From c5400c6e18d625da96909588a491a8eafcf6e491 Mon Sep 17 00:00:00 2001
From: Santiago Castro Dau <sanntiago5@gmail.com>
Date: Tue, 14 May 2024 14:21:29 +0200
Subject: [PATCH] in online mode download db to temp directory

---
 q2_moshpit/busco/busco.py            |  2 +-
 q2_moshpit/busco/tests/test_busco.py | 20 +++++++++-----
 q2_moshpit/plugin_setup.py           | 41 +++++++++++++++-------------
 3 files changed, 36 insertions(+), 27 deletions(-)

diff --git a/q2_moshpit/busco/busco.py b/q2_moshpit/busco/busco.py
index 4b0ac0db..a49880c7 100644
--- a/q2_moshpit/busco/busco.py
+++ b/q2_moshpit/busco/busco.py
@@ -70,7 +70,7 @@ def _run_busco(
             "-o",
             sample
         ])
-        run_command(cmd)
+        run_command(cmd,  cwd=os.path.dirname(output_dir))
 
         path_to_run_summary = os.path.join(
             output_dir, sample, "batch_summary.txt"
diff --git a/q2_moshpit/busco/tests/test_busco.py b/q2_moshpit/busco/tests/test_busco.py
index c8ee7b6b..d69e5f3b 100644
--- a/q2_moshpit/busco/tests/test_busco.py
+++ b/q2_moshpit/busco/tests/test_busco.py
@@ -61,15 +61,21 @@ def test_run_busco(self, mock_run):
         self.assertDictEqual(obs, exp)
         mock_run.assert_has_calls([
             call(
-                ['busco', '--lineage_dataset', 'bacteria_odb10',
-                 '--cpu', '7', '--in', self.get_data_path('mags/sample1'),
-                 '--out_path', self.temp_dir.name, '-o', 'sample1'],
+                [
+                    'busco', '--lineage_dataset', 'bacteria_odb10',
+                    '--cpu', '7', '--in', self.get_data_path('mags/sample1'),
+                    '--out_path', self.temp_dir.name, '-o', 'sample1'
+                ],
+                cwd=os.path.dirname(self.temp_dir.name)
             ),
             call(
-                ['busco', '--lineage_dataset', 'bacteria_odb10',
-                 '--cpu', '7', '--in', self.get_data_path('mags/sample2'),
-                 '--out_path', self.temp_dir.name, '-o', 'sample2'],
-            )
+                [
+                    'busco', '--lineage_dataset', 'bacteria_odb10',
+                    '--cpu', '7', '--in', self.get_data_path('mags/sample2'),
+                    '--out_path', self.temp_dir.name, '-o', 'sample2'
+                ],
+                cwd=os.path.dirname(self.temp_dir.name)
+            ),
         ])
 
     @patch('q2_moshpit.busco.busco._run_busco')
diff --git a/q2_moshpit/plugin_setup.py b/q2_moshpit/plugin_setup.py
index 96ef8fa3..6e8b9bce 100644
--- a/q2_moshpit/plugin_setup.py
+++ b/q2_moshpit/plugin_setup.py
@@ -1103,6 +1103,21 @@
     description="Collates BUSCO results."
 )
 
+plugin.visualizers.register_function(
+    function=q2_moshpit.busco._visualize_busco,
+    inputs={
+        "busco_results": BUSCOResults,
+    },
+    parameters={},
+    input_descriptions={
+        "busco_results": "BUSCO results table.",
+    },
+    parameter_descriptions={},
+    name="Visualize BUSCO results.",
+    description="This method generates a visualization "
+                "from the BUSCO results table.",
+    citations=[citations["manni_busco_2021"]],
+)
 
 plugin.methods.register_function(
     function=q2_moshpit.busco._evaluate_busco,
@@ -1117,7 +1132,9 @@
     input_descriptions={
         "bins": "MAGs to be analyzed.",
         "busco_db": "BUSCO database. If provided BUSCO will run in offline "
-                    "mode."
+                    "mode. If not provided a BUSCO database "
+                    "will be downloaded to a temporary location and then "
+                    "deleted."
     },
     parameter_descriptions=busco_param_descriptions,
     output_descriptions={
@@ -1131,22 +1148,6 @@
     citations=[citations["manni_busco_2021"]],
 )
 
-plugin.visualizers.register_function(
-    function=q2_moshpit.busco._visualize_busco,
-    inputs={
-        "busco_results": BUSCOResults,
-    },
-    parameters={},
-    input_descriptions={
-        "busco_results": "BUSCO results table.",
-    },
-    parameter_descriptions={},
-    name="Visualize BUSCO results.",
-    description="This method generates a visualization "
-                "from the BUSCO results table.",
-    citations=[citations["manni_busco_2021"]],
-)
-
 plugin.pipelines.register_function(
     function=q2_moshpit.busco.evaluate_busco,
     inputs={
@@ -1161,7 +1162,9 @@
     input_descriptions={
         "bins": "MAGs to be analyzed.",
         "busco_db": "BUSCO database. If provided BUSCO will run in offline "
-                    "mode."
+                    "mode. If not provided a BUSCO database "
+                    "will be downloaded to a temporary location and then "
+                    "deleted."
     },
     parameter_descriptions={
         **busco_param_descriptions, **partition_param_descriptions
@@ -1174,7 +1177,7 @@
     description="This method uses BUSCO "
                 "(Benchmarking Universal Single-Copy Ortholog assessment "
                 "tool) to assess the quality of assembled MAGs and generates "
-                "visualizations summarizing the results.",
+                "a table summarizing the results.",
     citations=[citations["manni_busco_2021"]],
 )