def __init__(self,
algorithm,
config,
database_name,
parameters=None,
checkpoint=None):
Runner.__init__(self, algorithm, parameters, checkpoint)
self._config = config
self._database = Database(database_name, config)
self._perceptops = PerceptOps(config)
def main():
parser = argparse.ArgumentParser(
description=
'Deletes percepts from the database by tag and deletes the percept data files.'
)
parser.add_argument('database', help='Name of database to use')
parser.add_argument('tag', help='Percepts with this tag will be deleted')
parser.add_argument(
'-c',
'--config',
type=str,
default='~/.rigor.ini',
help='Path to .rigor.ini config file. Default: ~/.rigor.ini')
parser.add_argument('--keep-percept-data',
action='store_true',
default=False,
help="Don't remove the percept data files")
parser.add_argument('-n',
'--dryrun',
action='store_true',
default=False,
help="Don't actually delete anything")
args = parser.parse_args()
config = RigorDefaultConfiguration(args.config)
db = Database(args.database, config)
ops = PerceptOps(config)
if args.dryrun:
print('DRY RUN')
with db.get_session() as session:
percepts = session.query(Percept).join(PerceptTag).filter(
PerceptTag.name == args.tag).all()
if len(percepts) == 0:
print('No percepts have the tag "{}"'.format(args.tag))
for ii, percept in enumerate(percepts):
print('{} of {}: deleting percept with id {}'.format(
ii, len(percepts), percept.id))
if args.dryrun:
continue
if args.keep_percept_data:
# only delete database entry, not percept file
session.delete(percept)
else:
# delete percept data file as well as database entries
ops.destroy(percept, session)
if args.dryrun:
print('DRY RUN')
def importdb():
shutil.copyfile(constants.kFixtureFile, constants.kImportDatabase)
database = Database(constants.kImportDatabase, kConfig)
with database.get_session() as session:
session.query(Percept).delete()
return database
def importToRigor(rowStream, configFn, dryrun=False, verbose=False, overwrite=False, numRows=None):
# set up database
kConfig = rigor.config.RigorDefaultConfiguration(configFn)
kDbName = 'YOUR_DB_NAME_HERE'
db = Database(kDbName, kConfig)
print('Connecting to database...')
with db.get_session(commit=not dryrun) as session:
print('...connected')
print('Importing rows...')
lastHash = None
lastLocator = None
lastPerceptId = None
start = time.time()
for ii, row in enumerate(rowStream):
# cast everything to a string, in case we're getting live Python objects
# instead of reading from a file
# TODO: move this to csvtoolkit
for k, v in row.data.items():
if v is None: v = '' # CSV module saves None as ''
row.data[k] = str(v)
if row.data['_kind'] == 'percept':
#---------------------------------------- PERCEPT
# check for existing percept with same 'hash'
hash = row.data['p:hash']
if hash:
sqlExistingPercept = session.query(rigor.types.Percept).filter(rigor.types.Percept.hash == hash).first()
if sqlExistingPercept:
if overwrite:
print('TODO: overwrite')
raise NotImplementedError
else:
# skip this row
#print('WARNING: {} line {}: the percept hash "{}" is already in the Rigor database. Skipping this percept.'.format(row.filename, row.lineNumber, hash))
continue
# build percept
byte_count = row.data['p:byte_count']
if byte_count == '': byte_count = 0
percept = rigor.types.Percept()
session.add(percept)
percept.byte_count = byte_count
percept.credentials = row.data['p:credentials']
percept.device_id = row.data['p:device_id']
percept.format = row.data['p:format']
percept.hash = row.data['p:hash']
percept.locator = row.data['p:locator']
percept.stamp = datetime.datetime.strptime(row.data['p:stamp'], "%Y-%m-%dT%H:%M:%SZ" )
percept.x_size = row.data['p:x_size'] or None
percept.y_size = row.data['p:y_size'] or None
# sample_count, sample_rate, sensors, collections
# tags, properties
# tags
tags = row.data['p:tags']
if tags:
tags = tags.split(',')
for tag in tags:
percept.tags.append(rigor.types.PerceptTag(tag))
# properties
for fieldName, value in row.data.items():
if not fieldName.startswith('p:property:'):
continue
propertyName = fieldName.replace('p:property:', '')
if propertyName == '' or value == '':
continue
percept.properties[propertyName] = rigor.types.PerceptProperty(name=propertyName, value=value)
if verbose:
print('percept ready for the database:')
print(pprint.pformat(percept.serialize()))
#---------------------------------------- END PERCEPT
elif row.data['_kind'] == 'annotation':
#---------------------------------------- ANNOTATION
# check for existing annotation with same 'uid' property
uid = row.data['a:property:uid']
if uid:
sqlExistingAnnotation = session.query(rigor.types.AnnotationProperty).filter(rigor.types.AnnotationProperty.name == 'uid', rigor.types.AnnotationProperty.value == uid).first()
if sqlExistingAnnotation:
if overwrite:
print('TODO: overwrite')
raise NotImplementedError
else:
# skip this row
# print('WARNING: {} line {}: the annotation uid "{}" is already in the Rigor database. Skipping this annotation.'.format(row.filename, row.lineNumber, uid))
continue
# find the percept id to attach this annotation to
perceptId = None
hash = row.data['a:percept_hash']
locator = row.data['a:percept_locator']
if bool(hash) == bool(locator):
raise Exception('{}: line {}: annotation must have either a:percept_hash or a:percept_locator, but not both or neither.'.format(row.filename, row.lineNumber))
if hash:
if lastHash == hash:
perceptId = lastPerceptId
else:
try:
sqlPercept = session.query(rigor.types.Percept).filter(rigor.types.Percept.hash == hash).one()
perceptId = sqlPercept.id
lastHash = hash
lastPerceptId = perceptId
lastLocator = None
except sqlalchemy.orm.exc.NoResultFound:
raise Exception('ERROR: {} line {}: percept hash from CSV not found in Rigor db: {}'.format(row.filename, row.lineNumber, hash))
elif locator:
print('TODO: look up percept id from a:percept_locator')
raise NotImplementedError
# build annotation
annotation = rigor.types.Annotation()
session.add(annotation)
if row.data['a:boundary'] != '':
boundary = json.loads(row.data['a:boundary'])
if boundary:
annotation.boundary = boundary
if row.data['a:confidence'] != '':
annotation.confidence = int(row.data['a:confidence'])
annotation.domain = row.data['a:domain']
annotation.percept_id = perceptId
annotation.model = row.data['a:model']
# parse iso6801 formatted timestamp in UTC ('Z' suffix)
annotation.stamp = datetime.datetime.strptime(row.data['a:stamp'], "%Y-%m-%dT%H:%M:%SZ" )
# tags
tags = row.data['a:tags']
if tags:
tags = tags.split(',')
for tag in tags:
annotation.tags.append(rigor.types.AnnotationTag(tag))
# properties
for fieldName, value in row.data.items():
if not fieldName.startswith('a:property:'):
continue
propertyName = fieldName.replace('a:property:', '')
if propertyName == '' or value == '':
continue
annotation.properties[propertyName] = rigor.types.AnnotationProperty(name=propertyName, value=value)
if verbose:
print('annotation ready for the database:')
print(pprint.pformat(annotation.serialize()))
#---------------------------------------- ANNOTATION
else: # _kind is neither annotation nor percept
raise Exception('{}: line {}: Unknown value in "_kind" column: "{}". Should be "percept" or "annotation".'.format(row.filename, row.lineNumber, row.data['_kind']))
# flush the session occasionally
# this prevents a very large sqlalchemy session from building up locally, filling up memory
if (ii+1) % 10 == 0:
if numRows:
seconds = time.time() - start
secondsPerRow = seconds/(ii+1)
remainingRows = numRows - (ii+1)
secondsLeft = remainingRows * secondsPerRow
rowsPerMinute = 60 / max(secondsPerRow, 0.001)
print('{}: {} of {} complete. {} minutes left. {:0.1f} rows per minute.'.format(row.filename, ii+1, numRows, int(secondsLeft/60), rowsPerMinute))
else:
print('{} complete'.format(ii+1))
session.flush()
if not dryrun:
session.commit()
yield row
# done consuming rows from the stream.
# finished adding all the rows. now flush the session.
if dryrun:
print('Rolling back (DRY RUN)...')
else:
print('Flushing one more time, then committing...')
session.flush()
# with statement is over
if dryrun:
print('Rolled back transaction.')
else:
print('Transaction was committed.')
def get_database():
shutil.copyfile(constants.kFixtureFile, constants.kTestFile)
database = Database(constants.kTestFile, kConfig)
return database
