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, value in annotations.iteritems():
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.iteritems()})
else:
elements = _to_list(value)
if all((isinstance(elem, basestring) 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) or isinstance(elem, long) 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 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 isPrivate: 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 date or blob annotations are supported, they are not
`documented <http://rest.synapse.org/org/sagebionetworks/repo/model/annotation/Annotations.html>`_
"""
if is_submission_status_annotations(annotations):
return annotations
synapseAnnos = {}
for key, value in annotations.iteritems():
if key in ['objectId', 'scopeId', 'stringAnnos','longAnnos','doubleAnnos']:
synapseAnnos[key] = value
elif isinstance(value, bool):
synapseAnnos.setdefault('stringAnnos', []).append({ 'key':key, 'value':unicode(value).lower(), 'isPrivate':is_private })
elif isinstance(value, int) or isinstance(value, long):
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, basestring):
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':unicode(value), 'isPrivate':is_private })
return synapseAnnos
