refactoring

tests/test_standardize_output.py

@@ -1,95 +1,93 @@
-import unittest 
+import unittest
 import os
 import subprocess
 
+def get_script_path():
+    script_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
+    return os.path.join(script_dir, 'srcs', 'standardize_yacht_output.py')
+
+def assert_file_exists(file_path):
+    assert os.path.exists(file_path)
+
+def assert_file_not_exists(file_path):
+    assert not os.path.exists(file_path)
+
+def create_outdir(outdir):
+    cmd = f'rm -rf {outdir}'
+    try:
+        subprocess.run(cmd, shell=True, check=True)
+    except:
+        pass
+    assert not os.path.exists(outdir)
+
+def cleanup_outdir(outdir):
+    cmd = f'rm -rf {outdir}'
+    res = subprocess.run(cmd, shell=True, check=True)
+    assert res.returncode == 0
+
 class TestScript(unittest.TestCase):
-    def test_everything_exists(self):
-        script_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
-        script_dir = os.path.join(script_dir, 'srcs')
-        script_full_path = os.path.join(script_dir, 'standardize_yacht_output.py')
-        assert os.path.exists(script_full_path)
+    def setUp(self):
+        self.script_full_path = get_script_path()
 
+    def test_everything_exists(self):
         yacht_output = os.path.join(os.path.dirname(__file__), 'testdata/standardize_output_testdata/result.xlsx')
-        assert os.path.exists(yacht_output)
-
         genome_to_taxid = os.path.join(os.path.dirname(__file__), 'testdata/standardize_output_testdata/toy_genome_to_taxid.tsv')
-        assert os.path.exists(genome_to_taxid)
-
         outdir = os.path.join(os.path.dirname(__file__), 'testdata')
-        assert os.path.exists(outdir)
 
-        cmd = f"python {script_full_path} --yacht_output {yacht_output} --sheet_name min_coverage0.2 --genome_to_taxid {genome_to_taxid} --outfile_prefix cami_result --outdir {outdir}"
+        assert_file_exists(self.script_full_path)
+        assert_file_exists(yacht_output)
+        assert_file_exists(genome_to_taxid)
+        assert_file_exists(outdir)
+
+        cmd = f"python {self.script_full_path} --yacht_output {yacht_output} --sheet_name min_coverage0.2 --genome_to_taxid {genome_to_taxid} --outfile_prefix cami_result --outdir {outdir}"
         res = subprocess.run(cmd, shell=True, check=True)
         assert res.returncode == 0
-        assert os.path.exists(os.path.join(outdir, 'cami_result.cami'))
+        assert_file_exists(os.path.join(outdir, 'cami_result.cami'))
 
     def test_wrong_yacht_output(self):
-        script_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
-        script_dir = os.path.join(script_dir, 'srcs')
-        script_full_path = os.path.join(script_dir, 'standardize_yacht_output.py')
-        assert os.path.exists(script_full_path)
-
         yacht_output = os.path.join(os.path.dirname(__file__), 'testdata/standardize_output_testdata/result_nonexisting.xlsx')
-        assert not os.path.exists(yacht_output)
-
         genome_to_taxid = os.path.join(os.path.dirname(__file__), 'testdata/standardize_output_testdata/toy_genome_to_taxid.tsv')
-        assert os.path.exists(genome_to_taxid)
-
         outdir = os.path.join(os.path.dirname(__file__), 'testdata')
-        assert os.path.exists(outdir)
-
-        cmd = f"python {script_full_path} --yacht_output {yacht_output} --sheet_name min_coverage0.2 --genome_to_taxid {genome_to_taxid} --outfile_prefix cami_result --outdir {outdir}"
+
+        assert_file_exists(self.script_full_path)
+        assert_file_not_exists(yacht_output)
+        assert_file_exists(genome_to_taxid)
+        assert_file_exists(outdir)
+
+        cmd = f"python {self.script_full_path} --yacht_output {yacht_output} --sheet_name min_coverage0.2 --genome_to_taxid {genome_to_taxid} --outfile_prefix cami_result --outdir {outdir}"
         with self.assertRaises(subprocess.CalledProcessError):
             res = subprocess.run(cmd, shell=True, check=True)
 
     def test_wrong_genome_to_taxid(self):
-        script_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
-        script_dir = os.path.join(script_dir, 'srcs')
-        script_full_path = os.path.join(script_dir, 'standardize_yacht_output.py')
-        assert os.path.exists(script_full_path)
-
         yacht_output = os.path.join(os.path.dirname(__file__), 'testdata/standardize_output_testdata/result.xlsx')
-        assert os.path.exists(yacht_output)
-
         genome_to_taxid = os.path.join(os.path.dirname(__file__), 'testdata/standardize_output_testdata/toy_genome_to_taxid_nonexisting.tsv')
-        assert not os.path.exists(genome_to_taxid)
-
         outdir = os.path.join(os.path.dirname(__file__), 'testdata')
-        assert os.path.exists(outdir)
 
-        cmd = f"python {script_full_path} --yacht_output {yacht_output} --sheet_name min_coverage0.2 --genome_to_taxid {genome_to_taxid} --outfile_prefix cami_result --outdir {outdir}"
+        assert_file_exists(self.script_full_path)
+        assert_file_exists(yacht_output)
+        assert_file_not_exists(genome_to_taxid)
+        assert_file_exists(outdir)
+
+        cmd = f"python {self.script_full_path} --yacht_output {yacht_output} --sheet_name min_coverage0.2 --genome_to_taxid {genome_to_taxid} --outfile_prefix cami_result --outdir {outdir}"
         with self.assertRaises(subprocess.CalledProcessError):
             res = subprocess.run(cmd, shell=True, check=True)
 
     def test_wrong_outdir(self):
-        script_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
-        script_dir = os.path.join(script_dir, 'srcs')
-        script_full_path = os.path.join(script_dir, 'standardize_yacht_output.py')
-        assert os.path.exists(script_full_path)
-
         yacht_output = os.path.join(os.path.dirname(__file__), 'testdata/standardize_output_testdata/result.xlsx')
-        assert os.path.exists(yacht_output)
-
         genome_to_taxid = os.path.join(os.path.dirname(__file__), 'testdata/standardize_output_testdata/toy_genome_to_taxid.tsv')
-        assert os.path.exists(genome_to_taxid)
-
         outdir = os.path.join(os.path.dirname(__file__), 'testdata_nonexisting')
-        cmd = 'rm -rf ' + outdir
-        try:
-            subprocess.run(cmd, shell=True, check=True)
-        except:
-            pass
-        assert not os.path.exists(outdir)
-
-        cmd = f"python {script_full_path} --yacht_output {yacht_output} --sheet_name min_coverage0.2 --genome_to_taxid {genome_to_taxid} --outfile_prefix cami_result --outdir {outdir}"
-        res = subprocess.run(cmd, shell=True, check=True)
-        assert res.returncode == 0
-        assert os.path.exists(outdir)
 
-        cmd = 'rm -rf ' + outdir
+        assert_file_exists(self.script_full_path)
+        assert_file_exists(yacht_output)
+        assert_file_exists(genome_to_taxid)
+        create_outdir(outdir)
+
+        cmd = f"python {self.script_full_path} --yacht_output {yacht_output} --sheet_name min_coverage0.2 --genome_to_taxid {genome_to_taxid} --outfile_prefix cami_result --outdir {outdir}"
         res = subprocess.run(cmd, shell=True, check=True)
         assert res.returncode == 0
+        assert_file_exists(outdir)
 
+        cleanup_outdir(outdir)
 
 if __name__ == '__main__':
     unittest.main()