def test_get_magni_info(self):
magni_info = _annotation.get_magni_info()
magni_info_keys = sorted(list(magni_info.keys()))
self.assertListEqual(self.ref_magni_info_keys, magni_info_keys)
def test_get_magni_info(self):
magni_info = _annotation.get_magni_info()
magni_info_keys = sorted(list(magni_info.keys()))
self.assertListEqual(self.ref_magni_info_keys, magni_info_keys)
def annotate_database(h5file):
"""
Annotate an HDF5 database with information about Magni and the platform.
The annotation consists of a group in the root of the `h5file` having nodes
that each provide information about Magni or the platform on which this
function is run.
Parameters
----------
h5file : tables.file.File
The handle to the HDF5 database that should be annotated.
See Also
--------
magni.reproducibility._annotation.get_conda_info : Conda annotation
magni.reproducibility._annotation.get_git_revision : Git annotation
magni.reproducibility._annotation.get_platform_info : Platform annotation
magni.reproducibility._annotation.get_datetime : Date and time annotation
magni.reproducibility._annotation.get_magni_config : Magni config
annotation
magni.reproducibility._annotation.get_magni_info : Magni info annotation
Notes
-----
The annotations of the database includes the following:
* conda_info - Information about Continuum Anacononda install
* git_revision - Git revision and tag of Magni
* platform_info - Information about the current platform (system)
* datetime - The current date and time
* magni_config - Infomation about the current configuration of Magni
* magni_info - Information from `help(magni)`
Examples
--------
Annotate the database named 'db.hdf5':
>>> import magni
>>> from magni.reproducibility.io import annotate_database
>>> with magni.utils.multiprocessing.File('db.hdf5', mode='a') as h5file:
... annotate_database(h5file)
"""
@_decorate_validation
def validate_input():
_generic('h5file', tables.file.File)
validate_input()
annotations = {
'conda_info': json.dumps(_annotation.get_conda_info()),
'git_revision': json.dumps(_annotation.get_git_revision()),
'platform_info': json.dumps(_annotation.get_platform_info()),
'datetime': json.dumps(_annotation.get_datetime()),
'magni_config': json.dumps(_annotation.get_magni_config()),
'magni_info': json.dumps(_annotation.get_magni_info())
}
try:
annotations_group = h5file.create_group('/', 'annotations')
for annotation in annotations:
h5file.create_array(annotations_group,
annotation,
obj=annotations[annotation].encode())
h5file.flush()
except tables.NodeError:
raise tables.NodeError('The database has already been annotated. ' +
'Remove the existing annotation prior to ' +
'(re)annotating the database.')
def annotate_database(h5file):
"""
Annotate an HDF5 database with information about Magni and the platform.
The annotation consists of a group in the root of the `h5file` having nodes
that each provide information about Magni or the platform on which this
function is run.
Parameters
----------
h5file : tables.file.File
The handle to the HDF5 database that should be annotated.
See Also
--------
magni.reproducibility._annotation.get_conda_info : Conda annotation
magni.reproducibility._annotation.get_git_revision : Git annotation
magni.reproducibility._annotation.get_platform_info : Platform annotation
magni.reproducibility._annotation.get_datetime : Date and time annotation
magni.reproducibility._annotation.get_magni_config : Magni config
annotation
magni.reproducibility._annotation.get_magni_info : Magni info annotation
Notes
-----
The annotations of the database includes the following:
* conda_info - Information about Continuum Anacononda install
* git_revision - Git revision and tag of Magni
* platform_info - Information about the current platform (system)
* datetime - The current date and time
* magni_config - Infomation about the current configuration of Magni
* magni_info - Information from `help(magni)`
Examples
--------
Annotate the database named 'db.hdf5':
>>> from magni.reproducibility.io import annotate_database
>>> with magni.utils.multiprocessing.File('db.hdf5', mode='a') as h5file:
... annotate_database(h5file)
"""
_validate_annotate_database(h5file)
annotations = {'conda_info': json.dumps(_annotation.get_conda_info()),
'git_revision': json.dumps(_annotation.get_git_revision()),
'platform_info': json.dumps(
_annotation.get_platform_info()),
'datetime': json.dumps(_annotation.get_datetime()),
'magni_config': json.dumps(_annotation.get_magni_config()),
'magni_info': json.dumps(_annotation.get_magni_info())}
try:
annotations_group = h5file.create_group('/', 'annotations')
for annotation in annotations:
h5file.create_array(annotations_group, annotation,
obj=annotations[annotation].encode())
h5file.flush()
except tables.NodeError:
raise tables.NodeError('The database has already been annotated. ' +
'Remove the existing annotation prior to ' +
'(re)annotating the database.')