diff --git a/frontend/src/components/SvDetails/AcmgRating.vue b/frontend/src/components/SvDetails/AcmgRating.vue index 45143333..e132f4b8 100644 --- a/frontend/src/components/SvDetails/AcmgRating.vue +++ b/frontend/src/components/SvDetails/AcmgRating.vue @@ -24,7 +24,7 @@ const resetAcmgRating = () => { if (!acmgRatingStore.acmgRating) { return } - acmgRatingStore.acmgRating.setUserPresenceAutoCNV() + acmgRatingStore.acmgRating.setUserToAutoCNV() } const calculateAcmgClass = computed((): string => { @@ -66,7 +66,6 @@ const switchCriteria = ( acmgRatingStore.acmgRating.setPresence(StateSourceCNV.User, criteria, Presence.Absent) } else { acmgRatingStore.acmgRating.setPresence(StateSourceCNV.User, criteria, Presence.Present) - console.log('setPresence, ', criteria, acmgRatingStore.acmgRating.getCriteriaCNVState(criteria)) } } @@ -128,17 +127,24 @@ const switchCriteria = ( acmgRatingStore.acmgRating.getCriteriaCNVState(criteria).presence ) " + color="primary" hide-details="auto" density="compact" class="switch" > + {{ acmgRatingStore.acmgRating.getCriteriaCNVState(criteria) }}
= 0.99 diff --git a/frontend/src/stores/svAcmgRating.ts b/frontend/src/stores/svAcmgRating.ts index 7df4d422..85bbc3be 100644 --- a/frontend/src/stores/svAcmgRating.ts +++ b/frontend/src/stores/svAcmgRating.ts @@ -4,8 +4,11 @@ import { defineStore } from 'pinia' import { ref } from 'vue' -import { API_INTERNAL_BASE_PREFIX } from '@/api/common' +// import { API_INTERNAL_BASE_PREFIX } from '@/api/common' import { + ACMG_CRITERIA_CNV_DEFS, + ACMG_CRITERIA_CNV_GAIN, + ACMG_CRITERIA_CNV_LOSS, AcmgCriteriaCNVGain, AcmgCriteriaCNVLoss, MultiSourceAcmgCriteriaCNVState, @@ -15,7 +18,7 @@ import { import { StoreState } from '@/stores/misc' import { type SvRecord } from '@/stores/svInfo' -const API_BASE_URL = API_INTERNAL_BASE_PREFIX +// const API_BASE_URL = API_INTERNAL_BASE_PREFIX export const useSvAcmgRatingStore = defineStore('svAcmgRating', () => { /** The current store state. */ @@ -38,14 +41,17 @@ export const useSvAcmgRatingStore = defineStore('svAcmgRating', () => { svRecord.value = null } - /** - * Capitalize the first letter of a string. + /** Helper function to get Enum key based on Enum value. * - * @param string The string to capitalize. - * @returns The capitalized string. + * @param myEnum The enum to search in. + * @param enumValue The enum value to search for. */ - function capitalizeFirstLetter(string: string): string { - return string.charAt(0).toUpperCase() + string.slice(1) + function getEnumKeyByEnumValue( + myEnum: T, + enumValue: string + ): keyof T | null { + const keys = Object.keys(myEnum).filter((x) => myEnum[x] == enumValue) + return keys.length > 0 ? keys[0] : null } /** @@ -68,46 +74,88 @@ export const useSvAcmgRatingStore = defineStore('svAcmgRating', () => { // Load data from AutoCNV via API storeState.value = StoreState.Loading try { - const chromosome = svRec.chromosome.replace('chr', '') - const start = svRec.start - const end = svRec.end - const svType = svRec.svType === 'DUP' ? 'dup' : 'del' - const response = await fetch( - `${API_BASE_URL}remote/cnv/acmg/?chromosome=${chromosome}&start=${start}&end=${end}&func=${svType}`, - { method: 'GET' } - ) - if (!response.ok) { - throw new Error('There was an error loading the ACMG data.') - } - const acmgRatingAutoCNVData = await response.json() + // const chromosome = svRec.chromosome.replace('chr', '') + // const start = svRec.start + // const end = svRec.end + // const svType = svRec.svType === 'DUP' ? 'dup' : 'del' + // const response = await fetch( + // `${API_BASE_URL}remote/cnv/acmg/?chromosome=${chromosome}&start=${start}&end=${end}&func=${svType}`, + // { method: 'GET' } + // ) + // if (!response.ok) { + // throw new Error('There was an error loading the ACMG data.') + // } + // const acmgRatingAutoCNVData = await response.json() // Go through the data and setPresense for each criteria - for (const [criteriaId, value] of Object.entries(acmgRatingAutoCNVData)) { - const criteriaIdKey = capitalizeFirstLetter(criteriaId) - if (value === true) { + // for (const [criteriaId, value] of Object.entries(acmgRatingAutoCNVData)) { + // const criteriaIdKey = capitalizeFirstLetter(criteriaId) + // if (value === true) { + // acmgRating.value.setPresence( + // StateSourceCNV.AutoCNV, + // svRec.svType === 'DUP' + // ? AcmgCriteriaCNVGain[criteriaIdKey as keyof typeof AcmgCriteriaCNVGain] + // : AcmgCriteriaCNVLoss[criteriaIdKey as keyof typeof AcmgCriteriaCNVLoss], + // Presence.Present + // ) + // acmgRating.value.setScore( + // StateSourceCNV.AutoCNV, + // svRec.svType === 'DUP' + // ? AcmgCriteriaCNVGain[criteriaIdKey as keyof typeof AcmgCriteriaCNVGain] + // : AcmgCriteriaCNVLoss[criteriaIdKey as keyof typeof AcmgCriteriaCNVLoss], + // 0 + // ) + // } else { + // acmgRating.value.setPresence( + // StateSourceCNV.AutoCNV, + // svRec.svType === 'DUP' + // ? AcmgCriteriaCNVGain[criteriaIdKey as keyof typeof AcmgCriteriaCNVGain] + // : AcmgCriteriaCNVLoss[criteriaIdKey as keyof typeof AcmgCriteriaCNVLoss], + // Presence.Absent + // ) + // } + // } + + // Set presence for all criteria to absent and score to default + if (svRec.svType === 'DUP') { + for (const criteria of ACMG_CRITERIA_CNV_GAIN) { + const criteriaKey = getEnumKeyByEnumValue(AcmgCriteriaCNVGain, criteria) acmgRating.value.setPresence( StateSourceCNV.AutoCNV, - svRec.svType === 'DUP' - ? AcmgCriteriaCNVGain[criteriaIdKey as keyof typeof AcmgCriteriaCNVGain] - : AcmgCriteriaCNVLoss[criteriaIdKey as keyof typeof AcmgCriteriaCNVLoss], - Presence.Present + AcmgCriteriaCNVGain[criteriaKey as keyof typeof AcmgCriteriaCNVGain], + Presence.Absent ) + const criteriaDef = ACMG_CRITERIA_CNV_DEFS.get(criteria) + if (criteriaDef === undefined) { + throw new Error('There was an error loading the ACMG data.') + } acmgRating.value.setScore( StateSourceCNV.AutoCNV, - svRec.svType === 'DUP' - ? AcmgCriteriaCNVGain[criteriaIdKey as keyof typeof AcmgCriteriaCNVGain] - : AcmgCriteriaCNVLoss[criteriaIdKey as keyof typeof AcmgCriteriaCNVLoss], - 0 + AcmgCriteriaCNVGain[criteriaKey as keyof typeof AcmgCriteriaCNVGain], + criteriaDef.defaultScore ) - } else { + } + acmgRating.value.setUserToAutoCNV() + } else if (svRec.svType === 'DEL') { + for (const criteria of ACMG_CRITERIA_CNV_LOSS) { + const criteriaKey = getEnumKeyByEnumValue(AcmgCriteriaCNVLoss, criteria) acmgRating.value.setPresence( StateSourceCNV.AutoCNV, - svRec.svType === 'DUP' - ? AcmgCriteriaCNVGain[criteriaIdKey as keyof typeof AcmgCriteriaCNVGain] - : AcmgCriteriaCNVLoss[criteriaIdKey as keyof typeof AcmgCriteriaCNVLoss], + AcmgCriteriaCNVLoss[criteriaKey as keyof typeof AcmgCriteriaCNVLoss], Presence.Absent ) + const criteriaDef = ACMG_CRITERIA_CNV_DEFS.get(criteria) + if (criteriaDef === undefined) { + throw new Error('There was an error loading the ACMG data.') + } + acmgRating.value.setScore( + StateSourceCNV.AutoCNV, + AcmgCriteriaCNVLoss[criteriaKey as keyof typeof AcmgCriteriaCNVLoss], + criteriaDef.defaultScore + ) } + acmgRating.value.setUserToAutoCNV() } + svRecord.value = svRec storeState.value = StoreState.Active } catch (e) {