@cosyte/terminology 0.0.4 → 0.0.6
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CHANGELOG.md +243 -0
- package/README.md +13 -2
- package/dist/index.cjs +92 -64
- package/dist/index.cjs.map +1 -1
- package/dist/index.d.cts +100 -10
- package/dist/index.d.ts +100 -10
- package/dist/index.mjs +92 -64
- package/dist/index.mjs.map +1 -1
- package/package.json +3 -3
package/CHANGELOG.md
CHANGED
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@@ -9,8 +9,237 @@ this file is maintained by hand (Changesets handles the version bump and publish
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## [Unreleased]
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### Changed
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- **Breaking: `ExpansionDiagnostic.system` is replaced by `ExpansionDiagnostic.path`.** The field
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used to carry the code system or value set URI the concern was about — consumer-supplied text of
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unbounded length on a diagnostic surface. It now carries a value-free structural locus into your
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own resource, built from integers and the engine's own field names: `"compose.include[2]"`,
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`"compose.include[0].valueSet[1]"`, `"expansion"`. A diagnostic raised while expanding a
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referenced value set is prefixed with the reference that reached it. This is strictly more precise
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than the URI, which cannot distinguish two `include` components naming the same system. `expand`
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and `validateCodeInValueSet` build the path identically, so a locus means the same thing in both;
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they do **not** always emit the same _set_ of diagnostics, because membership can decide an answer
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without evaluating a part expansion still has to report. Reading `d.system` is now a type error.
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The rationale, and the other three sites, are under **Fixed** below.
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### Fixed
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- **A `UnitNode` you assembled yourself could change how `reduce` and `ucumEqual` answer for a unit
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parsed out of the bundled UCUM table, for the rest of the process**
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(`TERMINOLOGY-ATOMMEMO-POISONING`). `reduce` is exported and takes a caller-built node, and
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nothing checks that the atoms on it came from the bundled table. Its per-atom memo, and the guard
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against a definition that leads back to itself, were keyed on `atom.code` — a **string** — so an
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atom you built wrote under the key of whichever shipped atom happened to share its code, and every
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later reduction of that shipped atom read what yours had left.
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Measured on `0.0.5`: one `reduce()` over a value-less atom coded `L`, as the first touch of `L` in
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the process, made `ucumEqual("L", "1")` and `ucumEqual("mg/L", "mg")` both answer `true` where the
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same calls without it answered `false`, and dropped `mmol/L` from `6.02214076e23 × m-3` to a
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dimensionless `6.02214076e20` — **a concentration comparing equal to a mass**, from an engine
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whose contract is never to fabricate. Two further readings on the same build: an atom coded `N`
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and defined as `N` left the cycle guard armed, so every later `ucumEqual("N", "kg.m/s2")` threw;
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and the value returned for a term with no factors was the engine's own module-global dimensionless
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object, so mutating a result you had been handed turned `kg.m/s2` into `999000 × m2.g.s-2` and
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made `ucumEqual("N", "kg.m/s2")` answer `false`.
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Four changes:
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- The memo and the cycle guard key on the **atom object**, in a `WeakMap` / `WeakSet`. The atoms
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`parseUcum` resolves are the unit table's cached singletons, so a parsed expression still gets
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one memo entry per atom; an atom you built gets its own entry and is collected with it. Measured
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warm over ten mixed expressions, best of seven trials of 2,000,000 `reduce` calls, on two
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different machines: identity-keyed came in at or ahead of string-keyed both times. Read that as
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no measured cost rather than as a speed-up; the absolute figures are machine- and load-dependent
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and are deliberately not quoted as a pair.
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- An atom carrying no linear definition, and which is neither a base nor an arbitrary unit, is now
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**refused** with `UCUM atom has no linear definition` rather than answered — and memoized — as
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dimensionless. No expression `parseUcum` accepts reaches this, though **not** because every atom
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in the bundled table has a linear definition: 21 of its 312 atoms, the special units, have none.
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It is that an expression containing a special unit short-circuits to the opaque `special` form
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before linear reduction, base and arbitrary units are answered directly, and every remaining atom
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resolves. A node you assemble can reach it — including by defining an atom in terms of a special
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unit such as `Cel`, which lands on the table's own `Cel`.
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- The cycle guard releases its atom in a `finally`, so a throw from inside the recursion no longer
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wedges that atom for the rest of the process.
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- `reduce` no longer returns the module-global dimensionless object. What you get back is per-call
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state, and mutating it cannot reach the engine.
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Keying on identity was chosen over validating that each atom came from the bundled table: it needs
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no provenance check on the hot path and adds no failure mode for real input, and it is the
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narrower change. The cost is that an atom you built is answered on its own terms only — the
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intended contract, not a regression. **No unit obtained from `parseUcum` changes its answer**: the
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530-case UCUM conformance suite and the rest of the suite are unchanged and green, and the new
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refusals are reachable only through a node you assembled. **The claim rests on one property, and
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it is the one this repo asserts: every atom in the bundled table reduces, and none of them reaches
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a refusal** (`test/ucum/reduce-memo.test.ts`, last case, over all 312). That is enough to cover
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every expression `parseUcum` accepts rather than sampling them — an expression containing a
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special unit short-circuits before linear reduction, linear reduction is compositional over atoms,
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and the table's own definitions close over that same set, so once every atom answers there is
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nothing left for a bigger corpus to vary. `test/ucum/functional.test.ts` separately drives the
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vendored UCUM functional-test suite's unit strings through `reduce`.
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**Do not restate this as more evidence than that.** Three drafts of this paragraph each claimed
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more than the tree holds — two cited generated-corpus sizes that were not reproducible from their
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own descriptions, and the third attributed a three-clause sweep to a file that pins one clause of
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it. A before/after differential is a two-tree measurement and **no in-tree test can pin one**, by
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construction; do not add a guard to make a sentence here true, shrink the sentence. The three
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guards are now covered by tests
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rather than by a `/* v8 ignore */` block, and each message is pinned by whole-message equality
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rather than by a substring match.
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- **Consumer-supplied strings reached `TerminologyError.message`, `err.stack` and an
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`ExpansionDiagnostic`, contradicting this package's own "value-free by construction" claim**
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(`PHI-WARNING-MESSAGE-LEAK`). Three sites, found by binding
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`assertNoDiagnosticPhiLeak` from `@cosyte/test-utils@0.0.2` to a 52-slot table covering the
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consumer-controlled positions across the readers and loaders that this repo has identified — which
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is not a proof that none was missed, as the fourth site below shows; **14 of the 52 slots were red on the
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base commit** — 4 CSV column-config slots, 1 `invertGem` slot, 4 in `expand.ts` and 5 in
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`validate.ts` — and the table was run there first for exactly that reason. (An earlier draft of
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this entry said 9. That was the measurement taken before the slot table was extended to the
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**second copy** of the `src/valueset/` diagnostic factories, and it was never re-taken; the five
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`validate.ts` slots are the difference. Re-measure after you widen a table.)
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1. `csv.ts` `requireHeader` interpolated the caller's configured column name into the
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`TERM_CODESYSTEM_MALFORMED` message. Measured against the published `0.0.5`: a 1,000,000-byte
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`columns.code` produced a 1,000,063-byte `err.message`, and the same bytes landed in
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`err.stack`. It now reads the message out of a frozen `MISSING_COLUMN_MESSAGE` table keyed on
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the column's **role** (`code` / `display` / `status` / `property`) and takes no value
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parameter. That is the `astm`/`transform` shape the ecosystem audit recorded for the designs
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that do not leak, and it is what this factory now is — a property of **this** factory, not a
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rule this package holds everywhere. Several factories here do take `string` parameters and are
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safe because every argument reaching them is engine-owned; they are named below, and reading
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the no-value-parameter shape as a package-wide rule is what made three drafts of this entry
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wrong.
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2. `invertGem` interpolated `GemMap.direction` into the `TERM_MAP_NOT_INVERTIBLE` message.
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`GemDirection` is a two-value union, but nothing validates it on load and a JavaScript caller
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can pass anything, so the echo was unbounded in practice. Now a closed-set `Map` lookup with a
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direction-free fallback; the direction is kept where it is one of the two authored values,
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because it tells the caller which file to load instead.
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3. `ExpansionDiagnostic.system` carried the caller's `include.system`, referenced `valueSet` URL,
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or `ValueSet.url` verbatim. **This site is not in the 2026-07-30 ecosystem audit, which
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recorded `terminology` as "one site, a CSV column name".** It is the only one of the three
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that is _document_-derived rather than caller-configuration. **Breaking:** the field is
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replaced by `path`, a value-free index locus (`compose.include[2]`,
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`compose.include[0].valueSet[1]`, `expansion`), built the same way in both `expand.ts` and
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`validate.ts` so a locus means the same thing in each, and prefixed with the reference that
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reached it when the diagnostic comes from a referenced value set. The two do **not** always
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emit the same _set_ of diagnostics and the changeset no longer says they do: membership
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short-circuits on a system mismatch and on an exclude that cannot change a decided verdict,
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where expansion still has to report the part it could not compute. Not a truncation: an index path is
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strictly more precise than the URI, which cannot distinguish two `include`s over one system.
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**Severity is medium-low and stays medium-low.** Sites 1 and 2 echo the caller's own
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configuration, not a patient's document; site 3 echoes a canonical URI out of reference content.
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The engine's genuinely patient-derived inputs are its _query_ values (a code off a parsed
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message, a unit off an observation, an NDC off a prescription, the `PatientContext` age/gender a
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complex map branches on), and **no query value reaches a message or a stack anywhere**: the
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engine throws only on an unusable source, never on a query. That is now asserted rather than
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argued.
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**A misfiled result field, corrected in the same docblock and shipped in `dist/index.d.ts`:
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`MapProvenance.sourceSystem`.** A draft of the "which result fields carry verbatim text" list put
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the whole of `MapProvenance` under _your loaded artifact_ — "reference data, not anything a
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patient supplied". That is true of `.targetSystem`, `.conceptMapUrl` and `.conceptMapVersion`
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(`group.target`, `map.url`, `map.version`) and **false of `.sourceSystem`**, which `translate`
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fills from the `system` on the `Coding` **you** passed it, verbatim and unbounded, falling back to
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the map's `group.source` only when the coding carries none. It is a query echo and is now listed
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as one, so a reader applies the log-it-only-if-you-would-log-the-code rule to it. This is a
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classification fix in prose: the value has always been the caller's own, it is not on a
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diagnostic-message surface, and **nothing about the runtime behaviour changed** — bounding it is
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not attempted here, and would be the same fabricate-a-miss trade-off as bounding any other echo.
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**The `@param` contract this broke** is `TerminologyError`'s own: _"a **value-free** structural
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description (path + fault; never an input value)"_. It now also tells a caller why, since the
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string reaches `err.stack`.
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**The "Value-free by construction" claim in `src/common/diagnostics.ts` was checked before being
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rewritten, and it was false** on two counts: the two messages above echoed arbitrary input, and
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"at most a code + system + version" described the leaking `ExpansionDiagnostic.system` as though
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it were the safety property. The new wording states the mechanical fact — **every string a message
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is assembled from is owned by the engine**: a literal, a frozen-table entry, or a locus this
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package built (a `line`, a column count, an index path of integers and FHIR field names) — and, in
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the same place, scopes it: it covers **diagnostics**, not **results**, which carry the caller's
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values by design. A first draft of that replacement said instead that "no message is built from a
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value parameter" and that every message is "a literal or a frozen-table entry". **That was false as
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written**, of factories it did not touch: `malformed(path, fault)` in `conceptmap/load.ts` and
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`valueset/load.ts`, and `cannotExpand` / `truncated` / `underPath` in `valueset/` — where
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`expand.ts` and `validate.ts` each carry their own copy — all of which do interpolate
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`string` parameters. **An earlier draft of this paragraph said "four", and the tree has seven**;
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a count in prose is the thing that goes stale, so it is derived now, not written down.
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The code is fine — every argument reaching them is engine-owned, each `fault`
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a literal at the call site and each `path` built from indices — but the sentence was stronger than
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the code, which is precisely the failure this entry exists to end. It now describes the arguments,
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not the signatures.
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**The mechanism is now stated as a general rule in exactly one place — the
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`src/common/diagnostics.ts` docblock.** `README.md`, `docs-content/troubleshooting.md` and
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`docs-content/concepts-archetype.md` carried the old "code + system + version" sentence, and the
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`test/phi/diagnostic-surface.test.ts` header (new in this slice) carried the same doctrine in a
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later wording; all four now state only the **consumer-facing property** — nothing you configured
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and nothing your release or resource contained reaches a `message`, `detail`, `reason` or
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`err.stack`, at any length — and none restates the general rule. An earlier draft of this slice
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moved all four to a _restatement_ of the mechanism instead, in the wording already found false of
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`malformed` / `cannotExpand` / `truncated`, and this entry claimed they had moved with the fix
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when what they had moved to was the superseded draft. No gate in this repo can grade an English
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sentence, which is the argument for one copy of the rule rather than four. **Statements scoped to
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a single factory are not copies of the rule and deliberately stay put** — `csv.ts` still says its
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own `MISSING_COLUMN_MESSAGE` lookup takes no value parameter, and `TerminologyError`'s `@param`
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still tells a caller what may go into the string it is handed. The `diagnostics` guidance in
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`troubleshooting.md`, which told readers to read a diagnostic for "which code system was missing",
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points at `path`.
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**What the gate proves is narrow, deliberately:** for each declared slot, no verbatim echo of
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four or more bytes of the planted value on any swept surface, and the slot provably reached the
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code it names. It does not prove the absence of a re-encoded echo, an echo under four bytes, or a
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leak through a slot nobody declared. Two limits are written into the file rather than implied
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away. First, `expectCode` shows the branch ran, not that the _marker_ ran it: about half the slots
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are **model-only** and pair the marker with a second marker-free malformed element so a diagnostic
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exists to sweep, and for those it is the sweep of **those diagnostics** that carries the proof. (An
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earlier draft said "the whole rendered result". The runner sweeps exactly what the two selectors
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return plus the thrown value, so for the `CodeSystem.url` slot the `url` itself is never swept —
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correctly, since it is payload, but not swept.) Second, `getModelIdentifiers` returns the model's
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real loci — a `RxNormLoadWarning.file`
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token, an `ExpansionDiagnostic.path` — which are also swept as part of their diagnostic, so it is
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redundant rather than load-bearing; it exists so the classification of every name-like string on
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every exported model type is executed and reviewable instead of collapsing to a `[]` a reader has
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to trust. `Property.code` and `RxNormEdge.predicate` are classified as payload on a checkable
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test: an HL7 v2 `segment.type` is spec-bounded to three characters, so bounding it discards
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nothing, while a FHIR `code` carries no `maxLength` and RxNorm's `RELA` is an open vocabulary, and
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both are the keys the engine and the caller match on, so truncating either turns a hit into a
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miss. The residual is
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named: that protects the lookup, not a future consumer who builds a locus out of one.
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`@cosyte/cli` is today the only package in the ecosystem that depends on this one, and it uses
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`loadConceptMap` + `translate` only.
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**A FOURTH site, found by the refuter after the three above: `reduce` echoed a forged atom's
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`code` into a plain `Error.message` and `err.stack`** — a second ~1 MB leak. `reduce` is exported
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and takes a caller-built
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`UnitNode`, and nothing checks that the atoms on it came from the vendored UCUM table, so a
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forged atom whose `value.unit` does not parse reaches the throw. Measured on `0.0.5`: a
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1,000,000-byte atom code produced a **1,000,042-byte** `Error.message`, with the same bytes in
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`err.stack`. Every `Error` message `reduce` can throw is a literal — two of them at that point,
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three after the memo fix recorded at the top of this section. The site had been marked `/* v8 ignore */` as
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"unreachable with the shipped data", and the throw was moved outside that block, with
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`test/ucum/reduce.test.ts` pinning the message and the stack. **The two branches still inside the
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block were not unreachable either, and the comment stopped saying they were.** A draft of that slice
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relabelled them "genuinely unreachable through the public API"; they were not, because `inProgress`
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and `atomMemo` keyed on the atom's `code` string and nothing checked that an atom came from the
|
|
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|
+
vendored table, so a caller-forged atom whose code collided with a shipped one re-entered the
|
|
226
|
+
cyclic guard (measured: `reduce` over a forged `mol` defined as `mol` threw it) and a forged atom
|
|
227
|
+
with no `value` fell through the second, which threw nothing — it memoized dimensionless and
|
|
228
|
+
returned. The "with the shipped data" scope was the defensible one and was restored, stated
|
|
229
|
+
as a coverage exclusion over a corrupt-table guard rather than as an assertion of unreachability.
|
|
230
|
+
Neither branch leaked — the one message inside the block was a literal — so nothing was deferred **on
|
|
231
|
+
the diagnostic surface**. What was deferred is not merely that the branches were reachable: that
|
|
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|
+
second branch wrote the forged atom's `code` into the module-global `atomMemo` before returning,
|
|
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|
+
so one `reduce()` over a forged, value-less atom whose code collided with a shipped one poisoned
|
|
234
|
+
every later reduction of that atom in the process — enough to make `ucumEqual("mg/L", "mg")`
|
|
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|
+
answer `true`. That is a **never-fabricate defect, not a diagnostic-surface one**, it was
|
|
236
|
+
byte-identical on `0.0.5`, and it was filed as its own item rather than folded in here. **It is
|
|
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|
+
fixed in this same unreleased window — see the memo-poisoning entry at the top of this section —
|
|
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|
+
and the `/* v8 ignore */` block is gone with it.** It is **not** in the slot table and
|
|
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|
+
cannot be: it throws an un-coded `Error`, so it can carry no `expectCode`, and every slot in
|
|
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|
+
that table names one. The 2026-07-30 ecosystem audit recorded this package as "one site"; with
|
|
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|
+
`ExpansionDiagnostic.system` and this, it was **three**.
|
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|
+
|
|
14
243
|
- **`LICENSE` was unqualified MIT over a tree that also distributes third-party material**
|
|
15
244
|
(`TERMINOLOGY-LICENSE-THIRD-PARTY`, residuals 1 and 2 of `TERMINOLOGY-RESIDUALS`). The README had
|
|
16
245
|
already grown a "What is bundled" carve-out; the licence file had not, so the two consumer-facing
|
|
@@ -207,6 +436,20 @@ has_ingredient IN`). RxNorm authors no such relationship in any release: the ing
|
|
|
207
436
|
the matcher can see a real autolink, so a green result cannot come from a pattern that matches
|
|
208
437
|
nothing. It reads bytes directly rather than shelling out to `grep`, which this repository has
|
|
209
438
|
already been burned by. Scoped to `docs-content/` only, for the reason above.
|
|
439
|
+
- **The README opens with the Cosyte mark, which follows the reader's color scheme.** A `<picture>`
|
|
440
|
+
block above the H1 offers a dark-ground tile behind a `prefers-color-scheme: dark` media query and
|
|
441
|
+
carries the light-ground tile as the inner `<img>`, so on a renderer that honors the switch the
|
|
442
|
+
mark sits on a ground that matches the page it is read on. This README carried no image at all
|
|
443
|
+
before, so the block is purely additive: the `# @cosyte/terminology` heading, the blockquote
|
|
444
|
+
tagline and every section below are unchanged, and because the lockup reads "Cosyte" while the
|
|
445
|
+
heading reads `@cosyte/terminology`, nothing is duplicated. The failure mode is safe: a renderer
|
|
446
|
+
that strips `<source>` renders the inner `<img>`, so the worst case is a light-ground mark on a
|
|
447
|
+
dark page, never a missing image. On the npm package page the `<img>` is hoisted out of its
|
|
448
|
+
`<picture>` by the anchor wrapper, so the light cut renders there, which is the correct one
|
|
449
|
+
because npmjs.com has no dark mode. The alt text describes the artwork rather than the package,
|
|
450
|
+
since it is what a screen reader reads out and what a reader gets when the image fails. Both tile
|
|
451
|
+
URLs were rechecked before push and returned `200 image/png`. No behaviour, API surface or bundled
|
|
452
|
+
content changed.
|
|
210
453
|
|
|
211
454
|
### Changed
|
|
212
455
|
|
package/README.md
CHANGED
|
@@ -1,3 +1,8 @@
|
|
|
1
|
+
<picture>
|
|
2
|
+
<source media="(prefers-color-scheme: dark)" srcset="https://cosyte.com/tile/cosyte-lockup-tile-on-dark-1200x300.png">
|
|
3
|
+
<img alt="Cosyte: a plus mark set in two overlapping rounded squares, one solid and one outlined, beside the Cosyte wordmark" src="https://cosyte.com/tile/cosyte-lockup-tile-on-light-1200x300.png">
|
|
4
|
+
</picture>
|
|
5
|
+
|
|
1
6
|
# @cosyte/terminology
|
|
2
7
|
|
|
3
8
|
> A **zero-dependency terminology engine** for US healthcare code systems — FHIR-shaped, BYO-data,
|
|
@@ -194,8 +199,14 @@ _names_, listed under [What is bundled](#what-is-bundled).
|
|
|
194
199
|
**are** bundled are named, with their copyright, under [What is bundled](#what-is-bundled).
|
|
195
200
|
- **Liberal load, conservative assertion.** Malformed input degrades to a typed diagnostic; a 1:many
|
|
196
201
|
mapping returns the full candidate set, never collapsed to one.
|
|
197
|
-
- **Value-free
|
|
198
|
-
a
|
|
202
|
+
- **Value-free diagnostic messages.** Nothing you configured and nothing your release or resource
|
|
203
|
+
contained reaches a `message`, `detail`, `reason` or `err.stack` — not a column name, not a
|
|
204
|
+
canonical URI, not a unit atom — at any length. What sits beside a message is a locus: a line
|
|
205
|
+
number, a column count, an index path into your own resource (`compose.include[2]`), or a fixed
|
|
206
|
+
token naming which file of a release it came from. The
|
|
207
|
+
**objects** are a different matter: a typed `unknown`/`unmapped` outcome names the code, unit or
|
|
208
|
+
NDC you asked about, so log the `code` and the locus rather than the whole result — a code _in
|
|
209
|
+
patient context_ can be PHI.
|
|
199
210
|
- **Zero runtime dependencies. Dual ESM + CJS.** Node stdlib only; built with `tsup`, validated with
|
|
200
211
|
`attw`. Immutable by construction (every returned value is deep-frozen).
|
|
201
212
|
|
package/dist/index.cjs
CHANGED
|
@@ -199,6 +199,9 @@ var TerminologyError = class _TerminologyError extends Error {
|
|
|
199
199
|
/**
|
|
200
200
|
* @param code - The stable {@link FatalCode} describing the fault.
|
|
201
201
|
* @param message - A **value-free** structural description (path + fault; never an input value).
|
|
202
|
+
* Every piece of it must be engine-owned — a literal, a frozen-table entry, or a locus this
|
|
203
|
+
* package built. This string reaches `err.stack`, so interpolating a caller-supplied or
|
|
204
|
+
* document-derived value into it is how a diagnostic becomes a leak.
|
|
202
205
|
*/
|
|
203
206
|
constructor(code, message) {
|
|
204
207
|
super(message);
|
|
@@ -652,13 +655,16 @@ function parseCsvRows(content) {
|
|
|
652
655
|
function parseCsv(content) {
|
|
653
656
|
return parseCsvRows(content).rows;
|
|
654
657
|
}
|
|
655
|
-
|
|
658
|
+
var MISSING_COLUMN_MESSAGE = Object.freeze({
|
|
659
|
+
code: "CSV source: the configured 'code' column is not present in the header row",
|
|
660
|
+
display: "CSV source: the configured 'display' column is not present in the header row",
|
|
661
|
+
status: "CSV source: the configured 'status' column is not present in the header row",
|
|
662
|
+
property: "CSV source: a configured property column is not present in the header row"
|
|
663
|
+
});
|
|
664
|
+
function requireHeader(header, name, role) {
|
|
656
665
|
const idx = header.indexOf(name);
|
|
657
666
|
if (idx < 0) {
|
|
658
|
-
throw new TerminologyError(
|
|
659
|
-
FATAL_CODES.TERM_CODESYSTEM_MALFORMED,
|
|
660
|
-
`CSV source: required column '${name}' is not present in the header row`
|
|
661
|
-
);
|
|
667
|
+
throw new TerminologyError(FATAL_CODES.TERM_CODESYSTEM_MALFORMED, MISSING_COLUMN_MESSAGE[role]);
|
|
662
668
|
}
|
|
663
669
|
return idx;
|
|
664
670
|
}
|
|
@@ -682,12 +688,12 @@ function parseCsvSource(source) {
|
|
|
682
688
|
})
|
|
683
689
|
);
|
|
684
690
|
}
|
|
685
|
-
const codeIdx = requireHeader(header, source.columns.code);
|
|
686
|
-
const displayIdx = requireHeader(header, source.columns.display);
|
|
687
|
-
const statusIdx = source.columns.status !== void 0 ? requireHeader(header, source.columns.status) : void 0;
|
|
691
|
+
const codeIdx = requireHeader(header, source.columns.code, "code");
|
|
692
|
+
const displayIdx = requireHeader(header, source.columns.display, "display");
|
|
693
|
+
const statusIdx = source.columns.status !== void 0 ? requireHeader(header, source.columns.status, "status") : void 0;
|
|
688
694
|
const propIdx = (source.columns.properties ?? []).map((n) => ({
|
|
689
695
|
name: n,
|
|
690
|
-
index: requireHeader(header, n)
|
|
696
|
+
index: requireHeader(header, n, "property")
|
|
691
697
|
}));
|
|
692
698
|
const needCols = Math.max(codeIdx, displayIdx, statusIdx ?? 0, ...propIdx.map((p) => p.index)) + 1;
|
|
693
699
|
const concepts = /* @__PURE__ */ new Map();
|
|
@@ -1291,48 +1297,54 @@ function makeCoding(system, code, display, version) {
|
|
|
1291
1297
|
if (display !== void 0) init.display = display;
|
|
1292
1298
|
return coding(init);
|
|
1293
1299
|
}
|
|
1294
|
-
function cannotExpand(detail,
|
|
1300
|
+
function cannotExpand(detail, path) {
|
|
1295
1301
|
const d = { code: "TERM_VALUESET_CANNOT_EXPAND", detail };
|
|
1296
|
-
if (
|
|
1302
|
+
if (path !== void 0) d.path = path;
|
|
1297
1303
|
return Object.freeze(d);
|
|
1298
1304
|
}
|
|
1299
|
-
function truncated(detail,
|
|
1305
|
+
function truncated(detail, path) {
|
|
1300
1306
|
const d = { code: "TERM_VALUESET_EXPANSION_TRUNCATED", detail };
|
|
1301
|
-
|
|
1307
|
+
d.path = path;
|
|
1302
1308
|
return Object.freeze(d);
|
|
1303
1309
|
}
|
|
1310
|
+
function underPath(d, prefix) {
|
|
1311
|
+
const out = { code: d.code, detail: d.detail };
|
|
1312
|
+
out.path = d.path === void 0 ? prefix : `${prefix}/${d.path}`;
|
|
1313
|
+
return Object.freeze(out);
|
|
1314
|
+
}
|
|
1304
1315
|
function intersectInto(into, other) {
|
|
1305
1316
|
for (const k of into.keys()) if (!other.has(k)) into.delete(k);
|
|
1306
1317
|
return into;
|
|
1307
1318
|
}
|
|
1308
|
-
function expandReferencedValueSets(urls, ctx, visited) {
|
|
1319
|
+
function expandReferencedValueSets(urls, ctx, visited, path) {
|
|
1309
1320
|
const diagnostics = [];
|
|
1310
1321
|
let complete = true;
|
|
1311
1322
|
let acc = null;
|
|
1312
|
-
for (const url of urls) {
|
|
1323
|
+
for (const [i, url] of urls.entries()) {
|
|
1324
|
+
const refPath = `${path}.valueSet[${String(i)}]`;
|
|
1313
1325
|
if (visited.has(url)) {
|
|
1314
|
-
diagnostics.push(cannotExpand("cyclic value set reference",
|
|
1326
|
+
diagnostics.push(cannotExpand("cyclic value set reference", refPath));
|
|
1315
1327
|
complete = false;
|
|
1316
1328
|
acc = /* @__PURE__ */ new Map();
|
|
1317
1329
|
continue;
|
|
1318
1330
|
}
|
|
1319
1331
|
const vs = ctx.valueSets?.get(url);
|
|
1320
1332
|
if (vs === void 0) {
|
|
1321
|
-
diagnostics.push(cannotExpand("referenced value set not supplied",
|
|
1333
|
+
diagnostics.push(cannotExpand("referenced value set not supplied", refPath));
|
|
1322
1334
|
complete = false;
|
|
1323
1335
|
acc = /* @__PURE__ */ new Map();
|
|
1324
1336
|
continue;
|
|
1325
1337
|
}
|
|
1326
1338
|
const exp = expandInternal(vs, ctx, /* @__PURE__ */ new Set([...visited, url]));
|
|
1327
1339
|
if (!exp.complete) complete = false;
|
|
1328
|
-
for (const d of exp.diagnostics) diagnostics.push(d);
|
|
1340
|
+
for (const d of exp.diagnostics) diagnostics.push(underPath(d, refPath));
|
|
1329
1341
|
const members = /* @__PURE__ */ new Map();
|
|
1330
1342
|
for (const c of exp.contains) members.set(codingKey(c.system, c.code), c);
|
|
1331
1343
|
acc = acc === null ? members : intersectInto(acc, members);
|
|
1332
1344
|
}
|
|
1333
1345
|
return { members: acc ?? /* @__PURE__ */ new Map(), complete, diagnostics };
|
|
1334
1346
|
}
|
|
1335
|
-
function expandComponent(component, ctx, visited) {
|
|
1347
|
+
function expandComponent(component, ctx, visited, path) {
|
|
1336
1348
|
const diagnostics = [];
|
|
1337
1349
|
let complete = true;
|
|
1338
1350
|
const { system, version, concept, filter, valueSet: valueSet2 } = component;
|
|
@@ -1347,18 +1359,18 @@ function expandComponent(component, ctx, visited) {
|
|
|
1347
1359
|
}
|
|
1348
1360
|
} else if (hasFilter || system !== void 0 && !hasVs) {
|
|
1349
1361
|
if (system === void 0) {
|
|
1350
|
-
diagnostics.push(cannotExpand("intensional filter without a code system 'system'"));
|
|
1362
|
+
diagnostics.push(cannotExpand("intensional filter without a code system 'system'", path));
|
|
1351
1363
|
return { members: /* @__PURE__ */ new Map(), complete: false, diagnostics };
|
|
1352
1364
|
}
|
|
1353
1365
|
const cs = ctx.codeSystems?.get(system);
|
|
1354
1366
|
if (cs === void 0) {
|
|
1355
|
-
diagnostics.push(cannotExpand("code system not supplied for intensional include",
|
|
1367
|
+
diagnostics.push(cannotExpand("code system not supplied for intensional include", path));
|
|
1356
1368
|
return { members: /* @__PURE__ */ new Map(), complete: false, diagnostics };
|
|
1357
1369
|
}
|
|
1358
1370
|
if (hasFilter) {
|
|
1359
1371
|
const unsupported = unsupportedOps(filter);
|
|
1360
1372
|
if (unsupported.length > 0) {
|
|
1361
|
-
diagnostics.push(cannotExpand("unsupported filter operator",
|
|
1373
|
+
diagnostics.push(cannotExpand("unsupported filter operator", path));
|
|
1362
1374
|
return { members: /* @__PURE__ */ new Map(), complete: false, diagnostics };
|
|
1363
1375
|
}
|
|
1364
1376
|
const sub = buildSubsumption(cs);
|
|
@@ -1382,7 +1394,7 @@ function expandComponent(component, ctx, visited) {
|
|
|
1382
1394
|
}
|
|
1383
1395
|
}
|
|
1384
1396
|
if (hasVs) {
|
|
1385
|
-
const refs = expandReferencedValueSets(valueSet2, ctx, visited);
|
|
1397
|
+
const refs = expandReferencedValueSets(valueSet2, ctx, visited, path);
|
|
1386
1398
|
for (const d of refs.diagnostics) diagnostics.push(d);
|
|
1387
1399
|
if (!refs.complete) complete = false;
|
|
1388
1400
|
base = base === null ? refs.members : intersectInto(base, refs.members);
|
|
@@ -1407,7 +1419,7 @@ function expandInternal(vs, ctx, visited) {
|
|
|
1407
1419
|
if (vs.expansion.truncated) {
|
|
1408
1420
|
complete = false;
|
|
1409
1421
|
diagnostics.push(
|
|
1410
|
-
truncated("pre-computed expansion is incomplete (truncated or too-costly)",
|
|
1422
|
+
truncated("pre-computed expansion is incomplete (truncated or too-costly)", "expansion")
|
|
1411
1423
|
);
|
|
1412
1424
|
}
|
|
1413
1425
|
const out = {
|
|
@@ -1422,14 +1434,14 @@ function expandInternal(vs, ctx, visited) {
|
|
|
1422
1434
|
const included = /* @__PURE__ */ new Map();
|
|
1423
1435
|
const diagnostics = [];
|
|
1424
1436
|
let complete = true;
|
|
1425
|
-
for (const inc of vs.compose.include) {
|
|
1426
|
-
const r = expandComponent(inc, ctx, visited);
|
|
1437
|
+
for (const [i, inc] of vs.compose.include.entries()) {
|
|
1438
|
+
const r = expandComponent(inc, ctx, visited, `compose.include[${String(i)}]`);
|
|
1427
1439
|
if (!r.complete) complete = false;
|
|
1428
1440
|
for (const d of r.diagnostics) diagnostics.push(d);
|
|
1429
1441
|
for (const [k, c] of r.members) if (!included.has(k)) included.set(k, c);
|
|
1430
1442
|
}
|
|
1431
|
-
for (const exc of vs.compose.exclude) {
|
|
1432
|
-
const r = expandComponent(exc, ctx, visited);
|
|
1443
|
+
for (const [i, exc] of vs.compose.exclude.entries()) {
|
|
1444
|
+
const r = expandComponent(exc, ctx, visited, `compose.exclude[${String(i)}]`);
|
|
1433
1445
|
for (const d of r.diagnostics) diagnostics.push(d);
|
|
1434
1446
|
for (const k of r.members.keys()) included.delete(k);
|
|
1435
1447
|
if (!r.complete) {
|
|
@@ -1456,12 +1468,17 @@ function expand(vs, ctx = {}) {
|
|
|
1456
1468
|
}
|
|
1457
1469
|
|
|
1458
1470
|
// src/valueset/validate.ts
|
|
1459
|
-
function cannotExpand2(detail,
|
|
1471
|
+
function cannotExpand2(detail, path) {
|
|
1460
1472
|
const d = { code: "TERM_VALUESET_CANNOT_EXPAND", detail };
|
|
1461
|
-
if (
|
|
1473
|
+
if (path !== void 0) d.path = path;
|
|
1462
1474
|
return Object.freeze(d);
|
|
1463
1475
|
}
|
|
1464
|
-
function
|
|
1476
|
+
function underPath2(d, prefix) {
|
|
1477
|
+
const out = { code: d.code, detail: d.detail };
|
|
1478
|
+
out.path = d.path === void 0 ? prefix : `${prefix}/${d.path}`;
|
|
1479
|
+
return Object.freeze(out);
|
|
1480
|
+
}
|
|
1481
|
+
function matchComponent(target, component, ctx, visited, path) {
|
|
1465
1482
|
const diagnostics = [];
|
|
1466
1483
|
const { system, concept, filter, valueSet: valueSet2 } = component;
|
|
1467
1484
|
const hasConcept = concept !== void 0;
|
|
@@ -1475,18 +1492,18 @@ function matchComponent(target, component, ctx, visited) {
|
|
|
1475
1492
|
baseMatched = concept.some((c) => c.code === target.code);
|
|
1476
1493
|
} else if (hasFilter || system !== void 0 && !hasVs) {
|
|
1477
1494
|
if (system === void 0) {
|
|
1478
|
-
diagnostics.push(cannotExpand2("intensional filter without a code system 'system'"));
|
|
1495
|
+
diagnostics.push(cannotExpand2("intensional filter without a code system 'system'", path));
|
|
1479
1496
|
baseMatched = false;
|
|
1480
1497
|
baseComplete = false;
|
|
1481
1498
|
} else {
|
|
1482
1499
|
const cs = ctx.codeSystems?.get(system);
|
|
1483
1500
|
if (cs === void 0) {
|
|
1484
|
-
diagnostics.push(cannotExpand2("code system not supplied for intensional include",
|
|
1501
|
+
diagnostics.push(cannotExpand2("code system not supplied for intensional include", path));
|
|
1485
1502
|
baseMatched = false;
|
|
1486
1503
|
baseComplete = false;
|
|
1487
1504
|
} else if (hasFilter) {
|
|
1488
1505
|
if (unsupportedOps(filter).length > 0) {
|
|
1489
|
-
diagnostics.push(cannotExpand2("unsupported filter operator",
|
|
1506
|
+
diagnostics.push(cannotExpand2("unsupported filter operator", path));
|
|
1490
1507
|
baseMatched = false;
|
|
1491
1508
|
baseComplete = false;
|
|
1492
1509
|
} else {
|
|
@@ -1501,21 +1518,22 @@ function matchComponent(target, component, ctx, visited) {
|
|
|
1501
1518
|
let refDefiniteFalse = false;
|
|
1502
1519
|
let refUndetermined = false;
|
|
1503
1520
|
if (hasVs) {
|
|
1504
|
-
for (const url of valueSet2) {
|
|
1521
|
+
for (const [i, url] of valueSet2.entries()) {
|
|
1522
|
+
const refPath = `${path}.valueSet[${String(i)}]`;
|
|
1505
1523
|
if (visited.has(url)) {
|
|
1506
|
-
diagnostics.push(cannotExpand2("cyclic value set reference",
|
|
1524
|
+
diagnostics.push(cannotExpand2("cyclic value set reference", refPath));
|
|
1507
1525
|
refUndetermined = true;
|
|
1508
1526
|
continue;
|
|
1509
1527
|
}
|
|
1510
1528
|
const vs = ctx.valueSets?.get(url);
|
|
1511
1529
|
if (vs === void 0) {
|
|
1512
|
-
diagnostics.push(cannotExpand2("referenced value set not supplied",
|
|
1530
|
+
diagnostics.push(cannotExpand2("referenced value set not supplied", refPath));
|
|
1513
1531
|
refUndetermined = true;
|
|
1514
1532
|
continue;
|
|
1515
1533
|
}
|
|
1516
1534
|
const m = validateInternal(target, vs, ctx, /* @__PURE__ */ new Set([...visited, url]));
|
|
1517
1535
|
if (m.undetermined) {
|
|
1518
|
-
for (const d of m.diagnostics) diagnostics.push(d);
|
|
1536
|
+
for (const d of m.diagnostics) diagnostics.push(underPath2(d, refPath));
|
|
1519
1537
|
refUndetermined = true;
|
|
1520
1538
|
} else if (!m.result) {
|
|
1521
1539
|
refDefiniteFalse = true;
|
|
@@ -1552,7 +1570,7 @@ function validateInternal(target, vs, ctx, visited) {
|
|
|
1552
1570
|
if (found) return decided(true, target);
|
|
1553
1571
|
if (vs.expansion.truncated) {
|
|
1554
1572
|
return undetermined(target, [
|
|
1555
|
-
cannotExpand2("pre-computed expansion is incomplete (truncated or too-costly)",
|
|
1573
|
+
cannotExpand2("pre-computed expansion is incomplete (truncated or too-costly)", "expansion")
|
|
1556
1574
|
]);
|
|
1557
1575
|
}
|
|
1558
1576
|
return decided(false, target);
|
|
@@ -1561,16 +1579,16 @@ function validateInternal(target, vs, ctx, visited) {
|
|
|
1561
1579
|
const diagnostics = [];
|
|
1562
1580
|
let includedDefinite = false;
|
|
1563
1581
|
let anyIncludeUndetermined = false;
|
|
1564
|
-
for (const inc of vs.compose.include) {
|
|
1565
|
-
const m = matchComponent(target, inc, ctx, visited);
|
|
1582
|
+
for (const [i, inc] of vs.compose.include.entries()) {
|
|
1583
|
+
const m = matchComponent(target, inc, ctx, visited, `compose.include[${String(i)}]`);
|
|
1566
1584
|
for (const d of m.diagnostics) diagnostics.push(d);
|
|
1567
1585
|
if (m.complete && m.matched) includedDefinite = true;
|
|
1568
1586
|
if (!m.complete) anyIncludeUndetermined = true;
|
|
1569
1587
|
}
|
|
1570
1588
|
let excludedDefinite = false;
|
|
1571
1589
|
let anyExcludeUndetermined = false;
|
|
1572
|
-
for (const exc of vs.compose.exclude) {
|
|
1573
|
-
const m = matchComponent(target, exc, ctx, visited);
|
|
1590
|
+
for (const [i, exc] of vs.compose.exclude.entries()) {
|
|
1591
|
+
const m = matchComponent(target, exc, ctx, visited, `compose.exclude[${String(i)}]`);
|
|
1574
1592
|
for (const d of m.diagnostics) diagnostics.push(d);
|
|
1575
1593
|
if (m.complete && m.matched) excludedDefinite = true;
|
|
1576
1594
|
if (!m.complete) anyExcludeUndetermined = true;
|
|
@@ -3893,32 +3911,37 @@ function power(r, p) {
|
|
|
3893
3911
|
}
|
|
3894
3912
|
return { kind: "linear", factor: Math.pow(r.factor, p), dims };
|
|
3895
3913
|
}
|
|
3896
|
-
var DIMENSIONLESS = {
|
|
3897
|
-
|
|
3898
|
-
|
|
3914
|
+
var DIMENSIONLESS = Object.freeze({
|
|
3915
|
+
kind: "linear",
|
|
3916
|
+
factor: 1,
|
|
3917
|
+
dims: Object.freeze({})
|
|
3918
|
+
});
|
|
3919
|
+
var atomMemo = /* @__PURE__ */ new WeakMap();
|
|
3920
|
+
var inProgress = /* @__PURE__ */ new WeakSet();
|
|
3899
3921
|
function reduceAtomLinear(atom) {
|
|
3900
3922
|
if (atom.base) return { kind: "linear", factor: 1, dims: { [atom.dim ?? atom.code]: 1 } };
|
|
3901
3923
|
if (atom.arbitrary) return { kind: "linear", factor: 1, dims: { [`arb:${atom.code}`]: 1 } };
|
|
3902
|
-
const cached2 = atomMemo.get(atom
|
|
3924
|
+
const cached2 = atomMemo.get(atom);
|
|
3903
3925
|
if (cached2) return cached2;
|
|
3904
|
-
if (inProgress.has(atom
|
|
3905
|
-
throw new Error(
|
|
3926
|
+
if (inProgress.has(atom)) {
|
|
3927
|
+
throw new Error("cyclic UCUM atom definition in the unit table");
|
|
3906
3928
|
}
|
|
3907
3929
|
if (!atom.value) {
|
|
3908
|
-
|
|
3909
|
-
return DIMENSIONLESS;
|
|
3930
|
+
throw new Error("UCUM atom has no linear definition");
|
|
3910
3931
|
}
|
|
3911
|
-
inProgress.add(atom
|
|
3912
|
-
|
|
3913
|
-
|
|
3914
|
-
|
|
3915
|
-
|
|
3932
|
+
inProgress.add(atom);
|
|
3933
|
+
try {
|
|
3934
|
+
const parsed = parseUcum(atom.value.unit);
|
|
3935
|
+
if (!parsed.ok) {
|
|
3936
|
+
throw new Error("unparseable UCUM essence definition in the unit table");
|
|
3937
|
+
}
|
|
3938
|
+
const reduced = linearReduceTerm(parsed.node);
|
|
3939
|
+
const result = multiply({ kind: "linear", factor: atom.value.factor, dims: {} }, reduced);
|
|
3940
|
+
atomMemo.set(atom, result);
|
|
3941
|
+
return result;
|
|
3942
|
+
} finally {
|
|
3943
|
+
inProgress.delete(atom);
|
|
3916
3944
|
}
|
|
3917
|
-
const reduced = linearReduceTerm(parsed.node);
|
|
3918
|
-
const result = multiply({ factor: atom.value.factor, dims: {} }, reduced);
|
|
3919
|
-
inProgress.delete(atom.code);
|
|
3920
|
-
atomMemo.set(atom.code, result);
|
|
3921
|
-
return result;
|
|
3922
3945
|
}
|
|
3923
3946
|
function reduceSimpleLinear(node) {
|
|
3924
3947
|
const base = reduceAtomLinear(node.atom);
|
|
@@ -3938,7 +3961,7 @@ function linearReduceComponent(comp) {
|
|
|
3938
3961
|
}
|
|
3939
3962
|
}
|
|
3940
3963
|
function linearReduceTerm(node) {
|
|
3941
|
-
let acc =
|
|
3964
|
+
let acc = { kind: "linear", factor: 1, dims: {} };
|
|
3942
3965
|
for (const { sign, node: comp } of node.factors) {
|
|
3943
3966
|
acc = multiply(acc, power(linearReduceComponent(comp), sign));
|
|
3944
3967
|
}
|
|
@@ -4120,10 +4143,15 @@ function applyGem(map, source) {
|
|
|
4120
4143
|
if (combinations !== void 0) matched.combinations = combinations;
|
|
4121
4144
|
return Object.freeze(matched);
|
|
4122
4145
|
}
|
|
4146
|
+
var NOT_INVERTIBLE_MESSAGE = /* @__PURE__ */ new Map([
|
|
4147
|
+
["9-to-10", "GEM map (direction 9-to-10) cannot be inverted \u2014 load the 10-to-9 GEM file instead"],
|
|
4148
|
+
["10-to-9", "GEM map (direction 10-to-9) cannot be inverted \u2014 load the 9-to-10 GEM file instead"]
|
|
4149
|
+
]);
|
|
4150
|
+
var NOT_INVERTIBLE_UNKNOWN_DIRECTION = "GEM map cannot be inverted \u2014 load the reverse GEM file instead";
|
|
4123
4151
|
function invertGem(map) {
|
|
4124
4152
|
throw new TerminologyError(
|
|
4125
4153
|
FATAL_CODES.TERM_MAP_NOT_INVERTIBLE,
|
|
4126
|
-
|
|
4154
|
+
NOT_INVERTIBLE_MESSAGE.get(map.direction) ?? NOT_INVERTIBLE_UNKNOWN_DIRECTION
|
|
4127
4155
|
);
|
|
4128
4156
|
}
|
|
4129
4157
|
|
|
@@ -4703,7 +4731,7 @@ function approximateMatch(graph, query, options = {}) {
|
|
|
4703
4731
|
}
|
|
4704
4732
|
|
|
4705
4733
|
// src/index.ts
|
|
4706
|
-
var VERSION = "0.0.
|
|
4734
|
+
var VERSION = "0.0.6";
|
|
4707
4735
|
|
|
4708
4736
|
exports.COMPLEX_MAP_SOURCE_SYSTEM = COMPLEX_MAP_SOURCE_SYSTEM;
|
|
4709
4737
|
exports.DIAGNOSTIC_CODES = DIAGNOSTIC_CODES;
|