Add parseAndClose to close streams automatically + minor fixes to support R4B

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/formats/IParser.java

@@ -4,6 +4,7 @@ package org.hl7.fhir.r5.formats;
 
 
 
+import java.io.FileInputStream;
 import java.io.IOException;
 
 /*
@@ -43,6 +44,7 @@ import java.io.UnsupportedEncodingException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.r5.model.DataType;
 import org.hl7.fhir.r5.model.Resource;
+import org.hl7.fhir.r5.model.SearchParameter;
 import org.xmlpull.v1.XmlPullParserException;
 
 
@@ -113,6 +115,8 @@ public interface IParser {
    */
   public Resource parse(InputStream input) throws IOException, FHIRFormatError;
 
+  public Resource parseAndClose(InputStream input) throws IOException, FHIRFormatError;
+
   /**
    * parse content that is known to be a resource  
  * @throws UnsupportedEncodingException 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/formats/ParserBase.java

@@ -36,7 +36,9 @@ package org.hl7.fhir.r5.formats;
 
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
+import java.io.FileInputStream;
 import java.io.IOException;
+import java.io.InputStream;
 import java.math.BigDecimal;
 import java.text.ParseException;
 import java.util.HashMap;
@@ -46,6 +48,7 @@ import org.apache.commons.codec.binary.Base64;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.r5.model.DataType;
 import org.hl7.fhir.r5.model.Resource;
+import org.hl7.fhir.r5.model.SearchParameter;
 import org.hl7.fhir.utilities.Utilities;
 
 public abstract class ParserBase extends FormatUtilities implements IParser {
@@ -101,6 +104,7 @@ public abstract class ParserBase extends FormatUtilities implements IParser {
     return bytes.toByteArray();
   }
 
+
   // -- Parser Configuration --------------------------------
 
   protected String xhtmlMessage;
@@ -233,5 +237,14 @@ public abstract class ParserBase extends FormatUtilities implements IParser {
     return value;
   }
 
+  @Override
+  public Resource parseAndClose(InputStream input) throws IOException, FHIRFormatError {
+    try {
+      return parse(input);
+    } finally {
+      input.close();
+    }
+  }
+
 
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Enumerations.java

@@ -33,6 +33,7 @@ package org.hl7.fhir.r5.model;
 
 
 import org.hl7.fhir.instance.model.api.*;
+import org.hl7.fhir.r5.model.Enumerations.FHIRVersion;
 import org.hl7.fhir.exceptions.FHIRException;
 
 public class Enumerations {
@@ -6478,6 +6479,9 @@ The primary difference between a medicationusage and a medicationadministration
          * added to help the parsers
          */
         NULL;
+      
+      public static final FHIRVersion R4B = FHIRVersion._4_0_1; 
+
         public static FHIRVersion fromCode(String codeString) throws FHIRException {
             if (codeString == null || "".equals(codeString))
                 return null;

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/TypesUtilities.java

@@ -80,9 +80,9 @@ public class TypesUtilities {
     
   }
   
-  public static List<String> wildcardTypes() {
+  public static List<String> wildcardTypes(String version) {
     List<String> res = new ArrayList<String>();
-    for (WildcardInformation wi : wildcards())
+    for (WildcardInformation wi : wildcards(version))
       res.add(wi.getTypeName());
     return res;
   }
@@ -94,7 +94,10 @@ public class TypesUtilities {
   //   Any of the IDMP data types
   // You have to walk into them to profile them.
   //
-  public static List<WildcardInformation> wildcards() {
+  public static List<WildcardInformation> wildcards(String version) {
+    if (version.startsWith("_")) {
+      throw new Error("underscore");
+    }
     List<WildcardInformation> res = new ArrayList<WildcardInformation>();
 
     // primitive types
@@ -108,7 +111,9 @@ public class TypesUtilities {
     res.add(new WildcardInformation("id", TypeClassification.PRIMITIVE));
     res.add(new WildcardInformation("instant", TypeClassification.PRIMITIVE));
     res.add(new WildcardInformation("integer", TypeClassification.PRIMITIVE));
+    if (!version.startsWith("4.0")) {
       res.add(new WildcardInformation("integer64", TypeClassification.PRIMITIVE));
+    }
     res.add(new WildcardInformation("markdown", TypeClassification.PRIMITIVE));
     res.add(new WildcardInformation("oid", TypeClassification.PRIMITIVE));
     res.add(new WildcardInformation("positiveInt", TypeClassification.PRIMITIVE));

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/client/FHIRToolingClient.java

@@ -80,6 +80,7 @@ public class FHIRToolingClient {
 
   private static final int TIMEOUT_NORMAL = 1500;
   private static final int TIMEOUT_OPERATION = 30000;
+  private static final int TIMEOUT_ENTRY = 500;
   private static final int TIMEOUT_OPERATION_LONG = 60000;
   private static final int TIMEOUT_OPERATION_EXPAND = 120000;
 
@@ -132,7 +133,7 @@ public class FHIRToolingClient {
       capabilities = (TerminologyCapabilities) client.issueGetResourceRequest(resourceAddress.resolveMetadataTxCaps(),
         getPreferredResourceFormat(), "TerminologyCapabilities", TIMEOUT_NORMAL).getReference();
     } catch (Exception e) {
-      handleException("An error has occurred while trying to fetch the server's terminology capabilities", e);
+      throw new FHIRException("Error fetching the server's terminology capabilities", e);
     }
     return capabilities;
   }
@@ -143,7 +144,7 @@ public class FHIRToolingClient {
       conformance = (CapabilityStatement) client.issueGetResourceRequest(resourceAddress.resolveMetadataUri(false),
         getPreferredResourceFormat(), "CapabilitiesStatement", TIMEOUT_NORMAL).getReference();
     } catch (Exception e) {
-      handleException("An error has occurred while trying to fetch the server's conformance statement", e);
+      throw new FHIRException("Error fetching the server's conformance statement", e);
     }
     return conformance;
   }
@@ -154,7 +155,7 @@ public class FHIRToolingClient {
       capabilities = (CapabilityStatement) client.issueGetResourceRequest(resourceAddress.resolveMetadataUri(true),
         getPreferredResourceFormat(), "CapabilitiesStatement-Quick", TIMEOUT_NORMAL).getReference();
     } catch (Exception e) {
-      handleException("An error fetching the server's capability statement: "+e.getMessage(), e);
+      throw new FHIRException("Error fetching the server's capability statement: "+e.getMessage(), e);
     }
     return capabilities;
   }
@@ -182,7 +183,7 @@ public class FHIRToolingClient {
         throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
       }
     } catch (Exception e) {
-      handleException("An error has occurred while trying to read this version of the resource", e);
+      throw new FHIRException("Error trying to read this version of the resource", e);
     }
     return result.getPayload();
   }
@@ -291,7 +292,7 @@ public class FHIRToolingClient {
   public Bundle transaction(Bundle batch) {
     Bundle transactionResult = null;
     try {
-      transactionResult = client.postBatchRequest(resourceAddress.getBaseServiceUri(), ByteUtils.resourceToByteArray(batch, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(), "transaction", TIMEOUT_NORMAL + batch.getEntry().size());
+      transactionResult = client.postBatchRequest(resourceAddress.getBaseServiceUri(), ByteUtils.resourceToByteArray(batch, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(), "transaction", TIMEOUT_OPERATION + (TIMEOUT_ENTRY * batch.getEntry().size()));
     } catch (Exception e) {
       handleException("An error occurred trying to process this transaction request", e);
     }