Updated BIGSdb API to be more tolerant towards failures

src/automlst/engine/data/mlst.py

@@ -9,5 +9,5 @@ class Allele:
 @dataclass(frozen=True)
 class MLSTProfile:
     alleles: Mapping[str, Sequence[Allele]]
-    sequence_type: int
+    sequence_type: str
     clonal_complex: str

src/automlst/engine/exceptions/database.py

@@ -0,0 +1,16 @@
+from typing import Union
+
+class BIGSDbDatabaseAPIException(Exception):
+    pass
+
+class NoBIGSdbExactMatchesException(BIGSDbDatabaseAPIException):
+    def __init__(self, database_name: str, database_schema_id: int, *args):
+        super().__init__(f"No exact match found with schema with ID {database_schema_id}  in the database \"{database_name}\".", *args)
+
+class NoSuchBIGSdbDatabaseException(BIGSDbDatabaseAPIException):
+    def __init__(self, database_name: str, *args):
+        super().__init__(f"No database \"{database_name}\" found.", *args)
+
+class NoSuchBigSdbSchemaException(BIGSDbDatabaseAPIException):
+    def __init__(self, database_name: str, database_schema_id: int, *args):
+        super().__init__(f"No schema with ID {database_schema_id}  in \"{database_name}\" found.", *args)

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

@@ -6,6 +6,7 @@ from aiohttp import ClientSession, ClientTimeout
 
 from automlst.engine.data.genomics import NamedString
 from automlst.engine.data.mlst import Allele, MLSTProfile
+from automlst.engine.exceptions.database import NoBIGSdbExactMatchesException, NoSuchBIGSdbDatabaseException
 
 class BIGSdbMLSTProfiler(AbstractAsyncContextManager):
 
@@ -25,12 +26,10 @@ class BIGSdbMLSTProfiler(AbstractAsyncContextManager):
             "sequence": sequence_string
         })
         sequence_response: dict = await response.json()
-        if "exact_matches" not in sequence_response:
-            # TODO throw exception for not finding matches.
-            pass
 
         if "exact_matches" not in sequence_response:
-            raise ValueError(f"Unable to find exact matches in \"{self._database_name}\" under schema ID \"{self._schema_id}\".")
+            raise NoBIGSdbExactMatchesException(self._database_name, self._schema_id)
+        
         exact_matches: dict[str, Sequence[dict[str, str]]] = sequence_response["exact_matches"]  
         for allele_loci, alleles in exact_matches.items():
             for allele in alleles:
@@ -48,11 +47,16 @@ class BIGSdbMLSTProfiler(AbstractAsyncContextManager):
         }
         async with self._http_client.post(uri_path, json=request_json) as response:
             response_json = await response.json()
-            if "fields" not in response_json:
+            if "exact_matches" not in response_json:
-                # TODO raise exception about invalid parameters or no exact parameterization found
+                raise NoBIGSdbExactMatchesException(self._database_name, self._schema_id)
-                pass
-            schema_fields_returned = response_json["fields"]
             schema_exact_matches: dict = response_json["exact_matches"]
+            if "fields" not in response_json:
+                schema_fields_returned = {
+                    "ST": "Unknown",
+                    "Clonal Complex": "Unknown"
+                }
+            else:
+                schema_fields_returned: Mapping[str, str] = response_json["fields"]
             allele_map: dict[str, list[Allele]] = defaultdict(list)
             for exact_match_loci, exact_match_alleles in schema_exact_matches.items():
                 for exact_match_allele in exact_match_alleles:
@@ -64,10 +68,14 @@ class BIGSdbMLSTProfiler(AbstractAsyncContextManager):
         return await self.fetch_mlst_st(alleles)
 
 
-    async def profile_multiple_strings(self, namedStrings: AsyncIterable[NamedString]) -> AsyncGenerator[tuple[str, MLSTProfile], Any]:
+    async def profile_multiple_strings(self, namedStrings: AsyncIterable[NamedString], stop_on_fail: bool = False) -> AsyncGenerator[Union[tuple[str, MLSTProfile], tuple[str, None]], Any]:
         async for named_string in namedStrings:
+            try:
                 yield (named_string.name, await self.profile_string(named_string.sequence))
-
+            except NoBIGSdbExactMatchesException as e:
+                if stop_on_fail:
+                    raise e
+                yield (named_string.name, None)
 
     async def close(self):
         await self._http_client.close()
@@ -107,7 +115,7 @@ class BIGSdbIndex(AbstractAsyncContextManager):
     async def get_bigsdb_api_from_seqdefdb(self, seqdef_db_name: str) -> str:
         known_databases = await self.get_known_seqdef_dbs()
         if seqdef_db_name not in known_databases:
-            raise ValueError(f"The database \"{seqdef_db_name}\" could not be found.")
+            raise NoSuchBIGSdbDatabaseException(seqdef_db_name)
         return known_databases[seqdef_db_name]     
 
     async def get_schemas_for_seqdefdb(self, seqdef_db_name: str, force: bool = False) -> Mapping[str, int]: