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authorAlexander Kabui2021-11-18 12:02:10 +0300
committerAlexander Kabui2021-11-18 12:02:10 +0300
commit56b574b903244a64aecaa54e5305b25bb642b254 (patch)
tree7077071db60f072acbbab6613d9cb5937f0cf1fc
parent1a3b85c4ebc66d54e3bda06c3742e8046e4c8159 (diff)
downloadgenenetwork2-56b574b903244a64aecaa54e5305b25bb642b254.tar.gz
pep8 formatting;minor fixes
-rw-r--r--wqflask/wqflask/correlation/pre_computes.py37
1 files changed, 23 insertions, 14 deletions
diff --git a/wqflask/wqflask/correlation/pre_computes.py b/wqflask/wqflask/correlation/pre_computes.py
index 241b0730..77592a3a 100644
--- a/wqflask/wqflask/correlation/pre_computes.py
+++ b/wqflask/wqflask/correlation/pre_computes.py
@@ -9,7 +9,7 @@ from base.webqtlConfig import TMPDIR
def fetch_all_cached_metadata(dataset_name):
"""in a gvein dataset fetch all the traits metadata"""
- file_name = f"{dataset_name}_metadata.json"
+ file_name = generate_file_name(dataset_name, suffix="metadata")
file_path = os.path.join(TMPDIR, file_name)
@@ -33,11 +33,11 @@ def cache_new_traits_metadata(dataset_metadata: dict, new_traits_metadata, file_
json.dump(dataset_metadata, file_handler)
-def generate_file_name(*args, prefix=""):
+def generate_file_name(*args, suffix="", file_ext="json"):
"""given a list of args generate a unique filename"""
- string_unicode = f"{*args,}{prefix}".encode()
- return hashlib.md5(string_unicode).hexdigest()
+ string_unicode = f"{*args,}".encode()
+ return f"{hashlib.md5(string_unicode).hexdigest()}_{suffix}.{file_ext}"
def generate_filename(base_dataset_name, target_dataset_name, base_timestamp, target_dataset_timestamp):
@@ -65,11 +65,12 @@ def cache_compute_results(base_dataset_type,
target_dataset_timestamp = base_timestamp
- file_name = generate_filename(
+ file_name = generate_file_name(
base_dataset_name, target_dataset_name,
- base_timestamp, target_dataset_timestamp)
+ base_timestamp, target_dataset_timestamp,
+ suffix="corr_precomputes")
- file_path = os.path.join(TMPDIR, f"{file_name}.json")
+ file_path = os.path.join(TMPDIR, file_name)
try:
with open(file_path, "r+") as json_file_handler:
@@ -91,16 +92,20 @@ def cache_compute_results(base_dataset_type,
json.dump(data, file_handler)
-def fetch_precompute_results(base_dataset_name, target_dataset_name, dataset_type, trait_name):
+def fetch_precompute_results(base_dataset_name,
+ target_dataset_name,
+ dataset_type,
+ trait_name):
"""function to check for precomputed results"""
base_timestamp = target_dataset_timestamp = query_table_timestamp(
dataset_type)
- file_name = generate_filename(
+ file_name = generate_file_name(
base_dataset_name, target_dataset_name,
- base_timestamp, target_dataset_timestamp)
+ base_timestamp, target_dataset_timestamp,
+ suffix="corr_precomputes")
- file_path = os.path.join(TMPDIR, f"{file_name}.json")
+ file_path = os.path.join(TMPDIR, file_name)
try:
with open(file_path, "r+") as json_handler:
@@ -112,7 +117,9 @@ def fetch_precompute_results(base_dataset_name, target_dataset_name, dataset_typ
pass
-def pre_compute_dataset_vs_dataset(base_dataset, target_dataset, corr_method):
+def pre_compute_dataset_vs_dataset(base_dataset,
+ target_dataset,
+ corr_method):
"""compute sample correlation between dataset vs dataset
wn:heavy function should be invoked less frequently
input:datasets_data(two dicts),corr_method
@@ -131,8 +138,10 @@ def pre_compute_dataset_vs_dataset(base_dataset, target_dataset, corr_method):
"trait_id": primary_trait_name
}
- trait_correlation_result = fast_compute_all_sample_correlation(
- corr_method=corr_method, this_trait=this_trait_data, target_dataset=target_traits_data)
+ trait_correlation_result = compute_all_sample_correlation(
+ corr_method=corr_method,
+ this_trait=this_trait_data,
+ target_dataset=target_traits_data)
dataset_correlation_results[primary_trait_name] = trait_correlation_result