update call to pass a test

EBIvariation · Apr 22, 2024 · 3f33912 · 3f33912
1 parent 8b0e334
commit 3f33912
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Showing 4 changed files with 6 additions and 8 deletions.
diff --git a/eva_submission/eload_ingestion.py b/eva_submission/eload_ingestion.py
@@ -206,7 +206,7 @@ def check_variant_db(self):
                     metadata_connection_handle=conn,
                     assembly_accession=assembly,
                     taxonomy_id=self.taxonomy,
-                    ncbi_api_key=cfg['eutils_api_key']
+                    ncbi_api_key=cfg.get('eutils_api_key')
                 )
 
         for db_info in assembly_to_db_name.values():

diff --git a/eva_submission/eload_utils.py b/eva_submission/eload_utils.py
@@ -26,14 +26,14 @@ def get_reference_fasta_and_report(species_name, reference_accession, output_dir
     if NCBIAssembly.is_assembly_accession_format(reference_accession):
         assembly = NCBIAssembly(
             reference_accession, species_name, output_directory,
-            eutils_api_key=cfg['eutils_api_key']
+            eutils_api_key=cfg.get('eutils_api_key')
         )
         if not os.path.isfile(assembly.assembly_fasta_path) or not os.path.isfile(assembly.assembly_report_path) or overwrite:
             assembly.download_or_construct(overwrite=overwrite)
         return assembly.assembly_fasta_path, assembly.assembly_report_path
     elif NCBISequence.is_genbank_accession_format(reference_accession):
         reference = NCBISequence(reference_accession, species_name, output_directory,
-                                 eutils_api_key=cfg['eutils_api_key'])
+                                 eutils_api_key=cfg.get('eutils_api_key'))
         if not os.path.isfile(reference.sequence_fasta_path) or overwrite:
             reference.download_contig_sequence_from_ncbi(genbank_only=True)
         return reference.sequence_fasta_path, None
@@ -54,7 +54,7 @@ def resolve_accession_from_text(reference_text):
     if NCBIAssembly.is_assembly_accession_format(reference_text):
         return [reference_text]
     # Search for a reference genome that resolve this text
-    accession = retrieve_genbank_assembly_accessions_from_ncbi(reference_text, api_key=cfg['eutils_api_key'])
+    accession = retrieve_genbank_assembly_accessions_from_ncbi(reference_text, api_key=cfg.get('eutils_api_key'))
     if accession:
         return accession
 

diff --git a/eva_submission/vep_utils.py b/eva_submission/vep_utils.py
@@ -139,7 +139,7 @@ def get_species_and_assembly(assembly_acc):
     Returns None if the taxonomy is not known.
     """
     # We first need to search for the species associated with the assembly
-    assembly_dicts = get_ncbi_assembly_dicts_from_term(assembly_acc, api_key=cfg['eutils_api_key'])
+    assembly_dicts = get_ncbi_assembly_dicts_from_term(assembly_acc, api_key=cfg.get('eutils_api_key'))
     taxid_and_assembly_name = set([
         (assembly_dict.get('taxid'), assembly_dict.get('assemblyname'))
         for assembly_dict in assembly_dicts
@@ -253,7 +253,7 @@ def recursive_nlst(ftp, root, pattern):
 
 @retry(tries=4, delay=2, backoff=1.2, jitter=(1, 3), logger=logger)
 def download_and_extract_vep_cache(ftp, vep_cache_file, taxonomy_id):
-    scientific_name = retrieve_species_scientific_name_from_tax_id_ncbi(taxonomy_id, api_key=cfg['eutils_api_key'])
+    scientific_name = retrieve_species_scientific_name_from_tax_id_ncbi(taxonomy_id, api_key=cfg.get('eutils_api_key'))
     species_name = scientific_name.replace(' ', '_').lower()
 
     tmp_dir = tempfile.TemporaryDirectory()

diff --git a/tests/resources/submission_config.yml b/tests/resources/submission_config.yml
@@ -45,5 +45,3 @@ ena:
   ftpport: 22
   username: demo
   password: password
-
-eutils_api_key: test