added ranks and rank_propagation (#207)

Thanks @VinzentRisch! LGTM!

- tests passed
- flake8 passed

I also ran the following and the taxonomy came out as expected:

qiime rescript get-ncbi-genomes --p-taxon 1322345 --p-assembly-source all --p-assembly-levels contig --p-no-only-reference --p-ranks phylum class subclass order family subfamily genus species --output-dir ncbi-genome-test-dl --verbose

INFO:2024-10-23 16:13:01,936:MainProcess:Downloading 1 records
INFO:2024-10-23 16:13:04,860:LokyProcess-3:got 1 records
Saved FeatureData[Sequence] to: ncbi-genome-test-dl/genome_assemblies.qza
Saved GenomeData[Loci] to: ncbi-genome-test-dl/loci.qza
Saved GenomeData[Proteins] to: ncbi-genome-test-dl/proteins.qza
Saved FeatureData[Taxonomy] to: ncbi-genome-test-dl/taxonomies.qza

rescript/ncbi_datasets.py

@@ -156,12 +156,14 @@ def _fetch_and_extract_dataset(
 def _fetch_taxonomy(
         all_acc_ids: list,
         all_tax_ids: list,
-        accession_to_assembly: pd.Series
+        accession_to_assembly: pd.Series,
+        ranks: list,
+        rank_propagation: bool
 ):
     manager = Manager()
     taxa, bad_accs = get_taxonomies(
         taxids={k: v for k, v in zip(all_acc_ids, all_tax_ids)},
-        ranks=_default_ranks, rank_propagation=True,
+        ranks=ranks, rank_propagation=rank_propagation,
         logging_level='INFO', n_jobs=2, request_lock=manager.Lock()
     )
     # technically, this should never happen as the taxa accession
@@ -213,6 +215,8 @@ def get_ncbi_genomes(
         only_genomic: bool = False,
         tax_exact_match: bool = False,
         page_size: int = 20,
+        ranks: list = _default_ranks,
+        rank_propagation: bool = True,
 ) -> (DNAFASTAFormat, LociDirectoryFormat,
       ProteinsDirectoryFormat, pd.DataFrame):
     # we use a deepcopy of assembly_levels because the new versions of
@@ -239,7 +243,9 @@ def get_ncbi_genomes(
         taxa = _fetch_taxonomy(
             assembly_to_taxon.keys(),
             assembly_to_taxon.values(),
-            accession_map.explode()
+            accession_map.explode(),
+            ranks,
+            rank_propagation
         )
 
     return genomes, loci, proteins, taxa

rescript/plugin_setup.py

@@ -1190,7 +1190,9 @@
         'assembly_levels': List[Str % Choices(
             ['complete_genome', 'chromosome', 'scaffold', 'contig'])],
         'tax_exact_match': Bool,
-        'page_size': Int % Range(20, 1000, inclusive_end=True)
+        'page_size': Int % Range(20, 1000, inclusive_end=True),
+        'ranks': List[Str % Choices(_allowed_ranks)],
+        'rank_propagation': Bool,
     },
     outputs=[
         ('genome_assemblies', FeatureData[Sequence]),
@@ -1217,6 +1219,10 @@
                      'request. If number of genomes to fetch is higher than '
                      'this number, requests will be repeated until all '
                      'assemblies are fetched.',
+        'ranks': 'List of taxonomic ranks for building a taxonomy from the '
+                 'NCBI Taxonomy database.',
+        'rank_propagation': RANK_PROPAGATE_DESCRIPTION,
+
     },
     output_descriptions={
         'genome_assemblies': 'Nucleotide sequences of requested genomes.',

rescript/tests/test_ncbi_datasets.py

@@ -198,7 +198,9 @@ def test_fetch_taxonomy(self, p):
             pd.Series(
                 {'GCF_123': ['AC_12.1'], 'GCF_234': ['AC_23.2']},
                 name="assembly_id"
-            ).explode()
+            ).explode(),
+            _default_ranks,
+            True
         )
 
         exp_taxa = pd.DataFrame(
@@ -221,7 +223,11 @@ def test_fetch_taxonomy_bad_accs(self, p):
             Exception, r'Invalid taxonomy.*\: ACC1, ACC2. Please check.*'
         ):
             _fetch_taxonomy(
-                self.fake_assembly_ids, self.fake_tax_ids, pd.Series()
+                self.fake_assembly_ids,
+                self.fake_tax_ids,
+                pd.Series(),
+                _default_ranks,
+                True
             )
 
     # just test that everything works together