diff options
| -rw-r--r-- | VERSION | 2 | ||||
| -rwxr-xr-x | bin/genenetwork2 | 82 | ||||
| -rw-r--r-- | wqflask/base/webqtlCaseData.py | 2 | ||||
| -rw-r--r-- | wqflask/runserver.py | 19 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 40 | ||||
| -rw-r--r-- | wqflask/wqflask/__init__.py | 6 |
6 files changed, 105 insertions, 46 deletions
diff --git a/VERSION b/VERSION index cd5ac039..144b089a 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -2.0 +2.10-pre1 diff --git a/bin/genenetwork2 b/bin/genenetwork2 index d926d6a1..889401fd 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -1,53 +1,93 @@ #! /bin/bash # -# This will run the GN2 server (with default settings if none supplied). Pass in -# your own settings file, e.g. +# This will run the GN2 server (with default settings if none +# supplied). Pass in your own settings file, e.g. # # ./bin/genenetwork2 ~/my_settings.py # +# But better is to retain the defaults and override them with +# JSON file (see the deploy docs). +# +# ./bin/genenetwork2 ~/my_overrides.json +# # To run a maintenance script with settings (instead of the webserver) add that with # a -c switch, e.g. # -# ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py +# ./bin/genenetwork2 ~/my_overrides.json -c ./wqflask/maintenance/gen_select_dataset.py # # Environment settings can be used to preconfigure as well as a # settings.py file. +# +# GN2_BASE_PATH is base directory of wqflask source code +# SCRIPT=$(readlink -f "$0") -GN2_BASE_PATH=$(dirname $(dirname "$SCRIPT")) +GN2_BASE_DIR=$(dirname $(dirname "$SCRIPT")) -GN2_GUIX_PATH=$GN2_BASE_PATH/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg -if [ -d $GN2_GUIX_PATH ]; then - echo GN2 is running from GUIX - GN2_BASE_PATH=$GN2_GUIX_PATH -fi -echo $GN2_BASE_PATH +echo GN2_BASE_DIR=$GN2_BASE_DIR -# Handle settings parameter + +# Handle settings parameter (can be .py or .json) settings=$1 -if [ -z $settings ]; then - # get default - settings=$GN2_BASE_PATH/etc/default_settings.py +ext="${settings##*.}" +if [ -z "$settings" -o "$ext" = "json" -o "$ext" = "JSON" ]; then + overrides=$settings + settings=$GN2_BASE_DIR/etc/default_settings.py else shift fi if [ ! -e $settings ]; then - echo "ERROR: can not locate settings file - pass it in the command line" - exit 1 + GUIX_ETC=$GN2_BASE_DIR/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg + if [ -d $GUIX_ETC ]; then + echo INFO: GN2 is actually running from GNU Guix + else + echo "ERROR: can not locate settings file - pass it in the command line" + exit 1 + fi +fi +export WQFLASK_SETTINGS=$settings # Python +export WQFLASK_OVERRIDES=$overrides # JSON + +echo WQFLASK_SETTINGS=$settings +echo WQFLASK_OVERRIDES=$overrides + +# ---- Checks and balances +if [ -z $GUIX_ETC ]; then + if [ -z $GN2_PROFILE ] ; then + echo "WARNING: GN2_PROFILE has not been set - I hope you know what you are doing" + else + export PYTHONPATH=$GN2_PROFILE/lib/python2.7/site-packages + export R_LIBS_SITE=$GN2_PROFILE/site-library + export GUIX_GTK3_PATH="$GN2_PROFILE/lib/gtk-3.0" + export GI_TYPELIB_PATH="$GN2_PROFILE/lib/girepository-1.0" + export XDG_DATA_DIRS="$GN2_PROFILE/share" + export GIO_EXTRA_MODULES="$GN2_PROFILE/lib/gio/modules" + fi + if [ -z $PYTHONPATH ] ; then + echo "WARNING PYTHONPATH has not been set" + fi + if [ ! -d $R_LIBS_SITE ] ; then + echo "ERROR: R_LIBS_SITE has not been set correctly (we only allow one path)" + echo "Paste in the output of, for example," + echo "guix package -p /usr/local/guix-profiles/gn2-staging --search-paths" + exit 1 + fi fi -export WQFLASK_SETTINGS=$settings # We may change this one: -export PYTHONPATH=$GN2_BASE_PATH/wqflask:$PYTHONPATH +export PYTHONPATH=$GN2_BASE_DIR/wqflask:$PYTHONPATH # TEMPDIR defaults to /tmp if nothing else if [ -z $TEMPDIR ]; then TEMPDIR="/tmp" fi +set|grep $GN2_PROFILE +set|grep TEMPDIR + # Now handle command parameter -c -if [ $1 = '-c' ] ; then - cd $GN2_BASE_PATH/wqflask +if [ "$1" = '-c' ] ; then + cd $GN2_BASE_DIR/wqflask cmd=${2#wqflask/} echo PYTHONPATH=$PYTHONPATH echo RUNNING COMMAND $cmd @@ -61,6 +101,6 @@ dbfilename gn2.rdb " | redis-server - & # Start the flask server running GN2 -cd $GN2_BASE_PATH/wqflask +cd $GN2_BASE_DIR/wqflask echo "Starting with $settings" /usr/bin/env python runserver.py diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index 8df9939e..2f88f778 100644 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -16,8 +16,6 @@ # Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) # at rwilliams@uthsc.edu and xzhou15@uthsc.edu # -# -# # This module is used by GeneNetwork project (www.genenetwork.org) # # Created by GeneNetwork Core Team 2010/08/10 diff --git a/wqflask/runserver.py b/wqflask/runserver.py index 12ec904e..0342b7ad 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -16,34 +16,37 @@ GREEN = '\033[92m' BOLD = '\033[1m' ENDC = '\033[0m' -logger.info("GN2 is running. Visit %shttp://localhost:5003/%s" % (BLUE,ENDC)) - import os app.config['SECRET_KEY'] = os.urandom(24) -from utility.tools import WEBSERVER_MODE +from utility.tools import WEBSERVER_MODE,get_setting_int + +port = get_setting_int("SERVER_PORT") + +logger.info("GN2 is running. Visit %shttp://localhost:%s/%s" % (BLUE,port,ENDC)) werkzeug_logger = logging.getLogger('werkzeug') if WEBSERVER_MODE == 'DEBUG': app.run(host='0.0.0.0', - port=app.config['SERVER_PORT'], + port=port, debug=True, - use_debugger=True, + use_debugger=False, threaded=False, + processes=0, use_reloader=True) elif WEBSERVER_MODE == 'DEV': werkzeug_logger.setLevel(logging.WARNING) app.run(host='0.0.0.0', - port=app.config['SERVER_PORT'], + port=port, debug=False, use_debugger=False, threaded=False, processes=0, use_reloader=True) -else: #production mode +else: # staging/production modes app.run(host='0.0.0.0', - port=app.config['SERVER_PORT'], + port=port, debug=False, use_debugger=False, threaded=True, diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 22779739..23d6fb62 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -3,6 +3,7 @@ import os import sys +import json from wqflask import app @@ -10,6 +11,8 @@ from wqflask import app import logging logger = logging.getLogger(__name__ ) +OVERRIDES = {} + def get_setting(command_id,guess=None): """Resolve a setting from the environment or the global settings in app.config, with valid_path is a function checking whether the @@ -45,13 +48,15 @@ def get_setting(command_id,guess=None): logger.debug("Looking for "+command_id+"\n") command = value(os.environ.get(command_id)) if command is None or command == "": - # ---- Check whether setting exists in app - command = value(app.config.get(command_id)) + command = OVERRIDES.get(command_id) if command is None: - command = value(guess) - if command is None or command == "": - print command - raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).') + # ---- Check whether setting exists in app + command = value(app.config.get(command_id)) + if command is None: + command = value(guess) + if command is None or command == "": + # print command + raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).') logger.debug("Set "+command_id+"="+str(command)) return command @@ -169,18 +174,20 @@ def show_settings(): log_level = getattr(logging, LOG_LEVEL.upper()) logging.basicConfig(level=log_level) + logger.info(OVERRIDES) logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC) - print "runserver.py: ****** The webserver has the following configuration ******" + print "runserver.py: ****** Webserver configuration ******" keylist = app.config.keys() 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(k),ENDC)) except: - print("%s %s%s%s%s" % (k,GREEN,BOLD,app.config[k],ENDC)) + print("%s: %s%s%s%s" % (k,GREEN,BOLD,app.config[k],ENDC)) # Cached values +HOME = get_setting('HOME') WEBSERVER_MODE = get_setting('WEBSERVER_MODE') GN_SERVER_URL = get_setting('GN_SERVER_URL') SQL_URI = get_setting('SQL_URI') @@ -199,3 +206,18 @@ PYLMM_COMMAND = pylmm_command() GEMMA_COMMAND = gemma_command() PLINK_COMMAND = plink_command() TEMPDIR = tempdir() + +from six import string_types + +if os.environ.get('WQFLASK_OVERRIDES'): + jsonfn = get_setting('WQFLASK_OVERRIDES') + logger.error("WQFLASK_OVERRIDES: %s" % jsonfn) + with open(jsonfn) as data_file: + overrides = json.load(data_file) + for k in overrides: + cmd = overrides[k] + if isinstance(cmd, string_types): + OVERRIDES[k] = eval(cmd) + else: + OVERRIDES[k] = cmd + logger.debug(OVERRIDES) diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index af271d02..2188ce17 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -14,11 +14,7 @@ app = Flask(__name__) app.config.from_object('cfg.default_settings') # Get the defaults from cfg.default_settings app.config.from_envvar('WQFLASK_SETTINGS') # See http://flask.pocoo.org/docs/config/#configuring-from-files - -logger.debug("System path is") -logger.debug(sys.path) -logger.debug("App.config is") -logger.debug(app.config) +# Note we also use WQFLASK_OVERRIDES app.jinja_env.globals.update( undefined = jinja2.StrictUndefined, |