def write_points(points, base_dir, service_suffix):
"""Write the sorted points into separate directories and files.
Args:
points (list of Point): A list of points sorted by species name.
base_dir (str): The base directory to write points.
service_suffix (str): The service suffix for the data files.
"""
current_species = None
out_file = None
for point in points:
if point.species_name != current_species:
if out_file:
out_file.close()
current_species = point.species_name
#print(point)
#print(current_species)
out_file = open(
get_species_filename(current_species, base_dir, service_suffix,
'.csv'), 'w')
if isinstance(point.flags, list):
flags = ','.join(point.flags)
elif isinstance(point.flags, str):
flags = point.flags
else:
flags = ''
out_file.write('{}, {}, {}, "{}"\n'.format(point.species_name, point.x,
point.y, flags))
if out_file:
out_file.close()
def get_gbif(species_key, species_name, base_dir):
"""Attempt to get gbif record for species."""
# Get points
json_points = get_points_from_gbif(species_key)
converted_points = []
if len(json_points) > 0:
# Convert points
converted_points = convert_json_to_point(
json_points,
itemgetter('species'),
itemgetter('decimalLongitude'),
itemgetter('decimalLatitude'),
flags_getter=itemgetter('issues'))
# Get file name
sp_filename = get_species_filename(species_name, base_dir, '_gbif', '.csv')
# Write points
write_points(sp_filename, converted_points)
def get_powo(species_key, species_name, base_dir):
"""Attempt to get powo record for species."""
# Get data
#try:
result = {}
fq_id = get_kew_id_for_species(species_name)
#except Exception:
# fq_id = None
if fq_id:
result = get_species_kew(fq_id)
# Get file name
sp_filename = get_species_filename(species_name, base_dir, '_powo',
'.json')
# Write
with open(sp_filename, 'w', encoding='utf8') as powo_out:
json.dump(result, powo_out)
def get_idigbio(species_key, species_name, base_dir):
"""Attempt to get idigbio record for species."""
# Get points
json_points = get_points_from_idigbio(species_key=species_key)
converted_points = []
if len(json_points) > 0:
# Convert points
converted_points = convert_json_to_point(
json_points,
species_chain_getter('indexTerms', 'canonicalname'),
chain_getter('indexTerms', 'geopoint', 'lon'),
chain_getter('indexTerms', 'geopoint', 'lat'),
flags_getter=chain_getter('indexTerms', 'flags'))
# Get file name
sp_filename = get_species_filename(species_name, base_dir, '_idigbio',
'.csv')
# Write points
write_points(sp_filename, converted_points)