diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/correlation/pre_computes.py | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 29 |
2 files changed, 13 insertions, 27 deletions
diff --git a/wqflask/wqflask/correlation/pre_computes.py b/wqflask/wqflask/correlation/pre_computes.py index b95ceba5..ad0bc6ef 100644 --- a/wqflask/wqflask/correlation/pre_computes.py +++ b/wqflask/wqflask/correlation/pre_computes.py @@ -16,12 +16,11 @@ def fetch_all_cached_metadata(dataset_name): try: with open(file_path, "r+") as file_handler: dataset_metadata = json.load(file_handler) + return (file_path, dataset_metadata) except FileNotFoundError: Path(file_path).touch(exist_ok=True) - return {} - - return (file_path, dataset_metadata) + return (file_path, {}) def cache_new_traits_metadata(dataset_metadata: dict, new_traits_metadata, file_path: str): @@ -46,16 +45,10 @@ def cache_compute_results(base_dataset_type, corr_method, correlation_results, trait_name): - # pass """function to cache correlation results for heavy computations""" - # init assumption only caching probeset type - # fix redis;issue potential redis_cache!=current_timestamp - base_timestamp = query_table_timestamp(base_dataset_type) - r.set(f"{base_dataset_type}timestamp", base_timestamp) - target_dataset_timestamp = base_timestamp file_name = generate_filename( diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 42010a1e..f5600f13 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -26,6 +26,9 @@ from base.trait import create_trait, jsonable from base.data_set import create_dataset from base.webqtlConfig import TMPDIR +from wqflask.correlation.pre_computes import fetch_all_cached_metadata +from wqflask.correlation.pre_computes import cache_new_traits_metadata + from utility import hmac @@ -34,7 +37,8 @@ def set_template_vars(start_vars, correlation_data): corr_method = start_vars['corr_sample_method'] if start_vars['dataset'] == "Temp": - this_dataset_ob = create_dataset(dataset_name="Temp", dataset_type="Temp", group_name=start_vars['group']) + this_dataset_ob = create_dataset( + dataset_name="Temp", dataset_type="Temp", group_name=start_vars['group']) else: this_dataset_ob = create_dataset(dataset_name=start_vars['dataset']) this_trait = create_trait(dataset=this_dataset_ob, @@ -86,25 +90,17 @@ def correlation_json_for_table(correlation_data, this_trait, this_dataset, targe corr_results = correlation_data['correlation_results'] results_list = [] - file_name = f"{target_dataset['name']}_metadata.json" - - file_path = os.path.join(TMPDIR, file_name) new_traits_metadata = {} - try: - with open(file_path,"r+") as file_handler: - dataset_metadata = json.load(file_handler) - - except FileNotFoundError: - Path(file_path).touch(exist_ok=True) - dataset_metadata = {} + (file_path, dataset_metadata) = fetch_all_cached_metadata( + target_dataset['name']) for i, trait_dict in enumerate(corr_results): trait_name = list(trait_dict.keys())[0] trait = trait_dict[trait_name] target_trait = dataset_metadata.get(trait_name) - if target_trait is None: + if target_trait is None: target_trait_ob = create_trait(dataset=target_dataset_ob, name=trait_name, get_qtl_info=True) @@ -184,12 +180,9 @@ def correlation_json_for_table(correlation_data, this_trait, this_dataset, targe results_list.append(results_dict) - - if bool(new_traits_metadata): - # that means new traits exists - dataset_metadata.update(new_traits_metadata) - with open(file_path,"w+") as file_handler: - json.dump(dataset_metadata, file_handler) + cache_new_traits_metadata(dataset_metadata, + new_traits_metadata, + file_path) return json.dumps(results_list) |