Guarantee mapping output for all variants

[bencap]

Enhancements to error handling:

• Added detailed error messages for cases where accession values cannot be determined during allele or haplotype annotation, replacing generic ValueError exceptions (src/dcd_mapping/annotate.py). [1] [2]
• Improved error messages for transcript selection failures, including specific reasons for the failure, such as missing gene symbols or matching transcripts (src/dcd_mapping/transcripts.py). [1] [2]
• Added error handling for unsupported sequence namespaces and intronic variants in genomic mapping, returning MappedScore objects with appropriate error messages (src/dcd_mapping/vrs_map.py). [1] [2]

Improvements to mapping logic:

• Introduced checks for mismatches between the number of mapped scores and total score records, with corresponding error messages (src/api/routers/map.py).

Codebase simplification:

• Removed hard-coded logic for specific datasets, such as manually selecting protein annotations or predefined results for certain score sets (src/dcd_mapping/annotate.py, src/dcd_mapping/transcripts.py). [1] [2]
• Simplified conditional statements by directly assigning error messages without redundant checks (src/dcd_mapping/annotate.py). [1] [2]

Performance and timeout adjustments:

• Increased the HTTP request timeout from 30 to 60 seconds in the http_download function to accommodate slower network conditions (src/dcd_mapping/resource_utils.py).

[sallybg]

This looks good! There are a few places where we are now returning individual variant-level errors when there is a problem with a reference sequence. I lean toward having the whole mapping job fail if these errors happen, although I recognize that for multi-target score sets we'd then be failing all targets if even one target fails.

[bencap]

Thanks @sallybg, totally agree.

I added some custom exceptions for those possibilities and included them in the try/except block during mapping. I also went ahead and refactored the other custom exceptions we have into a dedicated exception module to keep them a little more organized.

[sallybg]

Looks great!