def test_0025_uninstall_column_repository( self ):
'''uninstall column_maker, verify same section'''
installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name,
common.test_user_1_name )
self.uninstall_repository( installed_column_repository, remove_from_disk=True )
test_db_util.ga_refresh( installed_column_repository )
self.check_galaxy_repository_tool_panel_section( installed_column_repository, 'column_maker' )
def test_0070_uninstall_emboss_repository(self):
'''Uninstall the emboss_5 repository.'''
repository = test_db_util.get_installed_repository_by_name_owner(
emboss_repository_name, common.test_user_1_name)
self.uninstall_repository(repository, remove_from_disk=True)
strings_not_displayed = [
repository.name, repository.installed_changeset_revision
]
self.display_galaxy_browse_repositories_page(
strings_not_displayed=strings_not_displayed)
test_db_util.ga_refresh(repository)
self.check_galaxy_repository_tool_panel_section(
repository, 'emboss_5_0050')
# Now we have bismark, column_maker, and convert_chars installed, filtering and freebayes never installed, emboss_datatypes deactivated,
# and emboss uninstalled.
installed_repositories = [
(column_repository_name, common.test_user_1_name),
(convert_repository_name, common.test_user_1_name),
(bismark_repository_name, common.test_user_1_name)
]
uninstalled_repositories = [
(emboss_datatypes_repository_name, common.test_user_1_name),
(emboss_repository_name, common.test_user_1_name),
(filtering_repository_name, common.test_user_1_name),
(freebayes_repository_name, common.test_user_1_name)
]
self.verify_installed_uninstalled_repositories(
installed_repositories=installed_repositories,
uninstalled_repositories=uninstalled_repositories)
def test_0030_uninstall_convert_repository(self):
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name)
self.uninstall_repository(installed_convert_repository,
remove_from_disk=True)
test_db_util.ga_refresh(installed_convert_repository)
self.check_galaxy_repository_tool_panel_section(
installed_convert_repository, 'column_maker')
def test_0045_uninstall_freebayes_repository( self ):
'''Uninstall freebayes, verify tool panel section and missing repository dependency.'''
installed_freebayes_repository = test_db_util.get_installed_repository_by_name_owner( freebayes_repository_name, common.test_user_1_name )
installed_filtering_repository = test_db_util.get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name )
self.uninstall_repository( installed_freebayes_repository, remove_from_disk=True )
test_db_util.ga_refresh( installed_freebayes_repository )
self.check_galaxy_repository_tool_panel_section( installed_freebayes_repository, 'freebayes' )
strings_displayed = [ 'Missing repository', 'freebayes', 'filtering_0040', 'user1', "Galaxy's filtering tool for test 0040" ]
self.display_installed_repository_manage_page( installed_filtering_repository, strings_displayed=strings_displayed )
self.check_galaxy_repository_db_status( 'freebayes_0040',
'user1',
'Uninstalled' )
def test_0040_uninstall_filtering_repository( self ):
'''Uninstall filtering, verify tool panel section.'''
installed_filtering_repository = test_db_util.get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name )
installed_freebayes_repository = test_db_util.get_installed_repository_by_name_owner( freebayes_repository_name, common.test_user_1_name )
self.uninstall_repository( installed_filtering_repository, remove_from_disk=True )
test_db_util.ga_refresh( installed_filtering_repository )
self.check_galaxy_repository_tool_panel_section( installed_filtering_repository, '' )
strings_displayed = [ 'Missing repository', 'filtering' ]
self.display_installed_repository_manage_page( installed_freebayes_repository, strings_displayed=strings_displayed )
self.check_galaxy_repository_db_status( filtering_repository_name,
common.test_user_1_name,
'Uninstalled' )
def test_0045_uninstall_and_verify_tool_panel_sections( self ):
'''uninstall both and verify tool panel sections'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name,
common.test_user_1_name )
installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name,
common.test_user_1_name )
self.uninstall_repository( installed_column_repository, remove_from_disk=True )
self.uninstall_repository( installed_convert_repository, remove_from_disk=True )
test_db_util.ga_refresh( installed_convert_repository )
test_db_util.ga_refresh( installed_column_repository )
self.check_galaxy_repository_tool_panel_section( installed_column_repository, 'new_column_maker' )
self.check_galaxy_repository_tool_panel_section( installed_convert_repository, 'new_convert_chars' )
def test_0085_uninstall_all_repositories( self ):
'''Uninstall convert_chars and column_maker to verify that they are in the right tool panel sections.'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name,
common.test_user_1_name )
installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name,
common.test_user_1_name )
self.uninstall_repository( installed_column_repository, remove_from_disk=True )
self.uninstall_repository( installed_convert_repository, remove_from_disk=True )
test_db_util.ga_refresh( installed_column_repository )
test_db_util.ga_refresh( installed_convert_repository )
self.check_galaxy_repository_tool_panel_section( installed_column_repository, 'convert_maker' )
self.check_galaxy_repository_tool_panel_section( installed_convert_repository, 'convert_maker' )
def test_0015_reset_metadata_on_all_repositories(self):
"""Reset metadata on all repositories, then verify that it has not changed."""
repository_metadata = dict()
repositories = test_db_util.get_all_installed_repositories(actually_installed=True)
for repository in repositories:
repository_metadata[self.security.encode_id(repository.id)] = repository.metadata
self.reset_metadata_on_selected_installed_repositories(repository_metadata.keys())
for repository in repositories:
test_db_util.ga_refresh(repository)
old_metadata = repository_metadata[self.security.encode_id(repository.id)]
assert repository.metadata == old_metadata, (
"Metadata for installed repository %s changed after reset." % repository.name
)
def test_0015_reset_metadata_on_all_repositories(self):
'''Reset metadata on all repositories, then verify that it has not changed.'''
repository_metadata = dict()
repositories = test_db_util.get_all_installed_repositories(
actually_installed=True)
for repository in repositories:
repository_metadata[self.security.encode_id(
repository.id)] = repository.metadata
self.reset_metadata_on_selected_installed_repositories(
repository_metadata.keys())
for repository in repositories:
test_db_util.ga_refresh(repository)
old_metadata = repository_metadata[self.security.encode_id(
repository.id)]
assert repository.metadata == old_metadata, 'Metadata for installed repository %s changed after reset.' % repository.name
def test_0085_uninstall_all_repositories(self):
'''Uninstall convert_chars and column_maker to verify that they are in the right tool panel sections.'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name)
installed_column_repository = test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name)
self.uninstall_repository(installed_column_repository,
remove_from_disk=True)
self.uninstall_repository(installed_convert_repository,
remove_from_disk=True)
test_db_util.ga_refresh(installed_column_repository)
test_db_util.ga_refresh(installed_convert_repository)
self.check_galaxy_repository_tool_panel_section(
installed_column_repository, 'convert_maker')
self.check_galaxy_repository_tool_panel_section(
installed_convert_repository, 'convert_maker')
def test_0045_uninstall_and_verify_tool_panel_sections(self):
'''uninstall both and verify tool panel sections'''
installed_convert_repository = test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name)
installed_column_repository = test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name)
self.uninstall_repository(installed_column_repository,
remove_from_disk=True)
self.uninstall_repository(installed_convert_repository,
remove_from_disk=True)
test_db_util.ga_refresh(installed_convert_repository)
test_db_util.ga_refresh(installed_column_repository)
self.check_galaxy_repository_tool_panel_section(
installed_column_repository, 'new_column_maker')
self.check_galaxy_repository_tool_panel_section(
installed_convert_repository, 'new_convert_chars')
def test_0070_uninstall_emboss_repository( self ):
'''Uninstall the emboss_5 repository.'''
repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name )
self.uninstall_repository( repository, remove_from_disk=True )
strings_not_displayed = [ repository.name, repository.installed_changeset_revision ]
self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed )
test_db_util.ga_refresh( repository )
self.check_galaxy_repository_tool_panel_section( repository, 'emboss_5_0050' )
# Now we have bismark, column_maker, and convert_chars installed, filtering and freebayes never installed, emboss_datatypes deactivated,
# and emboss uninstalled.
installed_repositories = [ ( column_repository_name, common.test_user_1_name ),
( convert_repository_name, common.test_user_1_name ),
( bismark_repository_name, common.test_user_1_name ) ]
strings_displayed = [ 'column_maker_0050', 'convert_chars_0050', 'bismark_0050' ]
strings_not_displayed = [ 'emboss_0050', 'emboss_datatypes_0050', 'filtering_0050', 'freebayes_0050' ]
self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed )
self.verify_installed_repositories( installed_repositories )
def test_0040_uninstall_filtering_repository(self):
'''Uninstall filtering, verify tool panel section.'''
installed_filtering_repository = test_db_util.get_installed_repository_by_name_owner(
filtering_repository_name, common.test_user_1_name)
installed_freebayes_repository = test_db_util.get_installed_repository_by_name_owner(
freebayes_repository_name, common.test_user_1_name)
self.uninstall_repository(installed_filtering_repository,
remove_from_disk=True)
test_db_util.ga_refresh(installed_filtering_repository)
self.check_galaxy_repository_tool_panel_section(
installed_filtering_repository, '')
strings_displayed = ['Missing repository', 'filtering']
self.display_installed_repository_manage_page(
installed_freebayes_repository,
strings_displayed=strings_displayed)
self.check_galaxy_repository_db_status(filtering_repository_name,
common.test_user_1_name,
'Uninstalled')
def test_0035_verify_tool_panel_section( self ):
'''Check the tool panel section after repairing.'''
'''
This is step 4 - Make sure the filter_1430 repository is reinstalled and the tool is loaded into the tool panel
in the same section specified in step 1.
'''
filter_repository = test_db_util.get_installed_repository_by_name_owner( 'filter_1430', common.test_user_1_name )
strings_displayed = [ 'filter_1430',
"Galaxy's filter tool for test 1430",
filter_repository.installed_changeset_revision ]
self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed )
# Uninstall the filter repository again, so that the tool panel section metadata gets populated.
self.uninstall_repository( filter_repository, remove_from_disk=True )
test_db_util.ga_refresh( filter_repository )
tool_panel_section_metadata = filter_repository.metadata[ 'tool_panel_section' ]
for tool_id in tool_panel_section_metadata:
for panel_section in tool_panel_section_metadata[ tool_id ]:
assert panel_section[ 'name' ] == 'repair', 'Tool %s in tool panel section %s after repair, expected %s.' % \
( tool_id, panel_section[ 'name' ], 'repair' )
def test_0015_reset_metadata_on_all_repositories(self):
"""Reset metadata on all repositories, then verify that it has not changed."""
repository_metadata = dict()
repositories = test_db_util.get_all_installed_repositories(actually_installed=True)
for repository in repositories:
repository_metadata[self.security.encode_id(repository.id)] = repository.metadata
self.reset_metadata_on_selected_installed_repositories(repository_metadata.keys())
for repository in repositories:
test_db_util.ga_refresh(repository)
old_metadata = repository_metadata[self.security.encode_id(repository.id)]
# When a repository with tools to be displayed in a tool panel section is deactivated and reinstalled,
# the tool panel section remains in the repository metadata. However, when the repository's metadata
# is subsequently reset, the tool panel section is removed from the repository metadata. While this
# is normal and expected behavior, the functional tests assume that repository metadata will not change
# in any way after a reset. A workaround is to remove the tool panel section from the stored repository
# metadata dict, in order to eliminate the misleading detection of changed metadata.
if "tool_panel_section" in old_metadata and "tool_panel_section" not in repository.metadata:
del old_metadata["tool_panel_section"]
assert repository.metadata == old_metadata, (
"Metadata for %s repository %s changed after reset. \nOld: %s\nNew: %s"
% (repository.status, repository.name, old_metadata, repository.metadata)
)
def test_0015_reset_metadata_on_all_repositories(self):
'''Reset metadata on all repositories, then verify that it has not changed.'''
repository_metadata = dict()
repositories = test_db_util.get_all_installed_repositories(
actually_installed=True)
for repository in repositories:
repository_metadata[self.security.encode_id(
repository.id)] = repository.metadata
self.reset_metadata_on_selected_installed_repositories(
repository_metadata.keys())
for repository in repositories:
test_db_util.ga_refresh(repository)
old_metadata = repository_metadata[self.security.encode_id(
repository.id)]
# When a repository with tools to be displayed in a tool panel section is deactivated and reinstalled,
# the tool panel section remains in the repository metadata. However, when the repository's metadata
# is subsequently reset, the tool panel section is removed from the repository metadata. While this
# is normal and expected behavior, the functional tests assume that repository metadata will not change
# in any way after a reset. A workaround is to remove the tool panel section from the stored repository
# metadata dict, in order to eliminate the misleading detection of changed metadata.
if 'tool_panel_section' in old_metadata and 'tool_panel_section' not in repository.metadata:
del old_metadata['tool_panel_section']
assert repository.metadata == old_metadata, 'Metadata for %s repository %s changed after reset. \nOld: %s\nNew: %s' % \
( repository.status, repository.name, old_metadata, repository.metadata )
