Merge pull request #1877 from hapifhir/2025-01-gg-obligations

2025 01 gg obligations

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/VSACImporter.java

@@ -126,7 +126,7 @@ private void process(String source, String dest, boolean onlyNew, boolean onlyAc
   }
 
   private void cleanValueSets(List<String> allOids, String dest) throws IOException {
-    cleanValueSets(allOids, new File(Utilities.path(dest)));
+    cleanValueSets(allOids, ManagedFileAccess.file(Utilities.path(dest)));
   }
 
   private void cleanValueSets(List<String> allOids, File file) {

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR2.java

@@ -265,4 +265,10 @@ public Parameters translate(Parameters params) throws FHIRException {
     return (Parameters) VersionConvertorFactory_10_50.convertResource(client.translate((org.hl7.fhir.dstu2.model.Parameters) VersionConvertorFactory_10_50.convertResource(params)));
   }
 
+  @Override
+  public void setConversionLogger(ITerminologyConversionLogger logger) {
+    // TODO Auto-generated method stub
+
+  }
+
 }

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR3.java

@@ -268,4 +268,10 @@ public Parameters translate(Parameters params) throws FHIRException {
     return (Parameters) VersionConvertorFactory_30_50.convertResource(client.transform((org.hl7.fhir.dstu3.model.Parameters) VersionConvertorFactory_30_50.convertResource(params)));
   }
 
+  @Override
+  public void setConversionLogger(ITerminologyConversionLogger logger) {
+    // TODO Auto-generated method stub
+
+  }
+
 }

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR4.java

@@ -11,6 +11,8 @@
 import org.hl7.fhir.r4.model.Resource;
 import org.hl7.fhir.r4.utils.client.EFhirClientException;
 import org.hl7.fhir.r4.utils.client.FHIRToolingClient;
+import org.hl7.fhir.r5.formats.IParser.OutputStyle;
+import org.hl7.fhir.r5.formats.JsonParser;
 import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.CanonicalResource;
 import org.hl7.fhir.r5.model.CapabilityStatement;
@@ -28,9 +30,10 @@
 
 public class TerminologyClientR4 implements ITerminologyClient {
 
-  private final FHIRToolingClient client; // todo: use the R2 client
+  private final FHIRToolingClient client; 
   private ClientHeaders clientHeaders;
   private String id;
+  private ITerminologyConversionLogger logger;
 
   public TerminologyClientR4(String id, String address, String userAgent) throws URISyntaxException {
     this.client = new FHIRToolingClient(address, userAgent);
@@ -71,7 +74,7 @@ public FhirPublication getActualVersion() {
 
   @Override
   public TerminologyCapabilities getTerminologyCapabilities() throws FHIRException {
-    return (TerminologyCapabilities) VersionConvertorFactory_40_50.convertResource(client.getTerminologyCapabilities());
+    return (TerminologyCapabilities) convertResource("getTerminologyCapabilities.response", client.getTerminologyCapabilities());
   }
 
   @Override
@@ -81,29 +84,30 @@ public String getAddress() {
 
   @Override
   public ValueSet expandValueset(ValueSet vs, Parameters p) throws FHIRException {
-    org.hl7.fhir.r4.model.ValueSet vs2 = vs == null ? null : (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_40_50.convertResource(vs);
-    org.hl7.fhir.r4.model.Parameters p2 = p == null ? null :  (org.hl7.fhir.r4.model.Parameters) VersionConvertorFactory_40_50.convertResource(p);
+    org.hl7.fhir.r4.model.ValueSet vs2 = vs == null ? null : (org.hl7.fhir.r4.model.ValueSet) convertResource("expandValueset.valueset", vs);
+    org.hl7.fhir.r4.model.Parameters p2 = p == null ? null :  (org.hl7.fhir.r4.model.Parameters) convertResource("expandValueset.parameters", p);
     try {
       vs2 = client.expandValueset(vs2, p2); // todo: second parameter
-      return (ValueSet) VersionConvertorFactory_40_50.convertResource(vs2);
+      return (ValueSet) convertResource("expandValueset.response", vs2);
     } catch (org.hl7.fhir.r4.utils.client.EFhirClientException e) {
       if (e.getServerErrors().size() > 0) {
-        throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getCode(), e.getMessage(), (org.hl7.fhir.r5.model.OperationOutcome) VersionConvertorFactory_40_50.convertResource(e.getServerErrors().get(0)));
+        throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getCode(), e.getMessage(), (org.hl7.fhir.r5.model.OperationOutcome) convertResource("expandValueset.error", e.getServerErrors().get(0)));
       } else {
         throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getCode(), e.getMessage());        
       }
     }
   }
 
+
   @Override
   public Parameters validateCS(Parameters pin) throws FHIRException {
     try {
-      org.hl7.fhir.r4.model.Parameters p2 = (org.hl7.fhir.r4.model.Parameters) VersionConvertorFactory_40_50.convertResource(pin);
+      org.hl7.fhir.r4.model.Parameters p2 = (org.hl7.fhir.r4.model.Parameters) convertResource("validateCS.request", pin);
       p2 = client.operateType(org.hl7.fhir.r4.model.CodeSystem.class, "validate-code", p2);
-      return (Parameters) VersionConvertorFactory_40_50.convertResource(p2);
+      return (Parameters) convertResource("validateCS.response", p2);
     } catch (EFhirClientException e) {
       if (e.getServerErrors().size() == 1) {
-        OperationOutcome op =  (OperationOutcome) VersionConvertorFactory_40_50.convertResource(e.getServerErrors().get(0));
+        OperationOutcome op =  (OperationOutcome) convertResource("validateCS.error", e.getServerErrors().get(0));
         throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getCode(), e.getMessage(), op, e);
       } else {
         throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getCode(), e.getMessage(), e);        
@@ -117,12 +121,12 @@ public Parameters validateCS(Parameters pin) throws FHIRException {
   @Override
   public Parameters subsumes(Parameters pin) throws FHIRException {
     try {
-      org.hl7.fhir.r4.model.Parameters p2 = (org.hl7.fhir.r4.model.Parameters) VersionConvertorFactory_40_50.convertResource(pin);
+      org.hl7.fhir.r4.model.Parameters p2 = (org.hl7.fhir.r4.model.Parameters) convertResource("subsumes.request", pin);
       p2 = client.operateType(org.hl7.fhir.r4.model.CodeSystem.class, "subsumes", p2);
-      return (Parameters) VersionConvertorFactory_40_50.convertResource(p2);
+      return (Parameters) convertResource("subsumes.response", p2);
     } catch (EFhirClientException e) {
       if (e.getServerErrors().size() == 1) {
-        OperationOutcome op =  (OperationOutcome) VersionConvertorFactory_40_50.convertResource(e.getServerErrors().get(0));
+        OperationOutcome op =  (OperationOutcome) convertResource("subsumes.error", e.getServerErrors().get(0));
         throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getCode(), e.getMessage(), op, e);
       } else {
         throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getCode(), e.getMessage(), e);        
@@ -135,12 +139,12 @@ public Parameters subsumes(Parameters pin) throws FHIRException {
   @Override
   public Parameters validateVS(Parameters pin) throws FHIRException {
     try {
-      org.hl7.fhir.r4.model.Parameters p2 = (org.hl7.fhir.r4.model.Parameters) VersionConvertorFactory_40_50.convertResource(pin);
+      org.hl7.fhir.r4.model.Parameters p2 = (org.hl7.fhir.r4.model.Parameters) convertResource("validateVS.request", pin);
       p2 = client.operateType(org.hl7.fhir.r4.model.ValueSet.class, "validate-code", p2);
-      return (Parameters) VersionConvertorFactory_40_50.convertResource(p2);
+      return (Parameters) convertResource("validateVS.response", p2);
     } catch (EFhirClientException e) {
       if (e.getServerErrors().size() == 1) {
-        OperationOutcome op =  (OperationOutcome) VersionConvertorFactory_40_50.convertResource(e.getServerErrors().get(0));
+        OperationOutcome op =  (OperationOutcome) convertResource("validateVS.error", e.getServerErrors().get(0));
         throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getCode(), e.getMessage(), op, e);
       } else {
         throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getCode(), e.getMessage(), e);        
@@ -175,22 +179,22 @@ public ITerminologyClient setRetryCount(int retryCount) throws FHIRException {
 
   @Override
   public CapabilityStatement getCapabilitiesStatementQuick() throws FHIRException {
-    return (CapabilityStatement) VersionConvertorFactory_40_50.convertResource(client.getCapabilitiesStatementQuick());
+    return (CapabilityStatement) convertResource("getCapabilitiesStatementQuick.response", client.getCapabilitiesStatementQuick());
   }
 
   @Override
   public CapabilityStatement getCapabilitiesStatement() throws FHIRException {
-    return (CapabilityStatement) VersionConvertorFactory_40_50.convertResource(client.getCapabilitiesStatement());
+    return (CapabilityStatement) convertResource("getCapabilitiesStatement.response", client.getCapabilitiesStatement());
   }
 
   @Override
   public Parameters lookupCode(Map<String, String> params) throws FHIRException {
-    return (Parameters) VersionConvertorFactory_40_50.convertResource(client.lookupCode(params));
+    return (Parameters) convertResource("lookupCode.response", client.lookupCode(params));
   }
 
   @Override
   public Parameters lookupCode(Parameters params) throws FHIRException {
-    return (Parameters) VersionConvertorFactory_40_50.convertResource(client.lookupCode((org.hl7.fhir.r4.model.Parameters) VersionConvertorFactory_40_50.convertResource(params)));
+    return (Parameters) convertResource("lookupCode.response", client.lookupCode((org.hl7.fhir.r4.model.Parameters) convertResource("lookupCode.request", params)));
   }
 
   @Override
@@ -200,8 +204,8 @@ public int getRetryCount() throws FHIRException {
 
   @Override
   public Bundle validateBatch(Bundle batch) {
-    org.hl7.fhir.r4.model.Bundle result = client.transaction((org.hl7.fhir.r4.model.Bundle) VersionConvertorFactory_40_50.convertResource(batch));
-    return result == null ? null : (Bundle) VersionConvertorFactory_40_50.convertResource(result);
+    org.hl7.fhir.r4.model.Bundle result = client.transaction((org.hl7.fhir.r4.model.Bundle) convertResource("validateBatch.request", batch));
+    return result == null ? null : (Bundle) convertResource("validateBatch.response", result);
   }
 
   @Override
@@ -216,7 +220,7 @@ public CanonicalResource read(String type, String id) {
     if (r4 == null) {
       throw new FHIRException("Unable to fetch resource " + Utilities.pathURL(getAddress(), type, id));
     }
-    org.hl7.fhir.r5.model.Resource r5 = VersionConvertorFactory_40_50.convertResource(r4);
+    org.hl7.fhir.r5.model.Resource r5 = convertResource("read.result", r4);
     if (r5 == null) {
       throw new FHIRException("Unable to convert resource " + Utilities.pathURL(getAddress(), type, id) + " to R5 (internal representation)");
     }
@@ -278,12 +282,55 @@ public int getUseCount() {
   @Override
   public Bundle search(String type, String criteria) {    
     org.hl7.fhir.r4.model.Bundle result = client.search(type, criteria);
-    return result == null ? null : (Bundle) VersionConvertorFactory_40_50.convertResource(result);
+    return result == null ? null : (Bundle) convertResource("search.result", result);
   }
 
   @Override
   public Parameters translate(Parameters params) throws FHIRException {  
-    return (Parameters) VersionConvertorFactory_40_50.convertResource(client.translate((org.hl7.fhir.r4.model.Parameters) VersionConvertorFactory_40_50.convertResource(params)));
+    return (Parameters) convertResource("translate.response", client.translate((org.hl7.fhir.r4.model.Parameters) convertResource("translate.request", params)));
+  }
+
+  private org.hl7.fhir.r4.model.Resource convertResource(String name, org.hl7.fhir.r5.model.Resource resource) {
+    if (logger != null) {
+      try {
+        logger.log(name, resource.fhirType(), "r5", new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(resource));
+      } catch (IOException e) {
+        throw new FHIRException(e);
+      }
+    }
+    org.hl7.fhir.r4.model.Resource res = VersionConvertorFactory_40_50.convertResource(resource);
+    if (logger != null) {
+      try {
+        logger.log(name, resource.fhirType(), "r4", new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(org.hl7.fhir.r4.formats.IParser.OutputStyle.PRETTY).composeBytes(res));
+      } catch (IOException e) {
+        throw new FHIRException(e);
+      }
+    }
+    return res;
+  }
+
+  private org.hl7.fhir.r5.model.Resource convertResource(String name, org.hl7.fhir.r4.model.Resource resource) {
+    if (logger != null && name != null) {
+      try {
+        logger.log(name, resource.fhirType(), "r4", new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(org.hl7.fhir.r4.formats.IParser.OutputStyle.PRETTY).composeBytes(resource));
+      } catch (IOException e) {
+        throw new FHIRException(e);
+      }
+    }
+    org.hl7.fhir.r5.model.Resource res = VersionConvertorFactory_40_50.convertResource(resource);
+    if (logger != null && name != null) {
+      try {
+        logger.log(name, resource.fhirType(), "r5", new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(res));
+      } catch (IOException e) {
+        throw new FHIRException(e);
+      }
+    }
+    return res;
+  }
+
+  @Override
+  public void setConversionLogger(ITerminologyConversionLogger logger) {
+    this.logger = logger;    
   }
 
 }

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

@@ -420,7 +420,7 @@ public void renderTable(RenderingStatus status, ResourceWrapper res, List<XhtmlN
           if (ad == null) {
             actorId.addText(anActor.getCanonical());
           } else {
-            actorId.ah(ad.getWebPath()).tx(ad.getTitle());
+            actorId.ah(ad.getWebPath()).tx(ad.present());
           }
         }
 

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

@@ -679,7 +679,7 @@ private void scanObligations(List<Column> columns, List<ElementDefinition> list)
         if (actor == null) { 
           columns.add(new Column(col, tail(col), context.formatPhrase(RenderingContext.STRUC_DEF_UNDEF_ACT, col, col)+" "));           
         } else { 
-          columns.add(new Column(col, actor.getName(), context.formatPhrase(RenderingContext.STRUC_DEF_ACT, actor.present(), actor.getWebPath())+" "));                     
+          columns.add(new Column(col, actor.present(), context.formatPhrase(RenderingContext.STRUC_DEF_ACT, actor.present(), actor.getWebPath())+" "));                     
         } 
       } 
     } 
@@ -1761,7 +1761,6 @@ else if (definition.hasBinding())
             obr.seeObligations(profile.getExtensionsByUrl(ToolingExtensions.EXT_OBLIGATION_CORE, ToolingExtensions.EXT_OBLIGATION_TOOLS)); 
           } 
           obr.renderTable(status, res, gen, c, inScopeElements);
-
           if (definition.hasMaxLength() && definition.getMaxLength()!=0) { 
             if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); } 
             c.getPieces().add(checkForNoChange(definition.getMaxLengthElement(), gen.new Piece(null, context.formatPhrase(RenderingContext.GENERAL_MAX_LENGTH), null).addStyle("font-weight:bold"))); 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/client/ITerminologyClient.java

@@ -76,4 +76,10 @@ public interface ITerminologyClient {
   String getUserAgent();
   int getUseCount();
   Bundle search(String type, String criteria); 
+
+  // internal conversion logging
+  public interface ITerminologyConversionLogger {
+    void log(String name, String resourceType, String version, byte[] cnt);
+  }
+  void setConversionLogger(ITerminologyConversionLogger logger);
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/client/TerminologyClientR5.java

@@ -275,5 +275,11 @@ public Parameters translate(Parameters params) throws FHIRException {
     return client.translate(params);
   }
 
+  @Override
+  public void setConversionLogger(ITerminologyConversionLogger logger) {
+    // TODO Auto-generated method stub
+
+  }
+
 
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/testfactory/TestDataFactory.java

@@ -39,6 +39,7 @@
 import org.hl7.fhir.utilities.FhirPublication;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.http.HTTPResult;
 import org.hl7.fhir.utilities.http.ManagedWebAccess;
 import org.hl7.fhir.utilities.json.JsonException;
@@ -297,8 +298,8 @@ private void executeProfile() throws IOException {
   }
 
   private void checkDownloadBaseData() throws IOException {
-    localData = new File(Utilities.path("[tmp]", "fhir-test-data.db"));  
-    File localInfo = new File(Utilities.path("[tmp]", "fhir-test-data.json"));  
+    localData = ManagedFileAccess.file(Utilities.path("[tmp]", "fhir-test-data.db"));  
+    File localInfo = ManagedFileAccess.file(Utilities.path("[tmp]", "fhir-test-data.json"));  
     try {
       JsonObject local = localInfo.exists() ? JsonParser.parseObject(localInfo) : null; 
       JsonObject json = JsonParser.parseObjectFromUrl("http://fhir.org/downloads/test-data-versions.json");

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/testfactory/dataprovider/ExcelDataProvider.java

@@ -3,6 +3,7 @@
 import org.apache.poi.ss.usermodel.*;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.apache.poi.EncryptedDocumentException;
 import org.apache.poi.openxml4j.exceptions.InvalidFormatException;
 
@@ -37,7 +38,7 @@ public class ExcelDataProvider extends TableDataProvider {
    * @throws InvalidFormatException If the file format is invalid.
    */
   public ExcelDataProvider(String filename, String sheetName) throws IOException, InvalidFormatException {
-    FileInputStream fis = new FileInputStream(new File(filename));
+    FileInputStream fis = new FileInputStream(ManagedFileAccess.file(filename));
     this.workbook = WorkbookFactory.create(fis);
     if (sheetName != null) {
       this.sheet = workbook.getSheet(sheetName);
@@ -60,7 +61,7 @@ public ExcelDataProvider(String filename, String sheetName) throws IOException,
 
 
   public ExcelDataProvider(String filename) throws InvalidFormatException, IOException {
-    FileInputStream fis = new FileInputStream(new File(filename));
+    FileInputStream fis = new FileInputStream(ManagedFileAccess.file(filename));
     this.workbook = WorkbookFactory.create(fis);
     this.sheet = workbook.getSheetAt(0);
     loadColumnHeaders();

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java

@@ -477,6 +477,11 @@ public static File createDirectory(String path) throws IOException {
     return ManagedFileAccess.file(path);
   }
 
+  public static File createDirectoryNC(String path) throws IOException {
+    ManagedFileAccess.file(path).mkdirs();
+    return ManagedFileAccess.file(path);
+  }
+
   public static String changeFileExt(String name, String ext) {
     if (name.lastIndexOf('.') > -1)
       return name.substring(0, name.lastIndexOf('.')) + ext;

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/POGenerator.java

@@ -325,7 +325,7 @@ private void generate(String source, String src, String dest, String tgt, int co
     // save the destination file 
     String fn = Utilities.path(source, "source", dest);
     List<POObject> objects;
-    if (new File(fn).exists()) {
+    if (ManagedFileAccess.file(fn).exists()) {
       objects = loadPOFile(fn);
     } else {
       objects = new ArrayList<POGenerator.POObject>();

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/json/model/JsonObject.java

@@ -35,6 +35,18 @@ public JsonObject add(String name, JsonElement value) throws JsonException {
     propMap.put(name, p);
     return this;
   }
+
+  public JsonObject add(int index, String name, JsonElement value) throws JsonException {
+    check(name != null, "Json Property Name is null");
+    check(value != null, "Json Property Value is null");
+    if (get(name) != null) {
+      check(false, "Name '"+name+"' already exists (value = "+get(name).toString()+")");
+    }
+    JsonProperty p = new JsonProperty(name, value);
+    properties.add(index, p);
+    propMap.put(name, p);
+    return this;
+  }
 
   public JsonObject addIfNotNull(String name, JsonElement value) throws JsonException {
     if (value != null) {
@@ -347,6 +359,16 @@ public JsonArray forceArray(String name) throws JsonException {
     }
     return getJsonArray(name);
   }
+
+  public JsonArray forceArray(int index, String name) throws JsonException {
+    if (has(name) && !hasArray(name)) {
+      remove(name);
+    }
+    if (!has(name)) {
+      add(index, name, new JsonArray());
+    }
+    return getJsonArray(name);
+  }
 
   public List<JsonObject> getJsonObjects(String name) {
     List<JsonObject> res = new ArrayList<>();