def test_plugin_access_objects():
"""Test the plugin and check the access objects available"""
from tests.testplugins import alpha
assert isinstance(
alpha.AlphaSourcePlugin(CatalogTinyDb()).get_plugin_access(), dict)
plugin_access_objects = alpha.AlphaSourcePlugin(
CatalogTinyDb()).get_plugin_access()
assert list(plugin_access_objects.keys()) == [
basin3d.core.models.MeasurementTimeseriesTVPObservation,
basin3d.core.models.MonitoringFeature
]
assert plugin_access_objects[
basin3d.core.models.
MonitoringFeature].__class__.__name__ == 'tests.testplugins.alpha.AlphaMonitoringFeatureAccess'
assert plugin_access_objects[basin3d.core.models.MeasurementTimeseriesTVPObservation].__class__.__name__ == \
'tests.testplugins.alpha.AlphaMeasurementTimeseriesTVPObservationAccess'
def test_plugin_views(monkeypatch):
"""Import the alpha plugin and try to call the api directly"""
from tests.testplugins import alpha
monkeypatch.setattr(alpha.AlphaSourcePlugin, 'get_datasource', Mock())
plugin_views = alpha.AlphaSourcePlugin(CatalogTinyDb()).get_plugin_access()
assert isinstance(plugin_views, dict)
assert basin3d.core.models.MeasurementTimeseriesTVPObservation in plugin_views
assert basin3d.core.models.MonitoringFeature in plugin_views
def test_process_plugin_variable_mapping(catalog):
"""Test a bad mapping file with the wrong header"""
from tests.testplugins import alpha
from basin3d.core.catalog import CatalogException
with pytest.raises(CatalogException):
catalog._process_plugin_variable_mapping(
alpha.AlphaSourcePlugin(catalog),
map_filename='mapping_alpha_wrong_header.csv',
datasource=DataSource())
def plugin_access_alpha():
"""
Create a DataSourcePluginAccess object
"""
from tests.testplugins import alpha
from basin3d.core.catalog import CatalogTinyDb
catalog = CatalogTinyDb()
plugins = [alpha.AlphaSourcePlugin(catalog)]
catalog.initialize(plugins)
return plugins[0].access_classes[MeasurementTimeseriesTVPObservation]
def test_plugin_direct(monkeypatch):
"""Import the alpha plugin and try to call the api directly"""
from tests.testplugins import alpha
monkeypatch.setattr(alpha.AlphaSourcePlugin, 'get_datasource', Mock())
assert alpha.AlphaSourcePlugin().direct("path") is None
def test_create_catalog():
from tests.testplugins import alpha
from basin3d.core.catalog import CatalogTinyDb
catalog = CatalogTinyDb()
plugins = [alpha.AlphaSourcePlugin(catalog)]
catalog.initialize(plugins)
results = [{
'basin3d_id': 'ACT',
'datasource': {
'credentials': {},
'id': 'Alpha',
'id_prefix': 'A',
'location': 'https://asource.foo/',
'name': ''
},
'datasource_id': 'Alpha',
'datasource_variable_id': 'Acetate',
'observed_property': {
'datasource': {
'credentials': {},
'id': 'Alpha',
'id_prefix': 'A',
'location': 'https://asource.foo/',
'name': 'Alpha'
},
'datasource_description': '',
'datasource_variable': 'Acetate',
'observed_property_variable': {
'basin3d_id': 'ACT',
'categories': ['Biogeochemistry', 'Anions'],
'full_name': 'Acetate '
'(CH3COO)',
'units': 'mM'
},
'sampling_medium': 'WATER'
},
'observed_property_variable': {
'basin3d_id': 'ACT',
'categories': ['Biogeochemistry', 'Anions'],
'full_name': 'Acetate (CH3COO)',
'units': 'mM'
}
}, {
'basin3d_id': 'Ag',
'datasource': {
'credentials': {},
'id': 'Alpha',
'id_prefix': 'A',
'location': 'https://asource.foo/',
'name': ''
},
'datasource_id': 'Alpha',
'datasource_variable_id': 'Ag',
'observed_property': {
'datasource': {
'credentials': {},
'id': 'Alpha',
'id_prefix': 'A',
'location': 'https://asource.foo/',
'name': 'Alpha'
},
'datasource_description': '',
'datasource_variable': 'Ag',
'observed_property_variable': {
'basin3d_id': 'Ag',
'categories': ['Biogeochemistry', 'Trace '
'elements'],
'full_name': 'Silver '
'(Ag)',
'units': 'mg/L'
},
'sampling_medium': 'WATER'
},
'observed_property_variable': {
'basin3d_id': 'Ag',
'categories': ['Biogeochemistry', 'Trace elements'],
'full_name': 'Silver (Ag)',
'units': 'mg/L'
}
}, {
'datasource_id': 'Alpha',
'datasource': {},
'datasource_variable_id': 'Aluminum',
'observed_property': {},
'basin3d_id': 'Al',
'observed_property_variable': {}
}]
for item in catalog.in_memory_db:
idx = item.doc_id - 1
assert results[idx] == item
def test_get_observed_property_variables():
"""Test that all of the observed property variable are returned"""
from tests.testplugins import alpha
from basin3d.core.catalog import CatalogTinyDb
catalog = CatalogTinyDb()
plugins = [alpha.AlphaSourcePlugin(catalog)]
catalog.initialize(plugins)
assert [
'ACT', 'Br', 'Cl', 'DIN', 'DTN', 'F', 'NO3', 'NO2', 'PO4', 'SO4', 'S2',
'S2O3', 'HCO3', 'DIC', 'DOC', 'NPOC', 'POC', 'TIC', 'TOC', 'd13C',
'CO2_d13C_soilgas', 'CH4_d13C_soilgas', 'd15N', 'N2O_d15N_soilgas',
'CO2_d18O_soilgas', 'N2O_d18O_soilgas', 'SO4_d34S', 'U235', 'H2O_d18O',
'H2O_dD', 'NH4', 'Ca', 'Mg', 'K', 'Si', 'Na', 'MICRO_COV', 'MGO1',
'MGO2', 'MGO3', 'GENE_TRAN', 'MICRO_PEP', 'MICRO_PLFA', 'NH3', 'CO2',
'H2', 'H2S', 'CH4', 'N2', 'N2O', 'O2', 'Al', 'Sb', 'As', 'Ba', 'Be',
'B', 'Cd', 'Cs', 'Co', 'Cu', 'Eu', 'Ge', 'Fe2', 'Hg', 'Pb', 'Li',
'Mn2', 'Mo', 'Ni', 'Rb', 'Se', 'Ag', 'Sr', 'Th', 'Sn', 'Ti', 'Cr',
'FeT', 'Mn', 'P', 'U', 'V', 'Zn', 'Zr', 'AT', 'ALB', 'APA', 'APR',
'DP', 'ET', 'HI', 'PPT', 'PPT_TOT_5', 'PPT_TOT_10', 'PPT_TOT_60',
'PPT_TOT_DAY', 'UV_IN', 'UV_REF', 'NIR_IN', 'NIR_REF', 'PAR_IN',
'PAR_REF', 'LWIR_IN', 'LWIR_REF', 'BB_IN', 'BB_REF', 'RH', 'SD', 'SWE',
'SDEN', 'ST', 'PPT_SF', 'SRAD', 'WBT', 'W_DIR', 'W_GS', 'W_SPD',
'W_CH', 'ERT', 'CEC', 'EXAFS', 'SEQ', 'XRD', 'XRF', 'XANES', 'HCND',
'SED_SIZE', 'HCND_Sat', 'Porosity', 'SBD', 'SYD', 'HCND_Unsat',
'RET_CUR', 'LSE', 'GWF', 'Well logs', 'SAT', 'SDE', 'SMO', 'STM',
'SWP', 'SEC', 'FDOM', 'DO', 'EC', 'SC', 'SAL', 'GWL', 'PH', 'ORP',
'RDC', 'SWL', 'WLH', 'WLE', 'WT', 'TDS', 'TSS', 'TRB', 'STO_RES',
'LAI', 'PLT_HT', 'PAI', 'PFT', 'SAP', 'RGB', 'GCC', 'NDVI'
] == [i.basin3d_id for i in catalog.find_observed_property_variables()]
# This test creates a catalog
def test_create_catalog():
from tests.testplugins import alpha
from basin3d.core.catalog import CatalogTinyDb
catalog = CatalogTinyDb()
plugins = [alpha.AlphaSourcePlugin(catalog)]
catalog.initialize(plugins)
results = [{
'basin3d_id': 'ACT',
'datasource': {
'credentials': {},
'id': 'Alpha',
'id_prefix': 'A',
'location': 'https://asource.foo/',
'name': ''
},
'datasource_id': 'Alpha',
'datasource_variable_id': 'Acetate',
'observed_property': {
'datasource': {
'credentials': {},
'id': 'Alpha',
'id_prefix': 'A',
'location': 'https://asource.foo/',
'name': 'Alpha'
},
'datasource_description': '',
'datasource_variable': 'Acetate',
'observed_property_variable': {
'basin3d_id': 'ACT',
'categories': ['Biogeochemistry', 'Anions'],
'full_name': 'Acetate '
'(CH3COO)',
'units': 'mM'
},
'sampling_medium': 'WATER'
},
'observed_property_variable': {
'basin3d_id': 'ACT',
'categories': ['Biogeochemistry', 'Anions'],
'full_name': 'Acetate (CH3COO)',
'units': 'mM'
}
}, {
'basin3d_id': 'Ag',
'datasource': {
'credentials': {},
'id': 'Alpha',
'id_prefix': 'A',
'location': 'https://asource.foo/',
'name': ''
},
'datasource_id': 'Alpha',
'datasource_variable_id': 'Ag',
'observed_property': {
'datasource': {
'credentials': {},
'id': 'Alpha',
'id_prefix': 'A',
'location': 'https://asource.foo/',
'name': 'Alpha'
},
'datasource_description': '',
'datasource_variable': 'Ag',
'observed_property_variable': {
'basin3d_id': 'Ag',
'categories': ['Biogeochemistry', 'Trace '
'elements'],
'full_name': 'Silver '
'(Ag)',
'units': 'mg/L'
},
'sampling_medium': 'WATER'
},
'observed_property_variable': {
'basin3d_id': 'Ag',
'categories': ['Biogeochemistry', 'Trace elements'],
'full_name': 'Silver (Ag)',
'units': 'mg/L'
}
}, {
'datasource_id': 'Alpha',
'datasource': {},
'datasource_variable_id': 'Aluminum',
'observed_property': {},
'basin3d_id': 'Al',
'observed_property_variable': {}
}]
for item in catalog.in_memory_db:
idx = item.doc_id - 1
assert results[idx] == item