January 2010 - galaxy-dev - lists.galaxyproject.org

replacing deprecated <code> tags
by Martin Aryee 06 Jan '10

06 Jan '10

Hi, I'm trying to work out how to run custom python code as a tool is loaded (to get generate options for a select parameter) and after job completion (to set metadata). It looks like the <code> tags would have been the place to point to my code, but since they are now deprecated I was wondering if someone could point me in the right direction? Thanks, Martin Aryee.

2 4

Galaxy and GMOD at PAG
by Dave Clements, GMOD Help Desk 06 Jan '10

06 Jan '10

Hello all, GMOD will once again have a strong presence at the Plant and Animal Genome Conference (PAG 2010), being held January 9-13 in San Diego. There will be over 45 talks, workshops, demonstrations and posters about GMOD Components and projects that use them. This includes a workshop on Galaxy: Animal Genomics With Galaxy: Analyze, Publish, And Visualize Saturday, Jan 9, 1:30-2-30, California Room Anton will be presenting the workshop. See the PAG 2010 page on the GMOD wiki for a full listing and a flier showing highlights: http://gmod.org/wiki/PAG_2010 If you are attending PAG, please consider going to this and the other GMOD-related presentations. Thanks, Dave C. -- Please keep responses on the list! http://gmod.org/wiki/January_2010_GMOD_Meeting http://gmod.org/wiki/GMOD_News Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback

2 1

[hg] galaxy 3208: Add missing quickie icons, remove unused large...
by Greg Von Kuster 06 Jan '10

06 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/3863936b6f3e changeset: 3208:3863936b6f3e user: Kanwei Li <kanwei(a)gmail.com> date: Tue Jan 05 16:49:56 2010 -0500 description: Add missing quickie icons, remove unused large icons diffstat: static/images/qk/quickie1_lrg.png | 0 static/images/qk/quickie2_lrg.png | 0 static/images/qk/quickie3_lrg.png | 0 static/images/qk/quickie4_lrg.png | 0 static/images/qk/quickie5_lrg.png | 0 static/images/qk/quickie6_small.png | 0 static/images/qk/quickie7_small.png | 0 7 files changed, 0 insertions(+), 0 deletions(-) diffs (14 lines): diff -r 9500dce290d0 -r 3863936b6f3e static/images/qk/quickie1_lrg.png Binary file static/images/qk/quickie1_lrg.png has changed diff -r 9500dce290d0 -r 3863936b6f3e static/images/qk/quickie2_lrg.png Binary file static/images/qk/quickie2_lrg.png has changed diff -r 9500dce290d0 -r 3863936b6f3e static/images/qk/quickie3_lrg.png Binary file static/images/qk/quickie3_lrg.png has changed diff -r 9500dce290d0 -r 3863936b6f3e static/images/qk/quickie4_lrg.png Binary file static/images/qk/quickie4_lrg.png has changed diff -r 9500dce290d0 -r 3863936b6f3e static/images/qk/quickie5_lrg.png Binary file static/images/qk/quickie5_lrg.png has changed diff -r 9500dce290d0 -r 3863936b6f3e static/images/qk/quickie6_small.png Binary file static/images/qk/quickie6_small.png has changed diff -r 9500dce290d0 -r 3863936b6f3e static/images/qk/quickie7_small.png Binary file static/images/qk/quickie7_small.png has changed

1 0

[hg] galaxy 3207: Quickies: add close button, fix window height ...
by Greg Von Kuster 06 Jan '10

06 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/9500dce290d0 changeset: 3207:9500dce290d0 user: Kanwei Li <kanwei(a)gmail.com> date: Tue Jan 05 16:32:30 2010 -0500 description: Quickies: add close button, fix window height to fit flowplayer diffstat: static/scripts/galaxy.panels.js | 3 ++- static/welcome.html | 14 +++++++------- 2 files changed, 9 insertions(+), 8 deletions(-) diffs (73 lines): diff -r 84a9e0f0387b -r 9500dce290d0 static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js Tue Jan 05 15:17:10 2010 -0500 +++ b/static/scripts/galaxy.panels.js Tue Jan 05 16:32:30 2010 -0500 @@ -210,7 +210,8 @@ hide_modal(); $("#overlay-background").unbind( "click.overlay" ); }); - show_modal( null, $("<div style='margin: -5px;'><iframe style='margin: 0; padding: 0;' src='" + options.url + "' width='" + width + "' height='" + height + "' scrolling='" + scroll + "' frameborder='0'></iframe></div>" ) ); + show_modal( null, $("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:3px;top:3px;' src='../images/icon_error_sml.gif'><iframe style='margin: 0; padding: 0;' src='" + options.url + "' width='" + width + "' height='" + height + "' scrolling='" + scroll + "' frameborder='0'></iframe></div>" ) ); + $("#close_button").bind( "click", function() { hide_modal() } ); } // Tab management diff -r 84a9e0f0387b -r 9500dce290d0 static/welcome.html --- a/static/welcome.html Tue Jan 05 15:17:10 2010 -0500 +++ b/static/welcome.html Tue Jan 05 16:32:30 2010 -0500 @@ -75,49 +75,49 @@ <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr> <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/quickie1_TabSeq.flv',width:640,height:500,scroll:'no'})"> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/flow.html',width:640,height:480,scroll:'no'})"> <div class="quickie"> <img src="images/qk/quickie1_small.png" border="0"> </div> </a> </td> <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie2_Grouping/flow.html',width:640,height:500,scroll:'no'})"> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie2_Grouping/flow.html',width:640,height:480,scroll:'no'})"> <div class="quickie"> <img src="images/qk/quickie2_small.png" border="0"> </div> </a> </td> <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie3_Intervals/flow.html',width:640,height:500,scroll:'no'})"> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie3_Intervals/flow.html',width:640,height:480,scroll:'no'})"> <div class="quickie"> <img src="images/qk/quickie3_small.png" border="0"> </div> </a> </td> <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie4_whatsNew/flow.html',width:640,height:500,scroll:'no'})"> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie4_whatsNew/flow.html',width:640,height:480,scroll:'no'})"> <div class="quickie"> <img src="images/qk/quickie4_small.png" border="0"> </div> </a> </td> <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie5_join/flow.html',width:640,height:500,scroll:'no'})"> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie5_join/flow.html',width:640,height:480,scroll:'no'})"> <div class="quickie"> <img src="images/qk/quickie5_small.png" border="0"> </div> </a> </td> <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie6_share/flow.html',width:640,height:500,scroll:'no'})"> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie6_share/flow.html',width:640,height:480,scroll:'no'})"> <div class="quickie"> <img src="images/qk/quickie6_small.png" border="0"> </div> </a> </td> <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie7_sr_beta/flow.html',width:640,height:500,scroll:'no'})"> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie7_sr_beta/flow.html',width:640,height:480,scroll:'no'})"> <div class="quickie"> <img src="images/qk/quickie7_small.png" border="0"> </div>

1 0

[hg] galaxy 3206: Prevent sys.exit() from being caught by the tr...
by Greg Von Kuster 06 Jan '10

06 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/84a9e0f0387b changeset: 3206:84a9e0f0387b user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Jan 05 15:17:10 2010 -0500 description: Prevent sys.exit() from being caught by the try-except block in check_galaxy.py (since sys.exit() actually raises an exception, but one not derived from Exception). diffstat: scripts/check_python.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (10 lines): diff -r d81624fcac0b -r 84a9e0f0387b scripts/check_python.py --- a/scripts/check_python.py Tue Jan 05 14:47:55 2010 -0500 +++ b/scripts/check_python.py Tue Jan 05 15:17:10 2010 -0500 @@ -25,5 +25,5 @@ check_python() print check_virtualenv() sys.exit( 0 ) - except: + except Exception: sys.exit( 1 )

1 0

[hg] galaxy 3205: Bug fixes and code cleanup for managing users, ...
by Greg Von Kuster 05 Jan '10

05 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/d81624fcac0b changeset: 3205:d81624fcac0b user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Jan 05 14:47:55 2010 -0500 description: Bug fixes and code cleanup for managing users, groups and roles. diffstat: lib/galaxy/web/controllers/admin.py | 116 ++++++++------ templates/admin/dataset_security/group/group.mako | 2 +- templates/admin/dataset_security/group/group_rename.mako | 6 +- templates/admin/dataset_security/role/role.mako | 2 +- templates/admin/dataset_security/role/role_rename.mako | 6 +- templates/admin/user/user.mako | 2 +- test/base/twilltestcase.py | 18 +- test/functional/test_security_and_libraries.py | 4 +- 8 files changed, 89 insertions(+), 67 deletions(-) diffs (384 lines): diff -r f87019342f0a -r d81624fcac0b lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Tue Jan 05 14:36:09 2010 -0500 +++ b/lib/galaxy/web/controllers/admin.py Tue Jan 05 14:47:55 2010 -0500 @@ -159,7 +159,7 @@ columns = [ NameColumn( "Name", key="name", - link=( lambda item: dict( controller="admin", action="role", id=item.id ) ), + link=( lambda item: dict( operation="Manage users and groups", id=item.id ) ), model_class=model.Role, attach_popup=True, filterable="advanced" ), @@ -187,7 +187,8 @@ global_actions = [ grids.GridAction( "Add new role", dict( controller='admin', action='roles', operation='create' ) ) ] - operations = [ grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ), + operations = [ grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), allow_multiple=False ), + grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ), grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ), allow_multiple=True ), grids.GridOperation( "Purge", condition=( lambda item: item.deleted ), allow_multiple=True ) ] standard_filters = [ @@ -243,7 +244,7 @@ columns = [ NameColumn( "Name", key="name", - link=( lambda item: dict( controller="admin", action="group", id=item.id ) ), + link=( lambda item: dict( operation="Manage users and roles", id=item.id ) ), model_class=model.Group, attach_popup=True, filterable="advanced" ), @@ -261,7 +262,8 @@ global_actions = [ grids.GridAction( "Add new group", dict( controller='admin', action='groups', operation='create' ) ) ] - operations = [ grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ), + operations = [ grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), allow_multiple=False ), + grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ), grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ), allow_multiple=True ), grids.GridOperation( "Purge", condition=( lambda item: item.deleted ), allow_multiple=True ) ] standard_filters = [ @@ -327,8 +329,10 @@ return self.undelete_role( trans, **kwargs ) if operation == "purge": return self.purge_role( trans, **kwargs ) - if operation == "manage users & groups": - return self.role( trans, **kwargs ) + if operation == "manage users and groups": + return self.manage_users_and_groups_for_role( trans, **kwargs ) + if operation == "rename": + return self.rename_role( trans, **kwargs ) # Render the list view return self.role_list_grid( trans, **kwargs ) @web.expose @@ -389,7 +393,32 @@ messagetype=messagetype ) @web.expose @web.require_admin - def role( self, trans, **kwd ): + def rename_role( self, trans, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + role = get_role( trans, params.id ) + if params.get( 'rename_role_button', False ): + old_name = role.name + new_name = util.restore_text( params.name ) + new_description = util.restore_text( params.description ) + if not new_name: + msg = 'Enter a valid name' + return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, msg=msg, messagetype='error' ) + elif trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.name==new_name ).first(): + msg = 'A role with that name already exists' + return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, msg=msg, messagetype='error' ) + else: + role.name = new_name + role.description = new_description + trans.sa_session.add( role ) + trans.sa_session.flush() + msg = "Role '%s' has been renamed to '%s'" % ( old_name, new_name ) + return trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( msg ), status='done' ) ) + return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, msg=msg, messagetype=messagetype ) + @web.expose + @web.require_admin + def manage_users_and_groups_for_role( self, trans, **kwd ): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) @@ -413,26 +442,7 @@ trans.app.security_agent.set_entity_role_associations( roles=[ role ], users=in_users, groups=in_groups ) trans.sa_session.refresh( role ) msg = "Role '%s' has been updated with %d associated users and %d associated groups" % ( role.name, len( in_users ), len( in_groups ) ) - trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( msg ), status=messagetype ) ) - elif params.get( 'rename', False ): - if params.rename == 'submitted': - old_name = role.name - new_name = util.restore_text( params.name ) - new_description = util.restore_text( params.description ) - if not new_name: - msg = 'Enter a valid name' - return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, msg=msg, messagetype='error' ) - elif trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.name==new_name ).first(): - msg = 'A role with that name already exists' - return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, msg=msg, messagetype='error' ) - else: - role.name = new_name - role.description = new_description - trans.sa_session.add( role ) - trans.sa_session.flush() - msg = "Role '%s' has been renamed to '%s'" % ( old_name, new_name ) - return trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( msg ), status='done' ) ) - return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, msg=msg, messagetype=messagetype ) + trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( msg ), status=messagetype ) ) in_users = [] out_users = [] in_groups = [] @@ -561,13 +571,38 @@ return self.undelete_group( trans, **kwargs ) if operation == "purge": return self.purge_group( trans, **kwargs ) - if operation == "manage users & roles": - return self.group( trans, **kwargs ) + if operation == "manage users and roles": + return self.manage_users_and_roles_for_group( trans, **kwargs ) + if operation == "rename": + return self.rename_group( trans, **kwargs ) # Render the list view return self.group_list_grid( trans, **kwargs ) @web.expose @web.require_admin - def group( self, trans, **kwd ): + def rename_group( self, trans, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + group = get_group( trans, params.id ) + if params.get( 'rename_group_button', False ): + old_name = group.name + new_name = util.restore_text( params.name ) + if not new_name: + msg = 'Enter a valid name' + return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, msg=msg, messagetype='error' ) + elif trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.name==new_name ).first(): + msg = 'A group with that name already exists' + return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, msg=msg, messagetype='error' ) + else: + group.name = new_name + trans.sa_session.add( group ) + trans.sa_session.flush() + msg = "Group '%s' has been renamed to '%s'" % ( old_name, new_name ) + return trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype='done' ) ) + return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, msg=msg, messagetype=messagetype ) + @web.expose + @web.require_admin + def manage_users_and_roles_for_group( self, trans, **kwd ): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) @@ -579,23 +614,6 @@ trans.sa_session.refresh( group ) msg += "Group '%s' has been updated with %d associated roles and %d associated users" % ( group.name, len( in_roles ), len( in_users ) ) trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( msg ), status=messagetype ) ) - if params.get( 'rename', False ): - if params.rename == 'submitted': - old_name = group.name - new_name = util.restore_text( params.name ) - if not new_name: - msg = 'Enter a valid name' - return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, msg=msg, messagetype='error' ) - elif trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.name==new_name ).first(): - msg = 'A group with that name already exists' - return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, msg=msg, messagetype='error' ) - else: - group.name = new_name - trans.sa_session.add( group ) - trans.sa_session.flush() - msg = "Group '%s' has been renamed to '%s'" % ( old_name, new_name ) - return trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype='done' ) ) - return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, msg=msg, messagetype=messagetype ) in_roles = [] out_roles = [] in_users = [] @@ -943,7 +961,7 @@ if operation == "information": return self.user_info( trans, **kwargs ) if operation == "manage roles and groups": - return self.user( trans, **kwargs ) + return self.manage_roles_and_groups_for_user( trans, **kwargs ) # Render the list view return self.user_list_grid( trans, **kwargs ) @web.expose @@ -976,7 +994,7 @@ return ac_data @web.expose @web.require_admin - def user( self, trans, **kwd ): + def manage_roles_and_groups_for_user( self, trans, **kwd ): user_id = kwd.get( 'id', None ) message = '' status = '' diff -r f87019342f0a -r d81624fcac0b templates/admin/dataset_security/group/group.mako --- a/templates/admin/dataset_security/group/group.mako Tue Jan 05 14:36:09 2010 -0500 +++ b/templates/admin/dataset_security/group/group.mako Tue Jan 05 14:47:55 2010 -0500 @@ -50,7 +50,7 @@ <div class="toolForm"> <div class="toolFormTitle">Group '${group.name}'</div> <div class="toolFormBody"> - <form name="associate_group_role_user" id="associate_group_role_user" action="${h.url_for( action='group', group_id=group.id )}" method="post" > + <form name="associate_group_role_user" id="associate_group_role_user" action="${h.url_for( action='manage_users_and_roles_for_group', id=trans.security.encode_id( group.id ) )}" method="post" > <div class="form-row"> <div style="float: left; margin-right: 10px;"> <label>Roles associated with '${group.name}'</label> diff -r f87019342f0a -r d81624fcac0b templates/admin/dataset_security/group/group_rename.mako --- a/templates/admin/dataset_security/group/group_rename.mako Tue Jan 05 14:36:09 2010 -0500 +++ b/templates/admin/dataset_security/group/group_rename.mako Tue Jan 05 14:47:55 2010 -0500 @@ -8,7 +8,7 @@ <div class="toolForm"> <div class="toolFormTitle">Change group name</div> <div class="toolFormBody"> - <form name="library" action="${h.url_for( controller='admin', action='group' )}" method="post" > + <form name="library" action="${h.url_for( controller='admin', action='rename_group' )}" method="post" > <div class="form-row"> <label>Name:</label> <div style="float: left; width: 250px; margin-right: 10px;"> @@ -28,7 +28,9 @@ </div> <div style="clear: both"></div> </div> - <input type="submit" name="rename_group_button" value="Save"/> + <div class="form-row"> + <input type="submit" name="rename_group_button" value="Save"/> + </div> </form> </div> </div> diff -r f87019342f0a -r d81624fcac0b templates/admin/dataset_security/role/role.mako --- a/templates/admin/dataset_security/role/role.mako Tue Jan 05 14:36:09 2010 -0500 +++ b/templates/admin/dataset_security/role/role.mako Tue Jan 05 14:47:55 2010 -0500 @@ -50,7 +50,7 @@ <div class="toolForm"> <div class="toolFormTitle">Role '${role.name}'</div> <div class="toolFormBody"> - <form name="associate_role_user_group" id="associate_role_user_group" action="${h.url_for( action='role', role_id=role.id )}" method="post" > + <form name="associate_role_user_group" id="associate_role_user_group" action="${h.url_for( action='manage_users_and_groups_for_role', id=trans.security.encode_id( role.id ) )}" method="post" > <div class="form-row"> <div style="float: left; margin-right: 10px;"> <label>Users associated with '${role.name}'</label> diff -r f87019342f0a -r d81624fcac0b templates/admin/dataset_security/role/role_rename.mako --- a/templates/admin/dataset_security/role/role_rename.mako Tue Jan 05 14:36:09 2010 -0500 +++ b/templates/admin/dataset_security/role/role_rename.mako Tue Jan 05 14:47:55 2010 -0500 @@ -8,7 +8,7 @@ <div class="toolForm"> <div class="toolFormTitle">Change role name and description</div> <div class="toolFormBody"> - <form name="library" action="${h.url_for( controller='admin', action='role' )}" method="post" > + <form name="library" action="${h.url_for( controller='admin', action='rename_role' )}" method="post" > <div class="form-row"> <label>Name:</label> <div style="float: left; width: 250px; margin-right: 10px;"> @@ -35,7 +35,9 @@ </div> <div style="clear: both"></div> </div> - <input type="submit" name="rename_role_button" value="Save"/> + <div class="form-row"> + <input type="submit" name="rename_role_button" value="Save"/> + </div> </form> </div> </div> diff -r f87019342f0a -r d81624fcac0b templates/admin/user/user.mako --- a/templates/admin/user/user.mako Tue Jan 05 14:36:09 2010 -0500 +++ b/templates/admin/user/user.mako Tue Jan 05 14:47:55 2010 -0500 @@ -50,7 +50,7 @@ <div class="toolForm"> <div class="toolFormTitle">User '${user.email}'</div> <div class="toolFormBody"> - <form name="associate_user_role_group" id="associate_user_role_group" action="${h.url_for( action='user', id=trans.app.security.encode_id( user.id ) )}" method="post" > + <form name="associate_user_role_group" id="associate_user_role_group" action="${h.url_for( action='manage_roles_and_groups_for_user', id=trans.security.encode_id( user.id ) )}" method="post" > <div class="form-row"> <div style="float: left; margin-right: 10px;"> <label>Roles associated with '${user.email}'</label> diff -r f87019342f0a -r d81624fcac0b test/base/twilltestcase.py --- a/test/base/twilltestcase.py Tue Jan 05 14:36:09 2010 -0500 +++ b/test/base/twilltestcase.py Tue Jan 05 14:47:55 2010 -0500 @@ -960,21 +960,21 @@ def mark_user_deleted( self, user_id, email='' ): """Mark a user as deleted""" self.home() - self.visit_url( "%s/admin/mark_user_deleted?id=%s" % ( self.url, user_id ) ) + self.visit_url( "%s/admin/users?operation=delete&id=%s" % ( self.url, user_id ) ) check_str = "Deleted 1 users" self.check_page_for_string( check_str ) self.home() def undelete_user( self, user_id, email='' ): """Undelete a user""" self.home() - self.visit_url( "%s/admin/undelete_user?id=%s" % ( self.url, user_id ) ) + self.visit_url( "%s/admin/users?operation=undelete&id=%s" % ( self.url, user_id ) ) check_str = "Undeleted 1 users" self.check_page_for_string( check_str ) self.home() def purge_user( self, user_id, email ): """Purge a user account""" self.home() - self.visit_url( "%s/admin/purge_user?id=%s" % ( self.url, user_id ) ) + self.visit_url( "%s/admin/users?operation=purge&id=%s" % ( self.url, user_id ) ) check_str = "Purged 1 users" self.check_page_for_string( check_str ) self.home() @@ -983,7 +983,7 @@ in_group_ids=[], out_group_ids=[], check_str='' ): self.home() - url = "%s/admin/user?id=%s&user_roles_groups_edit_button=Save" % ( self.url, user_id ) + url = "%s/admin/manage_roles_and_groups_for_user?id=%s&user_roles_groups_edit_button=Save" % ( self.url, user_id ) if in_role_ids: url += "&in_roles=%s" % ','.join( in_role_ids ) if out_role_ids: @@ -1006,7 +1006,7 @@ create_group_for_role='no', private_role='' ): """Create a new role""" - url = "%s/admin/create_role?create_role_button=Save&name=%s&description=%s" % ( self.url, name.replace( ' ', '+' ), description.replace( ' ', '+' ) ) + url = "%s/admin/roles?operation=create&create_role_button=Save&name=%s&description=%s" % ( self.url, name.replace( ' ', '+' ), description.replace( ' ', '+' ) ) if in_user_ids: url += "&in_users=%s" % ','.join( in_user_ids ) if in_group_ids: @@ -1038,7 +1038,7 @@ def rename_role( self, role_id, name='Role One Renamed', description='This is Role One Re-described' ): """Rename a role""" self.home() - self.visit_url( "%s/admin/role?rename=True&id=%s" % ( self.url, role_id ) ) + self.visit_url( "%s/admin/roles?operation=rename&id=%s" % ( self.url, role_id ) ) self.check_page_for_string( 'Change role name and description' ) tc.fv( "1", "name", name ) tc.fv( "1", "description", description ) @@ -1081,7 +1081,7 @@ # Tests associated with groups def create_group( self, name='Group One', in_user_ids=[], in_role_ids=[] ): """Create a new group""" - url = "%s/admin/create_group?create_group_button=Save&name=%s" % ( self.url, name.replace( ' ', '+' ) ) + url = "%s/admin/groups?operation=create&create_group_button=Save&name=%s" % ( self.url, name.replace( ' ', '+' ) ) if in_user_ids: url += "&in_users=%s" % ','.join( in_user_ids ) if in_role_ids: @@ -1097,14 +1097,14 @@ def rename_group( self, group_id, name='Group One Renamed' ): """Rename a group""" self.home() - self.visit_url( "%s/admin/group?rename=True&id=%s" % ( self.url, group_id ) ) + self.visit_url( "%s/admin/groups?operation=rename&id=%s" % ( self.url, group_id ) ) self.check_page_for_string( 'Change group name' ) tc.fv( "1", "name", name ) tc.submit( "rename_group_button" ) self.home() def associate_users_and_roles_with_group( self, group_id, group_name, user_ids=[], role_ids=[] ): self.home() - url = "%s/admin/group?id=%s&group_roles_users_edit_button=Save" % ( self.url, group_id ) + url = "%s/admin/manage_users_and_roles_for_group?id=%s&group_roles_users_edit_button=Save" % ( self.url, group_id ) if user_ids: url += "&in_users=%s" % ','.join( user_ids ) if role_ids: diff -r f87019342f0a -r d81624fcac0b test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Tue Jan 05 14:36:09 2010 -0500 +++ b/test/functional/test_security_and_libraries.py Tue Jan 05 14:47:55 2010 -0500 @@ -21,7 +21,7 @@ self.check_page_for_string( not_logged_in_security_msg ) self.visit_url( "%s/admin/create_role" % self.url ) self.check_page_for_string( not_logged_in_security_msg ) - self.visit_url( "%s/admin/role" % self.url ) + self.visit_url( "%s/admin/manage_users_and_groups_for_role" % self.url ) self.check_page_for_string( not_logged_in_security_msg ) self.visit_url( "%s/admin/groups" % self.url ) self.check_page_for_string( not_logged_in_security_msg ) @@ -76,7 +76,7 @@ raise AssertionError( 'The DefaultHistoryPermission.action for history id %d is "%s", but it should be "%s"' \ % ( latest_history.id, dhp.action, galaxy.model.Dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS.action ) ) self.home() - self.visit_url( "%s/admin/user?id=%s" % ( self.url, self.security.encode_id( admin_user.id ) ) ) + self.visit_url( "%s/admin/manage_roles_and_groups_for_user?id=%s" % ( self.url, self.security.encode_id( admin_user.id ) ) ) self.check_page_for_string( admin_user.email ) # Try deleting the admin_user's private role check_str = "You cannot eliminate a user's private role association."

1 0

[hg] galaxy 3204: merge
by Greg Von Kuster 05 Jan '10

05 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/f87019342f0a changeset: 3204:f87019342f0a user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Tue Jan 05 14:36:09 2010 -0500 description: merge diffstat: buildbot_setup.sh | 3 +++ lib/galaxy/web/controllers/workflow.py | 3 ++- 2 files changed, 5 insertions(+), 1 deletions(-) diffs (32 lines): diff -r b142b116024c -r f87019342f0a buildbot_setup.sh --- a/buildbot_setup.sh Tue Jan 05 14:33:39 2010 -0500 +++ b/buildbot_setup.sh Tue Jan 05 14:36:09 2010 -0500 @@ -14,6 +14,9 @@ LINKS=" /depot/data2/galaxy/alignseq.loc +/depot/data2/galaxy/annotation_profiler/annotation_profiler.loc +/depot/data2/galaxy/annotation_profiler/annotation_profiler_options.xml +/depot/data2/galaxy/annotation_profiler/annotation_profiler_valid_builds.txt /depot/data2/galaxy/binned_scores.loc /depot/data2/galaxy/blastdb.loc /depot/data2/galaxy/bowtie_indices.loc diff -r b142b116024c -r f87019342f0a lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Tue Jan 05 14:33:39 2010 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Tue Jan 05 14:36:09 2010 -0500 @@ -315,13 +315,14 @@ upgrade_message = module.check_and_update_state() if upgrade_message: data['upgrade_messages'][step.order_index] = upgrade_message - # Pack atrributes into plain dictionary + # Pack attributes into plain dictionary step_dict = { 'id': step.order_index, 'type': module.type, 'tool_id': module.get_tool_id(), 'name': module.get_name(), 'tool_state': module.get_state(), + 'tooltip': module.get_tooltip(), 'tool_errors': module.get_errors(), 'data_inputs': module.get_data_inputs(), 'data_outputs': module.get_data_outputs(),

1 0

[hg] galaxy 3203: Smart converter for SOLiD, which takes care of...
by Greg Von Kuster 05 Jan '10

05 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/b142b116024c changeset: 3203:b142b116024c user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Tue Jan 05 14:33:39 2010 -0500 description: Smart converter for SOLiD, which takes care of F3-R3 pairing problem. Requires python2.5 diffstat: static/welcome.html | 95 +- test-data/f.fastq | 1996 +++++++++++++++++++++++++++++ test-data/fr.csf | 1001 ++++++++++++++ test-data/fr.qual | 1001 ++++++++++++++ test-data/fr_file1.fastq | 1988 ++++++++++++++++++++++++++++ test-data/fr_file2.fastq | 1988 ++++++++++++++++++++++++++++ test-data/rr.csf | 1001 ++++++++++++++ test-data/rr.qual | 1001 ++++++++++++++ tool_conf.xml.sample | 2 +- tools/fastx_toolkit/fastq_to_fasta.xml | 2 +- tools/fastx_toolkit/fastx_collapser.xml | 2 +- tools/next_gen_conversion/solid2fastq.py | 210 +++ tools/next_gen_conversion/solid2fastq.xml | 159 ++ 13 files changed, 10408 insertions(+), 38 deletions(-) diffs (truncated from 10545 to 3000 lines): diff -r 71928a8f9bf9 -r b142b116024c static/welcome.html --- a/static/welcome.html Tue Jan 05 10:31:32 2010 -0500 +++ b/static/welcome.html Tue Jan 05 14:33:39 2010 -0500 @@ -6,15 +6,26 @@ <meta name="generator" content="Docutils 0.3.9: http://docutils.sourceforge.net/" /> <link rel="stylesheet" href="style/base.css" type="text/css" /> <style type="text/css"> + .quickie { text-align: center; background: black; margin: 10px; } + .current-quickie { - width: 100%; - background: black; + width: 300px; + background: white; + margin: auto; } + + .current-quickie img { + padding: 15px; + border: 1px solid #ccc; + margin: auto; + background-color: white; + } + .previous { width: 100%; overflow: auto; @@ -30,42 +41,35 @@ margin-left: auto; margin-right: auto; } + </style> +<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.min.js"></script> +<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.cycle.all.2.72.js"></script> +<script type="text/javascript"> + +$(document).ready(function() { + $('.current-quickie').cycle({ + fx: 'fade', + pause: 1, + speed: 100 + }); +}); +</script> </head> +<body> +<div class="document"> +<h3 align="center">Galaxy in 2010...</h3> +<div align="center" class="current-quickie"> + <img src="http://galaxy.psu.edu/welcome_img/welcome_images.001.png" width="300" height="200" /> + <img src="http://galaxy.psu.edu/welcome_img/welcome_images.002.png" width="300" height="200" /> + <img src="http://galaxy.psu.edu/welcome_img/welcome_images.003.png" width="300" height="200" /> + <img src="http://galaxy.psu.edu/welcome_img/welcome_images.004.png" width="300" height="200" /> + <img src="http://galaxy.psu.edu/welcome_img/welcome_images.005.png" width="300" height="200" /> +</div> +<br> +<hr> - -<body> - -<div class="document"> -<div class="infomessagelarge"> - <strong>We are hiring!</strong> - <hr> - Thanks to your support and an unprecedented level of usage, we are looking for an experienced software developer to join our team. For more information about this position, please, click <a target="_blank" href="https://www.bx.psu.edu/cgi-bin/trac.cgi/galaxy/wiki/PythonDeveloper">here</a>. -</div> -<br/> - -<div id="screencasts"> - -<h2>Introducing Galactic Quickies</h2> -<p> - Galactic quickies are <i>super-short</i> screencasts that are <i>always</i> under 5 minutes. We thought it may be a good way to spread the word about Galaxy's functionality while keeping the "annoyance factor" to the minimum. The quickies will be updated weekly. -</p> - -<div class="current-quickie"> - <table border="0" cellpadding="0" cellspacing="0" width="100%"> - <tr> - <td align="center"> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie5_join/flow.html',width:640,height:500,scroll:'no'})"> - <img src="images/qk/quickie5_lrg.png" border="0"> - <br> - </a> - - </td> - </tr> - </table> -</div> - -<h3>Previous Quickies</h3> +<h3 align="center">Galaxy Quickies</h3> <div class="previous" id="previous"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> @@ -98,6 +102,27 @@ </div> </a> </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie5_join/flow.html',width:640,height:500,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie5_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie6_share/flow.html',width:640,height:500,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie6_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie7_sr_beta/flow.html',width:640,height:500,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie7_small.png" border="0"> + </div> + </a> + </td> </tr> </table> </div> diff -r 71928a8f9bf9 -r b142b116024c test-data/f.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/f.fastq Tue Jan 05 14:33:39 2010 -0500 @@ -0,0 +1,1996 @@ +@853_7_53_F3 +T..02.1120..22.2..230.22.3..033212.1.1....2221...12 ++ +!!14!3.15!!47!4!!8+1!$9!(!!,..1)&!3!(!!!!1/9&!!!,3 +@853_7_78_F3 +T..13.2222..22.2..222.22.2..222212.2.2....2222...22 ++ +!!##!###$!!##!&!!#$&!$&!&!!%&)'#'!$!#!!!!&)*(!!!&* +@853_7_88_F3 +T..23.2221..13.2..033.30.1..010220.1.2....2222...22 ++ +!!61!5551!!13!4!!.,)!/,!3!!.)/17+!&!5!!!!-'0.!!!,5 +@853_7_132_F3 +T..22.2032..32.2..222.22.2..222222.2.2....2222...22 ++ +!!$(!,#&#!!&#!#!!#($!%$!#!!#&%#$(!#!#!!!!)(*+!!!,2 +@853_7_141_F3 +T..22.2112..10.2..221.02.1..220112.0.2....0222...22 ++ +!!54!9518!!1&!5!!/31!)0!6!!)533/:!5!6!!!!)/<:!!!,7 +@853_7_146_F3 +T..12.1011..21.2..213.22.2..222222.2.2....2222...22 ++ +!!10!/240!!0)!2!!#&'!'5!(!!(.-*$3!*!4!!!!+#(.!!!.( +@853_7_269_F3 +T..12.2222..22.2..222.22.2..222222.2.2....2222...22 ++ +!!%&!('#%!!#*!#!!/##!&)!$!!'$',%,!%!2!!!!3,,*!!!,2 +@853_7_321_F3 +T..20.2322..21.3..222.12.1..120012.3.0....2000...22 ++ +!!+$!+21(!!*-!.!!)#1!8/!9!!6,3+%6!'!,!!!!2&6,!!!&2 +@853_7_386_F3 +T..12.2302..20.2..231.12.0..200232.3.2....0002...22 ++ +!!31!:7-%!!:,!-!!21,!77!)!!227:9:!2!;!!!!)',%!!!86 +@853_7_405_F3 +T..21.0221..31.2..000.23.2..020022.0.2....0313...12 ++ +!!<8!8;==!!;>!:!!7:7!7;!8!!7:>48=!2!=!!!!536*!!!;: +@853_7_411_F3 +T..10.2000..33.2..022.02.0..200222.2.0....0000...00 ++ +!!,/!13;,!!&,!+!!2/%!*1!$!!%*)+#,!,!&!!!!'-'&!!!++ +@853_7_445_F3 +T..30.3210..01.1..120.11.3..301222.1.2....3222...22 ++ +!!&'!*+'#!!'%!&!!,%#!)%!(!!'##$&'!#!$!!!!$$#,!!!#$ +@853_7_469_F3 +T..22.0102..20.3..200.21.0..002202.2.2....0203...02 ++ +!!##!*($&!!##!#!!%))!#1!%!!(,##$.!#!(!!!!##'#!!!&$ +@853_7_474_F3 +T..30.1122..22.3..111.21.3..222020.2.2....2203...23 ++ +!!54!6464!!56!:!!97:!88!8!!7/5)4/!4!8!!!!4#45!!!#) +@853_7_497_F3 +T..10.0200..22.1..112.03.0..100121.2.2....3132...21 ++ +!!9:!678;!!14!9!!:<:!77!;!!.76.(<!.!/!!!!2)(9!!!14 +@853_7_587_F3 +T..22.2022..01.2..323.23.0..323322.1.1....2212...20 ++ +!!2,!,33/!!7&!7!!916!)9!<!!;,<6,1!5!/!!!!,31;!!!/> +@853_7_630_F3 +T..13.0022..11.1..213.10.0..031113.3.3....1112...20 ++ +!!,8!&5/=!!>)!)!!;).!)7!6!!/2>,('!5!2!!!!)=,&!!!25 +@853_7_655_F3 +T..01.0023..02.2..301.32.3..232113.2.2....2222...22 ++ +!!##!###'!!#'!#!!,##!##!$!!%$###(!#!#!!!!#'##!!!## +@853_7_692_F3 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[hg] galaxy 3202: enable tooltip for existing nodes
by Greg Von Kuster 05 Jan '10

05 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/ab5af4830af3 changeset: 3202:ab5af4830af3 user: Kanwei Li <kanwei(a)gmail.com> date: Tue Jan 05 13:11:35 2010 -0500 description: enable tooltip for existing nodes diffstat: lib/galaxy/web/controllers/workflow.py | 3 ++- 1 files changed, 2 insertions(+), 1 deletions(-) diffs (19 lines): diff -r 77f309c46dd0 -r ab5af4830af3 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Tue Jan 05 13:01:37 2010 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Tue Jan 05 13:11:35 2010 -0500 @@ -315,13 +315,14 @@ upgrade_message = module.check_and_update_state() if upgrade_message: data['upgrade_messages'][step.order_index] = upgrade_message - # Pack atrributes into plain dictionary + # Pack attributes into plain dictionary step_dict = { 'id': step.order_index, 'type': module.type, 'tool_id': module.get_tool_id(), 'name': module.get_name(), 'tool_state': module.get_state(), + 'tooltip': module.get_tooltip(), 'tool_errors': module.get_errors(), 'data_inputs': module.get_data_inputs(), 'data_outputs': module.get_data_outputs(),

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using the 'user' information in the the "tool config file"
by Hotz, Hans-Rudolf 05 Jan '10

05 Jan '10

Hi By accident, my colleague found out, that we can use the $userEmail variable in the 'command' tag of the "tool config file", eg: <command interpreter="perl">script.pl $input $userEmail $output </command> Access to the 'user' information ('Anonymous' or the user's e-mail address if logged in) is very handy, as it gives the potential to execute the script differently depending on the value of $userEmail . Now, we would like to use the 'user' information in order to create different options in the interface for the tool, eg: <inputs> <param name="input" type="select" label="available files" display="radio" dynamic_options="ds_Options()"/> </inputs> <outputs> <data format="fasta" name="output"/> </outputs> <code file="more_code.py" /> where "ds_Options()" is defined in the extra python code "more_code.py" I can pass a value to "ds_Options()" which we get as an example from a first page of the interface, eg: <inputs> <page> <param name="dir" type="select" display="radio"> <option value="foo">FOO</option> <option value="bar">BAR</option> </param> </page> <page> <param name="input" type="select" label="available files" display="radio" dynamic_options="ds_Options(dir)"/> </page> </inputs> <outputs> <data format="fasta" name="output"/> </outputs> <code file="more_code.py" /> ...but how do I pass just the 'user' information to the function? As I can use '$userEmail' in the 'command' tag, I tried (with my limited understanding of galaxy and python) the obvious: dynamic_options="ds_Options(userEmail)" but I get NameError: name 'userEmail' is not defined Is there any way to pass the 'user' information? Alternatively, is there a direct way to get access to the 'user' information within the function? Thank you very much for your help Hans

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