diff options
| author | BonfaceKilz | 2021-05-05 12:50:19 +0300 |
|---|---|---|
| committer | GitHub | 2021-05-05 12:50:19 +0300 |
| commit | 402c21508f47a486dab6b2a9daa9e006f26beb61 (patch) | |
| tree | 11457fecd5b454962f1db4320f244554b13ce6e1 /gn3/api/correlation.py | |
| parent | 31ac939f58bf7b6d353ced995ca395376203b25f (diff) | |
| parent | 82a75b3efd23a8dba1c8eea15c4fc450219a1f86 (diff) | |
| download | genenetwork3-402c21508f47a486dab6b2a9daa9e006f26beb61.tar.gz | |
Merge pull request #9 from genenetwork/Feature/speed-up-correlation
Feature/speed up correlation
Diffstat (limited to 'gn3/api/correlation.py')
| -rw-r--r-- | gn3/api/correlation.py | 13 |
1 files changed, 7 insertions, 6 deletions
diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py index 2339088..e7e89cf 100644 --- a/gn3/api/correlation.py +++ b/gn3/api/correlation.py @@ -23,7 +23,6 @@ def compute_sample_integration(corr_method="pearson"): this_trait_data = correlation_input.get("trait_data") results = map_shared_keys_to_values(target_samplelist, target_data_values) - correlation_results = compute_all_sample_correlation(corr_method=corr_method, this_trait=this_trait_data, target_dataset=results) @@ -33,9 +32,10 @@ def compute_sample_integration(corr_method="pearson"): @correlation.route("/sample_r/<string:corr_method>", methods=["POST"]) def compute_sample_r(corr_method="pearson"): - """correlation endpoint for computing sample r correlations\ + """Correlation endpoint for computing sample r correlations\ api expects the trait data with has the trait and also the\ - target_dataset data""" + target_dataset data + """ correlation_input = request.get_json() # xtodo move code below to compute_all_sampl correlation @@ -53,9 +53,10 @@ def compute_sample_r(corr_method="pearson"): @correlation.route("/lit_corr/<string:species>/<int:gene_id>", methods=["POST"]) def compute_lit_corr(species=None, gene_id=None): - """api endpoint for doing lit correlation.results for lit correlation\ + """Api endpoint for doing lit correlation.results for lit correlation\ are fetched from the database this is the only case where the db\ - might be needed for actual computing of the correlation results""" + might be needed for actual computing of the correlation results + """ conn, _cursor_object = database_connector() target_traits_gene_ids = request.get_json() @@ -72,7 +73,7 @@ def compute_lit_corr(species=None, gene_id=None): @correlation.route("/tissue_corr/<string:corr_method>", methods=["POST"]) def compute_tissue_corr(corr_method="pearson"): - """api endpoint fr doing tissue correlation""" + """Api endpoint fr doing tissue correlation""" tissue_input_data = request.get_json() primary_tissue_dict = tissue_input_data["primary_tissue"] target_tissues_dict = tissue_input_data["target_tissues_dict"] |