Moved to a general BIGSdb implementation

Updated tests

Removed ABIF UI for the time being

Began updating CLI

tests/nsbdiagnosistoolkit/engine/local/test_abif.py

@@ -1,8 +1,12 @@
 import os
 
-from automlst.engine.local.abif import read_abif
+from automlst.engine.local.abif import read_abif, reference_consensus_assembly
 
 async def test_load_sanger_sequence_has_data():
     assert os.path.exists("tests/resources/1I1_F_P1815443_047.ab1")
     result_data = await read_abif("tests/resources/1I1_F_P1815443_047.ab1")
-    assert result_data is not None
+    assert result_data is not None
+
+async def test_consensus_assembly_with_ncbi():
+    consensus = reference_consensus_assembly("ON685494.1", [await read_abif("tests/resources/1I1_F_P1815443_047.ab1"), await read_abif("tests/resources/1I1_R_P1815443_094.ab1")])
+    # TODO complete implementing this

tests/nsbdiagnosistoolkit/engine/remote/databases/institutpasteur/test_mlst.py

@@ -1,54 +0,0 @@
-from Bio import SeqIO
-from automlst.engine.data.mlst import Allele, MLSTProfile
-from automlst.engine.remote.databases.institutpasteur.mlst import InstitutPasteurProfiler
-
-
-async def test_profiling_results_in_exact_matches_when_exact():
-    sequence = str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq)
-    async with InstitutPasteurProfiler(database_name="pubmlst_bordetella_seqdef") as dummy_profiler:
-        exact_matches = dummy_profiler.fetch_mlst_allele_variants(schema_id=3, sequence_string=sequence)
-        targets_left = {"adk", "fumC", "glyA", "tyrB", "icd", "pepA", "pgm"}
-        async for exact_match in exact_matches:
-            assert isinstance(exact_match, Allele)
-            assert exact_match.allele_variant == '1' # All of Tohama I has allele id I
-            targets_left.remove(exact_match.allele_loci)
-
-        assert len(targets_left) == 0
-
-async def test_profiling_results_in_correct_st():
-    async def dummy_allele_generator():
-        dummy_alleles = [
-        Allele("adk", "1"),
-        Allele("fumC", "1"),
-        Allele("glyA", "1"),
-        Allele("tyrB", "1"),
-        Allele("icd", "1"),
-        Allele("pepA", "1"),
-        Allele("pgm", "1"),
-        ]
-        for dummy_allele in dummy_alleles:
-            yield dummy_allele
-    async with InstitutPasteurProfiler(database_name="pubmlst_bordetella_seqdef") as dummy_profiler:
-        mlst_st_data = await dummy_profiler.fetch_mlst_st(3, dummy_allele_generator())
-        assert mlst_st_data is not None
-        assert isinstance(mlst_st_data, MLSTProfile)
-        assert mlst_st_data.clonal_complex == "ST-2 complex"
-        assert mlst_st_data.sequence_type == "1"
-
-async def test_sequence_profiling_is_correct():
-    sequence = str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq)
-    dummy_alleles = [
-        Allele("adk", "1"),
-        Allele("fumC", "1"),
-        Allele("glyA", "1"),
-        Allele("tyrB", "1"),
-        Allele("icd", "1"),
-        Allele("pepA", "1"),
-        Allele("pgm", "1"),
-    ]
-    async with InstitutPasteurProfiler(database_name="pubmlst_bordetella_seqdef") as dummy_profiler:
-        profile = await dummy_profiler.profile_string(3, sequence)
-        assert profile is not None
-        assert isinstance(profile, MLSTProfile)
-        assert profile.clonal_complex == "ST-2 complex"
-        assert profile.sequence_type == "1"

tests/nsbdiagnosistoolkit/engine/remote/databases/pubmlst/test_mlst.py

@@ -1,53 +0,0 @@
-import asyncio
-from Bio import SeqIO
-from automlst.engine.data.mlst import Allele, MLSTProfile
-from automlst.engine.remote.databases.pubmlst.mlst import PubMLSTProfiler
-
-
-async def test_profiling_results_in_exact_matches_when_exact():
-    dummy_alleles = {
-        Allele("adk", "1"),
-        Allele("atpG", "1"),
-        Allele("frdB", "1"),
-        Allele("fucK", "1"),
-        Allele("mdh", "1"),
-        Allele("pgi", "1"),
-        Allele("recA", "5"),
-    }
-    sequence = str(SeqIO.read("tests/resources/FDAARGOS_1560.fasta", "fasta").seq)
-    async with PubMLSTProfiler(database_name="pubmlst_hinfluenzae_seqdef") as dummy_profiler:
-        exact_matches = dummy_profiler.fetch_mlst_allele_variants(schema_id=1, sequence_string=sequence)
-        async for exact_match in exact_matches:
-            assert isinstance(exact_match, Allele)
-            dummy_alleles.remove(exact_match)
-
-        assert len(dummy_alleles) == 0
-
-async def test_profiling_results_in_correct_st():
-    async def generate_dummy_targets():
-        dummy_alleles = [
-                Allele("adk", "1"),
-                Allele("atpG", "1"),
-                Allele("frdB", "1"),
-                Allele("fucK", "1"),
-                Allele("mdh", "1"),
-                Allele("pgi", "1"),
-                Allele("recA", "5"),
-            ]
-        for dummy_allele in dummy_alleles:
-            yield dummy_allele
-    async with PubMLSTProfiler(database_name="pubmlst_hinfluenzae_seqdef") as dummy_profiler:
-        mlst_st_data = await dummy_profiler.fetch_mlst_st(1, generate_dummy_targets())
-        assert mlst_st_data is not None
-        assert isinstance(mlst_st_data, MLSTProfile)
-        assert mlst_st_data.clonal_complex == "ST-3 complex"
-        assert mlst_st_data.sequence_type == "3"
-
-async def test_sequence_profiling_is_correct():
-    sequence = str(SeqIO.read("tests/resources/FDAARGOS_1560.fasta", "fasta").seq)
-    async with PubMLSTProfiler(database_name="pubmlst_hinfluenzae_seqdef") as dummy_profiler:
-        profile = await dummy_profiler.profile_string(1, sequence)
-        assert profile is not None
-        assert isinstance(profile, MLSTProfile)
-        assert profile.clonal_complex == "ST-3 complex"
-        assert profile.sequence_type == "3"

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

@@ -0,0 +1,115 @@
+from Bio import SeqIO
+from automlst.engine.data.mlst import Allele, MLSTProfile
+from automlst.engine.remote.databases.bigsdb import BIGSdbIndex, BigSDBMLSTProfiler
+
+
+async def test_institutpasteur_profiling_results_in_exact_matches_when_exact():
+    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:
+        exact_matches = dummy_profiler.fetch_mlst_allele_variants(sequence_string=sequence)
+        targets_left = {"adk", "fumC", "glyA", "tyrB", "icd", "pepA", "pgm"}
+        async for exact_match in exact_matches:
+            assert isinstance(exact_match, Allele)
+            assert exact_match.allele_variant == '1' # All of Tohama I has allele id I
+            targets_left.remove(exact_match.allele_loci)
+
+        assert len(targets_left) == 0
+
+async def test_institutpasteur_profiling_results_in_correct_mlst_st():
+    async def dummy_allele_generator():
+        dummy_alleles = [
+        Allele("adk", "1"),
+        Allele("fumC", "1"),
+        Allele("glyA", "1"),
+        Allele("tyrB", "1"),
+        Allele("icd", "1"),
+        Allele("pepA", "1"),
+        Allele("pgm", "1"),
+        ]
+        for dummy_allele in dummy_alleles:
+            yield dummy_allele
+    async with BigSDBMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as dummy_profiler:
+        mlst_st_data = await dummy_profiler.fetch_mlst_st(dummy_allele_generator())
+        assert mlst_st_data is not None
+        assert isinstance(mlst_st_data, MLSTProfile)
+        assert mlst_st_data.clonal_complex == "ST-2 complex"
+        assert mlst_st_data.sequence_type == "1"
+
+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:
+        profile = await dummy_profiler.profile_string(sequence)
+        assert profile is not None
+        assert isinstance(profile, MLSTProfile)
+        assert profile.clonal_complex == "ST-2 complex"
+        assert profile.sequence_type == "1"
+
+
+async def test_pubmlst_profiling_results_in_exact_matches_when_exact():
+    dummy_alleles = {
+        Allele("adk", "1"),
+        Allele("atpG", "1"),
+        Allele("frdB", "1"),
+        Allele("fucK", "1"),
+        Allele("mdh", "1"),
+        Allele("pgi", "1"),
+        Allele("recA", "5"),
+    }
+    sequence = str(SeqIO.read("tests/resources/FDAARGOS_1560.fasta", "fasta").seq)
+    async with BigSDBMLSTProfiler(database_api="https://rest.pubmlst.org/", database_name="pubmlst_hinfluenzae_seqdef", schema_id=1) as dummy_profiler:
+        exact_matches = dummy_profiler.fetch_mlst_allele_variants(sequence_string=sequence)
+        async for exact_match in exact_matches:
+            assert isinstance(exact_match, Allele)
+            dummy_alleles.remove(exact_match)
+
+        assert len(dummy_alleles) == 0
+
+async def test_pubmlst_profiling_results_in_correct_st():
+    async def generate_dummy_targets():
+        dummy_alleles = [
+                Allele("adk", "1"),
+                Allele("atpG", "1"),
+                Allele("frdB", "1"),
+                Allele("fucK", "1"),
+                Allele("mdh", "1"),
+                Allele("pgi", "1"),
+                Allele("recA", "5"),
+            ]
+        for dummy_allele in dummy_alleles:
+            yield dummy_allele
+    async with BigSDBMLSTProfiler(database_api="https://rest.pubmlst.org/", database_name="pubmlst_hinfluenzae_seqdef", schema_id=1) as dummy_profiler:
+        mlst_st_data = await dummy_profiler.fetch_mlst_st(generate_dummy_targets())
+        assert mlst_st_data is not None
+        assert isinstance(mlst_st_data, MLSTProfile)
+        assert mlst_st_data.clonal_complex == "ST-3 complex"
+        assert mlst_st_data.sequence_type == "3"
+
+async def test_pubmlst_sequence_profiling_is_correct():
+    sequence = str(SeqIO.read("tests/resources/FDAARGOS_1560.fasta", "fasta").seq)
+    async with BigSDBMLSTProfiler(database_api="https://rest.pubmlst.org/", database_name="pubmlst_hinfluenzae_seqdef", schema_id=1) as dummy_profiler:
+        profile = await dummy_profiler.profile_string(sequence)
+        assert profile is not None
+        assert isinstance(profile, MLSTProfile)
+        assert profile.clonal_complex == "ST-3 complex"
+        assert profile.sequence_type == "3"
+
+async def test_bigsdb_index_all_databases_is_not_empty():
+    async with BIGSdbIndex() as bigsdb_index:
+        assert len(await bigsdb_index.get_known_seqdef_dbs()) > 0
+
+async def test_bigsdb_index_references_pubmlst_correctly():
+    async with BIGSdbIndex() as bigsdb_index:
+        assert (await bigsdb_index.get_bigsdb_api_from_seqdefdb("pubmlst_hinfluenzae_seqdef")) == "https://rest.pubmlst.org"
+
+async def test_bigsdb_index_references_institutpasteur_correctly():
+    async with BIGSdbIndex() as bigsdb_index:
+        assert (await bigsdb_index.get_bigsdb_api_from_seqdefdb("pubmlst_bordetella_seqdef")) == "https://bigsdb.pasteur.fr/api"
+
+
+async def test_bigsdb_index_instantiates_correct_profiler():
+    sequence = str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq)
+    async with BIGSdbIndex() as bigsdb_index:
+        async with await bigsdb_index.build_profiler_from_seqdefdb("pubmlst_bordetella_seqdef", 3) as profiler:
+            profile = await profiler.profile_string(sequence)
+            assert profile.clonal_complex == "ST-2 complex"
+            assert profile.sequence_type == "1"