Fixed concurrent profile_multiple_strings implementation

src/autobigs/engine/analysis/bigsdb.py

@@ -7,7 +7,7 @@ from os import path
 import os
 import shutil
 import tempfile
-from typing import Any, AsyncGenerator, AsyncIterable, Iterable, Mapping, Sequence, Set, Union
+from typing import Any, AsyncGenerator, AsyncIterable, Coroutine, Iterable, Mapping, Sequence, Set, Union
 
 from aiohttp import ClientSession, ClientTimeout
 
@@ -135,20 +135,24 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
         return await self.determine_mlst_st(alleles)
 
     async def profile_multiple_strings(self, query_named_string_groups: AsyncIterable[Iterable[NamedString]], stop_on_fail: bool = False) -> AsyncGenerator[NamedMLSTProfile, Any]:
-        tasks = []
+        tasks: list[Coroutine[Any, Any, Union[NamedMLSTProfile, MLSTProfile]]] = []
         async for named_strings in query_named_string_groups:
             tasks.append(self.profile_string(named_strings))
-            for task in asyncio.as_completed(tasks):
+        for task in asyncio.as_completed(tasks):
-                try:
+            named_mlst_profile = await task
-                    yield await task
+            try:
-                except NoBIGSdbMatchesException as e:
+                if isinstance(named_mlst_profile, NamedMLSTProfile):
-                    if stop_on_fail:
+                    yield named_mlst_profile
-                        raise e
+                else:
-                    causal_name = e.get_causal_query_name()
+                    raise TypeError("MLST profile is not named.")
-                    if causal_name is None:
+            except NoBIGSdbMatchesException as e:
-                        raise ValueError("Missing query name despite requiring names.")
+                if stop_on_fail:
-                    else:
+                    raise e
-                        yield NamedMLSTProfile(causal_name, None)
+                causal_name = e.get_causal_query_name()
+                if causal_name is None:
+                    raise ValueError("Missing query name despite requiring names.")
+                else:
+                    yield NamedMLSTProfile(causal_name, None)
 
     async def close(self):
         await self._http_client.close()

tests/autobigs/engine/analysis/test_bigsdb.py

@@ -102,6 +102,7 @@ class TestBIGSdbMLSTProfiler:
                     continue
                 scrambled = gene_scrambler(str(target_sequence.seq), 0.125)
                 async for partial_match in profiler.determine_mlst_allele_variants([scrambled]):
+                    assert isinstance(partial_match, Allele)
                     assert partial_match.partial_match_profile is not None
                     mlst_targets.remove(gene)
 
@@ -119,6 +120,7 @@ class TestBIGSdbMLSTProfiler:
         dummy_alleles = bad_profile.alleles
         async with bigsdb.get_BIGSdb_MLST_profiler(local_db, database_api, database_name, scheme_id) as dummy_profiler:
             mlst_profile = await dummy_profiler.determine_mlst_st(dummy_alleles)
+            assert isinstance(mlst_profile, MLSTProfile)
             assert mlst_profile.clonal_complex == "unknown"
             assert mlst_profile.sequence_type == "unknown"
 
@@ -207,5 +209,6 @@ class TestBIGSdbIndex:
             async with await bigsdb_index.build_profiler_from_seqdefdb(local, "pubmlst_bordetella_seqdef", 3) as profiler:
                 assert isinstance(profiler, BIGSdbMLSTProfiler)
                 profile = await profiler.profile_string(sequence)
+                assert isinstance(profile, MLSTProfile)
                 assert profile.clonal_complex == "ST-2 complex"
                 assert profile.sequence_type == "1"