fix/rename template of config file

lifemonitor/api/models/repositories/base.py

@@ -277,14 +277,16 @@ def write_zip(self, target_path: str):
             raise IllegalStateException(detail="Missing RO Crate metadata")
         return self.metadata.write_zip(target_path)
 
-    def write(self, target_path: str):
+    def write(self, target_path: str, overwrite: bool = False):
         for f in self.files:
             base_path = os.path.join(target_path, f.dir)
             file_path = os.path.join(base_path, f.name)
-            logger.debug("Writing file: %r", file_path)
             os.makedirs(base_path, exist_ok=True)
-            with open(file_path, "w") as out:
-                out.write(f.get_content())
+            file_exists = os.path.isfile(file_path)
+            if not file_exists or overwrite:
+                logger.debug("%s file: %r", "Overwriting" if file_exists else "Writing", file_path)
+                with open(file_path, "w") as out:
+                    out.write(f.get_content())
 
 
 class IssueCheckResult:

lifemonitor/api/models/repositories/config.py

@@ -40,7 +40,7 @@ class WorkflowRepositoryConfig(RepositoryFile):
 
     __BASE_FILENAME__ = "lifemonitor"
     DEFAULT_FILENAME = f".{__BASE_FILENAME__}.yaml"
-    TEMPLATE_FILENAME = f"{__BASE_FILENAME__}.yaml.j2"
+    TEMPLATE_FILENAME = f"{DEFAULT_FILENAME}.j2"
 
     def __init__(self, repo_path: str) -> None:
         config_file = self._search_for_config_file(repo_path)

lifemonitor/api/models/repositories/templates/__init__.py

@@ -131,8 +131,8 @@ def generate_metadata(self) -> WorkflowRepositoryMetadata:
         self._metadata.write(self._local_path)
         return self._metadata
 
-    def write(self, target_path: str):
-        super().write(target_path)
+    def write(self, target_path: str, overwrite: bool = False):
+        super().write(target_path, overwrite=overwrite)
         # rename files according to best practices
         if self.name == "galaxy":
             os.rename(os.path.join(target_path, 'workflow.ga'),

lifemonitor/templates/repositories/base/lifemonitor.yaml.j2 → lifemonitor/templates/repositories/base/.lifemonitor.yaml.j2

@@ -14,7 +14,7 @@ issues:
   # include: [{{issues|join(', ', attribute="identifier")}}]
   # csv of issues to ignore (none ignored by default)
   # exclude: [{{issues|join(', ', attribute="identifier")}}]
-    
+
 
 # Github Integration Settings
 push: