def handle(self, *args, **options):
# Get collection without taxa record
only_update_missing_class = options.get('only_update_missing_class')
if only_update_missing_class:
collections_non_taxa = BiologicalCollectionRecord.objects.filter(
Q(taxon_gbif_id__taxon_class__isnull=True)
| Q(taxon_gbif_id__taxon_class__exact=''))
else:
collections_non_taxa = BiologicalCollectionRecord.objects.filter(
taxon_gbif_id__isnull=True)
models.signals.post_save.disconnect(
collection_post_save_update_cluster, )
models.signals.post_save.disconnect(collection_post_save_handler, )
for collection in collections_non_taxa:
existed = BiologicalCollectionRecord.objects.filter(
original_species_name=collection.original_species_name,
taxon_gbif_id__isnull=False)
if existed and not only_update_missing_class:
collection.taxon_gbif_id = existed[0].taxon_gbif_id
collection.save()
else:
update_collection_record(collection)
models.signals.post_save.connect(collection_post_save_update_cluster, )
models.signals.post_save.connect(collection_post_save_handler, )
def handle(self, *args, **options):
# Get collection without taxa record
collections_non_taxa = BiologicalCollectionRecord.objects.filter(
taxon_gbif_id__isnull=True)
for collection in collections_non_taxa:
existed = BiologicalCollectionRecord.objects.filter(
original_species_name=collection.original_species_name,
taxon_gbif_id__isnull=False)
if existed:
collection.taxon_gbif_id = existed[0].taxon_gbif_id
collection.save()
else:
update_collection_record(collection)
def on_post_save(self):
if not self.taxonomy:
update_collection_record(self)
if not self.source_collection:
if preferences.SiteSetting.default_data_source:
self.source_collection = (
preferences.SiteSetting.default_data_source
)
self.save()
if self.taxonomy and not self.module_group:
# Get taxon group if exists
taxonomies = [self.taxonomy.id]
taxon_groups = TaxonGroup.objects.filter(
taxonomies__in=taxonomies,
category=TaxonomicGroupCategory.SPECIES_MODULE.name,
)
if taxon_groups.exists():
self.module_group = taxon_groups[0]
self.save()
def handle(self, *args, **options):
models.signals.pre_save.disconnect(
taxonomy_pre_save_handler,
)
models.signals.post_save.disconnect(
collection_post_save_handler,
)
taxonomy_gbif_keys = Taxonomy.objects.values_list(
'gbif_key',
flat=True
)
taxa = Taxon.objects.all().exclude(
gbif_id__in=taxonomy_gbif_keys
)
for taxon in taxa:
print('Migrate %s' % taxon.scientific_name)
taxon_identifier = process_taxon_identifier(taxon.gbif_id)
if taxon_identifier:
taxon_identifier.iucn_data = taxon.iucn_data
taxon_identifier.iucn_redlist_id = taxon.iucn_redlist_id
taxon_identifier.author = taxon.author
taxon_identifier.endemism = taxon.endemism
taxon_identifier.save()
if taxon.iucn_status:
iucn_status = IUCNStatus.objects.get(
pk=taxon.iucn_status.pk)
taxonomy = Taxonomy.objects.get(id=taxon_identifier.id)
taxonomy.iucn_status = iucn_status
taxonomy.save()
collections = BiologicalCollectionRecord.objects.filter(
taxonomy__isnull=True,
)
for collection in collections:
update_collection_record(collection)
models.signals.post_save.connect(
collection_post_save_handler,
)
def on_post_save(self):
if not self.taxon_gbif_id:
update_collection_record(self)
def form_valid(self, form):
form.save(commit=True)
collection_processed = {
'added': {
'count': 0,
'message': 'records added'
},
'duplicated': {
'count': 0,
'message': 'not accepted because duplicates'
},
'failed': {
'count': 0,
'message': 'failed'
},
'different_format': {
'count': 0,
'message': 'failed due to wrong format'
}
}
# Read csv
csv_file = form.instance.csv_file
# disconnect post save handler of location sites
# it is done from record signal
models.signals.post_save.disconnect(
location_site_post_save_handler,
)
models.signals.post_save.disconnect(
collection_post_save_update_cluster,
)
location_sites = []
with open(csv_file.path, 'r') as csvfile:
csv_reader = csv.DictReader(csvfile)
for record in csv_reader:
try:
print('------------------------------------')
print('Processing : %s' % record['species_name'])
location_type, status = LocationType.objects.get_or_create(
name='PointObservation',
allowed_geometry='POINT'
)
# Optional records for location site
optional_site_records = {}
# Optional fields and value
optional_records = {}
if sys.version_info > (3, 0):
# Python 3 code in this block
optional_fields_iter = self.additional_fields.items()
else:
# Python 2 code in this block
optional_fields_iter = self.additional_fields.\
iteritems()
for (opt_field, field_type) in optional_fields_iter:
if opt_field in record:
optional_record = self.parse_optional_record(
record[opt_field],
field_type
)
if not optional_record:
optional_record = ''
if opt_field[:4] == 'site':
optional_site_records[opt_field] = \
optional_record
else:
if optional_record:
optional_records[opt_field] = \
optional_record
record_point = Point(
float(record['longitude']),
float(record['latitude']))
try:
location_site, status = LocationSite.objects.\
get_or_create(
location_type=location_type,
geometry_point=record_point,
name=record['location_site']
)
except LocationSite.MultipleObjectsReturned:
location_site = LocationSite.objects.filter(
location_type=location_type,
geometry_point=record_point,
name=record['location_site']
)[0]
if sys.version_info > (3, 0):
optional_site_records_iter = \
optional_site_records.items()
else:
optional_site_records_iter = \
optional_site_records.iteritems()
for opt_key, opt_val in optional_site_records_iter:
setattr(location_site, opt_key, opt_val)
location_site.save()
location_sites.append(location_site)
# Get existed taxon
collections = self.collection_record.objects.filter(
original_species_name=record['species_name']
)
taxon_gbif = None
if collections:
taxon_gbif = collections[0].taxon_gbif_id
# custodian field
if 'custodian' in record:
optional_records['institution_id'] = \
record['custodian']
collection_records, created = self.collection_record.\
objects.\
get_or_create(
site=location_site,
original_species_name=record['species_name'],
category=record['category'].lower(),
collection_date=datetime.strptime(
record['date'], '%Y-%m-%d'),
collector=record['collector'],
notes=record['notes'],
taxon_gbif_id=taxon_gbif,
owner=self.request.user,
**optional_records
)
if created:
print('%s records added' % record['species_name'])
collection_processed['added']['count'] += 1
else:
collection_processed['duplicated']['count'] += 1
if not taxon_gbif:
print('Update taxon gbif')
update_collection_record(collection_records)
except KeyError:
collection_processed['different_format']['count'] += 1
except ValueError:
collection_processed['failed']['count'] += 1
print('------------------------------------')
csv_upload_message = ''
for processed in collection_processed:
if collection_processed[processed]['count'] > 0:
csv_upload_message += '%s %s <br/>' % (
collection_processed[processed]['count'],
collection_processed[processed]['message']
)
if collection_processed['added']['count'] > 0:
csv_upload_message += 'Verify your records ' \
'<a target="_blank" ' \
'href="/nonvalidated-user-list/">' \
'here</a> <br/>'
self.context_data['uploaded'] = csv_upload_message
# reconnect post save handler of location sites
models.signals.post_save.connect(
location_site_post_save_handler,
)
models.signals.post_save.connect(
collection_post_save_update_cluster,
)
return JsonResponse({
'message': self.context_data['uploaded']
})
def form_valid(self, form):
form.save(commit=True)
collection_processed = {
'added': {
'count': 0,
'message': 'records added'
},
'duplicated': {
'count': 0,
'message': 'not accepted because duplicates'
},
'failed': {
'count': 0,
'message': 'failed'
},
'different_format': {
'count': 0,
'message': 'failed due to wrong format'
}
}
# Read csv
csv_file = form.instance.csv_file
# disconnect post save handler of location sites
# it is done from record signal
models.signals.post_save.disconnect(location_site_post_save_handler, )
models.signals.post_save.disconnect(
collection_post_save_update_cluster, )
location_sites = []
with open(csv_file.path, 'r') as csvfile:
csv_reader = csv.DictReader(csvfile)
for record in csv_reader:
try:
print('------------------------------------')
print('Processing : %s' % record['species_name'])
location_type, status = LocationType.objects.get_or_create(
name='PointObservation', allowed_geometry='POINT')
# Optional records for location site
optional_site_records = {}
# Optional fields and value
optional_records = {}
if sys.version_info > (3, 0):
# Python 3 code in this block
optional_fields_iter = self.additional_fields.items()
else:
# Python 2 code in this block
optional_fields_iter = (
self.additional_fields.iteritems())
for (opt_field, field_type) in optional_fields_iter:
if opt_field in record:
optional_record = self.parse_optional_record(
record[opt_field], field_type)
if not optional_record:
optional_record = ''
if opt_field[:4] == 'site':
optional_site_records[opt_field] = \
optional_record
else:
if optional_record:
optional_records[opt_field] = \
optional_record
record_point = Point(float(record['longitude']),
float(record['latitude']))
try:
location_site, status = LocationSite.objects. \
get_or_create(
location_type=location_type,
geometry_point=record_point,
name=record['location_site']
)
except LocationSite.MultipleObjectsReturned:
location_site = LocationSite.objects.filter(
location_type=location_type,
geometry_point=record_point,
name=record['location_site'])[0]
if sys.version_info > (3, 0):
optional_site_records_iter = \
optional_site_records.items()
else:
optional_site_records_iter = \
optional_site_records.items()
for opt_key, opt_val in optional_site_records_iter:
setattr(location_site, opt_key, opt_val)
location_site.save()
location_sites.append(location_site)
# Get existed taxon
collections = self.collection_record.objects.filter(
original_species_name=record['species_name'])
# Endemism
endemism = None
if 'endemism' in record and record['endemism']:
endemism, endemism_created = (
Endemism.objects.get_or_create(
name=record['endemism']))
taxonomy = None
if collections:
taxonomy = collections[0].taxonomy
if taxonomy:
taxonomy.endemism = endemism
taxonomy.save()
# custodian field
if 'custodian' in record:
optional_records['institution_id'] = \
record['custodian']
category = ''
if 'category' in record:
category = record['category'].lower()
if 'origin' in record:
origin_choices = {
v: k
for k, v in
BiologicalCollectionRecord.CATEGORY_CHOICES
}
category = origin_choices[record['origin']]
if 'habitat' in record:
habitat_choices = {
v: k
for k, v in
BiologicalCollectionRecord.HABITAT_CHOICES
}
optional_records['collection_habitat'] = (
habitat_choices[record['habitat']])
# sampling method
sampling_method = None
if 'sampling_method' in record:
if record['sampling_method'] != 'unspecified':
sampling_method, sm_created = (
SamplingMethod.objects.get_or_create(
sampling_method=record['sampling_method']))
optional_records['sampling_method'] = (sampling_method)
# sampling effort
if sampling_method and 'effort_area' in record:
effort_area = record['effort_area']
if effort_area:
sampling_method.effort_measure = (effort_area +
' m2')
sampling_method.save()
if sampling_method and 'effort_time' in record:
effort_time = record['effort_time']
if effort_time:
sampling_method.effort_measure = (effort_time +
' min')
sampling_method.save()
# river
if 'river' in record and record['river']:
river, river_created = River.objects.get_or_create(
name=record['river'])
location_site.river = river
location_site.save()
allocate_site_codes_from_river(
location_id=location_site.id)
if record['date'].lower() == 'unspecified':
print('Unspecified date -> Next row')
continue
created = False
collection_records = None
if 'uuid' in record and record['uuid']:
try:
uuid_value = uuid.UUID(record['uuid']).hex
collection_records = (
BiologicalCollectionRecord.objects.filter(
uuid=uuid_value))
if collection_records.exists():
collection_records.update(
site=location_site,
original_species_name=record[
'species_name'],
collection_date=datetime.strptime(
record['date'], '%Y-%m-%d'),
taxonomy=taxonomy,
)
collection_records = collection_records[0]
else:
optional_records['uuid'] = uuid_value
except ValueError:
print('Bad uuid format')
if not collection_records:
collection_records, created = (
BiologicalCollectionRecord.objects.get_or_create(
site=location_site,
original_species_name=record['species_name'],
collection_date=datetime.strptime(
record['date'], '%Y-%m-%d'),
taxonomy=taxonomy,
category=category,
collector=record['collector'],
))
# Additional data
additional_data = {}
if 'effort_number_throws' in record:
additional_data['effort_number_throws'] = (
record['effort_number_throws'])
if 'catch_per_number' in record:
additional_data['catch_per_number'] = (
record['catch_per_number'])
if 'catch_per_unit_effort' in record:
additional_data['catch_per_unit_effort'] = (
record['catch_per_unit_effort'])
if 'number_of_replicates' in record:
additional_data['number_of_replicates'] = (
record['number_of_replicates'])
if 'hydraulic_biotope' in record:
additional_data['hydraulic_biotope'] = (
record['hydraulic_biotope'])
if 'substratum' in record:
additional_data['substratum'] = (record['substratum'])
if 'depth_m' in record:
additional_data['depth_m'] = (record['depth_m'])
if 'near_bed_velocity' in record:
additional_data['near_bed_velocity'] = (
record['near_bed_velocity'])
if 'conductivity' in record:
additional_data['conductivity'] = (
record['conductivity'])
if 'ph' in record:
additional_data['ph'] = (record['ph'])
if 'dissolved_oxygen' in record:
additional_data['dissolved_oxygen'] = (
record['dissolved_oxygen'])
if 'temperature' in record:
additional_data['temperature'] = (
record['temperature'])
if 'turbidity' in record:
additional_data['turbidity'] = (record['turbidity'])
collection_records.notes = record['notes']
collection_records.owner = self.request.user
collection_records.additional_data = additional_data
collection_records.save()
# update multiple fields
BiologicalCollectionRecord.objects.filter(
id=collection_records.id).update(**optional_records)
if created:
print('%s records added' % record['species_name'])
collection_processed['added']['count'] += 1
else:
collection_processed['duplicated']['count'] += 1
if not taxonomy:
print('Update taxon gbif')
update_collection_record(collection_records)
collection_records.taxonomy.endemism = endemism
collection_records.taxonomy.save()
except KeyError:
collection_processed['different_format']['count'] += 1
except ValueError:
collection_processed['failed']['count'] += 1
print('------------------------------------')
csv_upload_message = ''
for processed in collection_processed:
if collection_processed[processed]['count'] > 0:
csv_upload_message += '%s %s <br/>' % (
collection_processed[processed]['count'],
collection_processed[processed]['message'])
if collection_processed['added']['count'] > 0:
csv_upload_message += 'Verify your records ' \
'<a href="/nonvalidated-user-list/">' \
'here</a> <br/>'
self.context_data['uploaded'] = csv_upload_message
# reconnect post save handler of location sites
models.signals.post_save.connect(location_site_post_save_handler, )
models.signals.post_save.connect(collection_post_save_update_cluster, )
return JsonResponse({'message': self.context_data['uploaded']})
def handle(self, *args, **options):
folder_name = 'data'
source_collection = 'CFE Fish Data'
file_path = os.path.join(
os.path.abspath(os.path.dirname(__name__)),
'bims/static/{folder}/{filename}'.format(folder=folder_name,
filename=self.file_name))
with open(file_path, 'r') as csvfile:
csv_reader = csv.DictReader(csvfile)
for index, record in enumerate(csv_reader):
try:
log('Processing : %s' % record[SPECIES_NAME])
location_type, status = LocationType.objects.get_or_create(
name='PointObservation', allowed_geometry='POINT')
# Optional records for location site
optional_site_records = {}
# Optional fields and value
optional_records = {}
if sys.version_info > (3, 0):
# Python 3 code in this block
optional_fields_iter = self.additional_fields.items()
else:
# Python 2 code in this block
optional_fields_iter = (
self.additional_fields.iteritems())
for (opt_field, field_type) in optional_fields_iter:
if opt_field in record:
optional_record = self.parse_optional_record(
record[opt_field], field_type)
if not optional_record:
optional_record = ''
if opt_field[:4] == 'site':
optional_site_records[opt_field] = \
optional_record
else:
if optional_record:
optional_records[opt_field] = \
optional_record
record_point = Point(float(record[LONGITUDE]),
float(record[LATITUDE]))
# Create or get location site
try:
location_site, status = LocationSite.objects. \
get_or_create(
location_type=location_type,
geometry_point=record_point,
name=record[LOCATION_SITE]
)
except LocationSite.MultipleObjectsReturned:
location_site = LocationSite.objects.filter(
location_type=location_type,
geometry_point=record_point,
name=record[LOCATION_SITE])[0]
if sys.version_info > (3, 0):
optional_site_records_iter = (
optional_site_records.items())
else:
optional_site_records_iter = (
optional_site_records.iteritems())
for opt_key, opt_val in optional_site_records_iter:
setattr(location_site, opt_key, opt_val)
location_site.save()
# Get existed taxon
collections = BiologicalCollectionRecord.objects.filter(
original_species_name=record[SPECIES_NAME])
# Endemism
endemism = None
if ENDEMISM in record and record[ENDEMISM]:
endemism, endemism_created = (
Endemism.objects.get_or_create(
name=record[ENDEMISM]))
taxonomy = None
if collections:
taxonomy = collections[0].taxonomy
if taxonomy:
taxonomy.endemism = endemism
taxonomy.save()
# custodian field
if CUSTODIAN in record:
optional_records['institution_id'] = \
record[CUSTODIAN]
# reference
if REFERENCE in record:
optional_records['reference'] = record[REFERENCE]
if REFERENCE_CATEGORY in record:
optional_records['reference_category'] = (
record[REFERENCE_CATEGORY])
if PRESENT in record:
optional_records['present'] = bool(record[PRESENT])
category = ''
if CATEGORY in record:
category = record[CATEGORY].lower()
if ORIGIN in record:
origin_choices = {
v: k
for k, v in
BiologicalCollectionRecord.CATEGORY_CHOICES
}
category = origin_choices[record[ORIGIN]]
if HABITAT in record:
habitat_choices = {
v: k
for k, v in
BiologicalCollectionRecord.HABITAT_CHOICES
}
optional_records['collection_habitat'] = (
habitat_choices[record[HABITAT]])
# sampling method
sampling_method = None
if SAMPLING_METHOD in record:
if record[SAMPLING_METHOD] != 'unspecified':
sampling_method, sm_created = (
SamplingMethod.objects.get_or_create(
sampling_method=record[SAMPLING_METHOD]))
optional_records['sampling_method'] = (sampling_method)
# sampling effort
if sampling_method and EFFORT_AREA in record:
effort_area = record[EFFORT_AREA]
if effort_area:
sampling_method.effort_measure = (effort_area +
' m2')
sampling_method.save()
if sampling_method and EFFORT_TIME in record:
effort_time = record[EFFORT_TIME]
if effort_time:
sampling_method.effort_measure = (effort_time +
' min')
sampling_method.save()
if record[SAMPLING_DATE].lower() == 'unspecified':
self.add_to_error_summary(
'Unspecified date -> Next row', index)
continue
created = False
collection_records = None
if UUID in record and record[UUID]:
try:
uuid_value = uuid.UUID(record[UUID]).hex
collection_records = (
BiologicalCollectionRecord.objects.filter(
uuid=uuid_value))
if collection_records.exists():
collection_records.update(
site=location_site,
original_species_name=record[SPECIES_NAME],
collection_date=datetime.strptime(
record[SAMPLING_DATE], '%Y/%m/%d'),
taxonomy=taxonomy,
)
collection_records = collection_records[0]
else:
optional_records['uuid'] = uuid_value
except ValueError:
print('Bad uuid format')
if not collection_records:
collection_records, created = (
BiologicalCollectionRecord.objects.get_or_create(
site=location_site,
original_species_name=record[SPECIES_NAME],
collection_date=datetime.strptime(
record[SAMPLING_DATE], '%Y/%m/%d'),
taxonomy=taxonomy,
category=category,
collector=record[COLLECTOR],
))
# Additional data
additional_data = {}
if EFFORT_NUMBER_THROWS in record:
additional_data['effort_number_throws'] = (
record[EFFORT_NUMBER_THROWS])
if CATCH_NUMBER in record:
additional_data['catch_per_number'] = (
record[CATCH_NUMBER])
if CATCH_PER_UNIT in record:
additional_data['catch_per_unit_effort'] = (
record[CATCH_PER_UNIT])
if NUMBER_OF_REPLICATES in record:
additional_data['number_of_replicates'] = (
record[NUMBER_OF_REPLICATES])
if HYDRAULIC_BIOTOPE in record:
additional_data['hydraulic_biotope'] = (
record[HYDRAULIC_BIOTOPE])
if SUBSTRATUM in record:
additional_data['substratum'] = (record[SUBSTRATUM])
if DEPTH_M in record:
additional_data['depth_m'] = (record[DEPTH_M])
if NBV in record:
additional_data['near_bed_velocity'] = (record[NBV])
if CONDUCTIVITY in record:
additional_data['conductivity'] = (
record[CONDUCTIVITY])
if PH in record:
additional_data['ph'] = (record[PH])
if DISSOLVED_OXYGEN_PERCENT in record:
additional_data['dissolved_oxygen_percent'] = (
record[DISSOLVED_OXYGEN_PERCENT])
if DISSOLVED_OXYGEN_MG in record:
additional_data['dissolved_oxygen_mg_l'] = (
record[DISSOLVED_OXYGEN_MG])
if TEMP in record:
additional_data['temperature'] = (record[TEMP])
if TURBIDITY in record:
additional_data['turbidity'] = (record[TURBIDITY])
collection_records.notes = record[NOTES]
superusers = get_user_model().objects.filter(
is_superuser=True)
collection_records.owner = superusers[0]
collection_records.additional_data = additional_data
collection_records.source_collection = source_collection
collection_records.save()
# update multiple fields
BiologicalCollectionRecord.objects.filter(
id=collection_records.id).update(**optional_records)
if not created:
self.data_updated += 1
else:
self.data_added += 1
if not taxonomy:
log('Update taxon gbif')
update_collection_record(collection_records)
# If taxonomy still not found
if not collection_records.taxonomy:
self.add_to_error_summary(
'Taxonomy {} not found'.format(
record[SPECIES_NAME]), index)
collection_records.delete()
continue
collection_records.taxonomy.endemism = endemism
collection_records.taxonomy.save()
# Update common names
if COMMON_NAME in record and record[COMMON_NAME]:
common_name = record[COMMON_NAME]
try:
vernacular_name, vernacular_created = (
VernacularName.objects.get_or_create(
name=common_name, language='eng'))
except VernacularName.MultipleObjectsReturned:
vernacular_name = VernacularName.objects.filter(
name=common_name)[0]
collection_records.taxonomy.vernacular_names.clear()
collection_records.taxonomy.vernacular_names.add(
vernacular_name)
except KeyError as e:
self.add_to_error_summary(
'KeyError : {}'.format(e.message), index)
continue
except ValueError as e:
self.add_to_error_summary(
'ValueError : {}'.format(e.message), index)
continue
self.summary['data_added'] = self.data_added
self.summary['data_duplicated'] = self.data_updated
self.summary['data_failed'] = self.data_failed
self.summary['total_processed_data'] = (self.data_added +
self.data_updated +
self.data_failed)
self.summary['error_list'] = self.errors
log(json.dumps(self.summary))
def form_valid(self, form):
form.save(commit=True)
collection_processed = {'added': 0, 'failed': 0}
# Read csv
csv_file = form.instance.csv_file
# disconnect post save handler of location sites
# it is done from record signal
models.signals.post_save.disconnect(location_site_post_save_handler, )
models.signals.post_save.disconnect(
collection_post_save_update_cluster, )
location_sites = []
with open(csv_file.path, 'r') as csvfile:
csv_reader = csv.DictReader(csvfile)
for record in csv_reader:
try:
print('------------------------------------')
print('Processing : %s' % record['species_name'])
location_type, status = LocationType.objects.get_or_create(
name='PointObservation', allowed_geometry='POINT')
record_point = Point(float(record['longitude']),
float(record['latitude']))
location_site, status = LocationSite.objects.get_or_create(
location_type=location_type,
geometry_point=record_point,
name=record['location_site'],
)
location_sites.append(location_site)
# Get existed taxon
collections = self.collection_record.objects.filter(
original_species_name=record['species_name'])
taxon_gbif = None
if collections:
taxon_gbif = collections[0].taxon_gbif_id
# Optional fields and value
optional_records = {}
if (sys.version_info > (3, 0)):
# Python 3 code in this block
optional_fields_iter = self.additional_fields.items()
else:
# Python 2 code in this block
optional_fields_iter = self.additional_fields.\
iteritems()
for (opt_field, field_type) in optional_fields_iter:
if opt_field in record:
if field_type == 'bool':
record[opt_field] = record[opt_field] == '1'
elif field_type == 'str':
record[opt_field] = record[opt_field].lower()
optional_records[opt_field] = record[opt_field]
collection_records, created = self.collection_record.\
objects.\
get_or_create(
site=location_site,
original_species_name=record['species_name'],
category=record['category'].lower(),
collection_date=datetime.strptime(
record['date'], '%Y-%m-%d'),
collector=record['collector'],
notes=record['notes'],
taxon_gbif_id=taxon_gbif,
owner=self.request.user,
**optional_records
)
if created:
print('%s Added' % record['species_name'])
collection_processed['added'] += 1
else:
if not taxon_gbif:
print('Update taxon gbif')
update_collection_record(collection_records)
except (ValueError, KeyError):
collection_processed['failed'] += 1
print('------------------------------------')
self.context_data['uploaded'] = 'Collection added ' + \
str(collection_processed['added'])
# reconnect post save handler of location sites
models.signals.post_save.connect(location_site_post_save_handler, )
models.signals.post_save.connect(collection_post_save_update_cluster, )
return JsonResponse({'message': self.context_data['uploaded']})
