Review Galaxy Code for Dependency Injection Best Practices

Perform a Python code review on the provided code. Accept input in any of the following forms:

1. A working directory path (analyze git diff in that directory)
2. A Git commit reference (analyze changes in that commit)
3. A list of Python file paths (analyze those files)
4. A planning document (analyze the Python files in the plan)

Review Criteria

Review the code and ensure it follows best practices for dependency injection in Galaxy:

1. Avoid FastAPI-style injection - Prefer Galaxy-style DI using Lagom and type-based injection
2. Proper service/manager layer dependencies - Dependencies should be injected via constructors, not via app access
3. Avoid app property creation - Don't add new properties to the app object when DI can be used

Galaxy DI Architecture Background

The Problem: God Object Anti-pattern

Galaxy's app object was historically a "god object" - an object that knows/does too much. Every component, controller, and web transaction had a reference to app. This creates:

• Circular dependencies (manager imports UniverseApplication, which creates that manager)
• Difficult testing (hard to know what parts of app are needed, hard to mock)
• Brittle construction ordering

The Solution: Type-based Dependency Injection

Galaxy uses Lagom for type-based DI:

• Container keeps track of singletons and construction recipes
• Dependencies are resolved automatically based on type annotations
• Dependencies should form a DAG (directed acyclic graph)

Interface Pattern for Breaking Cycles

Use StructuredApp interface instead of UniverseApplication to break circular dependencies:

# BAD - creates circular dependency
class MyManager:
    def __init__(self, app: UniverseApplication):
        ...

# GOOD - uses interface, breaks cycle
class MyManager:
    def __init__(self, app: StructuredApp):
        ...

# BETTER - inject only what you need
class MyManager:
    def __init__(self, model: GalaxyModelMapping, security: IdEncodingHelper):
        ...

Code Patterns to Review

Manager/Service Pattern

Anti-pattern - using app directly:

class DatasetCollectionManager:
    def __init__(self, app):
        self.model = app.model
        self.security = app.security
        self.hda_manager = hdas.HDAManager(app)  # BAD: internal construction
        self.history_manager = histories.HistoryManager(app)

Correct pattern - injecting dependencies:

class DatasetCollectionManager:
    def __init__(
        self,
        model: GalaxyModelMapping,
        security: IdEncodingHelper,
        hda_manager: HDAManager,
        history_manager: HistoryManager,
    ):
        self.model = model
        self.security = security
        self.hda_manager = hda_manager
        self.history_manager = history_manager

Benefits:

• Type signature clearly delineates required dependencies
• Unit testing can inject precise mock dependencies
• No dependency on app object

FastAPI Controller Pattern

Anti-pattern - FastAPI Depends():

def get_tags_manager() -> TagsManager:
    return TagsManager()

@cbv(router)
class FastAPITags:
    manager: TagsManager = Depends(get_tags_manager)  # BAD: FastAPI style

Correct pattern - Galaxy's depends():

@cbv(router)
class FastAPITags:
    manager: TagsManager = depends(TagsManager)  # GOOD: Galaxy style

Legacy WSGI Controller Pattern

Anti-pattern:

class TagsController(BaseAPIController):
    def __init__(self, app):
        super().__init__(app)
        self.manager = TagsManager()  # BAD: manual construction

Correct pattern:

class TagsController(BaseGalaxyAPIController):
    manager: TagsManager = depends(TagsManager)  # GOOD: DI

Celery Task Pattern

Correct pattern - using @galaxy_task:

@celery_app.task(ignore_result=True)
@galaxy_task
def purge_hda(hda_manager: HDAManager, hda_id):
    hda = hda_manager.by_id(hda_id)
    hda_manager._purge(hda)

Dependencies are automatically injected based on type annotations.

Task with multiple dependencies:

@celery_app.task
@galaxy_task
def set_metadata(
    hda_manager: HDAManager,
    ldda_manager: LDDAManager,
    dataset_id,
    model_class='HistoryDatasetAssociation'
):
    ...

Related Code Paths

When reviewing, reference these Galaxy codebase locations for patterns:

• lib/galaxy/di/ - DI container setup
• lib/galaxy/structured_app.py - StructuredApp interface definition
• lib/galaxy/app.py - UniverseApplication implementation
• lib/galaxy/managers/ - Manager implementations using DI
• lib/galaxy/webapps/galaxy/api/ - FastAPI controllers using DI
• lib/galaxy/celery/tasks.py - Celery tasks using DI

Review Checklist

For each file/change, check:

• No app access for dependencies - Does code access app.some_manager instead of injecting?
• Type annotations present - Are constructor parameters properly type-annotated?
• Interface types used - Uses StructuredApp instead of UniverseApplication where needed?
• Galaxy-style depends() - Controllers use depends(Type) not FastAPI Depends()?
• No internal construction - Components don't construct their own dependencies internally?
• DAG structure - Dependencies form a directed acyclic graph (no cycles)?
• @galaxy_task for Celery - Celery tasks use @galaxy_task decorator with type-annotated parameters?

Output Format

For each issue found, report:

1. File and line number
2. Issue type (from review criteria above)
3. Current code snippet
4. Recommended fix
5. Severity (high/medium/low based on impact on architecture)

Summarize findings with counts by issue type and overall assessment of DI compliance.