From 837ce8b9c779b1da6e4390220ccd353b289c1fca Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 20 Dec 2017 09:11:31 -0600
Subject: Bring in some earlier work - mostly documentation and startup
handling
---
etc/default_settings.py | 11 ++++++++---
1 file changed, 8 insertions(+), 3 deletions(-)
(limited to 'etc')
diff --git a/etc/default_settings.py b/etc/default_settings.py
index c00f6c8f..59e22f1a 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -2,7 +2,7 @@
# webserver running in developer mode with limited console
# output. Copy this file and run it from ./bin/genenetwork2 configfile
#
-# Note that these settings are fetched in ./wqflask/utilities/tools.py
+# Note: these settings are fetched in ./wqflask/utilities/tools.py
# which has support for overriding them through environment variables,
# e.g.
#
@@ -14,8 +14,12 @@
# Note also that in the near future we will additionally fetch
# settings from a JSON file
#
-# Note that values for False and 0 have to be strings here - otherwise
+# Note: values for False and 0 have to be strings here - otherwise
# Flask won't pick them up
+#
+# For GNU Guix deployment also check the paths in
+#
+# ~/.guix-profile/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py
import os
import sys
@@ -34,7 +38,7 @@ SECURITY_RECOVERABLE = True
SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org"
SECURITY_POST_LOGIN_VIEW = "/thank_you"
-SERVER_PORT = 5003
+SERVER_PORT = 5003 # running on localhost
SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc'
# ---- Behavioural settings (defaults) note that logger and log levels can
@@ -42,6 +46,7 @@ SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a
WEBSERVER_MODE = 'DEV' # Python webserver mode (DEBUG|DEV|PROD)
WEBSERVER_BRANDING = None # Set the branding (nyi)
WEBSERVER_DEPLOY = None # Deployment specifics (nyi)
+WEBSERVER_URL = "http://localhost:"+str(SERVER_PORT)+"/" # external URL
LOG_LEVEL = 'WARNING' # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL)
LOG_LEVEL_DEBUG = '0' # logger.debugf log level (0-5, 5 = show all)
--
cgit v1.2.3
From a2325f723052ff951200020f9b072a2dd5140c01 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 20 Dec 2017 10:14:35 -0600
Subject: VERSION
---
VERSION | 2 +-
etc/VERSION | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
mode change 100644 => 120000 VERSION
(limited to 'etc')
diff --git a/VERSION b/VERSION
deleted file mode 100644
index 6a5fe6e8..00000000
--- a/VERSION
+++ /dev/null
@@ -1 +0,0 @@
-2.11
diff --git a/VERSION b/VERSION
new file mode 120000
index 00000000..a9a7884c
--- /dev/null
+++ b/VERSION
@@ -0,0 +1 @@
+etc/VERSION
\ No newline at end of file
diff --git a/etc/VERSION b/etc/VERSION
index 1785aa28..b624c74a 100644
--- a/etc/VERSION
+++ b/etc/VERSION
@@ -1 +1 @@
-2.10rc3
+2.10rc5
--
cgit v1.2.3
From 85316a82ec5df2c155f3c4d1dfd3739acf3d4145 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 29 Jan 2018 11:11:02 +0000
Subject: Bumped version
---
etc/VERSION | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
(limited to 'etc')
diff --git a/etc/VERSION b/etc/VERSION
index b624c74a..ca9e199c 100644
--- a/etc/VERSION
+++ b/etc/VERSION
@@ -1 +1 @@
-2.10rc5
+2.11-rc1
--
cgit v1.2.3
From 85819dbeaf922456dc205e482e7e338952945d9b Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 29 Jan 2018 15:10:09 +0000
Subject: Gunicorn works
---
bin/genenetwork2 | 28 +++++++++++++++++++---------
etc/default_settings.py | 2 +-
wqflask/gunicorn/__init__.py | 0
wqflask/gunicorn/genenetwork2.py | 10 ----------
wqflask/gunicorn/wsgi.py | 5 -----
wqflask/run_gunicorn.py | 19 +++++++++++++++++++
wqflask/runserver.py | 2 +-
wqflask/wsgi.py | 4 ++++
8 files changed, 44 insertions(+), 26 deletions(-)
delete mode 100644 wqflask/gunicorn/__init__.py
delete mode 100644 wqflask/gunicorn/genenetwork2.py
delete mode 100644 wqflask/gunicorn/wsgi.py
create mode 100644 wqflask/run_gunicorn.py
create mode 100644 wqflask/wsgi.py
(limited to 'etc')
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index f32c76eb..f6ae3807 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -31,7 +31,7 @@
#
# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./etc/default_settings.py -gunicorn "--bind 0.0.0.0:8000 --workers=2 --chdir wqflask/gunicorn/ wsgi"
-SCRIPT=$(readlink -f "$0")
+SCRIPT=$(realpath "$0")
GN2_BASE_DIR=$(dirname $(dirname "$SCRIPT"))
GN2_ID=$(cat /etc/hostname):$(basename $GN2_BASE_DIR)
@@ -50,15 +50,25 @@ else
fi
echo GN_VERSION=$GN_VERSION
+if [ "$1" = "-c" -o "$1" = "-gunicorn" ]; then
+ echo "Can not use $1 switch without default settings file"
+ exit 1
+fi
# Handle settings parameter (can be .py or .json)
-settings=$1
-ext="${settings##*.}"
-if [ -z "$settings" -o "$ext" = "json" -o "$ext" = "JSON" ]; then
- overrides=$settings
+settings=$(realpath "$1")
+if [ ! -e $settings ]; then
settings=$GN2_BASE_DIR/etc/default_settings.py
else
shift
fi
+
+ext="${settings##*.}"
+if [ "$ext" = "json" -o "$ext" = "JSON" ]; then
+ overrides=$settings
+else
+ echo $settings
+fi
+
if [ ! -e $settings ]; then
echo "ERROR: can not locate settings file - pass it in the command line"
exit 1
@@ -132,12 +142,12 @@ if [ "$1" = '-c' ] ; then
exit 0
fi
if [ "$1" = '-gunicorn' ] ; then
- cd $GN2_BASE_DIR
- cmd=${2}
+ cd $GN2_BASE_DIR/wqflask
+ cmd=$2
echo PYTHONPATH=$PYTHONPATH
- echo RUNNING COMMAND gunicorn $cmd
+ echo RUNNING gunicorn $cmd
gunicorn $cmd
- exit 0
+ exit $?
fi
echo "Starting the redis server:"
diff --git a/etc/default_settings.py b/etc/default_settings.py
index 59e22f1a..699d21f1 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -27,7 +27,7 @@ import sys
GN_VERSION = open("../etc/VERSION","r").read()
SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s"
SQL_ALCHEMY_POOL_RECYCLE = 3600
-GN_SERVER_URL = "http://localhost:8880/"
+GN_SERVER_URL = "http://localhost:8880/" # REST API server
# ---- Flask configuration (see website)
TRAP_BAD_REQUEST_ERRORS = True
diff --git a/wqflask/gunicorn/__init__.py b/wqflask/gunicorn/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/wqflask/gunicorn/genenetwork2.py b/wqflask/gunicorn/genenetwork2.py
deleted file mode 100644
index afbdc934..00000000
--- a/wqflask/gunicorn/genenetwork2.py
+++ /dev/null
@@ -1,10 +0,0 @@
-from flask import Flask
-application = Flask(__name__)
-
-@application.route("/")
-def hello():
- return "Hello There!
"
-
-if __name__ == "__main__":
- application.run(host='0.0.0.0')
-
diff --git a/wqflask/gunicorn/wsgi.py b/wqflask/gunicorn/wsgi.py
deleted file mode 100644
index 8c14ee6b..00000000
--- a/wqflask/gunicorn/wsgi.py
+++ /dev/null
@@ -1,5 +0,0 @@
-from genenetwork2 import application
-
-if __name__ == "__main__":
- application.run()
-
diff --git a/wqflask/run_gunicorn.py b/wqflask/run_gunicorn.py
new file mode 100644
index 00000000..14a2d689
--- /dev/null
+++ b/wqflask/run_gunicorn.py
@@ -0,0 +1,19 @@
+# Run with gunicorn, see ./bin/genenetwork2 for an example
+#
+# Run standalone with
+#
+# ./bin/genenetwork2 ./etc/default_settings.py -c run_gunicorn.py
+
+# from flask import Flask
+# application = Flask(__name__)
+
+print "Starting up Gunicorn process"
+
+from wqflask import app
+
+@app.route("/gunicorn")
+def hello():
+ return "Hello There!
"
+
+if __name__ == "__main__":
+ app.run(host='0.0.0.0')
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index e62e34f2..a0c76e51 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -1,6 +1,6 @@
# Starts the webserver with the ./bin/genenetwork2 command
#
-# This uses Werkzeug WSGI, see gunicorn.py for the alternative
+# This uses Werkzeug WSGI, see ./run_gunicorn.py for the alternative
#
# Please note, running with host set externally below combined with
# debug mode is a security risk unless you have a firewall setup, e.g.
diff --git a/wqflask/wsgi.py b/wqflask/wsgi.py
new file mode 100644
index 00000000..be9c7b37
--- /dev/null
+++ b/wqflask/wsgi.py
@@ -0,0 +1,4 @@
+from run_gunicorn import app as application # expect application as a name
+
+if __name__ == "__main__":
+ application.run()
--
cgit v1.2.3