def set_host_genus(self, value=None, attribute=None, format="empty_string"):
"""Set the host_genus from a value parsed from the indicated attribute.
The input data is split into multiple parts, and the first word is
used to set host_genus.
:param value:
the host genus of the phage genome
:type value: str
:param attribute:
the name of the genome attribute from which the
host_genus attribute will be set
:type attribute: str
:param format:
the default format if the input is an empty/null value.
:type format: str
"""
if value is None:
if (attribute is not None and hasattr(self, attribute)):
value = getattr(self, attribute)
else:
value = ""
if isinstance(value, str):
value = value.strip()
# The host_genus value may need to be split. But don't split until
# it is determined if the value is a null value.
value = basic.convert_empty(value, "empty_string")
if value != "":
self.host_genus = value.split(" ")[0]
else:
self.host_genus = basic.convert_empty(value, format)
def set_date(self, value, format="empty_datetime_obj"):
"""Set the date attribute.
:param value: Date
:type value: misc
:param format: Indicates the format if the value is empty.
:type format: str
"""
self.date = basic.convert_empty(value, format)
def set_accession(self, value, format="empty_string"):
"""Set the accession.
The Accession field in the MySQL database defaults to ''.
Some flat file accessions have the version number suffix, so discard
the version number.
:param value:
GenBank accession number.
:type value: str
:param format:
indicates the format of the data if it is not a
valid accession. Default is ''.
:type format: misc.
"""
if isinstance(value, str):
value = value.strip()
value = value.split(".")[0]
self.accession = basic.convert_empty(value, format)