def test_copy_dbase(pstore):
conn2 = pst.DictConnector("destination")
pst.util.copy_database(pstore.conn,
conn2,
overwrite=False,
progressbar=True)
return
def prj(request):
if request.param == "arctic":
connstr = "mongodb://localhost:27017/"
name = "test_project"
arc = arctic.Arctic(connstr)
if name in [lib.split(".")[0] for lib in arc.list_libraries()]:
connector = pst.ArcticConnector(name, connstr)
prj = pst.PastaStore(name, connector)
else:
connector = pst.ArcticConnector(name, connstr)
prj = initialize_project(connector)
elif request.param == "pystore":
name = "test_project"
path = "./tests/data/pystore"
pystore.set_path(path)
if name in pystore.list_stores():
connector = pst.PystoreConnector(name, path)
prj = pst.PastaStore(name, connector)
else:
connector = pst.PystoreConnector(name, path)
prj = initialize_project(connector)
elif request.param == "dict":
name = "test_project"
connector = pst.DictConnector(name)
prj = initialize_project(connector)
prj.type = request.param # added here for defining test dependencies
yield prj
def test_to_from_zip(pstore):
zipname = f"test_{pstore.type}.zip"
pstore.to_zip(zipname, progressbar=False, overwrite=True)
conn = pst.DictConnector("test")
try:
store = pst.PastaStore.from_zip(zipname, conn)
assert not store.oseries.empty
finally:
os.remove(zipname)
return store
def create_pastastore(oc,
pstore,
pstore_name='',
conn=pst.DictConnector("my_conn"),
add_metadata=True,
obs_column='stand_m_tov_nap',
kind='oseries',
verbose=False):
"""add observations to a new or existing pastastore
Parameters
----------
oc : observation.ObsCollection
collection of observations
pstore : pastastore.PastasProject, optional
Existing pastastore, if None a new project is created
pstore_name : str, optional
Name of the pastastore only used if pstore is None
conn : pastastore.connectors
connector for database
obs_column : str, optional
Name of the column in the Obs dataframe to be used
kind : str, optional
The kind of series that is added to the pastas project
add_metadata : boolean, optional
If True metadata from the observations added to the project.
verbose : boolean, optional
Print additional information to the screen (default is False).
Returns
-------
pstore : pastastore.PastasProject
the pastas project with the series from the ObsCollection
"""
if pstore is None:
pstore = pst.PastaStore(pstore_name, connector=conn)
for o in oc.obs.values:
if verbose:
print('add to pastastore -> {}'.format(o.name))
if add_metadata:
meta = _get_metadata_from_obs(o, verbose=verbose)
else:
meta = dict()
if kind == 'oseries':
pstore.conn.add_oseries(o[obs_column], o.name, metadata=meta)
else:
pstore.conn.add_stress(o[obs_column], o.name, kind, metadata=meta)
return pstore
def pr(request):
"""Fixture that yields connection object.
"""
name = f"test_{request.param}"
# connect to dbase
if request.param == "arctic":
connstr = "mongodb://localhost:27017/"
pr = pst.ArcticConnector(name, connstr)
elif request.param == "pystore":
path = "./tests/data/pystore"
pr = pst.PystoreConnector(name, path)
elif request.param == "dict":
pr = pst.DictConnector(name)
pr.type = request.param # added here for defining test dependencies
yield pr
def conn(request):
"""Fixture that yields connection object.
"""
name = f"test_{request.param}"
# connect to dbase
if request.param == "arctic":
connstr = "mongodb://localhost:27017/"
conn = pst.ArcticConnector(name, connstr)
elif request.param == "pystore":
path = "./tests/data/pystore"
conn = pst.PystoreConnector(name, path)
elif request.param == "dict":
conn = pst.DictConnector(name)
elif request.param == "pas":
conn = pst.PasConnector(name, "./tests/data/pas")
else:
raise ValueError("Unrecognized parameter!")
conn.type = request.param # added here for defining test dependencies
yield conn
def pstore(request):
if request.param == "arctic":
connstr = "mongodb://localhost:27017/"
name = "test_project"
connector = pst.ArcticConnector(name, connstr)
elif request.param == "pystore":
name = "test_project"
path = "./tests/data/pystore"
pystore.set_path(path)
connector = pst.PystoreConnector(name, path)
elif request.param == "dict":
name = "test_project"
connector = pst.DictConnector(name)
elif request.param == "pas":
name = "test_project"
connector = pst.PasConnector(name, "./tests/data/pas")
else:
raise ValueError("Unrecognized parameter!")
pstore = initialize_project(connector)
pstore.type = request.param # added here for defining test dependencies
yield pstore
