def reset_metadata_on_selected_installed_repositories(self, trans, **kwd):
repository_ids = util.listify(kwd.get("repository_ids"))
if repository_ids:
irmm = InstalledRepositoryMetadataManager(self.app)
failed = []
successful = []
for repository_id in repository_ids:
try:
repository = repository_util.get_installed_tool_shed_repository(
self.app, repository_id)
irmm.set_repository(repository)
irmm.reset_all_metadata_on_installed_repository()
if irmm.invalid_file_tups:
failed.append(repository_id)
else:
successful.append(repository_id)
except Exception:
failed.append(repository_id)
if successful:
message = "Successful reset of metadata for %s." % len(
successful)
if failed:
message += " Failed for %s." % len(failed)
elif failed:
message = "Failed to reset metadata for %s." % len(failed)
return dict(message=message, successful=successful, failed=failed)
else:
raise exceptions.MessageException(
"Please specify repository ids [repository_ids].")
def reset_metadata_on_installed_repositories(self, trans, payload, **kwd):
"""
PUT /api/tool_shed_repositories/reset_metadata_on_installed_repositories
Resets all metadata on all repositories installed into Galaxy in an "orderly fashion".
:param key: the API key of the Galaxy admin user.
"""
start_time = strftime("%Y-%m-%d %H:%M:%S")
results = dict(start_time=start_time,
successful_count=0,
unsuccessful_count=0,
repository_status=[])
# Make sure the current user's API key proves he is an admin user in this Galaxy instance.
if not trans.user_is_admin:
raise HTTPForbidden(
detail=
'You are not authorized to reset metadata on repositories installed into this Galaxy instance.'
)
irmm = InstalledRepositoryMetadataManager(self.app)
query = irmm.get_query_for_setting_metadata_on_repositories(
order=False)
# Now reset metadata on all remaining repositories.
for repository in query:
try:
irmm.set_repository(repository)
irmm.reset_all_metadata_on_installed_repository()
irmm_invalid_file_tups = irmm.get_invalid_file_tups()
if irmm_invalid_file_tups:
message = tool_util.generate_message_for_invalid_tools(
self.app,
irmm_invalid_file_tups,
repository,
None,
as_html=False)
results['unsuccessful_count'] += 1
else:
message = "Successfully reset metadata on repository %s owned by %s" % \
(str(repository.name), str(repository.owner))
results['successful_count'] += 1
except Exception as e:
message = "Error resetting metadata on repository %s owned by %s: %s" % \
(str(repository.name), str(repository.owner), util.unicodify(e))
results['unsuccessful_count'] += 1
results['repository_status'].append(message)
stop_time = strftime("%Y-%m-%d %H:%M:%S")
results['stop_time'] = stop_time
return json.dumps(results, sort_keys=True, indent=4)
def reset_metadata_on_installed_repositories( self, trans, payload, **kwd ):
"""
PUT /api/tool_shed_repositories/reset_metadata_on_installed_repositories
Resets all metadata on all repositories installed into Galaxy in an "orderly fashion".
:param key: the API key of the Galaxy admin user.
"""
start_time = strftime( "%Y-%m-%d %H:%M:%S" )
results = dict( start_time=start_time,
successful_count=0,
unsuccessful_count=0,
repository_status=[] )
# Make sure the current user's API key proves he is an admin user in this Galaxy instance.
if not trans.user_is_admin():
raise HTTPForbidden( detail='You are not authorized to reset metadata on repositories installed into this Galaxy instance.' )
irmm = InstalledRepositoryMetadataManager( self.app )
query = irmm.get_query_for_setting_metadata_on_repositories( order=False )
# Now reset metadata on all remaining repositories.
for repository in query:
try:
irmm.set_repository( repository )
irmm.reset_all_metadata_on_installed_repository()
irmm_invalid_file_tups = irmm.get_invalid_file_tups()
if irmm_invalid_file_tups:
message = tool_util.generate_message_for_invalid_tools( self.app,
irmm_invalid_file_tups,
repository,
None,
as_html=False )
results[ 'unsuccessful_count' ] += 1
else:
message = "Successfully reset metadata on repository %s owned by %s" % \
( str( repository.name ), str( repository.owner ) )
results[ 'successful_count' ] += 1
except Exception as e:
message = "Error resetting metadata on repository %s owned by %s: %s" % \
( str( repository.name ), str( repository.owner ), str( e ) )
results[ 'unsuccessful_count' ] += 1
results[ 'repository_status' ].append( message )
stop_time = strftime( "%Y-%m-%d %H:%M:%S" )
results[ 'stop_time' ] = stop_time
return json.dumps( results, sort_keys=True, indent=4 )
