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Merge pull request #566 from VariantEffect/release-2025.5.0
Release 2025.5.0
2 parents 2fe0807 + 58c4744 commit 22ce49c

37 files changed

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‎.gitignore‎

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# Sphinx documentation build cache
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.doctrees/
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# IDEs and editors
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.vscode/
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# OS X folder view option files
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*.DS_Store

‎package-lock.json‎

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‎package.json‎

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{
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"name": "mavedb-ui",
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"version": "2025.4.5",
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"version": "2025.5.0",
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"private": true,
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"type": "module",
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"scripts": {

‎src/assets/layout.css‎

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}
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.mavedb-screen-title-controls .p-button {
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margin-right: 10px;
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margin-right: 0.25rem;
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}
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.mavedb-screen-title-controls .p-button:last-child {

‎src/components/AssayFactSheet.vue‎

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<div class="mavedb-assay-facts-label">Assay Type</div>
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<div class="mavedb-assay-facts-value">
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<div v-if="scoreSet.experiment.keywords?.some((k) => k.keyword.key === 'Phenotypic Assay Method')">
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{{ scoreSet.experiment.keywords.find((k) => k.keyword.key === 'Phenotypic Assay Method').keyword.label }}
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{{ scoreSet.experiment.keywords.find((k) => k.keyword.key === 'Phenotypic Assay Method')?.keyword.label }}
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</div>
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<div v-else>Not specified</div>
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</div>
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<div class="mavedb-assay-facts-value">
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<div v-if="scoreSet.experiment.keywords?.some((k) => k.keyword.key === 'Molecular Mechanism Assessed')">
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{{
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scoreSet.experiment.keywords.find((k) => k.keyword.key === 'Molecular Mechanism Assessed').keyword.label
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scoreSet.experiment.keywords.find((k) => k.keyword.key === 'Molecular Mechanism Assessed')?.keyword.label
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}}
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</div>
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<div v-else>Not specified</div>
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<div class="mavedb-assay-facts-label">Variant Consequences Detected</div>
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<div class="mavedb-assay-facts-value">
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<div v-if="scoreSet.experiment.keywords?.some((k) => k.keyword.key === 'Phenotypic Assay Mechanism')">
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{{ scoreSet.experiment.keywords.find((k) => k.keyword.key === 'Phenotypic Assay Mechanism').keyword.label }}
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{{
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scoreSet.experiment.keywords.find((k) => k.keyword.key === 'Phenotypic Assay Mechanism')?.keyword.label
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}}
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</div>
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<div v-else>Not specified</div>
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</div>
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<div class="mavedb-assay-facts-value">
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<div v-if="scoreSet.experiment.keywords?.some((k) => k.keyword.key === 'Phenotypic Assay Model System')">
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{{
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scoreSet.experiment.keywords.find((k) => k.keyword.key === 'Phenotypic Assay Model System').keyword.label
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scoreSet.experiment.keywords.find((k) => k.keyword.key === 'Phenotypic Assay Model System')?.keyword.label
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}}
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</div>
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<div v-else>Not specified</div>
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</div>
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</div>
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</div>
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<div class="mavedb-assay-facts-section-title">Clinical Performance</div>
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<div class="mavedb-assay-facts-section-title">
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Clinical Performance<sup v-if="!primaryScoreRangeIsInvestigatorProvided">*</sup>
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</div>
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<div class="mavedb-assay-facts-section">
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<div v-if="scoreSet.scoreRanges?.investigatorProvided?.ranges[0]?.oddsPath?.ratio">
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<div v-if="primaryScoreRange?.functionalRanges?.some((r) => r.oddspathsRatio)">
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<div class="mavedb-assay-facts-row">
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<div class="mavedb-assay-facts-label">OddsPath – Normal</div>
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<div
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v-if="scoreSet.scoreRanges?.investigatorProvided?.ranges?.some((r) => r.classification === 'normal')"
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v-if="primaryScoreRange?.functionalRanges?.some((r) => r.classification === 'normal' && r.oddspathsRatio)"
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class="mavedb-assay-facts-value"
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>
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{{
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roundOddsPath(
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scoreSet.scoreRanges.investigatorProvided.ranges.find((r) => r.classification === 'normal').oddsPath
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?.ratio
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)
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}}
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<span class="mavedb-classification-badge mavedb-blue">
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{{
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scoreSet.scoreRanges.investigatorProvided.ranges.find((r) => r.classification === 'normal').oddsPath
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?.evidence
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}}
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{{ roundOddsPath(normalScoreRange?.oddspathsRatio) }}
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<span
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:class="[
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'mavedb-classification-badge',
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`mave-evidence-code-${
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normalScoreRange?.acmgClassification
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? formatEvidenceCodeForScoreRange(normalScoreRange)
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: 'INDETERMINATE'
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}`
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]"
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>
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{{ formatEvidenceCodeForScoreRange(normalScoreRange) }}
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</span>
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</div>
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<div v-else class="mavedb-assay-facts-value">OddsPath normal not provided</div>
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</div>
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<div class="mavedb-assay-facts-row">
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<div class="mavedb-assay-facts-label">OddsPath – Abnormal</div>
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<div
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v-if="scoreSet.scoreRanges?.investigatorProvided?.ranges?.some((r) => r.classification === 'abnormal')"
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v-if="primaryScoreRange?.functionalRanges?.some((r) => r.classification === 'abnormal' && r.oddspathsRatio)"
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class="mavedb-assay-facts-value"
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>
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{{
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roundOddsPath(
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scoreSet.scoreRanges.investigatorProvided.ranges.find((r) => r.classification === 'abnormal').oddsPath
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?.ratio
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)
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}}
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<span class="mavedb-classification-badge mavedb-red strong">
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{{
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scoreSet.scoreRanges.investigatorProvided.ranges.find((r) => r.classification === 'abnormal').oddsPath
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?.evidence
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}}
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{{ roundOddsPath(abnormalScoreRange?.oddspathsRatio) }}
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<span
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:class="[
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'mavedb-classification-badge',
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`mave-evidence-code-${
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abnormalScoreRange?.acmgClassification
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? formatEvidenceCodeForScoreRange(abnormalScoreRange)
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: 'INDETERMINATE'
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}`
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]"
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>
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{{ formatEvidenceCodeForScoreRange(abnormalScoreRange) }}
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</span>
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</div>
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<div v-else class="mavedb-assay-facts-value">OddsPath abnormal not provided</div>
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</div>
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<div v-if="!primaryScoreRangeIsInvestigatorProvided" style="font-size: 10px; margin-top: 4px">
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<sup>*</sup>OddsPath data from non-primary source(s):
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<template v-if="oddsPathSources">
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(
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<template v-for="(s, i) in oddsPathSources" :key="s.url">
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<a :href="s.url" rel="noopener" target="_blank">{{ shortCitationForPublication(s) }}</a
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><span v-if="i < oddsPathSources.length - 1">, </span>
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</template>
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).
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</template>
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<template v-else>.</template>
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</div>
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</div>
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<div v-else>OddsPath values are not provided for this score set.</div>
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import {defineComponent, PropType} from 'vue'
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import {getScoreSetFirstAuthor} from '@/lib/score-sets'
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import {shortCitationForPublication} from '@/lib/publication'
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import type {components} from '@/schema/openapi'
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export default defineComponent({
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}
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},
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setup() {
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return {
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shortCitationForPublication
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}
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},
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computed: {
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firstAuthor: function () {
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const firstAuthor = getScoreSetFirstAuthor(this.scoreSet)
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default:
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return null
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}
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},
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primaryScoreRange: function () {
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if (this.scoreSet.scoreCalibrations == null) {
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return null
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}
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return (
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Object.values(this.scoreSet.scoreCalibrations).filter((sr) => sr?.primary)[0] ||
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this.scoreSet.scoreCalibrations?.find((sr) => sr?.investigatorProvided) ||
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null
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)
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},
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primaryScoreRangeIsInvestigatorProvided: function () {
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if (this.scoreSet.scoreCalibrations == null) {
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return false
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}
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return this.primaryScoreRange === this.scoreSet.scoreCalibrations?.find((sr) => sr?.investigatorProvided)
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},
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abnormalScoreRange: function () {
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return this.primaryScoreRange?.functionalRanges?.find((r) => r.classification === 'abnormal') || null
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},
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normalScoreRange: function () {
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return this.primaryScoreRange?.functionalRanges?.find((r) => r.classification === 'normal') || null
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},
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oddsPathSources() {
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return this.primaryScoreRange?.classificationSources
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},
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sources: function () {
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return this.scoreSet.primaryPublicationIdentifiers.concat(this.scoreSet.secondaryPublicationIdentifiers)
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}
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},
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methods: {
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roundOddsPath: function (oddsPath: number | undefined) {
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return oddsPath?.toPrecision(5)
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roundOddsPath: function (oddsPath: number | null | undefined) {
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return oddsPath?.toFixed(3)
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},
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formatEvidenceCodeForScoreRange: function (functionalRange: components['schemas']['FunctionalRange'] | null) {
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if (!functionalRange?.acmgClassification?.evidenceStrength) {
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return ''
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}
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const criterion = functionalRange.acmgClassification.criterion
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const strength = functionalRange.acmgClassification.evidenceStrength.toUpperCase()
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return `${criterion}_${strength}`
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}
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}
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})
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background: #991b1b;
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color: white;
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}
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/* Evidence Strengths */
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.mave-evidence-code-PS3_VERY_STRONG {
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background-color: #943744;
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font-weight: bold;
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}
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.mave-evidence-code-PS3_STRONG {
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background-color: #b85c6b;
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font-weight: bold;
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}
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.mave-evidence-code-PS3_MODERATE_PLUS {
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background-color: #ca7682;
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font-weight: bold;
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}
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.mave-evidence-code-PS3_MODERATE {
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background-color: #d68f99;
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font-weight: bold;
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}
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.mave-evidence-code-PS3_SUPPORTING {
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background-color: #e6b1b8;
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font-weight: bold;
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}
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.mave-evidence-code-BS3_SUPPORTING {
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background-color: #e4f1f6;
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font-weight: bold;
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}
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.mave-evidence-code-BS3_MODERATE {
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background-color: #d0e8f0;
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font-weight: bold;
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}
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.mave-evidence-code-BS3_MODERATE_PLUS {
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background-color: #99c8dc;
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font-weight: bold;
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}
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.mave-evidence-code-BS3_STRONG {
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background-color: #7ab5d1;
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font-weight: bold;
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}
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.mave-evidence-code-BS3_VERY_STRONG {
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background-color: #4b91a6;
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font-weight: bold;
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}
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.mave-evidence-code-INDETERMINATE {
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background-color: #e0e0e0;
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font-weight: bold;
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}
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</style>

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