test(cladistics): correct the jplace weighted UniFrac expectation (follow-up to #239)

frontend/src/api/events.ts

@@ -13,12 +13,25 @@ export type SSEHandler = {
 export function openEventStream(handlers: SSEHandler & { onConnectedChange?: (connected: boolean) => void }): () => void {
   const es = new EventSource(apiUrl('/api/v1/events'))
 
+  // A malformed frame must not throw inside the listener: EventSource would
+  // keep the stream open but the exception surfaces as an uncaught error and
+  // the update is lost silently either way. Drop the bad frame instead.
+  const parseFrame = (data: string): unknown => {
+    try {
+      return JSON.parse(data)
+    } catch {
+      return undefined
+    }
+  }
+
   es.addEventListener('job_update', (e: MessageEvent) => {
-    handlers.onJobUpdate?.(JSON.parse(e.data) as Job)
+    const job = parseFrame(e.data)
+    if (job !== undefined) handlers.onJobUpdate?.(job as Job)
   })
 
   es.addEventListener('stage_update', (e: MessageEvent) => {
-    handlers.onStageUpdate?.(JSON.parse(e.data))
+    const ev = parseFrame(e.data)
+    if (ev !== undefined) handlers.onStageUpdate?.(ev as Parameters<NonNullable<SSEHandler['onStageUpdate']>>[0])
   })
 
   es.onopen = () => handlers.onConnectedChange?.(true)

frontend/src/api/types.ts

@@ -968,6 +968,17 @@ export interface CladeCumulusRequest {
 export interface CladeCumulusDiversity {
   samples: string[]
   mapped_tips: number
+  /**
+   * Reads per sample that no tip on the tree carries: a query whose kept
+   * `.jplace` like-weight ratios do not reach 1 contributes only that share,
+   * and an ASV the tree does not cover contributes nothing.
+   *
+   * These reads are excluded from the tree-tip abundances, but they are still
+   * counted in each sample's library size, which is the denominator the
+   * weighted UniFrac metrics divide by. That is what keeps the shortfall off
+   * the tree instead of renormalising a partially placed sample back up to
+   * abundance 1. Absent for responses produced before this field existed.
+   */
   unplaced_reads?: Record<string, number>
   faith_pd: Record<string, number>
   unweighted_unifrac: number[][]

frontend/src/components/CladeCumulusPanel.tsx

@@ -33,6 +33,11 @@ export interface CladeCumulusPanelProps {
   runs: CladeCumulusRunOption[]
 }
 
+/**
+ * Explore a study run's clade hierarchy, diversity and unplaced reads. Loads
+ * available sources and computes results on request; move checks can preview
+ * counterfactual trees or save sidecar proposals without changing canonical tables.
+ */
 export function CladeCumulusPanel({ study, runs }: CladeCumulusPanelProps) {
   const toast = useToast()
   const reqCounter = useRef(0)
@@ -249,6 +254,9 @@ export function CladeCumulusPanel({ study, runs }: CladeCumulusPanelProps) {
     return div.normalized_weighted_unifrac
   }, [result, unifracKind])
 
+  // Only samples that actually lost mass are worth naming; a run with a
+  // complete placement file (or one produced before the field existed) reports
+  // nothing here.
   const unplacedSamples = useMemo<[string, number][]>(() => {
     const div = result?.diversity
     if (!div?.unplaced_reads) return []
@@ -708,10 +716,25 @@ export function CladeCumulusPanel({ study, runs }: CladeCumulusPanelProps) {
                 ))}
               </div>
 
+              {/*
+                Reads no tip carries: like-weight mass a placement left on no
+                edge, plus ASVs the tree does not cover. They are absent from
+                the tree-tip abundances but they are *not* dropped from the
+                sample: each one still counts in its sample's library size,
+                which is the denominator the weighted UniFrac metrics divide
+                by. That is what keeps them off the tree instead of letting a
+                partially placed sample renormalise back up to abundance 1, so
+                the shortfall is stated here as well.
+              */}
               {unplacedSamples.length > 0 && (
                 <p style={{ fontSize: '.75rem', margin: '0 0 12px', color: 'var(--color-fg-muted, #57606a)' }}>
-                  Unplaced reads (like-weight mass left off reference edges, excluded from weighted abundances above):{' '}
-                  {unplacedSamples.map(([s, n]) => `${s} ${n.toFixed(2)}`).join(', ')}
+                  Unplaced reads (carried by no tip — like-weight mass left on no edge, plus
+                  ASVs the tree does not cover — excluded from the tree-tip abundances but
+                  counted in each sample’s library size, so they lower its relative
+                  abundances rather than being renormalised onto the placed tips):{' '}
+                  {unplacedSamples
+                    .map(([s, n]) => `${s} ${n.toFixed(2)}`)
+                    .join(', ')}
                 </p>
               )}
 

frontend/src/tree/model.ts

@@ -112,14 +112,14 @@ export function parseNewick(text: string): SourceTree {
     skipSpace()
     if (s[i] === "'" || s[i] === '"') {
       const q = s[i++]
-      let out = ''
+      const parts: string[] = []
       while (i < s.length) {
         if (s[i] === q) {
-          if (s[i + 1] === q) { out += q; i += 2; continue }
+          if (s[i + 1] === q) { parts.push(q); i += 2; continue }
           i++
-          return out
+          return parts.join('')
         }
-        out += s[i++]
+        parts.push(s[i++])
       }
       fail('unclosed quote')
     }
@@ -209,7 +209,18 @@ export function parseNewick(text: string): SourceTree {
 }
 
 export function parseJplace(text: string): SourceTree {
-  const doc = JSON.parse(text)
+  let doc: {
+    tree?: unknown
+    fields?: string[]
+    placements?: Record<string, unknown>[]
+    metadata?: Record<string, unknown>
+    version?: unknown
+  }
+  try {
+    doc = JSON.parse(text)
+  } catch {
+    throw new Error('jplace file is not valid JSON')
+  }
   const tree = parseNewick(String(doc.tree))
   const fields: string[] = doc.fields ?? []
   const col = (f: string) => fields.indexOf(f)

scripts/check-julia-syntax.jl

@@ -20,8 +20,15 @@ for file in files
                 issue = ex
                 break
             end
+            # A bare `end` at the top level parses without error and then fails
+            # at lowering (`syntax: "end" at top level`), which is how a file
+            # that lost its `module Foo` opener reaches CI looking syntactically
+            # fine. An `end` balances exactly one opener, so top level cannot
+            # hold one: this is a missing or duplicated opener, and the file
+            # would not load.
             if ex === :end
-                issue = "stray `end` at top level (missing or duplicated opener in this file)"
+                issue = "stray `end` at top level (a `module`/`function`/... opener " *
+                        "is missing or was duplicated in this file)"
                 break
             end
             next_position > position ||