1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/795a1799e7dc/ changeset: 795a1799e7dc user: carlfeberhard date: 2012-12-10 23:44:11 summary: Fixes to history functional tests; Twilltestcase: added function to parse and check json, exact string matcher affected #: 5 files

diff -r e19bf2b117638221414239698f840730a2cd0569 -r 795a1799e7dcf092b14f7e2a2dba3fb389403531 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -130,6 +130,7 @@ history_panel_template = "root/history.mako"

else: + # get all datasets server-side, client-side will get flags and render appropriately datasets = self.get_history_datasets( trans, history, show_deleted=True, show_hidden=True, show_purged=True )

diff -r e19bf2b117638221414239698f840730a2cd0569 -r 795a1799e7dcf092b14f7e2a2dba3fb389403531 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -241,8 +241,9 @@ try: os.makedirs( dir ) except OSError: - pass - print "Database connection:", database_connection + pass + log.info( "Database connection:", database_connection ) + # ---- Build Application -------------------------------------------------- app = None if start_server: @@ -412,6 +413,8 @@ if os.path.exists( tempdir ) and 'GALAXY_TEST_NO_CLEANUP' not in os.environ: log.info( "Cleaning up temporary files in %s" % tempdir ) shutil.rmtree( tempdir ) + else: + log.info( "GALAXY_TEST_NO_CLEANUP is on. Temporary files in %s" % tempdir ) except: pass if psu_production and 'GALAXY_TEST_NO_CLEANUP' not in os.environ:

diff -r e19bf2b117638221414239698f840730a2cd0569 -r 795a1799e7dcf092b14f7e2a2dba3fb389403531 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -310,11 +310,12 @@ // ostensibly, this is the App // LOAD INITIAL DATA IN THIS PAGE - since we're already sending it... // ...use mako to 'bootstrap' the models - var user = ${ get_current_user() }, + var page_show_deleted = ${ 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) }, + page_show_hidden = ${ 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) }, + + user = ${ get_current_user() }, history = ${ get_history( history.id ) }, hdas = ${ get_hdas( history.id, datasets ) }; - var currUser = new User( user ); - if( !Galaxy.currUser ){ Galaxy.currUser = currUser; }

// add user data to history // i don't like this history+user relationship, but user authentication changes views/behaviour @@ -326,8 +327,8 @@ urlTemplates : galaxy_paths.attributes, logger : ( debugging )?( console ):( null ), // is page sending in show settings? if so override history's - show_deleted : ${ 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) }, - show_hidden : ${ 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) } + show_deleted : page_show_deleted, + show_hidden : page_show_hidden }); historyPanel.render();

@@ -337,15 +338,16 @@ // urlTemplates : galaxy_paths.attributes, // logger : ( debugging )?( console ):( null ), // // is page sending in show settings? if so override history's - // show_deleted : ${ 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) }, - // show_hidden : ${ 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) } + // show_deleted : page_show_deleted, + // show_hidden : page_show_hidden //}); //historyPanel.model.loadFromApi( history.id );

// set it up to be accessible across iframes //TODO:?? mem leak top.Galaxy.currHistoryPanel = historyPanel; - + var currUser = new User( user ); + if( !Galaxy.currUser ){ Galaxy.currUser = currUser; }

// QUOTA METER is a cross-frame ui element (meter in masthead, over quota message in history) // create it and join them here for now (via events)

diff -r e19bf2b117638221414239698f840730a2cd0569 -r 795a1799e7dcf092b14f7e2a2dba3fb389403531 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -249,8 +249,9 @@ 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, show_deleted=False ): - """Looks for 'string' in history page""" + """Breaks patt on whitespace and searches for each element seperately in the history""" self.home() if show_deleted: self.visit_page( "history?show_deleted=True" ) @@ -264,11 +265,57 @@ errmsg = "no match to '%s'\npage content written to '%s'" % ( subpatt, fname ) raise AssertionError( errmsg ) self.home() + + def check_history_for_exact_string( self, string, show_deleted=False ): + """Looks for exact match to 'string' in history page""" + self.home() + if show_deleted: + self.visit_page( "history?show_deleted=True" ) + else: + self.visit_page( "history" ) + try: + tc.find( string ) + except: + fname = self.write_temp_file( tc.browser.get_html() ) + errmsg = "no match to '%s'\npage content written to '%s'" % ( string, fname ) + raise AssertionError( errmsg ) + self.home() + + def check_history_json( self, pattern, check_fn, show_deleted=None, multiline=True ): + """ + Tries to find a JSON string in the history page using the regex pattern, + parse it, and assert check_fn returns True when called on that parsed + data. + """ + self.home() + if show_deleted: + self.visit_page( "history?show_deleted=True" ) + elif show_deleted == False: + self.visit_page( "history?show_deleted=False" ) + else: + self.visit_page( "history" ) + try: + tc.find( pattern, flags=( 'm' if multiline else '' ) ) + # twill stores the regex match in a special stack variable + match = twill.namespaces.get_twill_glocals()[1][ '__match__' ] + json_data = from_json_string( match ) + assert check_fn( json_data ), 'failed check_fn' + + except Exception, exc: + log.error( exc, exc_info=True ) + fname = self.write_temp_file( tc.browser.get_html() ) + errmsg = ( "json '%s' could not be found or failed check_fn" % ( pattern ) + + "\npage content written to '%s'" % ( fname ) ) + raise AssertionError( errmsg ) + + self.home() + def clear_history( self ): """Empties a history of all datasets""" self.visit_page( "clear_history" ) self.check_history_for_string( 'Your history is empty' ) self.home() + def delete_history( self, id ): """Deletes one or more histories""" history_list = self.get_histories_as_data_list() @@ -279,6 +326,7 @@ check_str = 'Deleted %d %s' % ( num_deleted, iff( num_deleted != 1, "histories", "history" ) ) self.check_page_for_string( check_str ) self.home() + def delete_current_history( self, strings_displayed=[] ): """Deletes the current history""" self.home() @@ -286,16 +334,19 @@ for check_str in strings_displayed: self.check_page_for_string( check_str ) self.home() + def get_histories_as_data_list( self ): """Returns the data elements of all histories""" tree = self.histories_as_xml_tree() data_list = [ elem for elem in tree.findall("data") ] return data_list + def get_history_as_data_list( self, show_deleted=False ): """Returns the data elements of a history""" tree = self.history_as_xml_tree( show_deleted=show_deleted ) data_list = [ elem for elem in tree.findall("data") ] return data_list + def history_as_xml_tree( self, show_deleted=False ): """Returns a parsed xml object of a history""" self.home() @@ -303,6 +354,7 @@ xml = self.last_page() tree = ElementTree.fromstring(xml) return tree + def histories_as_xml_tree( self ): """Returns a parsed xml object of all histories""" self.home() @@ -310,6 +362,7 @@ xml = self.last_page() tree = ElementTree.fromstring(xml) return tree + def history_options( self, user=False, active_datasets=False, activatable_datasets=False, histories_shared_by_others=False ): """Mimics user clicking on history options link""" self.home() @@ -329,6 +382,7 @@ self.check_page_for_string( 'Rename</a> current history' ) self.check_page_for_string( 'Delete</a> current history' ) self.home() + def new_history( self, name=None ): """Creates a new, empty history""" self.home() @@ -338,6 +392,7 @@ self.visit_url( "%s/history_new" % self.url ) self.check_history_for_string('Your history is empty') self.home() + def rename_history( self, id, old_name, new_name ): """Rename an existing history""" self.home() @@ -345,6 +400,7 @@ check_str = 'History: %s renamed to: %s' % ( old_name, urllib.unquote( new_name ) ) self.check_page_for_string( check_str ) self.home() + def set_history( self ): """Sets the history (stores the cookies for this run)""" if self.history_id: @@ -353,6 +409,7 @@ else: self.new_history() self.home() + def share_current_history( self, email, strings_displayed=[], strings_displayed_after_submit=[], action='', action_strings_displayed=[], action_strings_displayed_after_submit=[] ): """Share the current history with different users""" @@ -372,6 +429,7 @@ for check_str in action_strings_displayed_after_submit: self.check_page_for_string( check_str ) self.home() + def share_histories_with_users( self, ids, emails, strings_displayed=[], strings_displayed_after_submit=[], action=None, action_strings_displayed=[] ): """Share one or more histories with one or more different users""" @@ -389,6 +447,7 @@ for check_str in action_strings_displayed: self.check_page_for_string( check_str ) self.home() + def unshare_history( self, history_id, user_id, strings_displayed=[] ): """Unshare a history that has been shared with another user""" self.visit_url( "%s/history/list?id=%s&operation=share+or+publish" % ( self.url, history_id ) ) @@ -396,12 +455,14 @@ self.check_page_for_string( check_str ) self.visit_url( "%s/history/sharing?unshare_user=%s&id=%s" % ( self.url, user_id, history_id ) ) self.home() + def switch_history( self, id='', name='' ): """Switches to a history in the current list of histories""" self.visit_url( "%s/history/list?operation=switch&id=%s" % ( self.url, id ) ) if name: - self.check_history_for_string( escape( name ) ) + self.check_history_for_exact_string( name ) self.home() + def view_stored_active_histories( self, strings_displayed=[] ): self.home() self.visit_page( "history/list" ) @@ -698,11 +759,13 @@ # if the server's env has GALAXY_TEST_SAVE, save the output file to that dir if self.keepOutdir: ofn = os.path.join( self.keepOutdir, os.path.basename( local_name ) ) + log.debug( 'keepoutdir: %s, ofn: %s', self.keepOutdir, ofn ) try: shutil.copy( temp_name, ofn ) except Exception, exc: error_log_msg = ( 'TwillTestCase could not save output file %s to %s: ' % ( temp_name, ofn ) ) error_log_msg += str( exc ) + log.error( error_log_msg, exc_info=True ) else: log.debug('## GALAXY_TEST_SAVE=%s. saved %s' % ( self.keepOutdir, ofn ) )

diff -r e19bf2b117638221414239698f840730a2cd0569 -r 795a1799e7dcf092b14f7e2a2dba3fb389403531 test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py +++ b/test/functional/test_history_functions.py @@ -250,8 +250,7 @@ sa_session.query( galaxy.model.HistoryDatasetAssociation ) .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3.id, galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) - .first() - ) + .first() ) assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" self.delete_history_item( str( hda_2_bed.id ) )

@@ -260,8 +259,7 @@ sa_session.query( galaxy.model.HistoryDatasetAssociation ) .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3.id, galaxy.model.HistoryDatasetAssociation.table.c.name=='3.bed' ) ) - .first() - ) + .first() ) assert hda_3_bed is not None, "Problem retrieving hda_3_bed from database" self.delete_history_item( str( hda_3_bed.id ) )

@@ -281,39 +279,52 @@ self.view_stored_active_histories( strings_displayed=[ "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 = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3_clone2.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) \ - .first() + hda_2_bed = ( + sa_session.query( 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 = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3_clone2.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='3.bed' ) ) \ - .first() + hda_3_bed = ( + sa_session.query( 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 ) + # check for encoded ids + # - these will be available bc the refreshed page will have bootstrapped json for the hdas + #NOTE: that these WON'T be available when refreshes become less common + # (when the backbone.js is fully integrated and refreshes aren't used after every history function) + self.check_history_for_exact_string( self.security.encode_id( hda_2_bed.id ), show_deleted=True ) + self.check_history_for_exact_string( self.security.encode_id( hda_3_bed.id ), show_deleted=True ) + # Test cloning only active datasets - self.clone_history( self.security.encode_id( history3.id ), - 'active', - strings_displayed_after_submit=[ 'is now included in your previously stored histories.' ] ) + self.clone_history( + self.security.encode_id( history3.id ), + 'active', + strings_displayed_after_submit=[ 'is now included in your previously stored histories.' ] ) global history3_clone3 - history3_clone3 = sa_session.query( 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() + history3_clone3 = ( + sa_session.query( 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( strings_displayed = ["Clone of '%s'" % history3.name ] ) - # Switch to the cloned history to make sure activatable datasets were cloned + + # Switch to the cloned history to make sure ONLY activatable datasets were cloned self.switch_history( id=self.security.encode_id( history3_clone3.id ) ) # Make sure the deleted datasets are NOT included in the cloned history + # - again using the bootstrapped json for the hdas try: - self.check_history_for_string( 'This dataset has been deleted.', show_deleted=True ) + self.check_history_for_exact_string( '"deleted": true', show_deleted=True ) + #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 @@ -349,6 +360,7 @@ # Shared history3 should be in regular_user3's list of shared histories self.view_shared_histories( cstrings_displayed=[ history3.name, admin_user.email ] ) """ + def test_045_change_permissions_on_current_history( self ): """Testing changing permissions on the current history""" # Logged in as regular_user3 @@ -402,6 +414,7 @@ current_history_permissions.sort() if current_history_permissions != history5_default_permissions: raise AssertionError, "With logout and login, the history default permissions are not preserved" + def test_050_sharing_restricted_history_by_making_datasets_public( self ): """Testing sharing a restricted history by making the datasets public""" # Logged in as admin_user @@ -432,6 +445,7 @@ self.check_history_for_string( 'chr1' ) self.logout() self.login( email=admin_user.email ) + def test_055_sharing_restricted_history_by_making_new_sharing_role( self ): """Testing sharing a restricted history by associating a new sharing role with protected datasets""" # At this point, history5 should have 1 item, 1.bed, which is public. We'll add another @@ -506,6 +520,7 @@ self.display_history_item( str( hda_2_bed.id ), strings_displayed=[ 'chr1' ] ) # Delete the clone so the next test will be valid self.delete_history( id=self.security.encode_id( history5_clone2.id ) ) + def test_060_sharing_restricted_history_with_multiple_users_by_changing_no_permissions( self ): """Testing sharing a restricted history with multiple users, making no permission changes""" # Logged in as regular_user2 @@ -515,10 +530,12 @@ # regular_user2 should be able to access history5's 2.bed dataset since it is associated with a # sharing role, and regular_user3 should be able to access history5's 1.bed, but not 2.bed even # though they can see it in their shared history. + # We first need to unshare history5 from regular_user2 so that we can re-share it. self.unshare_history( self.security.encode_id( history5.id ), self.security.encode_id( regular_user2.id ), strings_displayed=[ regular_user1.email, regular_user2.email ] ) + # Make sure the history was unshared correctly self.logout() self.login( email=regular_user2.email ) @@ -528,11 +545,14 @@ raise AssertionError, "history5 still shared with regular_user2 after unsharing it with that user." except: pass + self.logout() self.login( admin_user.email ) email = '%s,%s' % ( regular_user2.email, regular_user3.email ) - strings_displayed_after_submit = [ 'The following datasets can be shared with %s with no changes' % email, - 'The following datasets can be shared with %s by updating their permissions' % email ] + strings_displayed_after_submit = [ + 'The following datasets can be shared with %s with no changes' % email, + 'The following datasets can be shared with %s by updating their permissions' % email ] + # history5 will be shared with regular_user1, regular_user2 and regular_user3 self.share_current_history( email, strings_displayed_after_submit=strings_displayed_after_submit, @@ -547,30 +567,35 @@ 'activatable', strings_displayed_after_submit=[ 'is now included in your previously stored histories.' ] ) global history5_clone3 - history5_clone3 = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==regular_user2.id ) ) \ - .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ - .first() + history5_clone3 = ( + sa_session.query( galaxy.model.History ) + .filter( and_( galaxy.model.History.table.c.deleted==False, + galaxy.model.History.table.c.user_id==regular_user2.id ) ) + .order_by( desc( galaxy.model.History.table.c.create_time ) ) + .first() ) assert history5_clone3 is not None, "Problem retrieving history5_clone3 from database" + # Check list of histories to make sure shared history3 was cloned self.view_stored_active_histories( strings_displayed=[ "Clone of '%s'" % history5.name ] ) # Make sure the dataset is accessible self.switch_history( id=self.security.encode_id( history5_clone3.id ), name=history5_clone3.name ) - # Make sure both datasets are in the history + # Make sure both datasets are in the history self.check_history_for_string( '1.bed' ) self.check_history_for_string( '2.bed' ) # Get both new hdas from the db that were created for the shared history - hda_1_bed = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone3.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='1.bed' ) ) \ - .first() + hda_1_bed = ( + sa_session.query( galaxy.model.HistoryDatasetAssociation ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone3.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='1.bed' ) ) + .first() ) assert hda_1_bed is not None, "Problem retrieving hda_1_bed from database" - hda_2_bed = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone3.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) \ - .first() + hda_2_bed = ( + sa_session.query( galaxy.model.HistoryDatasetAssociation ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone3.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) + .first() ) assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" + # Make sure 1.bed is accessible since it is public self.display_history_item( str( hda_1_bed.id ), strings_displayed=[ 'chr1' ] ) # Make sure 2.bed is accessible since it is associated with a sharing role @@ -582,34 +607,39 @@ self.login( email=regular_user3.email ) # Shared history5 should be in regular_user2's list of shared histories self.view_shared_histories( strings_displayed=[ history5.name, admin_user.email ] ) + # Clone restricted history5 self.clone_history( self.security.encode_id( history5.id ), 'activatable', strings_displayed_after_submit=[ 'is now included in your previously stored histories.' ] ) global history5_clone4 - history5_clone4 = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==regular_user3.id ) ) \ - .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ - .first() + history5_clone4 = ( + sa_session.query( galaxy.model.History ) + .filter( and_( galaxy.model.History.table.c.deleted==False, + galaxy.model.History.table.c.user_id==regular_user3.id ) ) + .order_by( desc( galaxy.model.History.table.c.create_time ) ) + .first() ) assert history5_clone4 is not None, "Problem retrieving history5_clone4 from database" + # Check list of histories to make sure shared history3 was cloned self.view_stored_active_histories( strings_displayed=[ "Clone of '%s'" % history5.name ] ) # Make sure the dataset is accessible self.switch_history( id=self.security.encode_id( history5_clone4.id ), name=history5_clone4.name ) - # Make sure both datasets are in the history + # Make sure both datasets are in the history self.check_history_for_string( '1.bed' ) self.check_history_for_string( '2.bed' ) # Get both new hdas from the db that were created for the shared history - hda_1_bed = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone4.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='1.bed' ) ) \ - .first() + hda_1_bed = ( + sa_session.query( galaxy.model.HistoryDatasetAssociation ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone4.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='1.bed' ) ) + .first() ) assert hda_1_bed is not None, "Problem retrieving hda_1_bed from database" - hda_2_bed = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone4.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) \ - .first() + hda_2_bed = ( + sa_session.query( galaxy.model.HistoryDatasetAssociation ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone4.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) + .first() ) assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" # Make sure 1.bed is accessible since it is public self.display_history_item( str( hda_1_bed.id ), strings_displayed=[ 'chr1' ] ) @@ -619,20 +649,31 @@ raise AssertionError, "History item 2.bed is accessible by user %s when is should not be" % regular_user3.email except: pass - self.check_history_for_string( 'You do not have permission to view this dataset' ) + + # check the history page json for hda_2_bed and if it's accessible + def hda_2_bed_is_inaccessible( hda_list ): + for hda in hda_list: + if hda[ 'id' ] == self.security.encode_id( hda_2_bed.id ): + return ( not hda[ 'accessible' ] ) + return False + self.check_history_json( r'\bhdas\s*=\s*(.*);', hda_2_bed_is_inaccessible ) + # Admin users can view all datasets ( using the history/view feature ), so make sure 2.bed is accessible to the admin self.logout() self.login( email=admin_user.email ) self.view_history( str( hda_2_bed.history_id ), strings_displayed=[ '<td>NM_005997_cds_0_0_chr1_147962193_r</td>' ] ) self.logout() self.login( email=regular_user3.email ) + # Delete the clone so the next test will be valid self.delete_history( id=self.security.encode_id( history5_clone4.id ) ) + def test_065_sharing_private_history_by_choosing_to_not_share( self ): """Testing sharing a restricted history with multiple users by choosing not to share""" - # Logged in as regular_user3 + # Logged in as regular_user3 - login as admin self.logout() self.login( email=admin_user.email ) + # Unshare history5 from regular_user2 self.unshare_history( self.security.encode_id( history5.id ), self.security.encode_id( regular_user2.id ), @@ -641,7 +682,8 @@ self.unshare_history( self.security.encode_id( history5.id ), self.security.encode_id( regular_user3.id ), strings_displayed=[ regular_user1.email, regular_user3.email ] ) - # Make sure the history was unshared correctly + + # Make sure the histories were unshared correctly self.logout() self.login( email=regular_user2.email ) self.visit_page( "root/history_options" ) @@ -650,6 +692,7 @@ raise AssertionError, "history5 still shared with regular_user2 after unshaing it with that user." except: pass + self.logout() self.login( email=regular_user3.email ) self.visit_page( "root/history_options" ) @@ -660,42 +703,73 @@ pass self.logout() self.login( email=admin_user.email ) + def test_070_history_show_and_hide_deleted_datasets( self ): """Testing displaying deleted history items""" + #NOTE: due to the new client-side rendering of the history, this test isn't very apt + # (a) searching for strings in the dom doesn't work (they won't be twill's html) and + # (b) all datasets are included in the bootstrapped hda json regardless of the show_deleted setting + #CE: for now, I'm changing this to simply check whether the show_deleted flag + # is being properly passed to the history control + #TODO: this test needs to be moved to client-side testing framework (selenium or other) + # Logged in as admin_user + # create a new history and upload a new hda (1.bed) into it self.new_history( name=urllib.quote( 'show hide deleted datasets' ) ) - latest_history = sa_session.query( 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() + latest_history = ( + sa_session.query( 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 latest_history is not None, "Problem retrieving latest_history from database" self.upload_file('1.bed', dbkey='hg18') - latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ - .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ - .first() + latest_hda = ( + sa_session.query( galaxy.model.HistoryDatasetAssociation ) + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) + .first() ) + + # delete that item and make sure the 'history empty' message shows self.home() + log.info( 'deleting last hda' ) self.delete_history_item( str( latest_hda.id ) ) - self.check_history_for_string( 'Your history is empty' ) + # check the historyPanel settings.show_deleted for a null json value (no show_deleted in query string) + self.check_history_json( r'\bpage_show_deleted\s*=\s*(.*),', lambda x: x == None ) + + # reload this history with the show_deleted flag set in the query string + # the deleted dataset should be there with the proper 'deleted' text self.home() - self.visit_url( "%s/history/?show_deleted=True" % self.url ) - self.check_page_for_string( 'This dataset has been deleted.' ) - self.check_page_for_string( '1.bed' ) + log.info( 'turning show_deleted on' ) + #self.visit_url( "%s/history/?show_deleted=True" % self.url ) + # check the historyPanel settings.show_deleted for a true json value + self.check_history_json( r'\bpage_show_deleted\s*=\s*(.*),', lambda x: x == True, show_deleted=True ) + + # reload this history again with the show_deleted flag set TO FALSE in the query string + # make sure the 'history empty' message shows self.home() - self.visit_url( "%s/history/?show_deleted=False" % self.url ) - self.check_page_for_string( 'Your history is empty' ) + log.info( 'turning show_deleted off' ) + #self.visit_url( "%s/history/?show_deleted=False" % self.url ) + # check the historyPanel settings.show_deleted for a false json value + self.check_history_json( r'\bpage_show_deleted\s*=\s*(.*),', lambda x: x == False, show_deleted=False ) + + # delete this history self.delete_history( self.security.encode_id( latest_history.id ) ) + def test_075_deleting_and_undeleting_history_items( self ): """Testing deleting and un-deleting history items""" # logged in as admin_user + # Deleting the current history in the last method created a new history - latest_history = sa_session.query( 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() + latest_history = ( + sa_session.query( 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 latest_history is not None, "Problem retrieving latest_history from database" - self.rename_history( self.security.encode_id( latest_history.id ), latest_history.name, new_name=urllib.quote( 'delete undelete history items' ) ) + + self.rename_history( self.security.encode_id( latest_history.id ), + latest_history.name, new_name=urllib.quote( 'delete undelete history items' ) ) # Add a new history item self.upload_file( '1.bed', dbkey='hg15' ) latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ @@ -722,6 +796,7 @@ self.check_page_for_string( '1.bed' ) self.check_page_for_string( 'hg15' ) self.delete_history( self.security.encode_id( latest_history.id ) ) + def test_080_copying_history_items_between_histories( self ): """Testing copying history items between histories""" # logged in as admin_user @@ -776,6 +851,7 @@ self.check_history_for_string( hda1.name ) self.delete_history( self.security.encode_id( history6.id ) ) self.delete_history( self.security.encode_id( history7.id ) ) + def test_085_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to to be valid""" # logged in as admin_user

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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