diff options
| -rw-r--r-- | test/requests/correlation_tests.py | 99 | ||||
| -rwxr-xr-x | test/requests/test-website.py | 13 |
2 files changed, 111 insertions, 1 deletions
diff --git a/test/requests/correlation_tests.py b/test/requests/correlation_tests.py index 523dfc66..8a4dba12 100644 --- a/test/requests/correlation_tests.py +++ b/test/requests/correlation_tests.py @@ -1,7 +1,12 @@ +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(): @@ -124,3 +129,97 @@ def check_correlations(args_obj, parser): 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) diff --git a/test/requests/test-website.py b/test/requests/test-website.py index 7edb42bc..35a69c6c 100755 --- a/test/requests/test-website.py +++ b/test/requests/test-website.py @@ -9,7 +9,7 @@ from link_checker import check_links from link_checker import check_packaged_js_files from mapping_tests import check_mapping from navigation_tests import check_navigation -from correlation_tests import check_correlations +from correlation_tests import check_correlations, check_correlations_correctness from main_web_functionality import check_main_web_functionality import link_checker import sys @@ -43,6 +43,7 @@ def run_all(args_obj, parser): check_packaged_js_files(args_obj, parser) check_mapping(args_obj, parser) check_correlations(args_obj, parser) + # check_correlations_correctness(args_obj, parser) # activate once all correlations are verified # TODO: Add other functions as they are created. @@ -135,6 +136,16 @@ parser.add_argument( help="Checks that correlations run correctly.", ) +parser.add_argument( + "-e", + "--correlations-correctness", + dest="accumulate", + action="store_const", + const=check_correlations_correctness, + default=print_help, + help="Check that the correlation results are correct" +) + args = parser.parse_args() |