Merge pull request #168 from ARGA-Genomes/developPatch

Develop Merge Patch

Author: christopher-mangion

src/lib/data/database.py

@@ -172,9 +172,13 @@ def checkUpdateReady(self) -> bool:
         lastUpdate = self.downloadManager.getLastUpdate()
         return self.updateManager.isUpdateReady(lastUpdate)
 
-    def update(self) -> bool:
+    def update(self, flags: list[Flag]) -> bool:
+        for flag in [Flag.UPDATE, Flag.OUTPUT_OVERWRITE]:
+            if flag not in flags:
+                flags.append(flag)
+
         for step in (Step.DOWNLOAD, Step.PROCESSING, Step.CONVERSION):
-            self.create(step, (True, True), True)
+            self.create(step, flags)
 
         self.package()
 

src/tools/update.py

@@ -5,12 +5,12 @@
     parser = ArgParser(description="Run update on data source")
     parser.add_argument("-f", "--force", action="store_true", help="Force update regardless of config")
 
-    sources, overwrite, verbose, args = parser.parse_args()
+    sources, flags, args = parser.parse_args()
     kwargs = parser.namespaceKwargs(args)
     for source in sources:
         if not source.checkUpdateReady() and not args.force:
             logging.info(f"Data source '{source}' is not ready for update.")
             continue
 
-        source.update()
+        source.update(flags)
         outputFile = source.package()