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Handle full subspecies name in taxa upload #4094

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Jul 22, 2024
Merged

Handle full subspecies name in taxa upload #4094

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21 changes: 13 additions & 8 deletions bims/scripts/taxa_upload.py
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Original file line number Diff line number Diff line change
Expand Up @@ -200,8 +200,11 @@ def validate_parents(self, taxon, row):
csv_data = DataCSVUpload.row_value(
row, taxon_parent_rank.capitalize())
if taxon_parent_rank == SPECIES:
csv_data = DataCSVUpload.row_value(
row, GENUS) + ' ' + csv_data
genus = DataCSVUpload.row_value(
row, GENUS)
if genus not in csv_data:
csv_data = DataCSVUpload.row_value(
row, GENUS) + ' ' + csv_data
except KeyError:
parent = parent.parent
continue
Expand All @@ -218,7 +221,7 @@ def validate_parents(self, taxon, row):
print('Different parent for {}'.format(str(taxon)))
taxon_parent = self.get_parent(
row,
current_rank=taxon_parent_rank.upper()
current_rank=PARENT_RANKS.get(taxon_parent_rank.upper(), '')
)
print('Updated to {}'.format(str(taxon_parent)))
taxon.parent = taxon_parent
Expand All @@ -227,7 +230,7 @@ def validate_parents(self, taxon, row):
parent = parent.parent
if self.rank_name(taxon) != 'KINGDOM' and not parent:
parent = self.get_parent(
row, current_rank=taxon.rank.capitalize()
row, current_rank=PARENT_RANKS.get(taxon.rank.upper(), '')
)
if parent:
taxon.parent = parent
Expand Down Expand Up @@ -278,7 +281,9 @@ def get_parent(self, row, current_rank=GENUS):
if not taxon_name:
return None
if current_rank == SPECIES:
taxon_name = DataCSVUpload.row_value(row, GENUS) + ' ' + taxon_name
genus_name = DataCSVUpload.row_value(row, GENUS)
if genus_name not in taxon_name:
taxon_name = DataCSVUpload.row_value(row, GENUS) + ' ' + taxon_name
if current_rank == VARIETY:
taxon_name = (
DataCSVUpload.row_value(row, GENUS) + ' ' +
Expand All @@ -290,7 +295,7 @@ def get_parent(self, row, current_rank=GENUS):
taxon_name,
current_rank.upper()
)
while not taxon.gbif_key or not taxon.parent or taxon.parent.rank != 'KINGDOM':
while not taxon.gbif_key or not taxon.parent and taxon.parent.rank != 'KINGDOM':
parent_rank_name = parent_rank(current_rank)
if not parent_rank_name:
break
Expand Down Expand Up @@ -452,8 +457,8 @@ def process_data(self, row, taxon_group: TaxonGroup):

# Taxonomy found or created then validate it
if taxonomy:
if not taxonomy.parent:
taxonomy.parent = self.get_parent(row, parent_rank(rank))
if not taxonomy.parent and parent:
taxonomy.parent = parent

# Data from GBIF couldn't be found, so add it manually
if not taxonomy:
Expand Down