BXD90": "15.348",
+ "value:BXD91": "x",
+ "value:BXD93": "15.602",
+ "value:BXD94": "15.360",
+ "value:BXD95": "x",
+ "value:BXD98": "15.421",
+ "value:BXD99": "15.534",
+ "value:C3H/HeJ": "15.398",
+ "value:C57BL/6ByJ": "15.702",
+ "value:C57BL/6J": "15.281",
+ "value:CAST/EiJ": "15.890",
+ "value:CXB1": "15.774",
+ "value:CXB10": "15.518",
+ "value:CXB11": "15.922",
+ "value:CXB12": "15.753",
+ "value:CXB13": "15.608",
+ "value:CXB2": "15.320",
+ "value:CXB3": "15.492",
+ "value:CXB4": "15.541",
+ "value:CXB5": "15.353",
+ "value:CXB6": "15.454",
+ "value:CXB7": "15.547",
+ "value:CXB8": "15.496",
+ "value:CXB9": "15.880",
+ "value:D2B6F1": "15.265",
+ "value:DBA/2J": "15.287",
+ "value:KK/HlJ": "15.303",
+ "value:LG/J": "15.285",
+ "value:NOD/ShiLtJ": "15.348",
+ "value:NZO/HlLtJ": "15.028",
+ "value:PWD/PhJ": "15.535",
+ "value:PWK/PhJ": "15.382",
+ "value:WSB/EiJ": "15.424"}
diff --git a/test/lib/mapping.rb b/test/lib/mapping.rb
index 4c8ff632..d6a3cd7b 100644
--- a/test/lib/mapping.rb
+++ b/test/lib/mapping.rb
@@ -19,7 +19,7 @@ describe MappingTest do
       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
+      # 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'
@@ -37,7 +37,7 @@ describe MappingTest do
                          ({'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'
+      form.fields.select { |fld| fld.name == 'value:BXD1' }.first.value.must_equal "15.034"
     end
   end
 
@@ -50,7 +50,7 @@ describe MappingTest do
       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'
+      form.fields.select { |fld| fld.name == 'value:BXD1' }.first.value.must_equal "15.034"
     end
   end