def test_sync(self):
runner = CliRunner()
PlantnoteDataProvider.register_data_provider(
'plantnote_provider',
self.TEST_DB_PATH,
)
result = runner.invoke(
data_provider.sync,
['plantnote_provider', self.TEST_DB_PATH]
)
self.assertEqual(result.exit_code, 0)
result = runner.invoke(
data_provider.sync,
['plantnote_provider', self.TEST_DB_PATH]
)
self.assertEqual(result.exit_code, 0)
result = runner.invoke(
data_provider.sync,
['plantnote', self.TEST_DB_PATH]
)
self.assertEqual(result.exit_code, 1)
result = runner.invoke(
data_provider.sync,
['plantnote_provider', "yo"]
)
self.assertEqual(result.exit_code, 1)
def setUpClass(cls):
super(TestPlantnotePlotOccurrenceProvider, cls).setUpClass()
# Register Pl@ntnote data provider
PlantnoteDataProvider.register_data_provider(
'pl@ntnote_provider',
cls.TEST_DB_PATH,
)
# Populate taxon
populate.populate_ncpippn_taxon_database(
populate.load_ncpippn_taxon_dataframe_from_json(), )
def test_update_data_provider(self):
runner = CliRunner()
PlantnoteDataProvider.register_data_provider(
'test_data_provider_1'
)
result = runner.invoke(
data_provider.update_data_provider_cli,
['test_data_provider_1', '--new_name', 'YO'],
)
self.assertEqual(result.exit_code, 0)
def test_get_data_provider_list(self):
l1 = get_data_provider_list()
self.assertEqual(len(l1), 0)
TestDataProvider.register_data_provider('test_data_provider_1')
PlantnoteDataProvider.register_data_provider(
'pl@ntnote_provider_1',
self.TEST_DB_PATH,
)
PlantnoteDataProvider.register_data_provider(
'pl@ntnote_provider_2',
self.TEST_DB_PATH,
)
l2 = get_data_provider_list()
self.assertEqual(len(l2), 3)
def test_get_dataframe_and_sync(self):
pt_provider = PlantnoteDataProvider(
'pl@ntnote_provider',
self.TEST_DB_PATH,
)
with Connector.get_connection() as connection:
plot_provider = pt_provider.plot_provider
df1 = plot_provider.get_provider_plot_dataframe()
cols = df1.columns
for i in ['name', 'location', 'properties']:
self.assertIn(i, cols)
plot_provider.sync(connection)
df2 = plot_provider.get_niamoto_plot_dataframe(connection)
self.assertEqual(len(df1), len(df2))
def test_get_dataframe_and_sync(self):
pt_provider = PlantnoteDataProvider(
'pl@ntnote_provider',
self.TEST_DB_PATH,
)
with Connector.get_connection() as connection:
prov = pt_provider.plot_occurrence_provider
df1 = prov.get_niamoto_plot_occurrence_dataframe(connection)
self.assertEqual(len(df1), 0)
# Sync plots and occurrences
plot_prov = pt_provider.plot_provider
occ_prov = pt_provider.occurrence_provider
plot_prov.sync(connection)
occ_prov.sync(connection)
# Sync plot-occurrences
df2 = prov.get_provider_plot_occurrence_dataframe()
cols = df2.columns
for i in [
'occurrence_identifier',
]:
self.assertIn(i, cols)
prov.sync(connection)
df3 = prov.get_niamoto_plot_occurrence_dataframe(connection)
self.assertEqual(len(df2), len(df3))
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,
)