Merge pull request #448 from MannLabs/fix_fasta_in_cli

Fix fasta in cli

alphadia/cli.py

@@ -211,9 +211,9 @@ def run(*args, **kwargs):
     cli_params_config = {
         **({ConfigKeys.RAW_PATHS: raw_paths} if raw_paths else {}),
         **({ConfigKeys.LIBRARY_PATH: args.library} if args.library is not None else {}),
-        **({ConfigKeys.FASTA_PATHS: args.library} if args.fasta else {}),
+        **({ConfigKeys.FASTA_PATHS: args.fasta} if args.fasta else {}),
         **(
-            {ConfigKeys.QUANT_DIRECTORY: args.library}
+            {ConfigKeys.QUANT_DIRECTORY: args.quant_dir}
             if args.quant_dir is not None
             else {}
         ),

alphadia/utils.py

@@ -63,7 +63,7 @@ def ion_hash(precursor_idx, number, type, charge):
 
 
 @nb.njit
-def extended_ion_hash(precursor_idx, rank, number, type, charge):
+def extended_ion_hash(precursor_idx, rank, number, type, charge):  # TODO: unused?
     # create a 64 bit hash from the precursor_idx, number and type
     # the precursor_idx is the lower 32 bits
     # the number is the next 8 bits
@@ -73,7 +73,9 @@ def extended_ion_hash(precursor_idx, rank, number, type, charge):
     return precursor_idx + (rank << 32) + (number << 40) + (type << 48) + (charge << 56)
 
 
-def recursive_update(full_dict: dict, update_dict: dict):
+def recursive_update(
+    full_dict: dict, update_dict: dict
+):  # TODO merge with Config._update
     """recursively update a dict with a second dict. The dict is updated inplace.
 
     Parameters
@@ -99,12 +101,12 @@ def recursive_update(full_dict: dict, update_dict: dict):
             full_dict[key] = value
 
 
-def normal(x, mu, sigma):
+def normal(x, mu, sigma):  # TODO: unused?
     """ """
     return 1 / (sigma * np.sqrt(2 * np.pi)) * np.exp(-np.power((x - mu) / sigma, 2) / 2)
 
 
-def plt_limits(mobility_limits, dia_cycle_limits):
+def plt_limits(mobility_limits, dia_cycle_limits):  # TODO: unused?
     mobility_len = mobility_limits[1] - mobility_limits[0]
     dia_cycle_len = dia_cycle_limits[1] - dia_cycle_limits[0]
 
@@ -202,7 +204,7 @@ def amean0(array):
 
 
 @nb.njit()
-def astd0(array):
+def astd0(array):  # TODO: unused?
     out = np.zeros(array.shape[1])
     for i in range(len(out)):
         out[i] = np.std(array[:, i])
@@ -248,11 +250,11 @@ def mass_range(mz_list, ppm_tolerance):
     return out_mz
 
 
-def function_call(q):
+def function_call(q):  # TODO: unused?
     q.put("X" * 1000000)
 
 
-def modify(n, x, s, A):
+def modify(n, x, s, A):  # TODO: unused?
     n.value **= 2
     x.value **= 2
     s.value = s.value.upper()
@@ -261,7 +263,7 @@ def modify(n, x, s, A):
         a.y **= 2
 
 
-class Point(Structure):
+class Point(Structure):  # TODO: unused?
     _fields_ = [("x", c_double), ("y", c_double)]
 
 
@@ -315,7 +317,7 @@ def make_slice_2d(start_stop):
 
 
 @nb.njit
-def fourier_filter(dense_stack, kernel):
+def fourier_filter(dense_stack, kernel):  # TODO: unused?
     """Numba helper function to apply a gaussian filter to a dense stack.
     The filter is applied as convolution wrapping around the edges, calculated in fourier space.
 
@@ -512,7 +514,7 @@ def channel_score_groups(elution_group_idx, decoy, rank):
 
 
 @nb.njit()
-def profile_correlation(profile, tresh=3, shift=2, kernel_size=12):
+def profile_correlation(profile, tresh=3, shift=2, kernel_size=12):  # TODO: unused?
     mask = np.sum((profile >= tresh).astype(np.int8), axis=0) == profile.shape[0]
 
     output = np.zeros(profile.shape, dtype=np.float32)

tests/unit_tests/test_cli.py

@@ -1,10 +1,119 @@
-#!python -m unittest tests.test_utils
 """This module provides unit tests for alphadia.cli."""
 
-# builtin
-import unittest
+from unittest.mock import MagicMock, mock_open, patch
 
-# local
+import yaml
 
-if __name__ == "__main__":
-    unittest.main()
+from alphadia.cli import _get_config_from_args, _get_from_args_or_config, run
+
+# TODO add tests for _get_raw_path_list_from_args_and_config
+
+
+def test_get_config_from_args():
+    """Test the _get_config_from_args function correctly merges configs."""
+    mock_args = MagicMock(config="config.yaml", config_dict='{"key3": "value3"}')
+
+    yaml_content = {"key1": "value1", "key2": "value2"}
+    mock_yaml = yaml.dump(yaml_content)
+
+    with patch("builtins.open", mock_open(read_data=mock_yaml)):
+        result = _get_config_from_args(mock_args)
+
+    assert result == {"key1": "value1", "key2": "value2", "key3": "value3"}
+
+
+def test_get_from_args_or_config_returns_value_from_args():
+    """Test that the function returns the value from the args when it is not None."""
+    args = MagicMock(output="cli_output")
+    config = {"output_directory": "config_output"}
+
+    # when
+    result = _get_from_args_or_config(
+        args, config, args_key="output", config_key="output_directory"
+    )
+
+    assert result == "cli_output"
+
+
+def test_get_from_args_or_config_returns_value_from_config_when_args_none():
+    """Test that the function returns the value from the config when the args value is None."""
+    args = MagicMock(output=None)
+    config = {"output_directory": "config_output"}
+
+    # when
+    result = _get_from_args_or_config(
+        args, config, args_key="output", config_key="output_directory"
+    )
+
+    assert result == "config_output"
+
+
+@patch("alphadia.cli.parser.parse_known_args")
+@patch("builtins.print")
+@patch("alphadia.cli.SearchPlan")
+def test_cli_unknown_args(
+    mock_search_plan,
+    mock_print,
+    mock_parse_known_args,
+):
+    mock_parse_known_args.return_value = (MagicMock, ["unknown_arg"])
+
+    # when
+    run()
+
+    mock_print.assert_called_once_with("Unknown arguments: ['unknown_arg']")
+    mock_search_plan.assert_not_called()
+
+
+@patch("alphadia.cli.parser.parse_known_args")
+@patch("alphadia.cli.reporting.init_logging")
+@patch("alphadia.cli.SearchPlan")
+def test_cli_minimal_args(mock_search_plan, mock_init_logging, mock_parse_known_args):
+    """Test the run function of the CLI with minimal arguments maps correctly to SearchPlan."""
+    mock_args = MagicMock(config=None, version=None, output="/output")
+    mock_parse_known_args.return_value = (mock_args, [])
+
+    # when
+    run()
+
+    mock_search_plan.assert_called_once_with(
+        "/output",
+        {},
+        {
+            # TODO raw_paths missing here
+            "library_path": mock_args.library,
+            "fasta_paths": mock_args.fasta,
+            "quant_directory": mock_args.quant_dir,
+        },
+    )
+
+    mock_init_logging.assert_called_once_with("/output")
+
+
+@patch("alphadia.cli.parser.parse_known_args")
+@patch("alphadia.cli.reporting.init_logging")
+@patch("alphadia.cli.SearchPlan")
+def test_cli_minimal_args_all_none(
+    mock_search_plan, mock_init_logging, mock_parse_known_args
+):
+    """Test the run function of the CLI with minimal arguments maps correctly to SearchPlan if nothing given."""
+    mock_args = MagicMock(
+        config=None,
+        version=None,
+        output="/output",
+        fasta=None,
+        library=None,
+        quant_dir=None,
+    )
+    mock_parse_known_args.return_value = (mock_args, [])
+
+    # when
+    run()
+
+    mock_search_plan.assert_called_once_with(
+        "/output",
+        {},
+        {},
+    )
+
+    mock_init_logging.assert_called_once_with("/output")