class Data(BaseMetadata):
""" """
name = 'idsvc.data'
def __init__(self, *args, **kwargs):
"""
Required Parameter:
api_client # AgavePy client
Optional Parameters:
uuid # unique identifier for existing metadata object
body # information held in metadata 'value' field
meta # json or dictionary, values may include:
# uuid, owner, schemaId, internalUsername,
# associationIds, lastUpdated, name, value,
# created, _links
Explicit parameters take precedence over values found in the meta dictionary
"""
super(Data, self).__init__(*args, **kwargs)
self.system = None
system_id = kwargs.get('system_id', None)
path = kwargs.get('path', None)
sra_id = kwargs.get('sra_id', None)
if system_id is not None:
self.system_id = system_id
else:
self.system_id = self.value.get('system_id', None)
if self.system_id is not None:
self.value.update({'system_id': self.system_id})
if path is not None:
self.path = path
else:
self.path = self.value.get('path', None)
if self.path is not None:
self.value.update({'path': self.path})
if sra_id is not None:
self.sra_id = sra_id
else:
self.sra_id = self.value.get('sra_id', None)
if self.sra_id is not None:
self.value.update({'sra_id': self.sra_id})
@property
def title(self):
## When is the 'name' get set?
file_name = self.value.get('name')
if file_name:
return file_name
else:
return self.sra_id
@property
def project(self):
return next(iter([x for x in self.containers if x.name == 'idsvc.project']), None)
@property
def specimen(self):
return next(iter([x for x in self.containers if x.name == 'idsvc.specimen']), None)
@property
def process(self):
return next(iter([x for x in self.is_input_to + self.is_output_of if x.name == 'idsvc.process']), None)
@property
def datasets(self):
return [x for x in self.containers if x.name == 'idsvc.datasets']
@property
def input_to_process(self):
return [x for x in self.is_input_to if x.name == 'idsvc.process']
@property
def output_of_process(self):
return [x for x in self.is_output_of if x.name == 'idsvc.process']
def add_project(self, project):
""" """
self.add_container(project)
def load_file_info(self):
if self.system_id is None:
exception_msg = 'Missing system id, cannot load file info.'
logger.exception(exception_msg)
raise Exception(exception_msg)
if self.path is None:
exception_msg = 'Missing file path, cannot load file info.'
logger.exception(exception_msg)
raise Exception(exception_msg)
if self.system is None:
try:
self.system = System(api_client=self._api_client, system_id=self.system_id)
except Exception as e:
exception_msg = 'Unable to access system with system_id=%s.' % self.system_id
logger.error(exception_msg)
raise Exception(exception_msg)
try:
listing = self.system.listing(self.path)
file_info = next(iter(listing), None)
except Exception as e:
exception_msg = 'The path=%s could not be listed on system=%s. %s' \
% (self.path, self.system_id, e)
logger.error(exception_msg)
raise Exception(exception_msg)
try:
last_mod = file_info['lastModified']
file_info['lastModified'] = last_mod.strftime('%b %-d %I:%M')
except:
warning_msg = 'Listing response does not contain lastModified.'
logger.warning(warning_msg)
self.value = file_info
def _share(self, username, permission):
""""""
body=json.dumps({ 'username': username,
'permission': permission,
'recursive': False })
self._api_client.files.updatePermissions(
systemId=self.system_id,
filePath=self.value['path'],
body=body )
def save(self):
super(Data, self).save()
if self.path and self.system_id:
logger.debug('Sharing data with portal user...')
self._share(username='******', permission='READ')
def calculate_checksum(self):
""" """
name = "checksum"
app_id = "idsvc_checksum-0.1"
archive = True
portal_client = get_portal_api_client()
if self.sra_id:
parameters = {'UUID': self.uuid, 'SRA': self.sra_id}
body = {'name': name, 'appId': app_id, 'parameters': parameters}
else:
agave_url = "agave://%s/%s" % (self.system_id, self.path)
inputs = { 'AGAVE_URL': agave_url }
parameters = { 'UUID': self.uuid }
body={'name': name, 'appId': app_id, 'inputs': inputs, 'parameters': parameters, 'archive': archive}
try:
self.meta['value'].update(
{'checksum': None,
'lastChecksumUpdated': None,
'checksumConflict': None,
'checkStatus': None})
self.save()
except Exception as e:
exception_msg = 'Unable to initiate job. %s' % e
logger.error(exception_msg)
raise Exception(exception_msg)
try:
logger.debug("Job submission body: %s" % body)
import pprint
pprint.pprint(body)
# response = self._api_client.jobs.submit(body=body)
response = portal_client.jobs.submit(body=body)
logger.debug("Job submission response: %s" % response['id'])
except Exception as e:
exception_msg = 'Unable to initiate job. %s' % e
logger.error(exception_msg)
raise Exception(exception_msg)
return response
def delete(self):
"""Delete a data object, and remove relationships to it"""
if self.uuid is None:
raise Exception('Cannot delete without UUID.')
# delete all objects that have this object's uuid in their associationIds
for container in self.containers:
logger.debug('removing part (%s): %s - %s, from container (%s): : %s - %s' %
(self.name, self.uuid, self.title, container.name, container.uuid, container.title))
container.remove_part(self)
container.save()
logger.debug('deleting %s: %s - %s' % (self.name, self.uuid, self.title))
try:
self._api_client.meta.deleteMetadata(uuid=self.uuid)
except Exception as e:
logger.debug('Object does not exist, probably previously deleted. Error: %s' % e)
self.uuid = None
