Logging retrieved db config values before using default values

With reference to this commit:
#975 (comment)

So we have two key things to solve:
- Unnecessary variables like PATH, that may vary for each user to be removed (helps avoid "apple security" values).
- Need to see ENV vars values before being modified by default values in config.get() lines.

Two approaches:
1. Delete PATH, PYTHONPATH from the retrieved config.
- This wouldn't help much since we still need to handle the scenario when db config environment values haven't been set.

2. Using another config dictionary before modifying with default values
- If db config related keys exist, set it to the value from the retrieved config.
- Else if key does not exist in retrieved config, which means config file not present AND environment variables not set, then set it to None.
Note:
- This is not the same as changing the retrieved config value as the original dictionary is still intact.
- Additionally, in the case where config file not present AND environment variables not set, there are no values to before modifying with default values. So manually setting to None should be okay.

emission/core/get_database.py

@@ -15,9 +15,15 @@
 config = ecbc.get_config('conf/storage/db.conf',
     {"DB_HOST": "timeseries.url", "DB_RESULT_LIMIT": "timeseries.result_limit"})
 
+db_config = {}
+for key in ["DB_HOST", "DB_RESULT_LIMIT"]:
+    if key in config:
+        db_config[key] = config.get(key)
+    else:
+        db_config[key] = None
+print("Retrieved config: %s" % db_config)
 url = config.get("DB_HOST", "localhost")
 result_limit = config.get("DB_RESULT_LIMIT", 250000)
-print("Retrieved config: {'DB_HOST': '%s', 'DB_RESULT_LIMIT': '%s'}" % (url, result_limit))
 
 try:
     parsed=pymongo.uri_parser.parse_uri(url)

emission/tests/storageTests/TestTokenQueries.py

@@ -169,19 +169,23 @@ def test_run_script_show(self):
         esdt.insert({'token':'z'})
         sp = subprocess.run(["python3", "bin/auth/insert_tokens.py", "--show"], capture_output=True)
         # The first message is displayed when we run tests locally or run in the CI/CD, but with the local install 
-        # The second is displayed when we run tests locally in a docker container or run in the docker CI; the `DB_HOST` is set to `db` by default
+        # The second is displayed when we run tests (the `DB_HOST` is set to `db` by default):
+        #   a) in the docker CI or,
+        #   b) locally in a docker container (ad-hoc testing environment; do not expect this to be used)
         self.assertIn(sp.stdout,
-            [b'Config file not found, returning a copy of the environment variables instead...\nRetrieved config: {\'DB_HOST\': \'localhost\', \'DB_RESULT_LIMIT\': \'250000\'}\nURL not formatted, defaulting to "Stage_database"\nConnecting to database URL localhost\nx\ny\nz\n',
-             b'Config file not found, returning a copy of the environment variables instead...\nRetrieved config: {\'DB_HOST\': \'db\', \'DB_RESULT_LIMIT\': \'250000\'}\nURL not formatted, defaulting to "Stage_database"\nConnecting to database URL db\nx\ny\nz\n'
+            [b'Config file not found, returning a copy of the environment variables instead...\nRetrieved config: {\'DB_HOST\': None, \'DB_RESULT_LIMIT\': None}\nURL not formatted, defaulting to "Stage_database"\nConnecting to database URL localhost\nx\ny\nz\n',
+             b'Config file not found, returning a copy of the environment variables instead...\nRetrieved config: {\'DB_HOST\': \'db\', \'DB_RESULT_LIMIT\': None}\nURL not formatted, defaulting to "Stage_database"\nConnecting to database URL db\nx\ny\nz\n'
         ])
 
     def test_run_script_empty(self):
         sp = subprocess.run(["python3", "bin/auth/insert_tokens.py"], capture_output=True)
         # The first message is displayed when we run tests locally or run in the CI/CD, but with the local install 
-        # The second is displayed when we run tests locally in a docker container or run in the docker CI; the `DB_HOST` is set to `db` by default
+        # The second is displayed when we run tests (the `DB_HOST` is set to `db` by default):
+        #   a) in the docker CI or,
+        #   b) locally in a docker container (ad-hoc testing environment; do not expect this to be used)
         self.assertIn(sp.stdout,
-            [b'Config file not found, returning a copy of the environment variables instead...\nRetrieved config: {\'DB_HOST\': \'localhost\', \'DB_RESULT_LIMIT\': \'250000\'}\nURL not formatted, defaulting to "Stage_database"\nConnecting to database URL localhost\nPlease provide the script with an argument. Use the "--help" option for more details\n',
-             b'Config file not found, returning a copy of the environment variables instead...\nRetrieved config: {\'DB_HOST\': \'db\', \'DB_RESULT_LIMIT\': \'250000\'}\nURL not formatted, defaulting to "Stage_database"\nConnecting to database URL db\nPlease provide the script with an argument. Use the "--help" option for more details\n'
+            [b'Config file not found, returning a copy of the environment variables instead...\nRetrieved config: {\'DB_HOST\': None, \'DB_RESULT_LIMIT\': None}\nURL not formatted, defaulting to "Stage_database"\nConnecting to database URL localhost\nPlease provide the script with an argument. Use the "--help" option for more details\n',
+             b'Config file not found, returning a copy of the environment variables instead...\nRetrieved config: {\'DB_HOST\': \'db\', \'DB_RESULT_LIMIT\': None}\nURL not formatted, defaulting to "Stage_database"\nConnecting to database URL db\nPlease provide the script with an argument. Use the "--help" option for more details\n'
         ])
 
     #test that no two options can be used together