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# @author: Gunnar Schaefer
import logging
log = logging.getLogger('scitran.api')
import os
import copy
import shutil
import difflib
import datetime
import scitran.data
PROJECTION_FIELDS = ['timestamp', 'permissions', 'public']
def insert_file(dbc, _id, file_info, filepath, digest, data_path, quarantine_path):
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filename = os.path.basename(filepath)
if _id is None:
try:
log.info('Parsing %s' % filename)
dataset = scitran.data.parse(filepath)
except scitran.data.DataError:
q_path = tempfile.mkdtemp(prefix=datetime.datetime.now().strftime('%Y%m%d_%H%M%S_'), dir=quarantine_path)
shutil.move(filepath, q_path)
return 202, 'Quarantining %s (unparsable)' % filename
log.info('Sorting %s' % filename)
_id = _update_db(dbc.database, dataset)
file_spec = dict(
_id=_id,
files={'$elemMatch': {
'type': dataset.nims_file_type,
'kinds': dataset.nims_file_kinds,
'state': dataset.nims_file_state,
}},
)
file_info = dict(
name=dataset.nims_file_name,
ext=dataset.nims_file_ext,
size=os.path.getsize(filepath),
sha1=digest,
#hash=dataset.nims_hash, TODO: datasets should be able to hash themselves (but not here)
type=dataset.nims_file_type,
kinds=dataset.nims_file_kinds,
state=dataset.nims_file_state,
)
filename = dataset.nims_file_name + dataset.nims_file_ext
else:
file_spec = dict(
_id=_id,
files={'$elemMatch': {
'type': file_info['type'],
'kinds': file_info['kinds'],
'state': file_info['state'],
}},
)
container_path = os.path.join(data_path, str(_id)[-3:] + '/' + str(_id))
if not os.path.exists(container_path):
os.makedirs(container_path)
success = dbc.update(file_spec, {'$set': {'files.$': file_info}})
if not success['updatedExisting']:
dbc.update({'_id': _id}, {'$push': {'files': file_info}})
shutil.move(filepath, container_path + '/' + filename)
log.debug('Done %s' % os.path.basename(filepath)) # must use filepath, since filename is updated for sorted files
return 200, 'Success'
def _update_db(db, dataset):
#TODO: possibly try to keep a list of session IDs on the project, instead of having the session point to the project
# same for the session and acquisition
# queries might be more efficient that way
session_spec = {'uid': dataset.nims_session_id}
session = db.sessions.find_one(session_spec, ['project'])
if session: # skip project creation, if session exists
project = db.projects.find_one({'_id': session['project']}, fields=PROJECTION_FIELDS)
else:
existing_group_ids = [g['_id'] for g in db.groups.find(None, ['_id'])]
group_id_matches = difflib.get_close_matches(dataset.nims_group_id, existing_group_ids, cutoff=0.8)
if len(group_id_matches) == 1:
group_id = group_id_matches[0]
project_name = dataset.nims_project or 'untitled'
else:
group_id = 'unknown'
project_name = dataset.nims_group_id + ('/' + dataset.nims_project if dataset.nims_project else '')
group = db.groups.find_one({'_id': group_id})
project_spec = {'group_id': group['_id'], 'name': project_name}
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project = db.projects.find_and_modify(
project_spec,
{'$setOnInsert': {'group.name': group.get('name'), 'permissions': group['roles'], 'public': False, 'files': []}},
upsert=True,
new=True,
fields=PROJECTION_FIELDS,
)
session = db.sessions.find_and_modify(
session_spec,
{
'$setOnInsert': dict(project=project['_id'], permissions=project['permissions'], public=project['public'], files=[]),
'$set': _entity_metadata(dataset, dataset.session_properties, session_spec), # session_spec ensures non-empty $set
'$addToSet': {'domains': dataset.nims_file_domain},
},
upsert=True,
new=True,
fields=PROJECTION_FIELDS,
)
acquisition_spec = {'uid': dataset.nims_acquisition_id}
acquisition = db.acquisitions.find_and_modify(
acquisition_spec,
{
'$setOnInsert': dict(session=session['_id'], permissions=session['permissions'], public=session['public'], files=[]),
'$set': _entity_metadata(dataset, dataset.acquisition_properties, acquisition_spec), # acquisition_spec ensures non-empty $set
'$addToSet': {'types': {'$each': [{'domain': dataset.nims_file_domain, 'kind': kind} for kind in dataset.nims_file_kinds]}},
},
upsert=True,
new=True,
fields=[],
)
if dataset.nims_timestamp:
db.projects.update({'_id': project['_id']}, {'$max': dict(timestamp=dataset.nims_timestamp)})
db.sessions.update({'_id': session['_id']}, {'$min': dict(timestamp=dataset.nims_timestamp), '$set': dict(timezone=dataset.nims_timezone)})
return acquisition['_id']
def _entity_metadata(dataset, properties, metadata={}, parent_key=''):
metadata = copy.deepcopy(metadata)
if dataset.nims_metadata_status is not None:
parent_key = parent_key and parent_key + '.'
for key, attributes in properties.iteritems():
if attributes['type'] == 'object':
metadata.update(_entity_metadata(dataset, attributes['properties'], parent_key=key))
else:
value = getattr(dataset, attributes['field']) if 'field' in attributes else None
if value or value == 0: # drop Nones and empty iterables
metadata[parent_key + key] = value
return metadata
def hrsize(size):
if size < 1000:
return '%d%s' % (size, 'B')
for suffix in 'KMGTPEZY':
size /= 1024.
if size < 10.:
return '%.1f%s' % (size, suffix)
if size < 1000.:
return '%.0f%s' % (size, suffix)
return '%.0f%s' % (size, 'Y')
def mongo_dict(d):
def _mongo_list(d, pk=''):
pk = pk and pk + '.'
return sum([_mongo_list(v, pk+k) if isinstance(v, dict) else [(pk+k, v)] for k, v in d.iteritems()], [])
return dict(_mongo_list(d))