fhirsmith 0.18.2 → 1.0.0

package/config-template.json

@@ -1,10 +1,22 @@
 {
+  // A starting point for config.json: every section, with comments (config.json may have
+  // // and /* */ comments too). Every module is off: set "enabled": true on the ones you run
   "server": {
     "port": 3000,
     "cors": {
       "origin": true,
       "credentials": true
     }
+    // The largest request body accepted, in MB (bigger: 413). Optional; this is the default.
+    // "maxBodyMB": 50,
+    // Memory protection, as fractions of the memory limit (the cgroup limit - MemoryMax on the
+    // systemd unit - or else the machine's RAM), measured against process RSS (with a role,
+    // the whole cgroup's private memory: cluster.md). Above
+    // rejectFraction new requests get 503 + Retry-After; above abortFraction running operations
+    // are aborted with 422 too-costly. While refusing, the server forces a GC now and then;
+    // with trimAllocator it also returns the C allocator's free memory (malloc_trim, Linux):
+    // off by default, on by default with a role (cluster.md). Optional; these are the defaults.
+    // "memory": { "rejectFraction": 0.85, "abortFraction": 0.92, "trimAllocator": false }
   },
   // Usage statistics. Request counts are kept per module, per endpoint and per
   // operation, and written to a SQLite database every intervalMinutes so they
@@ -17,6 +29,8 @@
     "database": "stats.db",
     // how often the counters are written out
     "intervalMinutes": 10
+    // how often the graphs take a sample: intervalMinutes unless set; with a role, at most 60
+    // "sampleSeconds": 60
   },
   // Once a day the server checks its installed npm packages against the npm advisory
   // database (what `npm audit` does - report only, nothing is changed). Problems show on
@@ -45,6 +59,12 @@
     "enabled": true,
     "to": ["ops@example.org"]
   },
+  // Accessibility. checkPanel adds a button to the bottom of every page that checks the page,
+  // as it is in the browser, against WCAG 2.0 A/AA (using axe-core) and checks its heading
+  // structure. axe-core is only loaded when the button is pressed. Optional.
+  "accessibility": {
+    "checkPanel": false
+  },
   "modules": {
     "shl": {
       "enabled": false,
@@ -105,7 +125,29 @@
         "maxDownloadMB": 250,
         "maxUnpackedMB": 4096,
         "maxFileMB": 50,
-        "maxFiles": 250000
+        "maxFiles": 250000,
+        // publishers' package signatures, for feeds that list signing keys in package-feeds.json:
+        // "ignore"; "check" (the default: a signature that fails is logged, and the package
+        // stored anyway, unless the feed says signing.required); or "require" (an unsigned
+        // package, or one whose signature fails, is refused, and feeds that list no keys aren't
+        // read at all)
+        "signatures": "check"
+      },
+      // npm registry signatures (npm audit signatures). On by default. keyFile is the EC
+      // P-256 signing key (PEM), relative to the database's folder; made if it's not there
+      "npmSigning": {
+        "enabled": true,
+        "keyFile": "npm-signing-key.pem"
+      },
+      // /packages/feed-check: checks a package feed the way the crawler reads it, storing
+      // nothing; one check at a time. On by default; the other settings are the defaults.
+      // maxItems: items checked per run (each one's package is downloaded); maxTotalMB:
+      // downloaded per run; keepMinutes: how long a run's report is kept
+      "feedCheck": {
+        "enabled": true,
+        "maxItems": 50,
+        "maxTotalMB": 500,
+        "keepMinutes": 60
       },
       // /packages/npm-check: checks any registry against the npm registry protocol. On by
       // default; the other settings are the defaults. "control": false stops the daily
@@ -119,12 +161,15 @@
       }
     },
     "registry": {
-      "enabled": true,
+      "enabled": false,
       "masterUrl": "https://fhir.github.io/ig-registry/tx-servers.json",
       "crawlInterval": 30,
       "timeout": 30000,
       "userAgent": "YourServer/1.0",
       "apiKeys": {},
+      // OAuth2 client credentials for servers that need them to be scanned, by server code:
+      // "oauth": { "code": { "tokenEndpoint": "https://...", "clientId": "...", "clientSecret": "...", "scope": "" } }
+      "oauth": {},
       // the most a crawled server's response can be, once unzipped
       "maxResponseMB": 100,
       // how far back the software page reports each server's uptime, and how long scan outcomes are kept
@@ -139,11 +184,14 @@
       // }
     },
     "publisher": {
-      "enabled": true,
+      "enabled": false,
       "database": "/absolute/path/to/publisher.db",
       // required. Without it the publisher generates a random secret at startup, logs a
       // warning, and logins stop working across restarts.
       "sessionSecret": "change-this-to-a-secure-random-string",
+      // the password of the administrator, login 'admin' - set at every start, so changing it
+      // here changes it. Without it, the administrator gets a random password, which is logged
+      "adminPassword": "change-this-to-a-secure-password",
       // session cookies are marked Secure by default, so they only travel over HTTPS.
       // Set false only to run the publisher over plain HTTP - otherwise the browser will
       // not send the cookie back and logins will appear to do nothing. Behind a TLS
@@ -189,7 +237,7 @@
       }
     },
     "npmprojector": {
-      "enabled": true,
+      "enabled": false,
       "fhirVersion": "r4",  // Options: "r4", "r5", "stu3", "dstu2"
       "basePath": "/fhir",   // Default: "/npmprojector"
       "npmPath": "./data/fhir-package",
@@ -198,7 +246,7 @@
       "debounceMs": 500
     },
     "token": {
-      "enabled": true,
+      "enabled": false,
       "database": "/absolute/path/to/token.db",
       "sessionSecret": "change-this-to-a-secure-random-string-for-token-sessions",
       "oauth": {
@@ -247,7 +295,25 @@
       // (and a "Library" item in the tx nav bar), anything else gets the YAML file itself.
       // Off by default - the file names every database, cache and package the server runs.
       "publishLibrarySource": false,
+      // How SNOMED CT cache files are loaded (see tx/README.md, "Loading SNOMED CT"). Optional;
+      // without it every edition is read into the process, as before. "load": "read" or "mmap"
+      // for every edition; "prewarm": editions to map, then read through once in the background at startup;
+      // "read": editions to read into the process anyway. Entries are cache file names, edition
+      // version URIs or edition URIs
+      // "snomed": { "load": "mmap", "prewarm": ["sct_intl_20250201.cache", "sct_us_20250901b.cache"], "read": [] },
       "cacheTimeout": 30,
+      // Memory limits (see tx/README.md, "Configuration Options"); these are the defaults,
+      // which apply when a limit is left out or null; 0 = no limit. Logged at startup ("Limits: ...")
+      // concepts one client side cache may hold; more is refused with 422 too-costly
+      "cacheMaxConcepts": 250000,
+      // concepts an endpoint's client side caches hold between them; the least recently used
+      // caches are dropped (their cache-id then gets a 404 cache-id-unknown)
+      "cacheMaxTotalConcepts": 1000000,
+      // distinct codes, and longest code (characters), counted for usage-count; others aren't counted
+      "usageTrackerMaxCodes": 1000000,
+      "usageTrackerMaxCodeLength": 100,
+      // parsed language tags kept (least recently used dropped)
+      "languageTagCacheSize": 1000,
       // Optional. A short code (1-16 letters and digits) naming this server instance. Every
       // cache-id the server issues then starts with "<code>.", so a proxy in front of
       // several instances can route cached requests back to the instance that holds the
@@ -291,6 +357,8 @@
       },
       "expansionCacheSize": 1000,
       "expansionCacheMemoryThreshold": 0,
+      // most codes the expansion caches hold in all (default: a quarter of the heap limit, at 1 KB a code)
+      // "expansionCacheMaxCodes": 1000000,
       "endpoints": [
         {
           "path": "/tx/r5",
@@ -321,7 +389,7 @@
       ]
     },
     "ext-tracker": {
-      "enabled": true,
+      "enabled": false,
       "database": "/var/fhir/data/extension-tracker.db",
       "url": "/ext-tracker",
       // the token submissions must carry (Authorization: Bearer ...). The IG Publisher sends
@@ -419,8 +487,9 @@
         "port": 8082,
         "packages": ["hl7.fhir.uv.ips#1.1.0"],
         "timeout": 120000,
-        // the validator's own IPS code checks (default true)
-        "checkIpsCodes": true
+        // the analysis step looks up extension definitions in the validator: let it find, download
+        // and load the package that defines one it doesn't have (default true; validator 7.0.5)
+        "autoLoadPackages": true
         // , "profiles": ["http://hl7.org/fhir/uv/ips/StructureDefinition/Bundle-uv-ips"]
       }
     }

package/extension-tracker/extension-tracker-template.html

@@ -53,8 +53,6 @@
 		<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="/ext-tracker" style="color: gold">Extension Tracker</a>  &nbsp;|&nbsp;
   <a href="/ext-tracker/extensions" style="color: gold">Extensions</a>  &nbsp;|&nbsp;
@@ -72,7 +70,7 @@
             	<div class="inner-wrapper">
  <div class="col-9">
 
-  <h2><img border="0" src="../FHIRsmith32.png" style="vertical-align: text-bottom"/> [%title%] </h2>
+  <h2><a href="https://github.com/HealthIntersections/FHIRsmith/blob/main/README.md" title="FHIRsmith [%ver%]"><img border="0" src="/FHIRsmith32.png" alt="FHIRsmith Logo" style="vertical-align: text-bottom"/></a> [%title%] </h2>
 
 [%content%]
 
@@ -90,8 +88,7 @@
 		<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;
+                    <a href="https://github.com/HealthIntersections/FHIRsmith/blob/main/README.md" style="color: gold"><img border="0" src="/FHIRsmith16.png" alt="FHIRsmith Logo" style="vertical-align: text-bottom"/> FHIRsmith</a>  [%ver%]  &copy; HealthIntersections.com.au 2023+ &nbsp;|&nbsp;
                     [%total-packages%] packages tracked &nbsp;|
                     &nbsp; ([%ms%] ms)
                     [%sponsorMessage%]
@@ -113,10 +110,10 @@
 ================================================== -->
   <!-- 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/bootstrap.min.js"></script>
+<script src="/assets/js/respond.min.js"></script>
 
-<script src="/assets/js/fhir.js"/>
+<script src="/assets/js/fhir.js"></script>
 
   <!-- Analytics Below
 ================================================== -->

package/extension-tracker/extension-tracker.js

@@ -137,8 +137,6 @@ class ExtensionTrackerModule {
     router.get(this.urlBase + '/package/:pkg', (req, res) => this.handlePackageDetail(req, res));
 
     app.use('/', router);
-    const count = this.db.prepare('SELECT COUNT(*) as count FROM packages').get().count;
-    console.log(`Extension tracker: loaded (${count} packages in database) at ${this.urlBase}`);
   }
 
   createSchema() {

package/folder/folder.js

@@ -5,6 +5,7 @@ const USERS_FILE = '.users.json';
 const MAX_UPLOAD_BYTES = 10 * 1024 * 1024; // 10 MB
 const SAFE_NAME = /^[a-zA-Z0-9._-]+$/;
 const AUTH_FAIL_DELAY_MS = 5000;
+const folderLog = require('../library/logger').getInstance().child({ module: 'folder' });
 
 function escapeHtml(str) {
   return String(str)
@@ -30,12 +31,12 @@ class FolderModule {
         continue;
       }
       if (!fc.folder || !fc.url || !fc.name) {
-        console.log(`Folder config entry missing required fields (name, folder, url) - skipping`);
+        folderLog.warn(`config entry missing required fields (name, folder, url) - skipping`);
         continue;
       }
       const rootDir = path.resolve(fc.folder);
       if (!fs.existsSync(rootDir)) {
-        console.log(`Folder path ${rootDir} does not exist - skipping "${fc.name}"`);
+        folderLog.warn(`path ${rootDir} does not exist - skipping "${fc.name}"`);
         continue;
       }
 
@@ -57,11 +58,11 @@ class FolderModule {
 
       app.use('/', router);
       this.folders.push({ name: fc.name, folder: rootDir, url: urlBase });
-      console.log(`Folder module: serving "${fc.name}" from ${rootDir} at ${urlBase}`);
+      folderLog.info(`serving "${fc.name}" from ${rootDir} at ${urlBase}`);
     }
 
     if (this.folders.length === 0) {
-      console.log('Folder module: no folders configured');
+      folderLog.warn('no folders configured');
     }
   }
 
@@ -213,7 +214,7 @@ class FolderModule {
 
       return res.status(200).send('OK');
     }).catch(err => {
-      console.log(`Folder module: PUT error for ${fullPath}: ${err.message}`);
+      folderLog.error(`PUT failed for ${fullPath}: ${err.message}`);
       return res.status(500).send('Upload failed');
     });
   }
@@ -260,7 +261,7 @@ class FolderModule {
     let current = path.resolve(dir);
     const root = path.resolve(rootDir);
 
-    while (true) {
+    for (;;) {
       const usersPath = path.join(current, USERS_FILE);
       if (fs.existsSync(usersPath)) {
         try {