def run(args):
if fiona is None: # pragma: no cover
raise SystemExit(
'fiona and shapely must be installed for this command')
with fiona.collection(
str(args.repos.path("geo", "level2-shape/level2.shp")),
"r") as source:
regions = [f for f in source]
with update_ordered(args.repos.path("geo", "societies_tdwg.json"),
indent=4) as soc_tdwg:
for ds in args.repos.datasets:
for soc in ds.societies:
spec = soc_tdwg.get(
soc.id,
dict(lat=soc.Lat, lon=soc.Long, name=None, code=None))
if math.isclose(spec['lat'], soc.Lat) \
and math.isclose(spec['lon'], soc.Long) \
and spec['code']:
continue
region, dist = geo.match(spec['lon'], spec['lat'], regions)
spec['name'] = region['properties']['REGION_NAM']
spec['code'] = str(region['properties']['TDWG_CODE'])
if dist == 0: # pragma: no cover
args.log.info('{0} contained in region {1}'.format(
soc, spec['name']))
else:
args.log.warning(
'assigning {0} to nearest region {1}, distance {2}'.
format(soc, region['properties']['REGION_NAM'], dist))
soc_tdwg[soc.id] = spec
def test_match_contains_not(mocker):
mocker.patch(
'pydplace.geo.shape',
mocker.Mock(return_value=mocker.Mock(contains=lambda p: False)))
mocker.patch('pydplace.geo.Point',
mocker.Mock(return_value=mocker.Mock(distance=lambda p: 100)))
assert geo.match(0, 0, [mocker.MagicMock()])[1] == 100
def tdwg(args):
"""
Assign socities to TDWG regions
"""
try:
import fiona
from shapely.geometry import Point
except ImportError:
args.log.error('fiona and shapely must be installed for this command')
return
def isclose(a, b, rel_tol=1e-09, abs_tol=0.0):
return abs(a - b) <= max(rel_tol * max(abs(a), abs(b)), abs_tol)
with fiona.collection(
args.repos.path("geo", "level2-shape/level2.shp").as_posix(),
"r") as source:
regions = [f for f in source]
with update(args.repos.path("geo", "societies_tdwg.json"),
default={},
indent=4) as soc_tdwg:
for ds in args.repos.datasets:
for soc in ds.societies:
spec = soc_tdwg.get(
soc.id,
dict(lat=soc.Lat, lon=soc.Long, name=None, code=None))
if isclose(spec['lat'], soc.Lat) \
and isclose(spec['lon'], soc.Long) \
and spec['code']:
continue
region, dist = geo.match(Point(spec['lon'], spec['lat']),
regions)
spec['name'] = region['properties']['REGION_NAM']
spec['code'] = region['properties']['TDWG_CODE']
if dist == 0:
args.log.info('{0} contained in region {1}'.format(
soc, spec['name']))
else:
args.log.warn(
'assigning {0} to nearest region {1}, distance {2}'.
format(soc, region['properties']['REGION_NAM'], dist))
soc_tdwg[soc.id] = spec
def test_match_contains(mocker):
mocker.patch('pydplace.geo.shape', mocker.Mock())
mocker.patch('pydplace.geo.Point', mocker.Mock())
assert geo.match(0, 0, [mocker.MagicMock()])[1] == 0
def test_match():
with pytest.raises(AssertionError):
geo.match(0, 0, [])