fix: deal with undefined XRef

[tedil]

Some VariationArchive records seem to have no XRef (and/or XRefList) set; return an empty default on access.

Summary by CodeRabbit

• Bug Fixes
  • Enhanced progress indicator behavior for a smoother and more responsive visual display.
  • Improved data processing to gracefully handle missing information, reducing potential errors during conversions.

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📥 Commits

Reviewing files that changed from the base of the PR and between c2f178c and fd3ee4e.

📒 Files selected for processing (1)

• clinvar_data/conversion/__init__.py (2 hunks)

Walkthrough

The changes adjust the progress bar's behavior and improve dictionary key retrieval in the conversion modules. In the progress bar initialization, the smoothing value is modified from 1.0 to 0.001. In the dictionary-to-protobuf conversion routines, direct key indexing is replaced with the safer .get method for the "XRef" and "XRefList" fields, along with updates to several method signatures. These modifications enhance error handling without altering the core functionality.

Changes

File	Summary
clinvar_data/conversion/init.py	Updated the smoothing parameter in the tqdm.tqdm initialization from 1.0 to 0.001 in the convert function.
clinvar_data/conversion/dict_to_pb.py	Replaced direct dict indexing with .get for retrieving "XRef" and "XRefList" keys to prevent KeyError. Also updated method signatures in multiple conversion classes for clarity.

Sequence Diagram(s)

sequenceDiagram
    participant Caller
    participant ConversionFunction
    Note over ConversionFunction: Initialize progress bar with smoothing=0.001
    Caller->>ConversionFunction: Start conversion process
    ConversionFunction-->>Caller: Return progress updates

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sequenceDiagram
    participant Caller
    participant Converter
    participant DictData
    Caller->>Converter: Call parse_citations_xrefs_comments(value)
    Converter->>DictData: Retrieve "XRef" using .get (default empty list/dict)
    DictData-->>Converter: Return XRef data or default value
    Converter-->>Caller: Return processed conversion result

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Poem

Oh, I'm a happy little bunny,
Hopping through code with a smile so sunny.
My progress bar flows with smoother grace,
And safe key retrieval lights up the place!
With each hop, my code sings in delight—
A robust new path shining ever so bright!
🐰✨

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[github-actions]

Please format your code with black: make black.

[holtgrewe]

Looks good to me