def _get_dataset_partition_record(did, pid):
from databundles.identity import ObjectNumber, DatasetNumber, PartitionNumber
don = ObjectNumber.parse(did)
if not don or not isinstance(don, DatasetNumber):
raise exc.BadRequest('Dataset number {} is not valid'.format(did))
pon = ObjectNumber.parse(pid)
if not pon or not isinstance(pon, PartitionNumber):
raise exc.BadRequest('Partition number {} is not valid'.format(pid))
if str(pon.dataset) != str(don):
raise exc.BadRequest('Partition number {} does not belong to datset {}'.format(pid, did))
gr = get_library().get(did)
# Need to read the file early, otherwise exceptions here
# will result in the cilent's ocket disconnecting.
if not gr:
raise exc.NotFound('No dataset for id: {}'.format(did))
bundle = gr.bundle
partition = bundle.partitions.get(pid)
return bundle,partition
def get(self,bp_id):
'''Get a bundle or partition
Gets a bundle or Partition object, referenced by a string generated by
DatasetNumber or PartitionNumber, or by an object that has a name
or id_ field.
Args:
bp_id (Bundle|Partition|str) Specifies a bundle or partition to
fetch. bp_id may be:
An ObjectNumber string id for a partition or dataset
An ObjectNumber object
An Identity object, for a partition or bundle
Any object that has an 'identity' attribute that is an Identity object
Returns:
Bundle|Partition
'''
from databundles.identity import ObjectNumber, PartitionNumber, Identity
from databundles.orm import Dataset
from databundles.orm import Partition
import sqlalchemy.orm.exc
s = self.session
if isinstance(bp_id, basestring):
bp_id = ObjectNumber.parse(bp_id)
elif isinstance(bp_id, ObjectNumber):
pass
elif isinstance(bp_id, Identity):
if not bp_id.id_:
raise Exception("Identity does not have an id_ defined")
bp_id = ObjectNumber.parse(bp_id.id_)
else:
# hope that is has an identity field
bp_id = ObjectNumber.parse(bp_id.identity.id_)
dataset = None
partition = None
try:
if isinstance(bp_id, PartitionNumber):
query = s.query(Dataset, Partition).join(Partition).filter(Partition.id_ == str(bp_id))
dataset, partition = query.one();
else:
query = s.query(Dataset)
query = s.query(Dataset).filter(Dataset.id_ == str(bp_id))
dataset = query.one();
except sqlalchemy.orm.exc.NoResultFound as e: #@UnusedVariable
return None, None
#raise ResultCountError("Failed to find dataset or partition for: {}".format(str(bp_id)))
return dataset, partition
def add_column(self, name, **kwargs):
import sqlalchemy.orm.session
s = sqlalchemy.orm.session.Session.object_session(self)
name = Column.mangle_name(name)
if kwargs.get('sequence_id', False):
sequence = kwargs['sequence_id']
else:
sequence = None
row = Column(id=str(ColumnNumber(ObjectNumber.parse(self.id_),sequence)),
name=name,
t_id=self.id_,
**kwargs
)
for key, value in kwargs.items():
if key[0] != '_' and key not in ['d_id','t_id','name']:
setattr(row, key, value)
if isinstance(value, basestring) and len(value) == 0:
if key == 'is_primary_key':
value = False
setattr(row, key, value)
s.add(row)
if kwargs.get('commit', True):
s.commit()
return row
def before_update(mapper, conn, target):
'''Set the column id number based on the table number and the
sequence id for the column'''
if target.id_ is None:
table_on = ObjectNumber.parse(target.t_id)
target.id_ = str(ColumnNumber(table_on, target.sequence_id))
def __init__(self,table, **kwargs):
self.sequence_id = kwargs.get("sequence_id",len(table.columns)+1)
self.name = kwargs.get("name",None)
self.altname = kwargs.get("altname",None)
self.is_primary_key = _clean_flag(kwargs.get("is_primary_key",False))
self.datatype = kwargs.get("datatype",None)
self.size = kwargs.get("size",None)
self.precision = kwargs.get("precision",None)
self.width = kwargs.get("width",None)
self.sql = kwargs.get("sql",None)
self.flags = kwargs.get("flags",None)
self.description = kwargs.get("description",None)
self.keywords = kwargs.get("keywords",None)
self.measure = kwargs.get("measure",None)
self.units = kwargs.get("units",None)
self.universe = kwargs.get("universe",None)
self.scale = kwargs.get("scale",None)
self.data = kwargs.get("data",None)
# the table_name attribute is not stored. It is only for
# building the schema, linking the columns to tables.
self.table_name = kwargs.get("table_name",None)
if not self.name:
raise ValueError('Column must have a name')
self.t_id = table.id_
self.t_vid = table.vid
ton = ObjectNumber.parse(table.vid)
con = ColumnNumber(ton, self.sequence_id)
self.vid = str(con)
self.id = str(con.rev(None))
def _put(self, source, identity):
'''Put the source to the remote, creating a compressed version if
it is not originally compressed'''
from databundles.util import bundle_file_type
import gzip
import os, tempfile, uuid
from databundles.identity import ObjectNumber, DatasetNumber, PartitionNumber
id_ = identity.id_
on = ObjectNumber.parse(id_)
if not on:
raise ValueError("Failed to parse id: '{}'".format(id_))
if not isinstance(on, (DatasetNumber, PartitionNumber)):
raise ValueError("Object number '{}' is neither for a dataset nor partition".format(id_))
type_ = bundle_file_type(source)
if type_ == 'sqlite' or type_ == 'hdf':
import shutil
# If it is a plain sqlite file, compress it before sending it.
try:
cf = os.path.join(tempfile.gettempdir(),str(uuid.uuid4()))
with gzip.open(cf, 'wb') as out_f:
try:
shutil.copyfileobj(source, out_f)
except AttributeError:
with open(source) as in_f:
shutil.copyfileobj(in_f, out_f)
with open(cf) as sf_:
if isinstance(on,DatasetNumber ):
response = self.remote.datasets(id_).put(sf_)
else:
response = self.remote.datasets(str(on.dataset)).partitions(str(on)).put(sf_)
finally:
if os.path.exists(cf):
os.remove(cf)
elif type_ == 'gzip':
# the file is already gziped, so nothing to do.
if isinstance(on,DatasetNumber ):
response = self.remote.datasets(id_).put(source)
else:
response = self.remote.datasets(str(on.dataset)).partitions(str(on)).put(source)
else:
raise Exception("Bad file for id {} got type: {} ".format(id_, type_))
raise_for_status(response)
return response
def before_update(mapper, conn, target):
'''Set the Table ID based on the dataset number and the sequence number
for the table '''
if isinstance(target,Column):
raise TypeError('Got a column instead of a table')
if target.id_ is None:
dataset_id = ObjectNumber.parse(target.d_id)
target.id_ = str(TableNumber(dataset_id, target.sequence_id))
def _put(self, id_,source):
'''Put the source to the remote, creating a compressed version if
it is not originally compressed'''
from databundles.util import bundle_file_type
import gzip
import os, tempfile, uuid
from databundles.identity import ObjectNumber, DatasetNumber, PartitionNumber
on = ObjectNumber.parse(id_)
if not on:
raise ValueError("Failed to parse id: '{}'".format(id_))
if not isinstance(on, (DatasetNumber, PartitionNumber)):
raise ValueError("Object number '{}' is neither for a dataset nor partition".format(id_))
type_ = bundle_file_type(source)
if type_ == 'sqlite':
# If it is a plain sqlite file, compress it before sending it.
try:
cf = os.path.join(tempfile.gettempdir(),str(uuid.uuid4()))
f = gzip.open(cf, 'wb')
f.writelines(source)
f.close()
with open(cf) as source:
if isinstance(on,DatasetNumber ):
response = self.api.datasets(id_).put(source)
else:
response = self.api.datasets(str(on.dataset)).partitions(str(on)).put(source)
finally:
if os.path.exists(cf):
os.remove(cf)
elif type_ == 'gzip':
# the file is already gziped, so nothing to do.
if isinstance(on,DatasetNumber ):
response = self.api.datasets(id_).put(source)
else:
response = self.api.datasets(str(on.dataset)).partitions(str(on)).put(source)
else:
raise Exception("Bad file got type: {} ".format(type_))
raise_for_status(response)
return response
def __init__(self,dataset, **kwargs):
self.id_ = kwargs.get("id",kwargs.get("id_",None))
self.name = kwargs.get("name",kwargs.get("name",None))
self.vname = kwargs.get("vname",None)
self.sequence_id = kwargs.get("sequence_id",None)
self.d_id = kwargs.get("d_id",None)
self.space = kwargs.get("space",None)
self.time = kwargs.get("time",None)
self.t_id = kwargs.get("t_id",None)
self.grain = kwargs.get('grain',None)
self.format = kwargs.get('format',None)
self.segment = kwargs.get('segment',None)
self.data = kwargs.get('data',None)
self.d_id = dataset.id_
self.d_vid = dataset.vid
# See before_insert for setting self.vid and self.id_
if self.t_id:
don = ObjectNumber.parse(self.d_vid)
ton = ObjectNumber.parse(self.t_id)
self.t_vid = str(ton.rev( don.revision))
def __init__(self,**kwargs):
self.id_ = kwargs.get("oid",kwargs.get("id",kwargs.get("id_", None)) )
self.name = kwargs.get("name",None)
self.vname = kwargs.get("vname",None)
self.source = kwargs.get("source",None)
self.dataset = kwargs.get("dataset",None)
self.subset = kwargs.get("subset",None)
self.variation = kwargs.get("variation",None)
self.creator = kwargs.get("creator",None)
self.revision = kwargs.get("revision",None)
if not self.id_:
dn = DatasetNumber(None, self.revision )
self.vid = str(dn)
self.id_ = str(dn.rev(None))
elif not self.vid:
self.vid = str(ObjectNumber.parse(self.id_).rev(self.revision))
def before_insert(mapper, conn, target):
'''event.listen method for Sqlalchemy to set the seqience_id for this
object and create an ObjectNumber value for the id_'''
if target.sequence_id is None:
sql = text('''SELECT max(p_sequence_id)+1 FROM Partitions WHERE p_d_id = :did''')
max_id, = conn.execute(sql, did=target.d_id).fetchone()
if not max_id:
max_id = 1
target.sequence_id = max_id
don = ObjectNumber.parse(target.d_vid)
pon = PartitionNumber(don, target.sequence_id)
target.vid = str(pon)
target.id_ = str(pon.rev(None))
Partition.before_update(mapper, conn, target)
def __init__(self,dataset, **kwargs):
self.sequence_id = kwargs.get("sequence_id",None)
self.name = kwargs.get("name",None)
self.vname = kwargs.get("vname",None)
self.altname = kwargs.get("altname",None)
self.description = kwargs.get("description",None)
self.keywords = kwargs.get("keywords",None)
self.data = kwargs.get("data",None)
self.d_id = dataset.id_
self.d_vid = dataset.vid
don = ObjectNumber.parse(dataset.vid)
ton = TableNumber(don, self.sequence_id)
self.vid = str(ton)
self.id_ = str(ton.rev(None))
if self.name:
self.name = self.mangle_name(self.name)
self.init_on_load()
def get_ref(self,bp_id):
from databundles.identity import ObjectNumber, DatasetNumber, PartitionNumber, Identity, PartitionIdentity
if isinstance(bp_id, Identity):
if bp_id.id_:
bp_id = bp_id.id_
else:
bp_id = bp_id.name
# If dataset is not None, it means the file already is in the cache.
dataset = None
try:
on = ObjectNumber.parse(bp_id)
if not ( isinstance(on, DatasetNumber) or isinstance(on, PartitionNumber)):
raise ValueError("Object number must be for a Dataset or Partition: {} ".format(bp_id))
dataset, partition = self._get_bundle_path_from_id(bp_id) #@UnusedVariable
except:
pass
# Try it as a dataset name
if not dataset:
r = self.find(QueryCommand().identity(name = bp_id) )
if len(r) > 1:
raise Exception("Got more than one result")
elif len(r) == 0:
r = None
else:
r = r.pop()
if r:
dataset, partition = self._get_bundle_path_from_id(r.id_)
# Try the name as a partition name
if not dataset:
q = self.find(QueryCommand().partition(name = bp_id) )
if q:
r = q.pop(0)
if r:
dataset, partition = self._get_bundle_path_from_id(r.id_)
# No luck so far, so now try to get it from the remote library
if not dataset and self.remote:
import socket
try:
r = self.remote.find(bp_id)
if r:
r = r[0]
if r.is_partition:
dataset = r.as_dataset
partition = r
else:
dataset = r
partition = None
except socket.error:
self.logger.error("Connection to remote ")
elif dataset:
from identity import new_identity
dataset = Identity(**dataset.to_dict())
partition = new_identity(partition.to_dict()) if partition else None
if not dataset:
return False, False
return dataset, partition
def before_update(mapper, conn, target):
'''Set the column id number based on the table number and the
sequence id for the column'''
dataset = ObjectNumber.parse(target.d_id)
target.id_ = str(PartitionNumber(dataset, target.sequence_id))
def put_dataset(did):
'''Store a bundle, calling put() on the bundle file in the Library.
:param did: A dataset id string. must be parsable as a `DatasetNumber`
value
:rtype: string
:param pid: A partition id string. must be parsable as a `partitionNumber`
value
:rtype: string
:param payload: The bundle database file, which may be compressed.
:rtype: binary
'''
from databundles.identity import ObjectNumber, DatasetNumber
import stat
try:
cf = _read_body(request)
size = os.stat(cf).st_size
if size == 0:
raise exc.BadRequest("Got a zero size dataset file")
if not os.path.exists(cf):
raise exc.BadRequest("Non existent file")
# Now we have the bundle in cf. Stick it in the library.
# We're doing these exceptions here b/c if we don't read the body, the
# client will get an error with the socket closes.
try:
on = ObjectNumber.parse(did)
except ValueError:
raise exc.BadRequest("Unparse dataset id: {}".format(did))
if not isinstance(on, DatasetNumber):
raise exc.BadRequest("Bad dataset id, not for a dataset: {}".format(did))
# Is this a partition or a bundle?
try:
tb = DbBundle(cf)
type = tb.db_config.info.type
except Exception as e:
logger.error("Failed to access database: {}".format(cf))
raise
if( type == 'partition'):
raise exc.BadRequest("Bad data type: Got a partition")
if(tb.identity.id_ != did ):
raise exc.BadRequest("""Bad request. Dataset id of URL doesn't
match payload. {} != {}""".format(did,tb.identity.id_))
library_path, rel_path, url = get_library().put(tb) #@UnusedVariable
identity = tb.identity
# if that worked, OK to remove the temporary file.
finally :
pass
#os.remove(cf)
r = identity.to_dict()
r['url'] = url
return r
def get_ref(self,bp_id):
from databundles.identity import ObjectNumber, DatasetNumber, PartitionNumber, Identity
if isinstance(bp_id, Identity):
if bp_id.id_:
bp_id = bp_id.id_
else:
bp_id = bp_id.name
# If dataset is not None, it means the file already is in the cache.
dataset = None
try:
on = ObjectNumber.parse(bp_id)
if not ( isinstance(on, DatasetNumber) or isinstance(on, PartitionNumber)):
raise ValueError("Object number must be for a Dataset or Partition: {} ".format(bp_id))
dataset, partition = self._get_bundle_path_from_id(bp_id) #@UnusedVariable
except:
pass
# Try it as a dataset name
if not dataset:
r = self.find(QueryCommand().identity(name = bp_id) ).first()
if r:
dataset, partition = self._get_bundle_path_from_id(r[0].id_)
# Try the name as a partition name
if not dataset:
q = self.find(QueryCommand().partition(name = bp_id) )
r = q.first()
if r:
dataset, partition = self._get_bundle_path_from_id(r[1].id_)
# No luck so far, so now try to get it from the remote library
if not dataset and self.api:
from databundles.identity import Identity, PartitionIdentity
import socket
from databundles.orm import Dataset, Partition
try:
r = self.api.find(bp_id)
if r:
r = r[0]
if hasattr(r, 'Partition') and r.Partition is not None:
identity = PartitionIdentity(**(r.Partition._asdict()))
dataset = Dataset(**r.Dataset._asdict())
partition = ObjectNumber.parse(r.Partition.id)
else:
identity = Identity(**(r.Dataset._asdict()))
dataset = Dataset(**r.Dataset._asdict())
partition = None
except socket.error:
self.logger.error("Connection to remote {} failed".format(self.remote))
if not dataset:
return False, False
return dataset, partition
