Add setup configuration fixtures and setup command create table test

Author: karlnyr

tests/test_cli.py

@@ -4,10 +4,23 @@
 import pathlib
 
 import pytest
+import sqlalchemy
 from click.testing import CliRunner
 
 from microSALT.cli import root
-from microSALT.config import MicroSALTConfig
+from microSALT.config import (
+    Containers,
+    Database,
+    Folders,
+    MicroSALTConfig,
+    PasteurCredentials,
+    PubMLSTCredentials,
+    Regex,
+    Singularity,
+    SlurmHeader,
+    Threshold,
+)
+from microSALT.store.orm_models import Base
 
 
 @pytest.fixture
@@ -18,6 +31,48 @@ def config_file(config: MicroSALTConfig, tmp_path: pathlib.Path) -> pathlib.Path
     return path
 
 
+@pytest.fixture
+def setup_config(tmp_path: pathlib.Path) -> MicroSALTConfig:
+    """Fresh MicroSALTConfig whose directories do not yet exist — used to test `setup`."""
+    from importlib.resources import files as resource_files
+
+    base = tmp_path / "microsalt"
+    base.mkdir()
+    cfg = MicroSALTConfig(
+        slurm_header=SlurmHeader(time="1:00:00", threads="4", qos="normal",
+                                 job_prefix="MLST", project="test", type="core"),
+        regex=Regex(mail_recipient="test@test.com", file_pattern=".*", verified_organisms=[]),
+        folders=Folders(
+            results=str(base / "results"),
+            reports=str(base / "reports"),
+            log_file=str(base / "microsalt.log"),
+            seqdata=str(base / "seqdata"),
+            profiles=str(base / "profiles"),
+            references=str(base / "references"),
+            resistances=str(base / "resistances"),
+            genomes=str(base / "genomes"),
+            credentials=str(base / "credentials"),
+            adapters=str(base / "adapters"),
+        ),
+        database=Database(SQLALCHEMY_DATABASE_URI=f"sqlite:///{base / 'microsalt.db'}"),
+        threshold=Threshold(),
+        pubmlst=PubMLSTCredentials(),
+        pasteur=PasteurCredentials(),
+        singularity=Singularity(),
+        containers=Containers(),
+    )
+    cfg.folders.expec = str(resource_files("microSALT").joinpath("unique_references", "ExPEC.fsa"))
+    return cfg
+
+
+@pytest.fixture
+def setup_config_file(setup_config: MicroSALTConfig, tmp_path: pathlib.Path) -> pathlib.Path:
+    """Write the setup_config to a JSON file and return its path."""
+    path = tmp_path / "config.json"
+    path.write_text(setup_config.model_dump_json())
+    return path
+
+
 def invoke_root(config_file: pathlib.Path, *args: str):
     """Invoke the root CLI group with the test config and additional arguments."""
     runner = CliRunner()
@@ -48,55 +103,22 @@ def test_config_fields_propagated(config: MicroSALTConfig, config_file: pathlib.
     assert loaded.slurm_header.project == config.slurm_header.project
 
 
-def test_setup_command(tmp_path):
-    """setup command creates the configured directories without error."""
-    from importlib.resources import files as resource_files
-
-    from microSALT.config import (
-        Containers,
-        Database,
-        Folders,
-        PasteurCredentials,
-        PubMLSTCredentials,
-        Regex,
-        Singularity,
-        SlurmHeader,
-        Threshold,
-    )
-
-    base = tmp_path / "microsalt"
-    base.mkdir()
-
-    cfg = MicroSALTConfig(
-        slurm_header=SlurmHeader(time="1:00:00", threads="4", qos="normal",
-                                 job_prefix="MLST", project="test", type="core"),
-        regex=Regex(mail_recipient="test@test.com", file_pattern=".*", verified_organisms=[]),
-        folders=Folders(
-            results=str(base / "results"),
-            reports=str(base / "reports"),
-            log_file=str(base / "microsalt.log"),
-            seqdata=str(base / "seqdata"),
-            profiles=str(base / "profiles"),
-            references=str(base / "references"),
-            resistances=str(base / "resistances"),
-            genomes=str(base / "genomes"),
-            credentials=str(base / "credentials"),
-            adapters=str(base / "adapters"),
-        ),
-        database=Database(SQLALCHEMY_DATABASE_URI=f"sqlite:///{base}/microsalt.db"),
-        threshold=Threshold(),
-        pubmlst=PubMLSTCredentials(),
-        pasteur=PasteurCredentials(),
-        singularity=Singularity(),
-        containers=Containers(),
-    )
-    cfg.folders.expec = str(resource_files("microSALT").joinpath("unique_references", "ExPEC.fsa"))
+def test_setup_command(setup_config: MicroSALTConfig, setup_config_file: pathlib.Path):
+    """setup command creates the configured directories and reports success."""
+    result = invoke_root(setup_config_file, "setup")
+    assert result.exit_code == 0, result.output
+    assert "Directory setup complete" in result.output
+    assert "Database tables created" in result.output
+    assert pathlib.Path(setup_config.folders.results).exists()
+    assert pathlib.Path(setup_config.folders.reports).exists()
 
-    config_path = tmp_path / "config.json"
-    config_path.write_text(cfg.model_dump_json())
 
-    result = invoke_root(config_path, "setup")
+def test_setup_command_creates_tables(setup_config: MicroSALTConfig, setup_config_file: pathlib.Path):
+    """setup command creates every ORM-defined table in the database."""
+    result = invoke_root(setup_config_file, "setup")
     assert result.exit_code == 0, result.output
-    assert "Directory setup complete" in result.output
-    assert (base / "results").exists()
-    assert (base / "reports").exists()
+
+    engine = sqlalchemy.create_engine(setup_config.database.SQLALCHEMY_DATABASE_URI)
+    created = sqlalchemy.inspect(engine).get_table_names()
+    expected = set(Base.metadata.tables.keys())
+    assert expected == set(created), f"Missing tables: {expected - set(created)}"