def ac_method(name, description, required=True, default=AC_MODEL_NAIVE_BAYES):
return CaseSensitiveStringParameter(name, description,
required=required,
allow_multiple=False,
enum=[AC_MODEL_GMM, AC_MODEL_NAIVE_BAYES,
AC_MODEL_CUTPOINT],
default=default)
def chromosome_num(required=False, allow_multiple=True,
param_type=PARAMETER_TYPES.query): # @UndefinedVariable
""" Create a parameter instance for specifying chromosome number. """
return CaseSensitiveStringParameter(CHR_NUM, "Comma separated " \
"integers specifying chromosome " \
"numbers. ", required=required,
allow_multiple=allow_multiple,
param_type=param_type)
def sequence_names(required=False, allow_multiple=True,
param_type=PARAMETER_TYPES.query): # @UndefinedVariable
""" Create a parameter instance for specifying sequence name(s). """
return CaseSensitiveStringParameter(SEQUENCE_NAME, "Comma separated " \
"sequence name(s). ",
param_type=param_type,
required=required,
allow_multiple=allow_multiple)
def filenames(required=True, allow_multiple=True,
param_type=PARAMETER_TYPES.query): # @UndefinedVariable
""" Create a parameter instance for specifying filename(s). """
return CaseSensitiveStringParameter(FILENAMES, "Comma separated list " \
"of target filename(s) to delete.",
param_type=param_type,
required=required,
allow_multiple=allow_multiple)
def snpsearch_name(required=False, allow_multiple=True,
param_type=PARAMETER_TYPES.query): # @UndefinedVariable
""" Create a parameter instance for specifying chromosome number. """
return CaseSensitiveStringParameter(SNP_SEARCH_NAME, "Comma " \
"separated integers specifying " \
"snp search name. ",
required=required,
allow_multiple=allow_multiple,
param_type=param_type)
def format():
"""
Create a parameter instance for defining the return format of the
result.
"""
return CaseSensitiveStringParameter(FORMAT, "Format of result.",
FORMATS._fields,
default=FORMATS.json, # @UndefinedVariable
allow_multiple=False)
def available_stacks(cls, name, description, stack_type, required=True, allow_multiple=False):
existing_stacks = cls._DB_CONNECTOR.find(IMAGES_COLLECTION,
{STACK_TYPE: stack_type},
[NAME])
uniq_names = set([rec[NAME] for rec in existing_stacks])
return CaseSensitiveStringParameter(name, description,
required=required,
allow_multiple=allow_multiple,
enum=uniq_names)
def mon_camera_type(name=STACK_TYPE, description=None, required=True, allow_multiple=True,
default=None):
if not description:
description = "Comma separated list of available monitor cameras."
return CaseSensitiveStringParameter(name, description,
required=required,
allow_multiple=allow_multiple,
default=default,
enum={MONITOR1, MONITOR2})
def dyes(name=DYES, description=None, required=True, allow_multiple=True,
default=None):
if not description:
description = "Comma separated list of dye names."
return CaseSensitiveStringParameter(name, description,
required=required,
allow_multiple=allow_multiple,
default=default,
enum=get_dyes())
def cs_string(name, description, alias=None, required=True,
allow_multiple=False, enum=None):
return CaseSensitiveStringParameter(name, description,
alias=alias, required=required,
allow_multiple=allow_multiple)
def device(required=True, default=None):
return CaseSensitiveStringParameter(DEVICE, "Device name.",
required=required,
allow_multiple=False,
enum=get_devices(),
default=default)
def dye(name, description, required=False, default=None):
return CaseSensitiveStringParameter(name, description,
required=required,
allow_multiple=False,
enum=get_dyes(),
default=default)
def archive(required=True):
return CaseSensitiveStringParameter(ARCHIVE, "Archive directory name.",
required=required,
allow_multiple=False,
enum=get_archives())
def pa_data_source(required=True):
return CaseSensitiveStringParameter(PA_DATA_SOURCE, "Primary analysis data source.",
required=required,
allow_multiple=False,
enum=get_archives()+get_hdf5_dataset_names())
