Hello there,
I downloaded Galaxy (Dist) from
http://bitbucket.org/galaxy/galaxy-dist/
ran a basic setup and then "run.sh". Joy, Galaxy works fine.
But when trying to access Galaxy from another machine, the connection is refused. I've checked that it's not a funny misconfiguration of our network which would block traffic between the machines, so I deduce that it's Galaxy which rejects every traffic not coming from localhost.
I've searched a bit in the config files where to change that but did not find a place.
Where do I tell Galaxy it should accept traffic from a given host (or IP range).
Regards,
Bastien
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Hello all,
I am pleased to announce that we are now accepting applications for:
2010 GMOD Summer School - Americas
6-9 May 2010
NESCent, Durham, NC, USA
http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
This will be a hands-on multi-day course aimed at teaching new GMOD
users/administrators how to get GMOD Components up and running. The
course will introduce participants to the GMOD project and then focus
on installation, configuration and integration of popular GMOD
Components. The course will be held May 6-9, at NESCent in Durham, NC.
These components will be covered:
* Apollo - genome annotation editor
* Chado - a modular and extensible database schema
* Galaxy - workflow system
* GBrowse - the Generic Genome Browser
* GBrowse_syn - A generic synteny browser
* JBrowse - genome browser
* MAKER - genome annotation pipeline
* Tripal - web front end for Chado
The deadline for applying is the end of Friday, February 22. Admission
is competitive and is based on the strength of the application
(especially the statement of interest). In 2009 there were over 50
applications for the 25 slots. Any applications received after the
deadline will be placed on the waiting list.
See the course page for details and an application link:
http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
Thanks,
Dave Clements
GMOD Help Desk
PS: We are also investigating holding a GMOD course in the
Asia/Pacific region, sometime this fall. Watch the GMOD mailing lists
and the GMOD News page/RSS feed for updates.
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details: http://www.bx.psu.edu/hg/galaxy/rev/a4cd313cf84b
changeset: 3400:a4cd313cf84b
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Tue Feb 16 11:50:50 2010 -0500
description:
Filter out sharing roles from being displayed on permissions forms unless they belong to the current user.
diffstat:
lib/galaxy/security/__init__.py | 31 ++++++++++++++++++++++---------
1 files changed, 22 insertions(+), 9 deletions(-)
diffs (62 lines):
diff -r e783e000f7c3 -r a4cd313cf84b lib/galaxy/security/__init__.py
--- a/lib/galaxy/security/__init__.py Tue Feb 16 09:44:07 2010 -0500
+++ b/lib/galaxy/security/__init__.py Tue Feb 16 11:50:50 2010 -0500
@@ -139,13 +139,19 @@
if not trans.user:
return trans.sa_session.query( trans.app.model.Role ) \
.filter( and_( self.model.Role.table.c.deleted==False,
- self.model.Role.table.c.type != self.model.Role.types.PRIVATE ) ) \
+ self.model.Role.table.c.type != self.model.Role.types.PRIVATE,
+ self.model.Role.table.c.type != self.model.Role.types.SHARING ) ) \
.order_by( self.model.Role.table.c.name )
# Add the current user's private role
roles.add( self.get_private_user_role( trans.user ) )
+ # Add the current user's sharing roles
+ for role in self.get_sharing_roles( trans.user ):
+ roles.add( role )
+ # Add all remaining non-private, non-sharing roles
for role in trans.sa_session.query( trans.app.model.Role ) \
.filter( and_( self.model.Role.table.c.deleted==False,
- self.model.Role.table.c.type != self.model.Role.types.PRIVATE ) ) \
+ self.model.Role.table.c.type != self.model.Role.types.PRIVATE,
+ self.model.Role.table.c.type != self.model.Role.types.SHARING ) ) \
.order_by( self.model.Role.table.c.name ):
roles.add( role )
return sort_by_attr( [ role for role in roles ], 'name' )
@@ -172,15 +178,18 @@
return sort_by_attr( [ role for role in roles ], 'name' )
def ok_to_display( self, trans, role ):
"""
- Method for checking if a role is not private, unless it is the current user's
- private role. Private roles, except for the current user's private role, are
- never displayed, no matter what.
+ Method for checking if:
+ - a role is private and is the current user's private role
+ - a role is a sharing role and belongs to the current user
"""
- if trans.user and ( role.type != self.model.Role.types.PRIVATE or role == self.get_private_user_role( trans.user ) ):
+ if trans.user:
+ if role.type == self.model.Role.types.PRIVATE:
+ return role == self.get_private_user_role( trans.user )
+ if role.type == self.model.Role.types.SHARING:
+ return role in self.get_sharing_roles( trans.user )
+ # If role.type is neither private nor sharing, it's ok to display
return True
- if not trans.user and role.type != self.model.Role.types.PRIVATE:
- return True
- return False
+ return role.type != self.model.Role.types.PRIVATE and role.type != self.model.Role.types.SHARING
def allow_action( self, roles, action, item ):
"""
Method for checking a permission for the current user ( based on roles ) to perform a
@@ -287,6 +296,10 @@
else:
return None
return role
+ def get_sharing_roles( self, user ):
+ return self.sa_session.query( self.model.Role ) \
+ .filter( and_( ( self.model.Role.table.c.name ).like( "Sharing role for: %" + user.email + "%" ),
+ self.model.Role.table.c.type == self.model.Role.types.SHARING ) )
def user_set_default_permissions( self, user, permissions={}, history=False, dataset=False, bypass_manage_permission=False, default_access_private = False ):
# bypass_manage_permission is used to change permissions of datasets in a userless history when logging in
if user is None: