diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set/__init__.py | 4 | ||||
| -rw-r--r-- | wqflask/base/data_set/datasettype.py | 41 |
2 files changed, 21 insertions, 24 deletions
diff --git a/wqflask/base/data_set/__init__.py b/wqflask/base/data_set/__init__.py index 6d475df2..4667d5ce 100644 --- a/wqflask/base/data_set/__init__.py +++ b/wqflask/base/data_set/__init__.py @@ -37,7 +37,9 @@ def create_dataset(dataset_name, dataset_type=None, dataset_type = "Temp" if not dataset_type: - dataset_type = DatasetType(redis_conn)(dataset_name) + with database_connection() as db_conn, db_conn.cursor() as cursor: + dataset_type = DatasetType(redis_conn)( + dataset_name, redis_conn, cursor) dataset_ob = DS_NAME_MAP[dataset_type] dataset_class = globals()[dataset_ob] diff --git a/wqflask/base/data_set/datasettype.py b/wqflask/base/data_set/datasettype.py index ca6515b6..05f0f564 100644 --- a/wqflask/base/data_set/datasettype.py +++ b/wqflask/base/data_set/datasettype.py @@ -1,11 +1,8 @@ -# builtins imports +"DatasetType class ..." import json import requests -from dataclasses import field -from dataclasses import InitVar from typing import Optional, Dict -from dataclasses import dataclass from redis import Redis @@ -14,7 +11,7 @@ from redis import Redis from utility.tools import GN2_BASE_URL from wqflask.database import database_connection -@dataclass + class DatasetType: """Create a dictionary of samples where the value is set to Geno, Publish or ProbeSet. E.g. @@ -30,13 +27,13 @@ class DatasetType: 'B139_K_1206_R': 'ProbeSet' ... } """ - redis_instance: InitVar[Redis] - datasets: Optional[Dict] = field(init=False, default_factory=dict) - data: Optional[Dict] = field(init=False) - def __post_init__(self, redis_instance): - self.redis_instance = redis_instance - data = redis_instance.get("dataset_structure") + def __init__(self, redis_conn): + "Initialise the object" + self.datasets = {} + self.data = {} + # self.redis_instance = redis_instance + data = redis_conn.get("dataset_structure") if data: self.datasets = json.loads(data) else: @@ -61,11 +58,10 @@ class DatasetType: except Exception: # Do nothing pass - self.redis_instance.set("dataset_structure", - json.dumps(self.datasets)) + redis_conn.set("dataset_structure", json.dumps(self.datasets)) self.data = data - def set_dataset_key(self, t, name): + def set_dataset_key(self, t, name, redis_conn, db_cursor): """If name is not in the object's dataset dictionary, set it, and update dataset_structure in Redis args: @@ -102,21 +98,20 @@ class DatasetType: if t in ['pheno', 'other_pheno']: group_name = name.replace("Publish", "") - with database_connection() as conn, conn.cursor() as cursor: - cursor.execute(sql_query_mapping[t], (group_name,)) - if cursor.fetchone(): - self.datasets[name] = dataset_name_mapping[t] - self.redis_instance.set( - "dataset_structure", json.dumps(self.datasets)) - return True + db_cursor.execute(sql_query_mapping[t], (group_name,)) + if db_cursor.fetchone(): + self.datasets[name] = dataset_name_mapping[t] + redis_conn.set( + "dataset_structure", json.dumps(self.datasets)) + return True - def __call__(self, name): + def __call__(self, name, redis_conn, db_cursor): if name not in self.datasets: for t in ["mrna_expr", "pheno", "other_pheno", "geno"]: # This has side-effects, with the end result being a # truth-y value - if(self.set_dataset_key(t, name)): + if(self.set_dataset_key(t, name, redis_conn, db_cursor)): break # Return None if name has not been set return self.datasets.get(name, None) |