Create temp directory into output directory and download there

fusion_report.log.2023-11-27

@@ -0,0 +1,31 @@
+2023-11-27 10:01:30,030 - CRITICAL - fusion_report.common.net - table "mbca" already exists
+Traceback (most recent call last):
+  File "/Users/annick.renevey/anaconda3/envs/fusion-report/lib/python3.9/site-packages/fusion_report-2.1.5-py3.9.egg/fusion_report/common/db.py", line 61, in setup
+    self.create_database()
+  File "/Users/annick.renevey/anaconda3/envs/fusion-report/lib/python3.9/site-packages/fusion_report-2.1.5-py3.9.egg/fusion_report/common/db.py", line 84, in create_database
+    self.connection.executescript(schema.read().lower())
+sqlite3.OperationalError: table "mbca" already exists
+
+During handling of the above exception, another exception occurred:
+
+Traceback (most recent call last):
+  File "/Users/annick.renevey/anaconda3/envs/fusion-report/lib/python3.9/site-packages/fusion_report-2.1.5-py3.9.egg/fusion_report/app.py", line 72, in run
+    Download(params)
+  File "/Users/annick.renevey/anaconda3/envs/fusion-report/lib/python3.9/site-packages/fusion_report-2.1.5-py3.9.egg/fusion_report/download.py", line 23, in __init__
+    self.download_all(params)
+  File "/Users/annick.renevey/anaconda3/envs/fusion-report/lib/python3.9/site-packages/fusion_report-2.1.5-py3.9.egg/fusion_report/download.py", line 42, in download_all
+    Net.get_mitelman(self, return_err)
+  File "/Users/annick.renevey/anaconda3/envs/fusion-report/lib/python3.9/site-packages/fusion_report-2.1.5-py3.9.egg/fusion_report/common/net.py", line 204, in get_mitelman
+    db.setup(files, delimiter="\t", skip_header=False, encoding="ISO-8859-1")
+  File "/Users/annick.renevey/anaconda3/envs/fusion-report/lib/python3.9/site-packages/fusion_report-2.1.5-py3.9.egg/fusion_report/common/db.py", line 79, in setup
+    raise DbException(ex)
+fusion_report.common.exceptions.db.DbException: table "mbca" already exists
+
+During handling of the above exception, another exception occurred:
+
+Traceback (most recent call last):
+  File "/Users/annick.renevey/Projects/fusion-report/./bin/fusion_report", line 13, in <module>
+    app.run()
+  File "/Users/annick.renevey/anaconda3/envs/fusion-report/lib/python3.9/site-packages/fusion_report-2.1.5-py3.9.egg/fusion_report/app.py", line 79, in run
+    raise AppException(ex)
+fusion_report.common.exceptions.app.AppException: table "mbca" already exists

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: