Create temp directory into output directory and download there

fusion_report/common/net.py

@@ -206,12 +206,11 @@ def get_mitelman(self, return_err: List[str]) -> None:
 
     @staticmethod
     def clean():
-        """Remove all files except *db."""
-        for temp in glob.glob("*/"):
-            shutil.rmtree(temp)
-        for temp in glob.glob("*[!.db]"):
-            if not os.path.isdir(temp):
-                os.remove(temp)
+        """Remove all files except *db and move to output dir."""
+        for temp in glob.glob("*.db"):
+            shutil.copy(temp, "../")
+        os.chdir("../")
+        shutil.rmtree("tmp_dir")
 
     @staticmethod
     def timestamp():

fusion_report/download.py

@@ -36,7 +36,10 @@ def validate(self, params: Namespace) -> None:
     def download_all(self, params: Namespace) -> None:
         """Download all databases."""
         return_err: List[str] = []
-        os.chdir(params.output)
+        tmp_dir = os.path.join(params.output, "tmp_dir")
+        if not os.path.exists(tmp_dir):
+            os.mkdir(tmp_dir)
+        os.chdir(tmp_dir)
 
         # MITELMAN
         Net.get_mitelman(self, return_err)

fusion_report/modules/index_summary/index_summary.py

@@ -25,10 +25,8 @@ def tool_detection(self) -> List[List[Any]]:
         counts["together"] = 0
         running_tools_count: int = len(running_tools)
         for fusion in self.manager.fusions:
-            print(fusion.name)
             fusion_tools = fusion.tools.keys()
             for tool in fusion_tools:
-                print(tool)
                 counts[tool] += 1
             # intersection
             if len(fusion_tools) == running_tools_count: