Primary Score Ranges

src/components/AssayFactSheet.vue

@@ -77,48 +77,63 @@
         </div>
       </div>
     </div>
-    <div class="mavedb-assay-facts-section-title">Clinical Performance</div>
+    <div class="mavedb-assay-facts-section-title">
+      Clinical Performance<sup v-if="!primaryScoreRangeIsInvestigatorProvided">*</sup>
+    </div>
     <div class="mavedb-assay-facts-section">
-      <div v-if="scoreSet.scoreRanges?.investigatorProvided?.ranges[0]?.oddsPath?.ratio">
+      <div v-if="primaryScoreRange?.ranges.some((r) => r.oddsPath)">
         <div class="mavedb-assay-facts-row">
           <div class="mavedb-assay-facts-label">OddsPath – Normal</div>
           <div
-            v-if="scoreSet.scoreRanges?.investigatorProvided?.ranges?.some((r) => r.classification === 'normal')"
+            v-if="primaryScoreRange?.ranges?.some((r) => r.classification === 'normal' && r.oddsPath)"
             class="mavedb-assay-facts-value"
           >
             {{
               roundOddsPath(
-                scoreSet.scoreRanges.investigatorProvided.ranges.find((r) => r.classification === 'normal').oddsPath
+                primaryScoreRange?.ranges.find((r) => r.classification === 'normal').oddsPath
                   ?.ratio
               )
             }}
             <span class="mavedb-classification-badge mavedb-blue">
               {{
-                scoreSet.scoreRanges.investigatorProvided.ranges.find((r) => r.classification === 'normal').oddsPath
+                primaryScoreRange?.ranges.find((r) => r.classification === 'normal').oddsPath
                   ?.evidence
               }}
             </span>
           </div>
+          <div v-else class="mavedb-assay-facts-value">OddsPath normal not provided</div>
         </div>
         <div class="mavedb-assay-facts-row">
           <div class="mavedb-assay-facts-label">OddsPath – Abnormal</div>
           <div
-            v-if="scoreSet.scoreRanges?.investigatorProvided?.ranges?.some((r) => r.classification === 'abnormal')"
+            v-if="primaryScoreRange?.ranges?.some((r) => r.classification === 'abnormal' && r.oddsPath)"
             class="mavedb-assay-facts-value"
           >
             {{
               roundOddsPath(
-                scoreSet.scoreRanges.investigatorProvided.ranges.find((r) => r.classification === 'abnormal').oddsPath
+                primaryScoreRange?.ranges.find((r) => r.classification === 'abnormal').oddsPath
                   ?.ratio
               )
             }}
             <span class="mavedb-classification-badge mavedb-red strong">
               {{
-                scoreSet.scoreRanges.investigatorProvided.ranges.find((r) => r.classification === 'abnormal').oddsPath
+                primaryScoreRange?.ranges.find((r) => r.classification === 'abnormal').oddsPath
                   ?.evidence
               }}
             </span>
           </div>
+          <div v-else class="mavedb-assay-facts-value">OddsPath abnormal not provided</div>
+        </div>
+        <div v-if="!primaryScoreRangeIsInvestigatorProvided" style="font-size: 10px; margin-top: 4px">
+            <sup>*</sup>OddsPath data from non-primary source(s):
+            <template v-if="oddsPathSources">
+              (
+              <template v-for="(s,i) in oddsPathSources" :key="s.url">
+              <a :href="s.url" rel="noopener" target="_blank">{{ s.url }}</a><span v-if="i < oddsPathSources.length - 1">, </span>
+              </template>
+              ).
+            </template>
+            <template v-else>.</template>
         </div>
       </div>
       <div v-else>OddsPath values are not provided for this score set.</div>
@@ -130,7 +145,7 @@
 import _ from 'lodash'
 import {defineComponent, PropType} from 'vue'
 
-import {getScoreSetFirstAuthor} from '@/lib/score-sets'
+import {getScoreSetFirstAuthor, matchSources} from '@/lib/score-sets'
 import type {components} from '@/schema/openapi'
 
 export default defineComponent({
@@ -204,13 +219,38 @@ export default defineComponent({
         default:
           return null
       }
+    },
+
+    primaryScoreRange: function () {
+      if (this.scoreSet.scoreRanges == null) {
+        return null
+      }
+
+      return Object.values(this.scoreSet.scoreRanges).filter(
+          (sr) => sr?.primary
+        )[0] || this.scoreSet.scoreRanges?.investigatorProvided || null
+    },
+
+    primaryScoreRangeIsInvestigatorProvided: function () {
+      if (this.scoreSet.scoreRanges == null) {
+        return false
+      }
+
+      return this.primaryScoreRange === this.scoreSet.scoreRanges?.investigatorProvided
+    },
+    oddsPathSources() {
+      console.log(this.primaryScoreRange)
+      return matchSources(this.primaryScoreRange?.oddsPathSource, this.sources)
+    },
+    sources: function () {
+      return this.scoreSet.primaryPublicationIdentifiers.concat(this.scoreSet.secondaryPublicationIdentifiers)
     }
   },
 
   methods: {
     roundOddsPath: function (oddsPath: number | undefined) {
       return oddsPath?.toPrecision(5)
-    }
+    },
   }
 })
 </script>

src/components/RangeTable.vue

@@ -136,6 +136,10 @@ import Button from 'primevue/button'
 import {defineComponent, PropType} from 'vue'
 
 import {EVIDENCE_STRENGTHS_REVERSED, ScoreRanges, ScoreRange} from '@/lib/ranges'
+import {matchSources} from '@/lib/score-sets'
+import {components} from '@/schema/openapi'
+
+type PublicationIdentifiers = components['schemas']['ScoreSet']['primaryPublicationIdentifiers'][0]
 
 export default defineComponent({
   name: 'RangeTable',
@@ -152,7 +156,7 @@ export default defineComponent({
       required: true
     },
     sources: {
-      type: Array as PropType<{dbName: string; identifier: string; url: string}[]>,
+      type: Array as PropType<PublicationIdentifiers[]>,
       required: false,
       default: () => []
     }
@@ -198,10 +202,10 @@ export default defineComponent({
       return [...this.scoreRanges.ranges].sort(this.compareScoreRanges)
     },
     thresholdSources() {
-      return this.matchSources(this.scoreRanges.source)
+      return matchSources(this.scoreRanges.source, this.sources)
     },
     oddsPathSources() {
-      return this.matchSources(this.scoreRanges.oddsPathSource)
+      return matchSources(this.scoreRanges.oddsPathSource, this.sources)
     }
   },
 
@@ -238,17 +242,6 @@ export default defineComponent({
         .replace(/[-_]+(.)/g, (_, c) => ' ' + c.toUpperCase())
         .replace(/([a-z])([A-Z])/g, '$1 $2')
     },
-    matchSources(
-      sourceArr: Array<{dbName: string; identifier: string}> | undefined
-    ): {dbName: string; identifier: string; url: string}[] | null {
-      if (!Array.isArray(sourceArr) || !this.sources) return null
-      const matchedSources = []
-      for (const source of sourceArr) {
-        const match = this.sources.find((s) => s.dbName === source.dbName && s.identifier === source.identifier)
-        if (match) matchedSources.push(match)
-      }
-      return matchedSources.length > 0 ? matchedSources : null
-    },
     roundOddsPath(rangeBound: number) {
       return rangeBound.toPrecision(3)
     },

src/components/ScoreSetHistogram.vue

@@ -117,7 +117,7 @@
   <div v-if="showRanges && activeRange" class="mave-range-table-container">
     <Accordion collapse-icon="pi pi-minus" expand-icon="pi pi-plus">
       <AccordionTab class="mave-range-table-tab" header="Score Range Details">
-        <RangeTable :score-ranges="activeRange" :score-ranges-name="activeRangeKey?.label" :sources="allSources" />
+        <RangeTable :score-ranges="activeRange" :score-ranges-name="activeRangeKey.label" :sources="allSources" />
       </AccordionTab>
     </Accordion>
   </div>
@@ -251,7 +251,7 @@ export default defineComponent({
 
       activeViz: 0,
       showRanges: scoreSetHasRanges,
-      activeRangeKey: null as {label: string; value: string} | null,
+      activeRangeKey: {label: 'None', value: null} as {label: string; value: string | null},
 
       clinicalControls: [] as ClinicalControl[],
       clinicalControlOptions: [] as ClinicalControlOption[],
@@ -710,7 +710,7 @@ export default defineComponent({
           // Line 3: Score and classification
           if (variant.score) {
             let binClassificationLabel = ''
-            if (bin && this.activeRangeKey && this.activeRange) {
+            if (bin && this.activeRangeKey.value && this.activeRange) {
               // TODO#491: Refactor this calculation into the creation of variant objects so we may just access the property of the variant which tells us its classification.
               const binClassification = this.histogramShaders[this.activeRangeKey.value]?.find(
                 (range: HistogramShader) => shaderOverlapsBin(range, bin)
@@ -731,7 +731,7 @@ export default defineComponent({
           parts.push(`Bin range: ${bin.x0} to ${bin.x1}`)
 
           //Line 6: Bin Classification
-          if (this.activeRangeKey && this.activeRange) {
+          if (this.activeRangeKey.value && this.activeRange) {
             // TODO#491: Refactor this calculation into the creation of histogram bins so we don't need to repeat it every time we construct a tooltip.
             const binClassifications = this.histogramShaders[this.activeRangeKey.value]?.filter(
               (range: HistogramShader) => shaderOverlapsBin(range, bin)
@@ -980,7 +980,7 @@ export default defineComponent({
 
       // Only render clinical specific viz options if such features are enabled.
       if (this.config.CLINICAL_FEATURES_ENABLED && this.showRanges) {
-        this.histogram.renderShader(this.activeRangeKey?.value)
+        this.histogram.renderShader(this.activeRangeKey.value)
       } else {
         this.histogram.renderShader(null)
       }
@@ -1101,18 +1101,18 @@ export default defineComponent({
     },
 
     defaultRangeKey: function () {
-      if (this.activeRangeKey) {
+      if (this.activeRangeKey.value) {
         return this.activeRangeKey
       }
 
-      const defaultInvestigatorProvidedIndex = this.activeRangeOptions.findIndex(
-        (option) => option.value == 'investigatorProvided'
-      )
+      const primaryRange = this.activeRanges ? Object.entries(this.activeRanges).find(([, v]) => v.primary) : null
+      const primaryRangeKey = primaryRange ? primaryRange[0] : null
 
-      if (defaultInvestigatorProvidedIndex >= 0) {
-        return this.activeRangeOptions[defaultInvestigatorProvidedIndex]
+      // use the primary range if it exists, otherwise use investigatorProvided if it exists, otherwise none.
+      if (primaryRangeKey) {
+        return this.activeRangeOptions.find((option) => option.value === primaryRangeKey) || {label: 'None', value: null}
       } else if (this.activeRangeOptions.length > 0) {
-        return {label: 'None', value: null} // return this.activeRangeOptions[0]
+        return this.activeRangeOptions.find((option) => option.value === "investigatorProvided") || {label: 'None', value: null}
       } else {
         return {label: 'None', value: null}
       }

src/lib/ranges.ts

@@ -40,13 +40,16 @@ export interface pillarProjectParameterSet {
 // but we allow their implicit possibility as well.
 export interface ScoreSetRanges {
   investigatorProvided: ScoreRanges
-  pillarProject: ScoreRanges
+  zeibergCalibration: ScoreRanges
+  scottCalibration: ScoreRanges
+  fayerCalibration: ScoreRanges
   [key: string]: ScoreRanges
 }
 
 export interface ScoreRanges {
   title: string
   researchUseOnly: boolean
+  primary?: boolean
   baselineScore?: number
   baselineScoreDescription?: string | undefined
   oddsPathSource?: [{ identifier: string; dbName: string }] | undefined

src/lib/score-sets.ts

@@ -1,8 +1,9 @@
 import _ from 'lodash'
 
-import type {components} from '@/schema/openapi'
+import type { components } from '@/schema/openapi'
 
 type ScoreSet = components['schemas']['ScoreSet']
+type PublicationIdentifier = components['schemas']['ScoreSet']['primaryPublicationIdentifiers'][0]
 type Author = components["schemas"]["PublicationAuthors"]
 
 /**
@@ -51,3 +52,37 @@ export function getScoreSetShortName(scoreSet: ScoreSet): string {
   const parts = [authors, gene, year?.toString()].filter((x) => x != null)
   return parts.length > 0 ? parts.join(' ') : (scoreSet.title ?? scoreSet.shortDescription ?? 'Score set')
 }
+
+
+
+/**
+ * Filters a collection of publication identifier objects and returns only those
+ * that match the dbName + identifier pairs provided in a source array.
+ *
+ * Each element in sourceArr is treated as a (dbName, identifier) criterion. The
+ * function searches the sources list for exact matches (both dbName and
+ * identifier must match) and returns the subset that satisfies at least one
+ * criterion. If no matches are found, or if either input is missing/invalid,
+ * null is returned.
+ *
+ * Matching preserves the original objects from the sources list (it does not
+ * clone or transform them) and maintains the order in which matching criteria
+ * appear in sourceArr (not the original order in sources).
+ *
+ *
+ * @param sourceArr An array of (dbName, identifier) pairs to match against the sources list. If not an array, the function returns null.
+ * @param sources A list of publication identifiers to search (e.g., fetched from an API). Must support Array.prototype.find; if undefined, returns null.
+ * @returns An array of matched publication identifiers (in the order of the matching criteria) or null if there are no matches or inputs are invalid.
+ */
+export function matchSources(
+  sourceArr: Array<{ dbName: string; identifier: string }> | undefined,
+  sources: PublicationIdentifier[] | undefined
+): PublicationIdentifier[] | null {
+  if (!Array.isArray(sourceArr) || !sources) return null
+  const matchedSources = []
+  for (const source of sourceArr) {
+    const match = sources.find((s) => s.dbName === source.dbName && s.identifier === source.identifier)
+    if (match) matchedSources.push(match)
+  }
+  return matchedSources.length > 0 ? matchedSources : null
+}