def __init__(
self,
id_: uuid.UUID,
duid: DataUnitID,
sample_node_address: SampleNodeAddress,
created: datetime.datetime,
created_by: UserID,
expired: datetime.datetime = None,
expired_by: UserID = None):
'''
Create the link. If expired is provided expired_by must also be provided. If expired
is falsy expired_by is ignored.
:param id_: the link ID. This is generally expected to be unique per link.
:param duid: the data ID.
:param sample_node_address: the sample node address.
:param created: the creation time for the link.
:param created_by: the user that created the link.
:param expired: the expiration time for the link or None if the link is not expired.
:param expired_by: the user that expired the link or None if the link is not expired.
'''
# may need to make this non ws specific. YAGNI for now.
self.id = _not_falsy(id_, 'id_')
self.duid = _not_falsy(duid, 'duid')
self.sample_node_address = _not_falsy(sample_node_address, 'sample_node_address')
self.created = _check_timestamp(created, 'created')
self.created_by = _not_falsy(created_by, 'created_by')
self.expired = None
self.expired_by = None
if expired:
self.expired = _check_timestamp(expired, 'expired')
if expired < created:
raise ValueError('link cannot expire before it is created')
self.expired_by = _not_falsy(expired_by, 'expired_by')
def _resolve_timestamp(self,
timestamp: datetime.datetime = None
) -> datetime.datetime:
if timestamp:
_check_timestamp(timestamp, 'timestamp')
else:
timestamp = self._now()
return timestamp
def __init__(self,
id_: UUID,
user: UserID,
nodes: List[SampleNode],
savetime: datetime.datetime,
name: Optional[str] = None,
version: Optional[int] = None):
'''
Create the sample.
:param id_: The ID of the sample.
:param user: The user who saved the sample.
:param nodes: The tree nodes in the sample. BIOLOGICAL_REPLICATES must come first in
the list, and parents must come before children in the list.
:param savetime: The time the sample was saved. Cannot be a naive datetime.
:param name: The name of the sample. Cannot contain control characters or be longer than
255 characters.
:param version: The version of the sample, or None if unknown.
:raise MissingParameterError: if no nodes are provided.
:raises IllegalParameterError: if the name is too long or contains illegal characters,
the first node in the list is not a BIOLOGICAL_REPLICATE, all the BIOLOGICAL_REPLICATES
are not at the start of this list, node names are not unique, or parent nodes
do not appear in the list prior to their children.
'''
# having None as a possible version doesn't sit well with me, but that means we need
# yet another class, so...
super().__init__(nodes, name)
self.id = _not_falsy(id_, 'id_')
self.user = _not_falsy(user, 'user')
self.savetime = _check_timestamp(savetime, 'savetime')
if version is not None and version < 1:
raise ValueError('version must be > 0')
self.version = version
def __init__(self,
owner: UserID,
lastupdate: datetime.datetime,
admin: Sequence[UserID] = None,
write: Sequence[UserID] = None,
read: Sequence[UserID] = None,
public_read: bool = False):
'''
Create the ACLs.
:param owner: the owner username.
:param lastupdate: the last time the ACLs were updated.
:param admin: the list of admin usernames.
:param write: the list of usernames with write privileges.
:param read: the list of usernames with read privileges.
:param public_read: a boolean designating whether the sample is publically readable.
None is considered false.
:raises IllegalParameterError: If a user appears in more than one ACL
'''
self.owner = _not_falsy(owner, 'owner')
self.lastupdate = _check_timestamp(lastupdate, 'lastupdate')
super().__init__(admin, write, read, public_read)
all_ = (self.admin, self.write, self.read)
for i in range(len(all_)):
if self.owner in all_[i]:
raise _IllegalParameterError(
'The owner cannot be in any other ACL')