2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/2ea487b70602/
Changeset: 2ea487b70602
User: dannon
Date: 2015-01-26 13:54:29+00:00
Summary: Log when using virtualenv at Galaxy startup.
Affected #: 1 file
diff -r 36a5b25e0d33efdaaa0a6abb96468f648ee206f5 -r 2ea487b70602bd94f442243e27f00fca92693c33 run.sh
--- a/run.sh
+++ b/run.sh
@@ -6,6 +6,7 @@
# should run this instance in.
if [ -d .venv ];
then
+ printf "Activating virtualenv at %s/.venv\n" $(pwd)
. .venv/bin/activate
fi
https://bitbucket.org/galaxy/galaxy-central/commits/39f3f0586c48/
Changeset: 39f3f0586c48
User: dannon
Date: 2015-01-26 13:58:29+00:00
Summary: Allow admin users to change user information (like email addresses) when using remote_auth; otherwise should a user email address change you had to manually edit the database.
Affected #: 1 file
diff -r 2ea487b70602bd94f442243e27f00fca92693c33 -r 39f3f0586c48f81452e3a7a6af1f5e97c4ef8ed0 lib/galaxy/web/framework/middleware/remoteuser.py
--- a/lib/galaxy/web/framework/middleware/remoteuser.py
+++ b/lib/galaxy/web/framework/middleware/remoteuser.py
@@ -64,7 +64,7 @@
# If the secret header is enabled, we expect upstream to send along some key
# in HTTP_GX_SECRET, so we'll need to compare that here to the correct value
- #
+ #
# This is not an ideal location for this function. The reason being
# that because this check is done BEFORE the REMOTE_USER check, it is
# possible to attack the GX_SECRET key without having correct
@@ -79,8 +79,8 @@
title = "Access to Galaxy is denied"
message = """
Galaxy is configured to authenticate users via an external
- method (such as HTTP authentication in Apache), but an
- incorrect shared secret key was provided by the
+ method (such as HTTP authentication in Apache), but an
+ incorrect shared secret key was provided by the
upstream (proxy) server.</p><p>Please contact your local Galaxy administrator. The
variable <code>remote_user_secret</code> and
@@ -88,7 +88,7 @@
access Galaxy.
"""
return self.error( start_response, title, message )
-
+
if not environ.get(self.remote_user_header, '(null)').startswith('(null)'):
if not environ[ self.remote_user_header ].count( '@' ):
if self.maildomain is not None:
@@ -114,6 +114,8 @@
pass # admins can create users
elif path_info.startswith( '/user/logout' ) and environ[ self.remote_user_header ] in self.admin_users:
pass # Admin users may be impersonating, allow logout.
+ elif path_info.startswith( '/user/manage_user_info' ) and environ[ self.remote_user_header ] in self.admin_users:
+ pass # Admin users need to be able to change user information
elif path_info.startswith( '/user/api_keys' ):
pass # api keys can be managed when remote_user is in use
elif path_info.startswith( '/user/edit_username' ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/669da7067315/
Changeset: 669da7067315
User: jmchilton
Date: 2015-01-23 20:12:24+00:00
Summary: Merged in nsoranzo/galaxy-central (pull request #646)
Update rolling_restart.sh to treat .venv dir and GALAXY_CONFIG_FILE env variable as run.sh
Affected #: 2 files
diff -r de9bd9d7d47bfcdf45f3f170be391874b79e738f -r 669da7067315a6ce236a2ee753e9af6264279c01 rolling_restart.sh
--- a/rolling_restart.sh
+++ b/rolling_restart.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/sh
cd `dirname $0`
check_if_not_started(){
@@ -8,7 +8,7 @@
current_pid_in_file=$(cat $2);
# If they're equivalent, then the current pid file agrees with our logs
# and we've succesfully started
- if [[ $latest_pid -eq $current_pid_in_file ]];
+ if [ $latest_pid -eq $current_pid_in_file ];
then
echo 0;
else
@@ -16,17 +16,29 @@
fi
}
+# If there is a .venv/ directory, assume it contains a virtualenv that we
+# should run this instance in.
+if [ -d .venv ];
+then
+ . .venv/bin/activate
+fi
-GALAXY_CONFIG_FILE=config/galaxy.ini
-if [ ! -f $GALAXY_CONFIG_FILE ]; then
- GALAXY_CONFIG_FILE=universe_wsgi.ini
+if [ -z "$GALAXY_CONFIG_FILE" ]; then
+ if [ -f universe_wsgi.ini ]; then
+ GALAXY_CONFIG_FILE=universe_wsgi.ini
+ elif [ -f config/galaxy.ini ]; then
+ GALAXY_CONFIG_FILE=config/galaxy.ini
+ else
+ GALAXY_CONFIG_FILE=config/galaxy.ini.sample
+ fi
+ export GALAXY_CONFIG_FILE
fi
servers=`sed -n 's/^\[server:\(.*\)\]/\1/ p' $GALAXY_CONFIG_FILE | xargs echo`
for server in $servers;
do
# If there's a pid
- if [[ -e $server.pid ]]
+ if [ -e $server.pid ]
then
# Then kill it
echo "Killing $server"
@@ -44,12 +56,11 @@
pid=`cat $server.pid`
result=1
# Wait for the latest pid in the file to be the pid we've grabbed
- while [[ $result -eq 1 ]]
+ while [ $result -eq 1 ]
do
result=$(check_if_not_started $server.log $server.pid)
- echo -n "."
+ printf "."
sleep 1
done
- echo ""
+ echo
done
-
diff -r de9bd9d7d47bfcdf45f3f170be391874b79e738f -r 669da7067315a6ce236a2ee753e9af6264279c01 scripts/build_universe_config.py
--- a/scripts/build_universe_config.py
+++ b/scripts/build_universe_config.py
@@ -6,7 +6,10 @@
def merge():
- "Merges all .ini files in a specified directory into ./universe.ini"
+ """
+ Merges all .ini files in a specified directory into a file (defaults to
+ ./config/galaxy.ini ).
+ """
if len(argv) < 2:
message = "%s: Must specify directory to merge configuration files from." % argv[0]
raise Exception(message)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/0de04e073983/
Changeset: 0de04e073983
User: nsoranzo
Date: 2015-01-23 19:19:15+00:00
Summary: Fix merge() documentation.
Affected #: 1 file
diff -r 9ef517d8e767037e1633f6063c6edb3023f86499 -r 0de04e073983373e30775252efab83714eaa7184 scripts/build_universe_config.py
--- a/scripts/build_universe_config.py
+++ b/scripts/build_universe_config.py
@@ -6,7 +6,10 @@
def merge():
- "Merges all .ini files in a specified directory into ./universe.ini"
+ """
+ Merges all .ini files in a specified directory into a file (defaults to
+ ./config/galaxy.ini ).
+ """
if len(argv) < 2:
message = "%s: Must specify directory to merge configuration files from." % argv[0]
raise Exception(message)
https://bitbucket.org/galaxy/galaxy-central/commits/4f3f92ca8e74/
Changeset: 4f3f92ca8e74
User: nsoranzo
Date: 2015-01-23 19:23:41+00:00
Summary: Update rolling_restart.sh to treat .venv dir and GALAXY_CONFIG_FILE env variable as run.sh . Use POSIX shell syntax.
Affected #: 1 file
diff -r 0de04e073983373e30775252efab83714eaa7184 -r 4f3f92ca8e7488f4f5a90b8d57eddaeb3e1645d6 rolling_restart.sh
--- a/rolling_restart.sh
+++ b/rolling_restart.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/sh
cd `dirname $0`
check_if_not_started(){
@@ -8,7 +8,7 @@
current_pid_in_file=$(cat $2);
# If they're equivalent, then the current pid file agrees with our logs
# and we've succesfully started
- if [[ $latest_pid -eq $current_pid_in_file ]];
+ if [ $latest_pid -eq $current_pid_in_file ];
then
echo 0;
else
@@ -16,17 +16,29 @@
fi
}
+# If there is a .venv/ directory, assume it contains a virtualenv that we
+# should run this instance in.
+if [ -d .venv ];
+then
+ . .venv/bin/activate
+fi
-GALAXY_CONFIG_FILE=config/galaxy.ini
-if [ ! -f $GALAXY_CONFIG_FILE ]; then
- GALAXY_CONFIG_FILE=universe_wsgi.ini
+if [ -z "$GALAXY_CONFIG_FILE" ]; then
+ if [ -f universe_wsgi.ini ]; then
+ GALAXY_CONFIG_FILE=universe_wsgi.ini
+ elif [ -f config/galaxy.ini ]; then
+ GALAXY_CONFIG_FILE=config/galaxy.ini
+ else
+ GALAXY_CONFIG_FILE=config/galaxy.ini.sample
+ fi
+ export GALAXY_CONFIG_FILE
fi
servers=`sed -n 's/^\[server:\(.*\)\]/\1/ p' $GALAXY_CONFIG_FILE | xargs echo`
for server in $servers;
do
# If there's a pid
- if [[ -e $server.pid ]]
+ if [ -e $server.pid ]
then
# Then kill it
echo "Killing $server"
@@ -44,12 +56,11 @@
pid=`cat $server.pid`
result=1
# Wait for the latest pid in the file to be the pid we've grabbed
- while [[ $result -eq 1 ]]
+ while [ $result -eq 1 ]
do
result=$(check_if_not_started $server.log $server.pid)
- echo -n "."
+ printf "."
sleep 1
done
- echo ""
+ echo
done
-
https://bitbucket.org/galaxy/galaxy-central/commits/669da7067315/
Changeset: 669da7067315
User: jmchilton
Date: 2015-01-23 20:12:24+00:00
Summary: Merged in nsoranzo/galaxy-central (pull request #646)
Update rolling_restart.sh to treat .venv dir and GALAXY_CONFIG_FILE env variable as run.sh
Affected #: 2 files
diff -r de9bd9d7d47bfcdf45f3f170be391874b79e738f -r 669da7067315a6ce236a2ee753e9af6264279c01 rolling_restart.sh
--- a/rolling_restart.sh
+++ b/rolling_restart.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/sh
cd `dirname $0`
check_if_not_started(){
@@ -8,7 +8,7 @@
current_pid_in_file=$(cat $2);
# If they're equivalent, then the current pid file agrees with our logs
# and we've succesfully started
- if [[ $latest_pid -eq $current_pid_in_file ]];
+ if [ $latest_pid -eq $current_pid_in_file ];
then
echo 0;
else
@@ -16,17 +16,29 @@
fi
}
+# If there is a .venv/ directory, assume it contains a virtualenv that we
+# should run this instance in.
+if [ -d .venv ];
+then
+ . .venv/bin/activate
+fi
-GALAXY_CONFIG_FILE=config/galaxy.ini
-if [ ! -f $GALAXY_CONFIG_FILE ]; then
- GALAXY_CONFIG_FILE=universe_wsgi.ini
+if [ -z "$GALAXY_CONFIG_FILE" ]; then
+ if [ -f universe_wsgi.ini ]; then
+ GALAXY_CONFIG_FILE=universe_wsgi.ini
+ elif [ -f config/galaxy.ini ]; then
+ GALAXY_CONFIG_FILE=config/galaxy.ini
+ else
+ GALAXY_CONFIG_FILE=config/galaxy.ini.sample
+ fi
+ export GALAXY_CONFIG_FILE
fi
servers=`sed -n 's/^\[server:\(.*\)\]/\1/ p' $GALAXY_CONFIG_FILE | xargs echo`
for server in $servers;
do
# If there's a pid
- if [[ -e $server.pid ]]
+ if [ -e $server.pid ]
then
# Then kill it
echo "Killing $server"
@@ -44,12 +56,11 @@
pid=`cat $server.pid`
result=1
# Wait for the latest pid in the file to be the pid we've grabbed
- while [[ $result -eq 1 ]]
+ while [ $result -eq 1 ]
do
result=$(check_if_not_started $server.log $server.pid)
- echo -n "."
+ printf "."
sleep 1
done
- echo ""
+ echo
done
-
diff -r de9bd9d7d47bfcdf45f3f170be391874b79e738f -r 669da7067315a6ce236a2ee753e9af6264279c01 scripts/build_universe_config.py
--- a/scripts/build_universe_config.py
+++ b/scripts/build_universe_config.py
@@ -6,7 +6,10 @@
def merge():
- "Merges all .ini files in a specified directory into ./universe.ini"
+ """
+ Merges all .ini files in a specified directory into a file (defaults to
+ ./config/galaxy.ini ).
+ """
if len(argv) < 2:
message = "%s: Must specify directory to merge configuration files from." % argv[0]
raise Exception(message)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/892da4d5dcc9/
Changeset: 892da4d5dcc9
User: jmchilton
Date: 2015-01-23 20:08:37+00:00
Summary: Clarify default reports template cache location.
Affected #: 1 file
diff -r e361766bbcfd8976ee05cb8826ed239d0f2028f6 -r 892da4d5dcc979919c82d4a57ce897d3e93278ce config/reports_wsgi.ini.sample
--- a/config/reports_wsgi.ini.sample
+++ b/config/reports_wsgi.ini.sample
@@ -28,7 +28,7 @@
# Mako templates are compiled as needed and cached for reuse, this directory is
# used for the cache
-# template_cache_path = database/compiled_templates
+#template_cache_path = database/compiled_templates/reports
# Session support (beaker)
use_beaker_session = True
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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