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import csv
import sys
import html
import json
import requests
from lxml import etree
from pathlib import Path
from lxml.html import parse
from functools import reduce
from link_checker import check_page
def corrs_base_data():
return [
{
"dataset": "HC_M2_0606_P",
"trait_id": "1435464_at",
"corr_dataset": "HC_M2_0606_P",
},
{
"dataset": "HC_M2_0606_P",
"trait_id": "1457545_at",
"corr_dataset": "HC_M2_0606_R",
},
{
"dataset": "HC_M2_0606_P",
"trait_id": "1442370_at",
"corr_dataset": "BXDPublish",
}
]
def sample_vals():
return '{"C57BL/6J":"10.835","DBA/2J":"11.142","B6D2F1":"11.126","D2B6F1":"11.143","BXD1":"10.811","BXD2":"11.503","BXD5":"10.766","BXD6":"10.986","BXD8":"11.050","BXD9":"10.822","BXD11":"10.670","BXD12":"10.946","BXD13":"10.890","BXD14":"x","BXD15":"10.884","BXD16":"11.222","BXD18":"x","BXD19":"10.968","BXD20":"10.962","BXD21":"10.906","BXD22":"11.080","BXD23":"11.046","BXD24":"11.146","BXD24a":"x","BXD25":"x","BXD27":"11.078","BXD28":"11.034","BXD29":"10.808","BXD30":"x","BXD31":"11.087","BXD32":"11.029","BXD33":"10.662","BXD34":"11.482","BXD35":"x","BXD36":"x","BXD37":"x","BXD38":"10.836","BXD39":"10.926","BXD40":"10.638","BXD41":"x","BXD42":"10.974","BXD43":"10.828","BXD44":"10.900","BXD45":"11.358","BXD48":"11.042","BXD48a":"10.975","BXD49":"x","BXD50":"11.228","BXD51":"11.126","BXD52":"x","BXD53":"x","BXD54":"x","BXD55":"11.580","BXD56":"x","BXD59":"x","BXD60":"10.829","BXD61":"11.152","BXD62":"11.156","BXD63":"10.942","BXD64":"10.506","BXD65":"11.126","BXD65a":"11.272","BXD65b":"11.157","BXD66":"11.071","BXD67":"11.080","BXD68":"10.997","BXD69":"11.096","BXD70":"11.152","BXD71":"x","BXD72":"x","BXD73":"11.262","BXD73a":"11.444","BXD73b":"x","BXD74":"10.974","BXD75":"11.150","BXD76":"10.920","BXD77":"10.928","BXD78":"x","BXD79":"11.371","BXD81":"x","BXD83":"10.946","BXD84":"11.181","BXD85":"10.992","BXD86":"10.770","BXD87":"11.200","BXD88":"x","BXD89":"10.930","BXD90":"11.183","BXD91":"x","BXD93":"11.056","BXD94":"10.737","BXD95":"x","BXD98":"10.986","BXD99":"10.892","BXD100":"x","BXD101":"x","BXD102":"x","BXD104":"x","BXD105":"x","BXD106":"x","BXD107":"x","BXD108":"x","BXD109":"x","BXD110":"x","BXD111":"x","BXD112":"x","BXD113":"x","BXD114":"x","BXD115":"x","BXD116":"x","BXD117":"x","BXD119":"x","BXD120":"x","BXD121":"x","BXD122":"x","BXD123":"x","BXD124":"x","BXD125":"x","BXD126":"x","BXD127":"x","BXD128":"x","BXD128a":"x","BXD130":"x","BXD131":"x","BXD132":"x","BXD133":"x","BXD134":"x","BXD135":"x","BXD136":"x","BXD137":"x","BXD138":"x","BXD139":"x","BXD141":"x","BXD142":"x","BXD144":"x","BXD145":"x","BXD146":"x","BXD147":"x","BXD148":"x","BXD149":"x","BXD150":"x","BXD151":"x","BXD152":"x","BXD153":"x","BXD154":"x","BXD155":"x","BXD156":"x","BXD157":"x","BXD160":"x","BXD161":"x","BXD162":"x","BXD165":"x","BXD168":"x","BXD169":"x","BXD170":"x","BXD171":"x","BXD172":"x","BXD173":"x","BXD174":"x","BXD175":"x","BXD176":"x","BXD177":"x","BXD178":"x","BXD180":"x","BXD181":"x","BXD183":"x","BXD184":"x","BXD186":"x","BXD187":"x","BXD188":"x","BXD189":"x","BXD190":"x","BXD191":"x","BXD192":"x","BXD193":"x","BXD194":"x","BXD195":"x","BXD196":"x","BXD197":"x","BXD198":"x","BXD199":"x","BXD200":"x","BXD201":"x","BXD202":"x","BXD203":"x","BXD204":"x","BXD205":"x","BXD206":"x","BXD207":"x","BXD208":"x","BXD209":"x","BXD210":"x","BXD211":"x","BXD212":"x","BXD213":"x","BXD214":"x","BXD215":"x","BXD216":"x","BXD217":"x","BXD218":"x","BXD219":"x","BXD220":"x"}'
def do_request(url, data):
response = requests.post(
url,
data={
"dataset": "HC_M2_0606_P",
"trait_id": "1435464_at",
"corr_dataset": "HC_M2_0606_P",
"corr_sample_method": "pearson",
"corr_return_results": "100",
"corr_samples_group": "samples_primary",
"sample_vals": sample_vals(),
"location_type": "gene",
**data,
})
while response.text.find('<meta http-equiv="refresh" content="5">') >= 0:
response = requests.get(response.url)
pass
return response
def check_sample_correlations(baseurl, base_data):
data = {
**base_data,
"corr_type": "sample",
"corr_sample_method": "pearson",
"location_type": "gene",
"corr_return_results": "200"
}
top_n_message = "The top 200 correlations ranked by the Genetic Correlation"
result = do_request(f"{baseurl}/corr_compute", data)
assert result.status_code == 200
assert (result.text.find(f"Values of record {base_data['trait_id']}") >= 0), result.text
assert (result.text.find(top_n_message) >= 0), result.text
def check_tissue_correlations(baseurl, base_data):
data = {
**base_data,
"corr_type": "tissue",
"location_type": "gene",
}
result = do_request(f"{baseurl}/corr_compute", data)
assert result.status_code == 200
if (data["trait_id"] == "1442370_at"
and data["corr_dataset"] in ("BXDPublish",)):
top_n_message = (
"It is not possible to compute the 'Tissue' correlations between "
f"trait '{data['trait_id']}' and the data")
else:
top_n_message = "The top 100 correlations ranked by the Tissue Correlation"
assert (result.text.find(f"Values of record {base_data['trait_id']}") >= 0), result.text
assert (html.unescape(result.text).find(top_n_message) >= 0), (
f"NOT FOUND: {top_n_message}")
def check_lit_correlations(baseurl, base_data):
data = {
**base_data,
"corr_type": "lit",
"corr_return_results": "200"
}
result = do_request(f"{baseurl}/corr_compute", data)
assert result.status_code == 200
if (data["trait_id"] == "1442370_at"
and data["corr_dataset"] in ("BXDPublish",)):
top_n_message = (
"It is not possible to compute the 'Literature' correlations "
f"between trait '{data['trait_id']}' and the data")
else:
top_n_message = "The top 200 correlations ranked by the Literature Correlation"
assert (result.text.find(f"Values of record {base_data['trait_id']}") >= 0), result.text
assert (html.unescape(result.text).find(top_n_message) >= 0), (
f"NOT FOUND: {top_n_message}")
def check_correlations(args_obj, parser):
print("")
print("Checking the correlations...")
corr_type_fns = {
"sample": check_sample_correlations,
"tissue": check_tissue_correlations,
"lit": check_lit_correlations
}
host = args_obj.host
failure = False
for corr_type, corr_type_fn in corr_type_fns.items():
for corr_base in corrs_base_data():
try:
print(f"\tChecking {corr_type} correlations...", end="")
corr_type_fn(host, corr_base)
print(" ok")
except AssertionError as asserterr:
print (f" fail: {asserterr.args[0]}")
failure = True
if failure:
print("FAIL!")
sys.exit(1)
print("OK")
def thread(value, *functions):
return reduce(lambda result, func: func(result), functions, value)
def parse_results_from_html(raw_html):
doc = etree.HTML(raw_html)
# print(f"THE RESPONSE: {response.text}")
scripts = doc.xpath('//script')
for script in scripts:
script_content = thread(
script.xpath('.//child::text()'),
lambda val: "".join(val).strip())
if script_content.find("var tableJson") >= 0:
return json.loads(thread(
script_content,
lambda val: val[len("var tableJson = "):].strip()))
return []
def parse_expected(filepath):
with open(filepath, encoding="utf-8") as infl:
reader = csv.DictReader(infl, dialect=csv.unix_dialect)
for line in reader:
yield line
def verify_correctness(actual, expected):
# assert len(actual) == len(expected), (
# f"Expected {len(expected)} results but instead got {len(actual)} "
# "results")
def __assert(act_val, exp_val, title):
assert act_val == exp_val, (
f"Different '{title}' values: expected: '{exp_val}' but got "
f"'{act_val}'")
for act, exp in zip(actual, expected):
__assert(act["trait_id"], exp["Record ID"], "Trait/Record ID")
# __assert(act["dataset"], exp[""], "Dataset")
__assert(act["sample_r"], exp["Sample r ?"], "Sample r"),
__assert(act["num_overlap"], exp["N Cases"], "N Cases")
__assert(act["sample_p"], exp["Sample p(r) ?"], "Sample p")
__assert(act["symbol"], exp["Symbol"], "Symbol")
__assert(act["description"], exp["Description"], "Description")
__assert(act["location"], exp["Location Chr and Mb"], "Location Chr and Mb")
__assert(act["mean"], exp["Mean Expr"], "Mean")
# __assert(act["additive"], exp[], "Additive")
# __assert(act["lod_score"], exp[], "LOD Score")
__assert(act["lrs_location"], exp["Max LRS Location Chr and Mb"], "Max LRS Location Chr and Mb")
__assert(act["lit_corr"], exp["Lit Corr ?"], "Lit Corr")
__assert(act["tissue_corr"], exp["Tissue r ?"], "Tissue r")
__assert(act["tissue_pvalue"], exp["Tissue p(r) ?"], "Tissue p(r)")
# __assert(act[], exp[], "Different ...")
def check_correctness(host):
failures = tuple()
__idx = 1
tests = [
({"dataset": "HC_M2_0606_P", "trait_id": "1435464_at",
"corr_dataset": "HC_M2_0606_P", "corr_type": "sample",
"corr_sample_method": "pearson", "location_type": "gene",
"corr_samples_group": "samples_primary", "sample_vals": sample_vals(),
"corr_return_results": "500"},
"HC_M2_0606_P___1435464_at___sample_r___pearson__results.csv"),]
for test_data, expected_file in tests:
print(f"Test {__idx} ...", end="\t")
response = requests.post(f"{host}/corr_compute", data=test_data)
while response.text.find('<meta http-equiv="refresh" content="5">') >= 0:
response = requests.get(response.url)
pass
results = parse_results_from_html(response.text)
filepath = Path.cwd().parent.joinpath(
f"test/requests/correlation_results_text_files/{expected_file}")
try:
verify_correctness(results, tuple(parse_expected(filepath)))
print("OK")
except AssertionError as aerr:
failures = failures + ((__idx, aerr.args[0]),)
print("FAIL!")
__idx = __idx + 1
if len(failures) > 0:
print("\n\nFAILURES: ")
for test_num, err_msg in failures:
print(f"\tTest {test_num}: {err_msg}")
return False
return True
def check_correlations_correctness(args_obj, parser):
print("")
print("Checking the correctness of the correlations...")
if not check_correctness(args_obj.host):
sys.exit(1)
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