Test

[Nidhi091999]

checks

Summary by Sourcery

Introduce a custom configuration model and namespace existing settings under a dedicated 'custom' key, updating code references and documentation accordingly.

New Features:

• Define a Pydantic-based CustomConfig schema for typed application settings.
• Enable loading the custom configuration model via the custom_config_model parameter in app initialization.

Enhancements:

• Move all controller, TES, logging, middleware, and service information under a custom section in config.yaml.
• Update code paths to reference foca.config.custom instead of the root config fields.
• Add a Docker Compose reference link to the README for improved documentation.

Documentation:

• Extend README with a Docker Compose resource link.

[sourcery-ai]

Reviewer's Guide

This PR restructures the application’s configuration by introducing a new “custom” section in config.yaml backed by a Pydantic CustomConfig model, updates code to reference the nested custom settings (controllers, TES, logging, middlewares, serviceInfo), adjusts app initialization to use the new model, and adds a small documentation link.

File-Level Changes

Change	Details	Files
Nest existing settings under a new custom root in config.yaml	Moved controllers, serviceInfo, tes, storeLogs, and middlewares blocks under a top-level custom key Re-indented and adjusted key casing (e.g. serviceInfo, storeLogs) accordingly	pro_tes/config.yaml
Add Pydantic models for the new custom config structure	Created config_models.py defining BaseModel classes for controllers, tasks, TES, logging, middlewares, and CustomConfig Mapped all nested settings into typed attributes	pro_tes/config_models.py
Reference custom settings in code instead of flat foca config	Replaced references to foca_config.controllers, foca_config.storeLogs, foca_config.serviceInfo, and foca.tes with foca_config.custom.* Adjusted imports and attribute access in task_runs, service_info, middleware base, and track_task_progress	pro_tes/ga4gh/tes/task_runs.py pro_tes/ga4gh/tes/service_info.py pro_tes/plugins/middlewares/task_distribution/base.py pro_tes/tasks/track_task_progress.py
Configure the app to use the CustomConfig model	Passed custom_config_model="pro_tes.config_models.CustomConfig" to the Foca initializer	pro_tes/app.py
Update documentation with a new Docker Compose link	Appended a [res-docker compose] reference link in README	README.md

---

Tips and commands

Interacting with Sourcery

• Trigger a new review: Comment @sourcery-ai review on the pull request.
• Continue discussions: Reply directly to Sourcery's review comments.
• Generate a GitHub issue from a review comment: Ask Sourcery to create an
  issue from a review comment by replying to it. You can also reply to a
  review comment with @sourcery-ai issue to create an issue from it.
• Generate a pull request title: Write @sourcery-ai anywhere in the pull
  request title to generate a title at any time. You can also comment
  @sourcery-ai title on the pull request to (re-)generate the title at any time.
• Generate a pull request summary: Write @sourcery-ai summary anywhere in
  the pull request body to generate a PR summary at any time exactly where you
  want it. You can also comment @sourcery-ai summary on the pull request to
  (re-)generate the summary at any time.
• Generate reviewer's guide: Comment @sourcery-ai guide on the pull
  request to (re-)generate the reviewer's guide at any time.
• Resolve all Sourcery comments: Comment @sourcery-ai resolve on the
  pull request to resolve all Sourcery comments. Useful if you've already
  addressed all the comments and don't want to see them anymore.
• Dismiss all Sourcery reviews: Comment @sourcery-ai dismiss on the pull
  request to dismiss all existing Sourcery reviews. Especially useful if you
  want to start fresh with a new review - don't forget to comment
  @sourcery-ai review to trigger a new review!

Customizing Your Experience

Access your dashboard to:

• Enable or disable review features such as the Sourcery-generated pull request
  summary, the reviewer's guide, and others.
• Change the review language.
• Add, remove or edit custom review instructions.
• Adjust other review settings.

Getting Help

• Contact our support team for questions or feedback.
• Visit our documentation for detailed guides and information.
• Keep in touch with the Sourcery team by following us on X/Twitter, LinkedIn or GitHub.

[sourcery-ai]

Hey @Nidhi091999 - I've reviewed your changes - here's some feedback:

• The Celery config block was left at the root instead of under custom.controllers.celery—move it under the new custom.controllers hierarchy to match your CustomConfig model.
• YAML uses 'serviceInfo' but the Pydantic model defines 'service_info'; either rename the key or add an alias in the model so they align.
• You're indexing Pydantic models like dicts (e.g. custom.storeLogs["execution_trace"]); switch to attribute access (custom.storeLogs.execution_trace) for type safety and clarity.

Here's what I looked at during the review

• 🟡 General issues: 2 issues found
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Documentation: all looks good

---

Sourcery is free for open source - if you like our reviews please consider sharing them ✨

• X
• Mastodon
• LinkedIn
• Facebook

_{Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.}

[sourcery-ai]

issue (bug_risk): YAML key 'serviceInfo' does not match Pydantic field 'service_info'

Add Field(..., alias='serviceInfo') to service_info or rename it to serviceInfo so the YAML key aligns and loads correctly.

[sourcery-ai]

issue (bug_risk): Passing Pydantic model instead of raw list to middleware handler

Pass middlewares.__root__ or update the model to expose the list as a normal field, so set_middlewares receives an actual list.