def entity_date_to_timestamp(entity_date_time):
"""Convert Synapse object date/time string (from modifiedOn or createdOn properties) to a timestamp."""
date_and_time = entity_date_time.split(".")[0]
date_time_obj = datetime.datetime.strptime(date_and_time,
"%Y-%m-%dT%H:%M:%S")
return to_unix_epoch_time(date_time_obj)
def to_synapse_annotations(annotations):
"""Transforms a simple flat dictionary to a Synapse-style Annotation object."""
if is_synapse_annotations(annotations):
return annotations
synapseAnnos = {}
for key in Annotations.system_properties:
if hasattr(annotations, key):
synapseAnnos[key] = getattr(annotations, key)
for key, value in annotations.items():
if key in ['id', 'etag', 'blobAnnotations', 'creationDate', 'uri']:
synapseAnnos[key] = value
elif key in ['stringAnnotations', 'longAnnotations', 'doubleAnnotations', 'dateAnnotations']\
and isinstance(value, collections.Mapping):
synapseAnnos.setdefault(key, {}).update({k: to_list(v) for k, v in value.items()})
else:
elements = to_list(value)
if all((isinstance(elem, str) for elem in elements)):
synapseAnnos.setdefault('stringAnnotations', {})[key] = elements
elif all((isinstance(elem, bool) for elem in elements)):
synapseAnnos.setdefault('stringAnnotations', {})[key] = [str(element).lower() for element in elements]
elif all((isinstance(elem, int) for elem in elements)):
synapseAnnos.setdefault('longAnnotations', {})[key] = elements
elif all((isinstance(elem, float) for elem in elements)):
synapseAnnos.setdefault('doubleAnnotations', {})[key] = elements
elif all((is_date(elem) for elem in elements)):
synapseAnnos.setdefault('dateAnnotations', {})[key] = [to_unix_epoch_time(elem) for elem in elements]
# TODO: support blob annotations
# elif all((isinstance(elem, ???) for elem in elements)):
# synapseAnnos.setdefault('blobAnnotations', {})[key] = [???(elem) for elem in elements]
else:
synapseAnnos.setdefault('stringAnnotations', {})[key] = [str(elem) for elem in elements]
return synapseAnnos
def _convert_to_annotations_list(annotations):
nested_annos = {}
for key, value in annotations.items():
elements = to_list(value)
element_cls = _annotation_value_list_element_type(elements)
if issubclass(element_cls, str):
nested_annos[key] = {'type': 'STRING', 'value': elements}
elif issubclass(element_cls, bool):
nested_annos[key] = {
'type': 'BOOLEAN',
'value': ['true' if e else 'false' for e in elements]
}
elif issubclass(element_cls, int):
nested_annos[key] = {
'type': 'LONG',
'value': [str(e) for e in elements]
}
elif issubclass(element_cls, float):
nested_annos[key] = {
'type': 'DOUBLE',
'value': [str(e) for e in elements]
}
elif issubclass(element_cls, (datetime.date, datetime.datetime)):
nested_annos[key] = {
'type': 'TIMESTAMP_MS',
'value': [str(to_unix_epoch_time(e)) for e in elements]
}
else:
nested_annos[key] = {
'type': 'STRING',
'value': [str(e) for e in elements]
}
return nested_annos
def to_submission_status_annotations(annotations, is_private=True):
"""
Converts a normal dictionary to the format used to annotate submission statuses, which is different from the format
used to annotate entities.
:param annotations: A normal Python dictionary whose values are strings, floats, ints or doubles
:param is_private: Set privacy on all annotations at once. These can be set individually using
:py:func:`set_privacy`.
Example::
from synapseclient.annotations import to_submission_status_annotations, from_submission_status_annotations
from datetime import datetime as Datetime
## create a submission and get its status
submission = syn.submit(evaluation, 'syn11111111')
submission_status = syn.getSubmissionStatus(submission)
## add annotations
submission_status.annotations = {'foo':'bar', 'shoe_size':12, 'IQ':12, 'timestamp':Datetime.now()}
## convert annotations
submission_status.annotations = to_submission_status_annotations(submission_status.annotations)
submission_status = syn.store(submission_status)
Synapse categorizes these annotations by: stringAnnos, doubleAnnos, longAnnos.
"""
if is_submission_status_annotations(annotations):
return annotations
synapseAnnos = {}
for key, value in annotations.items():
if key in [
'objectId', 'scopeId', 'stringAnnos', 'longAnnos',
'doubleAnnos'
]:
synapseAnnos[key] = value
elif isinstance(value, bool):
synapseAnnos.setdefault('stringAnnos', []) \
.append({'key': key, 'value': str(value).lower(), 'isPrivate': is_private})
elif isinstance(value, int):
synapseAnnos.setdefault('longAnnos', []) \
.append({'key': key, 'value': value, 'isPrivate': is_private})
elif isinstance(value, float):
synapseAnnos.setdefault('doubleAnnos', []) \
.append({'key': key, 'value': value, 'isPrivate': is_private})
elif isinstance(value, str):
synapseAnnos.setdefault('stringAnnos', []) \
.append({'key': key, 'value': value, 'isPrivate': is_private})
elif is_date(value):
synapseAnnos.setdefault('longAnnos', []) \
.append({'key': key, 'value': to_unix_epoch_time(value), 'isPrivate': is_private})
else:
synapseAnnos.setdefault('stringAnnos', []) \
.append({'key': key, 'value': str(value), 'isPrivate': is_private})
return synapseAnnos
def _process(self, deleteSamplesDf, modifiedOn):
col = ("genieSampleId"
if self._fileType == "sampleRetraction" else "geniePatientId")
deleteSamplesDf.rename(columns={0: col}, inplace=True)
samples = [
process_functions.checkGenieId(sample, self.center)
for sample in deleteSamplesDf[col]
]
deleteSamplesDf[col] = samples
modifiedOn = to_unix_epoch_time(
datetime.datetime.strptime(modifiedOn, "%Y-%m-%dT%H:%M:%S"))
deleteSamplesDf["retractionDate"] = modifiedOn
deleteSamplesDf["center"] = self.center
return deleteSamplesDf
def string_to_unix_epoch_time_milliseconds(string_time):
"""
Takes dates in this format: 2018-10-25T20:16:07.959Z
and turns it into unix epoch time in milliseconds
Args:
string_time: string in this format: 2018-10-25T20:16:07.959Z
Returns:
unix epoch time in milliseconds
"""
datetime_obj = datetime.datetime.strptime(
string_time.split(".")[0], "%Y-%m-%dT%H:%M:%S")
return to_unix_epoch_time(datetime_obj)
