Finished adding partial allele matching

src/automlst/engine/remote/databases/bigsdb.py

@@ -59,28 +59,29 @@ class BIGSdbMLSTProfiler(AbstractAsyncContextManager):
 
 
 
-    async def fetch_mlst_st(self, alleles: AsyncIterable[Allele]) -> MLSTProfile:
+    async def fetch_mlst_st(self, alleles: Union[AsyncIterable[Allele], Iterable[Allele]]) -> MLSTProfile:
         uri_path = "designations"
         allele_request_dict: dict[str, list[dict[str, str]]] = defaultdict(list)
-        async for allele in alleles:
+        if isinstance(alleles, AsyncIterable):
-            allele_request_dict[allele.allele_loci].append({"allele": str(allele.allele_variant)})
+            async for allele in alleles:
-
+                allele_request_dict[allele.allele_loci].append({"allele": str(allele.allele_variant)})
+        else:
+            for allele in alleles:
+                allele_request_dict[allele.allele_loci].append({"allele": str(allele.allele_variant)})
         request_json = {
             "designations": allele_request_dict
         }
         async with self._http_client.post(uri_path, json=request_json) as response:
             response_json: dict = await response.json()
-            if "exact_matches" not in response_json:
+            allele_map: dict[str, list[Allele]] = defaultdict(list)
-                raise NoBIGSdbExactMatchesException(self._database_name, self._schema_id)
+            response_json.setdefault("fields", dict())
-            schema_exact_matches: dict = response_json["exact_matches"]
-            response_json.setdefault("fields", dict)
             schema_fields_returned: dict[str, str] = response_json["fields"]
             schema_fields_returned.setdefault("ST", "unknown")
             schema_fields_returned.setdefault("clonal_complex", "unknown")
-            allele_map: dict[str, list[Allele]] = defaultdict(list)
+            schema_exact_matches: dict = response_json["exact_matches"]
             for exact_match_loci, exact_match_alleles in schema_exact_matches.items():
                 for exact_match_allele in exact_match_alleles:
-                    allele_map[exact_match_loci].append(Allele(exact_match_loci, exact_match_allele["allele_id"]))
+                    allele_map[exact_match_loci].append(Allele(exact_match_loci, exact_match_allele["allele_id"], None))
             return MLSTProfile(allele_map, schema_fields_returned["ST"], schema_fields_returned["clonal_complex"])
 
     async def profile_string(self, string: str, exact: bool = False) -> MLSTProfile:

tests/automlst/engine/remote/databases/test_bigsdb.py

@@ -30,7 +30,7 @@ async def test_institutpasteur_profiling_results_in_exact_matches_when_exact():
         assert len(targets_left) == 0
 
 async def test_institutpasteur_sequence_profiling_non_exact_returns_non_exact():
-    sequences = SeqIO.parse("tests/resources/tohama_I_bpertussis_coding.fasta", "fasta")
+    sequences = list(SeqIO.parse("tests/resources/tohama_I_bpertussis_coding.fasta", "fasta"))
     mlst_targets = {"adk", "fumc", "glya", "tyrb", "icd", "pepa", "pgm"}
     async with BIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as profiler:
         for sequence in sequences:
@@ -40,13 +40,12 @@ async def test_institutpasteur_sequence_profiling_non_exact_returns_non_exact():
             gene = match.group(1)
             if gene.lower() not in mlst_targets:
                 continue
-            scrambled = gene_scrambler(str(sequence.seq), 0.2)
+            scrambled = gene_scrambler(str(sequence.seq), 0.125)
             async for partial_match in profiler.fetch_mlst_allele_variants(scrambled, False):
                 assert partial_match.partial_match_profile is not None
-                assert partial_match.allele_variant == '1'
                 mlst_targets.remove(gene.lower())
 
-            assert len(mlst_targets) == 0
+        assert len(mlst_targets) == 0
 
 async def test_institutpasteur_profiling_results_in_correct_mlst_st():
     async def dummy_allele_generator():
@@ -68,6 +67,22 @@ async def test_institutpasteur_profiling_results_in_correct_mlst_st():
         assert mlst_st_data.clonal_complex == "ST-2 complex"
         assert mlst_st_data.sequence_type == "1"
 
+async def test_institutpasteur_profiling_non_exact_results_in_list_of_mlsts():
+    dummy_alleles = [
+    Allele("adk", "1", None),
+    Allele("fumC", "2", None),
+    Allele("glyA", "36", None),
+    Allele("tyrB", "4", None),
+    Allele("icd", "4", None),
+    Allele("pepA", "1", None),
+    Allele("pgm", "5", None),
+    ]
+    async with BIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as dummy_profiler:
+        mlst_profile = await dummy_profiler.fetch_mlst_st(dummy_alleles)
+        assert mlst_profile.clonal_complex == "unknown"
+        assert mlst_profile.sequence_type == "unknown"
+
+
 async def test_institutpasteur_sequence_profiling_is_correct():
     sequence = str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq)
     async with BIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as dummy_profiler: