fhirsmith 0.13.4 → 0.14.1

package/testing/store.js

@@ -0,0 +1,410 @@
+//
+// Copyright 2026, Health Intersections Pty Ltd (http://www.healthintersections.com.au)
+//
+// Licensed under BSD-3: https://opensource.org/license/bsd-3-clause
+//
+
+/**
+ * SQLite storage for received TestReports.
+ *
+ * Each report is kept whole, as the JSON that was stored (with the server's id and
+ * meta.lastUpdated), alongside the columns the searches use. Reports are never edited
+ * once received, so there is no versioning. The submitter's IP address is recorded for
+ * tracing abuse, and is never returned by anything in this module.
+ *
+ * @module testing/store
+ */
+
+const Database = require('better-sqlite3');
+const { dateRange } = require('./search');
+
+const SCHEMA = `
+  CREATE TABLE IF NOT EXISTS reports (
+    id           TEXT PRIMARY KEY,
+    received     TEXT NOT NULL,      -- meta.lastUpdated
+    received_ms  INTEGER NOT NULL,
+    ip           TEXT,               -- never shared
+    name         TEXT NOT NULL,
+    name_lc      TEXT NOT NULL,
+    status       TEXT NOT NULL,
+    result       TEXT NOT NULL,
+    score        REAL,
+    tester       TEXT NOT NULL,
+    tester_lc    TEXT NOT NULL,
+    test_script  TEXT,
+    issued       TEXT NOT NULL,
+    issued_lo    INTEGER NOT NULL,
+    issued_hi    INTEGER NOT NULL,
+    size         INTEGER NOT NULL,
+    run_ms       INTEGER,            -- how long the run took, when the report says
+    test_count   INTEGER,            -- how many entries in TestReport.test
+    json         TEXT NOT NULL
+  );
+
+  CREATE TABLE IF NOT EXISTS participants (
+    report_id    TEXT NOT NULL REFERENCES reports(id) ON DELETE CASCADE,
+    seq          INTEGER NOT NULL,
+    type         TEXT,
+    uri          TEXT NOT NULL,
+    version      TEXT,
+    display      TEXT
+  );
+
+  -- people who can maintain the named links and delete reports. The administrator is not
+  -- in here: their password is in the configuration
+  CREATE TABLE IF NOT EXISTS users (
+    id                  INTEGER PRIMARY KEY AUTOINCREMENT,
+    login               TEXT UNIQUE NOT NULL,
+    name                TEXT NOT NULL,
+    password_hash       TEXT NOT NULL,
+    can_edit_links      INTEGER NOT NULL DEFAULT 0,
+    can_delete_reports  INTEGER NOT NULL DEFAULT 0,
+    created             TEXT NOT NULL
+  );
+
+  -- names (and links) shown in place of known canonical URLs
+  CREATE TABLE IF NOT EXISTS links (
+    id          INTEGER PRIMARY KEY AUTOINCREMENT,
+    canonical   TEXT UNIQUE NOT NULL,   -- without any |version
+    name        TEXT NOT NULL,
+    link        TEXT
+  );
+
+  CREATE INDEX IF NOT EXISTS idx_reports_received ON reports(received_ms);
+  CREATE INDEX IF NOT EXISTS idx_reports_name ON reports(name_lc);
+  CREATE INDEX IF NOT EXISTS idx_reports_tester ON reports(tester_lc);
+  CREATE INDEX IF NOT EXISTS idx_reports_status ON reports(status);
+  CREATE INDEX IF NOT EXISTS idx_reports_result ON reports(result);
+  CREATE INDEX IF NOT EXISTS idx_reports_score ON reports(score);
+  CREATE INDEX IF NOT EXISTS idx_reports_script ON reports(test_script);
+  CREATE INDEX IF NOT EXISTS idx_reports_issued ON reports(issued_lo, issued_hi);
+  CREATE INDEX IF NOT EXISTS idx_participants_report ON participants(report_id);
+  CREATE INDEX IF NOT EXISTS idx_participants_uri ON participants(uri);
+`;
+
+/**
+ * TestReport.testScript is a canonical in R5 and a Reference in R4; either way we want
+ * the URL.
+ */
+function testScriptOf(report) {
+  const ts = report.testScript;
+  if (typeof ts === 'string') {
+    return ts;
+  }
+  if (ts && typeof ts === 'object') {
+    if (typeof ts.reference === 'string') {
+      return ts.reference;
+    }
+    if (ts.identifier && typeof ts.identifier.value === 'string') {
+      return ts.identifier.value;
+    }
+  }
+  return null;
+}
+
+function str(v) {
+  return typeof v === 'string' ? v : null;
+}
+
+/**
+ * How long the run took, in milliseconds, if the report says: from the earliest
+ * period.start to the latest period.end across its tests. null if no test has a period
+ * with both ends.
+ */
+function runLengthOf(report) {
+  let lo = null;
+  let hi = null;
+  for (const t of Array.isArray(report.test) ? report.test : []) {
+    const p = t && typeof t === 'object' ? t.period : null;
+    if (!p || typeof p !== 'object') {
+      continue;
+    }
+    const s = typeof p.start === 'string' ? Date.parse(p.start) : NaN;
+    const e = typeof p.end === 'string' ? Date.parse(p.end) : NaN;
+    if (!Number.isNaN(s) && (lo === null || s < lo)) {
+      lo = s;
+    }
+    if (!Number.isNaN(e) && (hi === null || e > hi)) {
+      hi = e;
+    }
+  }
+  return lo !== null && hi !== null && hi >= lo ? hi - lo : null;
+}
+
+/** How many tests the report has (entries in TestReport.test). */
+function testCountOf(report) {
+  return Array.isArray(report.test) ? report.test.length : 0;
+}
+
+/** A canonical URL without its |version. */
+function unversioned(url) {
+  return typeof url === 'string' && url.includes('|') ? url.substring(0, url.indexOf('|')) : url;
+}
+
+class TestReportStore {
+  /**
+   * @param {string} dbPath - file name, or ':memory:'
+   */
+  constructor(dbPath) {
+    this.db = new Database(dbPath);
+    this.db.pragma('journal_mode = WAL');
+    this.db.pragma('foreign_keys = ON');
+    this.db.exec(SCHEMA);
+    this.migrate();
+    this.stmts = {
+      insert: this.db.prepare(`
+        INSERT INTO reports (id, received, received_ms, ip, name, name_lc, status, result, score,
+          tester, tester_lc, test_script, issued, issued_lo, issued_hi, size, run_ms, test_count, json)
+        VALUES (@id, @received, @received_ms, @ip, @name, @name_lc, @status, @result, @score,
+          @tester, @tester_lc, @test_script, @issued, @issued_lo, @issued_hi, @size, @run_ms, @test_count, @json)`),
+      insertParticipant: this.db.prepare(
+        'INSERT INTO participants (report_id, seq, type, uri, version, display) VALUES (?, ?, ?, ?, ?, ?)'),
+      read: this.db.prepare('SELECT json FROM reports WHERE id = ?'),
+      delete: this.db.prepare('DELETE FROM reports WHERE id = ?'),
+      purge: this.db.prepare('DELETE FROM reports WHERE received_ms < ?'),
+      count: this.db.prepare('SELECT COUNT(*) AS n FROM reports')
+    };
+  }
+
+  /** Bring a database made by an earlier version of the module up to date. */
+  migrate() {
+    const has = (table, col) => this.db.prepare(`PRAGMA table_info(${table})`).all().some(c => c.name === col);
+    if (!has('participants', 'version')) {
+      this.db.exec('ALTER TABLE participants ADD COLUMN version TEXT');
+    }
+    // columns worked out from the report: add them, and fill them in for the reports
+    // already there
+    const derived = [['run_ms', runLengthOf], ['test_count', testCountOf]];
+    for (const [col, fn] of derived) {
+      if (!has('reports', col)) {
+        this.db.exec(`ALTER TABLE reports ADD COLUMN ${col} INTEGER`);
+        const update = this.db.prepare(`UPDATE reports SET ${col} = ? WHERE id = ?`);
+        this.db.transaction(() => {
+          for (const row of this.db.prepare('SELECT id, json FROM reports').all()) {
+            const v = fn(JSON.parse(row.json));
+            if (v !== null) {
+              update.run(v, row.id);
+            }
+          }
+        })();
+      }
+    }
+  }
+
+  close() {
+    if (this.db) {
+      this.db.close();
+      this.db = null;
+    }
+  }
+
+  /**
+   * Store a report that has already been validated and given its id and meta.lastUpdated.
+   *
+   * @param {Object} report
+   * @param {{ip?: string, receivedMs: number}} info
+   */
+  insert(report, info) {
+    const json = JSON.stringify(report);
+    const issued = dateRange(report.issued);
+    const row = {
+      id: report.id,
+      received: report.meta.lastUpdated,
+      received_ms: info.receivedMs,
+      ip: info.ip || null,
+      name: report.name,
+      name_lc: report.name.toLowerCase(),
+      status: report.status,
+      result: report.result,
+      score: typeof report.score === 'number' && Number.isFinite(report.score) ? report.score : null,
+      tester: report.tester,
+      tester_lc: report.tester.toLowerCase(),
+      test_script: testScriptOf(report),
+      issued: report.issued,
+      issued_lo: issued.lo,
+      issued_hi: issued.hi,
+      size: Buffer.byteLength(json, 'utf8'),
+      run_ms: runLengthOf(report),
+      test_count: testCountOf(report),
+      json
+    };
+    this.db.transaction(() => {
+      this.stmts.insert.run(row);
+      report.participant.forEach((p, i) => {
+        this.stmts.insertParticipant.run(report.id, i, str(p.type), p.uri, str(p.version), str(p.display));
+      });
+    })();
+  }
+
+  /** @returns {Object|null} the stored report */
+  read(id) {
+    const row = this.stmts.read.get(id);
+    return row ? JSON.parse(row.json) : null;
+  }
+
+  /** @returns {boolean} whether there was such a report */
+  delete(id) {
+    return this.stmts.delete.run(id).changes > 0;
+  }
+
+  /** Delete reports received before the given time. @returns {number} how many */
+  purgeBefore(ms) {
+    return this.stmts.purge.run(ms).changes;
+  }
+
+  count() {
+    return this.stmts.count.get().n;
+  }
+
+  /**
+   * Run a parsed search (see search.js).
+   *
+   * @param {Object} search - from parseSearch
+   * @param {{withJson?: boolean}} options - include the stored JSON (FHIR API), or just
+   *   the columns the HTML list needs
+   * @returns {{total: number, rows: Object[]}}
+   */
+  search(search, options = {}) {
+    const where = search.where.length > 0 ? 'WHERE ' + search.where.join(' AND ') : '';
+    const total = this.db.prepare(`SELECT COUNT(*) AS n FROM reports r ${where}`).get(...search.args).n;
+    if (search.summaryCount || search.count === 0) {
+      return { total, rows: [] };
+    }
+    const cols = options.withJson
+      ? 'r.id, r.json'
+      : 'r.id, r.received, r.name, r.status, r.result, r.score, r.tester, r.test_script, r.issued, r.run_ms, r.test_count';
+    const rows = this.db.prepare(
+      `SELECT ${cols} FROM reports r ${where} ORDER BY ${search.orderBy} LIMIT ? OFFSET ?`
+    ).all(...search.args, search.count, search.offset);
+    if (!options.withJson && rows.length > 0) {
+      const byId = new Map(rows.map(r => [r.id, r]));
+      for (const r of rows) {
+        r.participants = [];
+      }
+      const ph = rows.map(() => '?').join(',');
+      const parts = this.db.prepare(
+        `SELECT report_id, type, uri, version, display FROM participants WHERE report_id IN (${ph}) ORDER BY report_id, seq`
+      ).all(...rows.map(r => r.id));
+      for (const p of parts) {
+        byId.get(p.report_id).participants.push(p);
+      }
+    }
+    return { total, rows };
+  }
+
+  /** Whether any report has a participant of this type. */
+  hasParticipantType(type) {
+    return !!this.db.prepare('SELECT 1 FROM participants WHERE type = ? LIMIT 1').get(type);
+  }
+
+  // ---- named links ----
+
+  /** @returns {Array<{id, canonical, name, link}>} sorted by name */
+  links() {
+    return this.db.prepare('SELECT id, canonical, name, link FROM links ORDER BY name COLLATE NOCASE, canonical').all();
+  }
+
+  /** Add a link, or replace the one for the same canonical. */
+  saveLink(canonical, name, link) {
+    this.db.prepare(`INSERT INTO links (canonical, name, link) VALUES (?, ?, ?)
+      ON CONFLICT(canonical) DO UPDATE SET name = excluded.name, link = excluded.link`)
+      .run(unversioned(canonical), name, link || null);
+  }
+
+  updateLink(id, canonical, name, link) {
+    return this.db.prepare('UPDATE links SET canonical = ?, name = ?, link = ? WHERE id = ?')
+      .run(unversioned(canonical), name, link || null, id).changes > 0;
+  }
+
+  deleteLink(id) {
+    return this.db.prepare('DELETE FROM links WHERE id = ?').run(id).changes > 0;
+  }
+
+  // ---- users ----
+
+  /** @returns {Array} users, without their password hashes */
+  users() {
+    return this.db.prepare('SELECT id, login, name, can_edit_links, can_delete_reports, created FROM users ORDER BY login').all();
+  }
+
+  /** @returns {Object|null} the user, including the password hash */
+  userByLogin(login) {
+    return this.db.prepare('SELECT * FROM users WHERE login = ?').get(login) || null;
+  }
+
+  userById(id) {
+    return this.db.prepare('SELECT id, login, name, can_edit_links, can_delete_reports FROM users WHERE id = ?').get(id) || null;
+  }
+
+  createUser(login, name, passwordHash, rights) {
+    this.db.prepare(`INSERT INTO users (login, name, password_hash, can_edit_links, can_delete_reports, created)
+      VALUES (?, ?, ?, ?, ?, ?)`).run(login, name, passwordHash, rights.editLinks ? 1 : 0, rights.deleteReports ? 1 : 0,
+      new Date().toISOString());
+  }
+
+  updateUser(id, name, rights, passwordHash) {
+    const n = this.db.prepare('UPDATE users SET name = ?, can_edit_links = ?, can_delete_reports = ? WHERE id = ?')
+      .run(name, rights.editLinks ? 1 : 0, rights.deleteReports ? 1 : 0, id).changes;
+    if (n > 0 && passwordHash) {
+      this.db.prepare('UPDATE users SET password_hash = ? WHERE id = ?').run(passwordHash, id);
+    }
+    return n > 0;
+  }
+
+  deleteUser(id) {
+    return this.db.prepare('DELETE FROM users WHERE id = ?').run(id).changes > 0;
+  }
+
+  /** The distinct values in a column, for filter drop-downs. */
+  distinct(column) {
+    if (!['status', 'result'].includes(column)) {
+      throw new Error('Not a filterable column: ' + column);
+    }
+    return this.db.prepare(`SELECT DISTINCT ${column} AS v FROM reports ORDER BY ${column}`).all().map(r => r.v);
+  }
+
+  /**
+   * How many reports each tester has sent, with how they came out, and when the latest
+   * was received. Most reports first.
+   *
+   * @returns {Array<{tester: string, reports: number, pass: number, fail: number, other: number,
+   *   latest: string}>}
+   */
+  testerCounts() {
+    return this.db.prepare(`
+      SELECT tester, COUNT(*) AS reports,
+        SUM(CASE WHEN result = 'pass' THEN 1 ELSE 0 END) AS pass,
+        SUM(CASE WHEN result = 'fail' THEN 1 ELSE 0 END) AS fail,
+        SUM(CASE WHEN result NOT IN ('pass', 'fail') THEN 1 ELSE 0 END) AS other,
+        MAX(received) AS latest
+      FROM reports GROUP BY tester ORDER BY reports DESC, tester_lc`).all();
+  }
+
+  /**
+   * The latest report for each test script against each participant (or tester): the
+   * one with the latest issued date, then the latest received. Test engines are not
+   * participants in this sense - the columns are the things that were tested.
+   *
+   * @param {'participant'|'tester'} by
+   * @returns {Array<{test_script: string|null, col: string, id: string, name: string,
+   *   result: string, score: number|null, issued: string, runs: number}>}
+   */
+  summary(by) {
+    const source = by === 'tester'
+      ? 'SELECT r.*, r.tester AS col FROM reports r'
+      : `SELECT r.*, p.uri AS col FROM reports r
+           JOIN (SELECT DISTINCT report_id, uri FROM participants
+                 WHERE type IS NULL OR type <> 'test-engine') p ON p.report_id = r.id`;
+    return this.db.prepare(`
+      SELECT test_script, col, id, name, result, score, issued, runs FROM (
+        SELECT s.*,
+          COUNT(*) OVER (PARTITION BY s.test_script, s.col) AS runs,
+          ROW_NUMBER() OVER (PARTITION BY s.test_script, s.col
+                             ORDER BY s.issued_lo DESC, s.received_ms DESC) AS rn
+        FROM (${source}) s
+      ) WHERE rn = 1
+      ORDER BY test_script, col`).all();
+  }
+}
+
+module.exports = { TestReportStore, testScriptOf, runLengthOf, testCountOf, unversioned };

package/testing/testing-template.html

@@ -0,0 +1,126 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<html xml:lang="en" lang="en">
+<head>
+    <title>FHIRsmith: [%title%]</title>
+
+  <meta charset="utf-8"/>
+  <meta content="width=device-width, initial-scale=1.0" name="viewport"/>
+  <meta content="http://hl7.org/fhir" name="author"/>
+  <meta charset="utf-8" http-equiv="X-UA-Compatible" content="IE=edge" />
+
+  <link rel="stylesheet" href="/fhir.css"/>
+
+
+    <!-- Bootstrap core CSS -->
+  <link rel="stylesheet" href="/assets/css/bootstrap.css"/>
+  <link rel="stylesheet" href="/assets/css/bootstrap-fhir.css"/>
+
+    <!-- Project extras -->
+  <link rel="stylesheet" href="/assets/css/project.css"/>
+  <link rel="stylesheet" href="/assets/css/pygments-manni.css"/>
+
+    <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
+    <!-- [if lt IE 9]>
+    <script src="/assets/js/html5shiv.js"></script>
+    <script src="/assets/js/respond.min.js"></script>
+    <![endif] -->
+
+    <!-- Favicons -->
+  <link sizes="144x144" rel="apple-touch-icon-precomposed" href="/assets/ico/apple-touch-icon-144-precomposed.png"/>
+  <link sizes="114x114" rel="apple-touch-icon-precomposed" href="/assets/ico/apple-touch-icon-114-precomposed.png"/>
+  <link sizes="72x72" rel="apple-touch-icon-precomposed" href="/assets/ico/apple-touch-icon-72-precomposed.png"/>
+  <link rel="apple-touch-icon-precomposed" href="/assets/ico/apple-touch-icon-57-precomposed.png"/>
+  <link rel="shortcut icon" href="/assets/ico/favicon.png"/>
+<script type="text/javascript" src="/assets/js/json2.js"></script>
+<script type="text/javascript" src="/assets/js/statuspage.js"></script>
+<script type="text/javascript" src="/assets/js/jquery.min.js"></script>
+<script type="text/javascript" src="/assets/js/jquery-ui.min.js"></script>
+<link rel="stylesheet" href="/assets/css/jquery.ui.all.css">
+<script type="text/javascript" src="/assets/js/jquery.ui.core.js"></script>
+<script type="text/javascript" src="/assets/js/jquery.ui.widget.js"></script>
+<script type="text/javascript" src="/assets/js/jquery.ui.mouse.js"></script>
+<script type="text/javascript" src="/assets/js/jquery.ui.resizable.js"></script>
+<script type="text/javascript" src="/assets/js/jquery.ui.draggable.js"></script>
+<script type="text/javascript" src="/assets/js/jtip.js"></script>
+<script type="text/javascript" src="/assets/js/jcookie.js"></script>
+<script type="text/javascript" src="/assets/js/fhir-gw.js"></script>
+</head>
+
+<body>
+  
+	<div id="segment-navbar" class="segment">  <!-- segment-breadcrumb -->
+		<div id="stripe"> </div>
+		<div class="container">  <!-- container -->
+		<div style="background-color: #ad1f2f; padding: 6px; color: white;">  <!-- container -->
+
+  <a href="http://www.hl7.org/fhir" style="color: gold" title="Fast Healthcare Interoperability Resources - Home Page"><img border="0" src="/icon-fhir-16.png" style="vertical-align: text-bottom"/> <b>FHIR</b></a> &copy; HL7.org &nbsp;|&nbsp;
+  <a href="https://github.com/HealthIntersections/FHIRsmith/blob/main/README.md" style="color: gold"><img border="0" src="/FHIRsmith16.png" style="vertical-align: text-bottom"/> FHIRsmith</a> [%ver%] &nbsp;|&nbsp;
+  <a href="/" style="color: gold"> Server Home</a> &nbsp;|&nbsp;
+  <a href="/testing" style="color: gold">Test Reports</a>  &nbsp;|&nbsp;
+  <a href="/testing/summary" style="color: gold">Summary</a>  &nbsp;|&nbsp;
+		</div>  <!-- /container -->
+		</div>  <!-- /container -->
+</div>
+
+	<!-- /segment-breadcrumb -->
+
+	<div id="segment-content" class="segment">  <!-- segment-content -->
+	<div class="container">  <!-- container -->
+            <div class="row">
+            	<div class="inner-wrapper">
+ <div class="col-12">
+
+  <h2><img border="0" src="/FHIRsmith32.png" style="vertical-align: text-bottom"/> [%title%] </h2>
+
+[%content%]
+
+
+ </div>
+
+
+				</div>  <!-- /inner-wrapper -->
+            </div>  <!-- /row -->
+        </div>  <!-- /container -->
+    </div>  <!-- /segment-content -->
+
+
+	<div id="segment-footer" class="segment">  <!-- segment-footer -->
+		<div class="container">  <!-- container -->
+			<div class="inner-wrapper">
+				<p>
+                    <a href="http://www.hl7.org/fhir" style="color: gold" title="Fast Healthcare Interoperability Resources - Home Page"><img border="0" src="/icon-fhir-16.png" style="vertical-align: text-bottom"/> <b>FHIR</b></a> &copy; HL7.org 2011+.  &nbsp;|&nbsp;
+                    <a href="https://github.com/HealthIntersections/FHIRsmith/blob/main/README.md" style="color: gold"><img border="0" src="/FHIRsmith16.png" style="vertical-align: text-bottom"/> FHIRsmith</a>  [%ver%]  &copy; HealthIntersections.com.au 2023+ &nbsp;|&nbsp;
+                    &nbsp; ([%ms%] ms)
+                    [%sponsorMessage%]
+        </p>
+			</div>  <!-- /inner-wrapper -->
+		</div>  <!-- /container -->
+	</div>  <!-- /segment-footer -->
+
+
+	<div id="segment-post-footer" class="segment hidden">  <!-- segment-post-footer -->
+		<div class="container">  <!-- container -->
+		</div>  <!-- /container -->
+	</div>  <!-- /segment-post-footer -->
+
+
+
+
+
+      <!-- JS and analytics only. -->
+      <!-- Bootstrap core JavaScript
+================================================== -->
+  <!-- Placed at the end of the document so the pages load faster -->
+<!-- <script src="/assets/js/jquery.js"/> -->
+<script src="/assets/js/bootstrap.min.js"/>
+<script src="/assets/js/respond.min.js"/>
+
+<script src="/assets/js/fhir.js"/>
+
+  <!-- Analytics Below
+================================================== -->
+
+</body>
+
+</html>