def test_add_single_synonym(self):
synonym_key = "synonym_key_1"
TaxonomyManager.register_synonym_key("synonym_key_1")
data = [
{
'id': 0,
'full_name': 'Family One',
'rank_name': 'One',
'rank': niamoto_db_meta.TaxonRankEnum.FAMILIA,
'parent_id': None,
'synonyms': {},
'mptt_left': 0,
'mptt_right': 0,
'mptt_tree_id': 0,
'mptt_depth': 0,
},
]
ins = niamoto_db_meta.taxon.insert().values(data)
with Connector.get_connection() as connection:
connection.execute(ins)
TaxonomyManager.add_synonym_for_single_taxon(0, synonym_key, 1)
df1 = TaxonomyManager.get_raw_taxon_dataframe()
self.assertEqual(df1.loc[0]['synonyms'], {synonym_key: 1})
TaxonomyManager.add_synonym_for_single_taxon(0, synonym_key, 2)
df2 = TaxonomyManager.get_raw_taxon_dataframe()
self.assertEqual(df2.loc[0]['synonyms'], {
synonym_key: 1,
synonym_key: 2,
})
def test_get_synonym_key(self):
self.assertRaises(NoRecordFoundError, TaxonomyManager.get_synonym_key,
'Not existing')
TaxonomyManager.register_synonym_key("test")
TaxonomyManager.get_synonym_key("test")
with Connector.get_connection() as connection:
TaxonomyManager.get_synonym_key("test", bind=connection)
def test_base_data_provider(self):
TestDataProvider.register_data_provider('test_data_provider_1')
test_data_provider = TestDataProvider('test_data_provider_1')
self.assertIsNotNone(test_data_provider)
self.assertIsNotNone(test_data_provider.db_id)
# Test with synonym key
TaxonomyManager.register_synonym_key("synonym")
TestDataProvider.register_data_provider(
'test_data_provider_2',
synonym_key="synonym"
)
def test_update_data_provider(self):
add_data_provider(
"pl@ntnote_provider_1",
"PLANTNOTE",
)
TaxonomyManager.register_synonym_key("YO")
update_data_provider(
"pl@ntnote_provider_1",
new_name="pl@ntnote",
synonym_key="YO"
)
l2 = get_data_provider_list()
self.assertIn("pl@ntnote", list(l2['name']))
self.assertIn("YO", list(l2['synonym_key']))
def test_register_unregister_synonym_key(self):
TaxonomyManager.register_synonym_key("synonym_key_1")
self.assertRaises(RecordAlreadyExistsError,
TaxonomyManager.register_synonym_key,
"synonym_key_1")
df = TaxonomyManager.get_synonym_keys()
self.assertEqual(len(df), 1)
TaxonomyManager.unregister_synonym_key("synonym_key_1")
self.assertRaises(NoRecordFoundError,
TaxonomyManager.unregister_synonym_key,
"synonym_key")
df = TaxonomyManager.get_synonym_keys()
self.assertEqual(len(df), 0)
# Test with bind
with Connector.get_connection() as connection:
TaxonomyManager.register_synonym_key("test", bind=connection)
TaxonomyManager.assert_synonym_key_exists("test", bind=connection)
TaxonomyManager.unregister_synonym_key("test", bind=connection)
TaxonomyManager.assert_synonym_key_does_not_exists("test",
bind=connection)
def test_duplicate_synonym(self):
synonym_key = "synonym_key_1"
TaxonomyManager.register_synonym_key("synonym_key_1")
data = [
{
'id': 0,
'full_name': 'Family One',
'rank_name': 'One',
'rank': niamoto_db_meta.TaxonRankEnum.FAMILIA,
'parent_id': None,
'synonyms': {},
'mptt_left': 0,
'mptt_right': 0,
'mptt_tree_id': 0,
'mptt_depth': 0,
},
{
'id': 1,
'full_name': 'Family Two',
'rank_name': 'Two',
'rank': niamoto_db_meta.TaxonRankEnum.FAMILIA,
'parent_id': None,
'synonyms': {},
'mptt_left': 0,
'mptt_right': 0,
'mptt_tree_id': 0,
'mptt_depth': 0,
},
]
ins = niamoto_db_meta.taxon.insert().values(data)
with Connector.get_connection() as connection:
connection.execute(ins)
TaxonomyManager.add_synonym_for_single_taxon(0, synonym_key, 1)
self.assertRaises(
IntegrityError,
TaxonomyManager.add_synonym_for_single_taxon,
1,
synonym_key,
1,
)
def test_get_synonyms_map(self):
synonym_key = "synonym_key_1"
TaxonomyManager.register_synonym_key("synonym_key_1")
data = [
{
'id': 0,
'full_name': 'Family One',
'rank_name': 'One',
'rank': niamoto_db_meta.TaxonRankEnum.FAMILIA,
'parent_id': None,
'synonyms': {
synonym_key: 10,
},
'mptt_left': 0,
'mptt_right': 0,
'mptt_tree_id': 0,
'mptt_depth': 0,
},
{
'id': 1,
'full_name': 'Family Two',
'rank_name': 'Two',
'rank': niamoto_db_meta.TaxonRankEnum.FAMILIA,
'parent_id': None,
'synonyms': {
synonym_key: 20,
},
'mptt_left': 0,
'mptt_right': 0,
'mptt_tree_id': 0,
'mptt_depth': 0,
},
]
ins = niamoto_db_meta.taxon.insert().values(data)
with Connector.get_connection() as connection:
connection.execute(ins)
synonyms = TaxonomyManager.get_synonyms_for_key(synonym_key)
self.assertEqual(synonyms.loc[10], 0)
self.assertEqual(synonyms.loc[20], 1)
def upgrade():
op.create_table('data_provider_type',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('name', sa.String(length=100), nullable=False),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint(
'name', name=op.f('uq_data_provider_type_name')),
schema='niamoto')
op.create_table('taxon',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('full_name', sa.Text(), nullable=False),
sa.Column('rank_name', sa.Text(), nullable=False),
sa.Column('rank', taxon_rank_enum, nullable=False),
sa.Column('parent_id',
sa.Integer(),
nullable=True,
index=True),
sa.Column('synonyms', postgresql.JSONB(), nullable=False),
sa.Column('mptt_left', sa.Integer(), nullable=False),
sa.Column('mptt_right', sa.Integer(), nullable=False),
sa.Column('mptt_tree_id', sa.Integer(), nullable=False),
sa.Column('mptt_depth', sa.Integer(), nullable=False),
sa.CheckConstraint('mptt_depth >= 0',
name=op.f('ck_taxon_mptt_depth_gt_0')),
sa.CheckConstraint('mptt_left >= 0',
name=op.f('ck_taxon_mptt_left_gt_0')),
sa.CheckConstraint('mptt_right >= 0',
name=op.f('ck_taxon_mptt_right_gt_0')),
sa.CheckConstraint(
'mptt_tree_id >= 0',
name=op.f('ck_taxon_mptt_tree_id_gt_0')),
sa.ForeignKeyConstraint(
['parent_id'],
['niamoto.taxon.id'],
deferrable=True,
),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint('full_name',
name=op.f('uq_taxon_full_name')),
schema='niamoto')
op.create_table('synonym_key_registry',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('name', sa.String(length=100), nullable=False),
sa.Column('date_create', sa.DateTime(), nullable=False),
sa.Column('date_update', sa.DateTime(), nullable=True),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint(
'name', name=op.f('uq_synonym_key_registry_name')),
schema='niamoto')
op.create_table('raster_registry',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('name', sa.String(length=100), nullable=False),
sa.Column('date_create', sa.DateTime(), nullable=False),
sa.Column('date_update', sa.DateTime(), nullable=True),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint('name',
name=op.f('uq_raster_registry_name')),
schema='niamoto')
op.create_table('vector_registry',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('name', sa.String(length=100), nullable=False),
sa.Column('date_create', sa.DateTime(), nullable=False),
sa.Column('date_update', sa.DateTime(), nullable=True),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint('name',
name=op.f('uq_vector_registry_name')),
schema='niamoto')
op.create_table('dimension_registry',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('name', sa.String(length=100), nullable=False),
sa.Column('dimension_key',
sa.String(length=100),
nullable=False),
sa.Column('date_create', sa.DateTime(), nullable=False),
sa.Column('date_update', sa.DateTime(), nullable=True),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint(
'name', name=op.f('uq_dimension_registry_name')),
schema='niamoto')
op.create_table('data_provider',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('name', sa.String(length=100), nullable=False),
sa.Column('provider_type_id',
sa.Integer(),
nullable=False,
index=True),
sa.Column('synonym_key_id',
sa.Integer(),
nullable=True,
index=True),
sa.Column('properties', postgresql.JSONB(),
nullable=False),
sa.Column('date_create', sa.DateTime(), nullable=False),
sa.Column('date_update', sa.DateTime(), nullable=True),
sa.Column('last_sync', sa.DateTime(), nullable=True),
sa.ForeignKeyConstraint(
['provider_type_id'],
['niamoto.data_provider_type.id'],
),
sa.ForeignKeyConstraint(
['synonym_key_id'],
['niamoto.synonym_key_registry.id'],
ondelete='SET NULL',
),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint('name',
name=op.f('uq_data_provider_name')),
schema='niamoto')
op.create_table(
'occurrence',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('provider_id', sa.Integer(), nullable=False, index=True),
sa.Column('provider_pk', sa.Integer(), nullable=False, index=True),
sa.Column(
'location',
geoalchemy2.types.Geometry(geometry_type='POINT', srid=4326),
),
sa.Column('taxon_id', sa.Integer(), nullable=True, index=True),
sa.Column('provider_taxon_id', sa.Integer(), nullable=True),
sa.Column('properties', postgresql.JSONB(), nullable=False),
sa.ForeignKeyConstraint(
['provider_id'],
['niamoto.data_provider.id'],
onupdate='CASCADE',
ondelete='CASCADE',
),
sa.ForeignKeyConstraint(
['taxon_id'],
['niamoto.taxon.id'],
onupdate="CASCADE",
ondelete="SET NULL",
deferrable=True,
),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint(
'id',
'provider_id',
'provider_pk',
name=op.f('uq_occurrence_id__provider_id__provider_pk')),
schema='niamoto')
op.create_table(
'plot',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('provider_id', sa.Integer(), nullable=False, index=True),
sa.Column('provider_pk', sa.Integer(), nullable=False),
sa.Column('name', sa.String(length=100), nullable=False),
sa.Column('location',
geoalchemy2.types.Geometry(geometry_type='POINT', srid=4326),
nullable=False),
sa.Column('properties', postgresql.JSONB(), nullable=False),
sa.ForeignKeyConstraint(
['provider_id'],
['niamoto.data_provider.id'],
onupdate='CASCADE',
ondelete='CASCADE',
),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint('id',
'provider_id',
'provider_pk',
name=op.f('uq_plot_id__provider_id__provider_pk')),
sa.UniqueConstraint('name', name=op.f('uq_plot_name')),
schema='niamoto')
op.create_table(
'plot_occurrence',
sa.Column('plot_id', sa.Integer(), nullable=False, index=True),
sa.Column('occurrence_id', sa.Integer(), nullable=False, index=True),
sa.Column('provider_id', sa.Integer(), nullable=True, index=True),
sa.Column('provider_plot_pk', sa.Integer(), nullable=True),
sa.Column('provider_occurrence_pk', sa.Integer(), nullable=True),
sa.Column('occurrence_identifier', sa.String(length=50),
nullable=True),
sa.ForeignKeyConstraint(
['occurrence_id', 'provider_id', 'provider_occurrence_pk'],
[
'niamoto.occurrence.id', 'niamoto.occurrence.provider_id',
'niamoto.occurrence.provider_pk'
],
onupdate='CASCADE',
ondelete='CASCADE',
),
sa.ForeignKeyConstraint(
['plot_id', 'provider_id', 'provider_plot_pk'],
[
'niamoto.plot.id', 'niamoto.plot.provider_id',
'niamoto.plot.provider_pk'
],
onupdate='CASCADE',
ondelete='CASCADE',
),
sa.PrimaryKeyConstraint('plot_id', 'occurrence_id'),
sa.UniqueConstraint(
'plot_id',
'occurrence_identifier',
name=op.f('uq_plot_occurrence_plot_id__occurrence_identifier'),
deferrable=True,
),
schema='niamoto')
connection = op.get_bind()
PlantnoteDataProvider.register_data_provider_type(bind=connection, )
CsvDataProvider.register_data_provider_type(bind=connection, )
TaxonomyManager.register_synonym_key(
'niamoto',
bind=connection,
)