Initialize alt ID mapping before loading ontologies

[jorgeMFS]

Summary

• initialize _alt_to_primary before ontology loading so alt IDs are indexed without raising an AttributeError

Testing

• pytest tests/test_mapping.py::TestOntologyMapper::test_alt_id_and_xref -q (fails: No module named 'yaml')

---

https://chatgpt.com/codex/tasks/task_e_6897f40728fc8327ba38387c1c91e630

Summary by Sourcery

Bug Fixes:

• Initialize _alt_to_primary mapping before ontologies are loaded to prevent AttributeError when populating alt IDs

[sourcery-ai]

Reviewer's guide (collapsed on small PRs)

Reviewer's Guide

The PR ensures that the _alt_to_primary mapping structure is initialized before ontology files are loaded by relocating its instantiation and adding a clarifying comment, preventing AttributeErrors during ontology parsing.

Class diagram for updated OntologyMapper initialization

classDiagram
    class OntologyMapper {
        - config_source
        - config
        - cache_expiry_days
        - _id_regex
        - _alt_to_primary: Dict[str, Dict[str, str]]
        - ontologies
        - default_ontologies
        + __init__(config_source)
        + load_ontologies()
        + _build_id_regex_from_config(config)
    }

    %% Highlight that _alt_to_primary is now initialized before ontologies
    OntologyMapper : _alt_to_primary initialized before ontologies
    OntologyMapper : ontologies = load_ontologies()

Loading

File-Level Changes

Change	Details	Files
Initialize alt-to-primary mapping before ontology loading	Added self._alt_to_primary instantiation before calling load_ontologies() Moved self.ontologies = self.load_ontologies() below the new initialization Inserted a comment explaining why the mapping must exist prior to loading	src/phenoqc/mapping.py

---

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 @jorgeMFS - I've reviewed your changes and they look great!

---

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.}