def uninstall_tools(galaxy_server, api_key, names, force):
galaxy_instance = GalaxyInstance(url=galaxy_server, key=api_key)
toolshed_client = ToolShedClient(galaxy_instance)
temp_tool_list_file = 'tmp/installed_tool_list.yml'
# TODO: Switch to using bioblend to obtain this list
# ephemeris uses bioblend but without using ephemeris we cut out the need to for a temp file
os.system('get-tool-list -g %s -a %s -o %s --get_all_tools' %
(galaxy_server, api_key, temp_tool_list_file))
tools_to_uninstall = []
with open(temp_tool_list_file) as tool_file:
installed_tools = yaml.safe_load(tool_file.read())['tools']
if not installed_tools:
raise Exception('No tools to uninstall')
os.system('rm %s' % temp_tool_list_file)
for name in names:
revision = None
if '@' in name:
(name, revision) = name.split('@')
matching_tools = [
t for t in installed_tools if t['name'] == name and (
not revision or revision in t['revisions'])
]
if len(matching_tools) == 0:
id_string = 'name %s revision %s' % (
name, revision) if revision else 'name %s' % name
sys.stderr.write('*** Warning: No tool with %s\n' % id_string)
elif len(matching_tools) > 1 and not force:
sys.stderr.write(
'*** Warning: More than one toolshed tool found for %s. ' %
name +
'Not uninstalling any of these tools. Run script with --force (-f) flag to uninstall anyway\n'
)
else: # Either there is only one matching tool for the name and revision, or there are many and force=True
for tool in matching_tools:
tool_copy = tool.copy()
if revision:
tool_copy['revisions'] = [revision]
tools_to_uninstall.append(tool_copy)
for tool in tools_to_uninstall:
try:
name = tool['name']
owner = tool['owner']
tool_shed_url = tool['tool_shed_url']
revision = tool['revisions'][0]
sys.stderr.write('Uninstalling %s at revision %s\n' %
(name, revision))
return_value = toolshed_client.uninstall_repository_revision(
name=name,
owner=owner,
changeset_revision=revision,
tool_shed_url=tool_shed_url)
sys.stderr.write(str(return_value) + '\n')
except KeyError as e:
sys.stderr.write(e)
def uninstall_tools(galaxy_server, api_key, names, force):
tools_to_uninstall = []
galaxy_instance = GalaxyInstance(url=galaxy_server, key=api_key)
toolshed_client = ToolShedClient(galaxy_instance)
installed_tools = [
t for t in toolshed_client.get_repositories()
if t['status'] != 'Uninstalled'
]
for name in names:
revision = None
if '@' in name:
(name, revision) = name.split('@')
matching_tools = [
t for t in installed_tools if (t['name'] == name and (
not revision or revision == t['changeset_revision']))
]
id_string = 'name %s revision %s' % (
name, revision) if revision else 'name %s' % name
if len(matching_tools) == 0:
print('*** Warning: No tool with %s' % id_string)
elif len(matching_tools) > 1 and not force:
print(
'*** Warning: More than one toolshed tool found for %s. ' %
id_string +
'Not uninstalling any of these tools. Run script with --force (-f) flag to uninstall anyway'
)
else: # Either there is only one matching tool for the name and revision, or there are many and force=True
tools_to_uninstall.extend(matching_tools)
for tool in tools_to_uninstall:
try:
print('Uninstalling %s at revision %s' %
(tool['name'], tool['changeset_revision']))
return_value = toolshed_client.uninstall_repository_revision(
name=tool['name'],
owner=tool['owner'],
changeset_revision=tool['changeset_revision'],
tool_shed_url=tool['tool_shed'],
)
print(return_value)
except Exception as e:
print(e)