@myelinbridge/cli 0.11.1 → 0.12.2

package/README.md

@@ -43,6 +43,18 @@ npx @myelinbridge/cli push  ./run_042 --dataset onco1-wes --submit
   every later delivery reconciles against it — a partial delivery (93 of 96) is
   reported as a state, never as a failure.
 
+- **Your client's own fields show up, read-only (0.12.0).** Clients can define
+  their own metadata fields on datasets (a sponsor study code, a work order, a
+  therapeutic area). `contract` prints them under CLIENT FIELDS — including a
+  required field nobody has filled in yet, shown as *"— required, not filled
+  in yet"* (0.12.2) — and `check` tells you the same thing via preflight;
+  informational only: their team fills them in Myelin, there is nothing to
+  change in your delivery, and metadata never moves the exit code. In
+  `--json`, datasets carry a `metadata` object
+  (`{key: {label, type, value, required?}}` — `required: true` and
+  `value: null` mark a required field with no value yet) and preflight
+  carries `metadata.missing_required`.
+
 - **A missing path in `roles set` is refused, not guessed (0.11.1).** Flags are
   not positional arguments: `roles set samplesheet --dataset onco1-wes` (path
   omitted) used to declare the samplesheet at the literal path `--dataset` and

package/bin/myelin.js

@@ -17,6 +17,29 @@
 // cannot validate either without deciding by hand, and hearing "all checks
 // pass" before uploading is the green-before-sending / red-after trap this
 // release exists to close.
+//
+// 0.12.0 — clients can define their own fields on datasets (sprint 22).
+// `contract` shows them read-only, and `check` reports the required ones the
+// client has not filled in yet — informational ONLY: metadata never moves the
+// exit code (the client fills these in Myelin; nothing for a partner to fix,
+// and a pipeline must never halt on it).
+//
+// 0.12.1 — three display-only fixes, no behavior change. `check`'s
+// human-readable output now labels every rule by `name` instead of
+// `check_type`: the type is the underlying evaluator (many-to-one with
+// rules), so two rules sharing one used to print identical, contradictory
+// lines. `check`/`push` now refuse an omitted <dir> the same way `roles set`
+// already refused an omitted <path> (0.11.1) — before, the following
+// --dataset flag was silently swallowed as the directory and the command
+// died with a raw ENOENT instead of its usage line. `resolve` no longer
+// doubles a project's code ("AML-CART-3B — AML-CART-3B — Phase 3…") when the
+// title already starts with it.
+//
+// 0.12.2 — a required field with no value yet used to be invisible in
+// `contract` (it only ever rendered keys the dataset already had a value
+// for), even though `check` correctly warned about it via preflight. The API
+// now includes required-but-empty fields in `metadata` too
+// (`required: true`, `value: null`), and `contract` renders them.
 
 import { readdirSync, statSync, createReadStream, readFileSync } from 'node:fs'
 import { resolve, join, relative, sep, basename } from 'node:path'
@@ -102,6 +125,11 @@ const VERDICT_LABEL = {
 const verdictMark = (v) => VERDICT_MARK[v] ?? '?'
 const verdictLabel = (v) => VERDICT_LABEL[v] ?? v
 
+// A client field value in human mode (0.12.0). Arrays joined, booleans said
+// in words, everything else printed as-is — never JSON punctuation.
+const fmtFieldValue = (v) =>
+  Array.isArray(v) ? v.join(', ') : v === true ? 'yes' : v === false ? 'no' : String(v ?? '—')
+
 // Column widths come from the content. padEnd() alone silently ran a long
 // value into the next column — a 28-character dataset slug swallowed the
 // STATUS header's gutter. Pass headers = null for an unheadered list.
@@ -565,13 +593,35 @@ async function cmdContract() {
     for (const c of manual) out(`  · ${c.name}`)
     out('')
   }
+  // 0.12.0 — the client's own fields on this dataset, read-only (their team
+  // writes them in Myelin; the API never accepts them from a partner key).
+  const meta = dataset.metadata ?? {}
+  const metaKeys = Object.keys(meta)
+  if (metaKeys.length > 0) {
+    out('CLIENT FIELDS — how your client describes this dataset (read-only)')
+    for (const k of metaKeys) {
+      const f = meta[k]
+      // A required field with no value yet is invisible unless we say so
+      // here too — `myelin check` already warns about it via preflight, and
+      // the two must agree on what's outstanding (0.12.0, cli-api-18).
+      out(
+        f.required
+          ? `  · ${f.label} — required, not filled in yet`
+          : `  · ${f.label}: ${fmtFieldValue(f.value)}`,
+      )
+    }
+    out('')
+  }
   out(`Run "myelin check <dir> --dataset ${dsRef}" to test ${s.checkable_before_upload} of these locally.`)
 }
 
 async function cmdCheck() {
   const dir = args[1]
   const dsRef = opt('dataset')
-  if (!dir || !dsRef) die('Usage: myelin check <dir> --dataset <slug|id>')
+  // Same trap as `roles set` (see the comment there): an omitted <dir> lets
+  // the following --dataset flag slide into its place, which used to reach
+  // resolve()/walkDir() and fail with a raw ENOENT instead of usage.
+  if (!dir || dir.startsWith('--') || !dsRef) die('Usage: myelin check <dir> --dataset <slug|id>')
   const root = resolve(dir)
   const files = walkDir(root)
   if (files.length === 0) die(`No files under ${root}`)
@@ -588,10 +638,15 @@ async function cmdCheck() {
   if (!JSON_MODE) {
     // One width across all three lists so the verdicts line up, and the hint
     // lines can still be interleaved under the check they belong to.
+    // Labelled by `name`, not `check_type` — the type is the underlying
+    // evaluator (e.g. "manifest_present") and is many-to-one with rules, so
+    // two rules of the same type used to print identical, contradictory
+    // lines. `name` is unique per rule and is what the manual list below
+    // already used.
     const w = Math.max(
       0,
-      ...j.evaluated.map((c) => c.check_type.length),
-      ...j.deferred.map((d) => d.check_type.length),
+      ...j.evaluated.map((c) => c.name.length),
+      ...j.deferred.map((d) => d.name.length),
       ...j.manual.map((m) => m.name.length),
     )
     for (const c of j.evaluated) {
@@ -600,7 +655,7 @@ async function cmdCheck() {
         : c.severity === 'blocking' && c.verdict === 'not_evaluated' ? ' — BLOCKING, and nobody looked'
         : c.severity === 'must_acknowledge' && c.verdict === 'failed' ? ' — your reviewer confirms this'
         : ''
-      out(`${verdictMark(c.verdict)} ${c.check_type.padEnd(w)}  ${verdictLabel(c.verdict)}${gate}`)
+      out(`${verdictMark(c.verdict)} ${c.name.padEnd(w)}  ${verdictLabel(c.verdict)}${gate}`)
       // Why we could not look, in the partner's terms. `abstained: 'rule'` is
       // the one that matters most: it says the fault is in the client's rule,
       // not in this delivery, and without the sentence the partner spends a
@@ -624,7 +679,7 @@ async function cmdCheck() {
         (c.verdict === 'not_evaluated' && c.details?.abstained !== 'rule')
       if (fixable && c.remediation) out(`    hint: ${c.remediation}`)
     }
-    for (const d of j.deferred) out(`… ${d.check_type.padEnd(w)}  ${d.reason}`)
+    for (const d of j.deferred) out(`… ${d.name.padEnd(w)}  ${d.reason}`)
     for (const m of j.manual) out(`○ ${m.name.padEnd(w)}  ${m.reason}`)
   }
 
@@ -662,6 +717,16 @@ async function cmdCheck() {
   if (j.must_acknowledge_failures > 0) {
     out(`${j.must_acknowledge_failures} check(s) your client asked to be told about — nothing to fix; their reviewer records a decision. Not a blocker.`)
   }
+  // 0.12.0 — required client fields not filled in yet. Informational ONLY:
+  // their team fills these in Myelin, nothing changes in the delivery, and
+  // metadata never moves the exit code (warn, never block — by design).
+  const gaps = j.metadata?.missing_required ?? []
+  if (gaps.length > 0) {
+    out(
+      `${gaps.length} field(s) your client asks for on this dataset ${gaps.length === 1 ? 'is' : 'are'} ` +
+        `not filled in yet: ${gaps.map((g) => g.label).join(', ')}. Their team fills these in Myelin — not a blocker.`,
+    )
+  }
 
   const k = j.counts
   // "All checks that run before upload pass" was written when every check
@@ -686,7 +751,10 @@ async function cmdCheck() {
 async function cmdPush() {
   const dir = args[1]
   const dsRef = opt('dataset')
-  if (!dir || !dsRef) die('Usage: myelin push <dir> --dataset <slug|id> [--submit] [--replace]')
+  // Same trap as `roles set` (see the comment there): an omitted <dir> lets
+  // the following --dataset flag slide into its place, which used to reach
+  // resolve()/walkDir() and fail with a raw ENOENT instead of usage.
+  if (!dir || dir.startsWith('--') || !dsRef) die('Usage: myelin push <dir> --dataset <slug|id> [--submit] [--replace]')
   const root = resolve(dir)
   const files = walkDir(root)
   if (files.length === 0) die(`No files under ${root}`)
@@ -1047,7 +1115,14 @@ async function cmdResolve() {
   const j = expectOk(await api('GET', `/deliveries/resolve?path=${encodeURIComponent(path)}`), 'resolve')
   emit(j)
   out(`${j.resolved} · ${j.query}`)
-  if (j.project) out(`  project   ${j.project.code} — ${j.project.title}`)
+  // Some seeded/client titles already embed the project code
+  // ("AML-CART-3B — Phase 3 CAR-T…") — only prepend it when the title
+  // doesn't already start with it, or the code prints twice.
+  if (j.project) {
+    const title =
+      j.project.title && j.project.title.startsWith(j.project.code) ? j.project.title : `${j.project.code} — ${j.project.title}`
+    out(`  project   ${title}`)
+  }
   if (j.dataset) out(`  dataset   ${j.dataset.name}${j.dataset.label ? ` (${j.dataset.label})` : ''}`)
   if (j.delivery) {
     out(`  batch     ${j.delivery.batch_name ?? j.delivery.batch_id} · #${j.delivery.sequence_number ?? '?'}`)

package/package.json

@@ -1,23 +1,23 @@
-{
-  "name": "@myelinbridge/cli",
-  "version": "0.11.1",
-  "description": "Myelin Partner Ingestion CLI — push R&D data deliveries from a pipeline: preflight against the client's quality rules, resumable upload, submit, track review outcomes.",
-  "type": "module",
-  "bin": {
-    "myelin": "bin/myelin.js"
-  },
-  "files": [
-    "bin/",
-    "README.md"
-  ],
-  "engines": {
-    "node": ">=20"
-  },
-  "keywords": [
-    "myelin",
-    "pharma",
-    "ingestion",
-    "s3"
-  ],
-  "license": "UNLICENSED"
-}
+{
+  "name": "@myelinbridge/cli",
+  "version": "0.12.2",
+  "description": "Myelin Partner Ingestion CLI — push R&D data deliveries from a pipeline: preflight against the client's quality rules, resumable upload, submit, track review outcomes.",
+  "type": "module",
+  "bin": {
+    "myelin": "bin/myelin.js"
+  },
+  "files": [
+    "bin/",
+    "README.md"
+  ],
+  "engines": {
+    "node": ">=20"
+  },
+  "keywords": [
+    "myelin",
+    "pharma",
+    "ingestion",
+    "s3"
+  ],
+  "license": "UNLICENSED"
+}