Fetch configs from app object not modulesdecouple_tools_and_wqflask_app

6 files changed, 30 insertions, 30 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:
 
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 37085448..21b2a716 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -7,7 +7,7 @@ from base import webqtlConfig
 from base.webqtlCaseData import webqtlCaseData
 from base.data_set import create_dataset
 from utility.authentication_tools import check_resource_availability
-from utility.tools import GN2_BASE_URL
+from utility.tools import get_setting
 from utility.redis_tools import get_redis_conn, get_resource_id
 
 from flask import g, request, url_for
@@ -173,11 +173,11 @@ class GeneralTrait:
         alias = 'Not available'
         if self.symbol:
             human_response = requests.get(
-                GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper())
+                get_setting(app, "GN2_BASE_URL") + "gn3/gene/aliases/" + self.symbol.upper())
             mouse_response = requests.get(
-                GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize())
+                get_setting(app, "GN2_BASE_URL") + "gn3/gene/aliases/" + self.symbol.capitalize())
             other_response = requests.get(
-                GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower())
+                get_setting(app, "GN2_BASE_URL") + "gn3/gene/aliases/" + self.symbol.lower())
 
             if human_response and mouse_response and other_response:
                 alias_list = json.loads(human_response.content) + json.loads(
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index dd6fad04..d144a342 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -21,11 +21,6 @@
 # Created by GeneNetwork Core Team 2010/08/10
 
 
-import utility.tools
-
-utility.tools.show_settings()
-
-
 class webqtlCaseData:
     """one case data in one trait"""