def chase_database(h5file):
"""
Chase an HDF5 database to track information about stack and source code.
The chase consist of a group in the root of the `h5file` having nodes that
each profide information about the program execution that led to this chase
of the database.
Parameters
----------
h5file : tables.file.File
The handle to the HDF5 database that should be chased.
See Also
--------
magni.reproducibility._chase.get_main_file_name : Name of main file
magni.reproducibility._chase.get_main_file_source : Main file source code
magni.reproducibility._chase.get_main_source : Source code around main
magni.reproducibility._chase.get_stack_trace : Complete stack trace
Notes
-----
The chase include the following information:
* main_file_name - Name of the main file/script that called this function
* main_file_source - Full source code of the main file/script
* main_source - Extract of main file source code that called this function
* stack_trace - Complete stack trace up until the call to this function
Examples
--------
Chase the database named 'db.hdf5':
>>> import magni
>>> from magni.reproducibility.io import chase_database
>>> with magni.utils.multiprocessing.File('db.hdf5', mode='a') as h5file:
... chase_database(h5file)
"""
@_decorate_validation
def validate_input():
_generic('h5file', tables.file.File)
validate_input()
chases = {
'main_file_name': json.dumps(_chase.get_main_file_name()),
'main_file_source': json.dumps(_chase.get_main_file_source()),
'main_source': json.dumps(_chase.get_main_source()),
'stack_trace': json.dumps(_chase.get_stack_trace())
}
try:
chase_group = h5file.create_group('/', 'chases')
for chase in chases:
h5file.create_array(chase_group, chase, obj=chases[chase].encode())
h5file.flush()
except tables.NodeError:
raise tables.NodeError('The database has already been chased. ' +
'Remove the existing chase prior to ' +
'(re)chasing the database.')
def test_get_stack_trace(self):
stack_trace = _chase.get_stack_trace()
self.assertIsInstance(stack_trace, str)
self.assertNotEqual(stack_trace, '')
self.assertNotIn('Failed', stack_trace)