Added check for HTTP 200 status

.vscode/extensions.json

@@ -1,5 +1,6 @@
 {
     "recommendations": [
-        "piotrpalarz.vscode-gitignore-generator"
+        "piotrpalarz.vscode-gitignore-generator",
+        "gruntfuggly.todo-tree"
     ]
 }

src/autobigs/engine/analysis/bigsdb.py

@@ -15,7 +15,7 @@ from autobigs.engine.reading import read_fasta
 from autobigs.engine.structures.alignment import PairwiseAlignment
 from autobigs.engine.structures.genomics import NamedString
 from autobigs.engine.structures.mlst import Allele, NamedMLSTProfile, AlignmentStats, MLSTProfile
-from autobigs.engine.exceptions.database import NoBIGSdbExactMatchesException, NoBIGSdbMatchesException, NoSuchBIGSdbDatabaseException
+from autobigs.engine.exceptions.database import BIGSdbResponseNotOkay, NoBIGSdbExactMatchesException, NoBIGSdbMatchesException, NoSuchBIGSdbDatabaseException
 
 from Bio.Align import PairwiseAligner
 
@@ -99,7 +99,10 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
                                 )
                                 yield result_allele if isinstance(sequence_string, str) else (sequence_string.name, result_allele)
                         else:
-                            raise NoBIGSdbMatchesException(self._database_name, self._scheme_id, sequence_string.name if isinstance(sequence_string, NamedString) else None)
+                            if response.status == 200:
+                                raise NoBIGSdbMatchesException(self._database_name, self._scheme_id, sequence_string.name if isinstance(sequence_string, NamedString) else None)
+                            else:
+                                raise BIGSdbResponseNotOkay(sequence_response)
                 except (ConnectionError, ServerDisconnectedError, ClientOSError) as e: # Errors we will retry
                     last_error = e
                     success = False
@@ -251,6 +254,16 @@ class BIGSdbIndex(AbstractAsyncContextManager):
 
     async def build_profiler_from_seqdefdb(self, local: bool, dbseqdef_name: str, scheme_id: int) -> BIGSdbMLSTProfiler:
         return get_BIGSdb_MLST_profiler(local, await self.get_bigsdb_api_from_seqdefdb(dbseqdef_name), dbseqdef_name, scheme_id)
+    
+    async def get_scheme_loci(self, dbseqdef_name: str, scheme_id: int) -> list[str]:
+        uri_path = f"{await self.get_bigsdb_api_from_seqdefdb(dbseqdef_name)}/db/{dbseqdef_name}/schemes/{scheme_id}"
+        async with self._http_client.get(uri_path) as response:
+            response_json = await response.json()
+            loci = response_json["loci"]
+            results = []
+            for locus in loci:
+                results.append(path.basename(locus))
+            return results
 
     async def close(self):
         await self._http_client.close()

src/autobigs/engine/exceptions/database.py

@@ -3,11 +3,13 @@ from typing import Union
 class BIGSDbDatabaseAPIException(Exception):
     pass
 
+class BIGSdbResponseNotOkay(BIGSDbDatabaseAPIException):
+    pass
 
 class NoBIGSdbMatchesException(BIGSDbDatabaseAPIException):
     def __init__(self, database_name: str, database_scheme_id: int, query_name: Union[None, str], *args):
         self._query_name = query_name
-        super().__init__(f"No matches found with scheme with ID {database_scheme_id}  in the database \"{database_name}\".", *args)
+        super().__init__(f"No matches found with scheme with ID {database_scheme_id} in the database \"{database_name}\".", *args)
     
     def get_causal_query_name(self) -> Union[str, None]:
         return self._query_name

src/autobigs/engine/writing.py

@@ -1,7 +1,7 @@
 from collections import defaultdict
 import csv
 from os import PathLike
-from typing import AsyncIterable, Collection, Mapping, Sequence, Union
+from typing import AsyncIterable, Collection, Iterable, Mapping, Sequence, Union
 
 from autobigs.engine.structures.mlst import Allele, MLSTProfile, NamedMLSTProfile
 
@@ -17,7 +17,7 @@ def alleles_to_text_map(alleles: Collection[Allele]) -> Mapping[str, Union[Seque
             result[locus] = tuple(result[locus]) # type: ignore
     return dict(result)
 
-async def write_mlst_profiles_as_csv(mlst_profiles_iterable: AsyncIterable[NamedMLSTProfile], handle: Union[str, bytes, PathLike[str], PathLike[bytes]]) -> Sequence[str]:
+async def write_mlst_profiles_as_csv(mlst_profiles_iterable: AsyncIterable[NamedMLSTProfile], handle: Union[str, bytes, PathLike[str], PathLike[bytes]], allele_names: Iterable[str]) -> Sequence[str]:
     failed = list()
     with open(handle, "w", newline='') as filehandle:
         header = None
@@ -30,7 +30,7 @@ async def write_mlst_profiles_as_csv(mlst_profiles_iterable: AsyncIterable[Named
                 continue
             allele_mapping = alleles_to_text_map(mlst_profile.alleles)
             if writer is None:
-                header = ["id", "st", "clonal-complex", *sorted(allele_mapping.keys())]
+                header = ["id", "st", "clonal-complex", *sorted(allele_names)]
                 writer = csv.DictWriter(filehandle, fieldnames=header)
                 writer.writeheader()
             row_dictionary = {

tests/autobigs/engine/analysis/test_bigsdb.py

@@ -222,3 +222,12 @@ class TestBIGSdbIndex:
                 assert isinstance(profile, MLSTProfile)
                 assert profile.clonal_complex == "ST-2 complex"
                 assert profile.sequence_type == "1"
+
+
+    @pytest.mark.parametrize(["bigsdb_name", "scheme_id", "expected"], [
+        ("pubmlst_bordetella_seqdef", 3, ["adk", "fumC", "glyA", "tyrB", "icd", "pepA", "pgm"])
+    ])
+    async def test_bigsdb_index_fetches_loci_names(self, bigsdb_name, scheme_id, expected):
+        async with BIGSdbIndex() as bigsdb_index:
+            loci = await bigsdb_index.get_scheme_loci(bigsdb_name, scheme_id)
+            assert set(loci) == set(expected)

tests/autobigs/engine/test_writing.py

@@ -27,7 +27,7 @@ async def test_column_order_is_same_as_expected_file(dummy_alphabet_mlst_profile
     dummy_profiles = [dummy_alphabet_mlst_profile]
     with tempfile.TemporaryDirectory() as temp_dir:
         output_path = path.join(temp_dir, "out.csv")
-        await write_mlst_profiles_as_csv(iterable_to_asynciterable(dummy_profiles), output_path)
+        await write_mlst_profiles_as_csv(iterable_to_asynciterable(dummy_profiles), output_path, ["A", "D", "B", "C"])
         with open(output_path) as csv_handle:
             csv_reader = reader(csv_handle)
             lines = list(csv_reader)
@@ -38,7 +38,7 @@ async def test_csv_writing_sample_name_not_repeated_when_single_sequence(dummy_a
     dummy_profiles = [dummy_alphabet_mlst_profile]
     with tempfile.TemporaryDirectory() as temp_dir:
         output_path = path.join(temp_dir, "out.csv")
-        await write_mlst_profiles_as_csv(iterable_to_asynciterable(dummy_profiles), output_path)
+        await write_mlst_profiles_as_csv(iterable_to_asynciterable(dummy_profiles), output_path, ["A", "D", "B", "C"])
         with open(output_path) as csv_handle:
             csv_reader = reader(csv_handle)
             lines = list(csv_reader)
@@ -63,7 +63,7 @@ async def test_csv_writing_includes_asterisk_for_non_exact(dummy_alphabet_mlst_p
     dummy_profiles = [dummy_alphabet_mlst_profile]
     with tempfile.TemporaryDirectory() as temp_dir:
         output_path = path.join(temp_dir, "out.csv")
-        await write_mlst_profiles_as_csv(iterable_to_asynciterable(dummy_profiles), output_path)
+        await write_mlst_profiles_as_csv(iterable_to_asynciterable(dummy_profiles), output_path, ["A", "D", "B", "C"])
         with open(output_path) as csv_handle:
             csv_reader = reader(csv_handle)
             lines = list(csv_reader)