Merge branch 'master' of github.com:hapifhir/org.hl7.fhir.core

Author: jamesagnew

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/importers/Mimic14Importer.java

@@ -80,6 +80,7 @@
 import org.hl7.fhir.dstu3.model.Type;
 import org.hl7.fhir.utilities.CSVReader;
 import org.hl7.fhir.utilities.IniFile;
+import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
 
 public class Mimic14Importer {
@@ -561,7 +562,7 @@ private void processNoteEvents(String src, String dest) throws FileNotFoundExcep
       } else {
         throw new FHIRException("Unhandled Note type '"+cat+"'/'"+desc+"'");
       }
-      dr.addContent().getAttachment().setContentType("text/plain; charset=UTF-8").setData(csv.cell("text").getBytes(Charset.forName("UTF-8")));
+      dr.addContent().getAttachment().setContentType("text/plain; charset=UTF-8").setData(TextFile.stringToBytes(csv.cell("text"), false));
       bnd.addEntry().setResource(dr);
     }
     System.out.println(Integer.toString(t)+" found");

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/importers/Mimic14Importer.java

@@ -76,6 +76,7 @@
 import org.hl7.fhir.r4.model.Type;
 import org.hl7.fhir.utilities.CSVReader;
 import org.hl7.fhir.utilities.IniFile;
+import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
 
 public class Mimic14Importer {
@@ -561,7 +562,7 @@ private void processNoteEvents(String src, String dest) throws FileNotFoundExcep
       } else {
         throw new FHIRException("Unhandled Note type '"+cat+"'/'"+desc+"'");
       }
-      dr.addContent().getAttachment().setContentType("text/plain; charset=UTF-8").setData(csv.cell("text").getBytes(Charset.forName("UTF-8")));
+      dr.addContent().getAttachment().setContentType("text/plain; charset=UTF-8").setData(TextFile.stringToBytes(csv.cell("text"), false));
       bnd.addEntry().setResource(dr);
     }
     System.out.println(Integer.toString(t)+" found");

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

@@ -324,7 +324,7 @@ public void finish() throws IOException {
   }
 
   private void buildIndexJson() throws IOException {
-    byte[] content = indexer.build().getBytes(Charset.forName("UTF-8"));
+    byte[] content = TextFile.stringToBytes(indexer.build(), false);
     addFile(Category.RESOURCE, ".index.json", content); 
   }
 

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/NpmPackage.java

@@ -182,10 +182,18 @@ public static NpmPackage fromPackage(InputStream tgz, boolean progress) throws I
           indexer.seeFile(n.substring(8), res.content.get(n));
         }          
       }
-      res.content.put("package/.index.json", indexer.build().getBytes(Charsets.UTF_8));
+      res.content.put("package/.index.json", TextFile.stringToBytes(indexer.build(), false));
+    }
+    try {
+      res.npm = JsonTrackingParser.parseJson(res.content.get("package/package.json"));
+    } catch (Exception e) {
+      throw new IOException("Error parsing package/package.json: "+e.getMessage(), e);
+    }
+    try {
+      res.readIndexFile((JsonObject) JsonTrackingParser.parseJson(new String(res.content.get("package/.index.json"))));
+    } catch (Exception e) {
+      throw new IOException("Error parsing package/.index.json: "+e.getMessage(), e);
     }
-    res.npm = JsonTrackingParser.parseJson(res.content.get("package/package.json"));
-    res.readIndexFile((JsonObject) new com.google.gson.JsonParser().parse(new String(res.content.get("package/.index.json"))));
     return res;
   }
 
@@ -518,7 +526,7 @@ public void save(OutputStream stream) throws IOException {
         tar.closeArchiveEntry();
       }
     }
-    byte[] cnt = new GsonBuilder().setPrettyPrinting().create().toJson(npm).getBytes(Charset.forName("UTF-8"));
+    byte[] cnt = TextFile.stringToBytes(new GsonBuilder().setPrettyPrinting().create().toJson(npm), false);
     TarArchiveEntry entry = new TarArchiveEntry("package/package.json");
     entry.setSize(cnt.length);
     tar.putArchiveEntry(entry);

pom.xml

@@ -17,7 +17,7 @@
 
     <properties>
         <hapi_fhir_version>4.1.0</hapi_fhir_version>
-        <validator_test_case_version>1.0.5-SNAPSHOT</validator_test_case_version>
+        <validator_test_case_version>1.0.6-SNAPSHOT</validator_test_case_version>
     </properties>
 
     <artifactId>org.hl7.fhir.core</artifactId>

release.bat

@@ -1,7 +1,7 @@
 @echo off
 
-set oldver=4.0.34
-set newver=4.0.35
+set oldver=4.0.35
+set newver=4.0.36
 
 echo ..
 echo =====================================================================