update data, fix head and neck

Author: Vincent-J-Z

.claude/settings.local.json

@@ -0,0 +1,7 @@
+{
+  "permissions": {
+    "allow": [
+      "Bash(python3:*)"
+    ]
+  }
+}

CLAUDE.md

@@ -0,0 +1,83 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+TrialMap is a Vue.js 3 SPA that helps researchers optimize clinical trial eligibility criteria using real-world EHR data. It guides users through a 4-step wizard to select a cancer type, trial, endpoint, and eligibility criteria, then visualizes optimized pathway combinations.
+
+Deployed to GitHub Pages at `/TrialMap/` base path. All source code lives in the `web/` subdirectory.
+
+## Commands
+
+All commands must be run from the `web/` directory:
+
+```bash
+cd web
+npm install       # Install dependencies
+npm run dev       # Start dev server (localhost:5173)
+npm run build     # Production build → web/dist/
+npm run preview   # Preview production build locally
+```
+
+There are no lint or test scripts configured.
+
+## Architecture
+
+**View switching** is managed entirely in `web/src/Main.vue` via an `activeView` ref (`'home'` | `'step'` | `'result'`). There is no Vue Router — navigation is pure component conditional rendering. `StepView` is force-remounted via `stepViewKey` counter to ensure clean state resets.
+
+**PrimeVue** (v4) is the UI component library with auto-import via `unplugin-vue-components`. Components are resolved automatically — no explicit imports needed for PrimeVue components in templates.
+
+## Data Sources
+
+`web/public/data/meta_data.xlsx` has 3 sheets (parsed via `xlsx` library):
+- **Sheet 0 (metadata)**: One row per trial. Columns: `cancer_type`, `trial_name`, `line_of_therapy`, `treatment`, `control`.
+- **Sheet 1 (trial_criteria)**: Maps trials to their eligibility criteria. Columns: `trial_name`, `criteria_name`, `must_apply` (truthy = criteria cannot be relaxed).
+- **Sheet 2 (criteria)**: Criteria details. Columns: `criteria_name`, `criteria_description`, `type`.
+
+`web/public/data/trail_dataset/[TrialName]_results_web.csv` — Per-trial result files. Each row is one pathway (criteria combination). Columns include: `criteria` (comma-separated criteria names), `hr_os`, `hr_pfs`, `selog_hr_os`, `selog_hr_pfs`, `sucra_os`, `sucra_pfs`, `ae`, `ease`, `g_index`, `number_of_patients`, `path_id`.
+
+## Data Pipeline: StepView (Selection)
+
+In `StepView.vue`, on mount:
+1. Fetches `meta_data.xlsx`, parses all 3 sheets into `metadata`, `trialCriteriaRows`, `criteria` refs.
+2. **Step 1** — Extracts unique `cancer_type` values from sheet 0 → radio button list.
+3. **Step 2** — Filters sheet 0 by selected cancer type → unique `trial_name` list. Displays each trial's `line_of_therapy`, `treatment`, `control` metadata.
+4. **Step 3** — User selects endpoint (OS or PFS). PFS is disabled for AHNC cancer type (no progression data in Flatiron DB).
+5. **Step 2→3 transition** (`onclickNextTreatment`): Also derives criteria for the selected trial:
+   - Filters sheet 1 by `trial_name` → `trialCriteria` (list of criteria names for this trial).
+   - Computes `mustApplyCriteria` set (criteria with `must_apply` truthy in sheet 1).
+   - Calls `computeAvailableTokensForTrial()`: fetches the trial CSV, parses all `criteria` column values (comma-split, normalized), builds a set of tokens that actually exist in the data. Falls back to sheet 1 names if CSV fetch fails.
+   - Builds `filteredCriteria`: joins sheet 2 rows by `criteria_name`, adds `must_apply` and `no_data` flags.
+6. **Step 4** — Shows criteria table. `must_apply` criteria are pre-checked and disabled. User selects which criteria to enforce.
+7. On "Result" click: emits `{ selectedCancerType, selectedTreatment, selectedEndpoint, selectedCriteria }` to `Main.vue`.
+
+## Data Pipeline: ResultView (Visualization)
+
+In `ResultView.vue`, on mount:
+1. Re-fetches `meta_data.xlsx` independently (does not share state with StepView). Extracts trial metadata and criteria rows for the selected trial.
+2. Fetches `[TrialName]_results_web.csv`, parses with `xlsx` library.
+3. Calls `buildAllPathways(trailResult, selectedCriteria, selectedEndpoint, criteriaNameToIndex)`:
+   - Normalizes all criteria tokens (lowercase, trimmed).
+   - Builds `availableTokens` set from all CSV `criteria` column values.
+   - Computes `effectiveSelected`: selected criteria that actually exist in the CSV (ignores missing ones for filtering).
+   - Filters CSV rows: keeps rows where `criteria` column contains ALL `effectiveSelected` tokens.
+   - Maps each row to a UI object with endpoint-specific fields: OS → `hr_os`/`selog_hr_os`/`sucra_os`, PFS → `hr_pfs`/`selog_hr_pfs`/`sucra_pfs`.
+   - `pathName` is built from criteria indices (1-based) matching the criteria table order.
+4. Calls `computeNormalizationParams(allCsvRows, endpoint)`: computes min/max for each metric (HR, selogHR, AE, EASE, G-Index, # patients) across the **entire** CSV (not filtered). Some metrics are reversed (lower=better: HR, selogHR, AE, EASE).
+5. **Top 4 paths**: Default sort by `sucra` (descending). `updateDisplayedTop4()` takes first 4 from sorted `AllPathwaysResult`.
+6. **Virtual scrolling table**: Full pathway list uses PrimeVue's `virtualScrollerOptions` with lazy loading (`loadPathwaysLazy`). Placeholder objects fill the virtual array; real data is loaded in chunks as user scrolls.
+7. **Sorting**: User can sort by any column (HR, AE, # patients, EASE, G-Index, selogHR). `getSortedData()` re-sorts `AllPathwaysResult`. Default (SUCRA) sorts descending; column sorts respect `sortOrder`. Sort changes reset the virtual array and reload.
+8. **Origami plots (radar charts)**: Top 4 paths rendered as Chart.js radar charts. Values are normalized to [0.4, 1.0] range via `normalizeRangeValue()` — maps [min, max] → [0.4, 1.0] with optional reversal. Chart labels alternate between metric names and empty strings (gap spacers for visual separation).
+9. **Row selection interaction**: Selecting a row in the top paths table highlights corresponding criteria rows in the left-panel criteria table via `criteriaIndices` → `selectedCriteriaPath` → `criteriaRowClass`.
+
+## State Restoration
+
+When user clicks "Return to Selection" in ResultView:
+- Emits `returnToSelection` with `{ step: '4' }` to Main.vue.
+- Main.vue increments `stepViewKey` to force StepView remount, passes `initialStep='4'` and the previous `resultPayload` as `initialData`.
+- StepView's `restoreState()` re-derives all intermediate data (treatment list, criteria, etc.) from the saved selections, then jumps to step 4.
+
+## Deployment
+
+Pushing to `main` triggers the GitHub Actions workflow (`.github/workflows/main.yml`) which builds and deploys to GitHub Pages automatically. The Vite `base` is hardcoded to `/TrialMap/` in `vite.config.js`.

web/public/data/meta_data.xlsx

@@ -289,9 +289,29 @@ const chartOptions = computed(() => ({
 // 缓存图表数据，避免每次渲染都创建新对象
 const chartDataList = shallowRef([])
 
+function computeNormParamsFromItems(items) {
+    const getNums = (key) => items.map(r => Number(r?.[key])).filter(n => Number.isFinite(n))
+    const makeParams = (arr, reverse) => {
+        const has = arr.length > 0
+        const min = has ? Math.min(...arr) : 0
+        const max = has ? Math.max(...arr) : 0
+        return { min, max, reverse, min_val: 0.4, max_val: 1 }
+    }
+    return {
+        hr: makeParams(getNums('hr'), true),
+        selog_hr: makeParams(getNums('selog_hr'), true),
+        ae: makeParams(getNums('ae'), true),
+        ease: makeParams(getNums('ease'), true),
+        g_index: makeParams(getNums('g_index'), false),
+        number_of_patients: makeParams(getNums('number_of_patients'), false)
+    }
+}
+
 function updateChartDataList() {
-    const p = normParams.value || {}
-    chartDataList.value = Top4PathwaysResult.value.map(item => {
+    const top4 = Top4PathwaysResult.value
+    if (!top4 || top4.length === 0) { chartDataList.value = []; return }
+    const p = computeNormParamsFromItems(top4)
+    chartDataList.value = top4.map(item => {
         const gap = 0.25
         const values = [
             normalizeRangeValue(item.hr, p.hr), gap,
@@ -321,8 +341,8 @@ function updateChartDataList() {
     })
 }
 
-// 只在 Top4PathwaysResult 或 normParams 变化时更新图表数据
-watch([Top4PathwaysResult, normParams], () => {
+// 只在 Top4PathwaysResult 变化时更新图表数据
+watch([Top4PathwaysResult], () => {
     updateChartDataList()
 }, { 
     deep: false, // 不使用深度监听，避免不必要的更新
@@ -480,8 +500,8 @@ function buildAllPathways(trailResult, criteria, endpoint, criteriaNameToIndex)
 
     // Map to UI items, keep all rows
     const keyMap = endpoint === 'Overall survival (OS)'
-        ? { srcHr: 'hr_os', srcSelog: 'selog_hr_os', srcSucra: 'sucra_os' }
-        : { srcHr: 'hr_pfs', srcSelog: 'selog_hr_pfs', srcSucra: 'sucra_pfs' }
+        ? { srcHr: 'hr_os', srcSelog: 'selog_hr_os', srcSucra: 'sucra_os', srcPareto: 'pareto_os' }
+        : { srcHr: 'hr_pfs', srcSelog: 'selog_hr_pfs', srcSucra: 'sucra_pfs', srcPareto: 'pareto_pfs' }
 
     return filtered.map((row, idx) => {
         const rowTokens = String(row.criteria ?? '').split(',').map(normalize)
@@ -506,6 +526,7 @@ function buildAllPathways(trailResult, criteria, endpoint, criteriaNameToIndex)
         if (row[keyMap.srcHr] != null) item.hr = row[keyMap.srcHr]
         if (row[keyMap.srcSelog] != null) item.selog_hr = row[keyMap.srcSelog]
         if (row[keyMap.srcSucra] != null) item.sucra = row[keyMap.srcSucra]
+        if (row[keyMap.srcPareto] != null) item.pareto = Number(row[keyMap.srcPareto])
         return item
     })
 }
@@ -519,8 +540,20 @@ function getSortedData() {
     }
     const metric = field || 'sucra'
     const isDefault = field == null
-    // For default (SUCRA): higher is better (desc). Otherwise respect sortOrder (1 asc, -1 desc)
-    const factor = isDefault ? -1 : (order === -1 ? -1 : 1)
+    if (isDefault) {
+        // Default sort: pareto first (descending), then SUCRA descending
+        const sorted = [...(AllPathwaysResult.value || [])].sort((a, b) => {
+            const ap = Number(a?.pareto) || 0
+            const bp = Number(b?.pareto) || 0
+            if (ap !== bp) return bp - ap  // pareto=1 first
+            const av = asNumber(a?.sucra, -Infinity)
+            const bv = asNumber(b?.sucra, -Infinity)
+            return bv - av  // higher sucra first
+        })
+        return sorted
+    }
+    // User-selected column sort: respect sortOrder (1 asc, -1 desc)
+    const factor = order === -1 ? -1 : 1
     const fallbackAsc = factor === 1 ? Infinity : -Infinity
     const sorted = [...(AllPathwaysResult.value || [])].sort((a, b) => {
         const av = asNumber(a?.[metric], fallbackAsc)

web/src/views/ResultView.vue

@@ -235,7 +235,7 @@ async function restoreState(data) {
   if (data.selectedCancerType) {
     selectedCancerType.value = data.selectedCancerType
     treatment.value = [...new Set(metadata.value.filter(item => item.cancer_type === data.selectedCancerType).map(item => item.trial_name))]
-    isAHNC.value = String(data.selectedCancerType).trim().toLowerCase() === 'advanced head and neck cancer (ahnc)'
+    isAHNC.value = String(data.selectedCancerType).trim().toLowerCase().includes('head and neck')
   }
   
   if (data.selectedTreatment) {
@@ -299,7 +299,7 @@ function onclickNextCancerType() {
   console.log('Selected Cancer Type:', selectedCancerType.value)
   treatment.value =[ ...new Set(metadata.value.filter(item => item.cancer_type === selectedCancerType.value).map(item => item.trial_name))]
   console.log('Parsed Excel treatment:', treatment.value)
-  isAHNC.value = String(selectedCancerType.value).trim().toLowerCase() === 'advanced head and neck cancer (ahnc)'
+  isAHNC.value = String(selectedCancerType.value).trim().toLowerCase().includes('head and neck')
   activeStep.value = '2'
 }