diff options
| -rw-r--r-- | test/requests/correlation_tests.py | 131 |
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 |