@cosyte/terminology 0.1.5 → 0.1.6

package/CHANGELOG.md

@@ -1,5 +1,15 @@
 # Changelog
 
+## 0.1.6
+
+### Patch Changes
+
+- 43eea2f: An internal tidy with no change to any result, warning, or diagnostic. The value set diagnostic factories now take the path every caller already gives them, a few expressions became statements so a coverage note can name the one arm no input reaches, and those arms now carry that note.
+- 43eea2f: A CSV source whose `columns.properties` list has a hole now fails with the typed `TERM_CODESYSTEM_MALFORMED` fatal for a missing property column, the same as an explicit `undefined` entry, instead of a `TypeError` from inside the loader.
+- 0cb5b88: Doc comments, which your editor shows on hover and the generated API reference prints, now match the code. `resolveSystem` lists the forms it accepts in the order it tries them, and no longer says it accepts a `v2-0203` mnemonic on its own (it does not; pass the table's OID or URI). `SYSTEM_IDENTITIES` and `resolveSystem` no longer say every accepted mnemonic comes from HL7 Table 0396: aliases such as `LOINC` and `CPT` are accepted too but are not Table 0396 codes. `NdcStatus` says that `loadRxNormGraph` reads no NDC history, so every NDC it resolves is `active`. `RxNormGraph.concepts` says a concept is typed by its first defining atom. The complex-map outcome types and `MAP_CATEGORIES.AMBIGUOUS` no longer say an ambiguous or context-dependent category stops a group on its own: the group's rules decide. Links that printed as a source path, such as `../crosswalk/gems.invertGem`, now link the symbol. No code changes.
+- e16570e: An RRF or fixed-width source whose property list has an entry that is not an object (a hole, `undefined`, or `null`) now fails with the typed `TERM_CODESYSTEM_MALFORMED` fatal, as a CSV source with a hole in its property columns does, instead of a `TypeError` from inside the loader.
+- 43eea2f: `validateCodeInValueSet` no longer admits a code through a `compose` component that selects nothing. A component with no `system`, `concept`, `filter`, or referenced value set (the loader accepts one with an empty `valueSet` list) matched every code, so an include admitted any code and an exclude removed every code, while `expand` gave the same component no members. Membership now agrees with `expand`: such a component matches no code, and a `valueSet` list that yields no reference is an intersection with nothing.
+
 ## 0.1.5
 
 ### Patch Changes

package/README.md

@@ -379,6 +379,9 @@ Questions, bug reports, and an answer the engine got wrong go in
 system, map, or value set that reproduces it. Use synthetic data only: a code in patient context can
 be PHI. [SUPPORT.md](https://github.com/cosyte/.github/blob/main/SUPPORT.md) says where to ask what.
 
+Need a terminology integration built, or hosted and run for you? See our
+[integration services](https://cosyte.com/integration-services).
+
 ## Security
 
 Report a vulnerability privately, never in a public issue, and with no real patient data in it:

package/dist/index.cjs

@@ -212,7 +212,7 @@ 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. Thrown by {@link ../crosswalk/gems.invertGem} so the
+   * inverse of the backward map. Thrown by {@link 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"
@@ -764,10 +764,10 @@ function parseCsvSource(source) {
   const codeIdx = requireHeader(header, source.columns.code, "code");
   const displayIdx = requireHeader(header, source.columns.display, "display");
   const statusIdx = source.columns.status !== void 0 ? requireHeader(header, source.columns.status, "status") : void 0;
-  const propIdx = (source.columns.properties ?? []).map((n) => ({
-    name: n,
-    index: requireHeader(header, n, "property")
-  }));
+  const propIdx = [];
+  for (const n of source.columns.properties ?? []) {
+    propIdx.push({ name: n, index: requireHeader(header, n, "property") });
+  }
   const needCols = Math.max(codeIdx, displayIdx, statusIdx ?? 0, ...propIdx.map((p) => p.index)) + 1;
   const concepts = /* @__PURE__ */ new Map();
   for (let r = 1; r < rows.length; r++) {
@@ -856,9 +856,10 @@ function collectConcepts(rawConcepts, into, warnings, parentCode) {
     if (code !== void 0 && code !== "" && !into.has(code)) {
       const props = [];
       for (const p of getArray(raw, "property") ?? []) {
+        if (!isJsonObject(p)) continue;
         const pcode = getString(p, "code");
         if (pcode === void 0) continue;
-        const value = isJsonObject(p) ? readPropertyValue(p) : void 0;
+        const value = readPropertyValue(p);
         if (value !== void 0) props.push(Object.freeze({ code: pcode, value }));
       }
       if (parentCode !== void 0 && !props.some((p) => p.code === "parent" && p.value === parentCode)) {
@@ -921,9 +922,21 @@ var ICD10CM_ORDER_FILE_FIELDS = Object.freeze({
     Object.freeze({ name: "shortDescription", slice: Object.freeze({ start: 16, end: 76 }) })
   ])
 });
+function requirePropertyFields(fields) {
+  for (const p of fields.properties ?? []) {
+    const entry = p;
+    if (typeof entry !== "object" || entry === null) {
+      throw new TerminologyError(
+        FATAL_CODES.TERM_CODESYSTEM_MALFORMED,
+        "fixed-width source: a configured property field is not an object"
+      );
+    }
+  }
+}
 function parseFixedWidth(source) {
   const statusMap = source.statusMap ?? defaultStatusMapper;
   const fields = source.fields;
+  requirePropertyFields(fields);
   const concepts = /* @__PURE__ */ new Map();
   const warnings = [];
   const lines = source.content.split(/\r?\n/);
@@ -985,7 +998,16 @@ function parseRrfLine(line) {
 function maxColumn(source) {
   const { code, display, status, properties } = source.columns;
   let max = Math.max(code, display, status ?? 0);
-  for (const p of properties ?? []) max = Math.max(max, p.column);
+  for (const p of properties ?? []) {
+    const entry = p;
+    if (typeof entry !== "object" || entry === null) {
+      throw new TerminologyError(
+        FATAL_CODES.TERM_CODESYSTEM_MALFORMED,
+        "RRF source: a configured property column is not an object"
+      );
+    }
+    max = Math.max(max, p.column);
+  }
   return max;
 }
 function cell(cells, index) {
@@ -1392,8 +1414,7 @@ function makeCoding(system, code, display, version) {
   return coding(init);
 }
 function cannotExpand(detail, path) {
-  const d = { code: "TERM_VALUESET_CANNOT_EXPAND", detail };
-  if (path !== void 0) d.path = path;
+  const d = { code: "TERM_VALUESET_CANNOT_EXPAND", detail, path };
   return Object.freeze(d);
 }
 function truncated(detail, path) {
@@ -1407,9 +1428,9 @@ function truncated(detail, path) {
 function enumeratedUndefined(detail, path) {
   const d = {
     code: "TERM_VALUESET_ENUMERATED_CODE_UNDEFINED",
-    detail
+    detail,
+    path
   };
-  if (path !== void 0) d.path = path;
   return Object.freeze(d);
 }
 function expansionIncompleteDetail(unclosed) {
@@ -1443,7 +1464,8 @@ function screenActive(members, component, ctx) {
 }
 function underPath(d, prefix) {
   const out = { code: d.code, detail: d.detail };
-  out.path = d.path === void 0 ? prefix : `${prefix}/${d.path}`;
+  if (d.path === void 0) out.path = prefix;
+  else out.path = `${prefix}/${d.path}`;
   return Object.freeze(out);
 }
 function intersectInto(into, other) {
@@ -1639,8 +1661,7 @@ function expand(vs, ctx = {}) {
 
 // src/valueset/validate.ts
 function cannotExpand2(detail, path) {
-  const d = { code: "TERM_VALUESET_CANNOT_EXPAND", detail };
-  if (path !== void 0) d.path = path;
+  const d = { code: "TERM_VALUESET_CANNOT_EXPAND", detail, path };
   return Object.freeze(d);
 }
 function expansionIncompleteDetail2(unclosed) {
@@ -1658,7 +1679,8 @@ function usableRelease2(component, system, ctx) {
 }
 function underPath2(d, prefix) {
   const out = { code: d.code, detail: d.detail };
-  out.path = d.path === void 0 ? prefix : `${prefix}/${d.path}`;
+  if (d.path === void 0) out.path = prefix;
+  else out.path = `${prefix}/${d.path}`;
   return Object.freeze(out);
 }
 function matchComponent(target, component, ctx, visited, path, activeOnly = false) {
@@ -1718,10 +1740,13 @@ function matchComponent(target, component, ctx, visited, path, activeOnly = fals
     }
   }
   if (system !== void 0 && target.system === void 0 && baseComplete) baseMatched = false;
+  if (baseMatched === null && !hasVs) return { matched: false, complete: true, diagnostics };
   let refDefiniteFalse = false;
   let refUndetermined = false;
   if (hasVs) {
+    let refsRead = 0;
     for (const [i, url] of valueSet2.entries()) {
+      refsRead++;
       const refPath = `${path}.valueSet[${String(i)}]`;
       if (visited.has(url)) {
         diagnostics.push(cannotExpand2("cyclic value set reference", refPath));
@@ -1742,6 +1767,7 @@ function matchComponent(target, component, ctx, visited, path, activeOnly = fals
         refDefiniteFalse = true;
       }
     }
+    if (refsRead === 0) refDefiniteFalse = true;
   }
   const baseDefiniteFalse = baseMatched === false && baseComplete;
   const baseDefiniteTrue = baseMatched === null || baseMatched === true && baseComplete;
@@ -3993,6 +4019,9 @@ function atBoundary(s, pos) {
   const c = s[pos];
   return c === "." || c === "/" || c === ")";
 }
+function prefixRank(m) {
+  return m.prefix ? 1 : 0;
+}
 function simpleMatches(essence, s, pos) {
   const out = [];
   for (const atom of essence.atoms) {
@@ -4007,7 +4036,7 @@ function simpleMatches(essence, s, pos) {
       }
     }
   }
-  out.sort((a, b) => b.len - a.len || (a.prefix ? 1 : 0) - (b.prefix ? 1 : 0));
+  out.sort((a, b) => b.len - a.len || prefixRank(a) - prefixRank(b));
   return out;
 }
 var MAX_PAREN_DEPTH = 100;
@@ -4412,7 +4441,7 @@ var MAP_CATEGORIES = {
   NO_MAP: "447638001",
   /** `447639009`: "Map of source concept is context dependent" (needs runtime patient context). */
   CONTEXT_DEPENDENT: "447639009",
-  /** `447640006`: "Source concept is ambiguous" (surface candidates, never pick one). */
+  /** `447640006`: "Source concept is ambiguous" (carried through on the result; the rule decides). */
   AMBIGUOUS: "447640006"
 };
 var NO_MAP_CATEGORIES = /* @__PURE__ */ new Set([MAP_CATEGORIES.NO_MAP]);
@@ -4545,8 +4574,15 @@ function evaluateConjunct(clause, context) {
     const bound = Number(ageMatch[2]);
     if (context.ageYears === void 0 || !Number.isFinite(bound)) return "unknown";
     const age = context.ageYears;
-    const ok = op === "<=" ? age <= bound : op === ">=" ? age >= bound : op === "<" ? age < bound : op === ">" ? age > bound : op === "=" ? age === bound : void 0;
-    if (ok === void 0) return "unknown";
+    let ok;
+    if (op === "<=") ok = age <= bound;
+    else if (op === ">=") ok = age >= bound;
+    else if (op === "<") ok = age < bound;
+    else if (op === ">") ok = age > bound;
+    else {
+      if (op === "=") ok = age === bound;
+      else return "unknown";
+    }
     return ok ? "match" : "no-match";
   }
   return "unknown";
@@ -4965,7 +5001,8 @@ function jaccard(a, b) {
   let inter = 0;
   for (const t of a) if (b.has(t)) inter++;
   const union = a.size + b.size - inter;
-  return union === 0 ? 0 : inter / union;
+  if (union === 0) return 0;
+  return inter / union;
 }
 function approximateMatch(graph, query, options = {}) {
   const minScore = options.minScore ?? 0.34;
@@ -4982,7 +5019,7 @@ function approximateMatch(graph, query, options = {}) {
 }
 
 // src/index.ts
-var VERSION = "0.1.5";
+var VERSION = "0.1.6";
 
 exports.COMPLEX_MAP_SOURCE_SYSTEM = COMPLEX_MAP_SOURCE_SYSTEM;
 exports.DIAGNOSTIC_CODES = DIAGNOSTIC_CODES;