XspecT 0.2.0__tar.gz → 0.2.3__tar.gz

{xspect-0.2.0/src/XspecT.egg-info → xspect-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: XspecT
-Version: 0.2.0
+Version: 0.2.3
 Summary: Tool to monitor and characterize pathogens using Bloom filters.
 License: MIT License
         

{xspect-0.2.0 → xspect-0.2.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "XspecT"
-version = "0.2.0"
+version = "0.2.3"
 description = "Tool to monitor and characterize pathogens using Bloom filters."
 readme = {file = "README.md", content-type = "text/markdown"}
 license = {file = "LICENSE"}

{xspect-0.2.0 → xspect-0.2.3/src/XspecT.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: XspecT
-Version: 0.2.0
+Version: 0.2.3
 Summary: Tool to monitor and characterize pathogens using Bloom filters.
 License: MIT License
         

{xspect-0.2.0 → xspect-0.2.3}/src/XspecT.egg-info/SOURCES.txt

@@ -75,6 +75,7 @@ src/xspect/train_filter/ncbi_api/ncbi_children_tree.py
 src/xspect/train_filter/ncbi_api/ncbi_taxon_metadata.py
 tests/__init__.py
 tests/conftest.py
+tests/test_cli.py
 tests/test_file_io.py
 tests/test_model_management.py
 tests/test_model_result.py

{xspect-0.2.0 → xspect-0.2.3}/src/xspect/fastapi.py

@@ -27,12 +27,16 @@ def classify(genus: str, file: str, meta: bool = False, step: int = 500):
     path = get_xspect_upload_path() / file
 
     pipeline = Pipeline(genus + " classification", "Test Author", "test@example.com")
-    species_execution = ModelExecution(genus + "-species", sparse_sampling_step=step)
+    species_execution = ModelExecution(
+        genus.lower() + "-species", sparse_sampling_step=step
+    )
     if meta:
         species_filtering_step = PipelineStep(
             StepType.FILTERING, genus, 0.7, species_execution
         )
-        genus_execution = ModelExecution(genus + "-genus", sparse_sampling_step=step)
+        genus_execution = ModelExecution(
+            genus.lower() + "-genus", sparse_sampling_step=step
+        )
         genus_execution.add_pipeline_step(species_filtering_step)
         pipeline.add_pipeline_step(genus_execution)
     else:

{xspect-0.2.0 → xspect-0.2.3}/src/xspect/main.py

@@ -59,12 +59,16 @@ def classify(genus, path, meta, step):
 
     # define pipeline
     pipeline = Pipeline(genus + " classification", "Test Author", "test@example.com")
-    species_execution = ModelExecution(genus + "-species", sparse_sampling_step=step)
+    species_execution = ModelExecution(
+        genus.lower() + "-species", sparse_sampling_step=step
+    )
     if meta:
         species_filtering_step = PipelineStep(
             StepType.FILTERING, genus, 0.7, species_execution
         )
-        genus_execution = ModelExecution(genus + "-genus", sparse_sampling_step=step)
+        genus_execution = ModelExecution(
+            genus.lower() + "-genus", sparse_sampling_step=step
+        )
         genus_execution.add_pipeline_step(species_filtering_step)
         pipeline.add_pipeline_step(genus_execution)
     else:

xspect-0.2.3/tests/test_cli.py

@@ -0,0 +1,61 @@
+"""Test XspecT CLI"""
+
+import json
+import pytest
+from click.testing import CliRunner
+from src.xspect.main import cli
+
+
+@pytest.mark.parametrize(
+    ["assembly_file_path", "genus", "species"],
+    [
+        (
+            "GCF_000069245.1_ASM6924v1_genomic.fna",
+            "Acinetobacter",
+            "470",
+        ),
+        (
+            "GCF_000018445.1_ASM1844v1_genomic.fna",
+            "Acinetobacter",
+            "470",
+        ),
+        ("GCF_000006945.2_ASM694v2_genomic.fna", "Salmonella", "28901"),
+    ],
+    indirect=["assembly_file_path"],
+)
+def test_species_assignment(assembly_file_path, genus, species):
+    """Test the species assignment"""
+    runner = CliRunner()
+    result = runner.invoke(cli, ["classify", genus, assembly_file_path])
+
+    run_path = result.output.strip().split("'")[1]
+    with open(run_path, encoding="utf-8") as f:
+        result_content = json.load(f)
+        assert result_content["results"][0]["prediction"] == species
+
+
+@pytest.mark.parametrize(
+    ["assembly_file_path", "genus", "species"],
+    [
+        (
+            "GCF_000069245.1_ASM6924v1_genomic.fna",
+            "Acinetobacter",
+            "470",
+        ),
+    ],
+    indirect=["assembly_file_path"],
+)
+def test_metagenome_mode(assembly_file_path, genus, species):
+    """Test the metagenome mode"""
+    runner = CliRunner()
+    result = runner.invoke(cli, ["classify", "-m", genus, assembly_file_path])
+
+    run_path = result.output.strip().split("'")[1]
+    with open(run_path, encoding="utf-8") as f:
+        result_content = json.load(f)
+        assert (
+            result_content["results"][0]["subprocessing_steps"][0]["result"][
+                "prediction"
+            ]
+            == species
+        )