adding tests for preparing commands

tests/test_prepare_commands.py

@@ -0,0 +1,64 @@
+import shutil
+import tempfile
+import unittest
+from pathlib import Path
+
+from pheval_gado.prepare.prepare_commands import CommandWriter, GADOProcessCLIArguments, GADOPrioritiseCLIArguments
+
+
+class TestCommandWriter(unittest.TestCase):
+    def setUp(self) -> None:
+        self.test_dir = tempfile.mkdtemp()
+        self.process_file_path = Path(self.test_dir).joinpath("process-command.txt")
+        self.process_command_writer = CommandWriter(output_file=self.process_file_path)
+        self.process_command_arguments = GADOProcessCLIArguments(input_output_dir=Path(self.test_dir),
+                                                                 data_dir=Path("/data_dir"),
+                                                                 gado_jar=Path("GADO/GADO.jar"),
+                                                                 hpo_ontology=Path("hp.obo"),
+                                                                 hpo_predictions_info=Path("predictions_auc_bonf.txt")
+                                                                 )
+        self.prioritise_file_path = Path(self.test_dir).joinpath("prioritise-command.txt")
+        self.prioritise_command_writer = CommandWriter(output_file=self.prioritise_file_path)
+        self.prioritise_command_arguments = GADOPrioritiseCLIArguments(input_output_dir=Path(self.test_dir),
+                                                                       data_dir=Path("/data_dir"),
+                                                                       gado_jar=Path("GADO/GADO.jar"),
+                                                                       hpo_predictions=Path(
+                                                                           "genenetwork_bonf_spiked/genenetwork_bonf_spiked.dat"),
+                                                                       genes=Path("hpo_prediction_genes.txt"),
+                                                                       results_dir=Path("results_dir")
+
+                                                                       )
+
+    def tearDown(self):
+        shutil.rmtree(self.test_dir)
+
+    def test_write_process_command(self):
+        self.process_command_writer.write_process_command(self.process_command_arguments)
+        self.process_command_writer.file.close()
+        with open(self.process_file_path) as f:
+            content = f.readlines()
+        f.close()
+        self.assertEqual(content, ['java -jar /data_dir/GADO/GADO.jar --mode PROCESS --output '
+                                   f'{self.test_dir}/hpoProcessed.txt '
+                                   '--caseHpo '
+                                   f'{self.test_dir}/input_cases.txt '
+                                   '--hpoOntology /data_dir/hp.obo --hpoPredictionsInfo '
+                                   '/data_dir/predictions_auc_bonf.txt\n'])
+
+    def test_write_prioritise_command(self):
+        self.prioritise_command_writer.write_prioritise_command(self.prioritise_command_arguments)
+        self.prioritise_command_writer.file.close()
+        with open(self.prioritise_file_path) as f:
+            content = f.readlines()
+        f.close()
+        self.assertEqual(content, ['java -jar /data_dir/GADO/GADO.jar --mode PRIORITIZE --output results_dir '
+                                   '--caseHpoProcessed '
+                                   f'{self.test_dir}/hpoProcessed.txt '
+                                   '--genes /data_dir/hpo_prediction_genes.txt --hpoPredictions '
+                                   '/data_dir/genenetwork_bonf_spiked/genenetwork_bonf_spiked.dat\n'])
+
+    def test_close(self):
+        self.prioritise_command_writer.close()
+        self.assertTrue(self.prioritise_command_writer.file.closed)
+        self.process_command_writer.close()
+        self.assertTrue(self.process_command_writer.file.closed)