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| author | Frederick Muriuki Muriithi | 2022-08-12 12:52:38 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2022-08-12 12:53:25 +0300 |
| commit | fbc7ea257028f07751d7ebaa9f8656569215e124 (patch) | |
| tree | bdef4a098b22b2bc1ebc6921f0e29e4cf493981e | |
| parent | 3c1cb6a94b64dae28c62f481e1f4499f8f5b89e7 (diff) | |
| download | genenetwork2-fbc7ea257028f07751d7ebaa9f8656569215e124.tar.gz | |
Fix some issues with the tests. Add notes in code for improvements.
| -rw-r--r-- | test/requests/correlation_tests.py | 9 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/rust_correlation.py | 2 |
2 files changed, 7 insertions, 4 deletions
diff --git a/test/requests/correlation_tests.py b/test/requests/correlation_tests.py index 0b8ba8cd..2d314833 100644 --- a/test/requests/correlation_tests.py +++ b/test/requests/correlation_tests.py @@ -12,6 +12,7 @@ def do_request(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(), @@ -34,7 +35,6 @@ def check_sample_correlations(baseurl): def check_tissue_correlations(baseurl): data = { "corr_type": "tissue", - "corr_sample_method": "pearson", "location_type": "gene", } top_n_message = "The top 100 correlations ranked by the Tissue Correlation" @@ -58,12 +58,13 @@ def check_correlations(args_obj, parser): print("") print("Checking the correlations...") corr_type_fns = { - "sample": check_sample_correlations,} + "sample": check_sample_correlations, + "tissue": check_tissue_correlations, + "tissue": check_lit_correlations + } host = args_obj.host for corr_type, corr_type_fn in corr_type_fns.items(): print(f"\tChecking {corr_type} correlations...", end="") corr_type_fn(host) print(" ok") - check_tissue_correlations(host) - check_lit_correlations(host) print("OK") diff --git a/wqflask/wqflask/correlation/rust_correlation.py b/wqflask/wqflask/correlation/rust_correlation.py index b4435887..3628f549 100644 --- a/wqflask/wqflask/correlation/rust_correlation.py +++ b/wqflask/wqflask/correlation/rust_correlation.py @@ -135,6 +135,7 @@ def compute_correlation_rust( (this_dataset, this_trait, target_dataset, sample_data) = ( target_trait_info) + ## Replace this with `match ...` once we hit Python 3.10 corr_type_fns = { "sample": __compute_sample_corr__, "tissue": __compute_tissue_corr__, @@ -142,6 +143,7 @@ def compute_correlation_rust( } results = corr_type_fns[corr_type]( start_vars, corr_type, method, n_top, target_trait_info) + ## END: Replace this with `match ...` once we hit Python 3.10 top_tissue_results = {} top_lit_results = {} |