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feat: optional deployment of schemas #71

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feat: optional deployment of schemas #71

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20 changes: 19 additions & 1 deletion snakedeploy/deploy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -70,6 +70,21 @@ def deploy_config(self):
shutil.copytree(config_dir, self.config, dirs_exist_ok=self.force)
return no_config

def deploy_schemas(self):
"""
Deploy the schemas directory.
"""
schema_dir = Path(self.repo_clone) / "workflow" / "schemas"
dest_dir = self.dest_path / "workflow" / "schemas"
if not schema_dir.exists():
logger.warning("No schemas directory found...")
else:
logger.info("Writing schemas...")
shutil.copytree(
schema_dir,
dest_dir,
)

Comment on lines +73 to +87
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⚠️ Potential issue

Add error handling and maintain consistency with other deploy methods

The deploy_schemas implementation needs improvements in error handling and consistency:

  1. Missing error handling for shutil.copytree
  2. Inconsistent with other deploy methods - missing dirs_exist_ok parameter
  3. Warning message could be more informative

Here's the suggested fix:

    def deploy_schemas(self):
        """
        Deploy the schemas directory.
        """
        schema_dir = Path(self.repo_clone) / "workflow" / "schemas"
        dest_dir = self.dest_path / "workflow" / "schemas"
        if not schema_dir.exists():
-           logger.warning("No schemas directory found...")
+           logger.warning(
+               "No schemas directory found in source repository. "
+               "This might be expected if the workflow doesn't use schema validation."
+           )
        else:
            logger.info("Writing schemas...")
+           try:
                shutil.copytree(
                    schema_dir,
                    dest_dir,
+                   dirs_exist_ok=self.force
                )
+           except OSError as e:
+               raise UserError(f"Failed to copy schemas: {e}")
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
def deploy_schemas(self):
"""
Deploy the schemas directory.
"""
schema_dir = Path(self.repo_clone) / "workflow" / "schemas"
dest_dir = self.dest_path / "workflow" / "schemas"
if not schema_dir.exists():
logger.warning("No schemas directory found...")
else:
logger.info("Writing schemas...")
shutil.copytree(
schema_dir,
dest_dir,
)
def deploy_schemas(self):
"""
Deploy the schemas directory.
"""
schema_dir = Path(self.repo_clone) / "workflow" / "schemas"
dest_dir = self.dest_path / "workflow" / "schemas"
if not schema_dir.exists():
logger.warning(
"No schemas directory found in source repository. "
"This might be expected if the workflow doesn't use schema validation."
)
else:
logger.info("Writing schemas...")
try:
shutil.copytree(
schema_dir,
dest_dir,
dirs_exist_ok=self.force
)
except OSError as e:
raise UserError(f"Failed to copy schemas: {e}")

@property
def repo_clone(self):
if self._cloned is None:
Expand All @@ -83,7 +98,7 @@ def repo_clone(self):

return self._cloned.name

def deploy(self, name: str):
def deploy(self, name: str, schemas: bool = False):
"""
Deploy a source to a destination.
"""
Expand All @@ -95,6 +110,9 @@ def deploy(self, name: str):
# Inspect repository to find existing snakefile
self.deploy_snakefile(self.repo_clone, name)

if schemas:
self.deploy_schemas()

logger.info(
self.env.get_template("post-instructions.txt.jinja").render(
no_config=no_config, dest_path=self.dest_path
Expand Down