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Merge pull request #455 from VariantEffect/release-2025.3.1
Release 2025.3.1
2 parents adba23d + 7ffea5f commit 406a104

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-246
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‎.env.dev‎

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@@ -2,3 +2,4 @@ VITE_API_URL=http://localhost:8002/api/v1
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VITE_APP_URL=https://127.0.0.1:8081
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VITE_SITE_TITLE=MaveDB (local API)
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VITE_CLINICAL_FEATURES_ENABLED=false
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VITE_PREVIEW_SITE=false

‎.env.live‎

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@@ -2,3 +2,4 @@ VITE_API_URL=https://api.mavedb.org/api/v1
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VITE_APP_URL=https://mavedb.org
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VITE_SITE_TITLE=MaveDB
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VITE_CLINICAL_FEATURES_ENABLED=false
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VITE_PREVIEW_SITE=false

‎.env.preview‎

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VITE_APP_URL=https://preview.mavedb.org
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VITE_SITE_TITLE=MaveDB (Preview Build)
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VITE_CLINICAL_FEATURES_ENABLED=true
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VITE_PREVIEW_SITE=true

‎.env.prodapi‎

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VITE_APP_URL=https://127.0.0.1:8081
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VITE_SITE_TITLE=MaveDB (prod API)
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VITE_CLINICAL_FEATURES_ENABLED=false
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VITE_PREVIEW_SITE=false

‎.env.staging‎

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@@ -2,3 +2,4 @@ VITE_API_URL=https://api.staging.mavedb.org/api/v1
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VITE_APP_URL=https://staging.mavedb.org
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VITE_SITE_TITLE=MaveDB (Staging)
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VITE_CLINICAL_FEATURES_ENABLED=false
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VITE_PREVIEW_SITE=false

‎src/assets/logo-mavedb-beta.png‎

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‎src/components/AssayFactSheet.vue‎

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<template>
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<div class="nutrition-card">
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<div class="nutrition-card-header">
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<span class="nutrition-author">{{ authorLine }}</span>
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</div>
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<div class="nutrition-section bottom-line">
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<div class="nutrition-row">
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<div class="nutrition-label">Gene (HGNC symbol)</div>
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<div class="nutrition-value">{{ scoreSet.targetGenes[0]?.name }}</div>
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</div>
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</div>
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<div class="nutrition-section">
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<div class="nutrition-row">
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<div class="nutrition-label">Assay Type</div>
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<div class="nutrition-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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</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 class="nutrition-row">
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<div class="nutrition-label">Molecular Mechanism Assessed</div>
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<div class="nutrition-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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</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 class="nutrition-row">
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<div class="nutrition-label">Model System</div>
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<div class="nutrition-value">
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<div
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v-if="scoreSet.experiment.keywords?.some((k) => k.keyword.key === 'Phenotypic Assay Model System')">
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{{ scoreSet.experiment.keywords.find((k) => k.keyword.key === "Phenotypic Assay Model System").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>
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<!--
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<div class="nutrition-row">
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<div class="nutrition-label">Detects Splicing Variants?</div>
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<div class="nutrition-value" :class="{ yellow: scoreSet.detectsSplicing === 'No' }">
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{{ scoreSet.detectsSplicing || "Yes" }}
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</div>
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</div>
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<div class="nutrition-row">
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<div class="nutrition-label">Detects NMD Variants?</div>
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<div class="nutrition-value" :class="{ yellow: scoreSet.detectsNmd === 'No' }">
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{{ scoreSet.detectsNmd || "Yes" }}
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</div>
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</div>
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-->
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<div class="nutrition-row">
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<div class="nutrition-label">Number of Variants</div>
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<div class="nutrition-value">
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<div>{{ scoreSet.numVariants }}</div>
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</div>
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</div>
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</div>
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<div class="nutrition-section-title">Clinical Performance</div>
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<div class="nutrition-section">
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<div v-if="scoreSet.scoreRanges?.investigatorProvided?.ranges[0]?.oddsPath?.ratio">
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<div class="nutrition-row">
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<div class="nutrition-label">OddsPath – Normal</div>
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<div class="nutrition-value" v-if="scoreSet.scoreRanges?.investigatorProvided?.ranges?.some((r) => r.classification === 'normal')">
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{{ scoreSet.scoreRanges.investigatorProvided.ranges.find((r) => r.classification === "normal").oddsPath?.ratio }}
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<span class="badge blue">
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{{ scoreSet.scoreRanges.investigatorProvided.ranges.find((r) => r.classification === "normal").oddsPath?.evidence }}
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</span>
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</div>
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</div>
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<div class="nutrition-row">
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<div class="nutrition-label">OddsPath – Abnormal</div>
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<div class="nutrition-value" v-if="scoreSet.scoreRanges?.investigatorProvided?.ranges?.some((r) => r.classification === 'abnormal')">
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{{ scoreSet.scoreRanges.investigatorProvided.ranges.find((r) => r.classification === "abnormal").oddsPath?.ratio }}
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<span class="badge strong red">
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{{ scoreSet.scoreRanges.investigatorProvided.ranges.find((r) => r.classification === "abnormal").oddsPath?.evidence }}
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</span>
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</div>
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</div>
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</div>
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<div v-else>
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OddsPath values are not provided for this score set.
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</div>
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</div>
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</div>
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</template>
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<script>
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import { defineComponent, computed } from 'vue'
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export default defineComponent({
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name: 'AssayFactSheet',
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props: {
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scoreSet: {
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type: Object,
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required: true
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},
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},
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computed: {
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authorLine: function(){
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const author = this.scoreSet.primaryPublicationIdentifiers[0]?.authors[0].name
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const gene = this.scoreSet.targetGenes?.[0]?.name || ""
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const year = this.scoreSet.primaryPublicationIdentifiers[0]?.publicationYear || ""
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if (author && author.length > 0) {
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return `${author} et al. ${gene} ${year}`
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}
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return `${gene} ${year}`
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}
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}
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})
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</script>
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<style scoped>
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/* Nutrition label */
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.nutrition-author {
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font-size: 21px;
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}
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.nutrition-card {
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width: 580px; /* fixed size */
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border: 1px solid #000;
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padding: 12px;
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font-family: sans-serif;
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font-size: 14px;
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line-height: 1.4;
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}
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.nutrition-card-header {
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font-weight: bold;
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border-bottom: 3px solid #000;
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padding-bottom: 4px;
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margin-bottom: 8px;
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}
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.nutrition-section {
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margin-bottom: 12px;
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}
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.nutrition-section-title {
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font-weight: bold;
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margin: 6px 0;
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border-top: 1.0px solid #3e3d3dbb;
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padding-top: 4px;
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font-size: 16px;
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font-weight: bold;
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}
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.nutrition-row {
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display: flex;
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justify-content: space-between;
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margin: 2px 0;
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}
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.nutrition-label {
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font-weight: bold;
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flex: 1;
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}
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.nutrition-value {
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flex: 1;
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text-align: left;
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}
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.nutrition-value.yellow {
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background: #fef3c7;
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padding: 2px 4px;
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border-radius: 4px;
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}
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.badge {
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display: inline-block;
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padding: 2px 6px;
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border-radius: 4px;
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font-size: 12px;
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font-weight: bold;
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margin-left: 4px;
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}
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.badge.blue {
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background: #1e40af;
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color: white;
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}
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.badge.red {
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background: #991b1b;
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color: white;
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}
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.bottom-line{
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border-bottom: 1px solid #3e3d3dbb;
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}
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</style>

‎src/components/RangeTable.vue‎

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}
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table.mave-range-table td.mave-evidence-code-PS3_VERY_STRONG {
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background-color: #7b1910;
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color: white;
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background-color: #943744;
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font-weight: bold;
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}
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table.mave-range-table td.mave-evidence-code-PS3_STRONG {
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background-color: #b02418;
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color: white;
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background-color: #D68F99;
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font-weight: bold;
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}
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table.mave-range-table td.mave-evidence-code-PS3_MODERATE+ {
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background-color: #ba6e68;
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color: white;
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background-color: #E6B1B8;
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font-weight: bold;
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}
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table.mave-range-table td.mave-evidence-code-PS3_MODERATE {
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background-color: #cf7b74;
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color: white;
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background-color: #F0D0D5;
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font-weight: bold;
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}
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table.mave-range-table td.mave-evidence-code-PS3_SUPPORTING {
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background-color: #e7bdb9;
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color: white;
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background-color: #F7E4E7;
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font-weight: bold;
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}
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table.mave-range-table td.mave-evidence-code-BS3_VERY_STRONG {
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background-color: #2c4374;
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color: white;
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background-color: #7AB5D1;
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font-weight: bold;
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}
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table.mave-range-table td.mave-evidence-code-BS3_STRONG {
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background-color: #385492;
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color: white;
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background-color: #E4F1F6;
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font-weight: bold;
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}
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table.mave-range-table td.mave-evidence-code-BS3_MODERATE+ {
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background-color: #5f76a7;
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color: white;
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background-color: #EDF6FA;
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font-weight: bold;
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}
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table.mave-range-table td.mave-evidence-code-BS3_MODERATE {
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background-color: #7387b2;
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color: white;
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background-color: #F4F9FC;
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font-weight: bold;
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}
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table.mave-range-table td.mave-evidence-code-BS3_SUPPORTING {
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background-color: #c3cbde;
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color: white;
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background-color: #F9FCFE;
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font-weight: bold;
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}
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table.mave-range-table td.mave-evidence-code-BS3_INDETERMINATE {
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background-color: #d9cb00;
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color: white;
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table.mave-range-table td.mave-evidence-code-INDETERMINATE {
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background-color: #c3cbde;
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font-weight: bold;
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}
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table.mave-range-table td.mave-evidence-code-undefined {
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background-color: #7b7b7b;
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color: white;
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background-color: #E0E0E0;
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font-weight: bold;
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}
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