@cosyte/terminology 0.0.1 → 0.0.2

package/dist/index.mjs

@@ -73,13 +73,13 @@ var DIAGNOSTIC_CODES = {
    * code system was not supplied, an unresolvable referenced value set, or a `filter` operator the
    * engine does not implement. Surfaced as a typed outcome that marks the expansion **incomplete**;
    * the engine **never** fabricates a member and **never** returns a silently-empty "no members"
-   * answer for a part it could not compute (roadmap §4.4 — a false "not a member" is a clinical error).
+   * answer for a part it could not compute (a false "not a member" is a clinical error).
    */
   TERM_VALUESET_CANNOT_EXPAND: "TERM_VALUESET_CANNOT_EXPAND",
   /**
    * A **pre-computed** `ValueSet.expansion` is **incomplete** — its `total` exceeds the number of
-   * `contains` entries, or it is flagged too-costly (the VSAC `$expand` >1200-code truncation hazard,
-   * roadmap §4.4). The engine **never treats a truncated expansion as complete membership**: a code
+   * `contains` entries, or it is flagged too-costly (the VSAC `$expand` >1200-code truncation
+   * hazard). The engine **never treats a truncated expansion as complete membership**: a code
    * absent from a truncated expansion is `undetermined`, never a confident "not a member".
    */
   TERM_VALUESET_EXPANSION_TRUNCATED: "TERM_VALUESET_EXPANSION_TRUNCATED",
@@ -87,7 +87,7 @@ var DIAGNOSTIC_CODES = {
    * A UCUM unit expression is **not valid** — it does not parse against the UCUM grammar, or it
    * names an atom absent from the vendored UCUM table. A **first-class typed outcome, never an
    * error and never a guess**: {@link validateUcum} returns `{ valid: false, reason }`, never a
-   * coerced or "nearest" unit (the never-fabricate invariant, applied to units — roadmap §4.3). The
+   * coerced or "nearest" unit (the never-fabricate invariant, applied to units). The
    * `reason` is value-free (a grammar fault or an unknown-atom shape), never PHI.
    */
   TERM_UCUM_INVALID: "TERM_UCUM_INVALID",
@@ -95,7 +95,7 @@ var DIAGNOSTIC_CODES = {
    * A crosswalk source code has an **authored No-Map** — the steward declares it has no valid target
    * in the other classification (a GEM `NoDx`/`NoPCS` sentinel, or a SNOMED complex-map `447638001`
    * "cannot be classified" category). A **first-class typed outcome, never an error and never a
-   * guess** (the never-fabricate invariant, applied to crosswalks — roadmap §4.1). Distinct from
+   * guess** (the never-fabricate invariant, applied to crosswalks). Distinct from
    * {@link TERM_CROSSWALK_UNMAPPED}: the source *is* in the map, and the map says "no target".
    */
   TERM_CROSSWALK_NO_MAP: "TERM_CROSSWALK_NO_MAP",
@@ -109,7 +109,7 @@ var DIAGNOSTIC_CODES = {
   /**
    * A SNOMED→ICD-10-CM complex-map group's decision needs **patient context** (an `IFA` age band or
    * gender) the caller did not supply. The engine surfaces the candidate rules + advice and **refuses
-   * to pick a branch** it lacks the data for (roadmap §4.1) — never a silently-chosen target.
+   * to pick a branch** it lacks the data for — never a silently-chosen target.
    */
   TERM_CROSSWALK_CONTEXT_REQUIRED: "TERM_CROSSWALK_CONTEXT_REQUIRED",
   /**
@@ -131,17 +131,27 @@ var DIAGNOSTIC_CODES = {
    * **silently** — they are expected, not faults.
    */
   TERM_RXNORM_MALFORMED_ROW: "TERM_RXNORM_MALFORMED_ROW",
+  /**
+   * An `RXCUI` appeared in the release's `SAB=RXNORM` atoms but **none of them could establish its
+   * term type**, so it is **not** in the graph. Either every atom carried a synonym-class `TTY`
+   * (`PSN`/`SY`/`TMSY`, which Appendix 5 defines as a "synonym of another TTY" and which therefore
+   * types a *name* rather than a concept) or every atom carried a `TTY` this engine does not model.
+   * The concept is skipped rather than typed from a synonym atom: an absent concept is already a
+   * first-class typed answer (`TERM_RXNORM_UNKNOWN_RXCUI`), while a concept whose term type reads
+   * `TMSY` is a fabricated claim about what a drug *is* that a caller cannot detect.
+   */
+  TERM_RXNORM_UNTYPED_CONCEPT: "TERM_RXNORM_UNTYPED_CONCEPT",
   /**
    * A RxNorm graph navigation was asked about an `RXCUI` **absent from the loaded release** — a
    * first-class typed outcome, never a fabricated concept and never an empty "success" (the
-   * never-fabricate invariant, applied to the drug graph — roadmap §4.2). Distinct from a *present*
+   * never-fabricate invariant, applied to the drug graph). Distinct from a *present*
    * concept that simply has no edge of the requested relationship (that is a found result with empty
    * targets).
    */
   TERM_RXNORM_UNKNOWN_RXCUI: "TERM_RXNORM_UNKNOWN_RXCUI",
   /**
    * An NDC could **not be resolved** to any `RXCUI` in the loaded RxNorm release — a typed, surfaced
-   * absence, never a guessed `RXCUI`. NDC↔RXCUI is many:1 and temporal (roadmap §4.2), so a resolution
+   * absence, never a guessed `RXCUI`. NDC↔RXCUI is many:1 and temporal, so a resolution
    * is always release-scoped; an NDC not present in the loaded release is this diagnostic.
    */
   TERM_RXNORM_NDC_UNMAPPED: "TERM_RXNORM_NDC_UNMAPPED"
@@ -176,7 +186,7 @@ var FATAL_CODES = {
   /**
    * An **inversion** of a directional crosswalk was requested — a forbidden operation. The GEMs and
    * the SNOMED→ICD-10-CM map are authoritative in **one direction only**; a forward map is not the
-   * inverse of the backward map (roadmap §4.1). Thrown by {@link ../crosswalk/gems.invertGem} so the
+   * inverse of the backward map. Thrown by {@link ../crosswalk/gems.invertGem} so the
    * never-invert refusal is a first-class, discoverable contract rather than a silent absence.
    */
   TERM_MAP_NOT_INVERTIBLE: "TERM_MAP_NOT_INVERTIBLE"
@@ -4358,12 +4368,17 @@ var TERM_TYPES = Object.freeze({
   BN: "Brand Name",
   SCDC: "Semantic Clinical Drug Component",
   SBDC: "Semantic Branded Drug Component",
+  SCDF: "Semantic Clinical Drug Form",
+  SBDF: "Semantic Branded Drug Form",
+  SCDFP: "Semantic Clinical Drug Form Precise",
+  SBDFP: "Semantic Branded Drug Form Precise",
   SCD: "Semantic Clinical Drug",
   SBD: "Semantic Branded Drug",
   SCDG: "Semantic Clinical Drug Group",
   SBDG: "Semantic Branded Drug Group",
+  SCDGP: "Semantic Clinical Drug Form Group Precise",
   GPCK: "Generic Pack",
-  BPCK: "Branded Pack",
+  BPCK: "Brand Name Pack",
   DF: "Dose Form",
   DFG: "Dose Form Group",
   PSN: "Prescribable Name",
@@ -4372,9 +4387,13 @@ var TERM_TYPES = Object.freeze({
   ET: "Entry Term"
 });
 var KNOWN = new Set(Object.keys(TERM_TYPES));
+var SYNONYM = /* @__PURE__ */ new Set(["PSN", "SY", "TMSY"]);
 function asTermType(tty) {
   return KNOWN.has(tty) ? tty : void 0;
 }
+function isSynonymTermType(tty) {
+  return SYNONYM.has(tty);
+}
 
 // src/rxnorm/load.ts
 var SAB_RXNORM = "RXNORM";
@@ -4388,13 +4407,13 @@ function cell2(cells, index) {
 }
 function parseConso(content, warnings) {
   const concepts = /* @__PURE__ */ new Map();
-  const lines = content.split(/\r?\n/);
-  for (let i = 0; i < lines.length; i++) {
-    const raw = lines[i] ?? "";
+  const conso = [];
+  const untyped = /* @__PURE__ */ new Map();
+  for (const [i, raw] of content.split(/\r?\n/).entries()) {
     if (raw === "") continue;
     const cells = parseRrfLine(raw);
     if (cells.length <= CONSO.STR) {
-      warnings.push(
+      conso.push(
         Object.freeze({
           code: "TERM_RXNORM_MALFORMED_ROW",
           file: "RXNCONSO",
@@ -4405,11 +4424,9 @@ function parseConso(content, warnings) {
       continue;
     }
     if (cell2(cells, CONSO.SAB) !== SAB_RXNORM) continue;
-    const tty = asTermType(cell2(cells, CONSO.TTY) ?? "");
-    if (tty === void 0) continue;
     const rxcui = cell2(cells, CONSO.RXCUI);
     if (rxcui === void 0 || rxcui === "") {
-      warnings.push(
+      conso.push(
         Object.freeze({
           code: "TERM_RXNORM_MALFORMED_ROW",
           file: "RXNCONSO",
@@ -4419,7 +4436,13 @@ function parseConso(content, warnings) {
       );
       continue;
     }
+    const tty = asTermType(cell2(cells, CONSO.TTY) ?? "");
+    if (tty === void 0 || isSynonymTermType(tty)) {
+      if (!concepts.has(rxcui) && !untyped.has(rxcui)) untyped.set(rxcui, i + 1);
+      continue;
+    }
     if (concepts.has(rxcui)) continue;
+    untyped.delete(rxcui);
     const name = cell2(cells, CONSO.STR) ?? "";
     const suppress = cell2(cells, CONSO.SUPPRESS) ?? "N";
     concepts.set(
@@ -4427,14 +4450,24 @@ function parseConso(content, warnings) {
       Object.freeze({ rxcui, tty, name, suppressed: suppress !== "" && suppress !== "N" })
     );
   }
+  for (const line of untyped.values()) {
+    conso.push(
+      Object.freeze({
+        code: "TERM_RXNORM_UNTYPED_CONCEPT",
+        file: "RXNCONSO",
+        line,
+        detail: "no RXNORM atom established this RXCUI's term type (every atom was synonym-class or an unmodelled TTY); skipped rather than typed from a synonym"
+      })
+    );
+  }
+  conso.sort((a, b) => a.line - b.line);
+  for (const w of conso) warnings.push(w);
   return concepts;
 }
 function parseRel(content, warnings) {
   const edges = /* @__PURE__ */ new Map();
   let edgeCount = 0;
-  const lines = content.split(/\r?\n/);
-  for (let i = 0; i < lines.length; i++) {
-    const raw = lines[i] ?? "";
+  for (const [i, raw] of content.split(/\r?\n/).entries()) {
     if (raw === "") continue;
     const cells = parseRrfLine(raw);
     if (cells.length <= REL.RELA) {
@@ -4463,9 +4496,7 @@ function parseRel(content, warnings) {
 }
 function parseNdcs(content, warnings) {
   const ndcs = /* @__PURE__ */ new Map();
-  const lines = content.split(/\r?\n/);
-  for (let i = 0; i < lines.length; i++) {
-    const raw = lines[i] ?? "";
+  for (const [i, raw] of content.split(/\r?\n/).entries()) {
     if (raw === "") continue;
     const cells = parseRrfLine(raw);
     if (cells.length <= SAT.ATV) {
@@ -4517,9 +4548,17 @@ function loadRxNormGraph(source) {
 
 // src/rxnorm/rela.ts
 var RELA = {
-  /** `has_ingredient` — subject (a drug/component) *has ingredient* object (an `IN`/`PIN`). */
+  /**
+   * `has_ingredient`: subject *has ingredient* object. Authored from the clinical side
+   * (`SCDC`/`SCDF`/`SCDG`) to an `IN` and from the branded side (`SBD`/`SBDC`/`SBDF`/`SBDG`) to a
+   * `BN`; RxNorm authors no `SCD ⟶ IN` row.
+   */
   HAS_INGREDIENT: "has_ingredient",
-  /** `ingredient_of` — subject (an `IN`/`PIN`) *is an ingredient of* object (a drug/component). */
+  /**
+   * `ingredient_of`: subject *is an ingredient of* object. The authored inverse, so an `IN` reaches
+   * clinical components and dose forms and a `BN` reaches branded concepts (the `SBD` included).
+   * Neither reaches an `SCD`.
+   */
   INGREDIENT_OF: "ingredient_of",
   /** `has_precise_ingredient` — subject *has precise ingredient* object (a `PIN`). */
   HAS_PRECISE_INGREDIENT: "has_precise_ingredient",
@@ -4662,8 +4701,8 @@ function approximateMatch(graph, query, options = {}) {
 }
 
 // src/index.ts
-var VERSION = "0.0.0";
+var VERSION = "0.0.2";
 
-export { COMPLEX_MAP_SOURCE_SYSTEM, DIAGNOSTIC_CODES, FATAL_CODES, HL7_V2_OID_ROOT, HL7_V2_URL_PREFIX, ICD10CM_ORDER_FILE_FIELDS, ICD10CM_SYSTEM, ICD9CM_SYSTEM, MAP_CATEGORIES, NO_MAP_CATEGORIES, RELA, RELA_INVERSE, RXNORM_SYSTEM, SNOMEDCT_SYSTEM, SYSTEM_IDENTITIES, TERM_TYPES, TerminologyError, VERSION, applyComplexMap, applyGem, approximateMatch, asTermType, brandsFor, buildSubsumption, codeableConcept, coding, consistsOf, defaultStatusMapper, doseFormsOf, expand, genericFor, getArray, getBoolean, getConcept, getNumber, getString, ingredientsOf, invertGem, isA, isJsonObject, isUnknownSystem, loadCodeSystem, loadComplexMap, loadConceptMap, loadGems, loadRxNormGraph, loadUcumEssence, loadValueSet, lookup, makeStatus, matchesFilter, parseCsv, parseCsvSource, parseFhirCodeSystem, parseFixedWidth, parseRrf, parseRrfLine, parseUcum, reduce, relatedByRela, resolveNdc, resolveSystem, sliceField, translate, ucumEqual, unsupportedOps, validateCode, validateCodeInValueSet, validateUcum };
+export { COMPLEX_MAP_SOURCE_SYSTEM, DIAGNOSTIC_CODES, FATAL_CODES, HL7_V2_OID_ROOT, HL7_V2_URL_PREFIX, ICD10CM_ORDER_FILE_FIELDS, ICD10CM_SYSTEM, ICD9CM_SYSTEM, MAP_CATEGORIES, NO_MAP_CATEGORIES, RELA, RELA_INVERSE, RXNORM_SYSTEM, SNOMEDCT_SYSTEM, SYSTEM_IDENTITIES, TERM_TYPES, TerminologyError, VERSION, applyComplexMap, applyGem, approximateMatch, asTermType, brandsFor, buildSubsumption, codeableConcept, coding, consistsOf, defaultStatusMapper, doseFormsOf, expand, genericFor, getArray, getBoolean, getConcept, getNumber, getString, ingredientsOf, invertGem, isA, isJsonObject, isSynonymTermType, isUnknownSystem, loadCodeSystem, loadComplexMap, loadConceptMap, loadGems, loadRxNormGraph, loadUcumEssence, loadValueSet, lookup, makeStatus, matchesFilter, parseCsv, parseCsvSource, parseFhirCodeSystem, parseFixedWidth, parseRrf, parseRrfLine, parseUcum, reduce, relatedByRela, resolveNdc, resolveSystem, sliceField, translate, ucumEqual, unsupportedOps, validateCode, validateCodeInValueSet, validateUcum };
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