Merge pull request #9 from BIONF/dev

fix cli

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "XspecT"
-version = "0.2.2"
+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"}

src/xspect/main.py

@@ -59,12 +59,16 @@ def classify(genus, path, meta, step):
 
     # define pipeline
     pipeline = Pipeline(genus + " classification", "Test Author", "[email protected]")
-    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:

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
+        )