"""
API operations allowing clients to determine datatype supported by Galaxy.
"""
import logging
from galaxy import exceptions
from galaxy.datatypes.data import Data
from galaxy.util import asbool
from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless
from galaxy.web.base.controller import BaseAPIController
log = logging.getLogger(__name__)
[docs]class DatatypesController(BaseAPIController):
[docs] @expose_api_anonymous_and_sessionless
def index(self, trans, **kwd):
"""
GET /api/datatypes
Return an object containing upload datatypes.
"""
datatypes_registry = self._datatypes_registry
try:
extension_only = asbool(kwd.get('extension_only', True))
upload_only = asbool(kwd.get('upload_only', True))
if extension_only:
if upload_only:
return datatypes_registry.upload_file_formats
else:
return [ext for ext in datatypes_registry.datatypes_by_extension]
else:
rval = []
for datatype_info_dict in datatypes_registry.datatype_info_dicts:
if not datatype_info_dict.get('display_in_upload') and upload_only:
continue
rval.append(datatype_info_dict)
return rval
except Exception as exception:
log.error('could not get datatypes: %s', str(exception), exc_info=True)
if not isinstance(exception, exceptions.MessageException):
raise exceptions.InternalServerError(str(exception))
else:
raise
[docs] @expose_api_anonymous_and_sessionless
def mapping(self, trans, **kwd):
'''
GET /api/datatypes/mapping
Return a dictionary of class to class mappings.
'''
try:
ext_to_class_name = dict()
classes = []
for k, v in self._datatypes_registry.datatypes_by_extension.items():
c = v.__class__
ext_to_class_name[k] = c.__module__ + "." + c.__name__
classes.append(c)
class_to_classes = dict()
def visit_bases(types, cls):
for base in cls.__bases__:
if issubclass(base, Data):
types.add(base.__module__ + "." + base.__name__)
visit_bases(types, base)
for c in classes:
n = c.__module__ + "." + c.__name__
types = set([n])
visit_bases(types, c)
class_to_classes[n] = dict((t, True) for t in types)
return dict(ext_to_class_name=ext_to_class_name, class_to_classes=class_to_classes)
except Exception as exception:
log.error('could not get datatype mapping: %s', str(exception), exc_info=True)
if not isinstance(exception, exceptions.MessageException):
raise exceptions.InternalServerError(str(exception))
else:
raise
[docs] @expose_api_anonymous_and_sessionless
def sniffers(self, trans, **kwd):
'''
GET /api/datatypes/sniffers
Return a list of sniffers.
'''
try:
rval = []
for sniffer_elem in self._datatypes_registry.sniffer_elems:
datatype = sniffer_elem.get('type')
if datatype is not None:
rval.append(datatype)
return rval
except Exception as exception:
log.error('could not get datatypes: %s', str(exception), exc_info=True)
if not isinstance(exception, exceptions.MessageException):
raise exceptions.InternalServerError(str(exception))
else:
raise
[docs] @expose_api_anonymous_and_sessionless
def converters(self, trans, **kwd):
converters = []
for (source_type, targets) in self._datatypes_registry.datatype_converters.items():
for target_type in targets:
converters.append({
'source': source_type,
'target': target_type,
'tool_id': targets[target_type].id,
})
return converters
[docs] @expose_api_anonymous_and_sessionless
def edam_data(self, trans, **kwds):
return self._datatypes_registry.edam_data
@property
def _datatypes_registry(self):
return self.app.datatypes_registry