refactor: consolidating protobuf definitions (#508)

[holtgrewe]

Release-As: 0.16.0

Summary by CodeRabbit

• New Features
  • Consolidated mitochondrial frequency settings into a unified structure for improved clarity.
• Bug Fixes
  • Updated references and field names to ensure consistency across the application.
• Documentation
  • Enhanced error handling and logging for better context during processing.
• Refactor
  • Renamed and removed outdated message types to streamline frequency annotations and queries.

[coderabbitai]

Caution

Review failed

The pull request is closed.

Walkthrough

The changes in this pull request involve significant modifications to several protocol buffer files and Rust source files, primarily focusing on the renaming and consolidation of message types related to mitochondrial frequency settings. The GnomadMitochondrialFrequency and HelixMtDbFrequency messages have been replaced with a unified MitochondrialFrequency message. Corresponding updates were made to various structures and functions across the codebase to reflect these changes, including adjustments to field names and the removal of obsolete settings.

Changes

File Path	Change Summary
protos/varfish/v1/seqvars/output.proto	- Renamed GnomadMitochondrialFrequency to MitochondrialFrequency. - Removed HelixMtDbFrequency. - Updated fields in FrequencyAnnotation.
protos/varfish/v1/seqvars/query.proto	- Renamed GnomadMitochondrialFrequencySettings to MitochondrialFrequencySettings. - Removed HelixMtDbFrequencySettings. - Renamed end to stop in Range.
src/seqvars/query/interpreter/frequency.rs	- Renamed frequency settings in passes function. - Updated test cases to reflect new settings.
src/seqvars/query/interpreter/regions_allowlist.rs	- Renamed parameter seqvar_end to seqvar_stop in overlaps function.
src/seqvars/query/mod.rs	- Updated FrequencyAnnotation fields to use MitochondrialFrequency. - Adjusted error handling in various functions.
src/seqvars/query/schema/query.rs	- Removed GnomadMitochondrialFrequencySettings. - Renamed HelixMtDbFrequencySettings to MitochondrialFrequencySettings. - Updated field end to stop.

Possibly related PRs

• feat: add mode of inheritance from HPO #493: This PR modifies the output.proto file by adding a new enumeration for modes of inheritance, which is related to the renaming and consolidation of frequency messages in the main PR.
• feat: adding more annotations to output (#504) #505: This PR enhances the output.proto file by adding new annotations, which may relate to the changes made in the main PR regarding the structure of frequency annotations.
• chore(main): release 0.15.0 #506: This release PR references the addition of more annotations to the output, which aligns with the changes made in the main PR regarding the consolidation of frequency message types.

🐇 In the meadow where the frequencies play,
A rabbit hops to greet the day.
With names now clear and messages bright,
Mitochondrial joy takes flight!
Consolidation brings a happy tune,
As we dance beneath the bright, full moon. 🌕

---

Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

🪧 Tips

Chat

There are 3 ways to chat with CodeRabbit:

• Review comments: Directly reply to a review comment made by CodeRabbit. Example:
  • I pushed a fix in commit <commit_id>, please review it.
  • Generate unit testing code for this file.
  • Open a follow-up GitHub issue for this discussion.
• Files and specific lines of code (under the "Files changed" tab): Tag @coderabbitai in a new review comment at the desired location with your query. Examples:
  • @coderabbitai generate unit testing code for this file.
  • @coderabbitai modularize this function.
• PR comments: Tag @coderabbitai in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples:
  • @coderabbitai gather interesting stats about this repository and render them as a table. Additionally, render a pie chart showing the language distribution in the codebase.
  • @coderabbitai read src/utils.ts and generate unit testing code.
  • @coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.
  • @coderabbitai help me debug CodeRabbit configuration file.

Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments.

CodeRabbit Commands (Invoked using PR comments)

• @coderabbitai pause to pause the reviews on a PR.
• @coderabbitai resume to resume the paused reviews.
• @coderabbitai review to trigger an incremental review. This is useful when automatic reviews are disabled for the repository.
• @coderabbitai full review to do a full review from scratch and review all the files again.
• @coderabbitai summary to regenerate the summary of the PR.
• @coderabbitai resolve resolve all the CodeRabbit review comments.
• @coderabbitai configuration to show the current CodeRabbit configuration for the repository.
• @coderabbitai help to get help.

Other keywords and placeholders

• Add @coderabbitai ignore anywhere in the PR description to prevent this PR from being reviewed.
• Add @coderabbitai summary to generate the high-level summary at a specific location in the PR description.
• Add @coderabbitai anywhere in the PR title to generate the title automatically.

CodeRabbit Configuration File (.coderabbit.yaml)

• You can programmatically configure CodeRabbit by adding a .coderabbit.yaml file to the root of your repository.
• Please see the configuration documentation for more information.
• If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: # yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json

Documentation and Community

• Visit our Documentation for detailed information on how to use CodeRabbit.
• Join our Discord Community to get help, request features, and share feedback.
• Follow us on X/Twitter for updates and announcements.

[codecov]

Codecov Report

Attention: Patch coverage is 94.73684% with 2 lines in your changes missing coverage. Please review.

Project coverage is 71%. Comparing base (fd08d42) to head (7c3b478).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/seqvars/query/mod.rs	0%	2 Missing ⚠️

Additional details and impacted files

@@          Coverage Diff          @@
##            main    #509   +/-   ##
=====================================
- Coverage     71%     71%   -1%     
=====================================
  Files         43      43           
  Lines      11844   11834   -10     
=====================================
- Hits        8514    8504   -10     
  Misses      3330    3330           

Files with missing lines	Coverage Δ
src/seqvars/query/interpreter/frequency.rs	85% <ø> (ø)
src/seqvars/query/interpreter/regions_allowlist.rs	51% <100%> (ø)
src/seqvars/query/schema/query.rs	96% <100%> (-1%)	⬇️
src/seqvars/query/mod.rs	9% <0%> (ø)