def load(self, filename):
"""Load a result from the given JSON file."""
LOGGER.info("Loading result from '%s'.", filename)
if filename.endswith(".gz"):
with gzip.open(filename, "rb") as file_handle:
result = MemoteResult(
json.loads(file_handle.read().decode("utf-8")))
else:
with open(filename, "r", encoding="utf-8") as file_handle:
result = MemoteResult(json.load(file_handle))
# TODO (Moritz Beber): Validate the read-in JSON maybe? Trade-off
# between extra time taken and correctness. Maybe we re-visit this
# issue when there was a new JSON format version needed.
return result
def load(self, filename):
"""Load a result from the given JSON file."""
# TODO: validate the read-in JSON maybe?
LOGGER.info("Loading result from '%s'.", filename)
with open(filename, encoding="utf-8") as file_handle:
result = MemoteResult(json.load(file_handle))
return result
def __init__(self,
model,
experimental_config=None,
exclusive=None,
skip=None,
**kwargs):
"""
Collect and store values during testing.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
experimental_config : memote.ExperimentConfiguration, optional
A description of experiments.
exclusive : iterable, optional
Names of test cases or modules to run and exclude all others. Takes
precedence over ``skip``.
skip : iterable, optional
Names of test cases or modules to skip.
"""
super(ResultCollectionPlugin, self).__init__(**kwargs)
self._model = model
self._exp_config = experimental_config
self.results = MemoteResult()
self._xcld = frozenset() if exclusive is None else frozenset(exclusive)
self._skip = frozenset() if skip is None else frozenset(skip)
def load(self, commit=None):
"""Load a result from the database."""
git_info = self.record_git_info(commit)
LOGGER.info("Loading result from '%s'.", git_info.hexsha)
result = MemoteResult(
self.session.query(Result.memote_result).
filter_by(hexsha=git_info.hexsha).
one().memote_result)
# Add git info so the object is equivalent to the one returned by the
# RepoResultManager.
self.add_git(result.meta, git_info)
return result
def __init__(self,
model,
sbml_version=None,
experimental_config=None,
exclusive=None,
skip=None,
**kwargs):
"""
Collect and store values during testing.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
sbml_version: tuple, optional
A tuple reporting on the level, version, and FBC use of
the SBML file.
experimental_config : memote.ExperimentConfiguration, optional
A description of experiments.
exclusive : iterable, optional
Names of test cases or modules to run and exclude all others. Takes
precedence over ``skip``.
skip : iterable, optional
Names of test cases or modules to skip.
"""
super(ResultCollectionPlugin, self).__init__(**kwargs)
self._model = model
self._sbml_ver = sbml_version
self._exp_config = experimental_config
self.results = MemoteResult()
self.results.add_environment_information(self.results.meta)
self._xcld = frozenset() if exclusive is None else frozenset(exclusive)
self._skip = frozenset() if skip is None else frozenset(skip)
if LOGGER.getEffectiveLevel() <= logging.DEBUG:
self._model.solver.configuration.verbosity = 3
def mock_history_manager():
"""Build a mock history manager that already contains results."""
result1 = MemoteResult({
"meta": {
"branch": "master",
"commit_author": "John Doe",
"commit_hash": "3f4665356a24d76a9461043f62a2b12dab56c75f",
"packages": {
"SomePackate": "0.1.0"
},
"platform": "Darwin",
"python": "2.7.10",
"release": "14.5.0",
"timestamp": "2017-05-03 18:26:11+02:00"
},
"tests": {
"test_parametrized": {
"data": {
"parameter1": ["item2", "item3"],
"parameter2": ["item4", "item3"]
},
"duration": {
"parameter1": 0.12,
"parameter2": 0.32
},
"format_type": 'percent',
"message": {
"parameter1": "Some Message 1",
"parameter2": "Some Message 2"
},
"metric": {
"parameter1": 0.5,
"parameter2": 0.9
},
"result": {
"parameter1": "failed",
"parameter2": "failed"
},
"summary": "Some description of the test",
"title": "Parametrized Test"
},
"test_number": {
"data": ['x', 'y', 'z'],
"duration": 0.002,
"format_type": "count",
"message": "Some Message 3",
"result": "passed",
"summary": "Some description again",
"metric": 0.2,
"title": "Non-Parametrized Test"
}
}
})
result2 = MemoteResult({
"meta": {
"branch": "develop",
"commit_author": "John Doe",
"commit_hash": "6e30d6236f5d47ebb4be39253eaa6a5dcb487687",
"packages": {
"SomePackate": "0.1.0"
},
"platform": "Darwin",
"python": "2.7.10",
"release": "14.5.0",
"timestamp": "2017-05-03 18:50:11+02:00"
},
"tests": {
"test_parametrized": {
"data": {
"parameter1": ["item1", "item2"],
"parameter2": ["item2", "item3"]
},
"duration": {
"parameter1": 0.2,
"parameter2": 0.1
},
"format_type": 'percent',
"message": {
"parameter1": "Some Message 1",
"parameter2": "Some Message 2"
},
"metric": {
"parameter1": 1.0,
"parameter2": 1.0
},
"result": {
"parameter1": "failed",
"parameter2": "failed"
},
"summary": "Some description of the test",
"title": "Parametrized Test"
},
"test_number": {
"data": ['x', 'y', 'z'],
"duration": 0.002,
"format_type": "count",
"message": "Some Message 3",
"result": "passed",
"summary": "Some description again",
"metric": 0.6,
"title": "Non-Parametrized Test"
}
}
})
branch_structure = {
"commits": {
"3f4665356a24d76a9461043f62a2b12dab56c75f": {
"timestamp": "2017-05-03 18:26:11+02:00",
"author": "John Doe",
"email": "*****@*****.**"
},
"6e30d6236f5d47ebb4be39253eaa6a5dcb487687": {
"timestamp": "2017-05-03 18:50:11+02:00",
"author": "John Doe",
"email": "*****@*****.**"
}
},
"branches": {
"master": ["3f4665356a24d76a9461043f62a2b12dab56c75f"],
"develop": [
"6e30d6236f5d47ebb4be39253eaa6a5dcb487687",
"3f4665356a24d76a9461043f62a2b12dab56c75f"
]
}
}
results = {
"3f4665356a24d76a9461043f62a2b12dab56c75f": result1,
"6e30d6236f5d47ebb4be39253eaa6a5dcb487687": result2,
}
# Create mock history manager.
class History(object):
def __init__(self, **kwargs):
super(History, self).__init__(**kwargs)
self._results = results
self._history = branch_structure
def get_result(self, commit):
return results[commit]
def iter_branches(self):
return iteritems(self._history["branches"])
def build_branch_structure(self):
pass
def load_history(self):
pass
return History()