Store all configs in the app object

1 files changed, 118 insertions, 114 deletions

diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 00b8368c..2969f31c 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -4,21 +4,22 @@
 import os
 import sys
 import json
+from typing import Any, Optional
 
-from wqflask import app
+from flask import Flask
 
 # Use the standard logger here to avoid a circular dependency
 import logging
 logger = logging.getLogger(__name__)
 
 
-def app_set(command_id, value):
+def app_set(app: Flask, command_id: str, value: Any) -> Any:
     """Set application wide value"""
     app.config.setdefault(command_id, value)
     return value
 
 
-def get_setting(command_id, guess=None):
+def get_setting(app: Flask, command_id: str, guess: Optional[Any] = None) -> Any:
     """Resolve a setting from the environment or the global settings in
     app.config, with valid_path is a function checking whether the
     path points to an expected directory and returns the full path to
@@ -45,7 +46,7 @@ def get_setting(command_id, guess=None):
     def value(command):
         if command:
             # sys.stderr.write("Found "+command+"\n")
-            app_set(command_id, command)
+            app_set(app, command_id, command)
             return command
         else:
             return app.config.get(command_id)
@@ -66,15 +67,15 @@ def get_setting(command_id, guess=None):
     return command
 
 
-def get_setting_bool(id):
-    v = get_setting(id)
+def get_setting_bool(app, id):
+    v = get_setting(app, id)
     if v not in [0, False, 'False', 'FALSE', None]:
         return True
     return False
 
 
-def get_setting_int(id):
-    v = get_setting(id)
+def get_setting_int(app, id):
+    v = get_setting(app, id)
     if isinstance(v, str):
         return int(v)
     if v is None:
@@ -100,43 +101,43 @@ def valid_path(dir):
     return None
 
 
-def js_path(module=None):
+def js_path(app, module=None):
     """
     Find the JS module in the two paths
     """
-    try_gn = get_setting("JS_GN_PATH") + "/" + module
+    try_gn = get_setting(app, "JS_GN_PATH") + "/" + module
     if valid_path(try_gn):
         return try_gn
-    try_guix = get_setting("JS_GUIX_PATH") + "/" + module
+    try_guix = get_setting(app, "JS_GUIX_PATH") + "/" + module
     if valid_path(try_guix):
         return try_guix
     raise "No JS path found for " + module + \
         " (if not in Guix check JS_GN_PATH)"
 
 
-def reaper_command(guess=None):
-    return get_setting("REAPER_COMMAND", guess)
+def reaper_command(app, guess=None):
+    return get_setting(app, "REAPER_COMMAND", guess)
 
 
-def gemma_command(guess=None):
-    return assert_bin(get_setting("GEMMA_COMMAND", guess))
+def gemma_command(app, guess=None):
+    return assert_bin(get_setting(app, "GEMMA_COMMAND", guess))
 
 
-def gemma_wrapper_command(guess=None):
-    return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND", guess))
+def gemma_wrapper_command(app, guess=None):
+    return assert_bin(get_setting(app, "GEMMA_WRAPPER_COMMAND", guess))
 
 
-def plink_command(guess=None):
-    return assert_bin(get_setting("PLINK_COMMAND", guess))
+def plink_command(app, guess=None):
+    return assert_bin(get_setting(app, "PLINK_COMMAND", guess))
 
 
-def flat_file_exists(subdir):
-    base = get_setting("GENENETWORK_FILES")
+def flat_file_exists(app, subdir):
+    base = get_setting(app, "GENENETWORK_FILES")
     return valid_path(base + "/" + subdir)
 
 
-def flat_files(subdir=None):
-    base = get_setting("GENENETWORK_FILES")
+def flat_files(app, subdir=None):
+    base = get_setting(app, "GENENETWORK_FILES")
     if subdir:
         return assert_dir(base + "/" + subdir)
     return assert_dir(base)
@@ -178,13 +179,13 @@ def mk_dir(dir):
     return assert_dir(dir)
 
 
-def locate(name, subdir=None):
+def locate(app: Flask, name: str, subdir=None) -> str:
     """
     Locate a static flat file in the GENENETWORK_FILES environment.
 
     This function throws an error when the file is not found.
     """
-    base = get_setting("GENENETWORK_FILES")
+    base = get_setting(app, "GENENETWORK_FILES")
     if subdir:
         base = base + "/" + subdir
     if valid_path(base):
@@ -198,18 +199,18 @@ def locate(name, subdir=None):
     raise Exception("Can not locate " + name + " in " + base)
 
 
-def locate_phewas(name, subdir=None):
-    return locate(name, '/phewas/' + subdir)
+def locate_phewas(app: Flask, name, subdir=None):
+    return locate(app, name, '/phewas/' + subdir)
 
 
-def locate_ignore_error(name, subdir=None):
+def locate_ignore_error(app: Flask, 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("GENENETWORK_FILES")
+    base = get_setting(app, "GENENETWORK_FILES")
     if subdir:
         base = base + "/" + subdir
     if valid_path(base):
@@ -219,11 +220,11 @@ def locate_ignore_error(name, subdir=None):
     return None
 
 
-def tempdir():
+def tempdir(app: Flask) -> str:
     """
     Get UNIX TMPDIR by default
     """
-    return valid_path(get_setting("TMPDIR", "/tmp"))
+    return valid_path(get_setting(app, "TMPDIR", "/tmp"))
 
 
 BLUE = '\033[94m'
@@ -232,15 +233,14 @@ BOLD = '\033[1m'
 ENDC = '\033[0m'
 
 
-def show_settings():
-    from utility.tools import LOG_LEVEL
+def show_settings(app: Flask) -> None:
+    LOG_LEVEL = get_setting(app, "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 ******",
@@ -248,89 +248,93 @@ def show_settings():
     keylist.sort()
     for k in keylist:
         try:
-            print(("%s: %s%s%s%s" % (k, BLUE, BOLD, get_setting(k), ENDC)),
+            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)
 
 
-# Cached values
-GN_VERSION = get_setting('GN_VERSION')
-HOME = get_setting('HOME')
-SERVER_PORT = get_setting('SERVER_PORT')
-WEBSERVER_MODE = get_setting('WEBSERVER_MODE')
-GN2_BASE_URL = get_setting('GN2_BASE_URL')
-GN2_BRANCH_URL = get_setting('GN2_BRANCH_URL')
-GN_SERVER_URL = get_setting('GN_SERVER_URL')
-GN_PROXY_URL = get_setting('GN_PROXY_URL')
-GN3_LOCAL_URL = get_setting('GN3_LOCAL_URL')
-SERVER_PORT = get_setting_int('SERVER_PORT')
-SQL_URI = get_setting('SQL_URI')
-LOG_LEVEL = get_setting('LOG_LEVEL')
-LOG_LEVEL_DEBUG = get_setting_int('LOG_LEVEL_DEBUG')
-LOG_SQL = get_setting_bool('LOG_SQL')
-LOG_SQL_ALCHEMY = get_setting_bool('LOG_SQL_ALCHEMY')
-LOG_BENCH = get_setting_bool('LOG_BENCH')
-LOG_FORMAT = "%(message)s"    # not yet in use
-USE_REDIS = get_setting_bool('USE_REDIS')
-REDIS_URL = get_setting('REDIS_URL')
-USE_GN_SERVER = get_setting_bool('USE_GN_SERVER')
-
-GENENETWORK_FILES = get_setting('GENENETWORK_FILES')
-JS_GUIX_PATH = get_setting('JS_GUIX_PATH')
-assert_dir(JS_GUIX_PATH)
-JS_GN_PATH = get_setting('JS_GN_PATH')
-# assert_dir(JS_GN_PATH)
-
-GITHUB_CLIENT_ID = get_setting('GITHUB_CLIENT_ID')
-GITHUB_CLIENT_SECRET = get_setting('GITHUB_CLIENT_SECRET')
-GITHUB_AUTH_URL = ""
-if GITHUB_CLIENT_ID != 'UNKNOWN' and GITHUB_CLIENT_SECRET:
-    GITHUB_AUTH_URL = "https://github.com/login/oauth/authorize?client_id=" + \
-                      GITHUB_CLIENT_ID + "&client_secret=" + GITHUB_CLIENT_SECRET
-    GITHUB_API_URL = get_setting('GITHUB_API_URL')
-
-ORCID_CLIENT_ID = get_setting('ORCID_CLIENT_ID')
-ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET')
-ORCID_AUTH_URL = None
-if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET:
-    ORCID_AUTH_URL = "https://orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id=" + \
-        ORCID_CLIENT_ID + "&client_secret=" + ORCID_CLIENT_SECRET + \
-        "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2"
-    ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL')
-
-
-SMTP_CONNECT = get_setting('SMTP_CONNECT')
-SMTP_USERNAME = get_setting('SMTP_USERNAME')
-SMTP_PASSWORD = get_setting('SMTP_PASSWORD')
-
-REAPER_COMMAND = app_set("REAPER_COMMAND", reaper_command())
-GEMMA_COMMAND = app_set("GEMMA_COMMAND", gemma_command())
-assert(GEMMA_COMMAND is not None)
-PLINK_COMMAND = app_set("PLINK_COMMAND", plink_command())
-GEMMA_WRAPPER_COMMAND = gemma_wrapper_command()
-TEMPDIR = tempdir()  # defaults to UNIX TMPDIR
-assert_dir(TEMPDIR)
-
-# ---- Handle specific JS modules
-JS_GUIX_PATH = get_setting("JS_GUIX_PATH")
-assert_dir(JS_GUIX_PATH)
-assert_dir(JS_GUIX_PATH + '/cytoscape-panzoom')
-
-CSS_PATH = JS_GUIX_PATH  # The CSS is bundled together with the JS
-# assert_dir(JS_PATH)
-
-JS_TWITTER_POST_FETCHER_PATH = get_setting(
-    "JS_TWITTER_POST_FETCHER_PATH", js_path("javascript-twitter-post-fetcher"))
-assert_dir(JS_TWITTER_POST_FETCHER_PATH)
-assert_file(JS_TWITTER_POST_FETCHER_PATH + "/js/twitterFetcher_min.js")
-
-JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH", js_path("cytoscape"))
-assert_dir(JS_CYTOSCAPE_PATH)
-assert_file(JS_CYTOSCAPE_PATH + '/cytoscape.min.js')
-
-# assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData")
-
-OAUTH2_CLIENT_ID = get_setting('OAUTH2_CLIENT_ID')
-OAUTH2_CLIENT_SECRET = get_setting('OAUTH2_CLIENT_SECRET')
+def set_mandatory_settings(app: Flask) -> Flask:
+    """Set the mandatory settings then return the `app` object."""
+    # Cached values
+    app.config["GN_VERSION"] = get_setting(app, 'GN_VERSION')
+    app.config["HOME"] = get_setting(app, 'HOME')
+    app.config["SERVER_PORT"] = get_setting(app, 'SERVER_PORT')
+    app.config["WEBSERVER_MODE"] = get_setting(app, 'WEBSERVER_MODE')
+    app.config["GN2_BASE_URL"] = get_setting(app, 'GN2_BASE_URL')
+    app.config["GN2_BRANCH_URL"] = get_setting(app, 'GN2_BRANCH_URL')
+    app.config["GN_SERVER_URL"] = get_setting(app, 'GN_SERVER_URL')
+    app.config["GN_PROXY_URL"] = get_setting(app, 'GN_PROXY_URL')
+    app.config["GN3_LOCAL_URL"] = get_setting(app, 'GN3_LOCAL_URL')
+    app.config["SERVER_PORT"] = get_setting_int(app, 'SERVER_PORT')
+    app.config["SQL_URI"] = get_setting(app, 'SQL_URI')
+    app.config["LOG_LEVEL"] = get_setting(app, 'LOG_LEVEL')
+    app.config["LOG_LEVEL_DEBUG"] = get_setting_int(app, 'LOG_LEVEL_DEBUG')
+    app.config["LOG_SQL"] = get_setting_bool(app, 'LOG_SQL')
+    app.config["LOG_SQL_ALCHEMY"] = get_setting_bool(app, 'LOG_SQL_ALCHEMY')
+    app.config["LOG_BENCH"] = get_setting_bool(app, 'LOG_BENCH')
+    app.config["LOG_FORMAT"] = "%(message)s"    # not yet in use
+    app.config["USE_REDIS"] = get_setting_bool(app, 'USE_REDIS')
+    app.config["REDIS_URL"] = get_setting(app, 'REDIS_URL')
+    app.config["USE_GN_SERVER"] = get_setting_bool(app, 'USE_GN_SERVER')
+
+    app.config["GENENETWORK_FILES"] = get_setting(app, 'GENENETWORK_FILES')
+    app.config["JS_GUIX_PATH"] = assert_dir(get_setting(app, 'JS_GUIX_PATH'))
+    app.config["JS_GN_PATH"] = get_setting(app, 'JS_GN_PATH')
+    # assert_dir(JS_GN_PATH)
+
+    app.config["GITHUB_CLIENT_ID"] = get_setting(app, 'GITHUB_CLIENT_ID')
+    app.config["GITHUB_CLIENT_SECRET"] = get_setting(app, 'GITHUB_CLIENT_SECRET')
+    app.config["GITHUB_AUTH_URL"] = ""
+    if app.config["GITHUB_CLIENT_ID"] != 'UNKNOWN' and app.config["GITHUB_CLIENT_SECRET"]:
+        app.config["GITHUB_AUTH_URL"] = "https://github.com/login/oauth/authorize?client_id=" + \
+                          app.config["GITHUB_CLIENT_ID"] + "&client_secret=" + \
+                          app.config["GITHUB_CLIENT_SECRET"]
+        app.config["GITHUB_API_URL"] = get_setting(app, 'GITHUB_API_URL')
+
+    app.config["ORCID_CLIENT_ID"] = get_setting(app, 'ORCID_CLIENT_ID')
+    app.config["ORCID_CLIENT_SECRET"] = get_setting(app, 'ORCID_CLIENT_SECRET')
+    app.config["ORCID_AUTH_URL"] = None
+    if app.config["ORCID_CLIENT_ID"] != 'UNKNOWN' and app.config["ORCID_CLIENT_SECRET"]:
+        app.config["ORCID_AUTH_URL"] = "https://orcid.org/oauth/authorize" + \
+            "?response_type=code&scope=/authenticate&show_login=true" + \
+            "&client_id=" + \
+            app.config["ORCID_CLIENT_ID"] + "&client_secret=" + \
+            app.config["ORCID_CLIENT_SECRET"] + "&redirect_uri=" + \
+            app.config["GN2_BRANCH_URL"] + "n/login/orcid_oauth2"
+        app.config["ORCID_TOKEN_URL"] = get_setting(app, 'ORCID_TOKEN_URL')
+
+
+    app.config["SMTP_CONNECT"] = get_setting(app, 'SMTP_CONNECT')
+    app.config["SMTP_USERNAME"] = get_setting(app, 'SMTP_USERNAME')
+    app.config["SMTP_PASSWORD"] = get_setting(app, 'SMTP_PASSWORD')
+
+    app.config["REAPER_COMMAND"] = app_set(app, "REAPER_COMMAND", reaper_command(app))
+    app.config["GEMMA_COMMAND"] = app_set(app, "GEMMA_COMMAND", gemma_command(app))
+    assert(app.config["GEMMA_COMMAND"] is not None)
+    app.config["PLINK_COMMAND"] = app_set(app, "PLINK_COMMAND", plink_command(app))
+    app.config["GEMMA_WRAPPER_COMMAND"] = gemma_wrapper_command(app)
+    app.config["TEMPDIR"] = assert_dir(tempdir(app))  # defaults to UNIX TMPDIR
+
+    # ---- Handle specific JS modules
+    app.config["JS_GUIX_PATH"] = assert_dir(get_setting(app, "JS_GUIX_PATH"))
+    assert_dir(app.config["JS_GUIX_PATH"] + '/cytoscape-panzoom')
+
+    app.config["CSS_PATH"] = app.config["JS_GUIX_PATH"]  # The CSS is bundled together with the JS
+    # assert_dir(JS_PATH)
+
+    app.config["JS_TWITTER_POST_FETCHER_PATH"] = assert_dir(get_setting(
+        app,
+        "JS_TWITTER_POST_FETCHER_PATH",
+        js_path(app, "javascript-twitter-post-fetcher")))
+    assert_file(app.config["JS_TWITTER_POST_FETCHER_PATH"] + "/js/twitterFetcher_min.js")
+
+    app.config["JS_CYTOSCAPE_PATH"] = assert_dir(get_setting(app, "JS_CYTOSCAPE_PATH", js_path(app, "cytoscape")))
+    assert_file(app.config["JS_CYTOSCAPE_PATH"] + '/cytoscape.min.js')
+
+    # assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData")
+
+    app.config["OAUTH2_CLIENT_ID"] = get_setting(app, 'OAUTH2_CLIENT_ID')
+    app.config["OAUTH2_CLIENT_SECRET"] = get_setting(app, 'OAUTH2_CLIENT_SECRET')
+    return app