def __init__(self,
app,
session,
file_info,
host_url=None,
external_endpoint=None,
custom_uri=None):
"""init
Parameters
----------
app : Flask
Flask app
session :
AskOmics session
file_info : dict
file info
host_url : None, optional
AskOmics url
"""
File.__init__(self,
app,
session,
file_info,
host_url,
external_endpoint=external_endpoint,
custom_uri=custom_uri)
self.entity_name = ''
self.category_values = {}
self.attributes = {}
self.attribute_abstraction = []
self.faldo_entity = True
def __init__(self,
app,
session,
file_info,
host_url=None,
external_endpoint=None,
custom_uri=None):
"""init
Parameters
----------
app : Flask
Flask app
session :
AskOmics session
file_info : dict
file info
host_url : None, optional
AskOmics url
"""
File.__init__(self,
app,
session,
file_info,
host_url,
external_endpoint=external_endpoint,
custom_uri=custom_uri)
self.type_dict = {
"rdf/ttl": "turtle",
"rdf/xml": "xml",
"rdf/nt": "nt"
}
def __init__(self,
app,
session,
file_info,
host_url=None,
external_endpoint=None,
custom_uri=None):
"""init
Parameters
----------
app : Flask
Flask app
session :
AskOmics session
file_info : dict
file info
host_url : None, optional
AskOmics url
"""
File.__init__(self,
app,
session,
file_info,
host_url,
external_endpoint=external_endpoint,
custom_uri=custom_uri)
def integrate(self, dataset_id, entities, public=True):
"""Integrate GFF file
Parameters
----------
entities : List
Entities to integrate
public : bool, optional
Insert in public dataset
"""
self.public = public
self.entities_to_integrate = entities
File.integrate(self, dataset_id=dataset_id)
def integrate(self, dataset_id, entity_name="", public=True):
"""Integrate BED file
Parameters
----------
entities : List
Entities to integrate
public : bool, optional
Insert in public dataset
"""
self.public = public
if entity_name:
self.entity_name = entity_name
else:
self.entity_name = self.human_name
File.integrate(self, dataset_id=dataset_id)
def integrate(self,
dataset_id,
forced_columns_type,
forced_header_names=None,
public=False):
"""Integrate the file
Parameters
----------
forced_columns_type : list
columns type
public : bool, optional
True if dataset will be public
"""
self.public = public
self.set_preview_and_header()
self.force_columns_type(forced_columns_type)
if forced_header_names:
self.force_header_names(forced_header_names)
File.integrate(self, dataset_id=dataset_id)
def __init__(self,
app,
session,
file_info,
host_url=None,
external_endpoint=None,
custom_uri=None):
"""init
Parameters
----------
app : Flask
Flask app
session :
AskOmics session
file_info : dict
file info
host_url : None, optional
AskOmics url
"""
File.__init__(self,
app,
session,
file_info,
host_url,
external_endpoint=external_endpoint,
custom_uri=custom_uri)
self.preview_limit = 30
try:
self.preview_limit = self.settings.getint("askomics", "npreview")
except Exception:
pass
self.header = []
self.preview = []
self.columns_type = []
self.category_values = {}