Fix taxa upload test (#4102)

bims/scripts/taxa_upload.py

@@ -287,33 +287,56 @@ def get_taxonomy(self, taxon_name, scientific_name, rank):
  return parent
 
  def get_parent(self, row, current_rank=GENUS):
+ # Retrieve the taxon name based on the current rank from the row data
  taxon_name = DataCSVUpload.row_value(row, current_rank)
  if not taxon_name:
  return None
+
+ # Handle concatenation for SPECIES rank
  if current_rank == SPECIES:
  genus_name = DataCSVUpload.row_value(row, GENUS)
  if genus_name not in taxon_name:
- taxon_name = DataCSVUpload.row_value(row, GENUS) + ' ' + taxon_name
+ taxon_name = genus_name + ' ' + taxon_name
+
+ # Handle concatenation for VARIETY rank
  if current_rank == VARIETY:
- taxon_name = (
- DataCSVUpload.row_value(row, GENUS) + ' ' +
- DataCSVUpload.row_value(row, SPECIES) + ' ' +
- DataCSVUpload.row_value(row, VARIETY)
- )
+ genus_name = DataCSVUpload.row_value(row, GENUS)
+ species_name = DataCSVUpload.row_value(row, SPECIES)
+ if species_name not in taxon_name:
+ taxon_name = species_name + ' ' + taxon_name
+ if genus_name not in taxon_name:
+ taxon_name = genus_name + ' ' + taxon_name
+
+ # Fetch the taxon using the constructed taxon name and current rank
  taxon = self.get_taxonomy(
  taxon_name,
  taxon_name,
  current_rank.upper()
  )
- while not taxon.gbif_key or not taxon.parent and taxon.parent.rank != 'KINGDOM':
+
+ # If the taxon already has a parent, return it
+ if taxon.parent and taxon.parent.rank:
+ return taxon
+
+ # Loop to find and assign the parent taxon until the conditions are met
+ while not taxon.gbif_key or (taxon.parent and taxon.parent.rank != 'KINGDOM'):
+ # Exit the loop if the current taxon rank is 'KINGDOM'
+ if taxon.rank == 'KINGDOM':
+ break
+
+ # Determine the parent rank name
  parent_rank_name = parent_rank(current_rank)
  if not parent_rank_name:
  break
+
+ # Recursively get the parent taxon
  parent = self.get_parent(row, parent_rank_name)
  if parent:
  taxon.parent = parent
  taxon.save()
  break
+
+ # Update the current rank for the next iteration
  current_rank = parent_rank_name
 
  return taxon