1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/299e9c8d29c5/ Changeset: 299e9c8d29c5 User: davebgx Date: 2014-04-23 22:46:14 Summary: Twill test framework cleanup. Fix functional tests for history functions. Affected #: 6 files

diff -r 0bc0fd94aaa4e7c1ede3e291b6c58544c83fc786 -r 299e9c8d29c5cd0b1603c38e6d805ecb33b1a58f test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -14,6 +14,7 @@ import urllib import zipfile

+from urlparse import urlparse from galaxy.web import security from galaxy.web.framework.helpers import iff from galaxy.util.json import from_json_string @@ -63,7 +64,6 @@ os.makedirs(self.keepOutdir) except: pass - self.home()

# Functions associated with files def files_diff( self, file1, file2, attributes=None ): @@ -232,7 +232,6 @@ tc.config("readonly_controls_writeable", 1) tc.fv( "tool_form", "NAME", name ) tc.submit( "runtool_btn" ) - self.home() except AssertionError, err: errmsg = "Uploading file resulted in the following exception. Make sure the file (%s) exists. " % filename errmsg += str( err ) @@ -251,13 +250,12 @@

def upload_url_paste( self, url_paste, ftype='auto', dbkey='unspecified (?)' ): """Pasted data in the upload utility""" - self.visit_page( "tool_runner/index?tool_id=upload1" ) + self.visit_url( "/tool_runner/index?tool_id=upload1" ) try: self.refresh_form( "file_type", ftype ) #Refresh, to support composite files tc.fv( "tool_form", "dbkey", dbkey ) tc.fv( "tool_form", "url_paste", url_paste ) tc.submit( "runtool_btn" ) - self.home() except Exception, e: errmsg = "Problem executing upload utility using url_paste: %s" % str( e ) raise AssertionError( errmsg ) @@ -271,8 +269,8 @@ # Wait for upload processing to finish (TODO: this should be done in each test case instead) self.wait()

- def json_from_url( self, url ): - self.visit_url( url ) + def json_from_url( self, url, params={} ): + self.visit_url( url, params ) return from_json_string( self.last_page() )

# Functions associated with histories @@ -283,8 +281,8 @@ params = dict() if show_deleted is not None: params[ 'deleted' ] = show_deleted - api_url = '/api/histories/%s/contents?%s' % ( encoded_history_id, urllib.urlencode( params ) ) - json_data = self.json_from_url( api_url ) + api_url = '/api/histories/%s/contents' % encoded_history_id + json_data = self.json_from_url( api_url, params=params ) if show_deleted is not None: hdas = [] for hda in json_data: @@ -296,8 +294,8 @@ json_data = hdas if show_details: params[ 'details' ] = ','.join( [ hda[ 'id' ] for hda in json_data ] ) - api_url = '/api/histories/%s/contents?%s' % ( encoded_history_id, urllib.urlencode( params ) ) - json_data = self.json_from_url( api_url ) + api_url = '/api/histories/%s/contents' % encoded_history_id + json_data = self.json_from_url( api_url, params=params ) log.debug( 'detailed url: %s' % api_url ) log.debug( 'detailed json data: %s' % json_data ) return json_data @@ -314,19 +312,18 @@

def check_history_for_errors( self ): """Raises an exception if there are errors in a history""" - self.home() - self.visit_page( "history" ) + self.visit_url( "/history" ) 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 ): """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" ) + params = dict( show_deleted=True ) + self.visit_url( "/history", params ) else: - self.visit_page( "history" ) + self.visit_url( "/history" ) for subpatt in patt.split(): try: tc.find( subpatt ) @@ -334,22 +331,19 @@ fname = self.write_temp_file( tc.browser.get_html() ) 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" ) + self.visit_url( "/history?show_deleted=True" ) else: - self.visit_page( "history" ) + self.visit_url( "/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, check_fn, show_deleted=None ): """ @@ -368,8 +362,6 @@ errmsg = ( "json could not be read\npage content written to '%s'" % ( fname ) ) raise AssertionError( errmsg )

- self.home() - def is_history_empty( self ): """ Uses history page JSON to determine whether this history is empty @@ -404,20 +396,15 @@ history_list = self.get_histories_as_data_list() self.assertTrue( history_list ) num_deleted = len( id.split( ',' ) ) - self.home() - self.visit_page( "history/list?operation=delete&id=%s" % ( id ) ) - + self.visit_url( "/history/list?operation=delete&id=%s" % ( id ) ) 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() - self.visit_page( "history/delete_current" ) + self.visit_url( "/history/delete_current" ) 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""" @@ -433,24 +420,21 @@

def history_as_xml_tree( self, show_deleted=False ): """Returns a parsed xml object of a history""" - self.home() - self.visit_page( 'history?as_xml=True&show_deleted=%s' % show_deleted ) + self.visit_url( '/history?as_xml=True&show_deleted=%s' % show_deleted ) 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() - self.visit_page( 'history/list_as_xml' ) + self.visit_url( '/history/list_as_xml' ) 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() - self.visit_page( "root/history_options" ) + self.visit_url( "/root/history_options" ) if user: self.check_page_for_string( 'Previously</a> stored histories' ) if active_datasets: @@ -465,35 +449,28 @@ self.check_page_for_string( 'Show deleted</a> datasets in current history' ) 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() if name: self.visit_url( "%s/history_new?name=%s" % ( self.url, name ) ) else: self.visit_url( "%s/history_new" % self.url ) self.check_page_for_string( 'New history created' ) assert self.is_history_empty(), 'Creating new history did not result in an empty history.' - self.home()

def rename_history( self, id, old_name, new_name ): """Rename an existing history""" - self.home() - self.visit_page( "history/rename?id=%s&name=%s" % ( id, new_name ) ) + self.visit_url( "/history/rename", params=dict( id=id, name=new_name ) ) 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: - self.home() - self.visit_page( "history?id=%s" % self.history_id ) + self.visit_url( "/history", params=dict( id=self.history_id ) ) 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=[] ): @@ -514,7 +491,6 @@ tc.submit( "share_restricted_button" ) 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=[] ): @@ -533,97 +509,70 @@

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 ) ) + self.visit_url( "/history/sharing", params=dict( id=history_id ) ) for check_str in strings_displayed: 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() + self.visit_url( "/history/sharing", params=dict( unshare_user=user_id, id=history_id ) )

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 ) ) + params = dict( operation='switch', id=id ) + self.visit_url( "/history/list", params ) if 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" ) + self.visit_url( "/history/list" ) self.check_page_for_string( 'Saved Histories' ) self.check_page_for_string( 'operation=Rename' ) self.check_page_for_string( 'operation=Switch' ) self.check_page_for_string( 'operation=Delete' ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.home()

def view_stored_deleted_histories( self, strings_displayed=[] ): - self.home() - self.visit_page( "history/list?f-deleted=True" ) + self.visit_url( "/history/list?f-deleted=True" ) self.check_page_for_string( 'Saved Histories' ) self.check_page_for_string( 'operation=Undelete' ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.home()

def view_shared_histories( self, strings_displayed=[] ): - self.home() - self.visit_page( "history/list_shared" ) + self.visit_url( "/history/list_shared" ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.home()

def copy_history( self, history_id, copy_choice, strings_displayed=[], strings_displayed_after_submit=[] ): - self.home() - self.visit_page( "history/copy?id=%s" % history_id ) + self.visit_url( "/history/copy?id=%s" % history_id ) for check_str in strings_displayed: self.check_page_for_string( check_str ) tc.fv( '1', 'copy_choice', copy_choice ) tc.submit( 'copy_choice_button' ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) - self.home()

def make_accessible_via_link( self, history_id, strings_displayed=[], strings_displayed_after_submit=[] ): - self.home() - self.visit_page( "history/list?operation=share+or+publish&id=%s" % history_id ) - for check_str in strings_displayed: - self.check_page_for_string( check_str ) # twill barfs on this form, possibly because it contains no fields, but not sure. # In any case, we have to mimic the form submission - self.home() - self.visit_page( 'history/sharing?id=%s&make_accessible_via_link=True' % history_id ) - for check_str in strings_displayed_after_submit: - self.check_page_for_string( check_str ) - self.home() + self.visit_url( '/history/sharing', dict( id=history_id, make_accessible_via_link=True ) ) + self.check_for_strings( strings_displayed=strings_displayed_after_submit )

def disable_access_via_link( self, history_id, strings_displayed=[], strings_displayed_after_submit=[] ): - self.home() - self.visit_page( "history/list?operation=share+or+publish&id=%s" % history_id ) - for check_str in strings_displayed: - self.check_page_for_string( check_str ) # twill barfs on this form, possibly because it contains no fields, but not sure. # In any case, we have to mimic the form submission - self.home() - self.visit_page( 'history/sharing?id=%s&disable_link_access=True' % history_id ) - for check_str in strings_displayed_after_submit: - self.check_page_for_string( check_str ) - self.home() + self.visit_url( '/history/sharing', dict( id=history_id, disable_link_access=True ) ) + self.check_for_strings( strings_displayed=strings_displayed_after_submit )

def import_history_via_url( self, history_id, email, strings_displayed_after_submit=[] ): - self.home() - self.visit_page( "history/imp?&id=%s" % history_id ) - for check_str in strings_displayed_after_submit: - self.check_page_for_string( check_str ) - self.home() + self.visit_url( "/history/imp", params=dict( id=history_id ) ) + self.check_for_strings( strings_displayed=strings_displayed_after_submit )

# Functions associated with datasets (history items) and meta data def _get_job_stream_output( self, hda_id, stream, format ): - self.visit_page( "datasets/%s/%s" % ( self.security.encode_id( hda_id ), stream ) ) + self.visit_url( "/datasets/%s/%s" % ( self.security.encode_id( hda_id ), stream ) )

output = self.last_page() return self._format_stream( output, stream, format ) @@ -657,7 +606,7 @@ elem = data_list[-1] hid = int( elem.get('hid') ) self.assertTrue( hid ) - self.visit_page( "dataset/edit?hid=%s" % hid ) + self.visit_url( "/dataset/edit?hid=%s" % hid ) for subpatt in patt.split(): tc.find(subpatt)

@@ -686,19 +635,16 @@ self.visit_url( '%s/datasets/%s/display/' % ( self.url, self.security.encode_id( hda_id ) ) ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.home()

def view_history( self, history_id, strings_displayed=[] ): """Displays a history for viewing""" self.visit_url( '%s/history/view?id=%s' % ( self.url, self.security.encode_id( history_id ) ) ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.home()

def edit_hda_attribute_info( self, hda_id, new_name='', new_info='', new_dbkey='', new_startcol='', strings_displayed=[], strings_not_displayed=[] ): """Edit history_dataset_association attribute information""" - self.home() self.visit_url( "%s/datasets/%s/edit" % ( self.url, self.security.encode_id( hda_id ) ) ) submit_required = False self.check_page_for_string( 'Edit Attributes' ) @@ -725,7 +671,6 @@ raise AssertionError( "String (%s) incorrectly displayed on Edit Attributes page." % check_str ) except: pass - self.home()

def check_hda_attribute_info( self, hda_id, strings_displayed=[] ): """Edit history_dataset_association attribute information""" @@ -734,7 +679,6 @@

def auto_detect_metadata( self, hda_id ): """Auto-detect history_dataset_association metadata""" - self.home() self.visit_url( "%s/datasets/%s/edit" % ( self.url, self.security.encode_id( hda_id ) ) ) self.check_page_for_string( 'This will inspect the dataset and attempt' ) tc.fv( 'auto_detect', 'detect', 'Auto-detect' ) @@ -745,28 +689,23 @@ except AssertionError: self.check_page_for_string( 'Attributes updated' ) #self.check_page_for_string( 'Attributes updated' ) - self.home()

def convert_format( self, hda_id, target_type ): """Convert format of history_dataset_association""" - self.home() self.visit_url( "%s/datasets/%s/edit" % ( self.url, self.security.encode_id( hda_id ) ) ) self.check_page_for_string( 'This will inspect the dataset and attempt' ) tc.fv( 'convert_data', 'target_type', target_type ) tc.submit( 'convert_data' ) self.check_page_for_string( 'The file conversion of Convert BED to GFF on data' ) self.wait() # wait for the format convert tool to finish before returning - self.home()

def change_datatype( self, hda_id, datatype ): """Change format of history_dataset_association""" - self.home() self.visit_url( "%s/datasets/%s/edit" % ( self.url, self.security.encode_id( hda_id ) ) ) self.check_page_for_string( 'This will change the datatype of the existing dataset but' ) tc.fv( 'change_datatype', 'datatype', datatype ) tc.submit( 'change' ) self.check_page_for_string( 'Changed the type of dataset' ) - self.home()

def copy_history_item( self, source_dataset_id=None, target_history_id=None, all_target_history_ids=[], deleted_history_ids=[] ): @@ -774,7 +713,6 @@ Copy 1 history_dataset_association to 1 history (Limited by twill since it doesn't support multiple field names, such as checkboxes """ - self.home() self.visit_url( "%s/dataset/copy_datasets?source_dataset_ids=%s" % ( self.url, source_dataset_id ) ) self.check_page_for_string( 'Source History:' ) # Make sure all of users active histories are displayed @@ -792,7 +730,6 @@ tc.submit( 'do_copy' ) check_str = '1 dataset copied to 1 history' self.check_page_for_string( check_str ) - self.home()

def get_hids_in_history( self ): """Returns the list of hid values for items in a history""" @@ -915,11 +852,10 @@ def __default_dataset_fetcher( self ): def fetcher( hda_id, filename=None ): if filename is None: - page_url = "display?encoded_id=%s" % hda_id - self.home() # I assume this is not needed. + page_url = "/display?encoded_id=%s" % hda_id else: - page_url = "datasets/%s/display/%s" % ( hda_id, filename ) - self.visit_page( page_url ) + page_url = "/datasets/%s/display/%s" % ( hda_id, filename ) + self.visit_url( page_url ) data = self.last_page() return data

@@ -1019,7 +955,8 @@ def create( self, cntrller='user', email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='' ): # HACK: don't use panels because late_javascripts() messes up the twill browser and it # can't find form fields (and hence user can't be logged in). - self.visit_url( "%s/user/create?cntrller=%s&use_panels=False" % ( self.url, cntrller ) ) + params = dict( cntrller=cntrller, use_panels=False ) + self.visit_url( "/user/create", params ) tc.fv( 'registration', 'email', email ) tc.fv( 'registration', 'redirect', redirect ) tc.fv( 'registration', 'password', password ) @@ -1095,7 +1032,6 @@ tc.submit( "edit_user_info_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) - self.home()

def user_set_default_permissions( self, cntrller='user', permissions_out=[], permissions_in=[], role_id='2' ): # role.id = 2 is Private Role for test2@bx.psu.edu @@ -1112,7 +1048,6 @@ url = "%s&%s=%s" % ( url, key, str( role_id ) ) self.visit_url( "%s/%s" % ( self.url, url ) ) self.check_page_for_string( 'Default new history permissions have been changed.' ) - self.home()

def history_set_default_permissions( self, permissions_out=[], permissions_in=[], role_id=3 ): # role.id = 3 is Private Role for test3@bx.psu.edu # NOTE: Twill has a bug that requires the ~/user/permissions page to contain at least 1 option value @@ -1126,10 +1061,8 @@ for pi in permissions_in: key = '%s_in' % pi url = "%s&%s=%s" % ( url, key, str( role_id ) ) - self.home() self.visit_url( "%s/%s" % ( self.url, url ) ) self.check_page_for_string( 'Default history permissions have been changed.' ) - self.home()

def login( self, email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='' ): # test@bx.psu.edu is configured as an admin user @@ -1139,14 +1072,12 @@ # The acount has previously been created, so just login. # HACK: don't use panels because late_javascripts() messes up the twill browser and it # can't find form fields (and hence user can't be logged in). - self.visit_url( "%s/user/login?use_panels=False" % self.url ) + self.visit_url( "/user/login?use_panels=False" ) self.submit_form( 1, 'login_button', email=email, redirect=redirect, password=password )

def logout( self ): - self.home() - self.visit_page( "user/logout" ) + self.visit_url( "%s/user/logout" % self.url ) self.check_page_for_string( "You have been logged out" ) - self.home()

# Functions associated with browsers, cookies, HTML forms and page visits

@@ -1208,9 +1139,6 @@ """Clears a form""" tc.formclear(str(form))

- def home( self ): - self.visit_url( self.url ) - def last_page( self ): return tc.browser.get_html()

@@ -1383,16 +1311,30 @@ # Submit for refresh tc.submit( '___refresh_grouping___' )

- def visit_page( self, page ): - # tc.go("./%s" % page) - if not page.startswith( "/" ): - page = "/" + page - tc.go( self.url + page ) - tc.code( 200 ) - - def visit_url( self, url ): - tc.go("%s" % url) - tc.code( 200 ) + def visit_url( self, url, params=None, checkbox_params=None, allowed_codes=[ 200 ] ): + if params is None: + params = dict() + parsed_url = urlparse( url ) + if len( parsed_url.netloc ) == 0: + url = 'http://%s:%s%s' % ( self.host, self.port, parsed_url.path ) + else: + url = '%s://%s%s' % ( parsed_url.scheme, parsed_url.netloc, parsed_url.path ) + if parsed_url.query: + for query_parameter in parsed_url.query.split( '&' ): + key, value = query_parameter.split( '=' ) + params[ key ] = value + if params: + url += '?%s' % urllib.urlencode( params ) + if checkbox_params is not None: + if params or parsed_url.query: + url += '&%s&%s' % ( urllib.urlencode( checkbox_params ), urllib.urlencode( checkbox_params ) ) + else: + url += '?%s&%s' % ( urllib.urlencode( checkbox_params ), urllib.urlencode( checkbox_params ) ) + new_url = tc.go( url ) + return_code = tc.browser.get_code() + assert return_code in allowed_codes, 'Invalid HTTP return code %s, allowed codes: %s' % \ + ( return_code, ', '.join( str( code ) for code in allowed_codes ) ) + return new_url

"""Functions associated with Galaxy tools""" def run_tool( self, tool_id, repeat_name=None, **kwd ): @@ -1412,9 +1354,9 @@ def run_ucsc_main( self, track_params, output_params ): """Gets Data From UCSC""" tool_id = "ucsc_table_direct1" - track_string = urllib.urlencode( track_params ) galaxy_url = urllib.quote_plus( "%s/tool_runner/index?" % self.url ) - self.visit_url( "http://genome.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=%s&hgta_compressType=..." % ( galaxy_url, tool_id, track_string ) ) + track_params.update( dict( GALAXY_URL=galaxy_url, hgta_compressType='none', tool_id=tool_id ) ) + self.visit_url( "http://genome.ucsc.edu/cgi-bin/hgTables", params=track_params ) tc.fv( "mainForm", "hgta_doTopSubmit", "get output" ) self.submit_form( button="get output" ) tc.fv( 2, "hgta_doGalaxyQuery", "Send query to Galaxy" ) @@ -1486,41 +1428,32 @@

def reset_password_as_admin( self, user_id, password='testreset' ): """Reset a user password""" - self.home() self.visit_url( "%s/admin/reset_user_password?id=%s" % ( self.url, user_id ) ) tc.fv( "1", "password", password ) tc.fv( "1", "confirm", password ) tc.submit( "reset_user_password_button" ) self.check_page_for_string( "Passwords reset for 1 user." ) - self.home()

def mark_user_deleted( self, user_id, email='' ): """Mark a user as deleted""" - self.home() self.visit_url( "%s/admin/users?operation=delete&id=%s" % ( self.url, user_id ) ) check_str = "Deleted 1 users" self.check_page_for_string( check_str ) - self.home()

def undelete_user( self, user_id, email='' ): """Undelete a user""" - self.home() self.visit_url( "%s/admin/users?operation=undelete&id=%s" % ( self.url, user_id ) ) check_str = "Undeleted 1 users" self.check_page_for_string( check_str ) - self.home()

def purge_user( self, user_id, email ): """Purge a user account""" - self.home() self.visit_url( "%s/admin/users?operation=purge&id=%s" % ( self.url, user_id ) ) check_str = "Purged 1 users" self.check_page_for_string( check_str ) - self.home()

def manage_roles_and_groups_for_user( self, user_id, in_role_ids=[], out_role_ids=[], in_group_ids=[], out_group_ids=[], strings_displayed=[] ): - self.home() url = "%s/admin/manage_roles_and_groups_for_user?id=%s" % ( self.url, user_id ) if in_role_ids: url += "&in_roles=%s" % ','.join( in_role_ids ) @@ -1535,7 +1468,6 @@ self.visit_url( url ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.home() # Tests associated with roles

def browse_roles( self, strings_displayed=[] ): @@ -1552,16 +1484,17 @@ private_role='', strings_displayed=[] ): """Create a new role""" - url = "%s/admin/roles?operation=create&create_role_button=Save&name=%s&description=%s" % \ - ( self.url, name.replace( ' ', '+' ), description.replace( ' ', '+' ) ) + url = "/admin/roles" + url_params = dict( operation='create', create_role_button='Save', name=name, description=description ) if in_user_ids: - url += "&in_users=%s" % ','.join( in_user_ids ) + url_params[ 'in_users' ] = ','.join( in_user_ids ) if in_group_ids: - url += "&in_groups=%s" % ','.join( in_group_ids ) + url_params[ 'in_groups' ] = ','.join( in_group_ids ) if create_group_for_role == 'yes': - url += '&create_group_for_role=yes&create_group_for_role=yes' - self.home() - self.visit_url( url ) + checkbox_params = dict( create_group_for_role='yes' ) + else: + checkbox_params = None + self.visit_url( url, url_params, checkbox_params=checkbox_params ) for check_str in strings_displayed: self.check_page_for_string( check_str ) if private_role: @@ -1573,47 +1506,36 @@ except AssertionError: # Reaching here is the behavior we want since no private roles should be displayed pass - self.home() self.visit_url( "%s/admin/roles" % self.url ) self.check_page_for_string( name ) - self.home()

def rename_role( self, role_id, name='Role One Renamed', description='This is Role One Re-described' ): """Rename a role""" - self.home() self.visit_url( "%s/admin/roles?operation=rename&id=%s" % ( self.url, role_id ) ) self.check_page_for_string( 'Change role name and description' ) tc.fv( "1", "name", name ) tc.fv( "1", "description", description ) tc.submit( "rename_role_button" ) - self.home()

def mark_role_deleted( self, role_id, role_name ): """Mark a role as deleted""" - self.home() self.visit_url( "%s/admin/roles?operation=delete&id=%s" % ( self.url, role_id ) ) check_str = "Deleted 1 roles: %s" % role_name self.check_page_for_string( check_str ) - self.home()

def undelete_role( self, role_id, role_name ): """Undelete an existing role""" - self.home() self.visit_url( "%s/admin/roles?operation=undelete&id=%s" % ( self.url, role_id ) ) check_str = "Undeleted 1 roles: %s" % role_name self.check_page_for_string( check_str ) - self.home()

def purge_role( self, role_id, role_name ): """Purge an existing role""" - self.home() self.visit_url( "%s/admin/roles?operation=purge&id=%s" % ( self.url, role_id ) ) check_str = "Purged 1 roles: %s" % role_name self.check_page_for_string( check_str ) - self.home()

def associate_users_and_groups_with_role( self, role_id, role_name, user_ids=[], group_ids=[] ): - self.home() url = "%s/admin/role?id=%s&role_members_edit_button=Save" % ( self.url, role_id ) if user_ids: url += "&in_users=%s" % ','.join( user_ids ) @@ -1622,26 +1544,25 @@ self.visit_url( url ) check_str = "Role '%s' has been updated with %d associated users and %d associated groups" % ( role_name, len( user_ids ), len( group_ids ) ) self.check_page_for_string( check_str ) - self.home()

# Tests associated with groups def create_group( self, name='Group One', in_user_ids=[], in_role_ids=[], create_role_for_group='', strings_displayed=[] ): """Create a new group""" - url = "%s/admin/groups?operation=create&create_group_button=Save&name=%s" % ( self.url, name.replace( ' ', '+' ) ) + url = "/admin/groups" + params = dict( operation='create', create_group_button='Save', name=name ) if in_user_ids: - url += "&in_users=%s" % ','.join( in_user_ids ) + params [ 'in_users' ] = ','.join( in_user_ids ) if in_role_ids: - url += "&in_roles=%s" % ','.join( in_role_ids ) + params[ 'in_roles' ] = ','.join( in_role_ids ) if create_role_for_group == 'yes': - url += '&create_role_for_group=yes&create_role_for_group=yes' - self.home() - self.visit_url( url ) + checkbox_params = dict( create_role_for_group='yes' ) + else: + checkbox_params = None + self.visit_url( url, params=params, checkbox_params=checkbox_params ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.home() - self.visit_url( "%s/admin/groups" % self.url ) + self.visit_url( "/admin/groups" ) self.check_page_for_string( name ) - self.home()

def browse_groups( self, strings_displayed=[] ): self.visit_url( '%s/admin/groups' % self.url ) @@ -1650,15 +1571,12 @@

def rename_group( self, group_id, name='Group One Renamed' ): """Rename a group""" - self.home() self.visit_url( "%s/admin/groups?operation=rename&id=%s" % ( self.url, group_id ) ) self.check_page_for_string( 'Change group name' ) tc.fv( "1", "name", name ) tc.submit( "rename_group_button" ) - self.home()

def associate_users_and_roles_with_group( self, group_id, group_name, user_ids=[], role_ids=[] ): - self.home() url = "%s/admin/manage_users_and_roles_for_group?id=%s&group_roles_users_edit_button=Save" % ( self.url, group_id ) if user_ids: url += "&in_users=%s" % ','.join( user_ids ) @@ -1667,31 +1585,24 @@ self.visit_url( url ) check_str = "Group '%s' has been updated with %d associated roles and %d associated users" % ( group_name, len( role_ids ), len( user_ids ) ) self.check_page_for_string( check_str ) - self.home()

def mark_group_deleted( self, group_id, group_name ): """Mark a group as deleted""" - self.home() self.visit_url( "%s/admin/groups?operation=delete&id=%s" % ( self.url, group_id ) ) check_str = "Deleted 1 groups: %s" % group_name self.check_page_for_string( check_str ) - self.home()

def undelete_group( self, group_id, group_name ): """Undelete an existing group""" - self.home() self.visit_url( "%s/admin/groups?operation=undelete&id=%s" % ( self.url, group_id ) ) check_str = "Undeleted 1 groups: %s" % group_name self.check_page_for_string( check_str ) - self.home()

def purge_group( self, group_id, group_name ): """Purge an existing group""" - self.home() self.visit_url( "%s/admin/groups?operation=purge&id=%s" % ( self.url, group_id ) ) check_str = "Purged 1 groups: %s" % group_name self.check_page_for_string( check_str ) - self.home()

# Form stuff def create_form( self, name, description, form_type, field_type='TextField', form_layout_name='', @@ -1743,12 +1654,10 @@ tc.submit( "save_changes_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) - self.home()

def edit_form( self, id, form_type='', new_form_name='', new_form_desc='', field_dicts=[], field_index=0, strings_displayed=[], strings_not_displayed=[], strings_displayed_after_submit=[] ): """Edit form details; name and description""" - self.home() self.visit_url( "%s/forms/edit_form_definition?id=%s" % ( self.url, id ) ) for check_str in strings_displayed: self.check_page_for_string( check_str ) @@ -1784,10 +1693,9 @@ tc.submit( "save_changes_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) - self.home() + def view_form( self, id, form_type='', form_name='', form_desc='', form_layout_name='', field_dicts=[] ): '''View form details''' - self.home() self.visit_url( "%s/forms/view_latest_form_definition?id=%s" % ( self.url, id ) ) #self.check_page_for_string( form_type ) self.check_page_for_string( form_name ) @@ -1800,15 +1708,13 @@ if field_dict[ 'type' ].lower() == 'selectfield': for option_index, option in enumerate( field_dict[ 'selectlist' ] ): self.check_page_for_string( option ) - self.home() + def mark_form_deleted( self, form_id ): """Mark a form_definition as deleted""" - self.home() url = "%s/forms/delete_form_definition?id=%s" % ( self.url, form_id ) self.visit_url( url ) check_str = "1 forms have been deleted." self.check_page_for_string( check_str ) - self.home()

# External services stuff def reload_external_service( self, external_service_type_id, strings_displayed=[], strings_displayed_after_submit=[] ): @@ -1819,6 +1725,7 @@ tc.submit( "reload_external_service_type_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) + def create_external_service( self, name, description, version, external_service_type_id, field_values={}, strings_displayed=[], strings_displayed_after_submit=[] ): self.visit_url( '%s/external_service/create_external_service' % self.url ) for check_str in strings_displayed: @@ -1832,10 +1739,12 @@ tc.submit( "create_external_service_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) + def view_external_service( self, external_service_id, strings_displayed=[] ): self.visit_url( '%s/external_service/view_external_service?id=%s' % ( self.url, external_service_id ) ) for check_str in strings_displayed: self.check_page_for_string( check_str ) + def edit_external_service( self, external_service_id, field_values={}, strings_displayed=[], strings_displayed_after_submit=[] ): self.visit_url( '%s/external_service/edit_external_service?id=%s' % ( self.url, external_service_id ) ) for check_str in strings_displayed: @@ -1852,7 +1761,6 @@ for check_str in strings_displayed: self.check_page_for_string( check_str ) def create_request_type( self, name, desc, request_form_id, sample_form_id, states, strings_displayed=[], strings_displayed_after_submit=[] ): - self.home() self.visit_url( "%s/request_type/create_request_type" % self.url ) for check_str in strings_displayed: self.check_page_for_string( check_str ) @@ -1876,14 +1784,11 @@ for pi in permissions_in: key = '%s_in' % pi url = "%s&%s=%s" % ( url, key, role_ids_str ) - self.home() self.visit_url( "%s/%s" % ( self.url, url ) ) check_str = "Permissions updated for request type '%s'" % request_type_name self.check_page_for_string( check_str ) - self.home() def view_request_type( self, request_type_id, request_type_name, sample_states, strings_displayed=[] ): '''View request_type details''' - self.home() self.visit_url( "%s/request_type/view_request_type?id=%s" % ( self.url, request_type_id ) ) self.check_page_for_string( '"%s" request type' % request_type_name ) for name, desc in sample_states: @@ -1926,7 +1831,6 @@ tc.submit( "create_request_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) - self.home() def view_request( self, cntrller, request_id, strings_displayed=[], strings_displayed_count=[], strings_not_displayed=[] ): self.visit_url( "%s/%s/browse_requests?operation=view_request&id=%s" % ( self.url, cntrller, request_id ) ) self.check_page( strings_displayed, strings_displayed_count, strings_not_displayed ) @@ -2121,7 +2025,6 @@ for check_str, count in strings_displayed_count: self.check_string_count_in_page( check_str, count ) def add_user_address( self, user_id, address_dict ): - self.home() self.visit_url( "%s/user/new_address?cntrller=user&user_id=%s" % ( self.url, user_id ) ) self.check_page_for_string( 'Add new address' ) for field_name, value in address_dict.items(): @@ -2137,7 +2040,6 @@ dis-inherit your template, call the manage_library_template_inheritance() below immediately after you call this method in your test code. Templates added to Requesttype objects are always inherited to samples. """ - self.home() if item_type == 'library': url = "%s/library_common/add_template?cntrller=%s&item_type=%s&form_type=%s&library_id=%s" % \ ( self.url, cntrller, item_type, form_type, library_id ) @@ -2155,10 +2057,9 @@ tc.fv( "select_template", "inheritable", '1' ) tc.submit( "add_template_button" ) self.check_page_for_string = 'A template based on the form "%s" has been added to this' % form_name - self.home() + def manage_library_template_inheritance( self, cntrller, item_type, library_id, folder_id=None, ldda_id=None, inheritable=True ): # If inheritable is True, the item is currently inheritable. - self.home() if item_type == 'library': url = "%s/library_common/manage_template_inheritance?cntrller=%s&item_type=%s&library_id=%s" % \ ( self.url, cntrller, item_type, library_id ) @@ -2173,7 +2074,7 @@ self.check_page_for_string = 'will no longer be inherited to contained folders and datasets' else: self.check_page_for_string = 'will now be inherited to contained folders and datasets' - self.home() + def browse_libraries_admin( self, deleted=False, strings_displayed=[], strings_not_displayed=[] ): self.visit_url( '%s/library_admin/browse_libraries?sort=name&f-description=All&f-name=All&f-deleted=%s' % ( self.url, str( deleted ) ) ) for check_str in strings_displayed: @@ -2214,7 +2115,7 @@ tc.submit( "create_library_button" ) check_str = "The new library named '%s' has been created" % name self.check_page_for_string( check_str ) - self.home() + def edit_template( self, cntrller, item_type, form_type, library_id, field_type, field_label_1, field_helptext_1, field_default_1, folder_id='', ldda_id='', action='add_field' ): """Edit the form fields defining a library template""" @@ -2251,7 +2152,7 @@ # Set the template field value tc.fv( "edit_info", field_name, field_value ) tc.submit( 'edit_info_button' ) - self.home() + def library_permissions( self, library_id, library_name, role_ids_str, permissions_in, permissions_out, cntrller='library_admin' ): # role_ids_str must be a comma-separated string of role ids url = "library_common/library_permissions?id=%s&cntrller=%s&update_roles_button=Save" % ( library_id, cntrller ) @@ -2261,11 +2162,10 @@ for pi in permissions_in: key = '%s_in' % pi url = "%s&%s=%s" % ( url, key, role_ids_str ) - self.home() self.visit_url( "%s/%s" % ( self.url, url ) ) check_str = "Permissions updated for library '%s'." % library_name self.check_page_for_string( check_str ) - self.home() + def make_library_item_public( self, library_id, id, cntrller='library_admin', item_type='library', contents=False, library_name='', folder_name='', ldda_name='' ): url = "%s/library_common/make_library_item_public?cntrller=%s&library_id=%s&item_type=%s&id=%s&contents=%s" % \ @@ -2293,7 +2193,7 @@ tc.submit( "new_folder_button" ) check_str = "The new folder named '%s' has been added to the data library." % name self.check_page_for_string( check_str ) - self.home() + def folder_info( self, cntrller, folder_id, library_id, name='', new_name='', description='', template_refresh_field_name='1_field_name', template_refresh_field_contents='', template_fields=[], strings_displayed=[], strings_not_displayed=[], strings_displayed_after_submit=[], strings_not_displayed_after_submit=[] ): @@ -2331,7 +2231,6 @@ raise AssertionError( "String (%s) incorrectly displayed." % check_str ) except: pass - self.home()

# Library dataset stuff def upload_library_dataset( self, cntrller, library_id, folder_id, filename='', server_dir='', replace_id='', @@ -2342,29 +2241,29 @@ """Add datasets to library using any upload_option""" # NOTE: due to the library_wait() method call at the end of this method, no tests should be done # for strings_displayed_after_submit. - url = "%s/library_common/upload_library_dataset?cntrller=%s&library_id=%s&folder_id=%s" % \ - ( self.url, cntrller, library_id, folder_id ) + params = dict( cntrller=cntrller, library_id=library_id, folder_id=folder_id ) + url = "%s/library_common/upload_library_dataset" % self.url if replace_id: # If we're uploading a new version of a library dataset, we have to include the replace_id param in the # request because the form field named replace_id will not be displayed on the upload form if we dont. - url += "&replace_id=%s" % replace_id - self.visit_url( url ) + params[ 'replace_id' ] = replace_id + self.visit_url( url, params=params ) if template_refresh_field_contents: # A template containing an AddressField is displayed on the upload form, so we need to refresh the form # with the received template_refresh_field_contents. self.refresh_form( template_refresh_field_name, template_refresh_field_contents ) for tup in template_fields: tc.fv( "1", tup[0], tup[1] ) - tc.fv( "1", "library_id", library_id ) - tc.fv( "1", "folder_id", folder_id ) - tc.fv( "1", "show_deleted", show_deleted ) - tc.fv( "1", "ldda_message", ldda_message ) - tc.fv( "1", "file_type", file_type ) - tc.fv( "1", "dbkey", dbkey ) + tc.fv( "upload_library_dataset", "library_id", library_id ) + tc.fv( "upload_library_dataset", "folder_id", folder_id ) + tc.fv( "upload_library_dataset", "show_deleted", show_deleted ) + tc.fv( "upload_library_dataset", "ldda_message", ldda_message ) + tc.fv( "upload_library_dataset", "file_type", file_type ) + tc.fv( "upload_library_dataset", "dbkey", dbkey ) if space_to_tab: - tc.fv( "1", "space_to_tab", space_to_tab ) + tc.fv( "upload_library_dataset", "space_to_tab", space_to_tab ) for role_id in roles: - tc.fv( "1", "roles", role_id ) + tc.fv( "upload_library_dataset", "roles", role_id ) # Refresh the form by selecting the upload_option - we do this here to ensure # all previously entered form contents are retained. self.refresh_form( 'upload_option', upload_option ) @@ -2380,21 +2279,21 @@ tc.submit( 'add_history_datasets_to_library_button' ) else: if upload_option in [ 'upload_paths', 'upload_directory' ]: - tc.fv( "1", "link_data_only", link_data_only ) + tc.fv( "upload_library_dataset", "link_data_only", link_data_only ) if upload_option == 'upload_paths': - tc.fv( "1", "filesystem_paths", filesystem_paths ) + tc.fv( "upload_library_dataset", "filesystem_paths", filesystem_paths ) if upload_option == 'upload_directory' and server_dir: - tc.fv( "1", "server_dir", server_dir ) + tc.fv( "upload_library_dataset", "server_dir", server_dir ) if upload_option == 'upload_file': if filename: filename = self.get_filename( filename ) - tc.formfile( "1", "files_0|file_data", filename ) + tc.formfile( "upload_library_dataset", "files_0|file_data", filename ) for check_str in strings_displayed: self.check_page_for_string( check_str ) tc.submit( "runtool_btn" ) # Give the files some time to finish uploading self.library_wait( library_id ) - self.home() + def ldda_permissions( self, cntrller, library_id, folder_id, id, role_ids_str, permissions_in=[], permissions_out=[], strings_displayed=[], ldda_name='' ): # role_ids_str must be a comma-separated string of role ids @@ -2413,7 +2312,7 @@ strings_displayed = [ "Permissions updated for dataset '%s'." % ldda_name ] for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.home() + def ldda_info( self, cntrller, library_id, folder_id, ldda_id, strings_displayed=[], strings_not_displayed=[] ): """View library_dataset_dataset_association information""" self.visit_url( "%s/library_common/ldda_info?cntrller=%s&library_id=%s&folder_id=%s&id=%s" % \ @@ -2426,7 +2325,7 @@ raise AssertionError( "String (%s) should not have been displayed on ldda info page." % check_str ) except: pass - self.home() + def ldda_edit_info( self, cntrller, library_id, folder_id, ldda_id, ldda_name, new_ldda_name='', template_refresh_field_name='1_field_name', template_refresh_field_contents='', template_fields=[], strings_displayed=[], strings_not_displayed=[] ): """Edit library_dataset_dataset_association information, optionally template element information""" @@ -2458,7 +2357,7 @@ raise AssertionError( "String (%s) should not have been displayed on ldda Edit Attributes page." % check_str ) except: pass - self.home() + def act_on_multiple_datasets( self, cntrller, library_id, do_action, ldda_ids='', strings_displayed=[] ): # Can't use the ~/library_admin/libraries form as twill barfs on it so we'll simulate the form submission # by going directly to the form action @@ -2474,7 +2373,6 @@ for check_str in strings_displayed: self.check_page_for_string( check_str ) def download_archive_of_library_files( self, cntrller, library_id, ldda_ids, format ): - self.home() # Here it would be ideal to have twill set form values and submit the form, but # twill barfs on that due to the recently introduced page wrappers around the contents # of the browse_library.mako template which enable panel layout when visiting the @@ -2494,7 +2392,6 @@ self.visit_url( url ) tc.code( 200 ) archive = self.write_temp_file( self.last_page(), suffix='.' + format ) - self.home() return archive def check_archive_contents( self, archive, lddas ): def get_ldda_path( ldda ): @@ -2542,7 +2439,6 @@

def move_library_item( self, cntrller, item_type, item_id, source_library_id, make_target_current, target_library_id=None, target_folder_id=None, strings_displayed=[], strings_displayed_after_submit=[] ): - self.home() params = dict( cntrller=cntrller, item_type=item_type, item_id=item_id, @@ -2552,7 +2448,7 @@ params[ 'target_library_id' ] = target_library_id if target_folder_id is not None: params[ 'target_folder_id' ] = target_folder_id - self.visit_url( "%s/library_common/move_library_item?%s" % ( self.url, urllib.urlencode( params ) ) ) + self.visit_url( "%s/library_common/move_library_item" % self.url, params=params ) if target_library_id: self.refresh_form( 'target_library_id', target_library_id, form_name='move_library_item' ) if target_folder_id: @@ -2562,39 +2458,36 @@ tc.submit( 'move_library_item_button' ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) - self.home()

def delete_library_item( self, cntrller, library_id, item_id, item_name, item_type='library_dataset' ): """Mark a library item as deleted""" - self.home() - self.visit_url( "%s/library_common/delete_library_item?cntrller=%s&library_id=%s&item_id=%s&item_type=%s" \ - % ( self.url, cntrller, library_id, item_id, item_type ) ) + params = dict( cntrller=cntrller, library_id=library_id, item_id=item_id, item_type=item_type ) + self.visit_url( "/library_common/delete_library_item", params ) if item_type == 'library_dataset': item_desc = 'Dataset' else: item_desc = item_type.capitalize() check_str = "marked deleted" - self.check_page_for_string( check_str ) - self.home() + self.check_for_strings( strings_displayed=[ item_desc, check_str ] ) + def undelete_library_item( self, cntrller, library_id, item_id, item_name, item_type='library_dataset' ): """Mark a library item as deleted""" - self.home() - self.visit_url( "%s/library_common/undelete_library_item?cntrller=%s&library_id=%s&item_id=%s&item_type=%s" \ - % ( self.url, cntrller, library_id, item_id, item_type ) ) + params = dict( cntrller=cntrller, library_id=library_id, item_id=item_id, item_type=item_type ) + self.visit_url( "/library_common/undelete_library_item", params ) if item_type == 'library_dataset': item_desc = 'Dataset' else: item_desc = item_type.capitalize() check_str = "marked undeleted" - self.check_page_for_string( check_str ) - self.home() + self.check_for_strings( strings_displayed=[ item_desc, check_str ] ) + def purge_library( self, library_id, library_name ): """Purge a library""" - self.home() - self.visit_url( "%s/library_admin/purge_library?id=%s" % ( self.url, library_id ) ) + params = dict( id=library_id ) + self.visit_url( "/library_admin/purge_library", params ) check_str = "Library '%s' and all of its contents have been purged" % library_name self.check_page_for_string( check_str ) - self.home() + def library_wait( self, library_id, cntrller='library_admin', maxiter=90 ): """Waits for the tools to finish""" count = 0

diff -r 0bc0fd94aaa4e7c1ede3e291b6c58544c83fc786 -r 299e9c8d29c5cd0b1603c38e6d805ecb33b1a58f test/functional/test_admin_features.py --- a/test/functional/test_admin_features.py +++ b/test/functional/test_admin_features.py @@ -232,7 +232,6 @@ # Rename the group rename = "Group One's been Renamed" self.rename_group( self.security.encode_id( group_one.id ), name=rename, ) - self.home() self.visit_url( '%s/admin/groups' % self.url ) self.check_page_for_string( rename ) # Reset the group back to the original name @@ -365,7 +364,6 @@ def test_065_mark_role_deleted( self ): """Testing marking a role as deleted""" # Logged in as admin_user - self.home() self.browse_roles( strings_displayed=[ role_two.name ] ) self.mark_role_deleted( self.security.encode_id( role_two.id ), role_two.name ) refresh( role_two )

diff -r 0bc0fd94aaa4e7c1ede3e291b6c58544c83fc786 -r 299e9c8d29c5cd0b1603c38e6d805ecb33b1a58f test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py +++ b/test/functional/test_history_functions.py @@ -1,4 +1,3 @@ -import urllib import galaxy.model from galaxy.model.orm import * from base.test_db_util import sa_session @@ -109,7 +108,7 @@ .first() assert history1 is not None, "Problem retrieving history1 from database" self.upload_file( '1.bed', dbkey='hg18' ) - self.new_history( name=urllib.quote( 'history2' ) ) + self.new_history( name='history2' ) global history2 history2 = sa_session.query( galaxy.model.History ) \ .filter( and_( galaxy.model.History.table.c.deleted == False, @@ -158,7 +157,7 @@ assert history3 is not None, "Problem retrieving history3 from database" if history3.deleted: raise AssertionError( "History id %d deleted when it should not be" % latest_history.id ) - self.rename_history( self.security.encode_id( history3.id ), history3.name, new_name=urllib.quote( 'history 3' ) ) + self.rename_history( self.security.encode_id( history3.id ), history3.name, new_name='history 3' ) sa_session.refresh( history3 )

def test_015_history_list( self ): @@ -348,7 +347,7 @@ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert history4 is not None, "Problem retrieving history4 from database" - self.rename_history( self.security.encode_id( history4.id ), history4.name, new_name=urllib.quote( 'history 4' ) ) + self.rename_history( self.security.encode_id( history4.id ), history4.name, new_name='history 4' ) sa_session.refresh( history4 ) # Galaxy's new history sharing code does not yet support sharing multiple histories; when support for sharing multiple histories is added, # this test will be uncommented and updated. @@ -383,7 +382,7 @@ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert history5 is not None, "Problem retrieving history5 from database" - self.rename_history( self.security.encode_id( history5.id ), history5.name, new_name=urllib.quote( 'history 5' ) ) + self.rename_history( self.security.encode_id( history5.id ), history5.name, new_name='history 5' ) # Current history is history5 sa_session.refresh( history5 ) # Due to the limitations of twill ( not functional with the permissions forms ), we're forced @@ -547,7 +546,7 @@ # Make sure the history was unshared correctly self.logout() self.login( email=regular_user2.email ) - self.visit_page( "root/history_options" ) + self.visit_url( "/root/history_options" ) try: self.check_page_for_string( 'List</a> histories shared with you by others' ) raise AssertionError( "history5 still shared with regular_user2 after unsharing it with that user." ) @@ -695,7 +694,7 @@ # Make sure the histories were unshared correctly self.logout() self.login( email=regular_user2.email ) - self.visit_page( "root/history_options" ) + self.visit_url( "/root/history_options" ) try: self.check_page_for_string( 'List</a> histories shared with you by others' ) raise AssertionError( "history5 still shared with regular_user2 after unshaing it with that user." ) @@ -704,7 +703,7 @@

self.logout() self.login( email=regular_user3.email ) - self.visit_page( "root/history_options" ) + self.visit_url( "/root/history_options" ) try: self.check_page_for_string( 'List</a> histories shared with you by others' ) raise AssertionError( "history5 still shared with regular_user3 after unshaing it with that user." ) @@ -724,7 +723,7 @@

# 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' ) ) + self.new_history( name='show hide deleted datasets' ) latest_history = ( sa_session.query( galaxy.model.History ) .filter( and_( galaxy.model.History.table.c.deleted == False, @@ -739,7 +738,6 @@ .first() )

# delete that item and make sure the history is not empty - self.home() log.info( 'deleting last hda' ) self.delete_history_item( str( latest_hda.id ) ) # check the number of items returned from the api @@ -776,13 +774,12 @@ 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' ) ) + latest_history.name, new_name='delete undelete history items' ) # Add a new history item self.upload_file( '1.bed', dbkey='hg15' ) latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ .first() - self.home() self.visit_url( "%s/history/?show_deleted=False" % self.url ) self.check_page_for_string( '1.bed' ) self.check_page_for_string( 'hg15' ) @@ -798,7 +795,6 @@ pass # Undelete the history item 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' ) self.check_page_for_string( 'hg15' ) @@ -807,7 +803,7 @@ def test_080_copying_history_items_between_histories( self ): """Testing copying history items between histories""" # logged in as admin_user - self.new_history( name=urllib.quote( 'copy history items' ) ) + self.new_history( name='copy history items' ) history6 = 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 ) ) \ @@ -836,7 +832,7 @@ if len( history6.datasets ) != 2: raise AssertionError( "Copying hda1 to the current history failed, history 6 has %d datasets, but should have 2" % len( history6.datasets ) ) # Test copying 1 hda to another history - self.new_history( name=urllib.quote( 'copy history items - 2' ) ) + self.new_history( name='copy history items - 2' ) history7 = 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 ) ) \

diff -r 0bc0fd94aaa4e7c1ede3e291b6c58544c83fc786 -r 299e9c8d29c5cd0b1603c38e6d805ecb33b1a58f test/functional/test_metadata_editing.py --- a/test/functional/test_metadata_editing.py +++ b/test/functional/test_metadata_editing.py @@ -27,7 +27,6 @@ latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ .first() - self.home() # Due to twill not being able to handle the permissions forms, we'll eliminate # DefaultHistoryPermissions prior to uploading a dataset so that the permission # form will not be displayed on ted edit attributes page.

diff -r 0bc0fd94aaa4e7c1ede3e291b6c58544c83fc786 -r 299e9c8d29c5cd0b1603c38e6d805ecb33b1a58f test/install_and_test_tool_shed_repositories/base/twilltestcase.py --- a/test/install_and_test_tool_shed_repositories/base/twilltestcase.py +++ b/test/install_and_test_tool_shed_repositories/base/twilltestcase.py @@ -39,7 +39,6 @@ # TODO: Figure out a way to alter these attributes during tests. self.galaxy_tool_dependency_dir = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR' ) self.shed_tools_dict = {} - self.home()

def initiate_installation_process( self, install_tool_dependencies=False, install_repository_dependencies=True, no_changes=True, new_tool_panel_section_label=None ):

diff -r 0bc0fd94aaa4e7c1ede3e291b6c58544c83fc786 -r 299e9c8d29c5cd0b1603c38e6d805ecb33b1a58f test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -61,7 +61,6 @@ # TODO: Figure out a way to alter these attributes during tests. self.galaxy_tool_dependency_dir = os.environ.get( 'GALAXY_TEST_TOOL_DEPENDENCY_DIR' ) self.shed_tools_dict = {} - self.home()

def add_repository_review_component( self, **kwd ): url = '/repository_review/create_component?operation=create' @@ -597,10 +596,8 @@ self.submit_form( '1', 'login_button', email=email, redirect=redirect, password=password )

def galaxy_logout( self ): - self.home() self.visit_galaxy_url( "/user/logout" ) self.check_page_for_string( "You have been logged out" ) - self.home()

def generate_complex_dependency_xml( self, filename, filepath, repository_tuples, package, version ): file_path = os.path.join( filepath, filename )

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

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