fhirsmith 0.7.6 → 0.8.0

package/tx/vs/vs-database.js

@@ -33,12 +33,31 @@ class ValueSetDatabase {
       db.all("PRAGMA table_info(valuesets)", [], (err, cols) => {
         if (err) { reject(err); return; }
         const hasCol = cols.some(c => c.name === 'date_first_seen');
-        if (hasCol) { resolve(); return; }
-        db.run(
-          "ALTER TABLE valuesets ADD COLUMN date_first_seen INTEGER DEFAULT 0",
-          [],
-          (err) => err ? reject(err) : resolve()
-        );
+        const migrations = [];
+        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()
+            );
+          }));
+        }
+        // Ensure vsac_runs table exists
+        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
+            )
+          `, [], (err) => err ? rej(err) : res());
+        }));
+        Promise.all(migrations).then(() => resolve()).catch(reject);
       });
     });
   }
@@ -204,6 +223,19 @@ class ValueSetDatabase {
               )
           `);
 
+          // 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 indexes for better search performance
           db.run('CREATE INDEX idx_valuesets_url ON valuesets(url, version)');
           db.run('CREATE INDEX idx_valuesets_version ON valuesets(version)');
@@ -231,6 +263,58 @@ class ValueSetDatabase {
     });
   }
 
+  /**
+   * Record the start of a VSAC sync run
+   * @returns {Promise<number>} The run ID
+   */
+  async startRun() {
+    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); }
+      );
+    });
+  }
+
+  /**
+   * Record the successful completion of a VSAC sync run
+   * @param {number} id - The run ID from startRun()
+   * @param {number} totalFetched - Total value sets fetched
+   * @param {number} totalNew - Number of new value sets found
+   * @returns {Promise<void>}
+   */
+  async finishRun(id, totalFetched, totalNew) {
+    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()
+      );
+    });
+  }
+
+  /**
+   * Record a failed VSAC sync run
+   * @param {number} id - The run ID from startRun()
+   * @param {string} errorMessage - The error message
+   * @returns {Promise<void>}
+   */
+  async failRun(id, errorMessage) {
+    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()
+      );
+    });
+  }
+
   /**
    * Insert or update a single ValueSet in the database
    * @param {Object} valueSet - The ValueSet resource
@@ -270,23 +354,23 @@ class ValueSetDatabase {
 
             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')
+                    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,

package/tx/vs/vs-vsac.js

@@ -98,6 +98,7 @@ class VSACValueSetProvider extends AbstractValueSetProvider {
       try {
         await this.refreshValueSets();
       } catch (error) {
+        debugLog(error);
         this.log.error(error, 'Error during scheduled refresh:');
       }
     }, intervalMs);
@@ -126,6 +127,7 @@ class VSACValueSetProvider extends AbstractValueSetProvider {
     this.queue = [];
 
     this.isRefreshing = true;
+    const runId = await this.database.startRun();
 
     try {
       // phase 1: list all value sets
@@ -202,10 +204,15 @@ class VSACValueSetProvider extends AbstractValueSetProvider {
 
       // Reload map with fresh data
       await this._reloadMap();
-      console.log(`VSAC refresh completed. Total: ${tracking.totalFetched} ValueSets, Deleted: ${tracking.deletedCount}`);
+      let msg = `VSAC refresh completed. Total: ${tracking.totalFetched} ValueSets, Deleted: ${tracking.deletedCount}`;
+      this.stats.taskDone('VSAC Sync', msg);
+      console.log(msg);
+
+      await this.database.finishRun(runId, tracking.totalFetched, tracking.totalNew);
     } catch (error) {
       debugLog(error, 'Error during VSAC refresh:');
-      this.stats.task('VSAC Sync', `Error (${error.message})`);
+      this.stats.taskError('VSAC Sync', `Error (${error.message})`);
+      await this.database.failRun(runId, error.message);
       throw error;
     } finally {
       this.isRefreshing = false;
@@ -265,7 +272,6 @@ class VSACValueSetProvider extends AbstractValueSetProvider {
     }
   }
 
-
   /**
    * Fetch a FHIR Bundle from the server
    * @param {string} url - Relative URL to fetch
@@ -511,7 +517,6 @@ class VSACValueSetProvider extends AbstractValueSetProvider {
     let logMsg = `VSAC (${tracking.count} of ${length}) ${q}: ${vcount} versions`;
     console.log(logMsg);
     this.stats.task('VSAC Sync', logMsg);
-
   }
 
   name() {
@@ -523,35 +528,77 @@ class VSACValueSetProvider extends AbstractValueSetProvider {
   }
 
   async info() {
+    const escape = require('escape-html');
     const db = await this.database._getReadConnection();
+
     const rows = await new Promise((resolve, reject) => {
       db.all(
-        `SELECT url, version, date_first_seen
+        `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
-          ORDER BY date_first_seen DESC
-          LIMIT 100`,
+         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)
       );
     });
 
-    const escape = require('escape-html');
-    let html = '<h3>Recently Value Sets Added to VSAC</h3>';
-    html += '<p>The last ' + rows.length + ' value sets found from VSAC, most recent first.</p>';
+    const fmt = ts => ts
+      ? new Date(ts * 1000).toISOString().replace('T', ' ').substring(0, 19) + ' UTC'
+      : '—';
+
+    let html = '<h3>VSAC Sync History</h3>';
     html += '<table class="grid">';
-    html += '<thead><tr><th>URL</th><th>Version</th><th>Date Observed</th></tr></thead>';
+    html += '<thead><tr><th>Time</th><th>Event</th><th>Detail</th></tr></thead>';
     html += '<tbody>';
+
     for (const row of rows) {
-      const date = row.date_first_seen
-        ? new Date(row.date_first_seen * 1000).toISOString().replace('T', ' ').substring(0, 19) + ' UTC'
-        : 'unknown';
-      html += '<tr>';
-      html += `<td>${escape(row.url || '')}</td>`;
-      html += `<td>${escape(row.version || '')}</td>`;
-      html += `<td>${escape(date)}</td>`;
-      html += '</tr>';
+      if (row.kind === 'run') {
+        const duration = row.finished_at ? `${row.finished_at - row.ts}s` : 'in progress';
+        let detail, colour;
+        if (row.status === 'ok') {
+          detail = `${row.total_fetched} fetched, ${row.total_new} new, ${duration}`;
+          colour = 'green';
+        } else if (row.status === 'error') {
+          detail = `Failed: ${escape(row.error_message || '')} (${duration})`;
+          colour = 'red';
+        } else {
+          detail = `Running... (started ${fmt(row.ts)})`;
+          colour = 'orange';
+        }
+        html += `<tr style="background:#f0f0f0">`;
+        html += `<td>${escape(fmt(row.ts))}</td>`;
+        html += `<td><strong style="color:${colour}">Sync run</strong></td>`;
+        html += `<td>${detail}</td>`;
+        html += `</tr>`;
+      } else {
+        html += `<tr>`;
+        html += `<td>${escape(fmt(row.ts))}</td>`;
+        html += `<td>New value set</td>`;
+        html += `<td>${escape(row.url || '')}#${escape(row.version || '')}</td>`;
+        html += `</tr>`;
+      }
     }
+
     html += '</tbody></table>';
     return html;
   }

package/tx/workers/search.js

@@ -35,7 +35,8 @@ class SearchWorker extends TerminologyWorker {
     '_offset', '_count', '_elements', '_sort', '_summary', '_total', '_format',
     'url', 'version', 'content-mode', 'date', 'description',
     'supplements', 'identifier', 'jurisdiction', 'name',
-    'publisher', 'status', 'system', 'title', 'text'
+    'publisher', 'status', 'system', 'title', 'text',
+    'source-system', 'target-system'
   ];
 
   // Summary elements for _summary=true (marked elements per resource type)

package/tx/workers/translate.js

@@ -115,8 +115,12 @@ class TranslateWorker extends TerminologyWorker {
     let targetSystem = null;
 
     // Get the source coding
+    // Accept both R5 names (sourceCoding, sourceCodeableConcept, sourceCode/sourceSystem)
+    // and R4 names (coding, codeableConcept, code/system) as aliases
     if (params.has('sourceCoding')) {
       coding = params.get('sourceCoding');
+    } else if (params.has('coding')) {
+      coding = params.get('coding');
     } else if (params.has('sourceCodeableConcept')) {
       const cc = params.get('sourceCodeableConcept');
       if (cc.coding && cc.coding.length > 0) {
@@ -125,16 +129,23 @@ class TranslateWorker extends TerminologyWorker {
         throw new Issue('error', 'invalid', null, null,
           'sourceCodeableConcept must contain at least one coding', null, 400);
       }
-    } else if (params.has('sourceCode')) {
-      if (!params.has('sourceSystem')) {
+    } else if (params.has('codeableConcept')) {
+      const cc = params.get('codeableConcept');
+      if (cc.coding && cc.coding.length > 0) {
+        coding = cc.coding[0];
+      } else {
         throw new Issue('error', 'invalid', null, null,
-          'sourceSystem parameter is required when using sourceCode', null, 400);
+          'codeableConcept must contain at least one coding', null, 400);
       }
-      coding = {
-        system: params.get('sourceSystem'),
-        version: params.get('sourceVersion'),
-        code: params.get('sourceCode')
-      };
+    } else if (params.has('sourceCode') || params.has('code')) {
+      const code = params.has('sourceCode') ? params.get('sourceCode') : params.get('code');
+      const system = params.has('sourceSystem') ? params.get('sourceSystem') : params.get('system');
+      if (!system) {
+        throw new Issue('error', 'invalid', null, null,
+          'system parameter is required when using code/sourceCode', null, 400);
+      }
+      const version = params.has('sourceVersion') ? params.get('sourceVersion') : params.get('version');
+      coding = { system, version, code };
     } else {
       throw new Issue('error', 'invalid', null, null,
         'Must provide sourceCode (with system), sourceCoding, or sourceCodeableConcept', null, 400);
@@ -169,7 +180,7 @@ class TranslateWorker extends TerminologyWorker {
     // If no explicit concept map, we need to find one based on source/target
     if (conceptMaps.length == 0) {
       await this.findConceptMapsInAdditionalResources(conceptMaps, coding.system, sourceScope, targetScope, targetSystem);
-      await this.provider.findConceptMapForTranslation(this.opContext, conceptMaps, coding.system, sourceScope, targetScope, targetSystem);
+      await this.provider.findConceptMapForTranslation(this.opContext, conceptMaps, coding.system, sourceScope, targetScope, targetSystem, coding.code);
       if (conceptMaps.length == 0) {
         throw new Issue('error', 'not-found', null, null, 'No suitable ConceptMaps found for the specified source and target', null, 404);
       }
@@ -208,10 +219,14 @@ class TranslateWorker extends TerminologyWorker {
     txp.readParams(params.jsonObj);
 
     // Get the source coding
+    // Accept both R5 names (sourceCoding, sourceCodeableConcept, sourceCode)
+    // and R4 names (coding, codeableConcept, code) as aliases
     let coding = null;
 
     if (params.has('sourceCoding')) {
       coding = params.get('sourceCoding');
+    } else if (params.has('coding')) {
+      coding = params.get('coding');
     } else if (params.has('sourceCodeableConcept')) {
       const cc = params.get('sourceCodeableConcept');
       if (cc.coding && cc.coding.length > 0) {
@@ -220,15 +235,25 @@ class TranslateWorker extends TerminologyWorker {
         throw new Issue('error', 'invalid', null, null,
           'sourceCodeableConcept must contain at least one coding', null, 400);
       }
-    } else if (params.has('sourceCode')) {
-      if (!params.has('system')) {
+    } else if (params.has('codeableConcept')) {
+      const cc = params.get('codeableConcept');
+      if (cc.coding && cc.coding.length > 0) {
+        coding = cc.coding[0];
+      } else {
+        throw new Issue('error', 'invalid', null, null,
+          'codeableConcept must contain at least one coding', null, 400);
+      }
+    } else if (params.has('sourceCode') || params.has('code')) {
+      const code = params.has('sourceCode') ? params.get('sourceCode') : params.get('code');
+      const system = params.has('system') ? params.get('system') : null;
+      if (!system) {
         throw new Issue('error', 'invalid', null, null,
-          'system parameter is required when using sourceCode', null, 400);
+          'system parameter is required when using code/sourceCode', null, 400);
       }
       coding = {
-        system: params.get('system'),
+        system,
         version: params.get('version'),
-        code: params.get('sourceCode')
+        code
       };
     } else {
       throw new Issue('error', 'invalid', null, null,

package/tx/workers/validate.js

@@ -1107,7 +1107,7 @@ class ValueSetChecker {
       codelist = !codelist ? '\'' + cc + '\'' : codelist + ', \'' + cc + '\'';
 
       if (v === false && !this.valueSet.jsonObj.internallyDefined && mode === 'codeableConcept') {
-        let m = this.worker.i18n.translate('None_of_the_provided_codes_are_in_the_value_set_one', this.params.HTTPLanguages, ['', this.valueSet.vurl, '\'' + cc + '\'']);
+        let m = this.worker.i18n.translate('None_of_the_provided_codes_are_in_the_value_set_one', this.params.HTTPLanguages, ['', this.valueSet.vurlOrMsg, '\'' + cc + '\'']);
         let p = issuePath + '.coding[' + i + '].code';
         op.addIssue(new Issue('information', 'code-invalid', p, 'None_of_the_provided_codes_are_in_the_value_set_one', m, 'this-code-not-in-vs'));
         if (cause.value === 'null') {
@@ -1284,10 +1284,10 @@ class ValueSetChecker {
       let mid, m, p;
       if (mode === 'codeableConcept') {
         mid = 'TX_GENERAL_CC_ERROR_MESSAGE';
-        m = this.worker.i18n.translate('TX_GENERAL_CC_ERROR_MESSAGE', this.params.HTTPLanguages, [this.valueSet.vurl]);
+        m = this.worker.i18n.translate('TX_GENERAL_CC_ERROR_MESSAGE', this.params.HTTPLanguages, [this.valueSet.vurlOrMsg]);
       } else {
         mid = 'None_of_the_provided_codes_are_in_the_value_set_one';
-        m = this.worker.i18n.translate('None_of_the_provided_codes_are_in_the_value_set_one', this.params.HTTPLanguages, ['', this.valueSet.vurl, codelist]);
+        m = this.worker.i18n.translate('None_of_the_provided_codes_are_in_the_value_set_one', this.params.HTTPLanguages, ['', this.valueSet.vurlOrMsg, codelist]);
       }
 
       if (mode === 'codeableConcept') {