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authorFrederick Muriuki Muriithi2022-08-11 06:57:11 +0300
committerFrederick Muriuki Muriithi2022-08-12 13:13:26 +0300
commit51a35646f1eb509b2f94204eb490715ce2abcdf2 (patch)
treec37c893e5d2047ebfb58739c58eef5a202ca2fd6
parente55aadbf0f1dd4752cd68b572ce6c66bcb6caed8 (diff)
downloadgenenetwork2-51a35646f1eb509b2f94204eb490715ce2abcdf2.tar.gz
Update format to prevent tissue correlation from failing
Update the data format of returned values so that it conforms with expectatitions.
-rw-r--r--wqflask/wqflask/correlation/rust_correlation.py53
1 files changed, 24 insertions, 29 deletions
diff --git a/wqflask/wqflask/correlation/rust_correlation.py b/wqflask/wqflask/correlation/rust_correlation.py
index 8a5021cc..4a22af72 100644
--- a/wqflask/wqflask/correlation/rust_correlation.py
+++ b/wqflask/wqflask/correlation/rust_correlation.py
@@ -1,5 +1,6 @@
"""module contains integration code for rust-gn3"""
import json
+from functools import reduce
from wqflask.correlation.correlation_functions import get_trait_symbol_and_tissue_values
from wqflask.correlation.correlation_gn3_api import create_target_this_trait
from wqflask.correlation.correlation_gn3_api import lit_for_trait_list
@@ -11,22 +12,21 @@ from gn3.computations.rust_correlation import parse_tissue_corr_data
from gn3.db_utils import database_connector
-def compute_top_n_lit(corr_results, this_dataset, this_trait):
+def compute_top_n_lit(corr_results, this_dataset, this_trait) -> dict:
(this_trait_geneid, geneid_dict, species) = do_lit_correlation(
this_trait, this_dataset)
geneid_dict = {trait_name: geneid for (trait_name, geneid) in geneid_dict.items() if
corr_results.get(trait_name)}
+ with database_connector() as conn:
+ return reduce(
+ lambda acc, corr: {**acc, **corr},
+ compute_all_lit_correlation(
+ conn=conn, trait_lists=list(geneid_dict.items()),
+ species=species, gene_id=this_trait_geneid),
+ {})
- conn = database_connector()
-
- with conn:
-
- correlation_results = compute_all_lit_correlation(
- conn=conn, trait_lists=list(geneid_dict.items()),
- species=species, gene_id=this_trait_geneid)
-
- return correlation_results
+ return {}
def compute_top_n_tissue(this_dataset, this_trait, traits, method):
@@ -55,25 +55,19 @@ def compute_top_n_tissue(this_dataset, this_trait, traits, method):
return {}
-def merge_results(dict_a, dict_b, dict_c):
+def merge_results(dict_a: dict, dict_b: dict, dict_c: dict) -> list[dict]:
"""code to merge diff corr into individual dicts
a"""
- correlation_results = []
-
- for (key, val) in dict_a.items():
-
- if key in dict_b:
-
- dict_a[key].update(dict_b[key])
-
- if key in dict_c:
-
- dict_a[key].update(dict_c[key])
-
- correlation_results.append({key: dict_a[key]})
-
- return correlation_results
+ def __merge__(trait_name, trait_corrs):
+ return {
+ trait_name: {
+ **trait_corrs,
+ **dict_b.get(trait_name, {}),
+ **dict_c.get(trait_name, {})
+ }
+ }
+ return [__merge__(tname, tcorrs) for tname, tcorrs in dict_a.items()]
def compute_correlation_rust(
@@ -109,7 +103,7 @@ def compute_correlation_rust(
top_lit_results = compute_top_n_lit(results,this_dataset,this_trait)
# merging the results
- results = merge_results(results,top_tissue_results,top_lit_results)
+ results = merge_results(results, top_tissue_results, top_lit_results)
if corr_type == "tissue":
@@ -125,8 +119,9 @@ def compute_correlation_rust(
dataset_vals=corr_result_tissue_vals_dict)
if data:
- results = run_correlation(
- data[1], data[0], method, ",", "tissue")
+ results = merge_results(
+ run_correlation(data[1], data[0], method, ",", "tissue"),
+ {}, {})
return {
"correlation_results": results,