aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorAlexander Kabui2021-11-17 08:27:05 +0300
committerAlexander Kabui2021-11-17 08:27:05 +0300
commit1090674ac9497dad22803e7bf8e51d77245f8a0c (patch)
treee8dd0d6f0c3ced2c3769c3c1d9517964649c9bda
parent5a407a34442860ebaea2886f2278be9e1eb33a8d (diff)
downloadgenenetwork2-1090674ac9497dad22803e7bf8e51d77245f8a0c.tar.gz
isolate function to fetch the traits metadata
-rw-r--r--wqflask/wqflask/correlation/pre_computes.py32
1 files changed, 19 insertions, 13 deletions
diff --git a/wqflask/wqflask/correlation/pre_computes.py b/wqflask/wqflask/correlation/pre_computes.py
index 355701f2..638ae860 100644
--- a/wqflask/wqflask/correlation/pre_computes.py
+++ b/wqflask/wqflask/correlation/pre_computes.py
@@ -9,6 +9,25 @@ from redis import Redis
r = Redis()
+# code to isolate metadata caching
+
+
+def fetch_all_cached_metadata(dataset_name):
+ """in a gvein dataset fetch all the traits metadata"""
+ file_name = f"{dataset_name}_metadata.json"
+
+ file_path = os.path.join(TMPDIR, file_name)
+
+ with open(file_path, "r+") as file_handler:
+ dataset_metadata = json.load(file_handler)
+
+ except FileNotFoundError:
+ Path(file_path).touch(exist_ok=True)
+ return {}
+
+ return dataset_metadata
+
+
def generate_filename(base_dataset_name, target_dataset_name, base_timestamp, target_dataset_timestamp):
"""generate unique filename"""
@@ -60,18 +79,10 @@ def cache_compute_results(base_dataset_type,
json.dump(data, file_handler)
- # create the file only if it does not exists
-
- # else open the file to cache the results
-
def fetch_precompute_results(base_dataset_name, target_dataset_name, dataset_type, trait_name):
"""function to check for precomputed results"""
- # check for redis timestamp
-
- # fix rely on the fact correlation run oftenly probeset is set
-
base_timestamp = target_dataset_timestamp = r.get(f"{dataset_type}timestamp")
if base_timestamp is None:
return
@@ -86,11 +97,9 @@ def fetch_precompute_results(base_dataset_name, target_dataset_name, dataset_typ
file_path = os.path.join(TMPDIR, f"{file_name}.json")
-
try:
with open(file_path, "r+") as json_handler:
correlation_results = json.load(json_handler)
- # print(correlation_results)
return correlation_results.get(trait_name)
@@ -131,8 +140,6 @@ def get_datasets_data(base_dataset, target_dataset_data):
(works for bxd only probeset datasets)
- # fix issue with fetching of the datasets
-
output:two dicts for datasets with key==trait and value==strains
"""
samples_fetched = base_dataset.group.all_samples_ordered()
@@ -142,7 +149,6 @@ def get_datasets_data(base_dataset, target_dataset_data):
base_traits_data = base_dataset.get_trait_data(
samples_fetched)
-
target_results = map_shared_keys_to_values(
samples_fetched, target_traits_data)
base_results = map_shared_keys_to_values(