fhirsmith 0.8.6 → 0.9.0

package/tx/vs/vs-database.js

@@ -37,9 +37,9 @@ class ValueSetDatabase {
         if (!hasCol) {
           migrations.push(new Promise((res, rej) => {
             db.run(
-              "ALTER TABLE valuesets ADD COLUMN date_first_seen INTEGER DEFAULT 0",
-              [],
-              (err) => err ? rej(err) : res()
+                "ALTER TABLE valuesets ADD COLUMN date_first_seen INTEGER DEFAULT 0",
+                [],
+                (err) => err ? rej(err) : res()
             );
           }));
         }
@@ -47,13 +47,22 @@ class ValueSetDatabase {
         migrations.push(new Promise((res, rej) => {
           db.run(`
             CREATE TABLE IF NOT EXISTS vsac_runs (
-              id INTEGER PRIMARY KEY AUTOINCREMENT,
-              started_at INTEGER NOT NULL,
-              finished_at INTEGER,
-              status TEXT NOT NULL DEFAULT 'running',
-              error_message TEXT,
-              total_fetched INTEGER,
-              total_new INTEGER
+                                                   id INTEGER PRIMARY KEY AUTOINCREMENT,
+                                                   started_at INTEGER NOT NULL,
+                                                   finished_at INTEGER,
+                                                   status TEXT NOT NULL DEFAULT 'running',
+                                                   error_message TEXT,
+                                                   total_fetched INTEGER,
+                                                   total_new INTEGER
+            )
+          `, [], (err) => err ? rej(err) : res());
+        }));
+        // Ensure vsac_settings table exists (for _lastUpdated tracking etc.)
+        migrations.push(new Promise((res, rej) => {
+          db.run(`
+            CREATE TABLE IF NOT EXISTS vsac_settings (
+              key TEXT PRIMARY KEY,
+              value TEXT
             )
           `, [], (err) => err ? rej(err) : res());
         }));
@@ -170,69 +179,77 @@ class ValueSetDatabase {
         db.serialize(() => {
           // Main value sets table
           db.run(`
-              CREATE TABLE valuesets (
-                                         id TEXT PRIMARY KEY,
-                                         url TEXT,
-                                         version TEXT,
-                                         date TEXT,
-                                         description TEXT,
-                                         effectivePeriod_start TEXT,
-                                         effectivePeriod_end TEXT,
-                                         expansion_identifier TEXT,
-                                         name TEXT,
-                                         publisher TEXT,
-                                         status TEXT,
-                                         title TEXT,
-                                         content TEXT NOT NULL,
-                                         last_seen INTEGER DEFAULT (strftime('%s', 'now')),
-                                         date_first_seen INTEGER DEFAULT (strftime('%s', 'now'))
-              )
+            CREATE TABLE valuesets (
+                                     id TEXT PRIMARY KEY,
+                                     url TEXT,
+                                     version TEXT,
+                                     date TEXT,
+                                     description TEXT,
+                                     effectivePeriod_start TEXT,
+                                     effectivePeriod_end TEXT,
+                                     expansion_identifier TEXT,
+                                     name TEXT,
+                                     publisher TEXT,
+                                     status TEXT,
+                                     title TEXT,
+                                     content TEXT NOT NULL,
+                                     last_seen INTEGER DEFAULT (strftime('%s', 'now')),
+                                     date_first_seen INTEGER DEFAULT (strftime('%s', 'now'))
+            )
           `);
 
           // Identifiers table (0..* Identifier)
           db.run(`
-              CREATE TABLE valueset_identifiers (
-                                                    valueset_id TEXT,
-                                                    system TEXT,
-                                                    value TEXT,
-                                                    use_code TEXT,
-                                                    type_system TEXT,
-                                                    type_code TEXT,
-                                                    FOREIGN KEY (valueset_id) REFERENCES valuesets(url)
-              )
+            CREATE TABLE valueset_identifiers (
+                                                valueset_id TEXT,
+                                                system TEXT,
+                                                value TEXT,
+                                                use_code TEXT,
+                                                type_system TEXT,
+                                                type_code TEXT,
+                                                FOREIGN KEY (valueset_id) REFERENCES valuesets(url)
+            )
           `);
 
           // Jurisdictions table (0..* CodeableConcept with 0..* Coding)
           db.run(`
-              CREATE TABLE valueset_jurisdictions (
-                                                      valueset_id TEXT,
-                                                      system TEXT,
-                                                      code TEXT,
-                                                      display TEXT,
-                                                      FOREIGN KEY (valueset_id) REFERENCES valuesets(url)
-              )
+            CREATE TABLE valueset_jurisdictions (
+                                                  valueset_id TEXT,
+                                                  system TEXT,
+                                                  code TEXT,
+                                                  display TEXT,
+                                                  FOREIGN KEY (valueset_id) REFERENCES valuesets(url)
+            )
           `);
 
           // Systems table (from compose.include[].system)
           db.run(`
-              CREATE TABLE valueset_systems (
-                                                valueset_id TEXT,
-                                                system TEXT,
-                                                version TEXT,
-                                                FOREIGN KEY (valueset_id) REFERENCES valuesets(url)
-              )
+            CREATE TABLE valueset_systems (
+                                            valueset_id TEXT,
+                                            system TEXT,
+                                            version TEXT,
+                                            FOREIGN KEY (valueset_id) REFERENCES valuesets(url)
+            )
           `);
 
           // Run tracking table
           db.run(`
-              CREATE TABLE vsac_runs (
-                                         id INTEGER PRIMARY KEY AUTOINCREMENT,
-                                         started_at INTEGER NOT NULL,
-                                         finished_at INTEGER,
-                                         status TEXT NOT NULL DEFAULT 'running',
-                                         error_message TEXT,
-                                         total_fetched INTEGER,
-                                         total_new INTEGER
+            CREATE TABLE vsac_runs (
+                                     id INTEGER PRIMARY KEY AUTOINCREMENT,
+                                     started_at INTEGER NOT NULL,
+                                     finished_at INTEGER,
+                                     status TEXT NOT NULL DEFAULT 'running',
+                                     error_message TEXT,
+                                     total_fetched INTEGER,
+                                     total_new INTEGER
+            )
+          `);
+
+          // Settings table (key-value store for _lastUpdated tracking etc.)
+          db.run(`
+              CREATE TABLE IF NOT EXISTS vsac_settings (
+                  key TEXT PRIMARY KEY,
+                  value TEXT
               )
           `);
 
@@ -271,9 +288,9 @@ class ValueSetDatabase {
     const db = await this._getWriteConnection();
     return new Promise((resolve, reject) => {
       db.run(
-        `INSERT INTO vsac_runs (started_at, status) VALUES (strftime('%s','now'), 'running')`,
-        [],
-        function(err) { err ? reject(err) : resolve(this.lastID); }
+          `INSERT INTO vsac_runs (started_at, status) VALUES (strftime('%s','now'), 'running')`,
+          [],
+          function(err) { err ? reject(err) : resolve(this.lastID); }
       );
     });
   }
@@ -289,10 +306,10 @@ class ValueSetDatabase {
     const db = await this._getWriteConnection();
     return new Promise((resolve, reject) => {
       db.run(
-        `UPDATE vsac_runs SET finished_at = strftime('%s','now'), status = 'ok',
-         total_fetched = ?, total_new = ? WHERE id = ?`,
-        [totalFetched, totalNew, id],
-        err => err ? reject(err) : resolve()
+          `UPDATE vsac_runs SET finished_at = strftime('%s','now'), status = 'ok',
+                                total_fetched = ?, total_new = ? WHERE id = ?`,
+          [totalFetched, totalNew, id],
+          err => err ? reject(err) : resolve()
       );
     });
   }
@@ -307,10 +324,43 @@ class ValueSetDatabase {
     const db = await this._getWriteConnection();
     return new Promise((resolve, reject) => {
       db.run(
-        `UPDATE vsac_runs SET finished_at = strftime('%s','now'), status = 'error',
-         error_message = ? WHERE id = ?`,
-        [errorMessage, id],
-        err => err ? reject(err) : resolve()
+          `UPDATE vsac_runs SET finished_at = strftime('%s','now'), status = 'error',
+                                error_message = ? WHERE id = ?`,
+          [errorMessage, id],
+          err => err ? reject(err) : resolve()
+      );
+    });
+  }
+
+  /**
+   * Get a setting value from the vsac_settings table
+   * @param {string} key - The setting key
+   * @returns {Promise<string|null>} The setting value, or null if not found
+   */
+  async getSetting(key) {
+    const db = await this._getReadConnection();
+    return new Promise((resolve, reject) => {
+      db.get('SELECT value FROM vsac_settings WHERE key = ?', [key], (err, row) => {
+        if (err) reject(err);
+        else resolve(row ? row.value : null);
+      });
+    });
+  }
+
+  /**
+   * Set a setting value in the vsac_settings table
+   * @param {string} key - The setting key
+   * @param {string} value - The setting value
+   * @returns {Promise<void>}
+   */
+  async setSetting(key, value) {
+    const db = await this._getWriteConnection();
+    return new Promise((resolve, reject) => {
+      db.run(
+          `INSERT INTO vsac_settings (key, value) VALUES (?, ?)
+         ON CONFLICT(key) DO UPDATE SET value = excluded.value`,
+          [key, value],
+          err => err ? reject(err) : resolve()
       );
     });
   }
@@ -353,24 +403,24 @@ class ValueSetDatabase {
             const expansionId = valueSet.expansion?.identifier || null;
 
             db.run(`
-                INSERT INTO valuesets (
-                    id, url, version, date, description, effectivePeriod_start, effectivePeriod_end,
-                    expansion_identifier, name, publisher, status, title, content, last_seen, date_first_seen
-                ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, strftime('%s', 'now'), strftime('%s', 'now'))
-                    ON CONFLICT(id) DO UPDATE SET
-                    url=excluded.url,
-                                           version=excluded.version,
-                                           date=excluded.date,
-                                           description=excluded.description,
-                                           effectivePeriod_start=excluded.effectivePeriod_start,
-                                           effectivePeriod_end=excluded.effectivePeriod_end,
-                                           expansion_identifier=excluded.expansion_identifier,
-                                           name=excluded.name,
-                                           publisher=excluded.publisher,
-                                           status=excluded.status,
-                                           title=excluded.title,
-                                           content=excluded.content,
-                                           last_seen=strftime('%s', 'now')
+              INSERT INTO valuesets (
+                id, url, version, date, description, effectivePeriod_start, effectivePeriod_end,
+                expansion_identifier, name, publisher, status, title, content, last_seen, date_first_seen
+              ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, strftime('%s', 'now'), strftime('%s', 'now'))
+                ON CONFLICT(id) DO UPDATE SET
+                url=excluded.url,
+                                     version=excluded.version,
+                                     date=excluded.date,
+                                     description=excluded.description,
+                                     effectivePeriod_start=excluded.effectivePeriod_start,
+                                     effectivePeriod_end=excluded.effectivePeriod_end,
+                                     expansion_identifier=excluded.expansion_identifier,
+                                     name=excluded.name,
+                                     publisher=excluded.publisher,
+                                     status=excluded.status,
+                                     title=excluded.title,
+                                     content=excluded.content,
+                                     last_seen=strftime('%s', 'now')
             `, [
               valueSet.id,
               valueSet.url,
@@ -414,10 +464,10 @@ class ValueSetDatabase {
 
     return new Promise((resolve, reject) => {
       db.run(`
-          update valuesets
-          set last_seen = strftime('%s', 'now')
-          where url = ?
-            and version = ?
+        update valuesets
+        set last_seen = strftime('%s', 'now')
+        where url = ?
+          and version = ?
       `, [
         valueSet.url,
         valueSet.version
@@ -466,9 +516,9 @@ class ValueSetDatabase {
         const typeCode = id.type?.coding?.[0]?.code || null;
 
         db.run(`
-            INSERT INTO valueset_identifiers (
-                valueset_id, system, value, use_code, type_system, type_code
-            ) VALUES (?, ?, ?, ?, ?, ?)
+          INSERT INTO valueset_identifiers (
+            valueset_id, system, value, use_code, type_system, type_code
+          ) VALUES (?, ?, ?, ?, ?, ?)
         `, [
           valueSet.id,
           id.system || null,
@@ -490,9 +540,9 @@ class ValueSetDatabase {
           for (const coding of jurisdiction.coding) {
             pendingOperations++;
             db.run(`
-                INSERT INTO valueset_jurisdictions (
-                    valueset_id, system, code, display
-                ) VALUES (?, ?, ?, ?)
+              INSERT INTO valueset_jurisdictions (
+                valueset_id, system, code, display
+              ) VALUES (?, ?, ?, ?)
             `, [
               valueSet.id,
               coding.system || null,
@@ -514,7 +564,7 @@ class ValueSetDatabase {
           pendingOperations++;
 
           db.run(`
-              INSERT INTO valueset_systems (valueset_id, system, version) VALUES (?, ?, ?)
+            INSERT INTO valueset_systems (valueset_id, system, version) VALUES (?, ?, ?)
           `, [valueSet.id, include.system, include.version], function(err) {
             if (err) {
               operationError(new Error(`Failed to insert system: ${err.message}`));
@@ -598,12 +648,12 @@ class ValueSetDatabase {
   async search(spaceId, map, searchParams, elements = null) {
     // Check if we can optimize by selecting only indexed columns
     const canOptimize = elements && elements.length > 0 &&
-      elements.every(e => INDEXED_COLUMNS.includes(e));
+        elements.every(e => INDEXED_COLUMNS.includes(e));
 
     // Always include 'id' in the columns to select when optimizing
     const columnsToSelect = canOptimize
-      ? (elements.includes('id') ? elements : ['id', ...elements])
-      : null;
+        ? (elements.includes('id') ? elements : ['id', ...elements])
+        : null;
 
     const db = await this._getReadConnection();
 

package/tx/vs/vs-vsac.js

@@ -78,7 +78,6 @@ class VSACValueSetProvider extends AbstractValueSetProvider {
     if (this.valueSetMap.size == 0) {
       await this.refreshValueSets();
     }
-
     // Start periodic refresh
     this._startRefreshTimer();
     this.initialized = true;
@@ -174,6 +173,14 @@ class VSACValueSetProvider extends AbstractValueSetProvider {
       console.log(`VSAC refresh phase 1 done. Total: ${count} with ${ncount} new items`);
       this.stats.task('VSAC Sync', `VSAC refresh phase 1 done. Total: ${count} with ${ncount} new items`);
 
+      // phase 1b: query for recently updated value sets via _lastUpdated
+      let lastUpdatedCount = await this._scanLastUpdated();
+      console.log(`VSAC refresh phase 1b done. ${lastUpdatedCount} additional items from _lastUpdated`);
+      this.stats.task('VSAC Sync', `Phase 1b: ${lastUpdatedCount} from _lastUpdated`);
+
+      // deduplicate the queue
+      this.queue = [...new Set(this.queue)];
+
       let tracking = { totalFetched: 0, totalNew: 0, count: 0, newCount : 0 };
       // phase 2: query for history & content
       this.requeue = [];
@@ -418,8 +425,8 @@ class VSACValueSetProvider extends AbstractValueSetProvider {
         isRefreshing: this.isRefreshing,
         refreshIntervalHours: this.refreshIntervalHours,
         nextRefresh: this.refreshTimer && this.lastRefresh
-          ? new Date(this.lastRefresh.getTime() + (this.refreshIntervalHours * 60 * 60 * 1000))
-          : null
+            ? new Date(this.lastRefresh.getTime() + (this.refreshIntervalHours * 60 * 60 * 1000))
+            : null
       }
     };
   }
@@ -506,8 +513,8 @@ class VSACValueSetProvider extends AbstractValueSetProvider {
     if (bundle.entry && bundle.entry.length > 0) {
       // Extract ValueSets from bundle entries
       const valueSets = bundle.entry
-        .filter(entry => entry.resource && entry.resource.resourceType === 'ValueSet')
-        .map(entry => entry.resource);
+          .filter(entry => entry.resource && entry.resource.resourceType === 'ValueSet')
+          .map(entry => entry.resource);
       if (valueSets.length > 0) {
         tracking.totalNew = tracking.totalNew + await this.batchUpsertValueSets(valueSets);
         tracking.totalFetched += valueSets.length;
@@ -519,6 +526,58 @@ class VSACValueSetProvider extends AbstractValueSetProvider {
     this.stats.task('VSAC Sync', logMsg);
   }
 
+  /**
+   * Scan VSAC for recently updated value sets using the _lastUpdated parameter.
+   * Uses a stored date from the previous run; if none exists, defaults to 4 days ago.
+   * Adds any found URLs to this.queue and stores the server's response date for next time.
+   * @returns {Promise<number>} Number of value set URLs added to the queue
+   * @private
+   */
+  async _scanLastUpdated() {
+    const SETTING_KEY = 'vsac_last_updated_date';
+
+    let sinceDate = await this.database.getSetting(SETTING_KEY);
+    if (!sinceDate) {
+      // No stored date — default to 10 days ago
+      const d = new Date();
+      d.setDate(d.getDate() - 10);
+      sinceDate = d.toISOString();
+    }
+
+    let url = `/res/ValueSet/?_lastUpdated=ge${sinceDate}&_offset=0&_count=100&_elements=id,url,version,status`;
+    let count = 0;
+    let serverDate = null;
+
+    while (url) {
+      console.log(`_lastUpdated scan: ${count} found so far`);
+      this.stats.task('VSAC Sync', `_lastUpdated scan: ${count} found`);
+
+      const bundle = await this._fetchBundle(url);
+
+      // Capture the server's lastUpdated from the first page
+      if (!serverDate && bundle.meta && bundle.meta.lastUpdated) {
+        serverDate = bundle.meta.lastUpdated;
+      }
+
+      for (let be of bundle.entry || []) {
+        let vs = be.resource;
+        if (vs && vs.url) {
+          this.queue.push(vs.url);
+          count++;
+        }
+      }
+
+      url = this._getNextUrl(bundle);
+    }
+
+    // Store the server date for next run
+    if (serverDate) {
+      await this.database.setSetting(SETTING_KEY, serverDate);
+    }
+
+    return count;
+  }
+
   name() {
     return "VSAC";
   }
@@ -533,38 +592,38 @@ class VSACValueSetProvider extends AbstractValueSetProvider {
 
     const rows = await new Promise((resolve, reject) => {
       db.all(
-        `SELECT 'vs' AS kind,
-                url,
-                version,
-                date_first_seen AS ts,
-                NULL AS status,
-                NULL AS error_message,
-                NULL AS finished_at,
-                NULL AS total_fetched,
-                NULL AS total_new
+          `SELECT 'vs' AS kind,
+                  url,
+                  version,
+                  date_first_seen AS ts,
+                  NULL AS status,
+                  NULL AS error_message,
+                  NULL AS finished_at,
+                  NULL AS total_fetched,
+                  NULL AS total_new
            FROM valuesets
-          WHERE date_first_seen > 0
-         UNION ALL
-         SELECT 'run' AS kind,
-                NULL,
-                NULL,
-                started_at AS ts,
-                status,
-                error_message,
-                finished_at,
-                total_fetched,
-                total_new
+           WHERE date_first_seen > 0
+           UNION ALL
+           SELECT 'run' AS kind,
+                  NULL,
+                  NULL,
+                  started_at AS ts,
+                  status,
+                  error_message,
+                  finished_at,
+                  total_fetched,
+                  total_new
            FROM vsac_runs
-         ORDER BY ts DESC
-         LIMIT 200`,
-        [],
-        (err, rows) => err ? reject(err) : resolve(rows)
+           ORDER BY ts DESC
+             LIMIT 200`,
+          [],
+          (err, rows) => err ? reject(err) : resolve(rows)
       );
     });
 
     const fmt = ts => ts
-      ? new Date(ts * 1000).toISOString().replace('T', ' ').substring(0, 19) + ' UTC'
-      : '—';
+        ? new Date(ts * 1000).toISOString().replace('T', ' ').substring(0, 19) + ' UTC'
+        : '—';
 
     let html = '<h3>VSAC Sync History</h3>';
     html += '<table class="grid">';

package/tx/workers/expand.js

@@ -646,6 +646,10 @@ class ValueSetExpander {
             throw new Issue('error', 'business-rule', null, null, 'The code system definition for ' + cset.system + ' has no content, so this expansion cannot be performed', 'invalid');
           } else if (cs.contentMode() === 'supplement') {
             throw new Issue('error', 'business-rule', null, null, 'The code system definition for ' + cset.system + ' defines a supplement, so this expansion cannot be performed', 'invalid');
+          } else if (cs.contentMode() === 'fragment') {
+            this.addParamUri(exp, 'used-fragment', cs.system() + '|' + cs.version());
+            Extensions.addBoolean(exp, "http://hl7.org/fhir/StructureDefinition/valueset-unclosed", true);
+            Extensions.addString(exp, "http://hl7.org/fhir/StructureDefinition/valueset-unclosed-reason","This extension is based on a fragment of the code system " + cset.system);
           } else {
             this.addParamUri(exp, cs.contentMode(), cs.system() + '|' + cs.version());
             Extensions.addBoolean(exp, "http://hl7.org/fhir/StructureDefinition/valueset-unclosed", true);
@@ -1010,7 +1014,7 @@ class ValueSetExpander {
           cds.clear();
           Extensions.checkNoModifiers(cc, 'ValueSetExpander.processCodes', 'set concept reference', vsSrc.vurl);
           const cctxt = await cs.locate(cc.code, this.allAltCodes);
-          if (cctxt && cctxt.context && (!this.params.activeOnly || !await cs.isInactive(cctxt)) && await this.passesFilters(cs, cctxt, prep, filters, 0)) {
+          if (cctxt && cctxt.context && (!this.params.activeOnly || !await cs.isInactive(cctxt.context)) && await this.passesFilters(cs, cctxt.context, prep, filters, 0)) {
             if (filter.passesDesignations(cds) || filter.passes(cc.code)) {
               let ov = Extensions.readString(cc, 'http://hl7.org/fhir/StructureDefinition/itemWeight');
               if (!ov) {

package/tx/workers/metadata.js

@@ -232,7 +232,8 @@ class MetadataHandler {
               ],
               operation: [
                 { name: 'expand', definition: 'http://hl7.org/fhir/OperationDefinition/ValueSet-expand' },
-                { name: 'validate-code', definition: 'http://hl7.org/fhir/OperationDefinition/ValueSet-validate-code' }
+                { name: 'validate-code', definition: 'http://hl7.org/fhir/OperationDefinition/ValueSet-validate-code' },
+                { name: 'related', definition: 'https://raw.githubusercontent.com/HealthIntersections/FHIRsmith/refs/heads/main/tx/data/OperationDefinition-ValueSet-related.json' }
               ]
             },
             {
@@ -265,6 +266,7 @@ class MetadataHandler {
             { name: 'validate-code', definition: 'http://hl7.org/fhir/OperationDefinition/Resource-validate-code' },
             { name: 'translate', definition: 'http://hl7.org/fhir/OperationDefinition/ConceptMap-translate' },
             { name: 'closure', definition: 'http://hl7.org/fhir/OperationDefinition/ConceptMap-closure' },
+            { name: 'related', definition: 'https://raw.githubusercontent.com/HealthIntersections/FHIRsmith/refs/heads/main/tx/data/OperationDefinition-ValueSet-related.json' },
             { name: 'versions', definition: 'http://hl7.org/fhir/OperationDefinition/fhir-versions' }
           ]
         }