fhirsmith 0.18.2 → 1.0.0

package/changelog-template.md

@@ -1,22 +0,0 @@
-## [m.n.p] - 2026-mm-dd
-
-### Security
-
-- 
-
-### Added
-
-- 
-
-### Changed
-
-- 
-
-### Fixed
-
-- 
-
-### Tx Conformance Statement
-
-(paste)
-

package/registry/test-runner.js

@@ -1,237 +0,0 @@
-// test-runner.js
-// Quick test runner to verify the fixes
-
-const { 
-  ServerRegistries, 
-  ServerRegistry, 
-  ServerInformation, 
-  ServerVersionInformation
-} = require('./registry-model');
-const RegistryCrawler = require('./registry/crawler');
-const RegistryAPI = require('./registry-api');
-
-// Create sample test data
-function createSampleData() {
-  const data = new ServerRegistries();
-  data.address = 'https://registry.example.org';
-  data.lastRun = new Date('2024-01-15T10:00:00Z');
-  data.outcome = 'Crawled 2 registries successfully, 0 errors';
-  data.doco = 'Test registry for unit tests';
-
-  // Registry 1: Main Registry
-  const reg1 = new ServerRegistry();
-  reg1.code = 'main';
-  reg1.name = 'Main Terminology Registry';
-  reg1.address = 'https://main.registry.org';
-  reg1.authority = 'HL7 International';
-
-  // Server 1.1: TX Server
-  const server11 = new ServerInformation();
-  server11.code = 'tx1';
-  server11.name = 'TX Terminology Server';
-  server11.address = 'https://tx.fhir.org';
-  server11.accessInfo = 'Public FHIR terminology server';
-  server11.authCSList = ['http://loinc.org*', 'http://snomed.info/sct*'];
-  server11.authVSList = ['http://hl7.org/fhir/ValueSet/loinc*'];
-  server11.usageList = ['production', 'public'];
-
-  // Version 4.0.1 for TX Server
-  const version111 = new ServerVersionInformation();
-  version111.version = '4.0.1';
-  version111.address = 'https://tx.fhir.org/r4';
-  version111.security = 'open';
-  version111.lastSuccess = new Date('2024-01-15T09:55:00Z');
-  version111.lastTat = '250ms';
-  version111.codeSystems = [
-    'http://loinc.org',
-    'http://snomed.info/sct',
-    'http://hl7.org/fhir/sid/icd-10',
-    'http://www.nlm.nih.gov/research/umls/rxnorm'
-  ].sort();
-  version111.valueSets = [
-    'http://hl7.org/fhir/ValueSet/observation-codes',
-    'http://hl7.org/fhir/ValueSet/condition-code',
-    'http://hl7.org/fhir/ValueSet/loinc-diagnostic-report-codes'
-  ].sort();
-  server11.versions.push(version111);
-
-  // Version 5.0.0 for TX Server (doesn't have loinc-diagnostic-report-codes)
-  const version112 = new ServerVersionInformation();
-  version112.version = '5.0.0';
-  version112.address = 'https://tx.fhir.org/r5';
-  version112.security = 'open';
-  version112.lastSuccess = new Date('2024-01-15T09:56:00Z');
-  version112.lastTat = '180ms';
-  version112.codeSystems = [
-    'http://loinc.org',
-    'http://snomed.info/sct',
-    'http://hl7.org/fhir/sid/icd-11'
-  ].sort();
-  version112.valueSets = [
-    'http://hl7.org/fhir/ValueSet/observation-codes'
-  ].sort();
-  server11.versions.push(version112);
-
-  // Server 1.2: Ontoserver
-  const server12 = new ServerInformation();
-  server12.code = 'onto';
-  server12.name = 'Ontoserver';
-  server12.address = 'https://ontoserver.example.org';
-  server12.accessInfo = 'Enterprise terminology server';
-  server12.authCSList = ['http://snomed.info/sct*'];
-  server12.authVSList = [];
-  server12.usageList = ['production'];
-
-  const version121 = new ServerVersionInformation();
-  version121.version = '6.4.0';
-  version121.address = 'https://ontoserver.example.org/fhir';
-  version121.security = 'oauth';
-  version121.lastSuccess = new Date('2024-01-15T09:50:00Z');
-  version121.lastTat = '180ms';
-  version121.codeSystems = [
-    'http://snomed.info/sct',
-    'http://snomed.info/sct/32506021000036107',
-    'http://loinc.org'
-  ].sort();
-  version121.valueSets = [
-    'http://snomed.info/sct?fhir_vs=ecl/<404684003',
-    'http://snomed.info/sct?fhir_vs=ecl/<373873005'
-  ].sort();
-  server12.versions.push(version121);
-
-  reg1.servers.push(server11);
-  reg1.servers.push(server12);
-
-  // Registry 2: Test Registry
-  const reg2 = new ServerRegistry();
-  reg2.code = 'test';
-  reg2.name = 'Test Terminology Registry';
-  reg2.address = 'https://test.registry.org';
-  reg2.authority = 'Testing Authority';
-
-  // Server 2.1: Test Server with error
-  const server21 = new ServerInformation();
-  server21.code = 'test-server';
-  server21.name = 'Test Server';
-  server21.address = 'https://test.server.org';
-  server21.accessInfo = 'Test server (currently down)';
-
-  const version211 = new ServerVersionInformation();
-  version211.version = '1.0.0';
-  version211.address = 'https://test.server.org/fhir';
-  version211.error = 'Connection timeout';
-  server21.versions.push(version211);
-
-  // Server 2.2: Local Dev Server
-  const server22 = new ServerInformation();
-  server22.code = 'local';
-  server22.name = 'Local Development Server';
-  server22.address = 'http://localhost:8080';
-  server22.accessInfo = 'Local development instance';
-  server22.authCSList = ['http://example.org/codesystem/*'];
-  server22.authVSList = ['http://example.org/valueset/*'];
-
-  const version221 = new ServerVersionInformation();
-  version221.version = '5.0.0';
-  version221.address = 'http://localhost:8080/fhir';
-  version221.security = 'open';
-  version221.lastSuccess = new Date('2024-01-15T08:00:00Z');
-  version221.lastTat = '50ms';
-  version221.codeSystems = [
-    'http://example.org/codesystem/test1',
-    'http://example.org/codesystem/test2',
-    'http://hl7.org/fhir/sid/icd-10'
-  ].sort();
-  version221.valueSets = [
-    'http://example.org/valueset/test1',
-    'http://example.org/valueset/test2'
-  ].sort();
-  server22.versions.push(version221);
-
-  reg2.servers.push(server21);
-  reg2.servers.push(server22);
-
-  data.registries.push(reg1);
-  data.registries.push(reg2);
-
-  return data;
-}
-
-// Run specific tests
-function runTests() {
-  const crawler = new RegistryCrawler();
-  crawler.loadData(createSampleData().toJSON());
-  const api = new RegistryAPI(crawler);
-  
-  console.log('\nRunning problematic tests:\n');
-  
-  // Test 1: should return all servers when no filter specified
-  console.log('Test 1: should return all servers when no filter specified');
-  const rows1 = api.buildRowsForCodeSystem({});
-  console.log(`  Expected: 4 working versions`);
-  console.log(`  Received: ${rows1.length} versions`);
-  console.log(`  Server codes: ${rows1.map(r => `${r.serverCode}(${r.version})`).join(', ')}`);
-  console.log(`  Test ${rows1.length === 4 ? '✓ PASSED' : '✗ FAILED'}\n`);
-  
-  // Test 2: should handle wildcard value set matching
-  console.log('Test 2: should handle wildcard value set matching');
-  const rows2 = api.buildRowsForValueSet({
-    valueSet: 'http://hl7.org/fhir/ValueSet/loinc-diagnostic-report-codes'
-  });
-  console.log(`  Query: 'http://hl7.org/fhir/ValueSet/loinc-diagnostic-report-codes'`);
-  console.log(`  TX server is authoritative for: 'http://hl7.org/fhir/ValueSet/loinc*'`);
-  console.log(`  Version 4.0.1 HAS this value set`);
-  console.log(`  Version 5.0.0 does NOT have this value set`);
-  console.log(`  Expected: 1 version (4.0.1 which has the value set) OR 2 versions (both authoritative)?`);
-  console.log(`  Received: ${rows2.length} version(s)`);
-  if (rows2.length > 0) {
-    console.log(`  Versions: ${rows2.map(r => `${r.version} (auth=${r.authoritative})`).join(', ')}`);
-  }
-  console.log(`  Test ${rows2.length === 1 && rows2[0].version === '4.0.1' ? '✓ PASSED (strict)' : rows2.length === 2 ? '✓ PASSED (lenient)' : '✗ FAILED'}\n`);
-  
-  // Test 3: should rank servers without errors higher
-  console.log('Test 3: should not include servers with errors even if authoritative');
-  const data = crawler.getData();
-  const testServer = data.registries[1].servers[0];
-  testServer.authCSList = ['http://test.org/*'];
-  
-  const rows3 = api.buildRowsForCodeSystem({
-    codeSystem: 'http://test.org/cs'
-  });
-  const hasErrorServer = rows3.some(r => r.serverCode === 'test-server');
-  console.log(`  Expected: No test-server in results`);
-  console.log(`  Received: ${hasErrorServer ? 'test-server found' : 'test-server not found'}`);
-  console.log(`  Servers in result: ${rows3.map(r => r.serverCode).join(', ')}`);
-  console.log(`  Test ${!hasErrorServer ? '✓ PASSED' : '✗ FAILED'}\n`);
-  
-  // Run all the other tests to make sure we didn't break anything
-  console.log('Running additional validation tests:\n');
-  
-  // Test: Find servers supporting LOINC
-  const loincRows = api.buildRowsForCodeSystem({
-    codeSystem: 'http://loinc.org'
-  });
-  console.log('Test: Find servers supporting LOINC');
-  console.log(`  Expected: 3 servers (tx1 v4, tx1 v5, onto v6)`);
-  console.log(`  Received: ${loincRows.length} servers`);
-  console.log(`  Test ${loincRows.length === 3 ? '✓ PASSED' : '✗ FAILED'}\n`);
-  
-  // Test: Filter by version
-  const versionRows = api.buildRowsForCodeSystem({
-    version: '4.0',
-    codeSystem: 'http://loinc.org'
-  });
-  console.log('Test: Filter by version 4.0');
-  console.log(`  Expected: 1 server (version 4.0.1)`);
-  console.log(`  Received: ${versionRows.length} server(s)`);
-  if (versionRows.length > 0) {
-    console.log(`  Version: ${versionRows[0].version}`);
-  }
-  console.log(`  Test ${versionRows.length === 1 && versionRows[0].version === '4.0.1' ? '✓ PASSED' : '✗ FAILED'}\n`);
-  
-  console.log('================================');
-  console.log('Test run complete!');
-}
-
-// Run the tests
-runTests();

package/release.sh

@@ -1,80 +0,0 @@
-#!/usr/bin/env bash
-#
-# Release FHIRsmith: ./release.sh 0.17.0
-#
-# Checks that the release is ready, submits the tx test report to the /testing server, then
-# tags the release and pushes the tag (which starts .github/workflows/release.yml).
-# Stops at the first problem, before anything is tagged.
-#
-# The test report: run the tx tests first (npx jest tests/tx/test-cases.test.js). If the
-# /testing server needs a token, set FHIRSMITH_TESTING_TOKEN.
-
-set -euo pipefail
-
-fail() {
-  echo "gr.sh: $*" >&2
-  exit 1
-}
-
-[ $# -eq 1 ] || fail "usage: ./gr.sh <version>, e.g. ./gr.sh 0.17.0"
-VERSION="${1#v}"
-TAG="v$VERSION"
-[[ "$VERSION" =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]] || fail "'$1' is not a release version (X.Y.Z)"
-
-cd "$(dirname "$0")"
-
-# --- git: on main, nothing uncommitted, and exactly what is on GitHub -------------------
-[ "$(git rev-parse --abbrev-ref HEAD)" = "main" ] || fail "not on main"
-[ -z "$(git status --porcelain --untracked-files=no)" ] || fail "there are uncommitted changes"
-git fetch --quiet origin main --tags
-[ "$(git rev-parse HEAD)" = "$(git rev-parse origin/main)" ] \
-  || fail "main is not the same as origin/main - push (or pull) first, so the tag is on a commit GitHub has"
-! git rev-parse -q --verify "refs/tags/$TAG" >/dev/null || fail "tag $TAG already exists"
-
-# --- versions: what release.yml's verify-version job checks ----------------------------
-check_version() {
-  local what="$1" found="$2"
-  [ "$found" = "$VERSION" ] || fail "$what is '$found', not $VERSION (npm version --no-git-tag-version $VERSION && npm install --package-lock-only)"
-}
-check_version "package.json version" "$(node -p "require('./package.json').version")"
-check_version "package-lock.json version" "$(node -p "require('./package-lock.json').version")"
-check_version 'package-lock.json packages[""]' "$(node -p "require('./package-lock.json').packages[''].version")"
-
-# --- CHANGELOG: a dated section for this version, with the conformance statement in -----
-HEADING=$(grep -E "^## \[v?${VERSION//./\\.}\]" CHANGELOG.md || true)
-[ -n "$HEADING" ] || fail "CHANGELOG.md has no section for $VERSION"
-[[ "$HEADING" =~ [0-9]{4}-[0-9]{2}-[0-9]{2}$ ]] || fail "the CHANGELOG.md section for $VERSION has no date: $HEADING"
-SECTION=$(sed -n "/^## \[v\{0,1\}${VERSION//./\\.}\]/,/^## \[/p" CHANGELOG.md | sed '$d')
-! grep -qx '(paste)' <<<"$SECTION" || fail "the Tx Conformance Statement for $VERSION hasn't been pasted into CHANGELOG.md"
-
-# --- the test report: this version, passed, and run on what is being released ----------
-REPORT=test-cases-report.json
-[ -f "$REPORT" ] || fail "no $REPORT - run the tx tests first (npx jest tests/tx/test-cases.test.js)"
-# the last commit that changed what the tests run - not the notes, nor the version bump
-CODE_COMMITTED=$(git log -1 --format=%cI -- . ':(exclude)*.md' ':(exclude)release.sh' ':(exclude)package.json' ':(exclude)package-lock.json')
-node - "$REPORT" "$VERSION" "$CODE_COMMITTED" <<'NODE' || exit 1
-const [file, version, committed] = process.argv.slice(2);
-const report = JSON.parse(require('fs').readFileSync(file, 'utf8'));
-const fhirsmith = (report.participant || []).find(p => p.uri === 'https://github.com/HealthIntersections/FHIRsmith');
-const problems = [];
-if (!fhirsmith || fhirsmith.version !== version) {
-  problems.push(`it is from FHIRsmith ${fhirsmith ? fhirsmith.version : '(unknown)'}, not ${version}`);
-}
-if (report.result !== 'pass') {
-  problems.push(`its result is '${report.result}', not 'pass'`);
-}
-if (!report.issued || new Date(report.issued) < new Date(committed)) {
-  problems.push(`it was run (${report.issued}) before the last change to the code (${committed})`);
-}
-if (problems.length > 0) {
-  console.error(`gr.sh: ${file} can't be submitted for ${version}: ${problems.join('; ')} - run the tx tests again`);
-  process.exit(1);
-}
-NODE
-
-# --- submit the report, then tag ---------------------------------------------------------
-node utilities/submit-test-report.js -file "$REPORT" || fail "the test report was not accepted, so $TAG has not been tagged"
-
-git tag -a "$TAG" -m "FHIRsmith $VERSION"
-git push origin "$TAG"
-echo "Tagged and pushed $TAG - the release workflow is now running"

package/test-scripts/repro-re2-wasm-leak.js

@@ -1,34 +0,0 @@
-// Historical reproducer for the re2-wasm WASM heap leak.
-// regex-utilities.js now sits on top of re2js (a pure-JS RE2 port), so the
-// underlying leak is gone. Kept as a stress test for the compile cache:
-//
-//   node test-scripts/repro-re2-wasm-leak.js            # same-pattern stress
-//   node test-scripts/repro-re2-wasm-leak.js --unique   # unique-pattern stress
-//
-// Background (re2-wasm era): without the cache, same-pattern OOMed at ~2965
-// iterations; with the cache, same-pattern ran indefinitely but unique-pattern
-// still OOMed because every distinct pattern was a real compile and re2-wasm
-// could not free its WASM heap. Under re2js both modes now run indefinitely
-// (unique-pattern is bounded only by ordinary V8 heap growth from the cache).
-
-const re = require('../library/regex-utilities');
-
-const mode = process.argv.includes('--unique') ? 'unique' : 'same';
-const basePattern =
-  'CYTO|HL7\\.CYTOGEN|HL7\\.GENETICS|^PATH(\\..*)?|^MOLPATH(\\..*)?|NR STATS|H&P\\.HX\\.LAB|CHALSKIN|LABORDERS';
-
-console.log(`mode: ${mode}-pattern`);
-
-let i = 0;
-try {
-  for (;;) {
-    const pattern = mode === 'unique' ? basePattern + `|UNIQUE${i}` : basePattern;
-    re.compile(pattern);
-    i++;
-    if (i % 100 === 0) console.log(`iter ${i}`);
-  }
-} catch (e) {
-  console.error(`OOMed at iteration ${i}: ${e.message}`);
-  process.exit(1);
-}
- 

package/tsconfig.eslint.json

@@ -1,9 +0,0 @@
-{
-  "compilerOptions": {
-    "allowJs": true, "checkJs": false, "noEmit": true,
-    "moduleResolution": "node", "target": "es2022", "module": "commonjs",
-    "strict": false, "skipLibCheck": true
-  },
-  "include": ["**/*.js"],
-  "exclude": ["node_modules", "static", "**/*.test.js", "tests", "coverage"]
-}

package/tx/html/dash-metrics.liquid

@@ -1,147 +0,0 @@
-<div style="display: flex; gap: 20px; margin-bottom: 20px;">
-  <div style="flex: 1;">
-    <h6>Memory Usage (Heap Used)</h6>
-    <canvas id="memoryChart" height="200"></canvas>
-  </div>
-  <div style="flex: 1;">
-    <h6>Turnaround Time</h6>
-    <canvas id="tatChart" height="200"></canvas>
-  </div>
-  <div style="flex: 1;">
-    <h6>Requests per Minute</h6>
-    <canvas id="requestChart" height="200"></canvas>
-  </div>
-</div>
-
-<script src="https://cdn.jsdelivr.net/npm/chart.js"></script>
-<script>
-(function() {
-  const historyData = {{ historyJson }};
-  const startTime = {{ startTime }};
-
-  function formatTime(timestamp) {
-    const d = new Date(timestamp);
-    return d.toLocaleTimeString([], { hour: '2-digit', minute: '2-digit' });
-  }
-
-  function formatMB(bytes) {
-    return (bytes / 1024 / 1024).toFixed(1);
-  }
-
-  function formatDuration(ms) {
-    const hours = ms / 3600000;
-    if (hours < 1) {
-      return Math.round(ms / 60000) + 'm ago';
-    }
-    return hours.toFixed(1) + 'h ago';
-  }
-
-  const chartOptions = {
-    responsive: false,
-    maintainAspectRatio: false,
-    scales: {
-      x: {
-        ticks: {
-          maxTicksAuto: 6
-        }
-      },
-      y: {
-        beginAtZero: true
-      }
-    },
-    plugins: {
-      legend: {
-        display: false
-      }
-    }
-  };
-
-  // Memory chart
-  new Chart(document.getElementById('memoryChart'), {
-    type: 'line',
-    data: {
-      labels: historyData.map(d => formatTime(d.time)),
-      datasets: [{
-        data: historyData.map(d => parseFloat(formatMB(d.mem))),
-        borderColor: '#007bff',
-        backgroundColor: 'rgba(0, 123, 255, 0.1)',
-        fill: true,
-        tension: 0.3,
-        pointRadius: 2
-      }]
-    },
-    options: {
-      ...chartOptions,
-      scales: {
-        ...chartOptions.scales,
-        y: {
-          ...chartOptions.scales.y,
-          title: {
-            display: true,
-            text: 'MB (𝚫 from start)'
-          }
-        }
-      }
-    }
-  });
-
-
-  // Tat chart
-  new Chart(document.getElementById('tatChart'), {
-    type: 'line',
-    data: {
-      labels: historyData.map(d => formatTime(d.time)),
-      datasets: [{
-        data: historyData.map(d => d.tat),
-        borderColor: '#7b7b7b',
-        backgroundColor: 'rgba(123, 123, 123, 0.1)',
-        fill: true,
-        tension: 0.3,
-        pointRadius: 2
-      }]
-    },
-    options: {
-      ...chartOptions,
-      scales: {
-        ...chartOptions.scales,
-        y: {
-          ...chartOptions.scales.y,
-          title: {
-            display: true,
-            text: 'ms'
-          }
-        }
-      }
-    }
-  });
-
-  // Requests chart
-  new Chart(document.getElementById('requestChart'), {
-    type: 'line',
-    data: {
-      labels: historyData.map(d => formatTime(d.time)),
-      datasets: [{
-        data: historyData.map(d => d.rpm.toFixed(2)),
-        borderColor: '#28a745',
-        backgroundColor: 'rgba(40, 167, 69, 0.1)',
-        fill: true,
-        tension: 0.3,
-        pointRadius: 2
-      }]
-    },
-    options: {
-      ...chartOptions,
-      scales: {
-        ...chartOptions.scales,
-        y: {
-          ...chartOptions.scales.y,
-          title: {
-            display: true,
-            text: 'req/min'
-          }
-        }
-      }
-    }
-  });
-})();
-</script>