add tests to increase coverage

q2_moshpit/busco/tests/test_busco.py

@@ -16,6 +16,7 @@
 from unittest.mock import patch, ANY, call, Mock, MagicMock
 from qiime2.plugin.testing import TestPluginBase
 from q2_types.per_sample_sequences._format import MultiMAGSequencesDirFmt
+from q2_moshpit.busco.types import BuscoDatabaseDirFmt
 
 
 class MockContext(Mock):
@@ -33,6 +34,10 @@ def setUp(self):
             path=self.get_data_path('mags'),
             mode="r",
         )
+        self.busco_db = BuscoDatabaseDirFmt(
+            path=self.get_data_path("busco_db"),
+            mode="r"
+        )
 
     def _prepare_summaries(self):
         for s in ['1', '2']:
@@ -110,7 +115,7 @@ def test_busco_helper(self, mock_len, mock_run):
         )
 
     @patch("q2_moshpit.busco.busco._busco_helper")
-    def test_evaluate_busco(self, mock_helper):
+    def test_evaluate_busco_online(self, mock_helper):
         _evaluate_busco(
             bins=self.mags, mode="some_mode", lineage_dataset="bacteria_odb10"
         )
@@ -121,6 +126,24 @@ def test_evaluate_busco(self, mock_helper):
              '--limit', '3']
         )
 
+    @patch("q2_moshpit.busco.busco._busco_helper")
+    def test_evaluate_busco_offline(self, mock_helper):
+        _evaluate_busco(
+            bins=self.mags,
+            busco_db=self.busco_db,
+            mode="some_mode",
+            lineage_dataset="lineage_1"
+        )
+        mock_helper.assert_called_with(
+            self.mags,
+            [
+                '--mode', 'some_mode', '--lineage_dataset', 'lineage_1',
+                '--cpu', '1', '--contig_break', '10', '--evalue', '0.001',
+                '--limit', '3', '--offline', "--download_path",
+                f"{str(self.busco_db)}/busco_downloads"
+            ]
+        )
+
     @patch(
         "q2_moshpit.busco.busco._draw_detailed_plots",
         return_value={"fake1": {"plot": "spec"}}

q2_moshpit/busco/tests/test_utils.py

@@ -7,16 +7,15 @@
 # ----------------------------------------------------------------------------
 import json
 import tempfile
-
 import pandas as pd
 from qiime2.plugin.testing import TestPluginBase
-
 from q2_moshpit.busco.utils import (
     _parse_busco_params, _collect_summaries, _parse_df_columns,
     _partition_dataframe, _get_feature_table, _calculate_summary_stats,
-    _get_mag_lengths,
+    _get_mag_lengths, _validate_lineage_dataset_input
 )
 from q2_types.per_sample_sequences._format import MultiMAGSequencesDirFmt
+from q2_moshpit.busco.types import BuscoDatabaseDirFmt
 
 
 class TestBUSCOUtils(TestPluginBase):
@@ -218,3 +217,67 @@ def test_get_mag_lengths(self):
             }, name="length"
         )
         pd.testing.assert_series_equal(obs, exp)
+
+    def test_validate_lineage_dataset_input_valid(self):
+        # Give path to valid database
+        p = self.get_data_path("busco_db")
+        busco_db = BuscoDatabaseDirFmt(path=p, mode="r")
+        _validate_lineage_dataset_input(
+            lineage_dataset="lineage_1",
+            auto_lineage=False,
+            auto_lineage_euk=False,
+            auto_lineage_prok=False,
+            busco_db=busco_db,
+            kwargs={}
+        )
+
+    def test_validate_lineage_dataset_input_invalid(self):
+        # Give path to valid database
+        p = self.get_data_path("busco_db")
+        busco_db = BuscoDatabaseDirFmt(path=p, mode="r")
+
+        with self.assertRaisesRegex(
+            ValueError,
+            "is not present in input database."
+        ):
+            # Run busco
+            _validate_lineage_dataset_input(
+                lineage_dataset="lineage2",
+                auto_lineage=False,
+                auto_lineage_euk=False,
+                auto_lineage_prok=False,
+                busco_db=busco_db,
+                kwargs={}
+            )
+
+    def test_validate_lineage_dataset_input_warning(self):
+        # Give path to valid database
+        p = self.get_data_path("busco_db")
+        busco_db = BuscoDatabaseDirFmt(path=p, mode="r")
+        kwargs = {
+            "auto_lineage": True,
+            "auto_lineage_euk": False,
+            "auto_lineage_prok": False
+        }
+        with self.assertWarnsRegex(
+            Warning,
+            "`--p-auto-lineage` flags will be ignored."
+        ):
+            # Run busco
+            _validate_lineage_dataset_input(
+                lineage_dataset="lineage_1",
+                auto_lineage=True,
+                auto_lineage_euk=False,
+                auto_lineage_prok=False,
+                busco_db=busco_db,
+                kwargs=kwargs
+            )
+
+        self.assertDictEqual(
+            kwargs,
+            {
+                "auto_lineage": False,
+                "auto_lineage_euk": False,
+                "auto_lineage_prok": False
+            }
+        )

q2_moshpit/busco/utils.py

@@ -12,6 +12,7 @@
 from typing import List
 import skbio.io
 from q2_types.per_sample_sequences import MultiMAGSequencesDirFmt
+from q2_moshpit.busco.types import BuscoDatabaseDirFmt
 
 arguments_with_hyphens = {
     "auto_lineage": "auto-lineage",
@@ -25,18 +26,18 @@
 
 
 def _validate_lineage_dataset_input(
-        lineage_dataset,
-        auto_lineage,
-        auto_lineage_euk,
-        auto_lineage_prok,
-        busco_db,
+        lineage_dataset: str,
+        auto_lineage: bool,
+        auto_lineage_euk: bool,
+        auto_lineage_prok: bool,
+        busco_db: BuscoDatabaseDirFmt,
         kwargs
         ) -> None:
     # When lineage_dataset is specified all other lineage flags are ignored
     if any([auto_lineage, auto_lineage_euk, auto_lineage_prok]):
         warnings.warn(
-            f"`--p-lineage-dataset` was specified as {lineage_dataset}. "
-            "--p-auto-lineage flags will be ignored."
+            f"`--p-lineage-dataset` was specified as '{lineage_dataset}'. "
+            "`--p-auto-lineage` flags will be ignored."
         )
         kwargs["auto_lineage"] = False
         kwargs["auto_lineage_euk"] = False
@@ -51,8 +52,8 @@ def _validate_lineage_dataset_input(
                 os.path.join(str(busco_db), "busco_downloads/lineages/")
             )
             raise ValueError(
-                f"The specified --p-lineage-dataset {lineage_dataset} "
-                "is not present in input database (--i-busco-db). \n"
+                f"The specified lineage_dataset ({lineage_dataset}) "
+                "is not present in input database. \n"
                 "Printing lineage datasets present in input database: \n"
                 f"{present_lineages}"
             )