From 8f3b998db0698298f828698e93e1f8f19a9c23d7 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 20 Jun 2023 08:11:04 +0300
Subject: Restore configuration variables' names

The names had been changed when refactoring the code but can now be restored.
---
 wqflask/base/data_set/datasetgroup.py |  2 +-
 wqflask/base/data_set/utils.py        |  4 ++--
 wqflask/base/webqtlConfig.py          | 35 +++++++++++++++++------------------
 3 files changed, 20 insertions(+), 21 deletions(-)

(limited to 'wqflask/base')

diff --git a/wqflask/base/data_set/datasetgroup.py b/wqflask/base/data_set/datasetgroup.py
index a44cf18d..7c3301fe 100644
--- a/wqflask/base/data_set/datasetgroup.py
+++ b/wqflask/base/data_set/datasetgroup.py
@@ -129,7 +129,7 @@ class DatasetGroup:
         return study_samples
 
     def get_genofiles(self):
-        jsonfile = "%s/%s.json" % (get_setting(app, "WEBQTL_GENODIR"), self.name)
+        jsonfile = "%s/%s.json" % (get_setting(app, "GENODIR"), self.name)
         try:
             f = open(jsonfile)
         except:
diff --git a/wqflask/base/data_set/utils.py b/wqflask/base/data_set/utils.py
index 11391d69..7f55989f 100644
--- a/wqflask/base/data_set/utils.py
+++ b/wqflask/base/data_set/utils.py
@@ -57,7 +57,7 @@ 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(app.config["WEBQTL_TMPDIR"], f"{file_name}.json")
+    file_path = os.path.join(app.config["TMPDIR"], f"{file_name}.json")
 
     with open(file_path, "w") as file_handler:
         json.dump(query_results, file_handler)
@@ -70,7 +70,7 @@ 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(app.config["WEBQTL_TMPDIR"], f"{file_name}.json")
+    file_path = os.path.join(app.config["TMPDIR"], f"{file_name}.json")
     try:
         with open(file_path, "r") as file_handler:
 
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 600c6800..a5797f60 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -91,34 +91,33 @@ def init_app(app):
     TEMPDIR = app.config["TEMPDIR"]
     mkdir_with_temp_dir = lambda child: mkdir_with_assert_writable(
         TEMPDIR, child)
-    WEBQTL_TMPDIR = mkdir_with_temp_dir("/gn2/")
-    app.config["WEBQTL_TMPDIR"] = WEBQTL_TMPDIR
-    app.config["TMPDIR"] = WEBQTL_TMPDIR
-    app.config["WEBQTL_CACHEDIR"] = mkdir_with_temp_dir(
-        f"{WEBQTL_TMPDIR}cache/")
+    TMPDIR = mkdir_with_temp_dir("/gn2/")
+    app.config["TMPDIR"] = TMPDIR
+    app.config["CACHEDIR"] = mkdir_with_temp_dir(
+        f"{TMPDIR}cache/")
 
     # We can no longer write into the git tree:
-    app.config["WEBQTL_GENERATED_IMAGE_DIR"] = mkdir_with_temp_dir(
-        f"{WEBQTL_TMPDIR}generated/")
-    app.config["WEBQTL_GENERATED_TEXT_DIR"] = mkdir_with_temp_dir(
-        f"{WEBQTL_TMPDIR}generated_text/")
+    app.config["GENERATED_IMAGE_DIR"] = mkdir_with_temp_dir(
+        f"{TMPDIR}generated/")
+    app.config["GENERATED_TEXT_DIR"] = mkdir_with_temp_dir(
+        f"{TMPDIR}generated_text/")
 
     # Flat file directories
-    app.config["WEBQTL_GENODIR"] = flat_files(app, 'genotype/')
+    app.config["GENODIR"] = flat_files(app, 'genotype/')
 
     # JSON genotypes are OBSOLETE
-    WEBQTL_JSON_GENODIR = flat_files(app, 'genotype/json/')
-    if not valid_path(WEBQTL_JSON_GENODIR):
+    JSON_GENODIR = flat_files(app, 'genotype/json/')
+    if not valid_path(JSON_GENODIR):
         # fall back on old location (move the dir, FIXME)
-        WEBQTL_JSON_GENODIR = flat_files('json')
-    app.config["WEBQTL_JSON_GENODIR"] = WEBQTL_JSON_GENODIR
+        JSON_GENODIR = flat_files('json')
+    app.config["JSON_GENODIR"] = JSON_GENODIR
 
 
-    app.config["WEBQTL_TEXTDIR"] = os.path.join(
+    app.config["TEXTDIR"] = os.path.join(
         app.config.get("GNSHARE", "/gnshare/gn/"),
         "web/ProbeSetFreeze_DataMatrix")
     # Are we using the following...?
-    app.config["WEBQTL_PORTADDR"] = "http://50.16.251.170"
-    app.config["WEBQTL_INFOPAGEHREF"] = '/dbdoc/%s.html'
-    app.config["WEBQTL_CGIDIR"] = '/webqtl/'  # XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
+    app.config["PORTADDR"] = "http://50.16.251.170"
+    app.config["INFOPAGEHREF"] = '/dbdoc/%s.html'
+    app.config["CGIDIR"] = '/webqtl/'  # XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
     return app
-- 
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