reimplement finding tips by processid

barcode_validator/__main__.py

@@ -7,6 +7,13 @@
 from barcode_validator.result import DNAAnalysisResult
 
 
+def get_tip_by_processid(process_id, tree):
+    for tip in tree.get_terminals():
+        if tip.guids['processid'] == process_id:
+            return tip
+    return None
+
+
 def main(fasta_file_path, bold_sheet, actions):
     logging.info(f"Starting analysis for file: {fasta_file_path}")
 
@@ -25,7 +32,7 @@ def main(fasta_file_path, bold_sheet, actions):
             logging.info(f'Processing FASTA record {process_id}')
 
             # Lookup species from process_id
-            tip = list(bold_tree.find_clades({'guid': {'processid': process_id}}))[0]
+            tip = get_tip_by_processid(process_id, bold_tree)
             species = tip.name
             for node in bold_tree.root.get_path(tip):
                 if node.rank == config.get('level'):

barcode_validator/taxonomy.py

@@ -15,11 +15,6 @@
 from nbt.Phylo.NCBITaxdmp import Parser as NCBIParser
 
 
-#def read_bold_taxonomy(spreadsheet):
-#    logging.info("Reading BOLD taxonomy")
-#    return BOLDParser(open(spreadsheet)).parse()
-
-
 def read_bold_taxonomy(spreadsheet):
     # Read the Excel file into a BytesIO object
     with open(spreadsheet, 'rb') as file: