fhirsmith 0.5.6 → 0.7.0

package/tx/vs/vs-vsac.js

@@ -4,6 +4,7 @@ const { AbstractValueSetProvider } = require('./vs-api');
 const { ValueSetDatabase } = require('./vs-database');
 const { VersionUtilities } = require('../../library/version-utilities');
 const folders = require('../../library/folder-setup');
+const {debugLog} = require("../operation-context");
 
 /**
  * VSAC (Value Set Authority Center) ValueSet provider
@@ -178,7 +179,7 @@ class VSACValueSetProvider extends AbstractValueSetProvider {
           await this.processContentAndHistory(q, tracking, this.queue.length);
         } catch (error) {
           this.requeue.push(q)
-          console.log(error);
+          debugLog(error);
           this.stats.task('VSAC Sync', error.message);
         }
         // `running (${totalFetched} fetched, ${totalNew} new)`)
@@ -190,7 +191,7 @@ class VSACValueSetProvider extends AbstractValueSetProvider {
         try {
           await this.processContentAndHistory(q, tracking, this.requeue.length);
         } catch (error) {
-          console.log(error);
+          debugLog(error);
           this.stats.task('VSAC Sync', error.message);
         }
         // `running (${totalFetched} fetched, ${totalNew} new)`)
@@ -201,7 +202,7 @@ class VSACValueSetProvider extends AbstractValueSetProvider {
       await this._reloadMap();
       console.log(`VSAC refresh completed. Total: ${tracking.totalFetched} ValueSets, Deleted: ${tracking.deletedCount}`);
     } catch (error) {
-      console.log(error, 'Error during VSAC refresh:');
+      debugLog(error, 'Error during VSAC refresh:');
       this.stats.task('VSAC Sync', `Error (${error.message})`);
       throw error;
     } finally {

package/tx/workers/batch-validate.js

@@ -15,6 +15,7 @@ const { TerminologyWorker } = require('./worker');
 const {OperationOutcome, Issue} = require("../library/operation-outcome");
 const {Parameters} = require("../library/parameters");
 const {ValidateWorker} = require("./validate");
+const {debugLog} = require("../operation-context");
 
 class BatchValidateWorker extends TerminologyWorker {
 
@@ -82,7 +83,7 @@ class BatchValidateWorker extends TerminologyWorker {
             output.push({name: "validation", resource : p});
           } catch (error) {
             this.log.error(error);
-            this.debugLog(error);
+            debugLog(error);
             if (error instanceof Issue) {
               let op = new OperationOutcome();
               op.addIssue(error);
@@ -98,7 +99,7 @@ class BatchValidateWorker extends TerminologyWorker {
       return res.json(result);
     } catch (error) {
       this.log.error(error);
-      this.debugLog(error);
+      debugLog(error);
       return res.status(error.statusCode || 500).json(this.operationOutcome(
         'error', error.issueCode || 'exception', error.message));
     }

package/tx/workers/batch.js

@@ -6,6 +6,7 @@
 
 const { TerminologyWorker } = require('./worker');
 const { Issue, OperationOutcome } = require('../library/operation-outcome');
+const {debugLog} = require("../operation-context");
 
 class BatchWorker extends TerminologyWorker {
   /**
@@ -40,7 +41,7 @@ class BatchWorker extends TerminologyWorker {
       await this.handleBatch(req, res);
     } catch (error) {
       this.log.error(error);
-      this.debugLog(error);
+      debugLog(error);
       if (error instanceof Issue) {
         const oo = new OperationOutcome();
         oo.addIssue(error);
@@ -160,7 +161,7 @@ class BatchWorker extends TerminologyWorker {
 
     } catch (error) {
       this.log.error(error);
-      this.debugLog(error);
+      debugLog(error);
       const statusCode = error.statusCode || 500;
       const issueCode = error.issueCode || 'exception';
 

package/tx/workers/expand.js

@@ -18,6 +18,7 @@ const {Issue, OperationOutcome} = require("../library/operation-outcome");
 const crypto = require('crypto');
 const ValueSet = require("../library/valueset");
 const {VersionUtilities} = require("../../library/version-utilities");
+const {debugLog} = require("../operation-context");
 
 // Expansion limits (from Pascal constants)
 const EXTERNAL_DEFAULT_LIMIT = 1000;
@@ -197,6 +198,7 @@ class ValueSetCounter {
 class ValueSetExpander {
   worker;
   params;
+  doingVersion = true;
   excludedSystems = new Set();
   excluded = new Set();
   hasExclusions = false;
@@ -495,7 +497,8 @@ class ValueSetExpander {
       }
     }
 
-    this.excluded.add(system + '|' + version + '#' + code);
+    let key = (this.doingVersion && !this.params.versionsMatch ? system + '|' + version : system) + '#' + code
+    this.excluded.add(key);
   }
 
   async checkCanExpandValueSet(uri, version) {
@@ -922,8 +925,20 @@ class ValueSetExpander {
       if (!cset.concept && !cset.filter) {
         this.worker.opContext.log('handle system');
         if (!cset.valueSet) {
-          // excluding a whole system - we don't list the codes in this case
-          this.excludedSystems.add(cset.system + (cset.version ? '|'+cset.version : ''));
+          if (!this.excludeSpecialCase) {
+            // excluding a whole system - we don't list the codes in this case
+            this.excludedSystems.add(cset.system + (this.doingVersion && cset.version ? '|' + cset.version : ''));
+          } else {
+            const iter = await cs.iteratorAll();
+            if (iter) {
+              let c = await cs.nextContext(iter);
+              while (c) {
+                this.worker.deadCheck('processCodes#3aa');
+                this.excludeCode(cs, cs.system(), cs.version(), await cs.code(c), expansion, valueSets, vsSrc.url);
+                c = await cs.nextContext(iter);
+              }
+            }
+          }
         } else {
           if (cs.isNotClosed(filter)) {
             if (cs.specialEnumeration()) {
@@ -1081,6 +1096,7 @@ class ValueSetExpander {
   async handleCompose(source, filter, expansion, notClosed, vsInfo) {
     this.worker.opContext.log('compose #1');
 
+    this.doingVersion = false;
     const ts = new Map();
     for (const c of source.jsonObj.compose.include || []) {
       this.worker.deadCheck('handleCompose#2');
@@ -1097,6 +1113,8 @@ class ValueSetExpander {
     if (vsInfo.handleByCS) {
       await this.processCodes("ValueSet.compose", source, source.jsonObj.compose, filter, expansion, this.excludeInactives(source), notClosed, vsInfo);
     } else {
+      this.checkForExclusionVersionSpecialCase(source, expansion);
+
       let i = 0;
       for (const c of source.jsonObj.compose.exclude || []) {
         this.worker.deadCheck('handleCompose#4');
@@ -1104,7 +1122,14 @@ class ValueSetExpander {
       }
 
       i = 0;
-      for (const c of source.jsonObj.compose.include || []) {
+      const includes = [...(source.jsonObj.compose.include || [])];
+      includes.sort((a, b) => {
+        if (a.system === b.system && a.version && b.version) {
+          return -VersionUtilities.compareVersionsGeneral(a.version, b.version);
+        }
+        return 0;
+      });
+      for (const c of includes) {
         this.worker.deadCheck('handleCompose#5');
         await this.includeCodes(c, "ValueSet.compose.include[" + i + "]", source, source.jsonObj.compose, filter, expansion, this.excludeInactives(source), notClosed);
         i++;
@@ -1197,6 +1222,9 @@ class ValueSetExpander {
     if (this.params.hasExcludeNested) {
       this.addParamBool(exp, 'excludeNested', this.params.excludeNested);
     }
+    if (this.params.versionsMatch) {
+      this.addParamBool(exp, 'versionsMatch', this.params.versionsMatch);
+    }
     if (this.params.hasActiveOnly) {
       this.addParamBool(exp, 'activeOnly', this.params.activeOnly);
     }
@@ -1388,17 +1416,28 @@ class ValueSetExpander {
   }
 
   checkCanonicalStatus(exp, vurl, status, standardsStatus, experimental, source) {
+    let sourceStatus = source ? source.status : undefined;
+    let sourceStandardsStatus= source ? Extensions.readString(source, 'http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status') : undefined;
     if (standardsStatus == 'deprecated') {
-      this.addParamUri(exp, 'warning-deprecated', vurl);
+      if (sourceStandardsStatus != 'deprecated') {
+        this.addParamUri(exp, 'warning-deprecated', vurl);
+      }
     } else if (standardsStatus == 'withdrawn') {
-      this.addParamUri(exp, 'warning-withdrawn', vurl);
+      if (sourceStandardsStatus != 'withdrawn') {
+        this.addParamUri(exp, 'warning-withdrawn', vurl);
+      }
     } else if (status == 'retired') {
-      this.addParamUri(exp, 'warning-retired', vurl);
-    } else if (experimental && !source.experimental) {
-      this.addParamUri(exp, 'warning-experimental', vurl)
-    } else if (((status == 'draft') || (standardsStatus == 'draft')) &&
-      !((source.status == 'draft') || (Extensions.readString(source, 'http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status') == 'draft'))) {
-      this.addParamUri(exp, 'warning-draft', vurl)
+      if (sourceStatus != 'retired') {
+        this.addParamUri(exp, 'warning-retired', vurl);
+      }
+    } else if (experimental) {
+      if (!source.experimental) {
+        this.addParamUri(exp, 'warning-experimental', vurl);
+      }
+    } else if (((status == 'draft') || (standardsStatus == 'draft'))) {
+      if (!((source.status == 'draft') || (Extensions.readString(source, 'http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status') == 'draft'))) {
+        this.addParamUri(exp, 'warning-draft', vurl)
+      }
     }
   }
 
@@ -1470,14 +1509,16 @@ class ValueSetExpander {
     if (this.excludedSystems.has(system)) {
       return true;
     }
-    if (this.excludedSystems.has(system+'|'+version)) {
+    let key = this.doingVersion && !this.params.versionsMatch? system+'|'+version : system;
+    if (this.excludedSystems.has(key)) {
       return true;
     }
-    return this.excluded.has(system+'|'+version+'#'+code);
+    key = (this.doingVersion && !this.params.versionsMatch ? system+'|'+version : system)+'#'+code;
+    return this.excluded.has(key);
   }
 
   keyS(system, version, code) {
-    return system+"~"+(this.doingVersion ? version+"~" : "")+code;
+    return system+"~"+(this.doingVersion && !this.params.versionsMatch ? version+"~" : "")+code;
   }
 
   keyC(contains) {
@@ -1625,6 +1666,31 @@ class ValueSetExpander {
     }
     return null;
   }
+
+
+  // special case: excluding a different version from the include
+  checkForExclusionVersionSpecialCase(source, exp) {
+    if (!this.params.hasVersionsMatch) {
+
+
+      const includes = source.jsonObj.compose.include || [];
+      const excludes = source.jsonObj.compose.exclude || [];
+
+      if (includes.length > 0 && excludes.length > 0) {
+        const system = includes[0].system;
+        const allSameSystem = includes.every(i => i.system === system && i.version)
+          && excludes.every(e => e.system === system && e.version);
+        const noOverlap = !includes.some(i => excludes.some(e => e.version === i.version));
+
+        if (allSameSystem && noOverlap) {
+          this.params.versionsMatch = true;
+          this.excludeSpecialCase = true;
+          this.addParamBool(exp, 'versionsMatch', this.params.versionsMatch);
+
+        }
+      }
+    }
+  }
 }
 
 class ExpandWorker extends TerminologyWorker {
@@ -1665,7 +1731,7 @@ class ExpandWorker extends TerminologyWorker {
       await this.handleTypeLevelExpand(req, res);
     } catch (error) {
       this.log.error(error);
-      this.debugLog(error);
+      debugLog(error);
       req.logInfo = this.usedSources.join("|")+" - error"+(error.msgId  ? " "+error.msgId : "");
       const statusCode = error.statusCode || 500;
       if (error instanceof Issue) {
@@ -1700,7 +1766,7 @@ class ExpandWorker extends TerminologyWorker {
       await this.handleInstanceLevelExpand(req, res);
     } catch (error) {
       this.log.error(error);
-      this.debugLog(error);
+      debugLog(error);
       req.logInfo = this.usedSources.join("|")+" - error"+(error.msgId  ? " "+error.msgId : "");
       const statusCode = error.statusCode || 500;
       const issueCode = error.issueCode || 'exception';
@@ -1797,7 +1863,48 @@ class ExpandWorker extends TerminologyWorker {
     req.logInfo = this.usedSources.join("|")+txp.logInfo();
     return res.json(result);
   }
-  
+
+  /**
+   * Handle type-level expand: /ValueSet/$expand
+   * ValueSet identified by url, or provided directly in body
+   */
+  async handleInternalExpand(valueSet, req) {
+    this.deadCheck('expand-internal');
+
+    if (!valueSet.jsonObj) {
+      valueSet = new ValueSet(valueSet);
+    }
+    // Determine how the request is structured
+    let params = null;
+    this.seeSourceVS(valueSet);
+
+    if (req.method === 'POST' && req.body) {
+      if (req.body.resourceType === 'ValueSet') {
+        params = this.queryToParameters(req.query);
+      } else if (req.body.resourceType === 'Parameters') {
+        // Body is a Parameters resource
+        params = req.body;
+      } else {
+        // Assume form body - convert to Parameters
+        params = this.formToParameters(req.body, req.query);
+      }
+    } else {
+      // GET request - convert query to Parameters
+      params = this.queryToParameters(req.query);
+    }
+    this.addHttpParams(req, params);
+
+    // Handle tx-resource and cache-id parameters
+    this.setupAdditionalResources(params);
+    const logExtraOutput = this.findParameter(params, 'logExtraOutput');
+
+    let txp = new TxParameters(this.opContext.i18n.languageDefinitions, this.opContext.i18n, false);
+    txp.readParams(params);
+
+    // Perform the expansion
+    return await this.doExpand(valueSet, txp, logExtraOutput);
+  }
+
   /**
    * Handle instance-level expand: /ValueSet/{id}/$expand
    * ValueSet identified by resource ID

package/tx/workers/lookup.js

@@ -13,6 +13,7 @@ const { Designations} = require("../library/designations");
 const {TxParameters} = require("../params");
 const {Parameters} = require("../library/parameters");
 const {Issue, OperationOutcome} = require("../library/operation-outcome");
+const {debugLog} = require("../operation-context");
 
 class LookupWorker extends TerminologyWorker {
   /**
@@ -45,7 +46,7 @@ class LookupWorker extends TerminologyWorker {
       await this.handleTypeLevelLookup(req, res);
     } catch (error) {
       this.log.error(error);
-      this.debugLog(error);
+      debugLog(error);
       req.logInfo = this.usedSources.join("|")+" - error"+(error.msgId  ? " "+error.msgId : "");
       const statusCode = error.statusCode || 500;
       const issueCode = error.issueCode || 'exception';
@@ -72,7 +73,7 @@ class LookupWorker extends TerminologyWorker {
       await this.handleInstanceLevelLookup(req, res);
     } catch (error) {
       this.log.error(error);
-      this.debugLog(error);
+      debugLog(error);
       req.logInfo = this.usedSources.join("|")+" - error"+(error.msgId  ? " "+error.msgId : "");
       const issueCode = error.issueCode || 'exception';
       return res.status(400).json({
@@ -159,7 +160,7 @@ class LookupWorker extends TerminologyWorker {
       return res.status(200).json(result);
     } catch (error) {
       this.log.error(error);
-      this.debugLog(error);
+      debugLog(error);
       req.logInfo = this.usedSources.join("|")+" - error"+(error.msgId  ? " "+error.msgId : "");
       if (error instanceof Issue) {
         let oo = new OperationOutcome();
@@ -223,7 +224,7 @@ class LookupWorker extends TerminologyWorker {
       return res.status(200).json(result);
     } catch (error) {
       this.log.error(error);
-      this.debugLog(error);
+      debugLog(error);
       req.logInfo = this.usedSources.join("|")+" - error"+(error.msgId  ? " "+error.msgId : "");
       if (error instanceof Issue) {
         let oo = new OperationOutcome();

package/tx/workers/read.js

@@ -5,6 +5,7 @@
 //
 
 const { TerminologyWorker } = require('./worker');
+const {debugLog} = require("../operation-context");
 
 class ReadWorker extends TerminologyWorker {
   /**
@@ -67,7 +68,7 @@ class ReadWorker extends TerminologyWorker {
       }
     } catch (error) {
       this.log.error(error);
-      this.debugLog(error);
+      debugLog(error);
       req.logInfo = this.usedSources.join("|")+" - error"+(error.msgId  ? " "+error.msgId : "");
       return res.status(500).json({
         resourceType: 'OperationOutcome',

package/tx/workers/related.js

@@ -16,6 +16,7 @@ const ValueSet = require("../library/valueset");
 const {ValueSetExpander} = require("./expand");
 const {SearchFilterText} = require("../library/designations");
 const {ArrayMatcher} = require("../../library/utilities");
+const {debugLog} = require("../operation-context");
 
 
 class RelatedWorker extends TerminologyWorker {
@@ -49,7 +50,7 @@ class RelatedWorker extends TerminologyWorker {
       await this.handleTypeLevelRelated(req, res);
     } catch (error) {
       this.log.error(error);
-      this.debugLog(error);
+      debugLog(error);
       req.logInfo = this.usedSources.join("|")+" - error"+(error.msgId  ? " "+error.msgId : "");
       const statusCode = error.statusCode || 500;
       if (error instanceof Issue) {
@@ -84,7 +85,7 @@ class RelatedWorker extends TerminologyWorker {
       await this.handleInstanceLevelRelated(req, res);
     } catch (error) {
       this.log.error(error);
-      this.debugLog(error);
+      debugLog(error);
       req.logInfo = this.usedSources.join("|")+" - error"+(error.msgId  ? " "+error.msgId : "");
       const statusCode = error.statusCode || 500;
       const issueCode = error.issueCode || 'exception';

package/tx/workers/search.js

@@ -7,6 +7,7 @@
 
 const { TerminologyWorker } = require('./worker');
 const {Utilities} = require("../../library/utilities");
+const {debugLog} = require("../operation-context");
 
 class SearchWorker extends TerminologyWorker {
   /**
@@ -114,7 +115,7 @@ class SearchWorker extends TerminologyWorker {
 
     } catch (error) {
       this.log.error(error);
-      this.debugLog(error);
+      debugLog(error);
       req.logInfo = "error "+(error.msgId || error.className);
       return res.status(500).json({
         resourceType: 'OperationOutcome',
@@ -137,7 +138,7 @@ class SearchWorker extends TerminologyWorker {
     const searchParams = {};
     for (const [key, value] of Object.entries(params)) {
       if (!key.startsWith('_') && value && SearchWorker.ALLOWED_PARAMS.includes(key)) {
-        searchParams[key] = value.toLowerCase();
+        searchParams[key] = key == 'url' ? value : value.toLowerCase();
       }
     }
 
@@ -146,6 +147,7 @@ class SearchWorker extends TerminologyWorker {
 
     for (const [key, cs] of this.provider.codeSystems) {
       this.deadCheck('searchCodeSystems');
+
       if (key == cs.vurl) {
         const json = cs.jsonObj;
 
@@ -157,10 +159,6 @@ class SearchWorker extends TerminologyWorker {
         // Check each search parameter for partial match
         let isMatch = true;
         for (const [param, searchValue] of Object.entries(searchParams)) {
-          // 'system' doesn't do anything for CodeSystem search
-          if (param === 'system') {
-            continue;
-          }
 
           // Map content-mode to content property
           const jsonProp = param === 'content-mode' ? 'content' : param;
@@ -177,9 +175,9 @@ class SearchWorker extends TerminologyWorker {
               isMatch = false;
               break;
             }
-          } else if (param === 'url') { // exact match
+          } else if (param === 'url' || param === 'system') { // exact match
             const propValue = json.url;
-            if (propValue != searchValue) {
+            if (propValue !== searchValue) {
               isMatch = false;
               break;
             }

package/tx/workers/subsumes.js

@@ -12,6 +12,7 @@ const { FhirCodeSystemProvider } = require('../cs/cs-cs');
 const {TxParameters} = require("../params");
 const {Parameters} = require("../library/parameters");
 const {Issue, OperationOutcome} = require("../library/operation-outcome");
+const {debugLog} = require("../operation-context");
 class SubsumesWorker extends TerminologyWorker {
   /**
    * @param {OperationContext} opContext - Operation context
@@ -43,7 +44,7 @@ class SubsumesWorker extends TerminologyWorker {
       await this.handleTypeLevelSubsumes(req, res);
     } catch (error) {
       this.log.error(error);
-      this.debugLog(error);
+      debugLog(error);
       req.logInfo = "error "+(error.msgId || error.className);
       if (error instanceof Issue) {
         let oo = new OperationOutcome();
@@ -67,7 +68,7 @@ class SubsumesWorker extends TerminologyWorker {
       await this.handleInstanceLevelSubsumes(req, res);
     } catch (error) {
       this.log.error(error);
-      this.debugLog(error);
+      debugLog(error);
       if (error instanceof Issue) {
         let oo = new OperationOutcome();
         oo.addIssue(error);

package/tx/workers/translate.js

@@ -12,6 +12,7 @@ const { TxParameters } = require('../params');
 const { Parameters } = require('../library/parameters');
 const { Issue, OperationOutcome } = require('../library/operation-outcome');
 const {ConceptMap} = require("../library/conceptmap");
+const {debugLog} = require("../operation-context");
 
 class TranslateWorker extends TerminologyWorker {
   /**
@@ -44,7 +45,7 @@ class TranslateWorker extends TerminologyWorker {
       await this.handleTypeLevelTranslate(req, res);
     } catch (error) {
       this.log.error(error);
-      this.debugLog(error);
+      debugLog(error);
       if (error instanceof Issue) {
         const oo = new OperationOutcome();
         oo.addIssue(error);
@@ -67,7 +68,7 @@ class TranslateWorker extends TerminologyWorker {
       await this.handleInstanceLevelTranslate(req, res);
     } catch (error) {
       this.log.error(error);
-      this.debugLog(error);
+      debugLog(error);
       if (error instanceof Issue) {
         const oo = new OperationOutcome();
         oo.addIssue(error);
@@ -410,7 +411,7 @@ class TranslateWorker extends TerminologyWorker {
       }
     } catch (error) {
       this.log.error(error);
-      this.debugLog(error);
+      debugLog(error);
       result.push({
         name: 'result',
         valueBoolean: false