Configs: Introduce Blueprints. Refactor configs in webqtlConfig.

* Introduce flask Blueprints to help with decoupling the various
  modules from the `wqflask/__init__.py` module
* Refactor settings: Create a function
  `base.webqtlConfig.init_app(...)` to handle setting up the
  configurations on the app correctly. Call this function at app
  creation time.
* Move configuration utility functions from `utility.tools` module to
  `utility.configuration` module.
* Use the `get_setting(...)` function to retrieve configuration
  settings from the application.

5 files changed, 193 insertions, 107 deletions

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 7d80b3fb..3d732228 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -1,7 +1,7 @@
 import json
 import requests
 
-from flask import g
+from flask import g, current_app as app
 from wqflask.database import database_connection
 from base import webqtlConfig
 
@@ -9,7 +9,7 @@ from utility.redis_tools import (get_redis_conn,
                                  get_resource_info,
                                  get_resource_id,
                                  add_resource)
-from utility.tools import GN_PROXY_URL
+from utility.configuration import get_setting
 
 Redis = get_redis_conn()
 
@@ -37,7 +37,7 @@ def check_resource_availability(dataset, user_id, trait_id=None):
         return webqtlConfig.SUPER_PRIVILEGES
 
     response = None
-    the_url = f"{GN_PROXY_URL}available?resource={resource_id}&user={user_id}"
+    the_url = f"{get_setting('GN_PROXY_URL')}available?resource={resource_id}&user={user_id}"
     try:
         response = json.loads(requests.get(the_url).content)
     except:
@@ -93,8 +93,9 @@ def get_group_code(dataset):
 
 
 def check_admin(resource_id=None):
-    the_url = GN_PROXY_URL + "available?resource={}&user={}".format(
-        resource_id, g.user_session.user_id)
+    the_url = (
+        f"{get_setting('GN_PROXY_URL')}available?resource={resource_id}"
+        f"&user={g.user_session.user_id}")
     try:
         response = json.loads(requests.get(the_url).content)['admin']
     except:
diff --git a/wqflask/utility/configuration.py b/wqflask/utility/configuration.py
new file mode 100644
index 00000000..933d9626
--- /dev/null
+++ b/wqflask/utility/configuration.py
@@ -0,0 +1,165 @@
+"""Functions used in setting up configurations."""
+import os # replace os.path with pathlib.Path
+import sys
+import logging
+
+from flask import current_app
+
+logger = logging.getLogger(__name__)
+
+def override_from_envvars(app):
+    """
+    Override `app` configuration values with those in the enviroment variables with the same names.
+    """
+    configs = dict((key, value.strip()) for key,value in
+                   ((key, os.environ.get(key)) for key in app.config.keys())
+                   if value is not None and value != "")
+    app.config.update(**configs)
+    return app
+
+def get_setting(app, setting_id, guess=None):
+    """Resolve a setting from the `app`."""
+    setting = app.config.get(setting_id, guess or "")
+    if setting is None or setting == "":
+        raise Exception(
+            f"{setting_id} setting unknown or faulty "
+            "(update default_settings.py?).")
+    return setting
+
+def get_setting_bool(app, setting_id):
+    v = get_setting(app, setting_id)
+    if v not in [0, False, 'False', 'FALSE', None]:
+        return True
+    return False
+
+
+def get_setting_int(app, setting_id):
+    val = get_setting(app, setting_id)
+    if isinstance(val, str):
+        return int(val)
+    if val is None:
+        return 0
+    return val
+
+def valid_bin(path):
+    if os.path.islink(path) or valid_file(path):
+        return path
+    return None
+
+def valid_file(path):
+    if os.path.isfile(path):
+        return path
+    return None
+
+def valid_path(path):
+    if os.path.isdir(path):
+        return path
+    return None
+
+def flat_file_exists(app, subdir):
+    base = get_setting(app, "GENENETWORK_FILES")
+    return valid_path(base + "/" + subdir)
+
+def flat_files(app, subdir=None):
+    base = get_setting(app, "GENENETWORK_FILES")
+    if subdir:
+        return assert_dir(base + "/" + subdir)
+    return assert_dir(base)
+
+def assert_bin(fn):
+    if not valid_bin(fn):
+        raise Exception("ERROR: can not find binary " + fn)
+    return fn
+
+
+def assert_dir(the_dir):
+    if not valid_path(the_dir):
+        raise FileNotFoundError(f"ERROR: can not find directory '{the_dir}'")
+    return the_dir
+
+def assert_writable_dir(path):
+    try:
+        fn = path + "/test.txt"
+        fh = open(fn, 'w')
+        fh.write("I am writing this text to the file\n")
+        fh.close()
+        os.remove(fn)
+    except IOError:
+        raise Exception(f"Unable to write test.txt to directory {path}")
+    return path
+
+def assert_file(fn):
+    if not valid_file(fn):
+        raise FileNotFoundError(f"Unable to find file '{fn}'")
+    return fn
+
+def mk_dir(path):
+    if not valid_path(path):
+        os.makedirs(path)
+    return assert_dir(path)
+
+def locate(app, name, subdir=None):
+    """
+    Locate a static flat file in the GENENETWORK_FILES environment.
+
+    This function throws an error when the file is not found.
+    """
+    base = get_setting(app, "GENENETWORK_FILES")
+    if subdir:
+        base = base + "/" + subdir
+    if valid_path(base):
+        lookfor = base + "/" + name
+        if valid_file(lookfor):
+            return lookfor
+        else:
+            raise Exception("Can not locate " + lookfor)
+    if subdir:
+        sys.stderr.write(subdir)
+    raise Exception("Can not locate " + name + " in " + base)
+
+def locate_ignore_error(app, name, subdir=None):
+    """
+    Locate a static flat file in the GENENETWORK_FILES environment.
+
+    This function does not throw an error when the file is not found
+    but returns None.
+    """
+    base = get_setting(app, "GENENETWORK_FILES")
+    if subdir:
+        base = base + "/" + subdir
+    if valid_path(base):
+        lookfor = base + "/" + name
+        if valid_file(lookfor):
+            return lookfor
+    return None
+
+def tempdir(app):
+    """Retrieve the configured temporary directory or `/tmp`."""
+    return valid_path(get_setting(app, "TMPDIR", "/tmp"))
+
+def show_settings(app):
+    """Print out the application configurations."""
+    BLUE = '\033[94m'
+    GREEN = '\033[92m'
+    BOLD = '\033[1m'
+    ENDC = '\033[0m'
+    app = app or current_app
+    LOG_LEVEL = app.config.get("LOG_LEVEL")
+
+    print(("Set global log level to " + BLUE + LOG_LEVEL + ENDC),
+          file=sys.stderr)
+    log_level = getattr(logging, LOG_LEVEL.upper())
+    logging.basicConfig(level=log_level)
+
+    logger.info(BLUE + "Mr. Mojo Risin 2" + ENDC)
+    keylist = list(app.config.keys())
+    print("runserver.py: ****** Webserver configuration - k,v pairs from app.config ******",
+          file=sys.stderr)
+    keylist.sort()
+    for k in keylist:
+        try:
+            print(("%s: %s%s%s%s" % (k, BLUE, BOLD, get_setting(app, k), ENDC)),
+                  file=sys.stderr)
+        except:
+            print(("%s: %s%s%s%s" % (k, GREEN, BOLD, app.config[k], ENDC)),
+                  file=sys.stderr)
diff --git a/wqflask/utility/hmac.py b/wqflask/utility/hmac.py
index 29891677..2fb8b106 100644
--- a/wqflask/utility/hmac.py
+++ b/wqflask/utility/hmac.py
@@ -1,9 +1,7 @@
 import hmac
 import hashlib
 
-from flask import url_for
-
-from wqflask import app
+from flask import url_for, current_app as app
 
 
 def hmac_creation(stringy):
@@ -37,7 +35,3 @@ def url_for_hmac(endpoint, **values):
     else:
         combiner = "?"
     return url + combiner + "hm=" + hm
-
-
-app.jinja_env.globals.update(url_for_hmac=url_for_hmac,
-                             data_hmac=data_hmac)
diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
index 69cac124..5ab43b1a 100644
--- a/wqflask/utility/startup_config.py
+++ b/wqflask/utility/startup_config.py
@@ -1,11 +1,10 @@
 
 from wqflask import app
 
-from utility.tools import WEBSERVER_MODE
-from utility.tools import show_settings
-from utility.tools import get_setting_int
-from utility.tools import get_setting
-from utility.tools import get_setting_bool
+from utility.configuration import show_settings
+from utility.configuration import get_setting_int
+from utility.configuration import get_setting
+from utility.configuration import get_setting_bool
 
 
 BLUE = '\033[94m'
@@ -14,28 +13,28 @@ BOLD = '\033[1m'
 ENDC = '\033[0m'
 
 
-def app_config():
+def app_config(app):
     app.config['SESSION_TYPE'] = app.config.get('SESSION_TYPE', 'filesystem')
     if not app.config.get('SECRET_KEY'):
         import os
         app.config['SECRET_KEY'] = str(os.urandom(24))
-    mode = WEBSERVER_MODE
+    mode = get_setting(app, "WEBSERVER_MODE")
     if mode in ["DEV", "DEBUG"]:
         app.config['TEMPLATES_AUTO_RELOAD'] = True
         if mode == "DEBUG":
             app.debug = True
 
     print("==========================================")
-    show_settings()
+    show_settings(app)
 
-    port = get_setting_int("SERVER_PORT")
+    port = get_setting_int(app, "SERVER_PORT")
 
-    if get_setting_bool("USE_GN_SERVER"):
+    if get_setting_bool(app, "USE_GN_SERVER"):
         print(f"GN2 API server URL is [{BLUE}GN_SERVER_URL{ENDC}]")
         import requests
-        page = requests.get(get_setting("GN_SERVER_URL"))
+        page = requests.get(get_setting(app, "GN_SERVER_URL"))
         if page.status_code != 200:
             raise Exception("API server not found!")
     print(f"GN2 is running. Visit {BLUE}"
           f"[http://localhost:{str(port)}/{ENDC}]"
-          f"({get_setting('WEBSERVER_URL')})")
+          f"({get_setting(app, 'WEBSERVER_URL')})")
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 5b3e9413..894bef76 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -7,6 +7,16 @@ import json
 
 from wqflask import app
 
+from .configuration import (
+    mk_dir,
+    valid_bin,
+    valid_file,
+    valid_path,
+    assert_bin,
+    assert_dir,
+    assert_file,
+    assert_writable_dir)
+
 # Use the standard logger here to avoid a circular dependency
 import logging
 logger = logging.getLogger(__name__)
@@ -86,24 +96,6 @@ def get_setting_int(id):
     return v
 
 
-def valid_bin(bin):
-    if os.path.islink(bin) or valid_file(bin):
-        return bin
-    return None
-
-
-def valid_file(fn):
-    if os.path.isfile(fn):
-        return fn
-    return None
-
-
-def valid_path(dir):
-    if os.path.isdir(dir):
-        return dir
-    return None
-
-
 def js_path(module=None):
     """
     Find the JS module in the two paths
@@ -146,42 +138,6 @@ def flat_files(subdir=None):
     return assert_dir(base)
 
 
-def assert_bin(fn):
-    if not valid_bin(fn):
-        raise Exception("ERROR: can not find binary " + fn)
-    return fn
-
-
-def assert_dir(the_dir):
-    if not valid_path(the_dir):
-        raise FileNotFoundError(f"ERROR: can not find directory '{the_dir}'")
-    return the_dir
-
-
-def assert_writable_dir(dir):
-    try:
-        fn = dir + "/test.txt"
-        fh = open(fn, 'w')
-        fh.write("I am writing this text to the file\n")
-        fh.close()
-        os.remove(fn)
-    except IOError:
-        raise Exception('Unable to write test.txt to directory ' + dir)
-    return dir
-
-
-def assert_file(fn):
-    if not valid_file(fn):
-        raise FileNotFoundError(f"Unable to find file '{fn}'")
-    return fn
-
-
-def mk_dir(dir):
-    if not valid_path(dir):
-        os.makedirs(dir)
-    return assert_dir(dir)
-
-
 def locate(name, subdir=None):
     """
     Locate a static flat file in the GENENETWORK_FILES environment.
@@ -230,35 +186,6 @@ def tempdir():
     return valid_path(get_setting("TMPDIR", "/tmp"))
 
 
-BLUE = '\033[94m'
-GREEN = '\033[92m'
-BOLD = '\033[1m'
-ENDC = '\033[0m'
-
-
-def show_settings():
-    from utility.tools import LOG_LEVEL
-
-    print(("Set global log level to " + BLUE + LOG_LEVEL + ENDC),
-          file=sys.stderr)
-    log_level = getattr(logging, LOG_LEVEL.upper())
-    logging.basicConfig(level=log_level)
-
-    logger.info(OVERRIDES)
-    logger.info(BLUE + "Mr. Mojo Risin 2" + ENDC)
-    keylist = list(app.config.keys())
-    print("runserver.py: ****** Webserver configuration - k,v pairs from app.config ******",
-          file=sys.stderr)
-    keylist.sort()
-    for k in keylist:
-        try:
-            print(("%s: %s%s%s%s" % (k, BLUE, BOLD, get_setting(k), ENDC)),
-                  file=sys.stderr)
-        except:
-            print(("%s: %s%s%s%s" % (k, GREEN, BOLD, app.config[k], ENDC)),
-                  file=sys.stderr)
-
-
 # Cached values
 GN_VERSION = get_setting('GN_VERSION')
 HOME = get_setting('HOME')