refactor: consolidating protobuf definitions (#508)

holtgrewe commented 1 month ago

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- Renamed and removed outdated message types to streamline frequency annotations and queries.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[bot] commented 1 month ago

[!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

#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.
#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.
#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. 🌕

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codecov[bot] commented 1 month ago

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 :warning:

Additional details and impacted files

```diff @@ 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](https://app.codecov.io/gh/varfish-org/varfish-server-worker/pull/509?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=varfish-org) | Coverage Δ | | |---|---|---| | [src/seqvars/query/interpreter/frequency.rs](https://app.codecov.io/gh/varfish-org/varfish-server-worker/pull/509?src=pr&el=tree&filepath=src%2Fseqvars%2Fquery%2Finterpreter%2Ffrequency.rs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=varfish-org#diff-c3JjL3NlcXZhcnMvcXVlcnkvaW50ZXJwcmV0ZXIvZnJlcXVlbmN5LnJz) | `85% <ø> (ø)` | | | [src/seqvars/query/interpreter/regions\_allowlist.rs](https://app.codecov.io/gh/varfish-org/varfish-server-worker/pull/509?src=pr&el=tree&filepath=src%2Fseqvars%2Fquery%2Finterpreter%2Fregions_allowlist.rs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=varfish-org#diff-c3JjL3NlcXZhcnMvcXVlcnkvaW50ZXJwcmV0ZXIvcmVnaW9uc19hbGxvd2xpc3QucnM=) | `51% <100%> (ø)` | | | [src/seqvars/query/schema/query.rs](https://app.codecov.io/gh/varfish-org/varfish-server-worker/pull/509?src=pr&el=tree&filepath=src%2Fseqvars%2Fquery%2Fschema%2Fquery.rs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=varfish-org#diff-c3JjL3NlcXZhcnMvcXVlcnkvc2NoZW1hL3F1ZXJ5LnJz) | `96% <100%> (-1%)` | :arrow_down: | | [src/seqvars/query/mod.rs](https://app.codecov.io/gh/varfish-org/varfish-server-worker/pull/509?src=pr&el=tree&filepath=src%2Fseqvars%2Fquery%2Fmod.rs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=varfish-org#diff-c3JjL3NlcXZhcnMvcXVlcnkvbW9kLnJz) | `9% <0%> (ø)` | |

varfish-org / varfish-server-worker