def import_new_tools(self, request, queryset):
"""
Import tools description from Galaxy server
"""
for galaxy_server in queryset:
tool_import_report = Tool.import_tools(galaxy_server)
if tool_import_report['new']:
self.message_user(request, "%s successfully imported new tools." % (len(tool_import_report['new'])))
else:
self.message_user(request, "No new tools imported.",
level=messages.WARNING
)
def import_tools(self, galaxy_url, query, tool_id, force):
tools_found = []
if galaxy_url:
galaxy_server, created = Server.objects.get_or_create(
url=galaxy_url)
else:
try:
galaxy_server = Server.objects.get(current=True)
except Server.DoesNotExist:
raise CommandError(
'Server Galaxy does not exist, please use --galaxyurl')
tools_url = '%s/%s/%s/' % (galaxy_server.url, 'api', 'tools')
if tool_id:
# search specific tool
tools_url_id = '%s/%s/' % (tools_url, tool_id)
connection = requests.get(tools_url_id).json()
if 'traceback' in connection:
raise CommandError('Tool {} was not found in {}'.format(
tool_id, galaxy_server.url))
tools_found.append(connection.get('id'))
else:
# fetch list of tools
connection = requests.get(tools_url, params={'in_panel': "false"})
if connection.status_code == 200:
tools_list = connection.json() or []
for tool in tools_list:
_m = [
tool.get('id').lower(),
tool.get('name').lower(),
str(tool.get('panel_section_name')).lower()
]
if query in _m:
tools_found.append(tool.get('id'))
if tools_found:
self.stdout.write("%s" % ('\n'.join(tools_found)))
response = 'y' if force else raw_input(
'Do you want (re)import this tool(s)? [y/N] from {}:'.format(
galaxy_server))
if response.lower() == 'y':
import_tools_report = Tool.import_tools(galaxy_server,
tools=tools_found,
force=force)
if import_tools_report['new']:
self.stdout.write(
self.style.SUCCESS(
"%s successfully imported new tools." %
(len(import_tools_report['new']))))
for ti in import_tools_report['new']:
self.stdout.write(
self.style.SUCCESS("%s %s successfully imported" %
(ti.name, ti.version)))
else:
self.stdout.write(
self.style.WARNING("No new tool has been imported"))
for tool_id in import_tools_report['error']:
self.stdout.write(
self.style.ERROR("import of %s has failed " %
(tool_id)))
else:
self.stdout.write("No result was found for query %s" % (query))
def import_tools(self, galaxy_url, query, tool_id, force):
tools_found = []
if galaxy_url:
galaxy_server, created = Server.objects.get_or_create(
url=galaxy_url)
else:
try:
galaxy_server = Server.objects.get(current=True)
except Server.DoesNotExist:
raise CommandError(
'Server Galaxy does not exist, please use --galaxyurl')
tools_url = '%s/%s/%s/' % (galaxy_server.url, 'api', 'tools')
if tool_id:
# search specific tool
tools_url_id = '%s/%s/' % (tools_url, tool_id)
connection = requests.get(tools_url_id).json()
if 'traceback' in connection:
raise CommandError('Tool {} was not found in {}'.format(
tool_id, galaxy_server.url))
tools_found.append(connection.get('id'))
else:
# fetch list of tools
connection = requests.get(tools_url, params={'in_panel': "false"})
if connection.status_code == 200:
tools_list = connection.json() or []
for tool in tools_list:
_m = [
tool.get('id').lower(),
tool.get('name').lower(),
str(tool.get('panel_section_name')).lower()
]
if query in _m:
tools_found.append(tool.get('id'))
else:
raise CommandError('Cannot connect to Galaxy server {}'.format(galaxy_server.url))
if tools_found:
self.stdout.write("%s" % ('\n'.join(tools_found)))
response = 'y' if force else raw_input(
'Do you want (re)import this tool(s)? [y/N] from {}:'.format(galaxy_server))
if response.lower() == 'y':
import_tools_report = Tool.import_tools(
galaxy_server, tools=tools_found,
force=force)
if import_tools_report['new']:
self.stdout.write(
self.style.SUCCESS(
"%s successfully imported new tools." %
(len(import_tools_report['new']))))
for ti in import_tools_report['new']:
self.stdout.write(
self.style.SUCCESS(
"%s %s successfully imported" %
(ti.name, ti.version))
)
else:
self.stdout.write(self.style.WARNING(
"No new tool has been imported"))
for tool_id in import_tools_report['error']:
self.stdout.write(
self.style.ERROR(
"import of %s has failed " % (tool_id))
)
else:
self.stdout.write("No result was found for query %s" % (query))
