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| author | Alexander Kabui | 2021-11-15 18:10:56 +0300 |
|---|---|---|
| committer | Alexander Kabui | 2021-11-15 18:10:56 +0300 |
| commit | 2982ba491e89acee5ead69206691c786be1cf728 (patch) | |
| tree | c22d60a36f14d83db12bcafbe7d20d5c3414c5d1 | |
| parent | 6f6e28d216e0a2adbf939b9b29f8794ae45d9aa8 (diff) | |
| download | genenetwork2-2982ba491e89acee5ead69206691c786be1cf728.tar.gz | |
test precomppute caching integration
| -rw-r--r-- | wqflask/wqflask/correlation/correlation_gn3_api.py | 23 |
1 files changed, 18 insertions, 5 deletions
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index 7b828016..191a748a 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -4,7 +4,8 @@ import time from functools import wraps from wqflask.correlation import correlation_functions - +from wqflask.correlation.pre_computes import fetch_precompute_results +from wqflask.correlation.pre_computes import cache_compute_results from base import data_set from base.trait import create_trait @@ -193,9 +194,21 @@ def compute_correlation(start_vars, method="pearson", compute_all=False): (this_trait_data, target_dataset_data) = fetch_sample_data( start_vars, this_trait, this_dataset, target_dataset) - correlation_results = fast_compute_all_sample_correlation(corr_method=method, - this_trait=this_trait_data, - target_dataset=target_dataset_data) + correlation_results = fetch_precompute_results( + this_dataset.name, target_dataset.name, this_dataset.type, this_trait.name) + + if correlation_results is None: + correlation_results = fast_compute_all_sample_correlation(corr_method=method, + this_trait=this_trait_data, + target_dataset=target_dataset_data) + + cache_compute_results(this_dataset.type, + this_dataset.name, + target_dataset.name, + corr_method, + correlation_results, + this_trait.name) + elif corr_type == "tissue": trait_symbol_dict = this_dataset.retrieve_genes("Symbol") tissue_input = get_tissue_correlation_input( @@ -295,7 +308,7 @@ def get_tissue_correlation_input(this_trait, trait_symbol_dict): """Gets tissue expression values for the primary trait and target tissues values""" primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( symbol_list=[this_trait.symbol]) - if this_trait.symbol.lower() in primary_trait_tissue_vals_dict: + if this_trait.symbol and this_trait.symbol.lower() in primary_trait_tissue_vals_dict: primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower( )] corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( |