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authorFrederick Muriuki Muriithi2022-11-28 12:35:34 +0300
committerFrederick Muriuki Muriithi2022-11-28 12:35:34 +0300
commit6e6fd71f3ee8df8c40fe82d5df93bec4a125ed29 (patch)
tree8434c8f5cb982d3deea7acd1c309f4334f40db8f /test
parentf935f79b95d1345583254e38d146cece75cd5cf4 (diff)
downloadgenenetwork2-6e6fd71f3ee8df8c40fe82d5df93bec4a125ed29.tar.gz
mechanical-rob: Add more tests for correctness
Diffstat (limited to 'test')
-rw-r--r--test/requests/correlation_tests.py131
1 files changed, 91 insertions, 40 deletions
diff --git a/test/requests/correlation_tests.py b/test/requests/correlation_tests.py
index 8a4dba12..552ef90e 100644
--- a/test/requests/correlation_tests.py
+++ b/test/requests/correlation_tests.py
@@ -135,7 +135,6 @@ def thread(value, *functions):
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(
@@ -154,66 +153,118 @@ def parse_expected(filepath):
for line in reader:
yield line
-def verify_correctness(actual, expected):
+def collect_failures(actual, expected, keys):
# 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 __equal(act_row, exp_row):
+ __eq = tuple()
+ for act_key, exp_key, title in keys:
+ act_val, exp_val = (act_row[act_key], exp_row[exp_key])
+ if act_val == exp_val:
+ # __eq = __eq + ("PASSED",)
+ continue
+ __eq = __eq + ((
+ f"Different '{title}' values: expected: '{exp_val}' but got "
+ f"'{act_val}'"),)
+ continue
+ return __eq
+
+ return tuple(
+ __equal(act_row, exp_row)
+ for act_row, exp_row in zip(actual, expected))
def check_correctness(host):
- failures = tuple()
- __idx = 1
+ pearsons_keys = (
+ ("trait_id", "Record ID", "Trait/Record ID"),
+ ("sample_r", "Sample r ?", "Sample r value"),
+ ("num_overlap", "N Cases", "N Cases"),
+ ("sample_p", "Sample p(r) ?", "Sample p value"),
+ ("symbol", "Symbol", "Symbol"),
+ ("description", "Description", "Description"),
+ ("location", "Location Chr and Mb", "Location Chr and Mb"),
+ ("mean", "Mean Expr", "Mean"),
+ ("lrs_location", "Max LRS Location Chr and Mb", "Max LRS Location Chr and Mb"),
+ ("lit_corr", "Lit Corr ?", "Literature Correlation"),
+ ("tissue_corr", "Tissue r ?", "Tissue Correlation r"),
+ ("tissue_pvalue", "Tissue p(r) ?", "Tissue Correlation p value"))
+
+ spearmans_keys = (
+ ("trait_id", "Record ID", "Trait/Record ID"),
+ ("sample_r", "Sample rho ?", "Sample rho value"),
+ ("num_overlap", "N Cases", "N Cases"),
+ ("sample_p", "Sample p(rho) ?", "Sample p(rho) value"),
+ ("symbol", "Symbol", "Symbol"),
+ ("description", "Description", "Description"),
+ ("location", "Location Chr and Mb", "Location Chr and Mb"),
+ ("mean", "Mean Expr", "Mean"),
+ ("lrs_location", "Max LRS Location Chr and Mb", "Max LRS Location Chr and Mb"),
+ ("lit_corr", "Lit Corr ?", "Literature Correlation"),
+ ("tissue_corr", "Tissue rho ?", "Tissue Correlation rho"),
+ ("tissue_pvalue", "Tissue p(rho) ?", "Tissue Correlation p(rho) value"))
+ failures = {}
tests = [
- ({"dataset": "HC_M2_0606_P", "trait_id": "1435464_at",
+ ("Trait '1435464_at' (Dataset 'HC_M2_0606_P'): Sample Correlation, Pearson, 500 results",
+ {"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",
+ pearsons_keys),
+ ("Trait '1435464_at' (Dataset 'HC_M2_0606_P'): Sample Correlation, Spearmans, 500 results",
+ {"dataset": "HC_M2_0606_P", "trait_id": "1435464_at",
"corr_dataset": "HC_M2_0606_P", "corr_type": "sample",
+ "corr_sample_method": "spearman", "location_type": "gene",
+ "corr_samples_group": "samples_primary", "sample_vals": sample_vals(),
+ "corr_return_results": "500"},
+ "HC_M2_0606_P___1435464_at___sample_r___spearman___no_filters__results.csv",
+ spearmans_keys),
+ ("Trait '1435464_at' (Dataset 'HC_M2_0606_P'): Tissue Correlation, Pearsons, 500 results",
+ {"dataset": "HC_M2_0606_P", "trait_id": "1435464_at",
+ "corr_dataset": "HC_M2_0606_P", "corr_type": "tissue",
"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"),]
+ "HC_M2_0606_P___1435464_at___tissue_r___pearson__results.csv",
+ pearsons_keys),
+ ("Trait '1435464_at' (Dataset 'HC_M2_0606_P'): Tissue Correlation, Spearmans, 500 results",
+ {"dataset": "HC_M2_0606_P", "trait_id": "1435464_at",
+ "corr_dataset": "HC_M2_0606_P", "corr_type": "tissue",
+ "corr_sample_method": "spearman", "location_type": "gene",
+ "corr_samples_group": "samples_primary", "sample_vals": sample_vals(),
+ "corr_return_results": "500"},
+ "HC_M2_0606_P___1435464_at___tissue_r___spearman__results.csv",
+ spearmans_keys)]
- for test_data, expected_file in tests:
- print(f"Test {__idx} ...", end="\t")
+ for test_title, test_data, expected_file, method_keys in tests:
+ print(f"Test: {test_title} ...", 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)
+ if len(results) == 0:
+ failures = {
+ **failures,
+ test_title: (("No results found.",),)}
+ continue
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
+ failures = {
+ **failures,
+ test_title: collect_failures(
+ results, tuple(parse_expected(filepath)), method_keys)
+ }
if len(failures) > 0:
print("\n\nFAILURES: ")
- for test_num, err_msg in failures:
- print(f"\tTest {test_num}: {err_msg}")
+ for test_title, failures in failures.items():
+ print(f"\nTest: {test_title}")
+ for result, result_failures in enumerate(failures):
+ for failure in result_failures:
+ print(f"\tResult {result}: {failure}")
+ print("")
return False
return True