@myelinbridge/cli 0.12.0 → 0.12.2

package/README.md

@@ -45,12 +45,15 @@ npx @myelinbridge/cli push  ./run_042 --dataset onco1-wes --submit
 
 - **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, and `check`
-  tells you when required ones are not filled in yet — 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}}`) and preflight carries
-  `metadata.missing_required`.
+  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

package/bin/myelin.js

@@ -23,6 +23,23 @@
 // 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'
@@ -582,7 +599,17 @@ async function cmdContract() {
   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) out(`  · ${meta[k].label}: ${fmtFieldValue(meta[k].value)}`)
+    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.`)
@@ -591,7 +618,10 @@ async function cmdContract() {
 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 ${root}`)
@@ -608,10 +638,15 @@ async function cmdCheck() {
   if (!JSON_MODE) {
     // One width across all three lists so the verdicts line up, and the hint
     // lines can still be interleaved under the check they belong to.
+    // Labelled by `name`, not `check_type` — the type is the underlying
+    // evaluator (e.g. "manifest_present") and is many-to-one with rules, so
+    // two rules of the same type used to print identical, contradictory
+    // lines. `name` is unique per rule and is what the manual list below
+    // already used.
     const w = Math.max(
       0,
-      ...j.evaluated.map((c) => c.check_type.length),
-      ...j.deferred.map((d) => d.check_type.length),
+      ...j.evaluated.map((c) => c.name.length),
+      ...j.deferred.map((d) => d.name.length),
       ...j.manual.map((m) => m.name.length),
     )
     for (const c of j.evaluated) {
@@ -620,7 +655,7 @@ async function cmdCheck() {
         : c.severity === 'blocking' && c.verdict === 'not_evaluated' ? ' — BLOCKING, and nobody looked'
         : c.severity === 'must_acknowledge' && c.verdict === 'failed' ? ' — your reviewer confirms this'
         : ''
-      out(`${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
@@ -644,7 +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}`)
   }
 
@@ -716,7 +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 ${root}`)
@@ -1077,7 +1115,14 @@ async function cmdResolve() {
   const j = expectOk(await api('GET', `/deliveries/resolve?path=${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

@@ -1,6 +1,6 @@
 {
   "name": "@myelinbridge/cli",
-  "version": "0.12.0",
+  "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": {