hide leading 1 for offset PositionalVariants

[mathieulemieux]

From JIRA https://www.bcgsc.ca/jira/browse/KBDEV-990

Problem:
PositionalVariant with a negative offset from the 1st position should hide the position '1' in their displayName as per HGVS standards (https://varnomen.hgvs.org/bg-material/numbering/), which is not the case at the moment.

Ex.:
"CEP72:c.1-2384C>T" should read "CEP72:c.-2384C>T"

Context:
When a PositionalVariant is added to GraphKB (let say through the web client interface, which uses the '/positionalvariants' POST route), the payload doesn't contain a displayName, neither a break1Repr nor a break2Repr. The parser is then used to format these fields.

[mathieulemieux]

@creisle & @elewis2 ,

Following the issue's description, when a POST request is sent to the GraphKB Api on the '/positionalvariants' route, the create() function is called (pori_graphkb_api/src/repo/commands/create.js), which will eventually lead to the GraphKB Parser :

1- the convertPositionToString() function will provide values for the break1Repr and break2Repr properties:

pori_graphkb_parser/src/position.ts

Lines 179 to 207 in 139af0d

	const convertPositionToString = (position) => {
	if (position.prefix === 'y') {
	let result = `${position.arm}`;
	if (position.majorBand !== undefined) {
	result = `${result}${position.majorBand || '?'}`;
	if (position.minorBand !== undefined) {
	result = `${result}.${position.minorBand || '?'}`;
	}
	}
	return result;
	} if (['c', 'r', 'n'].includes(position.prefix)) {
	let offset = '';
	if (position.offset === null) {
	offset = '?';
	} else if (position.offset) {
	if (position.offset > 0) {
	offset = '+';
	}
	offset = `${offset}${position.offset}`;
	}
	return `${position.pos || '?'}${offset}`;
	} if (position.prefix === 'p') {
	return `${position.refAA || '?'}${position.pos || '?'}`;
	}
	return `${position.pos || '?'}`;
	};

2- based in part on those properties, the stringifyVariant() function will provide the displayName's value:

pori_graphkb_parser/src/variant.ts

Lines 206 to 292 in 139af0d

	const stringifyVariant = (variant: VariantNotation): string => {
	const {
	multiFeature,
	noFeatures,
	reference1,
	reference2,
	break1Repr,
	break2Repr,
	untemplatedSeq,
	untemplatedSeqSize,
	truncation,
	refSeq,
	type,
	} = variant;
	let { notationType } = variant;
	if (notationType === undefined) {
	const variantType = ontologyTermRepr(type);
	notationType = TYPES_TO_NOTATION[variantType] || variantType.replace(/\s+/, '-');
	}
	const isMultiRef = multiFeature || (reference2 && (reference1 !== reference2));
	if (isMultiRef) {
	if (!break2Repr) {
	throw new InputValidationError('Multi-feature notation requires break2Repr');
	}
	// multi-feature notation
	let result = noFeatures
	? ''
	: `(${reference1},${reference2}):`;
	result = `${result}${notationType}(${stripParentheses(break1Repr)},${stripParentheses(break2Repr)})`;
	if (untemplatedSeq !== undefined) {
	result = `${result}${untemplatedSeq}`;
	} else if (untemplatedSeqSize !== undefined) {
	result = `${result}${untemplatedSeqSize}`;
	}
	return result;
	}
	// continuous notation
	const result: string[] = [];
	if (!noFeatures && !noFeatures) {
	result.push(`${reference1}:`);
	}
	result.push(break1Repr);
	if (break2Repr) {
	result.push(`_${break2Repr.slice(2)}`);
	}
	if (
	['ext', 'fs'].includes(notationType)
	|| (notationType === '>' && break1Repr.startsWith('p.'))
	) {
	if (untemplatedSeq) {
	result.push(untemplatedSeq);
	}
	}
	if (notationType === 'mis' && untemplatedSeq && break1Repr.startsWith('p.')) {
	result.push(untemplatedSeq);
	} else if (notationType !== '>') {
	if (notationType === 'delins') {
	result.push(`del${refSeq || ''}ins`);
	} else {
	result.push(notationType);
	}
	if (truncation && truncation !== 1) {
	if (truncation < 0) {
	result.push(`${truncation}`);
	} else {
	result.push(`*${truncation}`);
	}
	}
	if (refSeq && ['dup', 'del', 'inv'].includes(notationType)) {
	result.push(refSeq);
	}
	if ((untemplatedSeq || untemplatedSeqSize) && ['ins', 'delins'].includes(notationType)) {
	result.push(`${untemplatedSeq || untemplatedSeqSize}`);
	}
	} else if (!break1Repr.startsWith('p.')) {
	result.push(`${refSeq || '?'}${notationType}${untemplatedSeq || '?'}`);
	}
	return result.join('');
	};

Question:
Should we modify the break1Repr/break2Repr so the leading '1' is hidden, or would it be wiser to let these properties as is, and only change the displayName?

[mathieulemieux]

Here are the implementation of the 2 proposed solutions:

• Feature/hide leading 1 for offset positionalvariants 17 #18
• Feature/hide leading 1 for offset positionalvariants 17 stringifyvariant #19