galaxy-dev July 2009

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68 discussions

[hg] galaxy 2468: Add remote_user logout anchor href configurati...
by Greg Von Kuster 08 Jul '09

08 Jul '09

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

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[hg] galaxy 2469: Change folder.active_datasets mapper to a prop...
by Greg Von Kuster 08 Jul '09

08 Jul '09

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:

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[hg] galaxy 2467: Enhance history cloning to allow for cloning a...
by Greg Von Kuster 08 Jul '09

08 Jul '09

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

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[hg] galaxy 2466: Fix for popup menus on history grid - no longe...
by Greg Von Kuster 08 Jul '09

08 Jul '09

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>

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[hg] galaxy 2464: A bug fix for extract genomic dna to handle in...
by Greg Von Kuster 07 Jul '09

07 Jul '09

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:

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[hg] galaxy 2465: Fixes and additional functional tests associat...
by Greg Von Kuster 07 Jul '09

07 Jul '09

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:

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Re: [galaxy-dev] Question concerning interval definition
by Assaf Gordon 07 Jul '09

07 Jul '09

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

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[hg] galaxy 2463: Fix deleted user access bug discovered by Piet...
by Nate Coraor 06 Jul '09

06 Jul '09

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>

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galaxy-dev July 2009