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| author | Frederick Muriuki Muriithi | 2022-09-12 07:38:36 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2022-09-12 07:38:36 +0300 |
| commit | 185fc586d0f1c1faee4418805a1788e8d57680d8 (patch) | |
| tree | 5aeabb10c302332aef0f7222ec29d33bcaab732a /wqflask | |
| parent | 6341aef0a78f4e9c8c6d753ec799c0bbbd53ff66 (diff) | |
| download | genenetwork2-185fc586d0f1c1faee4418805a1788e8d57680d8.tar.gz | |
Check for species before calling `lower()`
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/correlation/correlation_gn3_api.py | 9 |
1 files changed, 4 insertions, 5 deletions
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index 1a375501..74796383 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -146,10 +146,7 @@ def lit_for_trait_list(corr_results, this_dataset, this_trait): geneid_dict = {trait_name: geneid for (trait_name, geneid) in geneid_dict.items() if trait_lists.get(trait_name)} - conn = database_connector() - - with conn: - + with database_connector() as conn: correlation_results = compute_all_lit_correlation( conn=conn, trait_lists=list(geneid_dict.items()), species=species, gene_id=this_trait_geneid) @@ -238,7 +235,9 @@ def compute_corr_for_top_results(start_vars, def do_lit_correlation(this_trait, this_dataset): """function for fetching lit inputs""" geneid_dict = this_dataset.retrieve_genes("GeneId") - species = this_dataset.group.species.lower() + species = this_dataset.group.species + if species: + species = species.lower() trait_geneid = this_trait.geneid return (trait_geneid, geneid_dict, species) |