Gracefully handle loading consequences not in enumeration

[grosscol]

Issue or current state

Reading vcfs into mongo backing data will throw errors if newer version of VEP is used with consequences that are not enumerated in snv_consequence2code:

bravo_api/bravo_api/models/readers.py

Lines 49 to 86 in 7a52032

	snv_consequence2code = { name: i for i, name in enumerate(reversed([
	'transcript_ablation',
	'splice_acceptor_variant',
	'splice_donor_variant',
	'stop_gained',
	'frameshift_variant',
	'stop_lost',
	'start_lost',
	'transcript_amplification',
	'inframe_insertion',
	'inframe_deletion',
	'missense_variant',
	'protein_altering_variant',
	'splice_region_variant',
	'incomplete_terminal_codon_variant',
	'start_retained_variant',
	'stop_retained_variant',
	'synonymous_variant',
	'coding_sequence_variant',
	'mature_miRNA_variant',
	'5_prime_UTR_variant',
	'3_prime_UTR_variant',
	'non_coding_transcript_exon_variant',
	'intron_variant',
	'NMD_transcript_variant',
	'non_coding_transcript_variant',
	'upstream_gene_variant',
	'downstream_gene_variant',
	'TFBS_ablation',
	'TFBS_amplification',
	'TF_binding_site_variant',
	'regulatory_region_ablation',
	'regulatory_region_amplification',
	'feature_elongation',
	'regulatory_region_variant',
	'feature_truncation',
	'intergenic_variant'
	]), 1)}

The error will crop up here:

bravo_api/bravo_api/models/readers.py

Line 103 in 7a52032

consequences = sorted(effect['Consequence'].split('&'), key = lambda x: snv_consequence2code[x], reverse = True)

Resolved when

A graceful method of handling consequences is implemented and demonstrated functioning with unit tests.