diff data_manager/bakta_build_database.py @ 6:97b1b5ad1cda draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e0ce56ac52cff0e8f85e546440d28ca46853b11d

--- a/data_manager/bakta_build_database.py	Wed Jun 05 14:20:59 2024 +0000
+++ b/data_manager/bakta_build_database.py	Thu Jun 20 19:13:58 2024 +0000
@@ -135,13 +135,9 @@
         try:
             with bakta_path.open("wb") as fh_out, requests.get(
                     self.db_url, stream=True) as resp:
-                total_length = resp.headers.get("content-length")
-                if total_length is None:  # no content length header
-                    for data in resp.iter_content(chunk_size=1024 * 1024):
-                        fh_out.write(data)
-                else:
-                    for data in resp.iter_content(chunk_size=1024 * 1024):
-                        fh_out.write(data)
+                # total_length = resp.headers.get("content-length")
+                for data in resp.iter_content(chunk_size=1024 * 1024):
+                    fh_out.write(data)
             print(f"Download bakta database {self.db_version}")
             self.tarball_path = bakta_path
         except IOError:
@@ -158,12 +154,19 @@
             ) as tar_file:
                 tar_file.extractall(path=db_path)
                 print(f"Untar the database in {db_path}")
-
-            if not self.test_mode:
-                self.move_files(db_path=db_path)
-
         except OSError:
             sys.exit(f"ERROR: Could not extract {self.tar_name} " f"to {db_path}")
+        if not self.test_mode:
+            self.move_files(db_path=db_path)
+        self.db_dir = db_path.resolve()
+
+    def delete_folder(self, path):
+        for sub in path.iterdir():
+            if sub.is_dir() and sub.name != "latest":
+                self.delete_folder(sub)
+            else:
+                sub.unlink()
+        path.rmdir()
 
     def move_files(self, db_path):
         if db_path.joinpath("db-light").is_dir():
@@ -173,9 +176,9 @@
         output_dir = db_path
         for file in input_dir.iterdir():
             if file.is_file():  # to avoid moving amrfinder-plus folder
-                input = input_dir.joinpath(file)
-                output = output_dir.joinpath(file)
-                input.rename(output)
+                output = output_dir.joinpath(file.name)
+                file.rename(output)
+        self.delete_folder(input_dir)
 
     def calc_md5_sum(self, buffer_size=1048576):
         tarball_path = Path(self.db_dir).joinpath(self.tar_name)