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from __future__ import print_function
import re
import copy
import json
import requests
from lxml.html import fromstring
def load_data_from_file():
filename = "../test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json"
file_handle = open(filename, "r")
file_data = json.loads(file_handle.read().encode("utf-8"))
return file_data
def check_pylmm_tool_selection(host, data):
print("")
print("pylmm mapping tool selection")
data["method"] = "pylmm"
page = requests.post(host+"/marker_regression", data=data)
doc = fromstring(page.text)
form = doc.forms[1]
assert form.fields["dataset"] == "HC_M2_0606_P"
assert form.fields["value:BXD1"] == "15.034" # Check value in the file
def check_R_qtl_tool_selection(host, data):
print("")
print("R/qtl mapping tool selection")
headers = {"Content-Type": "application/x-www-form-urlencoded"}
page = requests.post(host+"/marker_regression", data=data, headers=headers)
doc = fromstring(page.text)
form = doc.forms[1]
assert form.fields["dataset"] == "HC_M2_0606_P"
assert form.fields["value:BXD1"] == "15.034"
def check_CIM_tool_selection(host, data):
print("")
print("CIM mapping tool selection (using reaper)")
data["method"] = "reaper"
page = requests.post(host+"/marker_regression", data=data)
doc = fromstring(page.text)
form = doc.forms[1]
assert form.fields["dataset"] == "HC_M2_0606_P"
assert form.fields["value:BXD1"] == "15.034"
def check_mapping(args_obj, parser):
print("")
print("Checking mapping")
host = args_obj.host
data = load_data_from_file()
check_pylmm_tool_selection(host, copy.deepcopy(data))
check_R_qtl_tool_selection(host, copy.deepcopy(data)) ## Why does this fail?
check_CIM_tool_selection(host, copy.deepcopy(data))
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