[hg] galaxy 2468: Add remote_user logout anchor href configurati...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/035c0dc31963
changeset: 2468:035c0dc31963
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Wed Jul 08 15:25:57 2009 -0400
description:
Add remote_user logout anchor href configuration provided by Morita Hideyuki.
3 file(s) affected in this change:
lib/galaxy/config.py
templates/base_panels.mako
universe_wsgi.ini.sample
diffs (60 lines):
diff -r 319e2ba6a7be -r 035c0dc31963 lib/galaxy/config.py
--- a/lib/galaxy/config.py Wed Jul 08 14:10:45 2009 -0400
+++ b/lib/galaxy/config.py Wed Jul 08 15:25:57 2009 -0400
@@ -42,6 +42,7 @@
self.set_metadata_externally = string_as_bool( kwargs.get( "set_metadata_externally", "False" ) )
self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) )
self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None )
+ self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None )
self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) )
self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) )
self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) )
diff -r 319e2ba6a7be -r 035c0dc31963 templates/base_panels.mako
--- a/templates/base_panels.mako Wed Jul 08 14:10:45 2009 -0400
+++ b/templates/base_panels.mako Wed Jul 08 15:25:57 2009 -0400
@@ -199,16 +199,22 @@
</ul>
<ul class="loggedin-only" style="${style2}">
<li>Logged in as <span id="user-email">${user_email}</span></li>
- <li><a target="galaxy_main" href="${h.url_for( controller='user', action='index' )}">Preferences</a></li>
- <%
- if app.config.require_login:
- logout_target = ""
- logout_url = h.url_for( controller='root', action='index', m_c='user', m_a='logout' )
- else:
- logout_target = "galaxy_main"
- logout_url = h.url_for( controller='user', action='logout' )
- %>
- <li><a target="${logout_target}" href="${logout_url}">Logout</a></li>
+ %if app.config.use_remote_user:
+ %if app.config.remote_user_logout_href:
+ <li><a href="${app.config.remote_user_logout_href}" target="_top">Logout</a></li>
+ %endif
+ %else:
+ <li><a target="galaxy_main" href="${h.url_for( controller='user', action='index' )}">Preferences</a></li>
+ <%
+ if app.config.require_login:
+ logout_target = ""
+ logout_url = h.url_for( controller='root', action='index', m_c='user', m_a='logout' )
+ else:
+ logout_target = "galaxy_main"
+ logout_url = h.url_for( controller='user', action='logout' )
+ %>
+ <li><a target="${logout_target}" href="${logout_url}">Logout</a></li>
+ %endif
</ul>
</div>
</span>
diff -r 319e2ba6a7be -r 035c0dc31963 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample Wed Jul 08 14:10:45 2009 -0400
+++ b/universe_wsgi.ini.sample Wed Jul 08 15:25:57 2009 -0400
@@ -141,6 +141,9 @@
# method just returns bare usernames, set a default mail domain
#remote_user_maildomain = example.org
+# If use_remote_user is enabled, set a logout anchor href option
+#remote_user_logout_href = /logout
+
# this should be a comma-separated list of valid Galaxy users
#admin_users = user1@example.org,user2@example.org
11 years, 2 months
[hg] galaxy 2469: Change folder.active_datasets mapper to a prop...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/073c9a0b2467
changeset: 2469:073c9a0b2467
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Wed Jul 08 17:01:49 2009 -0400
description:
Change folder.active_datasets mapper to a property, and correct the list of library_datasets it returns - fixes the 'bug' part of ticket # 102 reported by Ross Lazarus.
3 file(s) affected in this change:
lib/galaxy/model/__init__.py
lib/galaxy/model/mapping.py
lib/galaxy/web/controllers/admin.py
diffs (54 lines):
diff -r 035c0dc31963 -r 073c9a0b2467 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py Wed Jul 08 15:25:57 2009 -0400
+++ b/lib/galaxy/model/__init__.py Wed Jul 08 17:01:49 2009 -0400
@@ -734,11 +734,17 @@
def active_components( self ):
return list( self.active_folders ) + list( self.active_datasets )
@property
+ def active_datasets( self ):
+ # This needs to be a list
+ return [ ld for ld in self.datasets if not ld.library_dataset_dataset_association.deleted ]
+ @property
def activatable_datasets( self ):
- return [ ld for ld in self.datasets if not ld.library_dataset_dataset_association.dataset.deleted ] #this needs to be a list
+ # This needs to be a list
+ return [ ld for ld in self.datasets if not ld.library_dataset_dataset_association.dataset.deleted ]
@property #make this a relation
def activatable_folders( self ):
- return [ folder for folder in self.folders if not folder.purged ] #this needs to be a list
+ # This needs to be a list
+ return [ folder for folder in self.folders if not folder.purged ]
class LibraryDataset( object ):
# This class acts as a proxy to the currently selected LDDA
diff -r 035c0dc31963 -r 073c9a0b2467 lib/galaxy/model/mapping.py
--- a/lib/galaxy/model/mapping.py Wed Jul 08 15:25:57 2009 -0400
+++ b/lib/galaxy/model/mapping.py Wed Jul 08 17:01:49 2009 -0400
@@ -706,11 +706,6 @@
primaryjoin=( ( LibraryDataset.table.c.folder_id == LibraryFolder.table.c.id ) ),
order_by=asc( LibraryDataset.table.c.order_id ),
lazy=False,
- viewonly=True ),
- active_datasets=relation( LibraryDataset,
- primaryjoin=( ( LibraryDataset.table.c.folder_id == LibraryFolder.table.c.id ) & ( not_( LibraryDataset.table.c.deleted ) ) ),
- order_by=asc( LibraryDataset.table.c.order_id ),
- lazy=False,
viewonly=True )
) )
diff -r 035c0dc31963 -r 073c9a0b2467 lib/galaxy/web/controllers/admin.py
--- a/lib/galaxy/web/controllers/admin.py Wed Jul 08 15:25:57 2009 -0400
+++ b/lib/galaxy/web/controllers/admin.py Wed Jul 08 17:01:49 2009 -0400
@@ -1937,10 +1937,11 @@
ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id )
ldda.deleted = True
ldda.flush()
- msg = "The selected datasets have been removed from this library"
+ msg = "The selected datasets have been removed from this library"
trans.response.send_redirect( web.url_for( controller='admin',
action='browse_library',
id=library_id,
+ show_deleted=False,
msg=util.sanitize_text( msg ),
messagetype='done' ) )
else:
11 years, 2 months
[hg] galaxy 2467: Enhance history cloning to allow for cloning a...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/319e2ba6a7be
changeset: 2467:319e2ba6a7be
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Wed Jul 08 14:10:45 2009 -0400
description:
Enhance history cloning to allow for cloning active or activatable datasets from the original history - resolves ticket # 29.
6 file(s) affected in this change:
lib/galaxy/model/__init__.py
lib/galaxy/web/controllers/history.py
templates/history/clone.mako
templates/history/list_shared.mako
test/base/twilltestcase.py
test/functional/test_history_functions.py
diffs (395 lines):
diff -r 539d481c8f59 -r 319e2ba6a7be lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py Tue Jul 07 20:32:00 2009 -0400
+++ b/lib/galaxy/model/__init__.py Wed Jul 08 14:10:45 2009 -0400
@@ -214,17 +214,21 @@
if genome_build not in [None, '?']:
self.genome_build = genome_build
self.datasets.append( dataset )
- def copy( self, name=None, target_user=None ):
+ def copy( self, name=None, target_user=None, activatable=False ):
if not name:
name = self.name
if not target_user:
target_user = self.user
new_history = History( name=name, user=target_user )
new_history.flush()
- for data in self.datasets:
- new_data = data.copy( copy_children=True, target_history=new_history )
- new_history.add_dataset( new_data, set_hid = False )
- new_data.flush()
+ if activatable:
+ hdas = self.activatable_datasets
+ else:
+ hdas = self.active_datasets
+ for hda in hdas:
+ new_hda = hda.copy( copy_children=True, target_history=new_history )
+ new_history.add_dataset( new_hda, set_hid = False )
+ new_hda.flush()
new_history.hid_counter = self.hid_counter
new_history.flush()
return new_history
diff -r 539d481c8f59 -r 319e2ba6a7be lib/galaxy/web/controllers/history.py
--- a/lib/galaxy/web/controllers/history.py Tue Jul 07 20:32:00 2009 -0400
+++ b/lib/galaxy/web/controllers/history.py Wed Jul 08 14:10:45 2009 -0400
@@ -310,8 +310,8 @@
email=email,
send_to_err=send_to_err )
if params.get( 'share_button', False ):
- can_change, cannot_change, no_change_needed = \
- self._populate_restricted( trans, user, histories, send_to_users, None )
+ can_change, cannot_change, no_change_needed, send_to_err = \
+ self._populate_restricted( trans, user, histories, send_to_users, None, send_to_err )
if can_change or cannot_change:
return trans.fill_template( "/history/share.mako",
histories=histories,
@@ -335,8 +335,8 @@
user = trans.get_user()
histories, send_to_users, send_to_err = self._get_histories_and_users( trans, user, id, email )
send_to_err = ''
- can_change, cannot_change, no_change_needed = \
- self._populate_restricted( trans, user, histories, send_to_users, action )
+ can_change, cannot_change, no_change_needed, send_to_err = \
+ self._populate_restricted( trans, user, histories, send_to_users, action, send_to_err )
# Now that we've populated the can_change, cannot_change, and no_change_needed dictionaries,
# we'll populate the histories_for_sharing dictionary from each of them.
histories_for_sharing = {}
@@ -430,7 +430,7 @@
elif history not in histories_for_sharing[ send_to_user ]:
histories_for_sharing[ send_to_user ].append( history )
return histories_for_sharing, send_to_err
- def _populate_restricted( self, trans, user, histories, send_to_users, action ):
+ def _populate_restricted( self, trans, user, histories, send_to_users, action, send_to_err ):
# The user may be attempting to share histories whose datasets cannot all be accessed by other users.
# If this is the case, the user sharing the histories can:
# 1) action=='public': choose to make the datasets public if he is permitted to do so
@@ -494,7 +494,7 @@
cannot_change[ send_to_user ][ history ] = [ hda ]
else:
cannot_change[ send_to_user ][ history ].append( hda )
- return can_change, cannot_change, no_change_needed
+ return can_change, cannot_change, no_change_needed, send_to_err
def _share_histories( self, trans, user, send_to_err, histories={} ):
# histories looks like: { userA: [ historyX, historyY ], userB: [ historyY ] }
msg = ""
@@ -585,8 +585,12 @@
return trans.show_message( "<p>%s" % change_msg, refresh_frames=['history'] )
@web.expose
@web.require_login( "clone shared Galaxy history" )
- def clone( self, trans, id ):
+ def clone( self, trans, id, **kwd ):
history = get_history( trans, id, check_ownership=False )
+ params = util.Params( kwd )
+ clone_choice = params.get( 'clone_choice', None )
+ if not clone_choice:
+ return trans.fill_template( "/history/clone.mako", history=history )
user = trans.get_user()
if history.user == user:
owner = True
@@ -598,7 +602,10 @@
name = "Clone of '%s'" % history.name
if not owner:
name += " shared by '%s'" % history.user.email
- new_history = history.copy( name=name, target_user=user )
+ if clone_choice == 'activatable':
+ new_history = history.copy( name=name, target_user=user, activatable=True )
+ elif clone_choice == 'active':
+ new_history = history.copy( name=name, target_user=user )
# Render the list view
return trans.show_ok_message( 'Clone with name "%s" is now included in your list of stored histories.' % new_history.name )
diff -r 539d481c8f59 -r 319e2ba6a7be templates/history/clone.mako
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/history/clone.mako Wed Jul 08 14:10:45 2009 -0400
@@ -0,0 +1,25 @@
+<% _=n_ %>
+<%inherit file="/base.mako"/>
+<%def name="title()">Clone History</%def>
+
+<div class="toolForm">
+ <div class="toolFormTitle">Clone History</div>
+ <div class="toolFormBody">
+ <form action="${h.url_for( controller='history', action='clone' )}" method="post" >
+ <div class="form-row">
+ <input type="hidden" name="id" value="${trans.security.encode_id( history.id )}">
+ You can clone the history such that the clone will include all items in the original
+ history, or you can eliminate the original history's deleted items from the clone.
+ </div>
+ <div class="form-row">
+ <input type="radio" name="clone_choice" value="activatable"> Clone all history items, including deleted items
+ </div>
+ <div class="form-row">
+ <input type="radio" name="clone_choice" value="active"> Clone only items that are not deleted
+ </div>
+ <div class="form-row">
+ <input type="submit" name="clone_choice_button" value="Clone">
+ </div>
+ </form>
+ </div>
+</div>
diff -r 539d481c8f59 -r 319e2ba6a7be templates/history/list_shared.mako
--- a/templates/history/list_shared.mako Tue Jul 07 20:32:00 2009 -0400
+++ b/templates/history/list_shared.mako Wed Jul 08 14:10:45 2009 -0400
@@ -18,7 +18,7 @@
${history.name}
<a id="shared-${i}-popup" class="popup-arrow" style="display: none;">▼</a>
<div popupmenu="shared-${i}-popup">
- <a class="action-button" href="${h.url_for( controller='history', action='clone', id=trans.security.encode_id( history.id ) )}">Clone</a>
+ <a class="action-button" href="${h.url_for( controller='history', action='clone', id=trans.security.encode_id( history.id ), clone_choice='activatable' )}">Clone</a>
</div>
</td>
<td>${history.user.email}</td>
diff -r 539d481c8f59 -r 319e2ba6a7be test/base/twilltestcase.py
--- a/test/base/twilltestcase.py Tue Jul 07 20:32:00 2009 -0400
+++ b/test/base/twilltestcase.py Wed Jul 08 14:10:45 2009 -0400
@@ -121,10 +121,13 @@
page = self.last_page()
if page.find( 'error' ) > -1:
raise AssertionError('Errors in the history for user %s' % self.user )
- def check_history_for_string( self, patt ):
+ def check_history_for_string( self, patt, show_deleted=False ):
"""Looks for 'string' in history page"""
self.home()
- self.visit_page( "history" )
+ if show_deleted:
+ self.visit_page( "history?show_deleted=True" )
+ else:
+ self.visit_page( "history" )
for subpatt in patt.split():
tc.find(subpatt)
self.home()
@@ -268,11 +271,6 @@
self.home()
def switch_history( self, id='', name='' ):
"""Switches to a history in the current list of histories"""
- data_list = self.get_histories_as_data_list()
- self.assertTrue( data_list )
- if not id:
- history = history_list[0]
- id = history.get( 'id' )
self.visit_url( "%s/history/list?operation=switch&id=%s" % ( self.url, id ) )
if name:
self.check_history_for_string( name )
@@ -305,11 +303,15 @@
if check_str2:
self.check_page_for_string( check_str2 )
self.home()
- def clone_history( self, history_id, check_str1='' ):
+ def clone_history( self, history_id, clone_choice, check_str1='', check_str_after_submit='' ):
self.home()
self.visit_page( "history/clone?id=%s" % history_id )
if check_str1:
self.check_page_for_string( check_str1 )
+ tc.fv( '1', 'clone_choice', clone_choice )
+ tc.submit( 'clone_choice_button' )
+ if check_str_after_submit:
+ self.check_page_for_string( check_str_after_submit )
self.home()
def enable_import_via_link( self, history_id, check_str='', check_str_after_submit='' ):
self.home()
@@ -366,34 +368,22 @@
self.visit_page( "edit?hid=%d" % hid )
for subpatt in patt.split():
tc.find(subpatt)
- def delete_history_item( self, hid, check_str='' ):
+ def delete_history_item( self, hda_id, check_str='' ):
"""Deletes an item from a history"""
try:
- hid = int( hid )
+ hda_id = int( hda_id )
except:
- raise AssertionError, "Invalid hid '%s' - must be int" % hid
- hid = str(hid)
- data_list = self.get_history_as_data_list()
- self.assertTrue( data_list )
- elems = [ elem for elem in data_list if elem.get( 'hid' ) == hid ]
- self.assertEqual( len( elems ), 1 )
- self.home()
- self.visit_page( "delete?id=%s" % elems[0].get( 'id' ) )
+ raise AssertionError, "Invalid hda_id '%s' - must be int" % hda_id
+ self.visit_url( "%s/root/delete?show_deleted_on_refresh=False&id=%s" % ( self.url, hda_id ) )
if check_str:
self.check_page_for_string( check_str )
- def undelete_history_item( self, hid, show_deleted=False, check_str='' ):
+ def undelete_history_item( self, hda_id, check_str='' ):
"""Un-deletes a deleted item in a history"""
try:
- hid = int( hid )
+ hda_id = int( hda_id )
except:
- raise AssertionError, "Invalid hid '%s' - must be int" % hid
- hid = str( hid )
- data_list = self.get_history_as_data_list( show_deleted=show_deleted )
- self.assertTrue( data_list )
- elems = [ elem for elem in data_list if elem.get( 'hid' ) == hid ]
- self.assertEqual( len( elems ), 1 )
- self.home()
- self.visit_url( "%s/dataset/undelete?id=%s" % ( self.url, elems[0].get( 'id' ) ) )
+ raise AssertionError, "Invalid hda_id '%s' - must be int" % hda_id
+ self.visit_url( "%s/dataset/undelete?id=%s" % ( self.url, hda_id ) )
if check_str:
self.check_page_for_string( check_str )
def display_history_item( self, id, check_str='' ):
diff -r 539d481c8f59 -r 319e2ba6a7be test/functional/test_history_functions.py
--- a/test/functional/test_history_functions.py Tue Jul 07 20:32:00 2009 -0400
+++ b/test/functional/test_history_functions.py Wed Jul 08 14:10:45 2009 -0400
@@ -168,11 +168,6 @@
# Test sharing history3 with an invalid user
self.share_current_history( 'jack(a)jill.com',
check_str_after_submit='jack(a)jill.com is not a valid Galaxy user.' )
-
-
-
-
-
def test_025_delete_shared_current_history( self ):
"""Testing deleting the current history after it was shared"""
# Logged in as admin_user
@@ -187,7 +182,8 @@
# Shared history3 should be in regular_user1's list of shared histories
self.view_shared_histories( check_str=history3.name, check_str2=admin_user.email )
self.clone_history( self.security.encode_id( history3.id ),
- check_str1='is now included in your list of stored histories.' )
+ 'activatable',
+ check_str_after_submit='is now included in your list of stored histories.' )
global history3_clone1
history3_clone1 = galaxy.model.History.filter( and_( galaxy.model.History.table.c.deleted==False,
galaxy.model.History.table.c.user_id==regular_user1.id ) ) \
@@ -201,8 +197,26 @@
# logged in as regular_user1
self.logout()
self.login( email=admin_user.email )
+ # Current history should be history3, add more datasets to history3, then delete them so we can
+ # test cloning activatable datasets as well as only the active datasets
+ self.upload_file( '2.bed', dbkey='hg18' )
+ hda_2_bed = galaxy.model.HistoryDatasetAssociation \
+ .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3.id,
+ galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) \
+ .first()
+ assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database"
+ self.delete_history_item( str( hda_2_bed.id ) )
+ self.upload_file( '3.bed', dbkey='hg18' )
+ hda_3_bed = galaxy.model.HistoryDatasetAssociation \
+ .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3.id,
+ galaxy.model.HistoryDatasetAssociation.table.c.name=='3.bed' ) ) \
+ .first()
+ assert hda_3_bed is not None, "Problem retrieving hda_3_bed from database"
+ self.delete_history_item( str( hda_3_bed.id ) )
+ # Test cloning activatable datasets
self.clone_history( self.security.encode_id( history3.id ),
- check_str1='is now included in your list of stored histories.' )
+ 'activatable',
+ check_str_after_submit='is now included in your list of stored histories.' )
global history3_clone2
history3_clone2 = galaxy.model.History.filter( and_( galaxy.model.History.table.c.deleted==False,
galaxy.model.History.table.c.user_id==admin_user.id ) ) \
@@ -210,6 +224,42 @@
assert history3_clone2 is not None, "Problem retrieving history3_clone2 from database"
# Check list of histories to make sure shared history3 was cloned
self.view_stored_active_histories( check_str="Clone of '%s'" % history3.name )
+ # Switch to the cloned history to make sure activatable datasets were cloned
+ self.switch_history( id=self.security.encode_id( history3_clone2.id ), name=history3_clone2.name )
+ hda_2_bed = galaxy.model.HistoryDatasetAssociation \
+ .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3_clone2.id,
+ galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) \
+ .first()
+ assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database"
+ hda_3_bed = galaxy.model.HistoryDatasetAssociation \
+ .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3_clone2.id,
+ galaxy.model.HistoryDatasetAssociation.table.c.name=='3.bed' ) ) \
+ .first()
+ assert hda_3_bed is not None, "Problem retrieving hda_3_bed from database"
+ # Make sure the deleted datasets are included in the cloned history
+ check_str = 'This dataset has been deleted. Click undelete id=%d"' % hda_2_bed.id
+ self.check_history_for_string( check_str, show_deleted=True )
+ check_str = 'This dataset has been deleted. Click undelete id=%d"' % hda_3_bed.id
+ self.check_history_for_string( check_str, show_deleted=True )
+ # Test cloning only active datasets
+ self.clone_history( self.security.encode_id( history3.id ),
+ 'active',
+ check_str_after_submit='is now included in your list of stored histories.' )
+ global history3_clone3
+ history3_clone3 = galaxy.model.History.filter( and_( galaxy.model.History.table.c.deleted==False,
+ galaxy.model.History.table.c.user_id==admin_user.id ) ) \
+ .order_by( desc( galaxy.model.History.table.c.create_time ) ).first()
+ assert history3_clone3 is not None, "Problem retrieving history3_clone3 from database"
+ # Check list of histories to make sure shared history3 was cloned
+ self.view_stored_active_histories( check_str="Clone of '%s'" % history3.name )
+ # Switch to the cloned history to make sure activatable datasets were cloned
+ self.switch_history( id=self.security.encode_id( history3_clone3.id ), name=history3_clone3.name )
+ # Make sure the deleted datasets are NOT included in the cloned history
+ try:
+ self.check_history_for_string( 'This dataset has been deleted.', show_deleted=True )
+ raise AssertionError, "Deleted datasets incorrectly included in cloned history history3_clone3"
+ except:
+ pass
def test_040_sharing_mulitple_histories_with_multiple_users( self ):
"""Testing sharing multiple histories containing only public datasets with multiple users"""
# Logged in as admin_user
@@ -304,7 +354,8 @@
self.view_shared_histories( check_str=history5.name, check_str2=admin_user.email )
# Clone restricted history5
self.clone_history( self.security.encode_id( history5.id ),
- check_str1='is now included in your list of stored histories.' )
+ 'activatable',
+ check_str_after_submit='is now included in your list of stored histories.' )
global history5_clone1
history5_clone1 = galaxy.model.History.filter( and_( galaxy.model.History.table.c.deleted==False,
galaxy.model.History.table.c.user_id==regular_user1.id ) ) \
@@ -359,7 +410,8 @@
self.view_shared_histories( check_str=history5.name, check_str2=admin_user.email )
# Clone restricted history5
self.clone_history( self.security.encode_id( history5.id ),
- check_str1='is now included in your list of stored histories.' )
+ 'activatable',
+ check_str_after_submit='is now included in your list of stored histories.' )
global history5_clone2
history5_clone2 = galaxy.model.History.filter( and_( galaxy.model.History.table.c.deleted==False,
galaxy.model.History.table.c.user_id==regular_user2.id ) ) \
@@ -431,7 +483,8 @@
self.view_shared_histories( check_str=history5.name, check_str2=admin_user.email )
# Clone restricted history5
self.clone_history( self.security.encode_id( history5.id ),
- check_str1='is now included in your list of stored histories.' )
+ 'activatable',
+ check_str_after_submit='is now included in your list of stored histories.' )
global history5_clone3
history5_clone3 = galaxy.model.History.filter( and_( galaxy.model.History.table.c.deleted==False,
galaxy.model.History.table.c.user_id==regular_user2.id ) ) \
@@ -468,7 +521,8 @@
self.view_shared_histories( check_str=history5.name, check_str2=admin_user.email )
# Clone restricted history5
self.clone_history( self.security.encode_id( history5.id ),
- check_str1='is now included in your list of stored histories.' )
+ 'activatable',
+ check_str_after_submit='is now included in your list of stored histories.' )
global history5_clone4
history5_clone4 = galaxy.model.History.filter( and_( galaxy.model.History.table.c.deleted==False,
galaxy.model.History.table.c.user_id==regular_user3.id ) ) \
@@ -587,16 +641,16 @@
self.check_page_for_string( 'hg15' )
self.assertEqual ( len( self.get_history_as_data_list() ), 1 )
# Delete the history item
- self.delete_history_item( latest_hda.hid, check_str="Your history is empty" )
+ self.delete_history_item( str( latest_hda.id ), check_str="Your history is empty" )
self.assertEqual ( len( self.get_history_as_data_list() ), 0 )
# Try deleting an invalid hid
try:
self.delete_history_item( 'XXX' )
- raise AssertionError, "Inproperly able to delete hid 'XXX' which is not an integer"
+ raise AssertionError, "Inproperly able to delete hda_id 'XXX' which is not an integer"
except:
pass
# Undelete the history item
- self.undelete_history_item( latest_hda.hid, show_deleted=True )
+ self.undelete_history_item( str( latest_hda.id ) )
self.home()
self.visit_url( "%s/history/?show_deleted=False" % self.url )
self.check_page_for_string( '1.bed' )
@@ -673,6 +727,7 @@
# Delete histories
self.delete_history( id=self.security.encode_id( history3.id ) )
self.delete_history( id=self.security.encode_id( history3_clone2.id ) )
+ self.delete_history( id=self.security.encode_id( history3_clone3.id ) )
self.delete_history( id=self.security.encode_id( history4.id ) )
self.delete_history( id=self.security.encode_id( history5.id ) )
# Eliminate Sharing role for: test(a)bx.psu.edu, test2(a)bx.psu.edu
11 years, 2 months
[hg] galaxy 2466: Fix for popup menus on history grid - no longe...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/539d481c8f59
changeset: 2466:539d481c8f59
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Tue Jul 07 20:32:00 2009 -0400
description:
Fix for popup menus on history grid - no longer necessary to encode ids in the template.
1 file(s) affected in this change:
templates/history/grid.mako
diffs (12 lines):
diff -r 3bbb2d2caa5f -r 539d481c8f59 templates/history/grid.mako
--- a/templates/history/grid.mako Tue Jul 07 14:48:01 2009 -0400
+++ b/templates/history/grid.mako Tue Jul 07 20:32:00 2009 -0400
@@ -168,7 +168,7 @@
<div popupmenu="grid-${i}-popup">
%for operation in grid.operations:
%if operation.allowed( item ):
- <a class="action-button" href="${url( operation=operation.label, id=trans.security.encode_id( item.id ) )}">${operation.label}</a>
+ <a class="action-button" href="${url( operation=operation.label, id=item.id )}">${operation.label}</a>
%endif
%endfor
</div>
11 years, 2 months
[hg] galaxy 2464: A bug fix for extract genomic dna to handle in...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/4c3282337a4c
changeset: 2464:4c3282337a4c
user: guru
date: Tue Jul 07 12:06:35 2009 -0400
description:
A bug fix for extract genomic dna to handle invalid chromosomes correctly.
1 file(s) affected in this change:
tools/extract/extract_genomic_dna.py
diffs (21 lines):
diff -r 3a4561684257 -r 4c3282337a4c tools/extract/extract_genomic_dna.py
--- a/tools/extract/extract_genomic_dna.py Mon Jul 06 20:41:24 2009 -0400
+++ b/tools/extract/extract_genomic_dna.py Tue Jul 07 12:06:35 2009 -0400
@@ -117,7 +117,7 @@
first_invalid_line = i + 1
invalid_line = line
continue
- elif seq_path and os.path.exists( seq_path ):
+ elif seq_path and os.path.isfile( seq_path ):
if chrom in twobits:
t = twobits[chrom]
else:
@@ -133,7 +133,7 @@
invalid_line = line
continue
else:
- warning = "Chrom '%s' was not found for build '%s'. " % ( chrom, dbkey )
+ warning = "Chromosome by name '%s' was not found for build '%s'. " % ( chrom, dbkey )
warnings.append( warning )
skipped_lines += 1
if not invalid_line:
11 years, 2 months
[hg] galaxy 2465: Fixes and additional functional tests associat...
by Greg Von Kuster
details: http://www.bx.psu.edu/hg/galaxy/rev/3bbb2d2caa5f
changeset: 2465:3bbb2d2caa5f
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Tue Jul 07 14:48:01 2009 -0400
description:
Fixes and additional functional tests associated with a user's private role:
- private roles are no longer displayed in the association forms, except for the currently selected user's private role
- a user's private role association can no longer be eliminated
- more than 1 association can no longer be made between a user and her private role
7 file(s) affected in this change:
lib/galaxy/model/mapping.py
lib/galaxy/security/__init__.py
lib/galaxy/web/controllers/admin.py
lib/galaxy/web/controllers/user.py
templates/admin/dataset_security/roles.mako
test/base/twilltestcase.py
test/functional/test_security_and_libraries.py
diffs (157 lines):
diff -r 4c3282337a4c -r 3bbb2d2caa5f lib/galaxy/model/mapping.py
--- a/lib/galaxy/model/mapping.py Tue Jul 07 12:06:35 2009 -0400
+++ b/lib/galaxy/model/mapping.py Tue Jul 07 14:48:01 2009 -0400
@@ -624,7 +624,7 @@
user=relation( User, backref="roles" ),
non_private_roles=relation( User,
backref="non_private_roles",
- primaryjoin=( ( User.table.c.id == UserRoleAssociation.table.c.user_id ) & ( UserRoleAssociation.table.c.role_id == Role.table.c.id ) & not_( Role.table.c.type == 'private' ) ) ),
+ primaryjoin=( ( User.table.c.id == UserRoleAssociation.table.c.user_id ) & ( UserRoleAssociation.table.c.role_id == Role.table.c.id ) & not_( Role.table.c.name == User.table.c.email & Role.table.c.type == 'private' ) ) ),
role=relation( Role )
)
)
diff -r 4c3282337a4c -r 3bbb2d2caa5f lib/galaxy/security/__init__.py
--- a/lib/galaxy/security/__init__.py Tue Jul 07 12:06:35 2009 -0400
+++ b/lib/galaxy/security/__init__.py Tue Jul 07 14:48:01 2009 -0400
@@ -422,8 +422,11 @@
for a in user.non_private_roles + user.groups:
a.delete()
a.flush()
+ user.refresh()
for role in roles:
- self.associate_components( user=user, role=role )
+ # Make sure we are not creating an additional association with a PRIVATE role
+ if role not in user.roles:
+ self.associate_components( user=user, role=role )
for group in groups:
self.associate_components( user=user, group=group )
def set_entity_group_associations( self, groups=[], users=[], roles=[], delete_existing_assocs=True ):
diff -r 4c3282337a4c -r 3bbb2d2caa5f lib/galaxy/web/controllers/admin.py
--- a/lib/galaxy/web/controllers/admin.py Tue Jul 07 12:06:35 2009 -0400
+++ b/lib/galaxy/web/controllers/admin.py Tue Jul 07 14:48:01 2009 -0400
@@ -623,22 +623,35 @@
msg = util.restore_text( params.get( 'msg', '' ) )
messagetype = params.get( 'messagetype', 'done' )
user = trans.app.model.User.get( int( params.user_id ) )
+ private_role = trans.app.security_agent.get_private_user_role( user )
if params.get( 'user_roles_groups_edit_button', False ):
+ # Make sure the user is not dis-associating himself from his private role
+ out_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.out_roles ) ]
+ if private_role in out_roles:
+ msg += "You cannot eliminate a user's private role association. "
+ messagetype = 'error'
in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.in_roles ) ]
+ out_groups = [ trans.app.model.Group.get( x ) for x in util.listify( params.out_groups ) ]
in_groups = [ trans.app.model.Group.get( x ) for x in util.listify( params.in_groups ) ]
- trans.app.security_agent.set_entity_user_associations( users=[ user ], roles=in_roles, groups=in_groups )
- user.refresh()
- msg += "User '%s' has been updated with %d associated roles and %d associated groups (private roles are not displayed)" % \
- ( user.email, len( in_roles ), len( in_groups ) )
- trans.response.send_redirect( web.url_for( action='users', msg=util.sanitize_text( msg ), messagetype=messagetype ) )
+ if in_roles:
+ trans.app.security_agent.set_entity_user_associations( users=[ user ], roles=in_roles, groups=in_groups )
+ user.refresh()
+ msg += "User '%s' has been updated with %d associated roles and %d associated groups (private roles are not displayed)" % \
+ ( user.email, len( in_roles ), len( in_groups ) )
+ trans.response.send_redirect( web.url_for( action='users', msg=util.sanitize_text( msg ), messagetype=messagetype ) )
in_roles = []
out_roles = []
in_groups = []
out_groups = []
- for role in trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.table.c.name ).all():
+ for role in trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ) \
+ .order_by( trans.app.model.Role.table.c.name ).all():
if role in [ x.role for x in user.roles ]:
in_roles.append( ( role.id, role.name ) )
- else:
+ elif role.type != trans.app.model.Role.types.PRIVATE:
+ # There is a 1 to 1 mapping between a user and a PRIVATE role, so private roles should
+ # not be listed in the roles form fields, except for the currently selected user's private
+ # role, which should always be in in_roles. The check above is added as an additional
+ # precaution, since for a period of time we were including private roles in the form fields.
out_roles.append( ( role.id, role.name ) )
for group in trans.app.model.Group.filter( trans.app.model.Group.table.c.deleted==False ).order_by( trans.app.model.Group.table.c.name ).all():
if group in [ x.group for x in user.groups ]:
diff -r 4c3282337a4c -r 3bbb2d2caa5f lib/galaxy/web/controllers/user.py
--- a/lib/galaxy/web/controllers/user.py Tue Jul 07 12:06:35 2009 -0400
+++ b/lib/galaxy/web/controllers/user.py Tue Jul 07 14:48:01 2009 -0400
@@ -81,7 +81,6 @@
@web.expose
def login( self, trans, email='', password='' ):
- log.debug( "###IN login, email:%s, password: %s" % ( email, password ))
email_error = password_error = None
# Attempt login
if trans.app.config.require_login:
diff -r 4c3282337a4c -r 3bbb2d2caa5f templates/admin/dataset_security/roles.mako
--- a/templates/admin/dataset_security/roles.mako Tue Jul 07 12:06:35 2009 -0400
+++ b/templates/admin/dataset_security/roles.mako Tue Jul 07 14:48:01 2009 -0400
@@ -44,7 +44,7 @@
%endif
%if len( roles ) == 0:
- There are no Galaxy roles
+ There are no non-private Galaxy roles
%else:
<table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
<%
diff -r 4c3282337a4c -r 3bbb2d2caa5f test/base/twilltestcase.py
--- a/test/base/twilltestcase.py Tue Jul 07 12:06:35 2009 -0400
+++ b/test/base/twilltestcase.py Tue Jul 07 14:48:01 2009 -0400
@@ -816,16 +816,23 @@
check_str = "User '%s' has been marked as purged." % email
self.check_page_for_string( check_str )
self.home()
- def associate_roles_and_groups_with_user( self, user_id, email, role_ids=[], group_ids=[] ):
+ def associate_roles_and_groups_with_user( self, user_id, email,
+ in_role_ids=[], out_role_ids=[],
+ in_group_ids=[], out_group_ids=[],
+ check_str='' ):
self.home()
url = "%s/admin/user?user_id=%s&user_roles_groups_edit_button=Save" % ( self.url, user_id )
- if role_ids:
- url += "&in_roles=%s" % ','.join( role_ids )
- if group_ids:
- url += "&in_groups=%s" % ','.join( group_ids )
+ if in_role_ids:
+ url += "&in_roles=%s" % ','.join( in_role_ids )
+ if out_role_ids:
+ url += "&out_roles=%s" % ','.join( out_role_ids )
+ if in_group_ids:
+ url += "&in_groups=%s" % ','.join( in_group_ids )
+ if out_group_ids:
+ url += "&out_groups=%s" % ','.join( out_group_ids )
self.visit_url( url )
- check_str = "User '%s' has been updated with %d associated roles and %d associated groups" % ( email, len( role_ids ), len( group_ids ) )
- self.check_page_for_string( check_str )
+ if check_str:
+ self.check_page_for_string( check_str )
self.home()
# Tests associated with roles
diff -r 4c3282337a4c -r 3bbb2d2caa5f test/functional/test_security_and_libraries.py
--- a/test/functional/test_security_and_libraries.py Tue Jul 07 12:06:35 2009 -0400
+++ b/test/functional/test_security_and_libraries.py Tue Jul 07 14:48:01 2009 -0400
@@ -72,6 +72,11 @@
self.home()
self.visit_url( "%s/admin/user?user_id=%s" % ( self.url, 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."
+ self.associate_roles_and_groups_with_user( str( admin_user.id ), admin_user.email,
+ out_role_ids=str( admin_user_private_role.id ),
+ check_str=check_str )
self.logout()
def test_010_login_as_regular_user1( self ):
"""Testing logging in as regular user test1(a)bx.psu.edu - tests private role creation and changing DefaultHistoryPermissions for new histories"""
@@ -430,7 +435,9 @@
group_ids = []
for uga in admin_user.groups:
group_ids.append( str( uga.group_id ) )
- self.associate_roles_and_groups_with_user( str( admin_user.id ), str( admin_user.email ), role_ids=role_ids, group_ids=group_ids )
+ check_str = "User '%s' has been updated with %d associated roles and %d associated groups" % ( admin_user.email, len( role_ids ), len( group_ids ) )
+ self.associate_roles_and_groups_with_user( str( admin_user.id ), str( admin_user.email ),
+ in_role_ids=role_ids, in_group_ids=group_ids, check_str=check_str )
admin_user.refresh()
# admin_user should now be associated with 4 roles: private, role_one, role_two, role_three
if len( admin_user.roles ) != 4:
11 years, 2 months
Re: [galaxy-dev] Question concerning interval definition
by Assaf Gordon
Hello Galaxy team and Eckart,
It seems questions about zero/one based coordinates are frequent by new
galaxy users.
Some time ago I wrote a short summary (with screen shots) about the
different between one-based and zero-based coordinates in UCSC browser
(and by extension - in galaxy).
You're welcome to put it on your wiki, if you'd like.
-Gordon.
Eckart Bindewald wrote, On 07/07/2009 02:14 PM:
> Hello:
> thank you for providing the Galaxy server, it is a very impressive
> web application. I have a seemingly dumb but important question, and
> I could not find the information anywhere: what is the precise
> definition of an interval? Or: has the first residue of a chromosome
> the index zero or the index one? Is the end residue (the second
> number of an interval) the last residue of the interval, or one
> residue downstream with respect to the last residue included in the
> interval?
> Maybe questions like this can be included in the FAQ...
>
> Thanks in advance,
>
> Eckart Bindewald
>
> _______________________________________________
> galaxy-bugs mailing list
> galaxy-bugs(a)bx.psu.edu
> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-bugs
11 years, 2 months
[hg] galaxy 2463: Fix deleted user access bug discovered by Piet...
by Nate Coraor
details: http://www.bx.psu.edu/hg/galaxy/rev/3a4561684257
changeset: 2463:3a4561684257
user: Nate Coraor <nate(a)bx.psu.edu>
date: Mon Jul 06 20:41:24 2009 -0400
description:
Fix deleted user access bug discovered by Pieter Neerincx
2 file(s) affected in this change:
lib/galaxy/web/framework/__init__.py
static/user_disabled.html
diffs (74 lines):
diff -r 8ad73e08978e -r 3a4561684257 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py Mon Jun 29 17:04:18 2009 -0400
+++ b/lib/galaxy/web/framework/__init__.py Mon Jul 06 20:41:24 2009 -0400
@@ -147,6 +147,9 @@
self.workflow_building_mode = False
# Always have a valid galaxy session
self.__ensure_valid_session( session_cookie )
+ # Prevent deleted users from accessing Galaxy
+ if self.app.config.use_remote_user and self.galaxy_session.user.deleted:
+ self.response.send_redirect( url_for( '/static/user_disabled.html' ) )
if self.app.config.require_login:
self.__ensure_logged_in_user( environ )
def setup_i18n( self ):
@@ -279,6 +282,9 @@
invalidate_existing_session = True
log.warning( "User '%s' is an external user with an existing session, invalidating session since external auth is disabled",
galaxy_session.user.email )
+ elif galaxy_session is not None and galaxy_session.user is not None and galaxy_session.user.deleted:
+ invalidate_existing_session = True
+ log.warning( "User '%s' is marked deleted, invalidating session" % galaxy_session.user.email )
# Do we need to invalidate the session for some reason?
if invalidate_existing_session:
prev_galaxy_session = galaxy_session
@@ -300,6 +306,9 @@
if prev_galaxy_session:
objects_to_flush.append( prev_galaxy_session )
sa_session.flush( objects_to_flush )
+ # If the old session was invalid, get a new history with our new session
+ if invalidate_existing_session:
+ self.new_history()
def __ensure_logged_in_user( self, environ ):
allowed_paths = (
url_for( controller='root', action='index' ),
@@ -368,8 +377,6 @@
# We set default user permissions, before we log in and set the default history permissions
self.app.security_agent.user_set_default_permissions( user )
#self.log_event( "Automatically created account '%s'", user.email )
- elif user.deleted:
- return self.show_error_message( "Your account is no longer valid, contact your Galaxy administrator to activate your account." )
return user
def __update_session_cookie( self, name='galaxysession' ):
"""
diff -r 8ad73e08978e -r 3a4561684257 static/user_disabled.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/static/user_disabled.html Mon Jul 06 20:41:24 2009 -0400
@@ -0,0 +1,28 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html lang="en">
+ <head>
+ <title>Galaxy</title>
+ <style type="text/css">
+ body {
+ min-width: 500px;
+ text-align: center;
+ }
+ .errormessage {
+ font: 75%% verdana, "Bitstream Vera Sans", geneva, arial, helvetica, helve, sans-serif;
+ padding: 10px;
+ margin: 100px auto;
+ min-height: 32px;
+ max-width: 500px;
+ border: 1px solid #AA6666;
+ background-color: #FFCCCC;
+ text-align: left;
+ }
+ </style>
+ </head>
+ <body>
+ <div class="errormessage">
+ <h4>Account Disabled</h4>
+ <p>Your account is no longer valid, contact your Galaxy administrator to activate your account.</p>
+ </div>
+ </body>
+</html>
11 years, 2 months