def open_connection(self):
"""
Internal function to open the connection to the database. Only after this function is called the database is
accessable.
"""
if self._database is None:
self._database = DatabaseAccess(self._configuration['sql_connection_string'],
self._configuration['sql_table_name'])
def setUpClass(cls):
"""
Set up whole class for testing
Returns:
"""
# we assume everything working on sqlite, should also work on postgres in sqlalchemy
cls.database = DatabaseAccess("sqlite:///test_database.db",
"simulation")
def switch_to_central_database(self):
if self._use_local_database:
self.close_connection()
self._database = DatabaseAccess(
self._configuration['sql_connection_string'],
self._configuration['sql_table_name'])
self._use_local_database = False
else:
print('Database is already in central mode!')
def open_connection(self):
"""
Internal function to open the connection to the database. Only after this function is called the database is
accessable.
"""
if self._database is None and not self.database_is_disabled:
self._database = DatabaseAccess(
self._configuration["sql_connection_string"],
self._configuration["sql_table_name"],
)
def setUp(self):
self.jobstatus = JobStatus()
self.database = DatabaseAccess('sqlite:///test_job_status.db',
'simulation')
par_dict = {
'chemicalformula': 'H',
'computer': 'localhost',
'hamilton': 'Test',
'hamversion': '0.1',
'job': 'testing',
'parentid': 0,
'project': 'database.testing',
'projectpath': '/TESTING',
'status': 'initialized',
'timestart': datetime(2016, 5, 2, 11, 31, 4, 253377),
'timestop': datetime(2016, 5, 2, 11, 31, 4, 371165),
'totalcputime': 0.117788,
'username': '******'
}
self.job_id = self.database.add_item_dict(par_dict)
self.jobstatus_database = JobStatus(db=self.database,
job_id=self.job_id)
def switch_to_central_database(self):
"""
Switch to central database
"""
if self._use_local_database and not self.database_is_disabled:
self.close_connection()
self._database = DatabaseAccess(
self._configuration["sql_connection_string"],
self._configuration["sql_table_name"],
)
self._use_local_database = False
else:
print("Database is already in central mode or disabled!")
def switch_to_local_database(self, file_name='pyiron.db', cwd=None):
if not self._use_local_database:
if cwd is None and not os.path.isabs(file_name):
file_name = os.path.join(os.path.abspath(os.path.curdir),
file_name)
elif cwd is not None:
file_name = os.path.join(cwd, file_name)
self.close_connection()
self._database = DatabaseAccess(
'sqlite:///' + file_name,
self._configuration['sql_table_name'])
self._use_local_database = True
else:
print('Database is already in local mode!')
def switch_to_user_mode(self):
"""
Switch from viewer mode to user mode - if viewer_mode is enable pyiron has read only access to the database.
"""
if self._configuration['sql_view_connection_string'] is not None:
if self._database.viewer_mode:
self.close_connection()
self._database = DatabaseAccess(self._configuration['sql_connection_string'],
self._configuration['sql_table_name'])
self._database.viewer_mode = True
else:
print('Database is already in user mode!')
else:
print('Viewer Mode is not available on this pyiron installation.')
def switch_to_user_mode(self):
"""
Switch from viewer mode to user mode - if viewer_mode is enable pyiron has read only access to the database.
"""
if self._configuration["sql_view_connection_string"] is not None and not self.database_is_disabled:
if self._database.viewer_mode:
self.close_connection()
self._database = DatabaseAccess(
self._configuration["sql_connection_string"],
self._configuration["sql_table_name"],
)
self._database.viewer_mode = True
else:
print("Database is already in user mode!")
else:
print("Viewer Mode is not available on this pyiron installation.")
def setUpClass(cls):
cls.sub_status = SubmissionStatus()
cls.database = DatabaseAccess('sqlite:///test_sub_status.db', 'simulation')
par_dict = {'chemicalformula': 'H',
'computer': 'localhost#1#3',
'hamilton': 'Test',
'hamversion': '0.1',
'job': 'testing',
'parentid': 0,
'project': 'database.testing',
'projectpath': '/TESTING',
'status': 'suspended',
'timestart': datetime(2016, 5, 2, 11, 31, 4, 253377),
'timestop': datetime(2016, 5, 2, 11, 31, 4, 371165),
'totalcputime': 0.117788,
'username': '******'}
cls.job_id = cls.database.add_item_dict(par_dict)
cls.sub_status_database = SubmissionStatus(db=cls.database, job_id=cls.job_id)
class TestSubmissionStatus(unittest.TestCase):
def setUp(self):
self.sub_status = SubmissionStatus()
self.database = DatabaseAccess('sqlite:///test_sub_status.db',
'simulation')
par_dict = {
'chemicalformula': 'H',
'computer': 'localhost#1#3',
'hamilton': 'Test',
'hamversion': '0.1',
'job': 'testing',
'parentid': 0,
'project': 'database.testing',
'projectpath': '/TESTING',
'status': 'suspended',
'timestart': datetime(2016, 5, 2, 11, 31, 4, 253377),
'timestop': datetime(2016, 5, 2, 11, 31, 4, 371165),
'totalcputime': 0.117788,
'username': '******'
}
self.job_id = self.database.add_item_dict(par_dict)
self.sub_status_database = SubmissionStatus(db=self.database,
job_id=self.job_id)
def doCleanups(self):
self.database.conn.close()
os.remove('test_sub_status.db')
def test_submit_next(self):
before = self.sub_status.submitted_jobs
self.sub_status.submit_next()
self.assertEqual(before + 1, self.sub_status.submitted_jobs)
before = self.sub_status_database.submitted_jobs
self.sub_status_database.submit_next()
self.assertEqual(before + 1, self.sub_status_database.submitted_jobs)
def test_refresh(self):
self.sub_status.submitted_jobs = 5
self.sub_status.refresh()
self.assertEqual(5, self.sub_status.submitted_jobs)
self.sub_status_database.submitted_jobs = 5
self.sub_status_database.refresh()
self.assertEqual(5, self.sub_status_database.submitted_jobs)
def switch_to_local_database(self, file_name='pyiron.db', cwd=None):
"""
Swtich to an local SQLite based database.
Args:
file_name (str): SQLite database file name
cwd (str/None): directory where the SQLite database file is located in
"""
if not self._use_local_database:
if cwd is None and not os.path.isabs(file_name):
file_name = os.path.join(os.path.abspath(os.path.curdir), file_name)
elif cwd is not None:
file_name = os.path.join(cwd, file_name)
self.close_connection()
self._database = DatabaseAccess('sqlite:///' + file_name,
self._configuration['sql_table_name'])
self._use_local_database = True
else:
print('Database is already in local mode!')
def setUpClass(cls):
cls.sub_status = SubmissionStatus()
cls.database = DatabaseAccess("sqlite:///test_sub_status.db", "simulation")
par_dict = {
"chemicalformula": "H",
"computer": "localhost#1#3",
"hamilton": "Test",
"hamversion": "0.1",
"job": "testing",
"parentid": 0,
"project": "database.testing",
"projectpath": "/TESTING",
"status": "suspended",
"timestart": datetime(2016, 5, 2, 11, 31, 4, 253377),
"timestop": datetime(2016, 5, 2, 11, 31, 4, 371165),
"totalcputime": 0.117788,
"username": "******",
}
cls.job_id = cls.database.add_item_dict(par_dict)
cls.sub_status_database = SubmissionStatus(db=cls.database, job_id=cls.job_id)
class TestJobStatus(unittest.TestCase):
def setUp(self):
self.jobstatus = JobStatus()
self.database = DatabaseAccess('sqlite:///test_job_status.db',
'simulation')
par_dict = {
'chemicalformula': 'H',
'computer': 'localhost',
'hamilton': 'Test',
'hamversion': '0.1',
'job': 'testing',
'parentid': 0,
'project': 'database.testing',
'projectpath': '/TESTING',
'status': 'initialized',
'timestart': datetime(2016, 5, 2, 11, 31, 4, 253377),
'timestop': datetime(2016, 5, 2, 11, 31, 4, 371165),
'totalcputime': 0.117788,
'username': '******'
}
self.job_id = self.database.add_item_dict(par_dict)
self.jobstatus_database = JobStatus(db=self.database,
job_id=self.job_id)
def doCleanups(self):
self.database.conn.close()
os.remove('test_job_status.db')
def test_initialized(self):
self.assertTrue(self.jobstatus.initialized)
self.jobstatus.string = 'finished'
self.assertFalse(self.jobstatus.initialized)
self.assertFalse(self.jobstatus.appended)
self.assertFalse(self.jobstatus.created)
self.assertFalse(self.jobstatus.submitted)
self.assertFalse(self.jobstatus.running)
self.assertFalse(self.jobstatus.aborted)
self.assertFalse(self.jobstatus.collect)
self.assertFalse(self.jobstatus.suspended)
self.assertFalse(self.jobstatus.refresh)
self.assertFalse(self.jobstatus.busy)
self.assertTrue(self.jobstatus.finished)
self.jobstatus.initialized = True
self.assertTrue(self.jobstatus.initialized)
self.assertFalse(self.jobstatus.appended)
self.assertFalse(self.jobstatus.created)
self.assertFalse(self.jobstatus.submitted)
self.assertFalse(self.jobstatus.running)
self.assertFalse(self.jobstatus.aborted)
self.assertFalse(self.jobstatus.collect)
self.assertFalse(self.jobstatus.suspended)
self.assertFalse(self.jobstatus.refresh)
self.assertFalse(self.jobstatus.busy)
self.assertFalse(self.jobstatus.finished)
def test_appended(self):
self.jobstatus.appended = True
self.assertFalse(self.jobstatus.initialized)
self.assertTrue(self.jobstatus.appended)
self.assertFalse(self.jobstatus.created)
self.assertFalse(self.jobstatus.submitted)
self.assertFalse(self.jobstatus.running)
self.assertFalse(self.jobstatus.aborted)
self.assertFalse(self.jobstatus.collect)
self.assertFalse(self.jobstatus.suspended)
self.assertFalse(self.jobstatus.refresh)
self.assertFalse(self.jobstatus.busy)
self.assertFalse(self.jobstatus.finished)
def test_created(self):
self.jobstatus.created = True
self.assertFalse(self.jobstatus.initialized)
self.assertFalse(self.jobstatus.appended)
self.assertTrue(self.jobstatus.created)
self.assertFalse(self.jobstatus.submitted)
self.assertFalse(self.jobstatus.running)
self.assertFalse(self.jobstatus.aborted)
self.assertFalse(self.jobstatus.collect)
self.assertFalse(self.jobstatus.suspended)
self.assertFalse(self.jobstatus.refresh)
self.assertFalse(self.jobstatus.busy)
self.assertFalse(self.jobstatus.finished)
def test_submitted(self):
self.jobstatus.submitted = True
self.assertFalse(self.jobstatus.initialized)
self.assertFalse(self.jobstatus.appended)
self.assertFalse(self.jobstatus.created)
self.assertTrue(self.jobstatus.submitted)
self.assertFalse(self.jobstatus.running)
self.assertFalse(self.jobstatus.aborted)
self.assertFalse(self.jobstatus.collect)
self.assertFalse(self.jobstatus.suspended)
self.assertFalse(self.jobstatus.refresh)
self.assertFalse(self.jobstatus.busy)
self.assertFalse(self.jobstatus.finished)
def test_running(self):
self.jobstatus.running = True
self.assertFalse(self.jobstatus.initialized)
self.assertFalse(self.jobstatus.appended)
self.assertFalse(self.jobstatus.created)
self.assertFalse(self.jobstatus.submitted)
self.assertTrue(self.jobstatus.running)
self.assertFalse(self.jobstatus.aborted)
self.assertFalse(self.jobstatus.collect)
self.assertFalse(self.jobstatus.suspended)
self.assertFalse(self.jobstatus.refresh)
self.assertFalse(self.jobstatus.busy)
self.assertFalse(self.jobstatus.finished)
def test_aborted(self):
self.jobstatus.aborted = True
self.assertFalse(self.jobstatus.initialized)
self.assertFalse(self.jobstatus.appended)
self.assertFalse(self.jobstatus.created)
self.assertFalse(self.jobstatus.submitted)
self.assertFalse(self.jobstatus.running)
self.assertTrue(self.jobstatus.aborted)
self.assertFalse(self.jobstatus.collect)
self.assertFalse(self.jobstatus.suspended)
self.assertFalse(self.jobstatus.refresh)
self.assertFalse(self.jobstatus.busy)
self.assertFalse(self.jobstatus.finished)
def test_collect(self):
self.jobstatus.collect = True
self.assertFalse(self.jobstatus.initialized)
self.assertFalse(self.jobstatus.appended)
self.assertFalse(self.jobstatus.created)
self.assertFalse(self.jobstatus.submitted)
self.assertFalse(self.jobstatus.running)
self.assertFalse(self.jobstatus.aborted)
self.assertTrue(self.jobstatus.collect)
self.assertFalse(self.jobstatus.suspended)
self.assertFalse(self.jobstatus.refresh)
self.assertFalse(self.jobstatus.busy)
self.assertFalse(self.jobstatus.finished)
def test_suspended(self):
self.jobstatus.suspended = True
self.assertFalse(self.jobstatus.initialized)
self.assertFalse(self.jobstatus.appended)
self.assertFalse(self.jobstatus.created)
self.assertFalse(self.jobstatus.submitted)
self.assertFalse(self.jobstatus.running)
self.assertFalse(self.jobstatus.aborted)
self.assertFalse(self.jobstatus.collect)
self.assertTrue(self.jobstatus.suspended)
self.assertFalse(self.jobstatus.refresh)
self.assertFalse(self.jobstatus.busy)
self.assertFalse(self.jobstatus.finished)
def test_refresh(self):
self.jobstatus.refresh = True
self.assertFalse(self.jobstatus.initialized)
self.assertFalse(self.jobstatus.appended)
self.assertFalse(self.jobstatus.created)
self.assertFalse(self.jobstatus.submitted)
self.assertFalse(self.jobstatus.running)
self.assertFalse(self.jobstatus.aborted)
self.assertFalse(self.jobstatus.collect)
self.assertFalse(self.jobstatus.suspended)
self.assertTrue(self.jobstatus.refresh)
self.assertFalse(self.jobstatus.busy)
self.assertFalse(self.jobstatus.finished)
def test_busy(self):
self.jobstatus.busy = True
self.assertFalse(self.jobstatus.initialized)
self.assertFalse(self.jobstatus.appended)
self.assertFalse(self.jobstatus.created)
self.assertFalse(self.jobstatus.submitted)
self.assertFalse(self.jobstatus.running)
self.assertFalse(self.jobstatus.aborted)
self.assertFalse(self.jobstatus.collect)
self.assertFalse(self.jobstatus.suspended)
self.assertFalse(self.jobstatus.refresh)
self.assertTrue(self.jobstatus.busy)
self.assertFalse(self.jobstatus.finished)
def test_finished(self):
self.jobstatus.finished = True
self.assertFalse(self.jobstatus.initialized)
self.assertFalse(self.jobstatus.appended)
self.assertFalse(self.jobstatus.created)
self.assertFalse(self.jobstatus.submitted)
self.assertFalse(self.jobstatus.running)
self.assertFalse(self.jobstatus.aborted)
self.assertFalse(self.jobstatus.collect)
self.assertFalse(self.jobstatus.suspended)
self.assertFalse(self.jobstatus.refresh)
self.assertFalse(self.jobstatus.busy)
self.assertTrue(self.jobstatus.finished)
def test_string(self):
self.jobstatus.string = 'initialized'
self.assertTrue(self.jobstatus.initialized)
self.assertEqual(str(self.jobstatus), 'initialized')
self.assertEqual(self.jobstatus.string, 'initialized')
self.jobstatus.string = 'appended'
self.assertTrue(self.jobstatus.appended)
self.assertEqual(str(self.jobstatus), 'appended')
self.assertEqual(self.jobstatus.string, 'appended')
self.jobstatus.string = 'created'
self.assertTrue(self.jobstatus.created)
self.assertEqual(str(self.jobstatus), 'created')
self.assertEqual(self.jobstatus.string, 'created')
self.jobstatus.string = 'submitted'
self.assertTrue(self.jobstatus.submitted)
self.assertEqual(str(self.jobstatus), 'submitted')
self.assertEqual(self.jobstatus.string, 'submitted')
self.jobstatus.string = 'running'
self.assertTrue(self.jobstatus.running)
self.assertEqual(str(self.jobstatus), 'running')
self.assertEqual(self.jobstatus.string, 'running')
self.jobstatus.string = 'aborted'
self.assertTrue(self.jobstatus.aborted)
self.assertEqual(str(self.jobstatus), 'aborted')
self.assertEqual(self.jobstatus.string, 'aborted')
self.jobstatus.string = 'collect'
self.assertTrue(self.jobstatus.collect)
self.assertEqual(str(self.jobstatus), 'collect')
self.assertEqual(self.jobstatus.string, 'collect')
self.jobstatus.string = 'suspended'
self.assertTrue(self.jobstatus.suspended)
self.assertEqual(str(self.jobstatus), 'suspended')
self.assertEqual(self.jobstatus.string, 'suspended')
self.jobstatus.string = 'refresh'
self.assertTrue(self.jobstatus.refresh)
self.assertEqual(str(self.jobstatus), 'refresh')
self.assertEqual(self.jobstatus.string, 'refresh')
self.jobstatus.string = 'busy'
self.assertTrue(self.jobstatus.busy)
self.assertEqual(str(self.jobstatus), 'busy')
self.assertEqual(self.jobstatus.string, 'busy')
self.jobstatus.string = 'finished'
self.assertTrue(self.jobstatus.finished)
self.assertEqual(str(self.jobstatus), 'finished')
self.assertEqual(self.jobstatus.string, 'finished')
def test_database_connection(self):
current_status = self.database.get_item_by_id(self.job_id)["status"]
self.assertTrue(self.jobstatus_database.initialized)
self.assertEqual(current_status, str(self.jobstatus_database))
self.jobstatus_database.created = True
new_status = self.database.get_item_by_id(self.job_id)["status"]
self.assertTrue(self.jobstatus_database.created)
self.assertNotEqual(current_status, str(self.jobstatus_database))
self.assertEqual(new_status, str(self.jobstatus_database))
self.database.item_update({'status': 'finished'}, self.job_id)
finished_status = self.database.get_item_by_id(self.job_id)["status"]
self.assertTrue(self.jobstatus_database.finished)
self.assertNotEqual(current_status, str(self.jobstatus_database))
self.assertNotEqual(new_status, str(self.jobstatus_database))
self.assertEqual(finished_status, str(self.jobstatus_database))
