def test_duplicate_user_species_error(self):
"""checks that an error is raised when a classifier description is
not present in the user value of species mapping
"""
config = {
"species": {
"species_classifier":
"classifier1",
"species_mapping": [
# note "a" is specified more than one time here
{
"user_species": "a",
"default_species": "Spruce"
},
{
"user_species": "a",
"default_species": "Oak"
}
]
}
}
ref = Mock(spec=SITCBMDefaults)
classifiers, classifier_values = self.get_mock_classifiers()
ref.get_afforestation_pre_types = lambda: []
species = pd.Series(["a", "a"])
with self.assertRaises(ValueError):
sit_mapping = SITMapping(config, ref)
sit_mapping.get_species(species, classifiers, classifier_values)
def test_undefined_single_default_spatial_unit_error(self):
"""Checks that an error is raised when the default mapping of spatial
unit does not match a defined value in the defaults reference.
"""
mapping = {
"spatial_units": {
"mapping_mode": "SingleDefaultSpatialUnit",
"default_spuid": 10
}
}
ref = Mock(spec=SITCBMDefaults)
def mock_get_spatial_unit(spatial_unit_id):
raise KeyError
ref.get_spatial_unit.side_effect = mock_get_spatial_unit
classifiers, classifier_values = self.get_mock_classifiers()
inventory = pd.DataFrame({
"classifier1": ["a", "b"],
"classifier2": ["a", "a"],
})
sit_mapping = SITMapping(mapping, ref)
with self.assertRaises(KeyError):
sit_mapping.get_spatial_unit(inventory, classifiers,
classifier_values)
self.assertTrue(ref.get_spatial_unit.called)
def test_get_disturbance_type_id_returns_expected_value(self):
"""Checks the expected output of SITMapping.get_disturbance_type_id
"""
config = {
"disturbance_types": [{
"user_dist_type": "fire",
"default_dist_type": "Wildfire"
}, {
"user_dist_type": "clearcut",
"default_dist_type": "ClearCut"
}]
}
ref = Mock(spec=SITCBMDefaults)
def mock_get_disturbance_type_id(name):
if name == "Wildfire":
return 1
if name == "ClearCut":
return 2
raise ValueError()
ref.get_disturbance_type_id.side_effect = mock_get_disturbance_type_id
sit_mapping = SITMapping(config, ref)
result = sit_mapping.get_default_disturbance_type_id(
pd.Series(["fire"] + ["clearcut"]))
self.assertTrue(list(result) == [1, 2])
def test_undefined_user_admin_error(self):
"""checks that an error is raised when a classifier description is
not present in the user value of admin mapping
"""
mapping = {
"spatial_units": {
"mapping_mode":
"SeparateAdminEcoClassifiers",
"admin_classifier":
"classifier1",
"eco_classifier":
"classifier2",
"admin_mapping": [{
"user_admin_boundary": "missing",
"default_admin_boundary": "Alberta"
}],
"eco_mapping": [{
"user_eco_boundary": "a",
"default_eco_boundary": "Montane Cordillera"
}]
}
}
ref = Mock(spec=SITCBMDefaults)
classifiers, classifier_values = self.get_mock_classifiers()
inventory = pd.DataFrame({
"classifier1": ["a", "b"],
"classifier2": ["a", "a"],
})
sit_mapping = SITMapping(mapping, ref)
with self.assertRaises(KeyError):
sit_mapping.get_spatial_unit(inventory, classifiers,
classifier_values)
def test_single_default_spatial_unit_admin_eco_specified(self):
"""Checks that an error is raised when the default mapping of spatial
unit does not match a defined value in the defaults reference.
"""
mapping = {
"spatial_units": {
"mapping_mode": "SingleDefaultSpatialUnit",
"admin_boundary": "a1",
"eco_boundary": "e1"
}
}
ref = Mock(spec=SITCBMDefaults)
def mock_get_spatial_unit_id(admin_boundary, eco_boundary):
self.assertTrue(admin_boundary == "a1")
self.assertTrue(eco_boundary == "e1")
return 1
ref.get_spatial_unit_id.side_effect = mock_get_spatial_unit_id
classifiers, classifier_values = self.get_mock_classifiers()
inventory = pd.DataFrame({
"classifier1": ["a", "b"],
"classifier2": ["a", "a"],
})
sit_mapping = SITMapping(mapping, ref)
result = sit_mapping.get_spatial_unit(inventory, classifiers,
classifier_values)
self.assertTrue((result == 1).all())
self.assertTrue(len(result) == inventory.shape[0])
ref.get_spatial_unit_id.assert_called_once()
def test_expected_result_with_species_nonforest_values(self):
"""checks that an error is raised when a the the species classifier
maps to at least one non forest value and a non-forest classifier is
used
"""
config = {
"species": {
"species_classifier":
"classifier1",
"species_mapping": [{
"user_species": "a",
"default_species": "Spruce"
}, {
"user_species": "b",
"default_species": "Gleysolic"
}]
}
}
ref = Mock(spec=SITCBMDefaults)
classifiers, classifier_values = self.get_mock_classifiers()
inventory = pd.DataFrame({"classifier1": ["a", "b", "a", "b"]})
def mock_get_afforestation_pre_types():
return [{
"afforestation_pre_type_name": "Gleysolic",
"afforestation_pre_type_id": 1001
}]
ref.get_afforestation_pre_types.side_effect = \
mock_get_afforestation_pre_types
ref.get_species.side_effect = lambda: [{"species_name": "Spruce"}]
sit_mapping = SITMapping(config, ref)
result = sit_mapping.get_nonforest_cover_ids(inventory, classifiers,
classifier_values)
self.assertTrue(list(result) == [-1, 1001, -1, 1001])
def test_get_species_expected_result(self):
"""checks the expected output of get_species
"""
config = {
"species": {
"species_classifier":
"classifier1",
"species_mapping": [
{
"user_species": "a",
"default_species": "Spruce"
},
{
"user_species": "b",
"default_species": "Oak"
},
{
"user_species": "nonforest",
"default_species": "Gleysolic"
},
]
}
}
ref = Mock(spec=SITCBMDefaults)
classifiers = pd.DataFrame(data=[(1, "classifier1"),
(2, "classifier2")],
columns=["id", "name"])
classifier_values = pd.DataFrame(
data=[(1, "a", "a"), (1, "b", "b"), (1, "nonforest", "nonforest"),
(2, "a", "a")],
columns=["classifier_id", "name", "description"])
def mock_get_species_id(species_name):
if species_name == "Spruce":
return 999
if species_name == "Oak":
return -999
raise ValueError()
species = pd.Series(["a", "b", "a", "b"])
ref.get_species_id.side_effect = mock_get_species_id
ref.get_afforestation_pre_types.side_effect = lambda: [{
"afforestation_pre_type_name":
"Gleysolic"
}]
sit_mapping = SITMapping(config, ref)
result = sit_mapping.get_species(species, classifiers,
classifier_values)
self.assertTrue(list(result) == [999, -999, 999, -999])
def test_undefined_user_disturbance_type_error(self):
"""checks that an error is raised when a disturbance type is
not present in the user value of disturbance type mapping
"""
config = {
"disturbance_types": [{
"user_dist_type": "fire",
"default_dist_type": "Wildfire"
}]
}
ref = Mock(spec=SITCBMDefaults)
sit_mapping = SITMapping(config, ref)
with self.assertRaises(KeyError):
sit_mapping.get_default_disturbance_type_id(
pd.Series(["missing_value"]))
def test_admin_eco_mapping_returns_expected_value(self):
"""Checks that an expected value is returned when admin-eco
classifier mapping is used.
"""
mapping = {
"spatial_units": {
"mapping_mode":
"SeparateAdminEcoClassifiers",
"admin_classifier":
"classifier1",
"eco_classifier":
"classifier2",
"admin_mapping": [{
"user_admin_boundary": "a",
"default_admin_boundary": "British Columbia"
}, {
"user_admin_boundary": "b",
"default_admin_boundary": "Alberta"
}],
"eco_mapping": [{
"user_eco_boundary": "a",
"default_eco_boundary": "Montane Cordillera"
}]
}
}
ref = Mock(spec=SITCBMDefaults)
classifiers, classifier_values = self.get_mock_classifiers()
inventory = pd.DataFrame({
"classifier1": ["a", "b"],
"classifier2": ["a", "a"],
})
def mock_get_spatial_unit_id(admin, eco):
if admin == "British Columbia" and eco == "Montane Cordillera":
return 1000
elif admin == "Alberta" and eco == "Montane Cordillera":
return 2000
else:
raise ValueError
ref.get_spatial_unit_id.side_effect = mock_get_spatial_unit_id
sit_mapping = SITMapping(mapping, ref)
result = sit_mapping.get_spatial_unit(inventory, classifiers,
classifier_values)
self.assertTrue(list(result) == [1000, 2000])
def test_duplicated_user_disturbance_type_error(self):
"""checks that an error is raised when a disturbance type is
duplicated in the sit json config
"""
config = {
"disturbance_types": [{
"user_dist_type": "duplicated",
"default_dist_type": "Wildfire"
}, {
"user_dist_type": "duplicated",
"default_dist_type": "Clearcut"
}]
}
ref = Mock(spec=SITCBMDefaults)
sit_mapping = SITMapping(config, ref)
with self.assertRaises(KeyError):
sit_mapping.get_default_disturbance_type_id(
pd.Series(["duplicated"]))
def test_undefined_mapped_default_spatial_unit_error(self):
"""Checks that an error is raised when the default mapping of spatial
unit does not match a defined value in the defaults reference in
spu classifier mode
"""
mapping = {
"spatial_units": {
"mapping_mode":
"JoinedAdminEcoClassifier",
"spu_classifier":
"classifier1",
"spu_mapping": [{
"user_spatial_unit": "a",
"default_spatial_unit": {
"admin_boundary": "British Columbia",
"eco_boundary": "Montane Cordillera"
}
}, {
"user_spatial_unit": "b",
"default_spatial_unit": {
"admin_boundary": "Alberta",
"eco_boundary": "Montane Cordillera"
}
}]
}
}
ref = Mock(spec=SITCBMDefaults)
classifiers, classifier_values = self.get_mock_classifiers()
inventory = pd.DataFrame({
"classifier1": ["a", "b"],
"classifier2": ["a", "a"],
})
def mock_get_spatial_unit_id(admin, eco):
# simulates a key error raised when the specified value is not
# present.
raise KeyError
ref.get_spatial_unit_id.side_effect = mock_get_spatial_unit_id
sit_mapping = SITMapping(mapping, ref)
with self.assertRaises(KeyError):
sit_mapping.get_spatial_unit(inventory, classifiers,
classifier_values)
self.assertTrue(ref.get_spatial_unit_id.called)
def test_get_landclass_undefined_id_error(self):
"""checks that an error is raised if an undefined id is used in the
input"""
ref = Mock(spec=SITCBMDefaults)
def mock_get_land_classes():
return [{
"code": "code1",
"land_class_id": 100
}, {
"code": "code2",
"land_class_id": 200
}]
ref.get_land_classes.side_effect = mock_get_land_classes
config = {}
sit_mapping = SITMapping(config, ref)
with self.assertRaises(ValueError):
sit_mapping.get_land_class_id(pd.Series([7000]))
def test_same_nonforest_classifier_and_species_classifier_error(self):
"""checks that an error is raised when a the the species classifier
maps to at least one non forest value and a non-forest classifier is
used
"""
config = {
"nonforest": {
"nonforest_classifier":
"classifier1",
"nonforest_mapping": [{
"user_nonforest_type": "a",
"default_nonforest_type": "Gleysolic"
}, {
"user_nonforest_type": "b",
"default_nonforest_type": None
}]
},
"species": {
"species_classifier":
"classifier1",
"species_mapping": [{
"user_species": "a",
"default_species": "Spruce"
}]
}
}
ref = Mock(spec=SITCBMDefaults)
classifiers, classifier_values = self.get_mock_classifiers()
inventory = pd.DataFrame({"classifier1": ["a"]})
def mock_get_afforestation_pre_types():
return [{
"afforestation_pre_type_name": "Gleysolic",
"afforestation_pre_type_id": "1"
}]
ref.get_afforestation_pre_types.side_effect = \
mock_get_afforestation_pre_types
ref.get_species.side_effect = lambda: []
with self.assertRaises(ValueError):
sit_mapping = SITMapping(config, ref)
sit_mapping.get_nonforest_cover_ids(inventory, classifiers,
classifier_values)
def test_undefined_default_nonforest_type_error(self):
"""Checks that an error is raised when the default mapping of
non-forest type does not match a defined value in the defaults
reference.
"""
config = {
"nonforest": {
"nonforest_classifier":
"classifier1",
"nonforest_mapping": [{
"user_nonforest_type": "a",
"default_nonforest_type": "missing"
}, {
"user_nonforest_type": "b",
"default_nonforest_type": None
}]
},
"species": {
"species_classifier":
"classifier2",
"species_mapping": [{
"user_species": "a",
"default_species": "Spruce"
}]
}
}
ref = Mock(spec=SITCBMDefaults)
classifiers, classifier_values = self.get_mock_classifiers()
inventory = pd.DataFrame({"classifier1": ["a"]})
def mock_get_afforestation_pre_types():
return [{
"afforestation_pre_type_name": "Gleysolic",
"afforestation_pre_type_id": "1"
}]
ref.get_afforestation_pre_types.side_effect = \
mock_get_afforestation_pre_types
ref.get_species.side_effect = None
with self.assertRaises(KeyError):
sit_mapping = SITMapping(config, ref)
sit_mapping.get_nonforest_cover_ids(inventory, classifiers,
classifier_values)
def test_get_landclass_id_expected_value_with_code(self):
"""tests the expected return of get_land_class_id when a Series of
land class code strings are passed"""
ref = Mock(spec=SITCBMDefaults)
def mock_get_land_classes():
return [{
"code": "code1",
"land_class_id": 1000
}, {
"code": "code2",
"land_class_id": 2000
}]
ref.get_land_classes.side_effect = mock_get_land_classes
config = {}
sit_mapping = SITMapping(config, ref)
result = sit_mapping.get_land_class_id(
pd.Series(["code1", "code2", "code1"]))
self.assertTrue(list(result) == [1000, 2000, 1000])
def test_get_landclass_id_expected_value(self):
"""tests the expected return of get_land_class_id when a Series of
land class id integers are passed"""
ref = Mock(spec=SITCBMDefaults)
def mock_get_land_classes():
return [{
"code": "code1",
"land_class_id": 100
}, {
"code": "code2",
"land_class_id": 200
}]
ref.get_land_classes.side_effect = mock_get_land_classes
config = {}
sit_mapping = SITMapping(config, ref)
result = sit_mapping.get_land_class_id(pd.Series([100, 200, 100]))
# for this case, a validated copy of the input series is returned
self.assertTrue(list(result) == [100, 200, 100])
def test_invalid_spatial_unit_mapping_mode_error(self):
"""checks that a non-supported mapping mode results in error
"""
mapping = {
"spatial_units": {
"mapping_mode": "UNSUPPORTED",
"default_spuid": 10
}
}
ref = Mock(spec=SITCBMDefaults)
classifiers, classifier_values = self.get_mock_classifiers()
inventory = pd.DataFrame({
"classifier1": ["a", "b"],
"classifier2": ["a", "a"],
})
sit_mapping = SITMapping(mapping, ref)
with self.assertRaises(ValueError):
sit_mapping.get_spatial_unit(inventory, classifiers,
classifier_values)
def test_undefined_default_disturbance_type_error(self):
"""checks that an error is raised when a default disturbance
type is not present in the disturbance type reference
"""
config = {
"disturbance_types": [{
"user_dist_type": "fire",
"default_dist_type": "Wildfire"
}]
}
ref = Mock(spec=SITCBMDefaults)
def mock_get_disturbance_type_id(name):
raise KeyError()
ref.get_disturbance_type_id.side_effect = \
mock_get_disturbance_type_id
sit_mapping = SITMapping(config, ref)
with self.assertRaises(KeyError):
sit_mapping.get_default_disturbance_type_id(pd.Series(["fire"]))
self.assertTrue(ref.get_disturbance_type_id.called)
def test_get_species_error_on_undefined_classifier(self):
"""checks that an error is thrown if an undefined species classifier
is used
"""
config = {
"species": {
"species_classifier":
"undefined",
"species_mapping": [
{
"user_species": "a",
"default_species": "Spruce"
},
{
"user_species": "b",
"default_species": "Oak"
},
{
"user_species": "nonforest",
"default_species": "Gleysolic"
},
]
}
}
ref = Mock(spec=SITCBMDefaults)
classifiers, classifier_values = self.get_mock_classifiers()
pd.DataFrame({
"classifier1": ["a", "b"],
"classifier2": ["a", "a"],
})
species = pd.Series(["a", "b", "a", "b"])
ref.get_afforestation_pre_types.side_effect = lambda: [{
"afforestation_pre_type_name":
"Gleysolic"
}]
sit_mapping = SITMapping(config, ref)
with self.assertRaises(ValueError):
sit_mapping.get_species(species, classifiers, classifier_values)
def test_undefined_default_species_error(self):
"""Checks that an error is raised when the default mapping of species
does not match a defined value in the defaults reference.
"""
config = {
"species": {
"species_classifier":
"classifier1",
"species_mapping": [{
"user_species": "a",
"default_species": "Spruce"
}, {
"user_species": "b",
"default_species": "Oak"
}]
}
}
ref = Mock(spec=SITCBMDefaults)
classifiers, classifier_values = self.get_mock_classifiers()
pd.DataFrame({
"classifier1": ["a", "b"],
"classifier2": ["a", "a"],
})
def mock_get_species_id(species_name):
# simulates a key error raised when the specified value is not
# present.
raise KeyError()
species = pd.Series(["a", "b"])
ref.get_species_id.side_effect = mock_get_species_id
ref.get_afforestation_pre_types.side_effect = lambda: []
with self.assertRaises(KeyError):
sit_mapping = SITMapping(config, ref)
sit_mapping.get_species(species, classifiers, classifier_values)
self.assertTrue(ref.get_species_id.called)
def test_undefined_classifier_joined_admin_eco_error(self):
"""checks that an error is raised when any mapping references a
non-existant classifier name
"""
mapping = {
"spatial_units": {
"mapping_mode":
"JoinedAdminEcoClassifier",
"spu_classifier":
"NOT_DEFINED",
"spu_mapping": [{
"user_spatial_unit": "a",
"default_spatial_unit": {
"admin_boundary": "British Columbia",
"eco_boundary": "Montane Cordillera"
}
}, {
"user_spatial_unit": "b",
"default_spatial_unit": {
"admin_boundary": "Alberta",
"eco_boundary": "Montane Cordillera"
}
}]
}
}
ref = Mock(spec=SITCBMDefaults)
classifiers, classifier_values = self.get_mock_classifiers()
inventory = pd.DataFrame({
"classifier1": ["a", "b"],
"classifier2": ["a", "a"],
})
with self.assertRaises(KeyError):
sit_mapping = SITMapping(mapping, ref)
sit_mapping.get_spatial_unit(inventory, classifiers,
classifier_values)
def test_undefined_user_species_error(self):
"""checks that an error is raised when a classifier description is
not present in the user value of species mapping
"""
config = {
"species": {
"species_classifier":
"classifier1",
"species_mapping": [{
"user_species": "UNDEFINED",
"default_species": "Spruce"
}, {
"user_species": "b",
"default_species": "Oak"
}]
}
}
ref = Mock(spec=SITCBMDefaults)
classifiers, classifier_values = self.get_mock_classifiers()
ref.get_afforestation_pre_types = lambda: []
species = pd.Series(["b", "b"])
with self.assertRaises(KeyError):
sit_mapping = SITMapping(config, ref)
sit_mapping.get_species(species, classifiers, classifier_values)
def initialize_sit_objects(sit, db_path=None, locale_code="en-CA"):
"""Load and attach objects required for the SIT to the specified namespace
Args:
sit (types.SimpleNamespace): object with parsed SIT data, such as the
return value of :py:func:`read_sit_config`.
db_path (str, optional): path to a cbm_defaults database. If None, the
default database is used. Defaults to None.
locale_code (str, optional): a locale code used to fetch the
corresponding translated version of default parameter strings
"""
if not db_path:
db_path = resources.get_cbm_defaults_path()
sit_defaults = SITCBMDefaults(sit, db_path, locale_code=locale_code)
sit.sit_mapping = SITMapping(sit.config["mapping_config"], sit_defaults)
sit.sit_data.disturbance_types.insert(
0, "default_disturbance_type_id",
sit.sit_mapping.get_default_disturbance_type_id(
sit.sit_data.disturbance_types.name))
sit.db_path = db_path
sit.defaults = sit_defaults
_create_classifier_value_maps(sit)
_create_disturbance_type_maps(sit)
return sit