diff options
| -rw-r--r-- | wqflask/wqflask/correlation/pre_computes.py | 9 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/rust_correlation.py | 19 |
2 files changed, 12 insertions, 16 deletions
diff --git a/wqflask/wqflask/correlation/pre_computes.py b/wqflask/wqflask/correlation/pre_computes.py index 2831bd39..720eab09 100644 --- a/wqflask/wqflask/correlation/pre_computes.py +++ b/wqflask/wqflask/correlation/pre_computes.py @@ -25,17 +25,16 @@ def cache_trait_metadata(dataset_name, data): current_date = datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S') txn.put(b"creation_date", current_date.encode()) return "success" - except lmdb.Error as error: pass -def read_trait_metadata(dataset_name): +def read_trait_metadata(dataset_name,dataset_type): try: - with lmdb.open(os.path.join(TMPDIR,f"metadata_{dataset_name}"), + with lmdb.open(os.path.join("/tmp/",f"metadata_{dataset_type}"), readonly=True, lock=False) as env: with env.begin() as txn: - db_name = txn.get(dataset_name.encode()) - return (pickle.loads(db_name) if db_name else {}) + metadata = txn.get(dataset_name.encode()) + return (pickle.loads(metadata)["data"] if metadata else {}) except lmdb.Error as error: return {} diff --git a/wqflask/wqflask/correlation/rust_correlation.py b/wqflask/wqflask/correlation/rust_correlation.py index 41dd77a1..18f8c622 100644 --- a/wqflask/wqflask/correlation/rust_correlation.py +++ b/wqflask/wqflask/correlation/rust_correlation.py @@ -64,12 +64,13 @@ def get_metadata(dataset, traits): def __location__(probe_chr, probe_mb): if probe_mb: return f"Chr{probe_chr}: {probe_mb:.6f}" - return f"Chr{probe_chr}: ???" - cached_metadata = read_trait_metadata(dataset.name) - to_fetch_metadata = list( - set(traits).difference(list(cached_metadata.keys()))) - if to_fetch_metadata: - results = {**({trait_name: { + return f"Chr{probe_chr}: ???" + + cached_metadata = read_trait_metadata(dataset.name,"ProbeSet") + if cached_metadata: + return {trait:cached_metadata.get(trait) for trait in traits} + else: + return {**({trait_name: { "name": trait_name, "view": True, "symbol": symbol, @@ -88,11 +89,7 @@ def get_metadata(dataset, traits): } for trait_name, probe_chr, probe_mb, symbol, mean, description, additive, lrs, chr_score, mb - in query_probes_metadata(dataset, to_fetch_metadata)}), **cached_metadata} - cache_trait_metadata(dataset.name, results) - return results - return cached_metadata - + in query_probes_metadata(dataset, traits)})} def chunk_dataset(dataset, steps, name): |