Merge pull request #1883 from hapifhir/2025-01-gg-ai

2025 01 gg ai
hapifhir · Jan 16, 2025 · ac4b187 · ac4b187
2 parents cf0d398 + 3d0a3c4
commit ac4b187
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Showing 52 changed files with 1,549 additions and 99 deletions.
diff --git a/org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/terminologies/CodeSystemUtilities.java b/org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/terminologies/CodeSystemUtilities.java
@@ -240,7 +240,7 @@ public static String getOID(CodeSystem cs) {
     return null;
   }
 
-  private static ConceptDefinitionComponent findCode(List<ConceptDefinitionComponent> list, String code) {
+  public static ConceptDefinitionComponent findCode(List<ConceptDefinitionComponent> list, String code) {
     for (ConceptDefinitionComponent c : list) {
       if (c.getCode().equals(code))
         return c;

diff --git a/org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/elementmodel/ObjectConverter.java b/org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/elementmodel/ObjectConverter.java
@@ -72,7 +72,7 @@ public Element convert(Resource ig) throws IOException, FHIRException {
     ByteArrayInputStream bi = new ByteArrayInputStream(bs.toByteArray());
     List<NamedElement> list = new JsonParser(context).parse(bi);
     if (list.size() != 1) {
-      throw new FHIRException("Unable to convert because the source contains multieple resources");
+      throw new FHIRException("Unable to convert because the source contains multiple resources");
     }
     return list.get(0).getElement();
   }

diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/ProfileUtilities.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/ProfileUtilities.java
@@ -2853,7 +2853,7 @@ else if (ToolingExtensions.hasExtension(expBase.getValueset().getExpansion(), To
                 } else {
                   boolean ok = true;
                   for (ValueSetExpansionContainsComponent cc : expDerived.getValueset().getExpansion().getContains()) {
-                    ValidationResult vr = context.validateCode(null, cc.getSystem(), cc.getVersion(), cc.getCode(), null, baseVs);
+                    ValidationResult vr = context.validateCode(new ValidationOptions(), cc.getSystem(), cc.getVersion(), cc.getCode(), null, baseVs);
                     if (!vr.isOk()) {
                       ok = false;
                       break;                      

diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
@@ -942,7 +942,10 @@ public ValueSetExpansionOutcome expandVS(ITerminologyOperationDetails opCtxt, Co
 
     try {
       ValueSet result = tc.getClient().expandValueset(vs, p);
-      res = new ValueSetExpansionOutcome(result).setTxLink(txLog.getLastId());  
+      res = new ValueSetExpansionOutcome(result).setTxLink(txLog.getLastId());
+      if (res != null && res.getValueset() != null) { 
+        res.getValueset().setUserData(UserDataNames.VS_EXPANSION_SOURCE, tc.getHost());
+      }
     } catch (Exception e) {
       res = new ValueSetExpansionOutcome(e.getMessage() == null ? e.getClass().getName() : e.getMessage(), TerminologyServiceErrorClass.UNKNOWN, true);
       if (txLog != null) {
@@ -1012,7 +1015,10 @@ public ValueSetExpansionOutcome expandVS(String url, boolean cacheOk, boolean hi
           throw new Error(formatMessage(I18nConstants.NO_URL_IN_EXPAND_VALUE_SET_2));
         }
       }
-      res = new ValueSetExpansionOutcome(result).setTxLink(txLog.getLastId());  
+      res = new ValueSetExpansionOutcome(result).setTxLink(txLog.getLastId()); 
+      if (res != null && res.getValueset() != null) { 
+        res.getValueset().setUserData(UserDataNames.VS_EXPANSION_SOURCE, tc.getHost());
+      } 
     } catch (Exception e) {
       res = new ValueSetExpansionOutcome((e.getMessage() == null ? e.getClass().getName() : e.getMessage()), TerminologyServiceErrorClass.UNKNOWN, allErrors, true).setTxLink(txLog == null ? null : txLog.getLastId());
     }
@@ -1085,6 +1091,9 @@ public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean h
     res = null;
     try {
       res = vse.expand(vs, p);
+      if (res != null && res.getValueset() != null) { 
+        res.getValueset().setUserData(UserDataNames.VS_EXPANSION_SOURCE, vse.getSource());
+      }
     } catch (Exception e) {
       allErrors.addAll(vse.getAllErrors());
       e.printStackTrace();
@@ -1098,7 +1107,7 @@ public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean h
       txCache.cacheExpansion(cacheToken, res, TerminologyCache.TRANSIENT);
       return res;
     }
-    if (res.getErrorClass() == TerminologyServiceErrorClass.INTERNAL_ERROR || isNoTerminologyServer()) { // this class is created specifically to say: don't consult the server
+    if (res.getErrorClass() == TerminologyServiceErrorClass.INTERNAL_ERROR || isNoTerminologyServer() || res.getErrorClass() == TerminologyServiceErrorClass.VALUESET_UNKNOWN) { // this class is created specifically to say: don't consult the server
       return new ValueSetExpansionOutcome(res.getError(), res.getErrorClass(), false);
     }
 
@@ -1133,6 +1142,9 @@ public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean h
         res = new ValueSetExpansionOutcome((e.getMessage() == null ? e.getClass().getName() : e.getMessage()), TerminologyServiceErrorClass.UNKNOWN, allErrors, true).setTxLink(txLog == null ? null : txLog.getLastId());
       }
     }
+    if (res != null && res.getValueset() != null) {
+      res.getValueset().setUserData(UserDataNames.VS_EXPANSION_SOURCE, tc.getHost());
+    }
     txCache.cacheExpansion(cacheToken, res, TerminologyCache.PERMANENT);
     return res;
   }

diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/ObjectConverter.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/ObjectConverter.java
@@ -73,7 +73,7 @@ public Element convert(Resource ig) throws IOException, FHIRException {
     ByteArrayInputStream bi = new ByteArrayInputStream(bs.toByteArray());
     List<ValidatedFragment> list = new JsonParser(context).parse(bi);
     if (list.size() != 1) {
-      throw new FHIRException("Unable to convert because the source contains multieple resources");
+      throw new FHIRException("Unable to convert because the source contains multiple resources");
     }
     return list.get(0).getElement();
   }

diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ValueSetRenderer.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ValueSetRenderer.java
@@ -90,7 +90,20 @@ public void buildNarrative(RenderingStatus status, XhtmlNode x, ResourceWrapper
         if (vs.hasCopyright())
           generateCopyright(x, r);
       }
-
+      if (vs.hasExtension(ToolingExtensions.EXT_VS_CS_SUPPL_NEEDED)) {
+        var p = x.para();
+        p.tx("This ValueSet requires the Code system Supplement ");
+        String u = ToolingExtensions.readStringExtension(vs, ToolingExtensions.EXT_VS_CS_SUPPL_NEEDED);
+        CodeSystem cs = context.getContext().fetchResource(CodeSystem.class, u);
+        if (cs == null) {
+          p.code().tx(u);
+        } else if (!cs.hasWebPath()) {
+          p.ah(u).tx(cs.present());
+        } else {
+          p.ah(cs.getWebPath()).tx(cs.present());          
+        }
+        p.tx(".");
+      }
       if (vs.hasExpansion()) {
         // for now, we just accept an expansion if there is one
         generateExpansion(status, r, x, vs, false, maps);
@@ -498,14 +511,26 @@ private void generateVersionNotice(XhtmlNode x, ValueSetExpansionComponent expan
         if (versions.size() == 1 && versions.get(s).size() == 1) {
           for (String v : versions.get(s)) { // though there'll only be one
             XhtmlNode p = x.para().style("border: black 1px dotted; background-color: #EEEEEE; padding: 8px; margin-bottom: 8px");
-            p.tx(context.formatPhrase(RenderingContext.VALUE_SET_EXPANSION)+" ");
+            if (!vs.hasUserData(UserDataNames.VS_EXPANSION_SOURCE)) {
+              p.tx(context.formatPhrase(RenderingContext.VALUE_SET_EXPANSION)+" ");
+            } else if ("internal".equals(vs.getUserString(UserDataNames.VS_EXPANSION_SOURCE))) {
+              p.tx(context.formatPhrase(RenderingContext.VALUE_SET_EXPANSION_INTERNAL)+" ");              
+            } else {
+              p.tx(context.formatPhrase(RenderingContext.VALUE_SET_EXPANSION_SRVR, vs.getUserString(UserDataNames.VS_EXPANSION_SOURCE))+" ");
+            }
             expRef(p, s, v, vs);
           }
         } else {
           for (String v : versions.get(s)) {
             if (first) {
               div = x.div().style("border: black 1px dotted; background-color: #EEEEEE; padding: 8px; margin-bottom: 8px");
-              div.para().tx(context.formatPhrase(RenderingContext.VALUE_SET_EXPANSIONS));
+              if (!vs.hasUserData(UserDataNames.VS_EXPANSION_SOURCE)) {
+                div.para().tx(context.formatPhrase(RenderingContext.VALUE_SET_EXPANSIONS));                
+              } else if ("internal".equals(vs.getUserString(UserDataNames.VS_EXPANSION_SOURCE))) {
+                div.para().tx(context.formatPhrase(RenderingContext.VALUE_SET_EXPANSIONS_INTERNAL));                
+              } else {
+                div.para().tx(context.formatPhrase(RenderingContext.VALUE_SET_EXPANSIONS_SRVR, vs.getUserString(UserDataNames.VS_EXPANSION_SOURCE)));
+              }
               ul = div.ul();
               first = false;
             }

diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetUtilities.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetUtilities.java
@@ -48,8 +48,10 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import org.hl7.fhir.r5.model.IntegerType;
 import org.hl7.fhir.r5.model.Enumerations.FilterOperator;
 import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
+import org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent;
 import org.hl7.fhir.r5.model.Identifier;
 import org.hl7.fhir.r5.model.Meta;
+import org.hl7.fhir.r5.model.Parameters;
 import org.hl7.fhir.r5.model.UriType;
 import org.hl7.fhir.r5.model.ValueSet;
 import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
@@ -65,6 +67,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionPropertyComponent;
 import org.hl7.fhir.r5.terminologies.CodeSystemUtilities.ConceptDefinitionComponentSorter;
 import org.hl7.fhir.r5.terminologies.CodeSystemUtilities.ConceptStatus;
+import org.hl7.fhir.r5.terminologies.utilities.TerminologyCache.SourcedValueSet;
 import org.hl7.fhir.r5.utils.CanonicalResourceUtilities;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
 import org.hl7.fhir.r5.utils.UserDataNames;
@@ -501,4 +504,97 @@ private static void addCodes(Set<String> res, ConceptSetComponent inc, List<Conc
       }
     }    
   }
+
+
+
+  public static String versionFromExpansionParams(Parameters expParameters, String system, String defaultVersion) {
+    for (ParametersParameterComponent p : expParameters.getParameter()) {
+      if ("system-version".equals(p.getName()) || "force-system-version".equals(p.getName())) {
+        String v = p.getValue().primitiveValue();
+        if (v.startsWith(system+"|")) {
+          String ver = v.substring(v.indexOf("|")+1);
+          if (defaultVersion == null || ver.startsWith(defaultVersion) || "force-system-version".equals(p.getName())) {
+            return ver;
+          }
+        }
+      }
+    }
+    return defaultVersion;
+  }
+
+  public static boolean isImplicitLoincValueSet(String url) {
+    return url.startsWith("http://loinc.org/vs");    
+  }
+
+  public static boolean isImplicitSCTValueSet(String url) {
+    return url.startsWith("http://snomed.info/sct") && url.contains("?fhir_vs");
+  }
+
+  public static ValueSet makeImplicitValueSet(String url, String version) {
+    if (url.startsWith("http://snomed.info/sct")) {
+      return makeImplicitSCTVS(url, version);
+    } else if (url.startsWith("http://loinc.org/vs")) {
+      return makeImplicitLoincVS(url, version);
+    } else {
+      throw new FHIRException("Unknown implicit value set URL "+url);
+    }
+  }
+
+  private static ValueSet makeImplicitSCTVS(String url, String version) {
+    String query = url.substring(url.indexOf("?")+1);
+    if ("fhir_vs".equals(query)) {
+      ValueSet vs = new ValueSet();
+      vs.setUrl(url);
+      vs.setVersion(version);
+      vs.getCompose().addInclude().setSystem("http://snomed.info/sct");
+      return vs;
+    } else if (query.startsWith("fhir_vs=isa/")) {
+      ValueSet vs = new ValueSet();
+      vs.setUrl(url);
+      vs.setVersion(version);
+      vs.getCompose().addInclude().setSystem("http://snomed.info/sct").addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue(query.substring(12));
+      return vs;
+    } else if (query.equals("fhir_vs=refset")) {
+      ValueSet vs = new ValueSet();
+      vs.setUrl(url);
+      vs.setVersion(version);
+      vs.getCompose().addInclude().setSystem("http://snomed.info/sct").addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("refset-base");
+      return vs;      
+    } else if (query.startsWith("fhir_vs=refset/")) {
+      ValueSet vs = new ValueSet();
+      vs.setUrl(url);
+      vs.setVersion(version);
+      vs.getCompose().addInclude().setSystem("http://snomed.info/sct").addFilter().setProperty("concept").setOp(FilterOperator.IN).setValue(query.substring(15));
+      return vs;      
+    } else {
+      throw new FHIRException("Unknown implicit SNOMED CT value set URL "+url);
+    }
+  }
+
+  private static ValueSet makeImplicitLoincVS(String url, String version) {
+    if (url.equals("http://loinc.org/vs")) {
+      ValueSet vs = new ValueSet();
+      vs.setUrl(url);
+      vs.setVersion(version);
+      vs.getCompose().addInclude().setSystem("http://loinc.org");
+      return vs;
+    } else if (url.startsWith("http://loinc.org/vs/LP")) {
+      ValueSet vs = new ValueSet();
+      vs.setUrl(url);
+      vs.setVersion(version);
+      vs.getCompose().addInclude().setSystem("http://loinc.org").addFilter().setProperty("ancestor").setOp(FilterOperator.EQUAL).setValue(url.substring(21));
+      return vs;      
+    } else if (url.startsWith("http://loinc.org/vs/LL")) {
+      ValueSet vs = new ValueSet();
+      vs.setUrl(url);
+      vs.setVersion(version);
+      // this isn't the actual definition, but it won't matter to us internally
+      vs.getCompose().addInclude().setSystem("http://loinc.org").addFilter().setProperty("answer-list").setOp(FilterOperator.EQUAL).setValue(url.substring(21));      
+      return vs;
+    } else {
+      throw new FHIRException("Unknown implicit LOINC value set URL "+url);
+    }
+  }
+
+
 }
diff --git a/....fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/client/TerminologyClientContext.java b/....fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/client/TerminologyClientContext.java
@@ -1,6 +1,8 @@
 package org.hl7.fhir.r5.terminologies.client;
 
 import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Map;
@@ -218,5 +220,14 @@ public static boolean isCanUseCacheId() {
   public static void setCanUseCacheId(boolean canUseCacheId) {
     TerminologyClientContext.canUseCacheId = canUseCacheId;
   }
+
+  public String getHost() {
+    try {
+      URL uri = new URL(getAddress());
+      return uri.getHost();
+    } catch (MalformedURLException e) {
+      return getAddress();
+    }
+  }
 
 }
diff --git a/....fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/client/TerminologyClientManager.java b/....fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/client/TerminologyClientManager.java
@@ -22,6 +22,7 @@
 import org.hl7.fhir.r5.model.Parameters;
 import org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent;
 import org.hl7.fhir.r5.model.TerminologyCapabilities.TerminologyCapabilitiesCodeSystemComponent;
+import org.hl7.fhir.r5.model.UriType;
 import org.hl7.fhir.r5.model.TerminologyCapabilities;
 import org.hl7.fhir.r5.model.ValueSet;
 import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
@@ -562,7 +563,28 @@ public SourcedValueSet findValueSetOnServer(String canonical) {
     if (IGNORE_TX_REGISTRY || getMasterClient() == null) {
       return null;
     }
-    String request = Utilities.pathURL(monitorServiceURL, "resolve?fhirVersion="+factory.getVersion()+"&valueSet="+Utilities.URLEncode(canonical));
+    String request = null;
+    boolean isImplicit = false;
+    String iVersion = null;
+    if (ValueSetUtilities.isImplicitSCTValueSet(canonical)) {
+      isImplicit = true;
+      iVersion = canonical.substring(0, canonical.indexOf("?fhir_vs"));
+      if ("http://snomed.info/sct".equals(iVersion) && canonical.contains("|")) {
+        iVersion = canonical.substring(canonical.indexOf("|")+1);
+      } 
+      iVersion = ValueSetUtilities.versionFromExpansionParams(expParameters, "http://snomed.info/sct", iVersion); 
+      request = Utilities.pathURL(monitorServiceURL, "resolve?fhirVersion="+factory.getVersion()+"&url="+Utilities.URLEncode("http://snomed.info/sct"+(iVersion == null ? "": "|"+iVersion)));
+    } else if (ValueSetUtilities.isImplicitLoincValueSet(canonical)) {
+      isImplicit = true;
+      iVersion = null;
+      if (canonical.contains("|")) {
+        iVersion = canonical.substring(canonical.indexOf("|")+1);
+      } 
+      iVersion = ValueSetUtilities.versionFromExpansionParams(expParameters, "http://loinc.org", iVersion); 
+      request = Utilities.pathURL(monitorServiceURL, "resolve?fhirVersion="+factory.getVersion()+"&url="+Utilities.URLEncode("http://loinc.org"+(iVersion == null ? "": "|"+iVersion)));
+    } else {
+      request = Utilities.pathURL(monitorServiceURL, "resolve?fhirVersion="+factory.getVersion()+"&valueSet="+Utilities.URLEncode(canonical));
+    }
     String server = null;
     try {
       if (!useEcosystem) {
@@ -628,7 +650,23 @@ public SourcedValueSet findValueSetOnServer(String canonical) {
       Bundle bnd = client.getClient().search("ValueSet", criteria);
       String rid = null;
       if (bnd.getEntry().size() == 0) {
-        return null;
+        if (isImplicit) {
+          // couldn't find it, but can we expand on it? 
+          Parameters p= new Parameters();
+          p.addParameter("url", new UriType(canonical));
+          p.addParameter("count", 0);
+          p.addParameters(expParameters);
+          try {
+            ValueSet vs = client.getClient().expandValueset(null, p);
+            if (vs != null) {
+              return new SourcedValueSet(server, ValueSetUtilities.makeImplicitValueSet(canonical, iVersion));
+            }
+          } catch (Exception e) {
+            return null;
+          }
+        } else {
+          return null;
+        }
       } else if (bnd.getEntry().size() > 1) {
         List<ValueSet> vslist = new ArrayList<>();
         for (BundleEntryComponent be : bnd.getEntry()) {
@@ -659,7 +697,6 @@ public SourcedValueSet findValueSetOnServer(String canonical) {
       return null;
     }
   }
-
   public SourcedCodeSystem findCodeSystemOnServer(String canonical) {
     if (IGNORE_TX_REGISTRY || getMasterClient() == null || !useEcosystem) {
       return null;