diff options
Diffstat (limited to 'wqflask/base/data_set')
| -rw-r--r-- | wqflask/base/data_set/__init__.py | 5 | ||||
| -rw-r--r-- | wqflask/base/data_set/datasetgroup.py | 25 | ||||
| -rw-r--r-- | wqflask/base/data_set/datasettype.py | 6 | ||||
| -rw-r--r-- | wqflask/base/data_set/utils.py | 11 |
4 files changed, 26 insertions, 21 deletions
diff --git a/wqflask/base/data_set/__init__.py b/wqflask/base/data_set/__init__.py index e49c6a93..27955f8a 100644 --- a/wqflask/base/data_set/__init__.py +++ b/wqflask/base/data_set/__init__.py @@ -6,11 +6,12 @@ import pickle as pickle # 3rd-party imports from redis import Redis +from flask import current_app as app # local imports from .dataset import DataSet from base import webqtlConfig -from utility.tools import USE_REDIS +from utility.tools import get_setting_bool from .datasettype import DatasetType from .tempdataset import TempDataSet from .datasetgroup import DatasetGroup @@ -113,7 +114,7 @@ def datasets(group_name, this_group=None, redis_conn=Redis()): dataset_menu.append(dict(tissue=tissue_name, datasets=[(dataset, dataset_short)])) - if USE_REDIS: + if get_setting_bool(app, "USE_REDIS"): redis_conn.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL)) redis_conn.expire(key, 60 * 5) diff --git a/wqflask/base/data_set/datasetgroup.py b/wqflask/base/data_set/datasetgroup.py index 72577f38..10556dbf 100644 --- a/wqflask/base/data_set/datasetgroup.py +++ b/wqflask/base/data_set/datasetgroup.py @@ -3,6 +3,8 @@ import os import json +from flask import current_app as app + from base import webqtlConfig from .markers import Markers, HumanMarkers @@ -13,9 +15,10 @@ from maintenance import get_group_samplelists from wqflask.database import database_connection from utility.tools import ( locate, - USE_REDIS, flat_files, + get_setting, flat_file_exists, + get_setting_bool, locate_ignore_error) class DatasetGroup: @@ -87,8 +90,8 @@ class DatasetGroup: def get_markers(self): def check_plink_gemma(): - if flat_file_exists("mapping"): - MAPPING_PATH = flat_files("mapping") + "/" + if flat_file_exists(app, "mapping"): + MAPPING_PATH = flat_files(app, "mapping") + "/" if os.path.isfile(MAPPING_PATH + self.name + ".bed"): return True return False @@ -117,7 +120,7 @@ class DatasetGroup: def get_study_samplelists(self): study_sample_file = locate_ignore_error( - self.name + ".json", 'study_sample_lists') + app, self.name + ".json", 'study_sample_lists') try: f = open(study_sample_file) except: @@ -126,7 +129,7 @@ class DatasetGroup: return study_samples def get_genofiles(self): - jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name) + jsonfile = "%s/%s.json" % (get_setting(app, 'GENODIR'), self.name) try: f = open(jsonfile) except: @@ -137,20 +140,20 @@ class DatasetGroup: def get_samplelist(self, redis_conn): result = None key = "samplelist:v3:" + self.name - if USE_REDIS: + if get_setting_bool(app, "USE_REDIS"): result = redis_conn.get(key) if result is not None: self.samplelist = json.loads(result) else: - genotype_fn = locate_ignore_error(self.name + ".geno", 'genotype') + genotype_fn = locate_ignore_error(app, self.name + ".geno", 'genotype') if genotype_fn: self.samplelist = get_group_samplelists.get_samplelist( "geno", genotype_fn) else: self.samplelist = None - if USE_REDIS: + if get_setting_bool(app, "USE_REDIS"): redis_conn.set(key, json.dumps(self.samplelist)) redis_conn.expire(key, 60 * 5) @@ -169,11 +172,11 @@ class DatasetGroup: if self.genofile: if "RData" in self.genofile: # ZS: This is a temporary fix; I need to change the way the JSON files that point to multiple genotype files are structured to point to other file types like RData full_filename = str( - locate(self.genofile.split(".")[0] + ".geno", 'genotype')) + locate(app, self.genofile.split(".")[0] + ".geno", 'genotype')) else: - full_filename = str(locate(self.genofile, 'genotype')) + full_filename = str(locate(app, self.genofile, 'genotype')) else: - full_filename = str(locate(self.name + '.geno', 'genotype')) + full_filename = str(locate(app, self.name + '.geno', 'genotype')) genotype_1 = gen_geno_ob.genotype(full_filename) if genotype_1.type == "group" and self.parlist: diff --git a/wqflask/base/data_set/datasettype.py b/wqflask/base/data_set/datasettype.py index 05f0f564..c8b78a43 100644 --- a/wqflask/base/data_set/datasettype.py +++ b/wqflask/base/data_set/datasettype.py @@ -6,9 +6,9 @@ from typing import Optional, Dict from redis import Redis +from flask import current_app as app - -from utility.tools import GN2_BASE_URL +from utility.tools import get_setting from wqflask.database import database_connection @@ -41,7 +41,7 @@ class DatasetType: # emptied try: data = json.loads(requests.get( - GN2_BASE_URL + "/api/v_pre1/gen_dropdown", + get_setting(app, "GN2_BASE_URL") + "/api/v_pre1/gen_dropdown", timeout=5).content) for _species in data['datasets']: for group in data['datasets'][_species]: diff --git a/wqflask/base/data_set/utils.py b/wqflask/base/data_set/utils.py index 703fee04..bb17a6c7 100644 --- a/wqflask/base/data_set/utils.py +++ b/wqflask/base/data_set/utils.py @@ -6,9 +6,10 @@ import json import hashlib from typing import List +from flask import current_app as app -from utility.tools import SQL_URI -from base.webqtlConfig import TMPDIR + +from utility.tools import get_setting from wqflask.database import parse_db_url, database_connection def geno_mrna_confidentiality(ob): @@ -27,7 +28,7 @@ def query_table_timestamp(dataset_type: str): # computation data and actions with database_connection() as conn, conn.cursor() as cursor: - fetch_db_name = parse_db_url(SQL_URI) + fetch_db_name = parse_db_url(get_setting(app, "SQL_URI")) cursor.execute( "SELECT UPDATE_TIME FROM " "information_schema.tables " @@ -57,7 +58,7 @@ def cache_dataset_results(dataset_name: str, dataset_type: str, samplelist: List samplelist_as_str = ",".join(samplelist) file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp, samplelist_as_str) - file_path = os.path.join(TMPDIR, f"{file_name}.json") + file_path = os.path.join(get_setting(app, "TMPDIR"), f"{file_name}.json") with open(file_path, "w") as file_handler: json.dump(query_results, file_handler) @@ -70,7 +71,7 @@ def fetch_cached_results(dataset_name: str, dataset_type: str, samplelist: List) samplelist_as_str = ",".join(samplelist) file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp, samplelist_as_str) - file_path = os.path.join(TMPDIR, f"{file_name}.json") + file_path = os.path.join(get_setting(app, "TMPDIR"), f"{file_name}.json") try: with open(file_path, "r") as file_handler: |