opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Explicitly uninstall tool dependencies that are in an error state.

Browse Source
This commit is contained in:
Dave Bouvier
2013-10-14 16:46:41 -04:00
parent 3e8f294ea5
commit ff28741642
2 changed files with 37 additions and 1 deletions
Download Patch File Download Diff File Expand all files Collapse all files
test/install_and_test_tool_shed_repositories/base/test_db_util.py
+20
View File
@@ -8,39 +8,59 @@ log = logging.getLogger(__name__)
def delete_obj( obj ):
sa_session.delete( obj )
sa_session.flush()
def delete_user_roles( user ):
for ura in user.roles:
sa_session.delete( ura )
sa_session.flush()
def flush( obj ):
sa_session.add( obj )
sa_session.flush()
def get_repository( repository_id ):
return sa_session.query( model.ToolShedRepository ) \
.filter( model.ToolShedRepository.table.c.id == repository_id ) \
.first()
def get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ):
return sa_session.query( model.ToolShedRepository ) \
.filter( and_( model.ToolShedRepository.table.c.name == name,
model.ToolShedRepository.table.c.owner == owner,
model.ToolShedRepository.table.c.installed_changeset_revision == changeset_revision ) ) \
.one()
def get_private_role( user ):
for role in user.all_roles():
if role.name == user.email and role.description == 'Private Role for %s' % user.email:
return role
raise AssertionError( "Private role not found for user '%s'" % user.email )
def get_tool_dependencies_for_installed_repository( repository_id, status=None ):
if status is not None:
return sa_session.query( model.ToolDependency ) \
.filter( and_( model.ToolDependency.table.c.tool_shed_repository_id == repository_id,
model.ToolDependency.table.c.status == status ) ) \
.all()
else:
return sa_session.query( model.ToolDependency ) \
.filter( model.ToolDependency.table.c.tool_shed_repository_id == repository_id ) \
.all()
def mark_obj_deleted( obj ):
obj.deleted = True
sa_session.add( obj )
sa_session.flush()
def refresh( obj ):
sa_session.refresh( obj )
def get_private_role( user ):
for role in user.all_roles():
if role.name == user.email and role.description == 'Private Role for %s' % user.email:
return role
raise AssertionError( "Private role not found for user '%s'" % user.email )
def get_user( email ):
return sa_session.query( model.User ) \
.filter( model.User.table.c.email==email ) \
test/install_and_test_tool_shed_repositories/base/twilltestcase.py
+17 -1
View File
@@ -149,4 +149,20 @@ class InstallTestRepository( TwillTestCase ):
strings_displayed.append( 'has been deactivated' )
else:
strings_displayed.append( 'has been uninstalled' )
self.check_for_strings( strings_displayed, strings_not_displayed=[] )
self.check_for_strings( strings_displayed, strings_not_displayed=[] )
# Get all tool dependencies that are in an error state and uninstall them explicitly, so that the next installation attempt
# may succeed.
error_state = model.ToolDependency.installation_status.ERROR
tool_dependencies = test_db_util.get_tool_dependencies_for_installed_repository( installed_repository.id, status=error_state )
if len( tool_dependencies ) > 0:
encoded_tool_dependency_ids = [ self.security.encode_id( tool_dependency.id ) for tool_dependency in tool_dependencies ]
self.uninstall_tool_dependencies( self.security.encode_id( installed_repository.id ), encoded_tool_dependency_ids )
def uninstall_tool_dependencies( self, encoded_repository_id, encoded_tool_dependency_ids ):
tool_dependency_ids = ','.join( encoded_tool_dependency_ids )
url = '/admin_toolshed/uninstall_tool_dependencies?repository_id=%s&inst_td_ids=%s&operation=uninstall' % \
( encoded_repository_id, tool_dependency_ids )
self.visit_url( url )
tc.fv( 'uninstall_tool_dependencies', 'tool_dependency_ids', tool_dependency_ids )
tc.submit( 'uninstall_tool_dependencies_button' )