From 070d7487fe4574bb04d21ab752383f179b7c1f79 Mon Sep 17 00:00:00 2001
From: gbouras13 <george.bouras@adelaide.edu.au>
Date: Fri, 8 Mar 2024 11:57:05 +1030
Subject: [PATCH] Fix #49 ensure --force works 2

---
 src/plassembler/__init__.py |  6 +++---
 src/plassembler/utils/db.py | 25 +++++++++++++------------
 tests/test_db.py            |  6 +++---
 3 files changed, 19 insertions(+), 18 deletions(-)

diff --git a/src/plassembler/__init__.py b/src/plassembler/__init__.py
index 9606994..9c45803 100644
--- a/src/plassembler/__init__.py
+++ b/src/plassembler/__init__.py
@@ -434,7 +434,7 @@ def run(
     # check the mash database is installed
 
     logger.info("Checking database installation.")
-    check_db_installation(Path(database), install_flag=False)
+    check_db_installation(Path(database), force=False, install_flag=False)
     # will only continue if successful
     logger.info("Database successfully checked.")
 
@@ -996,7 +996,7 @@ def assembled(
     # check the mash database is installed
 
     logger.info("Checking database installation.")
-    check_db_installation(Path(database), install_flag=False)
+    check_db_installation(Path(database), force=False, install_flag=False)
     # will only continue if successful
     logger.info("Database successfully checked.")
 
@@ -1319,7 +1319,7 @@ def long(
 
     # check the mash database is installed
     logger.info("Checking database installation.")
-    check_db_installation(Path(database), install_flag=False)
+    check_db_installation(Path(database), force=False, install_flag=False)
     # will only continue if successful
     logger.info("Database successfully checked.")
 
diff --git a/src/plassembler/utils/db.py b/src/plassembler/utils/db.py
index 724f447..75dc14d 100755
--- a/src/plassembler/utils/db.py
+++ b/src/plassembler/utils/db.py
@@ -29,19 +29,20 @@ def check_db_installation(db_dir: Path, force: bool, install_flag: bool):
     f1: Path = db_dir / f"{mash_db_names[0]}"
     f2: Path = db_dir / f"{mash_db_names[1]}"
 
-    if force is True:
-        if os.path.isdir(db_dir) is True:
-            logger.info(f"Removing the directory {db_dir} as --force was specified")
-            shutil.rmtree(db_dir)
+    if install_flag is True:
+        if force is True:
+            if os.path.isdir(db_dir) is True:
+                logger.info(f"Removing the directory {db_dir} as --force was specified")
+                shutil.rmtree(db_dir)
+            else:
+                logger.info(
+                    f"--force was specified even though the directory {db_dir} does not already exist. Continuing"
+                )
         else:
-            logger.info(
-                f"--force was specified even though the directory {db_dir} does not already exist. Continuing"
-            )
-    else:
-        if os.path.isdir(db_dir) is True:
-            logger.error(
-                f"Directory {db_dir} already exists and force was not specified. Please specify -f or --force to overwrite {db_dir}"
-            )
+            if os.path.isdir(db_dir) is True:
+                logger.error(
+                    f"Directory {db_dir} already exists and force was not specified. Please specify -f or --force to overwrite {db_dir}"
+                )
 
     # instantiate outdir
     if os.path.isdir(db_dir) is False:
diff --git a/tests/test_db.py b/tests/test_db.py
index 4d53db7..45c98d4 100644
--- a/tests/test_db.py
+++ b/tests/test_db.py
@@ -40,15 +40,15 @@ class test_install(unittest.TestCase):
 
     # for plassembler run
     def test_check_db_installation_good(self):
-        check_db_installation(db_path, False)
+        check_db_installation(db_path, force=False, install_flag=False)
 
     # for plassembler download
     def test_check_db_installation_good_d(self):
-        check_db_installation(db_path, True)
+        check_db_installation(db_path, force=True, install_flag=True)
 
     def test_check_db_installation_bad(self):
         with self.assertRaises(SystemExit):
-            check_db_installation(val_data, False)
+            check_db_installation(val_data, force=False, install_flag=False)
 
     def test_get_database_zenodo(self):
         expected_return = True