Merge pull request #586 from hapifhir/gg-202108-vr-system

Gg 202108 vr system

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java

@@ -1062,6 +1062,8 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     boolean ok = false;
     String message = "No Message returned";
     String display = null;
+    String system = null;
+    String code = null;
     TerminologyServiceErrorClass err = TerminologyServiceErrorClass.UNKNOWN;
     for (ParametersParameterComponent p : pOut.getParameter()) {
       if (p.hasValue()) {
@@ -1071,6 +1073,10 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
           message = ((StringType) p.getValue()).getValue();
         } else if (p.getName().equals("display")) {
           display = ((StringType) p.getValue()).getValue();
+        } else if (p.getName().equals("system")) {
+          system = ((StringType) p.getValue()).getValue();
+        } else if (p.getName().equals("code")) {
+          code = ((StringType) p.getValue()).getValue();
         } else if (p.getName().equals("cause")) {
           try {
             IssueType it = IssueType.fromCode(((StringType) p.getValue()).getValue());
@@ -1089,11 +1095,11 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     if (!ok) {
       return new ValidationResult(IssueSeverity.ERROR, message+" (from "+txClient.getAddress()+")", err).setTxLink(txLog.getLastId());
     } else if (message != null && !message.equals("No Message returned")) { 
-      return new ValidationResult(IssueSeverity.WARNING, message+" (from "+txClient.getAddress()+")", new ConceptDefinitionComponent().setDisplay(display)).setTxLink(txLog.getLastId());
+      return new ValidationResult(IssueSeverity.WARNING, message+" (from "+txClient.getAddress()+")", system, new ConceptDefinitionComponent().setDisplay(display).setCode(code)).setTxLink(txLog.getLastId());
     } else if (display != null) {
-      return new ValidationResult(new ConceptDefinitionComponent().setDisplay(display)).setTxLink(txLog.getLastId());
+      return new ValidationResult(system, new ConceptDefinitionComponent().setDisplay(display).setCode(code)).setTxLink(txLog.getLastId());
     } else {
-      return new ValidationResult(new ConceptDefinitionComponent()).setTxLink(txLog.getLastId());
+      return new ValidationResult(system, new ConceptDefinitionComponent().setCode(code)).setTxLink(txLog.getLastId());
     }
   }
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/IWorkerContext.java

@@ -538,6 +538,7 @@ public interface IWorkerContext {
 
   class ValidationResult {
     private ConceptDefinitionComponent definition;
+    private String system;
     private IssueSeverity severity;
     private String message;
     private TerminologyServiceErrorClass errorClass;
@@ -548,13 +549,15 @@ public interface IWorkerContext {
       this.message = message;
     }
     
-    public ValidationResult(ConceptDefinitionComponent definition) {
+    public ValidationResult(String system, ConceptDefinitionComponent definition) {
+      this.system = system;
       this.definition = definition;
     }
 
-    public ValidationResult(IssueSeverity severity, String message, ConceptDefinitionComponent definition) {
+    public ValidationResult(IssueSeverity severity, String message, String system, ConceptDefinitionComponent definition) {
       this.severity = severity;
       this.message = message;
+      this.system = system;
       this.definition = definition;
     }
     
@@ -568,12 +571,18 @@ public interface IWorkerContext {
       return severity == null || severity == IssueSeverity.INFORMATION || severity == IssueSeverity.WARNING;
     }
 
+    public String getSystem() {
+      return system;
+    }
+
     public String getDisplay() {
-// We don't want to return question-marks because that prevents something more useful from being displayed (e.g. the code) if there's no display value
-//      return definition == null ? "??" : definition.getDisplay();
       return definition == null ? null : definition.getDisplay();
     }
 
+    public String getCode() {
+      return definition == null ? null : definition.getCode();
+    }
+
     public ConceptDefinitionComponent asConceptDefinition() {
       return definition;
     }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/TerminologyCache.java

@@ -333,6 +333,8 @@ public class TerminologyCache {
         } else {
           sw.write("v: {\r\n");
           sw.write("  \"display\" : \""+Utilities.escapeJson(ce.v.getDisplay()).trim()+"\",\r\n");
+          sw.write("  \"code\" : \""+Utilities.escapeJson(ce.v.getCode()).trim()+"\",\r\n");
+          sw.write("  \"system\" : \""+Utilities.escapeJson(ce.v.getSystem()).trim()+"\",\r\n");
           sw.write("  \"severity\" : "+(ce.v.getSeverity() == null ? "null" : "\""+ce.v.getSeverity().toCode().trim()+"\"")+",\r\n");
           sw.write("  \"error\" : \""+Utilities.escapeJson(ce.v.getMessage()).trim()+"\"\r\n}\r\n");
         }
@@ -379,7 +381,9 @@ public class TerminologyCache {
               } else {
                 IssueSeverity severity = o.get("severity") instanceof JsonNull ? null :  IssueSeverity.fromCode(o.get("severity").getAsString());
                 String display = loadJS(o.get("display"));
-                ce.v = new ValidationResult(severity, error, new ConceptDefinitionComponent().setDisplay(display));
+                String code = loadJS(o.get("code"));
+                String system = loadJS(o.get("system"));
+                ce.v = new ValidationResult(severity, error, system, new ConceptDefinitionComponent().setDisplay(display).setCode(code));
               }
               nc.map.put(String.valueOf(hashNWS(ce.request)), ce);
               nc.list.add(ce);

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/DiagnosticReportRenderer.java

@@ -189,9 +189,9 @@ public class DiagnosticReportRenderer extends ResourceRenderer {
         ObservationNode obs = new ObservationNode();
         obs.ref = b.get("reference").primitiveValue();
         obs.obs = resolveReference(rw, obs.ref);
-        if (obs.obs.getResource() != null) {
+        if (obs.obs != null && obs.obs.getResource() != null) {
           PropertyWrapper t = getProperty(obs.obs.getResource(), "contained");
-          if (t.hasValues()) {
+          if (t != null && t.hasValues()) {
             obs.contained = fetchObservations(t.getValues(), rw);
           }
         }
@@ -239,7 +239,7 @@ public class DiagnosticReportRenderer extends ResourceRenderer {
 
   private boolean scanObsForRefRange(List<ObservationNode> observations) {
     for (ObservationNode o : observations) {
-      if (o.obs.getResource() != null) {
+      if (o.obs != null && o.obs.getResource() != null) {
         PropertyWrapper pw = getProperty(o.obs.getResource(), "referenceRange");
         if (valued(pw)) {
           return true;
@@ -256,7 +256,7 @@ public class DiagnosticReportRenderer extends ResourceRenderer {
 
   private boolean scanObsForNote(List<ObservationNode> observations) {
     for (ObservationNode o : observations) {
-      if (o.obs.getResource() != null) {
+      if (o.obs != null && o.obs.getResource() != null) {
         PropertyWrapper pw = getProperty(o.obs.getResource(), "note");
         if (valued(pw)) {
           return true;
@@ -273,7 +273,7 @@ public class DiagnosticReportRenderer extends ResourceRenderer {
 
   private boolean scanObsForIssued(List<ObservationNode> observations, DataType iss) throws UnsupportedEncodingException, FHIRException, IOException {
     for (ObservationNode o : observations) {
-      if (o.obs.getResource() != null) {
+      if (o.obs != null && o.obs.getResource() != null) {
         PropertyWrapper pw = getProperty(o.obs.getResource(), "issued");
         if (valued(pw)) {
           if (!Base.compareDeep(pw.value().getBase(), iss, true)) {
@@ -292,7 +292,7 @@ public class DiagnosticReportRenderer extends ResourceRenderer {
 
   private boolean scanObsForEffective(List<ObservationNode> observations, DataType eff) throws UnsupportedEncodingException, FHIRException, IOException {
     for (ObservationNode o : observations) {
-      if (o.obs.getResource() != null) {
+      if (o.obs != null && o.obs.getResource() != null) {
         PropertyWrapper pw = getProperty(o.obs.getResource(), "effective[x]");
         if (valued(pw)) {
           if (!Base.compareDeep(pw.value().getBase(), eff, true)) {
@@ -311,7 +311,7 @@ public class DiagnosticReportRenderer extends ResourceRenderer {
 
   private boolean scanObsForFlags(List<ObservationNode> observations) throws UnsupportedEncodingException, FHIRException, IOException {
     for (ObservationNode o : observations) {
-      if (o.obs.getResource() != null) {
+      if (o.obs != null && o.obs.getResource() != null) {
         PropertyWrapper pw = getProperty(o.obs.getResource(), "interpretation");
         if (valued(pw)) {
           return true;
@@ -335,15 +335,15 @@ public class DiagnosticReportRenderer extends ResourceRenderer {
 
   private void addObservationToTable(XhtmlNode tbl, ObservationNode o, int i, String cs, boolean refRange, boolean flags, boolean note, boolean effectiveTime, boolean issued, DataType eff, DataType iss) throws UnsupportedEncodingException, FHIRException, IOException {
     XhtmlNode tr = tbl.tr();
-    if (o.obs.getReference()  == null) {
+    if (o.obs != null && o.obs.getReference()  == null) {
       XhtmlNode td = tr.td().colspan(cs);
       td.i().tx("This Observation could not be resolved");
     } else {
-      if (o.obs.getResource() != null) {
+      if (o.obs != null && o.obs.getResource() != null) {
         addObservationToTable(tr, o.obs.getResource(), i, o.obs.getReference(), refRange, flags, note, effectiveTime, issued, eff, iss);
       } else {
         XhtmlNode td = tr.td().colspan(cs);
-        td.i().ah(o.obs.getReference()).tx("Observation");
+        td.i().tx("Observation");
       }
       if (o.contained != null) {
         for (ObservationNode c : o.contained) {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetCheckerSimple.java

@@ -176,7 +176,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
         res = validateCode(code, cs);
       } else if (cs == null && valueset.hasExpansion() && inExpansion) {
         // we just take the value set as face value then
-        res = new ValidationResult(new ConceptDefinitionComponent().setCode(code.getCode()).setDisplay(code.getDisplay()));
+        res = new ValidationResult(system, new ConceptDefinitionComponent().setCode(code.getCode()).setDisplay(code.getDisplay()));
       } else {
         // well, we didn't find a code system - try the expansion? 
         // disabled waiting for discussion
@@ -193,7 +193,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
         Boolean ok = codeInValueSet(system, code.getCode());
         if (ok == null || !ok) {
           if (res == null) {
-            res = new ValidationResult(null, null);
+            res = new ValidationResult((IssueSeverity) null, null);
           }
           if (!inExpansion && !inInclude) {
             res.setMessage("Not in value set "+valueset.getUrl()).setSeverity(IssueSeverity.ERROR);
@@ -258,7 +258,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
         ConceptDefinitionComponent ccd = new ConceptDefinitionComponent();
         ccd.setCode(containsComponent.getCode());
         ccd.setDisplay(containsComponent.getDisplay());
-        ValidationResult res = new ValidationResult(ccd);
+        ValidationResult res = new ValidationResult(code.getSystem(), ccd);
         return res;
       }
       if (containsComponent.hasContains()) {
@@ -300,19 +300,19 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
       }
     }
     if (code.getDisplay() == null) {
-      return new ValidationResult(cc);
+      return new ValidationResult(code.getSystem(), cc);
     }
     CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
     if (cc.hasDisplay()) {
       b.append(cc.getDisplay());
       if (code.getDisplay().equalsIgnoreCase(cc.getDisplay())) {
-        return new ValidationResult(cc);
+        return new ValidationResult(code.getSystem(), cc);
       }
     }
     for (ConceptDefinitionDesignationComponent ds : cc.getDesignation()) {
       b.append(ds.getValue());
       if (code.getDisplay().equalsIgnoreCase(ds.getValue())) {
-        return new ValidationResult(cc);
+        return new ValidationResult(code.getSystem(), cc);
       }
     }
     // also check to see if the value set has another display
@@ -321,17 +321,17 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
       if (vs.hasDisplay()) {
         b.append(vs.getDisplay());
         if (code.getDisplay().equalsIgnoreCase(vs.getDisplay())) {
-          return new ValidationResult(cc);
+          return new ValidationResult(code.getSystem(), cc);
         }
       }
       for (ConceptReferenceDesignationComponent ds : vs.getDesignation()) {
         b.append(ds.getValue());
         if (code.getDisplay().equalsIgnoreCase(ds.getValue())) {
-          return new ValidationResult(cc);
+          return new ValidationResult(code.getSystem(), cc);
         }
       }
     }
-    return new ValidationResult(IssueSeverity.WARNING, context.formatMessage(I18nConstants.DISPLAY_NAME_FOR__SHOULD_BE_ONE_OF__INSTEAD_OF_, code.getSystem(), code.getCode(), b.toString(), code.getDisplay()), cc);
+    return new ValidationResult(IssueSeverity.WARNING, context.formatMessage(I18nConstants.DISPLAY_NAME_FOR__SHOULD_BE_ONE_OF__INSTEAD_OF_, code.getSystem(), code.getCode(), b.toString(), code.getDisplay()), code.getSystem(), cc);
   }
 
   private ConceptReferenceComponent findValueSetRef(String system, String code) {