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-rw-r--r--wqflask/utility/authentication_tools.py11
-rw-r--r--wqflask/utility/configuration.py165
-rw-r--r--wqflask/utility/hmac.py8
-rw-r--r--wqflask/utility/startup_config.py23
-rw-r--r--wqflask/utility/tools.py93
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')
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-25 21:12:21 +0000