@cosyte/synth 0.1.5 → 0.1.7

package/dist/fhir/index.d.cts

@@ -397,6 +397,12 @@ interface FhirCorpusOptions {
     readonly count?: number;
     /** The resource kinds to cycle through. Defaults to the full US Core clinical spine + a Bundle. */
     readonly mix?: readonly FhirResourceKind[];
+    /**
+     * Whether each artifact is read back through its parser and the parser's findings recorded as its
+     * `warnings`. Defaults to `true`. `false` skips the read, a large share of a corpus's time; every
+     * artifact's `warnings` is then empty without having been checked.
+     */
+    readonly verify?: boolean;
 }
 /**
  * Build a reproducible {@link Corpus} of spec-clean FHIR resources across the supported kinds. Each

package/dist/fhir/index.d.ts

@@ -397,6 +397,12 @@ interface FhirCorpusOptions {
     readonly count?: number;
     /** The resource kinds to cycle through. Defaults to the full US Core clinical spine + a Bundle. */
     readonly mix?: readonly FhirResourceKind[];
+    /**
+     * Whether each artifact is read back through its parser and the parser's findings recorded as its
+     * `warnings`. Defaults to `true`. `false` skips the read, a large share of a corpus's time; every
+     * artifact's `warnings` is then empty without having been checked.
+     */
+    readonly verify?: boolean;
 }
 /**
  * Build a reproducible {@link Corpus} of spec-clean FHIR resources across the supported kinds. Each

package/dist/fhir/index.mjs

@@ -1,6 +1,12 @@
-import { list, complex, primitive, decimal, serializeResource, parseResource, validateResource } from '@cosyte/fhir';
+import { createRequire } from 'module';
+import { fileURLToPath } from 'url';
 
-// src/fhir/patient.ts
+var __require = /* @__PURE__ */ ((x) => typeof require !== "undefined" ? require : typeof Proxy !== "undefined" ? new Proxy(x, {
+  get: (a, b) => (typeof require !== "undefined" ? require : a)[b]
+}) : x)(function(x) {
+  if (typeof require !== "undefined") return require.apply(this, arguments);
+  throw Error('Dynamic require of "' + x + '" is not supported');
+});
 
 // src/rng/splitmix32.ts
 function splitmix32(seed) {
@@ -551,42 +557,64 @@ var SYSTEM = Object.freeze({
   /** US Core `us-core-provenance-participant-type`, `Provenance.agent.type` (`transmitter`). */
   US_CORE_PROVENANCE_PARTICIPANT_TYPE: "http://hl7.org/fhir/us/core/CodeSystem/us-core-provenance-participant-type"
 });
+function defaultHost() {
+  if (typeof import.meta.resolve !== "function") return { require: __require, resolve: void 0 };
+  return { require: createRequire(import.meta.url), resolve: (s) => import.meta.resolve(s) };
+}
+function isRequireEsmRefusal(error) {
+  return error?.code === "ERR_REQUIRE_ESM";
+}
+function loadPeer(specifier, host) {
+  if (host.resolve === void 0) return host.require(specifier);
+  const entry = fileURLToPath(host.resolve(specifier));
+  try {
+    return host.require(entry);
+  } catch (error) {
+    if (!isRequireEsmRefusal(error)) throw error;
+    return host.require(specifier);
+  }
+}
+function lazyPeer(specifier, host) {
+  let loaded;
+  return () => loaded ??= loadPeer(specifier, defaultHost());
+}
+var fhirPeer = lazyPeer("@cosyte/fhir");
 
 // src/fhir/builder.ts
 function prop(name2, value) {
   return { name: name2, value };
 }
 function str(value) {
-  return primitive(value);
+  return fhirPeer().primitive(value);
 }
 function dec(raw) {
-  return primitive(decimal(raw));
+  return fhirPeer().primitive(fhirPeer().decimal(raw));
 }
 function bool(value) {
-  return primitive(value);
+  return fhirPeer().primitive(value);
 }
 function coding(concept) {
-  return complex([
+  return fhirPeer().complex([
     prop("system", str(concept.system)),
     prop("code", str(concept.code)),
     prop("display", str(concept.display))
   ]);
 }
 function codeableConcept(concept) {
-  return complex([prop("coding", list([coding(concept)]))]);
+  return fhirPeer().complex([prop("coding", fhirPeer().list([coding(concept)]))]);
 }
 function reference(ref) {
-  return complex([prop("reference", str(ref))]);
+  return fhirPeer().complex([prop("reference", str(ref))]);
 }
 function narrative(text) {
   const escaped = text.replace(/&/g, "&amp;").replace(/</g, "&lt;").replace(/>/g, "&gt;");
-  return complex([
+  return fhirPeer().complex([
     prop("status", str("generated")),
     prop("div", str(`<div xmlns="http://www.w3.org/1999/xhtml"><p>${escaped}</p></div>`))
   ]);
 }
 function meta(profiles) {
-  return complex([prop("profile", list(profiles.map((p) => str(p))))]);
+  return fhirPeer().complex([prop("profile", fhirPeer().list(profiles.map((p) => str(p))))]);
 }
 function toFhirDate(ymd) {
   return `${ymd.slice(0, 4)}-${ymd.slice(4, 6)}-${ymd.slice(6, 8)}`;
@@ -603,13 +631,13 @@ function fhirPatientIdentity(rng) {
   return { id, person, mrn, birthDate, gender, address: address2, phone: phone2, email: email2 };
 }
 function mrnIdentifier(mrn) {
-  return complex([
+  return fhirPeer().complex([
     prop(
       "type",
-      complex([
+      fhirPeer().complex([
         prop(
           "coding",
-          list([
+          fhirPeer().list([
             coding({
               system: SYSTEM.IDENTIFIER_TYPE,
               code: "MR",
@@ -905,13 +933,16 @@ function resolveMix(allowed, requested, fallback) {
 // src/fhir/patient.ts
 var PATIENT_PROFILES = Object.freeze(["base", "us-core"]);
 function ombExtension(url, category) {
-  return complex([
+  return fhirPeer().complex([
     prop("url", str(url)),
     prop(
       "extension",
-      list([
-        complex([prop("url", str("ombCategory")), prop("valueCoding", coding(category))]),
-        complex([prop("url", str("text")), prop("valueString", str(category.display))])
+      fhirPeer().list([
+        fhirPeer().complex([
+          prop("url", str("ombCategory")),
+          prop("valueCoding", coding(category))
+        ]),
+        fhirPeer().complex([prop("url", str("text")), prop("valueString", str(category.display))])
       ])
     )
   ]);
@@ -942,24 +973,27 @@ function generatePatient(options = {}) {
     props.push(
       prop(
         "extension",
-        list([
+        fhirPeer().list([
           ombExtension(US_CORE_RACE_EXTENSION, race),
           ombExtension(US_CORE_ETHNICITY_EXTENSION, ethnicity),
-          complex([prop("url", str(US_CORE_BIRTHSEX_EXTENSION)), prop("valueCode", str(birthsex))])
+          fhirPeer().complex([
+            prop("url", str(US_CORE_BIRTHSEX_EXTENSION)),
+            prop("valueCode", str(birthsex))
+          ])
         ])
       )
     );
   }
-  props.push(prop("identifier", list([mrnIdentifier(id.mrn)])));
+  props.push(prop("identifier", fhirPeer().list([mrnIdentifier(id.mrn)])));
   props.push(prop("active", bool(true)));
   props.push(
     prop(
       "name",
-      list([
-        complex([
+      fhirPeer().list([
+        fhirPeer().complex([
           prop("use", str("official")),
           prop("family", str(id.person.family)),
-          prop("given", list([str(id.person.given)]))
+          prop("given", fhirPeer().list([str(id.person.given)]))
         ])
       ])
     )
@@ -967,13 +1001,13 @@ function generatePatient(options = {}) {
   props.push(
     prop(
       "telecom",
-      list([
-        complex([
+      fhirPeer().list([
+        fhirPeer().complex([
           prop("system", str("phone")),
           prop("value", str(id.phone)),
           prop("use", str("home"))
         ]),
-        complex([prop("system", str("email")), prop("value", str(id.email))])
+        fhirPeer().complex([prop("system", str("email")), prop("value", str(id.email))])
       ])
     )
   );
@@ -982,10 +1016,10 @@ function generatePatient(options = {}) {
   props.push(
     prop(
       "address",
-      list([
-        complex([
+      fhirPeer().list([
+        fhirPeer().complex([
           prop("use", str("home")),
-          prop("line", list([str(id.address.street)])),
+          prop("line", fhirPeer().list([str(id.address.street)])),
           prop("city", str(id.address.city)),
           prop("state", str(id.address.state)),
           prop("postalCode", str(id.address.zip))
@@ -993,8 +1027,10 @@ function generatePatient(options = {}) {
       ])
     )
   );
-  return complex(props);
+  return fhirPeer().complex(props);
 }
+
+// src/fhir/condition.ts
 function generateCondition(options = {}) {
   const { seed = 0, subject = "Patient/syn-patient-1", usCore = true } = options;
   const rng = createRng(seed);
@@ -1024,7 +1060,7 @@ function generateCondition(options = {}) {
   props.push(
     prop(
       "category",
-      list([
+      fhirPeer().list([
         codeableConcept({
           system: SYSTEM.CONDITION_CATEGORY,
           code: "problem-list-item",
@@ -1035,15 +1071,17 @@ function generateCondition(options = {}) {
   );
   props.push(prop("code", codeableConcept(code)));
   props.push(prop("subject", reference(subject)));
-  return complex(props);
+  return fhirPeer().complex(props);
 }
+
+// src/fhir/observation.ts
 function drawValue(rng, concept) {
   const span = concept.high - concept.low;
   const raw = concept.low + rng.float() * span;
   return raw.toFixed(concept.decimals);
 }
 function valueQuantity(rng, concept) {
-  return complex([
+  return fhirPeer().complex([
     prop("value", dec(drawValue(rng, concept))),
     prop("unit", str(concept.unit)),
     prop("system", str(SYSTEM.UCUM)),
@@ -1065,7 +1103,7 @@ function buildObservation(seed, subject, usCore, profileUrl, category, pool, eff
   props.push(
     prop(
       "category",
-      list([
+      fhirPeer().list([
         codeableConcept({
           system: SYSTEM.OBSERVATION_CATEGORY,
           code: category.code,
@@ -1081,7 +1119,7 @@ function buildObservation(seed, subject, usCore, profileUrl, category, pool, eff
   const d = String(rng.int(1, 28)).padStart(2, "0");
   if (effective) props.push(prop("effectiveDateTime", str(`${String(y)}-${m}-${d}`)));
   props.push(prop("valueQuantity", valueQuantity(rng, concept)));
-  return complex(props);
+  return fhirPeer().complex(props);
 }
 function generateObservationLab(options = {}) {
   const { seed = 0, subject = "Patient/syn-patient-1", usCore = true } = options;
@@ -1107,6 +1145,8 @@ function generateVitalSign(options = {}) {
     true
   );
 }
+
+// src/fhir/medication-request.ts
 function generateMedicationRequest(options = {}) {
   const {
     seed = 0,
@@ -1131,8 +1171,10 @@ function generateMedicationRequest(options = {}) {
   props.push(prop("subject", reference(subject)));
   props.push(prop("authoredOn", str(`${String(y)}-${m}-${d}`)));
   props.push(prop("requester", reference(requester)));
-  return complex(props);
+  return fhirPeer().complex(props);
 }
+
+// src/fhir/encounter.ts
 function generateEncounter(options = {}) {
   const { seed = 0, subject = "Patient/syn-patient-1", usCore = true } = options;
   const rng = createRng(seed);
@@ -1149,8 +1191,8 @@ function generateEncounter(options = {}) {
   props.push(
     prop(
       "identifier",
-      list([
-        complex([
+      fhirPeer().list([
+        fhirPeer().complex([
           prop("system", str(`urn:oid:${id.assigningAuthorityOid}`)),
           prop("value", str(id.value))
         ])
@@ -1159,11 +1201,13 @@ function generateEncounter(options = {}) {
   );
   props.push(prop("status", str("finished")));
   props.push(prop("class", coding(cls)));
-  props.push(prop("type", list([codeableConcept(type)])));
+  props.push(prop("type", fhirPeer().list([codeableConcept(type)])));
   props.push(prop("subject", reference(subject)));
-  props.push(prop("period", complex([prop("start", str(`${start}T09:00:00Z`))])));
-  return complex(props);
+  props.push(prop("period", fhirPeer().complex([prop("start", str(`${start}T09:00:00Z`))])));
+  return fhirPeer().complex(props);
 }
+
+// src/fhir/immunization.ts
 function generateImmunization(options = {}) {
   const { seed = 0, patient = "Patient/syn-patient-1", usCore = true } = options;
   const rng = createRng(seed);
@@ -1180,8 +1224,10 @@ function generateImmunization(options = {}) {
   props.push(prop("patient", reference(patient)));
   props.push(prop("occurrenceDateTime", str(occurrence)));
   props.push(prop("primarySource", bool(true)));
-  return complex(props);
+  return fhirPeer().complex(props);
 }
+
+// src/fhir/allergy-intolerance.ts
 function generateAllergyIntolerance(options = {}) {
   const { seed = 0, patient = "Patient/syn-patient-1", usCore = true } = options;
   const rng = createRng(seed);
@@ -1214,11 +1260,17 @@ function generateAllergyIntolerance(options = {}) {
   props.push(
     prop(
       "reaction",
-      list([complex([prop("manifestation", list([codeableConcept(manifestation)]))])])
+      fhirPeer().list([
+        fhirPeer().complex([
+          prop("manifestation", fhirPeer().list([codeableConcept(manifestation)]))
+        ])
+      ])
     )
   );
-  return complex(props);
+  return fhirPeer().complex(props);
 }
+
+// src/fhir/procedure.ts
 function generateProcedure(options = {}) {
   const { seed = 0, subject = "Patient/syn-patient-1", usCore = true } = options;
   const rng = createRng(seed);
@@ -1234,8 +1286,10 @@ function generateProcedure(options = {}) {
   props.push(prop("code", codeableConcept(code)));
   props.push(prop("subject", reference(subject)));
   props.push(prop("performedDateTime", str(`${performed}T10:00:00Z`)));
-  return complex(props);
+  return fhirPeer().complex(props);
 }
+
+// src/fhir/provenance.ts
 function generateProvenance(options = {}) {
   const { seed = 0, target = "Patient/syn-patient-1", usCore = true } = options;
   const rng = createRng(seed);
@@ -1248,19 +1302,19 @@ function generateProvenance(options = {}) {
   ];
   if (usCore) props.push(prop("meta", meta([US_CORE_PROFILE.PROVENANCE])));
   props.push(prop("text", narrative("Synthetic provenance for a generated fixture.")));
-  props.push(prop("target", list([reference(target)])));
+  props.push(prop("target", fhirPeer().list([reference(target)])));
   props.push(prop("recorded", str(`${recorded}T10:00:00Z`)));
   props.push(
     prop(
       "agent",
-      list([
-        complex([
+      fhirPeer().list([
+        fhirPeer().complex([
           prop(
             "type",
-            complex([
+            fhirPeer().complex([
               prop(
                 "coding",
-                list([
+                fhirPeer().list([
                   coding({
                     system: SYSTEM.PROVENANCE_PARTICIPANT_TYPE,
                     code: "author",
@@ -1281,8 +1335,10 @@ function generateProvenance(options = {}) {
       ])
     )
   );
-  return complex(props);
+  return fhirPeer().complex(props);
 }
+
+// src/fhir/diagnostic-report.ts
 function generateDiagnosticReport(options = {}) {
   const { seed = 0, subject = "Patient/syn-patient-1", results = [], usCore = true } = options;
   const rng = createRng(seed);
@@ -1298,7 +1354,7 @@ function generateDiagnosticReport(options = {}) {
   props.push(
     prop(
       "category",
-      list([
+      fhirPeer().list([
         codeableConcept({
           system: SYSTEM.DIAGNOSTIC_SERVICE_SECTION,
           code: "LAB",
@@ -1312,12 +1368,13 @@ function generateDiagnosticReport(options = {}) {
   props.push(prop("effectiveDateTime", str(`${day}T08:30:00Z`)));
   props.push(prop("issued", str(`${day}T09:00:00.000Z`)));
   if (results.length > 0) {
-    props.push(prop("result", list(results.map((r) => reference(r)))));
+    props.push(prop("result", fhirPeer().list(results.map((r) => reference(r)))));
   }
-  return complex(props);
+  return fhirPeer().complex(props);
 }
 
 // src/corpus.ts
+var UNCHECKED = Object.freeze([]);
 function makeCorpus(seed, artifacts, quirks = []) {
   const counts = {};
   const formats = /* @__PURE__ */ new Set();
@@ -1337,11 +1394,13 @@ function makeCorpus(seed, artifacts, quirks = []) {
     artifacts: Object.freeze(frozenArtifacts)
   });
 }
+
+// src/fhir/composition.ts
 function section(sec) {
-  return complex([
+  return fhirPeer().complex([
     prop("title", str(sec.title)),
     prop("code", codeableConcept({ system: SYSTEM.LOINC, code: sec.code, display: sec.title })),
-    prop("entry", list(sec.entries.map((e) => reference(e))))
+    prop("entry", fhirPeer().list(sec.entries.map((e) => reference(e))))
   ]);
 }
 function buildComposition(rng, input) {
@@ -1360,18 +1419,20 @@ function buildComposition(rng, input) {
     ),
     prop("subject", reference(input.subject)),
     prop("date", str(`${input.date}T09:00:00Z`)),
-    prop("author", list([reference(input.organization)])),
+    prop("author", fhirPeer().list([reference(input.organization)])),
     prop("title", str("Synthetic Continuity of Care Document")),
     prop("custodian", reference(input.organization)),
-    prop("section", list(input.sections.map((s) => section(s))))
+    prop("section", fhirPeer().list(input.sections.map((s) => section(s))))
   ];
-  return complex(props);
+  return fhirPeer().complex(props);
 }
+
+// src/fhir/round-trip.ts
 function roundTrip(resource, options = {}) {
-  const content = serializeResource(resource);
-  const { resource: reparsed } = parseResource(content);
-  const byteStable = serializeResource(reparsed) === content;
-  const result = validateResource(
+  const content = fhirPeer().serializeResource(resource);
+  const { resource: reparsed } = fhirPeer().parseResource(content);
+  const byteStable = fhirPeer().serializeResource(reparsed) === content;
+  const result = fhirPeer().validateResource(
     reparsed,
     options.profiles !== void 0 ? { mode: "strict", profiles: options.profiles } : { mode: "strict" }
   );
@@ -1380,6 +1441,13 @@ function roundTrip(resource, options = {}) {
   const valid = result.valid;
   return { content, errors, warnings, byteStable, valid, specClean: valid && byteStable };
 }
+function fhirCorpusArtifact(resource, verify) {
+  const content = fhirPeer().serializeResource(resource);
+  if (!verify) return { content, warnings: UNCHECKED };
+  const { resource: reparsed } = fhirPeer().parseResource(content);
+  const warnings = fhirPeer().validateResource(reparsed, { mode: "strict" }).issues.filter((i) => i.severity === "error" || i.severity === "fatal").map((i) => i.code);
+  return { content, warnings };
+}
 
 // src/fhir/bundle.ts
 var BUNDLE_TYPES = Object.freeze([
@@ -1393,14 +1461,14 @@ function resourceTypeOf(resource) {
 }
 function buildOrganization(rng) {
   const id = safe.identifier(rng, "AN");
-  return complex([
+  return fhirPeer().complex([
     prop("resourceType", str("Organization")),
     prop("id", str(`syn-org-${rng.digits(8)}`)),
     prop("text", narrative("Synthetic health organization.")),
     prop(
       "identifier",
-      list([
-        complex([
+      fhirPeer().list([
+        fhirPeer().complex([
           prop("system", str(`urn:oid:${id.assigningAuthorityOid}`)),
           prop("value", str(id.value))
         ])
@@ -1513,11 +1581,14 @@ function generateBundle(options = {}) {
       entryProps.push(
         prop(
           "request",
-          complex([prop("method", str("POST")), prop("url", str(resourceTypeOf(member.resource)))])
+          fhirPeer().complex([
+            prop("method", str("POST")),
+            prop("url", str(resourceTypeOf(member.resource)))
+          ])
         )
       );
     }
-    return complex(entryProps);
+    return fhirPeer().complex(entryProps);
   });
   const props = [
     prop("resourceType", str("Bundle")),
@@ -1528,7 +1599,7 @@ function generateBundle(options = {}) {
     props.push(
       prop(
         "identifier",
-        complex([
+        fhirPeer().complex([
           prop("system", str(`urn:oid:${id.assigningAuthorityOid}`)),
           prop("value", str(`urn:uuid:${safe.uuid(rng)}`))
         ])
@@ -1537,8 +1608,8 @@ function generateBundle(options = {}) {
   }
   props.push(prop("type", str(type)));
   if (type === "document") props.push(prop("timestamp", str(`${spine.date}T09:00:00.000Z`)));
-  props.push(prop("entry", list(entries)));
-  return complex(props);
+  props.push(prop("entry", fhirPeer().list(entries)));
+  return fhirPeer().complex(props);
 }
 var ALL_KINDS = Object.freeze([
   "Patient",
@@ -1599,13 +1670,13 @@ function generateKind(kind, seed) {
   }
 }
 function fhirCorpus(options) {
-  const { seed, count = 1 } = options;
+  const { seed, count = 1, verify = true } = options;
   const kinds = resolveMix(ALL_KINDS, options.mix, DEFAULT_MIX);
   const seedStream = createRng(seed);
   const artifacts = Array.from({ length: count }, (_unused, i) => {
     const kind = kinds[i % kinds.length] ?? "USCorePatient";
-    const rt = roundTrip(generateKind(kind, seedStream.nextUint32()));
-    return { format: "fhir", kind, content: rt.content, warnings: rt.errors };
+    const rt = fhirCorpusArtifact(generateKind(kind, seedStream.nextUint32()), verify);
+    return { format: "fhir", kind, content: rt.content, warnings: rt.warnings };
   });
   return makeCorpus(seed, artifacts);
 }