Merge pull request #1590 from hapifhir/2024-04-gg-fixes

2024 04 gg fixes

.mvn/wrapper/MavenWrapperDownloader.java

@@ -50,17 +50,17 @@ public class MavenWrapperDownloader {
 
     public static void main(String args[]) {
         System.out.println("- Downloader started");
-        File baseDirectory = new File(args[0]);
+        File baseDirectory = ManagedFileAccess.file(args[0]);
         System.out.println("- Using base directory: " + baseDirectory.getAbsolutePath());
 
         // If the maven-wrapper.properties exists, read it and check if it contains a custom
         // wrapperUrl parameter.
-        File mavenWrapperPropertyFile = new File(baseDirectory, MAVEN_WRAPPER_PROPERTIES_PATH);
+        File mavenWrapperPropertyFile = ManagedFileAccess.file(baseDirectory, MAVEN_WRAPPER_PROPERTIES_PATH);
         String url = DEFAULT_DOWNLOAD_URL;
         if(mavenWrapperPropertyFile.exists()) {
             FileInputStream mavenWrapperPropertyFileInputStream = null;
             try {
-                mavenWrapperPropertyFileInputStream = new FileInputStream(mavenWrapperPropertyFile);
+                mavenWrapperPropertyFileInputStream = ManagedFileAccess.inStream(mavenWrapperPropertyFile);
                 Properties mavenWrapperProperties = new Properties();
                 mavenWrapperProperties.load(mavenWrapperPropertyFileInputStream);
                 url = mavenWrapperProperties.getProperty(PROPERTY_NAME_WRAPPER_URL, url);
@@ -78,7 +78,7 @@ public class MavenWrapperDownloader {
         }
         System.out.println("- Downloading from: : " + url);
 
-        File outputFile = new File(baseDirectory.getAbsolutePath(), MAVEN_WRAPPER_JAR_PATH);
+        File outputFile = ManagedFileAccess.file(baseDirectory.getAbsolutePath(), MAVEN_WRAPPER_JAR_PATH);
         if(!outputFile.getParentFile().exists()) {
             if(!outputFile.getParentFile().mkdirs()) {
                 System.out.println(
@@ -101,7 +101,7 @@ public class MavenWrapperDownloader {
         URL website = new URL(urlString);
         ReadableByteChannel rbc;
         rbc = Channels.newChannel(website.openStream());
-        FileOutputStream fos = new FileOutputStream(destination);
+        FileOutputStream fos = ManagedFileAccess.outStream(destination);
         fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
         fos.close();
         rbc.close();

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/R2R3ConversionManager.java

@@ -67,6 +67,7 @@ import org.hl7.fhir.dstu3.utils.StructureMapUtilities;
 import org.hl7.fhir.dstu3.utils.StructureMapUtilities.ITransformerServices;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.utilities.TextFile;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 /**
  * This class manages conversion from R2 to R3 and vice versa
@@ -113,8 +114,8 @@ public class R2R3ConversionManager implements ITransformerServices {
       self.setR3Definitions(getNamedParam(args, "-d3"));
       self.setMappingLibrary(getNamedParam(args, "-maps"));
       FhirFormat fmt = hasParam(args, "-fmt") ? getNamedParam(args, "-fmt").equalsIgnoreCase("json") ? FhirFormat.JSON : FhirFormat.XML : FhirFormat.XML;
-      InputStream src = new FileInputStream(getNamedParam(args, "-src"));
+      InputStream src = ManagedFileAccess.inStream(getNamedParam(args, "-src"));
-      OutputStream dst = new FileOutputStream(getNamedParam(args, "-dest"));
+      OutputStream dst = ManagedFileAccess.outStream(getNamedParam(args, "-dest"));
       self.convert(src, dst, hasParam(args, "-r2"), fmt);
     }
   }
@@ -164,9 +165,9 @@ public class R2R3ConversionManager implements ITransformerServices {
   }
 
   public void setR2Definitions(String source) throws IOException, FHIRException {
-    File f = new File(source);
+    File f = ManagedFileAccess.file(source);
     if (f.exists())
-      setR2Definitions(new FileInputStream(f));
+      setR2Definitions(ManagedFileAccess.inStream(f));
     else
       setR2Definitions(fetch(source));
   }
@@ -184,9 +185,9 @@ public class R2R3ConversionManager implements ITransformerServices {
   }
 
   public void setR3Definitions(String source) throws IOException, FHIRException {
-    File f = new File(source);
+    File f = ManagedFileAccess.file(source);
     if (f.exists())
-      setR3Definitions(new FileInputStream(f));
+      setR3Definitions(ManagedFileAccess.inStream(f));
     else
       setR3Definitions(fetch(source));
   }
@@ -201,9 +202,9 @@ public class R2R3ConversionManager implements ITransformerServices {
   }
 
   public void setMappingLibrary(String source) throws IOException, FHIRException {
-    File f = new File(source);
+    File f = ManagedFileAccess.file(source);
     if (f.exists())
-      setMappingLibrary(new FileInputStream(f));
+      setMappingLibrary(ManagedFileAccess.inStream(f));
     else
       setMappingLibrary(fetch(source));
   }

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/SpecDifferenceEvaluator.java

@@ -42,6 +42,7 @@ import org.hl7.fhir.utilities.IniFile;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
 import org.hl7.fhir.utilities.ZipGenerator;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.xhtml.NodeType;
 import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
@@ -132,7 +133,7 @@ public class SpecDifferenceEvaluator {
   }
 
   private static void loadSD4(Map<String, StructureDefinition> map, String fn) throws FHIRException, IOException {
-    org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) new org.hl7.fhir.r4.formats.XmlParser().parse(new FileInputStream(fn));
+    org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) new org.hl7.fhir.r4.formats.XmlParser().parse(ManagedFileAccess.inStream(fn));
     for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
       if (be.getResource() instanceof org.hl7.fhir.r4.model.StructureDefinition) {
         org.hl7.fhir.r4.model.StructureDefinition sd = (org.hl7.fhir.r4.model.StructureDefinition) be.getResource();
@@ -143,7 +144,7 @@ public class SpecDifferenceEvaluator {
   }
 
   private static void loadSD(Map<String, StructureDefinition> map, String fn) throws FHIRFormatError, IOException {
-    Bundle bundle = (Bundle) new XmlParser().parse(new FileInputStream(fn));
+    Bundle bundle = (Bundle) new XmlParser().parse(ManagedFileAccess.inStream(fn));
     for (BundleEntryComponent be : bundle.getEntry()) {
       if (be.getResource() instanceof StructureDefinition) {
         StructureDefinition sd = (StructureDefinition) be.getResource();
@@ -153,7 +154,7 @@ public class SpecDifferenceEvaluator {
   }
 
   private static void loadVS4(Map<String, ValueSet> map, String fn) throws FHIRException, IOException {
-    org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) new org.hl7.fhir.r4.formats.XmlParser().parse(new FileInputStream(fn));
+    org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) new org.hl7.fhir.r4.formats.XmlParser().parse(ManagedFileAccess.inStream(fn));
     for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
       if (be.getResource() instanceof org.hl7.fhir.r4.model.ValueSet) {
         org.hl7.fhir.r4.model.ValueSet sd = (org.hl7.fhir.r4.model.ValueSet) be.getResource();
@@ -163,7 +164,7 @@ public class SpecDifferenceEvaluator {
   }
 
   private static void loadVS(Map<String, ValueSet> map, String fn) throws FHIRFormatError, IOException {
-    Bundle bundle = (Bundle) new XmlParser().parse(new FileInputStream(fn));
+    Bundle bundle = (Bundle) new XmlParser().parse(ManagedFileAccess.inStream(fn));
     for (BundleEntryComponent be : bundle.getEntry()) {
       if (be.getResource() instanceof ValueSet) {
         ValueSet sd = (ValueSet) be.getResource();

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/analytics/PackageVisitor.java

@@ -18,6 +18,7 @@ import org.hl7.fhir.utilities.SimpleHTTPClient;
 import org.hl7.fhir.utilities.SimpleHTTPClient.HTTPResult;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.json.model.JsonArray;
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.json.parser.JsonParser;
@@ -230,14 +231,14 @@ public class PackageVisitor {
         String[] p = url.split("\\/");
         String repo = "https://build.fhir.org/ig/"+p[0]+"/"+p[1];
         JsonObject manifest = JsonParser.parseObjectFromUrl(repo+"/package.manifest.json");
-        File co = new File(Utilities.path(cache, pid+"."+manifest.asString("date")+".tgz"));
+        File co = ManagedFileAccess.file(Utilities.path(cache, pid+"."+manifest.asString("date")+".tgz"));
         if (!co.exists()) {
           SimpleHTTPClient fetcher = new SimpleHTTPClient();
           HTTPResult res = fetcher.get(repo+"/package.tgz?nocache=" + System.currentTimeMillis());
           res.checkThrowException();
           TextFile.bytesToFile(res.getContent(), co);
         }
-        NpmPackage npm = NpmPackage.fromPackage(new FileInputStream(co));          
+        NpmPackage npm = NpmPackage.fromPackage(ManagedFileAccess.inStream(co));          
         String fv = npm.fhirVersion();
         long ms2 = System.currentTimeMillis();
 

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

@@ -9,11 +9,12 @@ import java.io.InputStreamReader;
 
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class BOMRemover {
 
   public static void main(String[] args) throws FileNotFoundException, IOException {
-    new BOMRemover().execute(new File(args[0]));
+    new BOMRemover().execute(ManagedFileAccess.file(args[0]));
 
   }
 

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

@@ -9,20 +9,21 @@ import java.io.IOException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.r5.formats.JsonParser;
 import org.hl7.fhir.r5.model.CodeSystem;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class BigCodeSystemGenerator {
 
   public static void main(String[] args) throws FileNotFoundException, IOException {
-    new BigCodeSystemGenerator().execute(new File("/Users/grahamegrieve/work/test-cases/tx/big/codesystem-big.json"));
+    new BigCodeSystemGenerator().execute(ManagedFileAccess.file("/Users/grahamegrieve/work/test-cases/tx/big/codesystem-big.json"));
   }
 
   private void execute(File file) throws FHIRFormatError, FileNotFoundException, IOException {
-    CodeSystem cs = (CodeSystem) new JsonParser().parse(new FileInputStream(file));
+    CodeSystem cs = (CodeSystem) new JsonParser().parse(ManagedFileAccess.inStream(file));
     cs.getConcept().clear();
     for (int i = 1; i <= 2000; i++) {
       cs.addConcept().setCode("code"+i).setDisplay("Display "+i).setDefinition("This is code "+i);
     }
-    new JsonParser().compose(new FileOutputStream(file), cs);
+    new JsonParser().compose(ManagedFileAccess.outStream(file), cs);
     
   }
   

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

@@ -44,6 +44,7 @@ import org.hl7.fhir.utilities.SimpleHTTPClient;
 import org.hl7.fhir.utilities.SimpleHTTPClient.HTTPResult;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -115,9 +116,9 @@ public class CKMImporter {
     String src = Utilities.path(Utilities.path("[tmp]"), id + ".xml");
     String dst = Utilities.path(dest, id + ".xml");
 
-    if (!new File(src).exists())
+    if (!ManagedFileAccess.file(src).exists())
       downloadArchetype(id);
-    if (cfg != null && new File(cfg).exists())
+    if (cfg != null && ManagedFileAccess.file(cfg).exists())
       ADLImporter.main(new String[]{"-source", src, "-dest", dst, "-config", config, "-info", cfg});
     else
       ADLImporter.main(new String[]{"-source", src, "-dest", dst, "-config", config});

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

@@ -32,6 +32,7 @@ import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
 import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
 import org.hl7.fhir.utilities.CSVReader;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class CPTImporter {
 
@@ -89,12 +90,12 @@ public class CPTImporter {
     System.out.println(c);
     System.out.println(k);
     
-    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dst), cs); 
+    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(dst), cs); 
     produceDB(Utilities.changeFileExt(dst, ".db"), cs);
     
     cs.setContent(CodeSystemContentMode.FRAGMENT);
     cs.getConcept().removeIf(cc -> !Utilities.existsInList(cc.getCode(), "metadata-kinds", "metadata-designations", "99202", "99203", "0001A", "99252", "25", "P1", "1P", "F1", "95"));
-    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.changeFileExt(dst, "-fragment.json")), cs); 
+    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.changeFileExt(dst, "-fragment.json")), cs); 
     produceDB(Utilities.changeFileExt(dst, "-fragment.db"), cs);
   }
 
@@ -146,7 +147,7 @@ public class CPTImporter {
   }
 
 
-  private void produceDB(String path, CodeSystem cs) throws ClassNotFoundException, SQLException {
+  private void produceDB(String path, CodeSystem cs) throws ClassNotFoundException, SQLException, IOException {
     Connection con = connect(path);
 
     Statement stmt = con.createStatement();
@@ -185,10 +186,10 @@ public class CPTImporter {
   }
 
 
-  private Connection connect(String dest) throws SQLException, ClassNotFoundException {
+  private Connection connect(String dest) throws SQLException, ClassNotFoundException, IOException {
     //    Class.forName("com.mysql.jdbc.Driver");  
     //    con = DriverManager.getConnection("jdbc:mysql://localhost:3306/omop?useSSL=false","root",{pwd}); 
-    new File(dest).delete();
+    ManagedFileAccess.file(dest).delete();
     Connection con = DriverManager.getConnection("jdbc:sqlite:"+dest); 
     makeMetadataTable(con);
     makeConceptsTable(con);
@@ -267,7 +268,7 @@ public class CPTImporter {
   }
 
   private int processModifiers(CodeSystem cs, String path) throws FHIRException, FileNotFoundException, IOException {
-    CSVReader csv = new CSVReader(new FileInputStream(path));
+    CSVReader csv = new CSVReader(ManagedFileAccess.inStream(path));
     csv.readHeaders();
 
     int res = 0;
@@ -309,7 +310,7 @@ public class CPTImporter {
     FileInputStream inputStream = null;
     Scanner sc = null;
     try {
-        inputStream = new FileInputStream(path);
+        inputStream = ManagedFileAccess.inStream(path);
         sc = new Scanner(inputStream, "UTF-8");
         while (sc.hasNextLine()) {
           String line = sc.nextLine();

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

@@ -24,6 +24,7 @@ import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.DateTimeType;
 import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.terminologies.CodeSystemUtilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -58,7 +59,7 @@ public class CVXImporter {
   }
 
   private void doUpdate(String source, String dest) throws FHIRFormatError, FileNotFoundException, IOException, ParserConfigurationException, SAXException {
-    CodeSystem cvx = (CodeSystem) new JsonParser().parse(new FileInputStream(dest));
+    CodeSystem cvx = (CodeSystem) new JsonParser().parse(ManagedFileAccess.inStream(dest));
     
     String ldate = null;
     
@@ -94,7 +95,7 @@ public class CVXImporter {
     Collections.sort(cvx.getConcept(), new CVXSorter());
     cvx.setDateElement(new DateTimeType(ldate));
     cvx.setVersion(ldate.replace("-", ""));
-    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), cvx);
+    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(dest), cvx);
   }
 
   private ConceptDefinitionComponent findCVXCode(CodeSystem cvx, String code) {

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

@@ -7,6 +7,7 @@ import java.io.IOException;
 
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.json.parser.JsonParser;
 import org.hl7.fhir.utilities.npm.NpmPackage;
@@ -26,12 +27,12 @@ public class CorePackageTools {
   private void buildPackage(String path, String output) throws IOException {
     NpmPackage npm = NpmPackage.fromFolder(path);
     npm.loadAllFiles();
-    npm.save(new FileOutputStream(output));
+    npm.save(ManagedFileAccess.outStream(output));
 
   }
 
   private void buildXml(String json, String xml, String version) throws FHIRFormatError, IOException {
-    for (File f : new File(Utilities.path(json, "package")).listFiles()) {
+    for (File f : ManagedFileAccess.file(Utilities.path(json, "package")).listFiles()) {
       if (f.getName().endsWith(".json")) {
         JsonObject j = JsonParser.parseObject(f);
         if (j.has("resourceType")) {
@@ -39,8 +40,8 @@ public class CorePackageTools {
             String n = f.getName();
             System.out.println(n);
             String xn = Utilities.changeFileExt(n, ".xml");
-            org.hl7.fhir.dstu2016may.model.Resource r = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(new FileInputStream(f));
+            org.hl7.fhir.dstu2016may.model.Resource r = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(ManagedFileAccess.inStream(f));
-            new org.hl7.fhir.dstu2016may.formats.XmlParser().setOutputStyle(org.hl7.fhir.dstu2016may.formats.IParser.OutputStyle.NORMAL).compose(new FileOutputStream(Utilities.path(xml, "package", xn)), r);
+            new org.hl7.fhir.dstu2016may.formats.XmlParser().setOutputStyle(org.hl7.fhir.dstu2016may.formats.IParser.OutputStyle.NORMAL).compose(ManagedFileAccess.outStream(Utilities.path(xml, "package", xn)), r);
           }
         }
       }

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

@@ -45,6 +45,7 @@ import org.hl7.fhir.r4.model.CodeType;
 import org.hl7.fhir.r4.model.ContactPoint.ContactPointSystem;
 import org.hl7.fhir.r4.model.DateTimeType;
 import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -123,10 +124,10 @@ public class CountryCodesConverter {
     cs1.setCount(cs1.getConcept().size());
     cs2.setCount(cs2.getConcept().size());
     throw new Error("Needs revisiting");
-//    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "4.0.1", "package", "CodeSstem-iso3166.json")), cs1);
+//    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "4.0.1", "package", "CodeSstem-iso3166.json")), cs1);
-//    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "3.0.2", "package", "CodeSstem-iso3166.json")), cs1); // format hasn't changed
+//    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "3.0.2", "package", "CodeSstem-iso3166.json")), cs1); // format hasn't changed
-//    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "4.0.1", "package", "CodeSstem-iso3166-2.json")), cs2);
+//    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "4.0.1", "package", "CodeSstem-iso3166-2.json")), cs2);
-//    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "3.0.2", "package", "CodeSstem-iso3166-2.json")), cs2); // format hasn't changed
+//    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "3.0.2", "package", "CodeSstem-iso3166-2.json")), cs2); // format hasn't changed
   }
 
   public void setMetadata(Document src, CodeSystem cs, String id, String url, String partName, String partTitle) {
@@ -360,7 +361,7 @@ public class CountryCodesConverter {
     factory.setNamespaceAware(true);
     DocumentBuilder builder = factory.newDocumentBuilder();
 
-    return builder.parse(new FileInputStream(source));
+    return builder.parse(ManagedFileAccess.inStream(source));
   }
 
 

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

@@ -23,6 +23,7 @@ import org.hl7.fhir.r4.model.ValueSet;
 import org.hl7.fhir.r4.utils.NPMPackageGenerator;
 import org.hl7.fhir.r4.utils.NPMPackageGenerator.Category;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -73,8 +74,8 @@ public class DicomPackageBuilder {
     Set<String> ids = new HashSet<>();
     ids.add(vs.getId());
     
-    for (File f : new File(Utilities.path(source, "Resources", "valuesets", "fhir", "json")).listFiles()) {
+    for (File f : ManagedFileAccess.file(Utilities.path(source, "Resources", "valuesets", "fhir", "json")).listFiles()) {
-      vs = (ValueSet) JsonParser.loadFile(new FileInputStream(f));
+      vs = (ValueSet) JsonParser.loadFile(ManagedFileAccess.inStream(f));
       vs.setVersion(version);
       if (vs.getId().length() > 64) {
         vs.setId(vs.getId().substring(0, 64));
@@ -133,7 +134,7 @@ public class DicomPackageBuilder {
     DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
     factory.setNamespaceAware(true);
     DocumentBuilder builder = factory.newDocumentBuilder();
-    Document doc = builder.parse(new FileInputStream(Utilities.path(source, "Resources", "Ontology", "DCM", "dcm.owl")));
+    Document doc = builder.parse(ManagedFileAccess.inStream(Utilities.path(source, "Resources", "Ontology", "DCM", "dcm.owl")));
     Element rdf = doc.getDocumentElement();
     Element d = XMLUtil.getFirstChild(rdf);
     version = processVersion(XMLUtil.getNamedChildText(d, "versionInfo"));

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

@@ -10,6 +10,7 @@ import java.util.Set;
 import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.TextFile;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.json.parser.JsonParser;
 
@@ -22,9 +23,9 @@ public class ExamplesPackageBuilder {
 
   private void process(String source) throws FHIRFormatError, FileNotFoundException, IOException {
     Set<String> set = new HashSet<>();
-    for (File f : new File(source).listFiles()) {
+    for (File f : ManagedFileAccess.file(source).listFiles()) {
       if (f.getName().endsWith(".json")) {
-        JsonObject obj = JsonParser.parseObject(new FileInputStream(f));
+        JsonObject obj = JsonParser.parseObject(ManagedFileAccess.inStream(f));
         if (obj.has("resourceType") && obj.has("id")) {
           String type = obj.asString("resourceType");
           String id = obj.asString("id");

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

@@ -23,6 +23,7 @@ import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
 import org.hl7.fhir.r5.model.ValueSet;
 import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
 import org.hl7.fhir.utilities.npm.NpmPackage;
@@ -131,7 +132,7 @@ public class ExtensionExtractor {
       save(cs, dst,s, ids);
     }
     
-    deleteMatchingResources(ids, new File("/Users/grahamegrieve/work/r5/source"));
+    deleteMatchingResources(ids, ManagedFileAccess.file("/Users/grahamegrieve/work/r5/source"));
   }
 
   private void deleteMatchingResources(Set<String> ids, File folder) {
@@ -172,9 +173,9 @@ public class ExtensionExtractor {
     ids.add(cr.getId());
     String fn = Utilities.path(dst, folder, cr.fhirType()+"-"+cr.getId()+".xml"); 
     cr.setUserData("folder", folder);
-    if (!new File(fn).exists()) {
+    if (!ManagedFileAccess.file(fn).exists()) {
       Utilities.createDirectory(Utilities.getDirectoryForFile(fn));
-      new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(fn), cr);
+      new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(fn), cr);
     }
   }
 

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

@@ -43,13 +43,14 @@ import org.hl7.fhir.dstu2.model.Resource;
 import org.hl7.fhir.dstu2.model.ValueSet;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class GenValueSetExpansionConvertor {
 
   public static void main(String[] args) throws FHIRFormatError, IOException {
     String src = args[0];
     String tgt = args[1];
-    Bundle bundle = (Bundle) new XmlParser().parse(new FileInputStream(src));
+    Bundle bundle = (Bundle) new XmlParser().parse(ManagedFileAccess.inStream(src));
     for (BundleEntryComponent be : bundle.getEntry()) {
       Resource res = be.getResource();
       if (res != null) {
@@ -58,7 +59,7 @@ public class GenValueSetExpansionConvertor {
           id = tail(((ValueSet) res).getUrl());
         String dst = Utilities.path(tgt, res.fhirType() + "-" + id + ".json");
         System.out.println(dst);
-        new JsonParser().setOutputStyle(OutputStyle.NORMAL).compose(new FileOutputStream(dst), res);
+        new JsonParser().setOutputStyle(OutputStyle.NORMAL).compose(ManagedFileAccess.outStream(dst), res);
       }
     }
   }

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ICD11Generator.java

@@ -28,6 +28,7 @@ import org.hl7.fhir.r4.utils.ToolingExtensions;
 import org.hl7.fhir.utilities.SimpleHTTPClient;
 import org.hl7.fhir.utilities.SimpleHTTPClient.HTTPResult;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.json.model.JsonElement;
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.json.parser.JsonParser;
@@ -49,7 +50,7 @@ public class ICD11Generator {
       processMMSEntity(cs, base, child.asString(), cs.addConcept(), dest);
       System.out.println();
     }
-    new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "icd-11-mms.xml")), cs);
+    new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "icd-11-mms.xml")), cs);
     makeFullVs(dest, cs);
 
     cs = makeEntityCodeSystem();
@@ -62,7 +63,7 @@ public class ICD11Generator {
       processEntity(cs, ids, base, tail(child.asString()), dest);
       System.out.println();
     }
-    new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "icd-11-foundation.xml")), cs);
+    new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "icd-11-foundation.xml")), cs);
     makeFullVs2(dest, cs);
     System.out.println("finished");
   }
@@ -153,7 +154,7 @@ public class ICD11Generator {
     vs.setStatus(cs.getStatus());
     ConceptSetComponent inc = vs.getCompose().addInclude();
     inc.setSystem(cs.getUrl());
-    new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "vs-all-MMS.xml")), vs);
+    new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "vs-all-MMS.xml")), vs);
   }
 
   private void makeFullVs2(String dest, CodeSystem cs) throws IOException {
@@ -172,7 +173,7 @@ public class ICD11Generator {
     vs.setStatus(cs.getStatus());
     ConceptSetComponent inc = vs.getCompose().addInclude();
     inc.setSystem(cs.getUrl());
-    new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "vs-all-foundation.xml")), vs);
+    new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "vs-all-foundation.xml")), vs);
   }
 
   private void processMMSEntity(CodeSystem cs, String base, String ref, org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, String dest) throws IOException {
@@ -281,7 +282,7 @@ public class ICD11Generator {
     for (JsonElement e : o.getJsonArray("scaleEntity")) {
       inc.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue(tail(e.asString()));
     }
-    new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "vs-" + id + ".xml")), vs);
+    new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "vs-" + id + ".xml")), vs);
     return url;
   }
 

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

@@ -19,6 +19,7 @@ import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
 import org.hl7.fhir.r5.model.CodeSystem.PropertyType;
 import org.hl7.fhir.r5.model.CodeType;
 import org.hl7.fhir.utilities.CSVReader;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class ICFImporter {
 
@@ -28,7 +29,7 @@ public class ICFImporter {
   }
 
   private void doImport(String src, String dst) throws FHIRException, FileNotFoundException, IOException {
-    CSVReader csv = new CSVReader(new FileInputStream(src));
+    CSVReader csv = new CSVReader(ManagedFileAccess.inStream(src));
     csv.setDelimiter('\t');
     csv.readHeaders();
 
@@ -98,7 +99,7 @@ public class ICFImporter {
     
     }
     csv.close();
-    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dst), cs); 
+    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(dst), cs); 
   }
 //
 //  private String processLink(String cell) {

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ICPC2Importer.java

@@ -53,6 +53,7 @@ import org.hl7.fhir.dstu3.model.ValueSet;
 import org.hl7.fhir.dstu3.terminologies.CodeSystemUtilities;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -122,7 +123,7 @@ public class ICPC2Importer {
     DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
     factory.setNamespaceAware(false);
     DocumentBuilder builder = factory.newDocumentBuilder();
-    Document doc = builder.parse(new FileInputStream(sourceFileName));
+    Document doc = builder.parse(ManagedFileAccess.inStream(sourceFileName));
 
     ValueSet vs = new ValueSet();
     vs.setUrl("http://hl7.org/fhir/sid/icpc2/vs");
@@ -170,8 +171,8 @@ public class ICPC2Importer {
 
     XmlParser xml = new XmlParser();
     xml.setOutputStyle(OutputStyle.PRETTY);
-    xml.compose(new FileOutputStream(targetFileNameVS), vs);
+    xml.compose(ManagedFileAccess.outStream(targetFileNameVS), vs);
-    xml.compose(new FileOutputStream(targetFileNameCS), cs);
+    xml.compose(ManagedFileAccess.outStream(targetFileNameCS), cs);
   }
 
   private void processClass(Element cls, Map<String, ConceptDefinitionComponent> concepts, CodeSystem define) throws FHIRFormatError {

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/IEEE11073Convertor.java

@@ -68,6 +68,7 @@ import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.utilities.CSVReader;
 import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class IEEE11073Convertor {
 
@@ -113,7 +114,7 @@ public class IEEE11073Convertor {
     g.setSource("urn:iso:std:iso:11073:10101");
     g.setTarget("http://loinc.org");
 
-    CSVReader csv = new CSVReader(new FileInputStream(src));
+    CSVReader csv = new CSVReader(ManagedFileAccess.inStream(src));
     csv.readHeaders();
     while (csv.line()) {
       SourceElementComponent e = g.addElement();
@@ -124,13 +125,13 @@ public class IEEE11073Convertor {
       t.setCode(csv.cell("LOINC_NUM"));
       t.setDisplay(csv.cell("LOINC_LONG_COMMON_NAME"));
     }
-    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dst, "conceptmap-" + cm.getId() + ".xml")), cm);
+    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dst, "conceptmap-" + cm.getId() + ".xml")), cm);
     System.out.println("Done");
     return cm;
   }
 
   public static CodeSystem generateMDC(String src, String dst, UcumService ucum) throws IOException, FHIRException {
-    CSVReader csv = new CSVReader(new FileInputStream(src));
+    CSVReader csv = new CSVReader(ManagedFileAccess.inStream(src));
     csv.readHeaders();
     CodeSystem cs = new CodeSystem();
     Map<String, String> ucumIssues = new HashMap<String, String>();
@@ -206,7 +207,7 @@ public class IEEE11073Convertor {
       }
     }
     csv.close();
-    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dst, "codesystem-" + cs.getId() + ".xml")), cs);
+    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dst, "codesystem-" + cs.getId() + ".xml")), cs);
     System.out.println(errorCount + "UCUM errors");
 
     for (String u : sorted(ucumIssues.keySet()))

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/IGPackConverter102.java

@@ -49,6 +49,7 @@ import org.hl7.fhir.dstu3.model.ValueSet;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.utilities.FhirPublication;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class IGPackConverter102 extends BaseAdvisor_10_30 {
 
@@ -60,21 +61,21 @@ public class IGPackConverter102 extends BaseAdvisor_10_30 {
 
   private void process() throws IOException, FHIRException {
     initCSList();
-    for (String s : new File(Utilities.path("[tmp]", "igpack2")).list()) {
+    for (String s : ManagedFileAccess.file(Utilities.path("[tmp]", "igpack2")).list()) {
       if (s.endsWith(".xml") && !s.startsWith("z-") && !Utilities.existsInList(s, "expansions.xml", "v3-codesystems.xml", "v2-tables.xml")) {
         System.out.println("process " + s);
         org.hl7.fhir.dstu2.formats.XmlParser xp = new org.hl7.fhir.dstu2.formats.XmlParser();
-        org.hl7.fhir.dstu2.model.Resource r10 = xp.parse(new FileInputStream(Utilities.path("[tmp]", "igpack2\\" + s)));
+        org.hl7.fhir.dstu2.model.Resource r10 = xp.parse(ManagedFileAccess.inStream(Utilities.path("[tmp]", "igpack2\\" + s)));
         org.hl7.fhir.dstu3.model.Resource r17 = VersionConvertorFactory_10_30.convertResource(r10, this);
         org.hl7.fhir.dstu3.formats.XmlParser xc = new org.hl7.fhir.dstu3.formats.XmlParser();
         xc.setOutputStyle(OutputStyle.PRETTY);
-        xc.compose(new FileOutputStream(Utilities.path("[tmp]", "igpack2\\" + s)), r17);
+        xc.compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "igpack2\\" + s)), r17);
       }
     }
     System.out.println("save codesystems");
     org.hl7.fhir.dstu3.formats.XmlParser xc = new org.hl7.fhir.dstu3.formats.XmlParser();
     xc.setOutputStyle(OutputStyle.PRETTY);
-    xc.compose(new FileOutputStream(Utilities.path("[tmp]", "igpack2\\codesystems.xml")), cslist);
+    xc.compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "igpack2\\codesystems.xml")), cslist);
     System.out.println("done");
   }
 

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/IGPackConverter140.java

@@ -37,20 +37,21 @@ import java.io.FileOutputStream;
 import org.hl7.fhir.convertors.factory.VersionConvertorFactory_14_30;
 import org.hl7.fhir.dstu3.formats.IParser.OutputStyle;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class IGPackConverter140 {
 
   public static void main(String[] args) throws Exception {
-    for (String s : new File(Utilities.path("[tmp]", "igpack")).list()) {
+    for (String s : ManagedFileAccess.file(Utilities.path("[tmp]", "igpack")).list()) {
 //      if (s.endsWith(".xml") && !s.contains("z-")) {
       if (s.equals("expansions.xml")) {
         System.out.println("process " + s);
         org.hl7.fhir.dstu2016may.formats.XmlParser xp = new org.hl7.fhir.dstu2016may.formats.XmlParser();
-        org.hl7.fhir.dstu2016may.model.Resource r14 = xp.parse(new FileInputStream(Utilities.path("[tmp]", "igpack\\" + s)));
+        org.hl7.fhir.dstu2016may.model.Resource r14 = xp.parse(ManagedFileAccess.inStream(Utilities.path("[tmp]", "igpack\\" + s)));
         org.hl7.fhir.dstu3.model.Resource r17 = VersionConvertorFactory_14_30.convertResource(r14);
         org.hl7.fhir.dstu3.formats.XmlParser xc = new org.hl7.fhir.dstu3.formats.XmlParser();
         xc.setOutputStyle(OutputStyle.PRETTY);
-        xc.compose(new FileOutputStream(Utilities.path("[tmp]", "igpack\\z-" + s)), r17);
+        xc.compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "igpack\\z-" + s)), r17);
       }
     }
     System.out.println("done");

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

@@ -3,6 +3,7 @@ package org.hl7.fhir.convertors.misc;
 import java.io.FileOutputStream;
 import java.io.IOException;
 
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.json.parser.JsonParser;
 
@@ -15,7 +16,7 @@ public class JsonProcessor {
   private void process(String source) throws IOException {
     JsonObject json = JsonParser.parseObjectFromFile(source);
     process(json);
-    JsonParser.compose(json, new FileOutputStream(source), true);
+    JsonParser.compose(json, ManagedFileAccess.outStream(source), true);
     
   }
 

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

@@ -1,33 +1,33 @@
 package org.hl7.fhir.convertors.misc;
 
-/*
+/*
-  Copyright (c) 2011+, HL7, Inc.
+  Copyright (c) 2011+, HL7, Inc.
-  All rights reserved.
+  All rights reserved.
-  
+  
-  Redistribution and use in source and binary forms, with or without modification, 
+  Redistribution and use in source and binary forms, with or without modification, 
-  are permitted provided that the following conditions are met:
+  are permitted provided that the following conditions are met:
-    
+    
-   * Redistributions of source code must retain the above copyright notice, this 
+   * Redistributions of source code must retain the above copyright notice, this 
-     list of conditions and the following disclaimer.
+     list of conditions and the following disclaimer.
-   * Redistributions in binary form must reproduce the above copyright notice, 
+   * Redistributions in binary form must reproduce the above copyright notice, 
-     this list of conditions and the following disclaimer in the documentation 
+     this list of conditions and the following disclaimer in the documentation 
-     and/or other materials provided with the distribution.
+     and/or other materials provided with the distribution.
-   * Neither the name of HL7 nor the names of its contributors may be used to 
+   * Neither the name of HL7 nor the names of its contributors may be used to 
-     endorse or promote products derived from this software without specific 
+     endorse or promote products derived from this software without specific 
-     prior written permission.
+     prior written permission.
-  
+  
-  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
-  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
+  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
-  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
+  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
-  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
+  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
-  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
+  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
-  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
+  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
-  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
-  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
-  POSSIBILITY OF SUCH DAMAGE.
+  POSSIBILITY OF SUCH DAMAGE.
-  
+  
- */
+ */
 
 
 
@@ -50,6 +50,7 @@ import org.hl7.fhir.r5.model.DateTimeType;
 import org.hl7.fhir.r5.model.InstantType;
 import org.hl7.fhir.r5.model.Meta;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -151,12 +152,12 @@ public class LoincToDEConvertor {
 		factory.setNamespaceAware(true);
 		DocumentBuilder builder = factory.newDocumentBuilder();
 
-		xml = builder.parse(new FileInputStream(definitions)); 
+		xml = builder.parse(ManagedFileAccess.inStream(definitions)); 
 	}
 
 	private void saveBundle() throws FHIRFormatError, IOException, XmlPullParserException {
 		XmlParser xml = new XmlParser();
-		FileOutputStream s = new FileOutputStream(dest);
+		FileOutputStream s = ManagedFileAccess.outStream(dest);
     xml.compose(s, bundle, true);
     s.close();
 	}

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

@@ -48,6 +48,7 @@ import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
 import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.utilities.CSVReader;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class NUCCConvertor {
 
@@ -56,7 +57,7 @@ public class NUCCConvertor {
   }
 
   public void execute() throws IOException, FHIRException {
-    CSVReader csv = new CSVReader(new FileInputStream(Utilities.path("[tmp]", "nucc.csv")));
+    CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path("[tmp]", "nucc.csv")));
     CodeSystem cs = new CodeSystem();
     cs.setId("nucc-provider-taxonomy");
     cs.setUrl("http://nucc.org/provider-taxonomy");
@@ -79,7 +80,7 @@ public class NUCCConvertor {
     }
     csv.close();
     cs.sort();
-    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "nucc.json")), cs);
+    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "nucc.json")), cs);
   }
 
   private void processLine(CodeSystem cs, String[] values) throws FHIRFormatError {

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

@@ -39,6 +39,7 @@ import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.json.model.JsonArray;
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.json.parser.JsonParser;
@@ -80,7 +81,7 @@ public class NpmPackageVersionConverter {
   }
 
   public void execute() throws IOException {
-    Map<String, byte[]> content = loadContentMap(new FileInputStream(source));
+    Map<String, byte[]> content = loadContentMap(ManagedFileAccess.inStream(source));
 
     Map<String, byte[]> output = new HashMap<>();
     output.put("package/package.json", convertPackage(content.get("package/package.json")));
@@ -141,7 +142,7 @@ public class NpmPackageVersionConverter {
       tar.write(cnt);
       tar.closeArchiveEntry();
       cnt = TextFile.fileToBytes(e.getValue().getDbFilename());
-      new File(e.getValue().getDbFilename()).delete();
+      ManagedFileAccess.file(e.getValue().getDbFilename()).delete();
       entry = new TarArchiveEntry(e.getKey() + "/.index.db");
       entry.setSize(cnt.length);
       tar.putArchiveEntry(entry);

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

@@ -3,10 +3,12 @@ package org.hl7.fhir.convertors.misc;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
+import java.io.IOException;
 
 import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
 import org.hl7.fhir.utilities.IniFile;
 import org.hl7.fhir.utilities.VersionUtilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class OIDAssigner {
 
@@ -15,9 +17,9 @@ public class OIDAssigner {
     new OIDAssigner().execute(args[0], args[1], args[2]);
   }
 
-  private void execute(String oidSource, String folder, String version) {
+  private void execute(String oidSource, String folder, String version) throws IOException {
    IniFile oids = new IniFile(oidSource);
-   File f = new File(folder);
+   File f = ManagedFileAccess.file(folder);
    process(oids, f, version);
   }
 
@@ -47,7 +49,7 @@ public class OIDAssigner {
     org.hl7.fhir.dstu2.formats.IParser parser = fmt == FhirFormat.JSON ? new  org.hl7.fhir.dstu2.formats.JsonParser() : new org.hl7.fhir.dstu2.formats.XmlParser();
     try {
       boolean save = false;
-      org.hl7.fhir.dstu2.model.Resource r = parser.parse(new FileInputStream(f));
+      org.hl7.fhir.dstu2.model.Resource r = parser.parse(ManagedFileAccess.inStream(f));
       if (r instanceof org.hl7.fhir.dstu2.model.ValueSet) { 
         org.hl7.fhir.dstu2.model.ValueSet vs = (org.hl7.fhir.dstu2.model.ValueSet) r;
         boolean hasOid = isOid(vs.getIdentifier());
@@ -81,7 +83,7 @@ public class OIDAssigner {
         }
       }
       if (save) {
-        parser.setOutputStyle(org.hl7.fhir.dstu2.formats.IParser.OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
+        parser.setOutputStyle(org.hl7.fhir.dstu2.formats.IParser.OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), r);
       }
     } catch (Exception e) {
       System.out.println("Erro processing "+f.getAbsolutePath()+": "+e.getMessage());
@@ -93,7 +95,7 @@ public class OIDAssigner {
     org.hl7.fhir.dstu3.formats.IParser parser = fmt == FhirFormat.JSON ? new  org.hl7.fhir.dstu3.formats.JsonParser() : new org.hl7.fhir.dstu3.formats.XmlParser();
     try {
       boolean save = false;
-      org.hl7.fhir.dstu3.model.Resource r = parser.parse(new FileInputStream(f));
+      org.hl7.fhir.dstu3.model.Resource r = parser.parse(ManagedFileAccess.inStream(f));
       if (r instanceof org.hl7.fhir.dstu3.model.CodeSystem) { 
         org.hl7.fhir.dstu3.model.CodeSystem cs = (org.hl7.fhir.dstu3.model.CodeSystem) r;
         boolean hasOid = isOid(cs.getIdentifier());
@@ -141,7 +143,7 @@ public class OIDAssigner {
         }
       }
       if (save) {
-        parser.setOutputStyle(org.hl7.fhir.dstu3.formats.IParser.OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
+        parser.setOutputStyle(org.hl7.fhir.dstu3.formats.IParser.OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), r);
       }
     } catch (Exception e) {
       System.out.println("Erro processing "+f.getAbsolutePath()+": "+e.getMessage());
@@ -153,7 +155,7 @@ public class OIDAssigner {
     org.hl7.fhir.r4.formats.IParser parser = fmt == FhirFormat.JSON ? new  org.hl7.fhir.r4.formats.JsonParser() : new org.hl7.fhir.r4.formats.XmlParser();
     try {
       boolean save = false;
-      org.hl7.fhir.r4.model.Resource r = parser.parse(new FileInputStream(f));
+      org.hl7.fhir.r4.model.Resource r = parser.parse(ManagedFileAccess.inStream(f));
       if (r instanceof org.hl7.fhir.r4.model.CodeSystem) { 
         org.hl7.fhir.r4.model.CodeSystem cs = (org.hl7.fhir.r4.model.CodeSystem) r;
         boolean hasOid = false;
@@ -206,7 +208,7 @@ public class OIDAssigner {
         }
       }
       if (save) {
-        parser.setOutputStyle(org.hl7.fhir.r4.formats.IParser.OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
+        parser.setOutputStyle(org.hl7.fhir.r4.formats.IParser.OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), r);
       }
     } catch (Exception e) {
       System.out.println("Erro processing "+f.getAbsolutePath()+": "+e.getMessage());
@@ -217,7 +219,7 @@ public class OIDAssigner {
     org.hl7.fhir.r4b.formats.IParser parser = fmt == FhirFormat.JSON ? new  org.hl7.fhir.r4b.formats.JsonParser() : new org.hl7.fhir.r4b.formats.XmlParser();
     try {
       boolean save = false;
-      org.hl7.fhir.r4b.model.Resource r = parser.parse(new FileInputStream(f));
+      org.hl7.fhir.r4b.model.Resource r = parser.parse(ManagedFileAccess.inStream(f));
       if (r instanceof org.hl7.fhir.r4b.model.CanonicalResource) { 
         org.hl7.fhir.r4b.model.CanonicalResource cs = (org.hl7.fhir.r4b.model.CanonicalResource) r;
         boolean hasOid = false;
@@ -233,7 +235,7 @@ public class OIDAssigner {
         }
       }
       if (save) {
-        parser.setOutputStyle(org.hl7.fhir.r4b.formats.IParser.OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
+        parser.setOutputStyle(org.hl7.fhir.r4b.formats.IParser.OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), r);
       }
     } catch (Exception e) {
       System.out.println("Erro processing "+f.getAbsolutePath()+": "+e.getMessage());
@@ -245,7 +247,7 @@ public class OIDAssigner {
     org.hl7.fhir.r5.formats.IParser parser = fmt == FhirFormat.JSON ? new  org.hl7.fhir.r5.formats.JsonParser() : new org.hl7.fhir.r5.formats.XmlParser();
     try {
       boolean save = false;
-      org.hl7.fhir.r5.model.Resource r = parser.parse(new FileInputStream(f));
+      org.hl7.fhir.r5.model.Resource r = parser.parse(ManagedFileAccess.inStream(f));
       if (r instanceof org.hl7.fhir.r5.model.CanonicalResource) { 
         org.hl7.fhir.r5.model.CanonicalResource cs = (org.hl7.fhir.r5.model.CanonicalResource) r;
         boolean hasOid = false;
@@ -261,7 +263,7 @@ public class OIDAssigner {
         }
       }
       if (save) {
-        parser.setOutputStyle(org.hl7.fhir.r5.formats.IParser.OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
+        parser.setOutputStyle(org.hl7.fhir.r5.formats.IParser.OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), r);
       }
     } catch (Exception e) {
       System.out.println("Erro processing "+f.getAbsolutePath()+": "+e.getMessage());

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

@@ -15,6 +15,7 @@ import java.util.Map;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.utilities.CSVReader;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class OMOPImporter {
 
@@ -107,15 +108,15 @@ public class OMOPImporter {
   }
 
 
-  private void connect(String dest) throws SQLException, ClassNotFoundException {
+  private void connect(String dest) throws SQLException, ClassNotFoundException, IOException {
     //    Class.forName("com.mysql.jdbc.Driver");  
     //    con = DriverManager.getConnection("jdbc:mysql://localhost:3306/omop?useSSL=false","root",{pwd}); 
-    new File("/Users/grahamegrieve/temp/omop/omop.db").delete();
+    ManagedFileAccess.file("/Users/grahamegrieve/temp/omop/omop.db").delete();
     con = DriverManager.getConnection("jdbc:sqlite:"+dest); 
   }
   private void processRelationships(String folder, boolean process) throws FHIRException, FileNotFoundException, IOException, SQLException {
     Tracker t = new Tracker("Relationships", 700);
-    CSVReader csv = new CSVReader(new FileInputStream(Utilities.path(folder, "RELATIONSHIP.csv")));
+    CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "RELATIONSHIP.csv")));
     csv.setDelimiter('\t');
     csv.readHeaders();
     csv.setDoingQuotes(false);
@@ -147,7 +148,7 @@ public class OMOPImporter {
       stmt.execute("Create Index `RelationshipsId` on Relationships  (`relationship_id`)");
       stmt.execute("Create Index`RelationshipsReverse` on Relationships (`reverse_relationship_id`)");
 
-      csv = new CSVReader(new FileInputStream(Utilities.path(folder, "RELATIONSHIP.csv")));
+      csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "RELATIONSHIP.csv")));
       csv.setDelimiter('\t');
       csv.readHeaders();
       csv.setDoingQuotes(false);
@@ -182,7 +183,7 @@ public class OMOPImporter {
 
   private void processVocabularies(String folder, boolean process) throws FHIRException, FileNotFoundException, IOException, SQLException {
     Tracker t = new Tracker("Vocabularies", 60);
-    CSVReader csv = new CSVReader(new FileInputStream(Utilities.path(folder, "VOCABULARY.csv")));
+    CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "VOCABULARY.csv")));
     csv.setDelimiter('\t');
     csv.readHeaders();
     csv.setDoingQuotes(false);
@@ -217,7 +218,7 @@ public class OMOPImporter {
           "\r\n");
       stmt.execute("CREATE INDEX `VocabulariesId` on Vocabularies (`vocabulary_id`)");
 
-      csv = new CSVReader(new FileInputStream(Utilities.path(folder, "VOCABULARY.csv")));
+      csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "VOCABULARY.csv")));
       csv.setDelimiter('\t');
       csv.readHeaders();
       csv.setDoingQuotes(false);
@@ -244,7 +245,7 @@ public class OMOPImporter {
   private void processDomains(String folder, boolean process) throws FHIRException, FileNotFoundException, IOException, SQLException {
     Tracker t = new Tracker("Domains", 50);
 
-    CSVReader csv = new CSVReader(new FileInputStream(Utilities.path(folder, "DOMAIN.csv")));
+    CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "DOMAIN.csv")));
     csv.setDelimiter('\t');
     csv.readHeaders();
     csv.setDoingQuotes(false);
@@ -275,7 +276,7 @@ public class OMOPImporter {
 
       stmt.execute("CREATE INDEX `DomainId` on Domains (`domain_id`)");
 
-      csv = new CSVReader(new FileInputStream(Utilities.path(folder, "DOMAIN.csv")));
+      csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "DOMAIN.csv")));
       csv.setDelimiter('\t');
       csv.readHeaders();
       csv.setDoingQuotes(false);
@@ -299,7 +300,7 @@ public class OMOPImporter {
   private void processConceptClasses(String folder, boolean process) throws FHIRException, FileNotFoundException, IOException, SQLException {
     Tracker t = new Tracker("ConceptClasses", 400);
 
-    CSVReader csv = new CSVReader(new FileInputStream(Utilities.path(folder, "CONCEPT_CLASS.csv")));
+    CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "CONCEPT_CLASS.csv")));
     csv.setDelimiter('\t');
     csv.readHeaders();
     csv.setDoingQuotes(false);
@@ -325,7 +326,7 @@ public class OMOPImporter {
           "  PRIMARY KEY (`concept_class_concept_id`)\r\n"+
           ") \r\n"+
           "\r\n");
-      csv = new CSVReader(new FileInputStream(Utilities.path(folder, "CONCEPT_CLASS.csv")));
+      csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "CONCEPT_CLASS.csv")));
       csv.setDelimiter('\t');
       csv.readHeaders();
       csv.setDoingQuotes(false);
@@ -356,7 +357,7 @@ public class OMOPImporter {
       return;
     }
 
-    CSVReader csv = new CSVReader(new FileInputStream(Utilities.path(folder, "DRUG_STRENGTH.csv")));
+    CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "DRUG_STRENGTH.csv")));
     csv.setDelimiter('\t');
     csv.readHeaders();
     csv.setDoingQuotes(false);
@@ -398,7 +399,7 @@ public class OMOPImporter {
         "  PRIMARY KEY (`drug_concept_id`,`ingredient_concept_id`)\r\n"+
         ") \r\n"+
         "\r\n");
-    csv = new CSVReader(new FileInputStream(Utilities.path(folder, "DRUG_STRENGTH.csv")));
+    csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "DRUG_STRENGTH.csv")));
     csv.setDelimiter('\t');
     csv.readHeaders();
     csv.setDoingQuotes(false);
@@ -446,7 +447,7 @@ public class OMOPImporter {
       return;
     }
 
-    CSVReader csv = new CSVReader(new FileInputStream(Utilities.path(folder, "CONCEPT.csv")));
+    CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "CONCEPT.csv")));
     csv.setDelimiter('\t');
     csv.readHeaders();
     csv.setDoingQuotes(false);
@@ -485,7 +486,7 @@ public class OMOPImporter {
     stmt.execute("CREATE INDEX `ConceptVocabulary` on Concepts (`vocabulary_id`,`concept_code`)");
     stmt.execute("CREATE INDEX `ConceptClass` on Concepts (`concept_class_id`)");
 
-    csv = new CSVReader(new FileInputStream(Utilities.path(folder, "CONCEPT.csv")));
+    csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "CONCEPT.csv")));
     csv.setDelimiter('\t');
     csv.readHeaders();
     csv.setDoingQuotes(false);
@@ -523,7 +524,7 @@ public class OMOPImporter {
     }    
     t.scan();
 
-    CSVReader csv = new CSVReader(new FileInputStream(Utilities.path(folder, "CONCEPT_SYNONYM.csv")));
+    CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "CONCEPT_SYNONYM.csv")));
     csv.setDelimiter('\t');
     csv.readHeaders();
     csv.setDoingQuotes(false);
@@ -545,7 +546,7 @@ public class OMOPImporter {
     stmt.execute("CREATE INDEX `SynonymId` on ConceptSynonyms (`concept_id`)");
     stmt.execute("CREATE INDEX `SynonymLang` on ConceptSynonyms (`language_concept_id`)");
 
-    csv = new CSVReader(new FileInputStream(Utilities.path(folder, "CONCEPT_SYNONYM.csv")));
+    csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "CONCEPT_SYNONYM.csv")));
     csv.setDelimiter('\t');
     csv.readHeaders();
     csv.setDoingQuotes(false);
@@ -575,7 +576,7 @@ public class OMOPImporter {
     }
 
     t.process();
-    CSVReader csv = new CSVReader(new FileInputStream(Utilities.path(folder, "CONCEPT_ANCESTOR.csv")));
+    CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "CONCEPT_ANCESTOR.csv")));
     csv.setDelimiter('\t');
     csv.readHeaders();
     csv.setDoingQuotes(false);
@@ -614,7 +615,7 @@ public class OMOPImporter {
     }
 
     t.scan();
-    CSVReader csv = new CSVReader(new FileInputStream(Utilities.path(folder, "CONCEPT_RELATIONSHIP.csv")));
+    CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "CONCEPT_RELATIONSHIP.csv")));
     csv.setDelimiter('\t');
     csv.readHeaders();
     csv.setDoingQuotes(false);
@@ -641,7 +642,7 @@ public class OMOPImporter {
 //  stmt.execute("CREATE INDEX `type1` on ConceptRelationships (`relationship_id`,`concept_id_1`,`concept_id_2`)");
 //  stmt.execute("CREATE INDEX `type2` on ConceptRelationships (`relationship_id`,`concept_id_2`,`concept_id_1`)");
 
-    csv = new CSVReader(new FileInputStream(Utilities.path(folder, "CONCEPT_RELATIONSHIP.csv")));
+    csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "CONCEPT_RELATIONSHIP.csv")));
     csv.setDelimiter('\t');
     csv.readHeaders();
     csv.setDoingQuotes(false);

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

@@ -51,6 +51,7 @@ import org.hl7.fhir.dstu3.model.Type;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class ObservationStatsBuilder {
 
@@ -78,7 +79,7 @@ public class ObservationStatsBuilder {
     vitals(b, base, 130, 95, 133, 97, 37.2);
     vitals(b, base, 150, 85, 125, 98, 37.1);
 
-    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "vitals.xml")), b);
+    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "vitals.xml")), b);
   }
 
   private static void vitals(Bundle b, Calendar base, int minutes, int diastolic, int systolic, int sat, double temp) throws FHIRFormatError {
@@ -202,7 +203,7 @@ public class ObservationStatsBuilder {
     addAge(b, 10, 0, "31.9");
 
 
-    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "obs.xml")), b);
+    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "obs.xml")), b);
   }
 
   private static void addAge(Bundle b, int y, int m, String v) throws FHIRException {

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

@@ -7,6 +7,7 @@ import java.util.List;
 
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.json.parser.JsonParser;
 
@@ -67,15 +68,15 @@ public class PackageMaintainer {
           System.out.println("Examples contains " + s + " but core doesn't");
       }
     }
-    strip(new File(Utilities.path(PATH, "hl7.fhir." + ver + ".core", "package")));
+    strip(ManagedFileAccess.file(Utilities.path(PATH, "hl7.fhir." + ver + ".core", "package")));
-    strip(new File(Utilities.path(PATH, "hl7.fhir." + ver + ".expansions", "package")));
+    strip(ManagedFileAccess.file(Utilities.path(PATH, "hl7.fhir." + ver + ".expansions", "package")));
     if (!ver.equals("r2b"))
-      strip(new File(Utilities.path(PATH, "hl7.fhir." + ver + ".elements", "package")));
+      strip(ManagedFileAccess.file(Utilities.path(PATH, "hl7.fhir." + ver + ".elements", "package")));
   }
 
 
-  private List<String> listResources(String dir) {
+  private List<String> listResources(String dir) throws IOException {
-    File folder = new File(dir);
+    File folder = ManagedFileAccess.file(dir);
     List<String> res = new ArrayList<>();
     for (String fn : folder.list()) {
       if (fn.endsWith(".json") && fn.contains("-")) {

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

@@ -7,6 +7,7 @@ import java.io.IOException;
 import org.hl7.fhir.r5.formats.JsonParser;
 import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.r5.utils.ResourceMinifier;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
 import org.hl7.fhir.utilities.npm.NpmPackage;
 import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
@@ -33,7 +34,7 @@ public class PackageMinifier {
         }
       }
     }
-    tgt.save(new FileOutputStream(target));
+    tgt.save(ManagedFileAccess.outStream(target));
   }
   
 }

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

@@ -3,6 +3,7 @@ package org.hl7.fhir.convertors.misc;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
+import java.io.IOException;
 
 /*
   Copyright (c) 2011+, HL7, Inc.
@@ -38,6 +39,7 @@ import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 /*
  * load reosurces in xml format, and sve them in package format (json, with correct name
@@ -48,10 +50,10 @@ import org.hl7.fhir.utilities.Utilities;
 public class PackagePreparer {
 
 
-  public static void main(String[] args) {
+  public static void main(String[] args) throws IOException {
-    for (File f : new File("C:\\work\\fhirserver\\resources\\mihin").listFiles()) {
+    for (File f : ManagedFileAccess.file("C:\\work\\fhirserver\\resources\\mihin").listFiles()) {
       try {
-        org.hl7.fhir.dstu3.model.Resource r = new org.hl7.fhir.dstu3.formats.JsonParser().parse(new FileInputStream(f));
+        org.hl7.fhir.dstu3.model.Resource r = new org.hl7.fhir.dstu3.formats.JsonParser().parse(ManagedFileAccess.inStream(f));
         if (r instanceof Bundle) {
           Bundle b = (Bundle) r;
           for (BundleEntryComponent be : b.getEntry()) {
@@ -60,7 +62,7 @@ public class PackagePreparer {
               if (r4.getId().startsWith(r4.fhirType() + "-"))
                 be.getResource().setId(r4.getId().substring(r4.fhirType().length() + 1));
               if (be.getResource().hasId())
-                new org.hl7.fhir.r4.formats.JsonParser().compose(new FileOutputStream(Utilities.path("C:\\work\\fhirserver\\resources\\fhir.test.data\\3.5.0\\package", be.getResource().fhirType() + "-" + be.getResource().getId() + ".json")), r4);
+                new org.hl7.fhir.r4.formats.JsonParser().compose(ManagedFileAccess.outStream(Utilities.path("C:\\work\\fhirserver\\resources\\fhir.test.data\\3.5.0\\package", be.getResource().fhirType() + "-" + be.getResource().getId() + ".json")), r4);
               else
                 System.out.println(f.getName() + " bundle entry has no id");
             } catch (Exception e) {
@@ -68,7 +70,7 @@ public class PackagePreparer {
             }
           }
         } else if (r.hasId())
-          new org.hl7.fhir.r4.formats.JsonParser().compose(new FileOutputStream(Utilities.path(Utilities.getDirectoryForFile(f.getAbsolutePath()), r.fhirType() + "-" + r.getId() + ".json")), VersionConvertorFactory_30_40.convertResource(r));
+          new org.hl7.fhir.r4.formats.JsonParser().compose(ManagedFileAccess.outStream(Utilities.path(Utilities.getDirectoryForFile(f.getAbsolutePath()), r.fhirType() + "-" + r.getId() + ".json")), VersionConvertorFactory_30_40.convertResource(r));
         else
           System.out.println(f.getName() + " has no id");
       } catch (Exception e) {

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

@@ -18,6 +18,7 @@ import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.utilities.CSVReader;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class PhinVadsImporter extends OIDBasedValueSetImporter {
 
@@ -32,13 +33,13 @@ public class PhinVadsImporter extends OIDBasedValueSetImporter {
     self.process(args[0], args[1]);
   }
 
-  private void process(String source, String dest) {
+  private void process(String source, String dest) throws IOException {
-    for (File f : new File(source).listFiles()) {
+    for (File f : ManagedFileAccess.file(source).listFiles()) {
       try {
         System.out.println("Process " + f.getName());
         ValueSet vs = importValueSet(TextFile.fileToBytes(f));
         if (vs.getId() != null) {
-          new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "ValueSet-" + vs.getId() + ".json")), vs);
+          new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "ValueSet-" + vs.getId() + ".json")), vs);
         }
       } catch (Exception e) {
         e.printStackTrace();

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

@@ -23,6 +23,7 @@ import org.hl7.fhir.r5.utils.ResourceDependencyWalker;
 import org.hl7.fhir.r5.utils.ResourceDependencyWalker.IResourceDependencyNotifier;
 import org.hl7.fhir.r5.utils.ResourceMinifier;
 import org.hl7.fhir.utilities.VersionUtilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.json.JsonException;
 import org.hl7.fhir.utilities.json.parser.JsonParser;
 import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
@@ -47,7 +48,7 @@ public class ResourceDependencyPackageBuilder {
     
     new ResourceDependencyWalker(ctxt, pckBuilder).walk(ctxt.fetchResource(CapabilityStatement.class, args[2]));
     
-    pckBuilder.npm.save(new FileOutputStream(args[4]));
+    pckBuilder.npm.save(ManagedFileAccess.outStream(args[4]));
   }
 
   private static NpmPackage makeNpm(String vid, String version) throws JsonException, IOException {

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

@@ -13,6 +13,7 @@ import org.hl7.fhir.r4.terminologies.CodeSystemUtilities;
 import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.json.parser.JsonParser;
 
@@ -27,7 +28,7 @@ public class SPDXImporter {
   
   public void generate(String[] args) throws Exception {
     JsonObject json = JsonParser.parseObjectFromUrl("https://raw.githubusercontent.com/spdx/license-list-data/main/json/licenses.json");
-    CodeSystem cs = (CodeSystem) new org.hl7.fhir.r4.formats.JsonParser().parse(new FileInputStream(args[0]));
+    CodeSystem cs = (CodeSystem) new org.hl7.fhir.r4.formats.JsonParser().parse(ManagedFileAccess.inStream(args[0]));
     cs.getConcept().clear();
     cs.getProperty().clear();
     cs.addProperty().setCode("reference").setType(PropertyType.STRING);
@@ -58,7 +59,7 @@ public class SPDXImporter {
       }
     }
     CodeSystemUtilities.sortAllCodes(cs);
-    new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(args[1]), cs);
+    new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(args[1]), cs);
     b = new StringBuilder();
     generateEnum("SPDXLicense", cs);
     TextFile.stringToFile(b.toString(), Utilities.changeFileExt(args[1], ".java"));

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

@@ -45,6 +45,7 @@ import org.hl7.fhir.dstu3.formats.JsonParser;
 import org.hl7.fhir.dstu3.formats.XmlParser;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class Test {
   public final static String DEF_TS_SERVER = "http://fhir-dev.healthintersections.com.au/open";
@@ -58,13 +59,13 @@ public class Test {
   public static void main(String[] args) {
     try {
       CCDAConverter c = new CCDAConverter(new UcumEssenceService(UCUM_PATH), SimpleWorkerContext.fromPack(Utilities.path(SRC_PATH, "validation.zip")));
-      Bundle a = c.convert(new FileInputStream(DEF_PATH + "ccda.xml"));
+      Bundle a = c.convert(ManagedFileAccess.inStream(DEF_PATH + "ccda.xml"));
       String fx = DEF_PATH + "output.xml";
       IParser x = new XmlParser().setOutputStyle(OutputStyle.PRETTY);
-      x.compose(new FileOutputStream(fx), a);
+      x.compose(ManagedFileAccess.outStream(fx), a);
       String fj = DEF_PATH + "output.json";
       IParser j = new JsonParser().setOutputStyle(OutputStyle.PRETTY);
-      j.compose(new FileOutputStream(fj), a);
+      j.compose(ManagedFileAccess.outStream(fj), a);
       System.out.println("done. save as " + fx + " and " + fj);
     } catch (Exception e) {
       e.printStackTrace();

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

@@ -30,6 +30,7 @@ import org.hl7.fhir.r4.utils.client.FHIRToolingClient;
 import org.hl7.fhir.r4.terminologies.JurisdictionUtilities;
 import org.hl7.fhir.utilities.CSVReader;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.json.model.JsonArray;
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.json.model.JsonProperty;
@@ -47,7 +48,7 @@ public class VSACImporter extends OIDBasedValueSetImporter {
   }
 
   private void process(String source, String dest, String apiKey, boolean onlyNew) throws FHIRException, IOException, URISyntaxException {
-    CSVReader csv = new CSVReader(new FileInputStream(source));
+    CSVReader csv = new CSVReader(ManagedFileAccess.inStream(source));
     csv.readHeaders();
     Map<String, String> errs = new HashMap<>();
 
@@ -59,13 +60,13 @@ public class VSACImporter extends OIDBasedValueSetImporter {
 
     CapabilityStatement cs = fhirToolingClient.getCapabilitiesStatement();
     JsonParser json = new JsonParser();
-    json.setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "vsac-capability-statmenet.json")), cs);
+    json.setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "vsac-capability-statmenet.json")), cs);
 
     System.out.println("Loading");
     List<String> oids = new ArrayList<>();
     while (csv.line()) {
       String oid = csv.cell("OID");
-      if (!onlyNew || !(new File(Utilities.path(dest, "ValueSet-" + oid + ".json")).exists())) {
+      if (!onlyNew || !(ManagedFileAccess.file(Utilities.path(dest, "ValueSet-" + oid + ".json")).exists())) {
         oids.add(oid);
       }
     }
@@ -99,7 +100,7 @@ public class VSACImporter extends OIDBasedValueSetImporter {
     for (String oid : errs.keySet()) {
       oo.addIssue().setSeverity(IssueSeverity.ERROR).setCode(IssueType.EXCEPTION).setDiagnostics(errs.get(oid)).addLocation(oid);
     }
-    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "other", "OperationOutcome-vsac-errors.json")), oo);
+    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "other", "OperationOutcome-vsac-errors.json")), oo);
     System.out.println("Done. " + i + " ValueSets in "+Utilities.describeDuration(System.currentTimeMillis() - tt));
   }
 
@@ -164,7 +165,7 @@ public class VSACImporter extends OIDBasedValueSetImporter {
       }
       vs.setName(makeValidName(vs.getName()));
       JurisdictionUtilities.setJurisdictionCountry(vs.getJurisdiction(), "US");
-      new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "ValueSet-" + oid + ".json")), vs);
+      new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "ValueSet-" + oid + ".json")), vs);
     
     return true;
   }

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

@@ -4,6 +4,7 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.json.model.JsonProperty;
 import org.hl7.fhir.utilities.npm.NpmPackage;
@@ -11,7 +12,7 @@ import org.hl7.fhir.utilities.npm.NpmPackage;
 public class XMLPackageConvertor {
 
   public static void main(String[] args) throws IOException {
-    new XMLPackageConvertor().process(new File("C:\\web\\hl7.org\\fhir"));
+    new XMLPackageConvertor().process(ManagedFileAccess.file("C:\\web\\hl7.org\\fhir"));
   }
 
   private void process(File folder) throws IOException {
@@ -21,7 +22,7 @@ public class XMLPackageConvertor {
       } else {
         if (f.getName().endsWith(".tgz")) {
           System.out.println("Package " + f.getAbsolutePath());
-          NpmPackage p = NpmPackage.fromPackage(new FileInputStream(f));
+          NpmPackage p = NpmPackage.fromPackage(ManagedFileAccess.inStream(f));
           if (p.getNpm().has("dependencies")) {
             JsonObject dep = p.getNpm().getJsonObject("dependencies");
             if (dep.getProperties().isEmpty()) {

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

@@ -19,6 +19,7 @@ import org.hl7.fhir.dstu2.model.StructureDefinition;
 import org.hl7.fhir.dstu2.model.StructureDefinition.StructureDefinitionSnapshotComponent;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.json.JsonTrackingParser;
 import org.xml.sax.SAXException;
 
@@ -66,7 +67,7 @@ public class XVerPackegeFixer {
 
   public static void main(String[] args) throws FileNotFoundException, ParserConfigurationException, SAXException, IOException {
     modCount = 0;
-    for (File f : new File(args[0]).listFiles()) {
+    for (File f : ManagedFileAccess.file(args[0]).listFiles()) {
       if (f.getName().startsWith("xver-") && f.getName().contains("1.0")) {
         JsonObject j = JsonTrackingParser.parseJson(f);
         fixUp(j, f.getName());
@@ -164,7 +165,7 @@ public class XVerPackegeFixer {
     if (map5.containsKey(tn)) {
       sd = map5.get(tn);
     } else {
-      sd = (org.hl7.fhir.r5.model.StructureDefinition) new org.hl7.fhir.r5.formats.JsonParser().parse(new FileInputStream(Utilities.path(R5_FOLDER, "StructureDefinition-"+tn+".json")));
+      sd = (org.hl7.fhir.r5.model.StructureDefinition) new org.hl7.fhir.r5.formats.JsonParser().parse(ManagedFileAccess.inStream(Utilities.path(R5_FOLDER, "StructureDefinition-"+tn+".json")));
       map5.put(tn, sd);
     }
     for (org.hl7.fhir.r5.model.ElementDefinition ed : sd.getSnapshot().getElement()) {
@@ -220,7 +221,7 @@ public class XVerPackegeFixer {
     if (map4.containsKey(tn)) {
       sd = map4.get(tn);
     } else {
-      sd = (org.hl7.fhir.r4.model.StructureDefinition) new org.hl7.fhir.r4.formats.JsonParser().parse(new FileInputStream(Utilities.path(R4_FOLDER, "StructureDefinition-"+tn+".json")));
+      sd = (org.hl7.fhir.r4.model.StructureDefinition) new org.hl7.fhir.r4.formats.JsonParser().parse(ManagedFileAccess.inStream(Utilities.path(R4_FOLDER, "StructureDefinition-"+tn+".json")));
       map4.put(tn, sd);
     }
     for (org.hl7.fhir.r4.model.ElementDefinition ed : sd.getSnapshot().getElement()) {
@@ -277,7 +278,7 @@ public class XVerPackegeFixer {
     if (map3.containsKey(tn)) {
       sd = map3.get(tn);
     } else {
-      sd = (org.hl7.fhir.dstu3.model.StructureDefinition) new org.hl7.fhir.dstu3.formats.JsonParser().parse(new FileInputStream(Utilities.path(R3_FOLDER, "StructureDefinition-"+tn+".json")));
+      sd = (org.hl7.fhir.dstu3.model.StructureDefinition) new org.hl7.fhir.dstu3.formats.JsonParser().parse(ManagedFileAccess.inStream(Utilities.path(R3_FOLDER, "StructureDefinition-"+tn+".json")));
       map3.put(tn, sd);
     }
     for (org.hl7.fhir.dstu3.model.ElementDefinition ed : sd.getSnapshot().getElement()) {
@@ -383,7 +384,7 @@ public class XVerPackegeFixer {
     if (map2.containsKey(tn)) {
       sd = map2.get(tn);
     } else {
-      sd = (org.hl7.fhir.dstu2.model.StructureDefinition) new org.hl7.fhir.dstu2.formats.JsonParser().parse(new FileInputStream(Utilities.path(R2_FOLDER, "StructureDefinition-"+tn+".json")));
+      sd = (org.hl7.fhir.dstu2.model.StructureDefinition) new org.hl7.fhir.dstu2.formats.JsonParser().parse(ManagedFileAccess.inStream(Utilities.path(R2_FOLDER, "StructureDefinition-"+tn+".json")));
       map2.put(tn, sd);
     }
     return sd;
@@ -431,7 +432,7 @@ public class XVerPackegeFixer {
     if (map2b.containsKey(tn)) {
       sd = map2b.get(tn);
     } else {
-      sd = (org.hl7.fhir.dstu2016may.model.StructureDefinition) new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(new FileInputStream(Utilities.path(R2B_FOLDER, "StructureDefinition-"+tn+".json")));
+      sd = (org.hl7.fhir.dstu2016may.model.StructureDefinition) new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(ManagedFileAccess.inStream(Utilities.path(R2B_FOLDER, "StructureDefinition-"+tn+".json")));
       map2b.put(tn, sd);
     }
     for (org.hl7.fhir.dstu2016may.model.ElementDefinition ed : sd.getSnapshot().getElement()) {

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/adl/ADLImporter.java

@@ -46,6 +46,7 @@ import org.hl7.fhir.dstu3.formats.XmlParser;
 import org.hl7.fhir.dstu3.model.ElementDefinition;
 import org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus;
 import org.hl7.fhir.dstu3.model.StructureDefinition;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.w3c.dom.Element;
 
@@ -91,11 +92,11 @@ public class ADLImporter {
     DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
     factory.setNamespaceAware(true);
     DocumentBuilder builder = factory.newDocumentBuilder();
-    adlConfig = builder.parse(new FileInputStream(config)).getDocumentElement();
+    adlConfig = builder.parse(ManagedFileAccess.inStream(config)).getDocumentElement();
 
     // load ADL
     builder = factory.newDocumentBuilder();
-    adl = builder.parse(new FileInputStream(source)).getDocumentElement();
+    adl = builder.parse(ManagedFileAccess.inStream(source)).getDocumentElement();
 
     check("root", adl.getNamespaceURI(), "http://schemas.openehr.org/v1", "Wrong namespace for ADL XML");
     check("root", adl.getNodeName(), "archetype", "Wrong XML for ADL XML");
@@ -150,7 +151,7 @@ public class ADLImporter {
     genElements(sd, root.getName(), root);
 
     // save
-    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), sd);
+    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(dest), sd);
     System.out.println("done. saved as " + dest);
   }
 

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/argonaut/ArgonautConverter.java

@@ -110,6 +110,7 @@ import org.hl7.fhir.dstu3.utils.NarrativeGenerator;
 import org.hl7.fhir.dstu3.utils.ResourceUtilities;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.ZipGenerator;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 import org.hl7.fhir.utilities.xhtml.NodeType;
@@ -178,7 +179,7 @@ public class ArgonautConverter extends ConverterBase {
   }
 
   public void convert(String sourceFolder, Coding clss) throws Exception {
-    File source = new File(sourceFolder);
+    File source = ManagedFileAccess.file(sourceFolder);
     for (String f : source.list()) {
       convert(sourceFolder, f, clss);
     }
@@ -221,13 +222,13 @@ public class ArgonautConverter extends ConverterBase {
   }
 
   private void convert(String sourceFolder, String filename, Coding clss) throws IOException {
-    if (new File(Utilities.path(sourceFolder, filename)).length() == 0)
+    if (ManagedFileAccess.file(Utilities.path(sourceFolder, filename)).length() == 0)
       return;
 
     CDAUtilities cda;
     try {
       System.out.println("Process " + Utilities.path(sourceFolder, filename));
-      cda = new CDAUtilities(new FileInputStream(Utilities.path(sourceFolder, filename)));
+      cda = new CDAUtilities(ManagedFileAccess.inStream(Utilities.path(sourceFolder, filename)));
       zipJ = new ZipGenerator(Utilities.path(destFolder, "json/doc", Utilities.changeFileExt(filename, ".json.zip")));
       zipX = new ZipGenerator(Utilities.path(destFolder, "xml/doc", Utilities.changeFileExt(filename, ".xml.zip")));
       Element doc = cda.getElement();
@@ -1320,7 +1321,7 @@ public class ArgonautConverter extends ConverterBase {
     Binary binary = new Binary();
     binary.setId(context.getBaseId() + "-binary");
     binary.setContentType("application/hl7-v3+xml");
-    binary.setContent(IOUtils.toByteArray(new FileInputStream(Utilities.path(sourceFolder, filename))));
+    binary.setContent(IOUtils.toByteArray(ManagedFileAccess.inStream(Utilities.path(sourceFolder, filename))));
     saveResource(binary);
   }
 

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/iso21090/ISO21090Importer.java

@@ -59,6 +59,7 @@ import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.dstu3.utils.ToolingExtensions;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -125,7 +126,7 @@ public class ISO21090Importer {
       addParentProperties(sd.getSnapshot().getElement(), dt.getName(), dt.getParent(), false, true);
     produceProperties(sd.getSnapshot().getElement(), dt.getName(), dt.getProperties(), false, true);
     ed.getBase().setPath(ed.getPath()).setMin(ed.getMin()).setMax(ed.getMax());
-    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "iso21090\\StructureDefinition-" + dt.getName() + ".xml")), sd);
+    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "iso21090\\StructureDefinition-" + dt.getName() + ".xml")), sd);
   }
 
   private void addParentProperties(List<ElementDefinition> elements, String name, String parent, boolean attrMode, boolean snapshot) throws FHIRFormatError {
@@ -176,7 +177,7 @@ public class ISO21090Importer {
     for (String code : evs.getCodes()) {
       inc.addConcept().setCode(code);
     }
-    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "iso21090\\ValueSet-" + evs.getName() + ".xml")), vs);
+    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "iso21090\\ValueSet-" + evs.getName() + ".xml")), vs);
   }
 
   private void processDataTypes() {
@@ -319,7 +320,7 @@ public class ISO21090Importer {
     DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
     factory.setNamespaceAware(false);
     DocumentBuilder builder = factory.newDocumentBuilder();
-    Document doc = builder.parse(new FileInputStream("C:\\work\\projects\\org.hl7.v3.dt\\iso\\iso-21090-datatypes.xsd"));
+    Document doc = builder.parse(ManagedFileAccess.inStream("C:\\work\\projects\\org.hl7.v3.dt\\iso\\iso-21090-datatypes.xsd"));
     schema = doc.getDocumentElement();
   }
 

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/searchparam/SearchParameterProcessor.java

@@ -49,6 +49,7 @@ import org.hl7.fhir.r5.model.Enumerations.ConceptMapRelationship;
 import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
 import org.hl7.fhir.utilities.CSVReader;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class SearchParameterProcessor {
 
@@ -120,7 +121,7 @@ public class SearchParameterProcessor {
         e.addTarget().setCode(d).setRelationship(ConceptMapRelationship.RELATEDTO);
       }
     }
-    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(ROOT, "ConceptMap-" + map.getId() + ".json")), map);
+    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(ROOT, "ConceptMap-" + map.getId() + ".json")), map);
   }
 
   private SourceElementComponent makeElement(String code, ConceptMapGroupComponent group) {
@@ -208,7 +209,7 @@ public class SearchParameterProcessor {
   }
 
   private void load4() throws FHIRFormatError, IOException {
-    org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) new org.hl7.fhir.r4.formats.JsonParser().parse(new FileInputStream(Utilities.path("[tmp]", "sp4.json")));
+    org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) new org.hl7.fhir.r4.formats.JsonParser().parse(ManagedFileAccess.inStream(Utilities.path("[tmp]", "sp4.json")));
     for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
       org.hl7.fhir.r4.model.SearchParameter sp = (org.hl7.fhir.r4.model.SearchParameter) be.getResource();
       for (org.hl7.fhir.r4.model.CodeType br : sp.getBase()) {
@@ -221,7 +222,7 @@ public class SearchParameterProcessor {
   }
 
   private void load3() throws FHIRFormatError, IOException {
-    org.hl7.fhir.dstu3.model.Bundle bundle = (org.hl7.fhir.dstu3.model.Bundle) new org.hl7.fhir.dstu3.formats.JsonParser().parse(new FileInputStream(Utilities.path("[tmp]", "sp3.json")));
+    org.hl7.fhir.dstu3.model.Bundle bundle = (org.hl7.fhir.dstu3.model.Bundle) new org.hl7.fhir.dstu3.formats.JsonParser().parse(ManagedFileAccess.inStream(Utilities.path("[tmp]", "sp3.json")));
     for (org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
       org.hl7.fhir.dstu3.model.SearchParameter sp = (org.hl7.fhir.dstu3.model.SearchParameter) be.getResource();
       for (org.hl7.fhir.dstu3.model.CodeType br : sp.getBase()) {
@@ -234,7 +235,7 @@ public class SearchParameterProcessor {
   }
 
   private void load2() throws FHIRFormatError, IOException {
-    org.hl7.fhir.dstu2.model.Bundle bundle = (org.hl7.fhir.dstu2.model.Bundle) new org.hl7.fhir.dstu2.formats.JsonParser().parse(new FileInputStream(Utilities.path("[tmp]", "sp2.json")));
+    org.hl7.fhir.dstu2.model.Bundle bundle = (org.hl7.fhir.dstu2.model.Bundle) new org.hl7.fhir.dstu2.formats.JsonParser().parse(ManagedFileAccess.inStream(Utilities.path("[tmp]", "sp2.json")));
     for (org.hl7.fhir.dstu2.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
       org.hl7.fhir.dstu2.model.SearchParameter sp = (org.hl7.fhir.dstu2.model.SearchParameter) be.getResource();
       String br = sp.getBase();
@@ -246,7 +247,7 @@ public class SearchParameterProcessor {
   }
 
   private void load2b() throws FHIRFormatError, IOException {
-    org.hl7.fhir.dstu2016may.model.Bundle bundle = (org.hl7.fhir.dstu2016may.model.Bundle) new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(new FileInputStream(Utilities.path("[tmp]", "sp2b.json")));
+    org.hl7.fhir.dstu2016may.model.Bundle bundle = (org.hl7.fhir.dstu2016may.model.Bundle) new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(ManagedFileAccess.inStream(Utilities.path("[tmp]", "sp2b.json")));
     for (org.hl7.fhir.dstu2016may.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
       org.hl7.fhir.dstu2016may.model.SearchParameter sp = (org.hl7.fhir.dstu2016may.model.SearchParameter) be.getResource();
       String br = sp.getBase();
@@ -258,7 +259,7 @@ public class SearchParameterProcessor {
   }
 
   private void loadCsv() throws IOException, FHIRException {
-    CSVReader csv = new CSVReader(new FileInputStream("C:\\work\\org.hl7.fhir\\org.fhir.interversion\\work\\search-params.csv"));
+    CSVReader csv = new CSVReader(ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\org.fhir.interversion\\work\\search-params.csv"));
     csv.readHeaders();
     while (csv.line()) {
       String r4 = csv.cell("R4");

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/utg/UTGCaseSensitivePopulator.java

@@ -21,11 +21,12 @@ import org.hl7.fhir.r4.model.Provenance;
 import org.hl7.fhir.r4.model.Provenance.ProvenanceAgentComponent;
 import org.hl7.fhir.r4.model.Resource;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class UTGCaseSensitivePopulator {
 
   public static void main(String[] args) throws FileNotFoundException, IOException {
-    new UTGCaseSensitivePopulator().process(new File(args[0]));
+    new UTGCaseSensitivePopulator().process(ManagedFileAccess.file(args[0]));
 
   }
 
@@ -35,7 +36,7 @@ public class UTGCaseSensitivePopulator {
     bundle.setId("hxutg1-1-0-12");
     
     scanFolders(root, bundle);
-    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(root.getAbsolutePath(), "input", "sourceOfTruth", "history", "utgrel1hx-1-0-12.json")), bundle);
+    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(root.getAbsolutePath(), "input", "sourceOfTruth", "history", "utgrel1hx-1-0-12.json")), bundle);
     System.out.println("Done");
   }
 
@@ -60,10 +61,10 @@ public class UTGCaseSensitivePopulator {
 
   private void processFile(File f, Bundle bundle, IParser parser, Date d, Date dt) {
     try {
-      Resource r = parser.parse(new FileInputStream(f));
+      Resource r = parser.parse(ManagedFileAccess.inStream(f));
       if (r instanceof CodeSystem) {
         if (processCodeSystem((CodeSystem) r, bundle, d, dt)) {
-          parser.setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
+          parser.setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), r);
         }
       }
     } catch (Exception e) {

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/utg/UTGVersionSorter.java

@@ -29,6 +29,7 @@ import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.r5.model.ValueSet;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
 import org.hl7.fhir.utilities.npm.NpmPackage;
 import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
@@ -47,7 +48,7 @@ public class UTGVersionSorter {
   private void execute(String source) throws IOException {
     List<CanonicalResourceAnalysis> list = new ArrayList<>();
     System.out.println("Loading UTG");
-    loadFromSource(list, new File(source));
+    loadFromSource(list, ManagedFileAccess.file(source));
 
     Map<String, CanonicalResource> r2 = loadPackageR2("hl7.fhir.r2.core");
     Map<String, CanonicalResource> r3 = loadPackageR3("hl7.fhir.r3.core");
@@ -58,7 +59,7 @@ public class UTGVersionSorter {
       cr.analyse(r2, r3, r4);
     }
 
-    Bundle b = (Bundle) new JsonParser().parse(new FileInputStream("C:\\work\\org.hl7.fhir.igs\\UTG\\input\\sourceOfTruth\\history\\utgrel1hx-1-0-6.json"));
+    Bundle b = (Bundle) new JsonParser().parse(ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir.igs\\UTG\\input\\sourceOfTruth\\history\\utgrel1hx-1-0-6.json"));
 
     System.out.println("Summary");
     for (CanonicalResourceAnalysis cr : list) {
@@ -79,10 +80,10 @@ public class UTGVersionSorter {
       pa.getWho().setDisplay("Vocabulary WG");
       CanonicalResource res = cr.resource;
       res.setVersion(cr.recommendation);
-      new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(cr.filename), res);
+      new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(cr.filename), res);
     }
     System.out.println();
-    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream("C:\\work\\org.hl7.fhir.igs\\UTG\\input\\sourceOfTruth\\history\\utgrel1hx-1-0-6.json"), b);
+    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream("C:\\work\\org.hl7.fhir.igs\\UTG\\input\\sourceOfTruth\\history\\utgrel1hx-1-0-6.json"), b);
     System.out.println("Done");
   }
 
@@ -134,7 +135,7 @@ public class UTGVersionSorter {
         loadFromSource(list, f);
       } else if (f.getName().endsWith(".xml")) {
         try {
-          Resource r = new XmlParser().parse(new FileInputStream(f));
+          Resource r = new XmlParser().parse(ManagedFileAccess.inStream(f));
           if (r instanceof CanonicalResource) {
             CanonicalResource cr = (CanonicalResource) r;
             cr.setWebPath(f.getAbsolutePath());

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/xver/CorePackageVersionConvertor.java

@@ -15,6 +15,7 @@ import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_50;
 import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.json.model.JsonArray;
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.json.parser.JsonParser;
@@ -479,7 +480,7 @@ public class CorePackageVersionConvertor {
     // build a new package
     System.out.println("Convert "+packageSource+" to "+versionTarget);
     
-    NpmPackage src = NpmPackage.fromPackage(new FileInputStream(packageSource));
+    NpmPackage src = NpmPackage.fromPackage(ManagedFileAccess.inStream(packageSource));
     IContentConvertor conv = contentConvertorFactory(src.fhirVersion(), versionTarget);
     
     NpmPackage dst = NpmPackage.empty();
@@ -510,7 +511,7 @@ public class CorePackageVersionConvertor {
         }
       }
     }
-    dst.save(new FileOutputStream(Utilities.changeFileExt(packageSource, ".as."+VersionUtilities.getNameForVersion(versionTarget).toLowerCase()+".tgz")));
+    dst.save(ManagedFileAccess.outStream(Utilities.changeFileExt(packageSource, ".as."+VersionUtilities.getNameForVersion(versionTarget).toLowerCase()+".tgz")));
   }
 
   private IContentConvertor contentConvertorFactory(String fhirVersion, String versionTarget) throws Exception {

org.hl7.fhir.core.generator/configuration/tests/RoundTripTests.java

@@ -33,7 +33,7 @@ public class RoundTripTests {
 
   @Parameters(name = "{index}: file {0}")
   public static Iterable<Object[]> data() throws ParserConfigurationException, SAXException, IOException {
-    File dir = new File(EXAMPLES_DIR);
+    File dir = ManagedFileAccess.file(EXAMPLES_DIR);
 
     String[] list = dir.list();
     List<Object[]> objects = new ArrayList<Object[]>(list.length);
@@ -77,7 +77,7 @@ public class RoundTripTests {
   }
 
   private void save(byte[] src, String path) throws IOException {
-    File f = new File(path);
+    File f = ManagedFileAccess.file(path);
     if (f.exists()) {
       f.delete();
     }

org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/codegen/Configuration.java

@@ -23,7 +23,7 @@ public class Configuration {
   public Configuration(String path) throws FileNotFoundException, IOException {
     license = TextFile.fileToString(Utilities.path(path, "license.txt"));
     ini = new IniFile(Utilities.path(path, "configuration.ini"));
-    for (File jfn : new File(path).listFiles()) {
+    for (File jfn : ManagedFileAccess.file(path).listFiles()) {
       if (jfn.getName().endsWith(".java")) {
         adornments.put(Utilities.changeFileExt(jfn.getName(), ""), TextFile.fileToString(jfn));
       }

org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/codegen/JavaResourceGenerator.java

@@ -483,7 +483,7 @@ public class JavaResourceGenerator extends JavaBaseGenerator {
 ////    write("  }\r\n"); 
 ////
 ////    // now, generate the implementation
-////    JavaPatternImplGenerator jrg = new JavaPatternImplGenerator(new FileOutputStream(javaPatternDir+jn+namenn+"Impl.java"), definitions, adornments, enumInfo);
+////    JavaPatternImplGenerator jrg = new JavaPatternImplGenerator(ManagedFileAccess.outStream(javaPatternDir+jn+namenn+"Impl.java"), definitions, adornments, enumInfo);
 ////    jrg.generate(resourceDefn.getRoot(), jn, JavaGenClass.Resource, null, genDate, version, false, null, null, namenn, root);
 ////    jrg.close();
 ////

org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/codegen/extensions/JavaExtensionsGenerator.java

@@ -58,9 +58,9 @@ public class JavaExtensionsGenerator {
       }
     }    
 
-    JavaExtensionsFactoryGenerator gen = new JavaExtensionsFactoryGenerator(new FileOutputStream(Utilities.path(path, "Extensions.java")), master, config, version, date, jid, elementInfo, genClassList);
+    JavaExtensionsFactoryGenerator gen = new JavaExtensionsFactoryGenerator(ManagedFileAccess.outStream(Utilities.path(path, "Extensions.java")), master, config, version, date, jid, elementInfo, genClassList);
     gen.start();
-    JavaConstantsGenerator cgen = new JavaConstantsGenerator(new FileOutputStream(Utilities.path(path, "ExtensionConstants.java")), master, config, version, date, jid);
+    JavaConstantsGenerator cgen = new JavaConstantsGenerator(ManagedFileAccess.outStream(Utilities.path(path, "ExtensionConstants.java")), master, config, version, date, jid);
     cgen.start();
     for (String url : urls) {
       StructureDefinition sd = extensions.get(url);

org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/engine/JavaCoreGenerator.java

@@ -89,19 +89,19 @@ public class JavaCoreGenerator {
     
     System.out.println("Generate Model in "+dest);   
     System.out.println(" .. Constants");
-    JavaConstantsGenerator cgen = new JavaConstantsGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "Constants.java")), master, config, date, npm.version(), jid);
+    JavaConstantsGenerator cgen = new JavaConstantsGenerator(ManagedFileAccess.outStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "Constants.java")), master, config, date, npm.version(), jid);
     cgen.generate();
     cgen.close();
     System.out.println(" .. Enumerations");
-    JavaEnumerationsGenerator egen = new JavaEnumerationsGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "Enumerations.java")), master, config, date, npm.version(), jid);
+    JavaEnumerationsGenerator egen = new JavaEnumerationsGenerator(ManagedFileAccess.outStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "Enumerations.java")), master, config, date, npm.version(), jid);
     egen.generate();
     egen.close();
     
-    JavaFactoryGenerator fgen = new JavaFactoryGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "ResourceFactory.java")), master, config, date, npm.version(), jid);
+    JavaFactoryGenerator fgen = new JavaFactoryGenerator(ManagedFileAccess.outStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "ResourceFactory.java")), master, config, date, npm.version(), jid);
-    JavaTypeGenerator tgen = new JavaTypeGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "ResourceType.java")), master, config, date, npm.version(), jid);
+    JavaTypeGenerator tgen = new JavaTypeGenerator(ManagedFileAccess.outStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "ResourceType.java")), master, config, date, npm.version(), jid);
-    JavaParserJsonGenerator jgen = new JavaParserJsonGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "formats", "JsonParser.java")), master, config, date, npm.version(), jid);
+    JavaParserJsonGenerator jgen = new JavaParserJsonGenerator(ManagedFileAccess.outStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "formats", "JsonParser.java")), master, config, date, npm.version(), jid);
-    JavaParserXmlGenerator xgen = new JavaParserXmlGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "formats", "XmlParser.java")), master, config, date, npm.version(), jid);
+    JavaParserXmlGenerator xgen = new JavaParserXmlGenerator(ManagedFileAccess.outStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "formats", "XmlParser.java")), master, config, date, npm.version(), jid);
-    JavaParserRdfGenerator rgen = new JavaParserRdfGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "formats", "RdfParser.java")), master, config, date, npm.version(), jid);
+    JavaParserRdfGenerator rgen = new JavaParserRdfGenerator(ManagedFileAccess.outStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "formats", "RdfParser.java")), master, config, date, npm.version(), jid);
     
     if (VersionUtilities.isR4BVer(version)) {
       StructureDefinition sd = master.getStructures().get("http://hl7.org/fhir/StructureDefinition/Element");
@@ -206,7 +206,7 @@ public class JavaCoreGenerator {
     Analysis analysis = jca.analyse(sd, elementInfo);
     
     String fn = Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", name+".java");
-    JavaResourceGenerator gen = new JavaResourceGenerator(new FileOutputStream(fn), master, config, date, npm.version(), jid);
+    JavaResourceGenerator gen = new JavaResourceGenerator(ManagedFileAccess.outStream(fn), master, config, date, npm.version(), jid);
     gen.generate(analysis); 
     gen.close();
     jgen.seeClass(analysis);

org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/terminologies/LoincToDEConvertor.java

@@ -54,6 +54,7 @@ import org.hl7.fhir.dstu2.model.Meta;
 import org.hl7.fhir.dstu2.utils.ToolingExtensions;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -165,12 +166,12 @@ public class LoincToDEConvertor {
     factory.setNamespaceAware(true);
     DocumentBuilder builder = factory.newDocumentBuilder();
 
-    xml = builder.parse(new FileInputStream(definitions));
+    xml = builder.parse(ManagedFileAccess.inStream(definitions));
   }
 
   private void saveBundle() throws FHIRFormatError, IOException, XmlPullParserException {
     XmlParser xml = new XmlParser();
-    FileOutputStream s = new FileOutputStream(dest);
+    FileOutputStream s = ManagedFileAccess.outStream(dest);
     xml.compose(s, bundle, true);
     s.close();
   }

org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/terminologies/ValueSetExpansionCache.java

@@ -75,6 +75,7 @@ import org.hl7.fhir.dstu2.utils.IWorkerContext;
 import org.hl7.fhir.dstu2.utils.ToolingExtensions;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
 
 public class ValueSetExpansionCache implements ValueSetExpanderFactory {
@@ -91,7 +92,7 @@ public class ValueSetExpansionCache implements ValueSetExpanderFactory {
         // well, we'll see if the designated server can expand it, and if it can, we'll
         // cache it locally
         vso = context.expandVS(source, false);
-        FileOutputStream s = new FileOutputStream(Utilities.path(cacheFolder, makeFile(source.getUrl())));
+        FileOutputStream s = ManagedFileAccess.outStream(Utilities.path(cacheFolder, makeFile(source.getUrl())));
         context.newXmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, vso.getValueset());
         s.close();
       }
@@ -125,10 +126,10 @@ public class ValueSetExpansionCache implements ValueSetExpanderFactory {
   }
 
   private void loadCache() throws FHIRFormatError, IOException {
-    File[] files = new File(cacheFolder).listFiles();
+    File[] files = ManagedFileAccess.file(cacheFolder).listFiles();
     for (File f : files) {
       if (f.getName().endsWith(".xml")) {
-        final FileInputStream is = new FileInputStream(f);
+        final FileInputStream is = ManagedFileAccess.inStream(f);
         try {
           Resource r = context.newXmlParser().setOutputStyle(OutputStyle.PRETTY).parse(is);
           if (r instanceof OperationOutcome) {

org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/BatchLoader.java

@@ -47,6 +47,7 @@ import org.hl7.fhir.dstu2.model.Resource;
 import org.hl7.fhir.dstu2.utils.client.FHIRToolingClient;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class BatchLoader {
 
@@ -66,7 +67,7 @@ public class BatchLoader {
         throw new FHIRException("Unimplemented file type " + file);
       } else if (file.endsWith(".zip")) {
         LoadZipFile(server, file, p, size, 0, -1);
-      } else if (new File(file).isDirectory()) {
+      } else if (ManagedFileAccess.file(file).isDirectory()) {
         LoadDirectory(server, file, p, size);
       } else
         throw new FHIRException("Unknown file type " + file);
@@ -99,7 +100,7 @@ public class BatchLoader {
     Bundle b = new Bundle();
     b.setType(BundleType.COLLECTION);
     b.setId(UUID.randomUUID().toString().toLowerCase());
-    ZipInputStream zip = new ZipInputStream(new FileInputStream(file));
+    ZipInputStream zip = new ZipInputStream(ManagedFileAccess.inStream(file));
     ZipEntry entry;
     while ((entry = zip.getNextEntry()) != null) {
       try {

org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/SimpleWorkerContext.java

@@ -60,8 +60,8 @@ import org.hl7.fhir.dstu2.utils.client.FHIRToolingClient;
 import org.hl7.fhir.dstu2.utils.validation.IResourceValidator;
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
-import org.hl7.fhir.utilities.CSFileInputStream;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.CSFileInputStream;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 

org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/Translations.java

@@ -38,7 +38,7 @@ import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 
-import org.hl7.fhir.utilities.CSFileInputStream;
+import org.hl7.fhir.utilities.filesystem.CSFileInputStream;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;

org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/Unbundler.java

@@ -42,6 +42,7 @@ import org.hl7.fhir.dstu2.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.dstu2.model.Resource;
 import org.hl7.fhir.dstu2.model.ValueSet;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class Unbundler {
 
@@ -51,7 +52,7 @@ public class Unbundler {
 
   private static void unbundle(String src) throws FHIRFormatError, FileNotFoundException, IOException {
     String folder = Utilities.getDirectoryForFile(src);
-    Bundle bnd = (Bundle) new JsonParser().parse(new FileInputStream(src));
+    Bundle bnd = (Bundle) new JsonParser().parse(ManagedFileAccess.inStream(src));
     for (BundleEntryComponent be : bnd.getEntry()) {
       Resource r = be.getResource();
       if (r != null) {
@@ -61,7 +62,7 @@ public class Unbundler {
         }
         if (!StringUtils.isBlank(r.getId())) {
           String tgt = Utilities.path(folder, r.fhirType() + "-" + r.getId() + ".json");
-          new JsonParser().compose(new FileOutputStream(tgt), r);
+          new JsonParser().compose(ManagedFileAccess.outStream(tgt), r);
         }
       }
     }

org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/FluentPathTests.java

@@ -7,6 +7,7 @@ import org.hl7.fhir.dstu2.utils.FHIRPathEngine;
 import org.hl7.fhir.dstu2.utils.SimpleWorkerContext;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.junit.jupiter.api.*;
 import org.junit.jupiter.params.ParameterizedTest;
@@ -55,7 +56,7 @@ public class FluentPathTests {
         fp.check(null, null, null, node);
       else {
         res = new XmlParser()
-            .parse(new FileInputStream(Utilities.path("C:\\work\\org.hl7.fhir.dstu2\\build\\publish", input)));
+            .parse(ManagedFileAccess.inStream(Utilities.path("C:\\work\\org.hl7.fhir.dstu2\\build\\publish", input)));
         fp.check(res, res.getResourceType().toString(), res.getResourceType().toString(), node);
       }
       outcome = fp.evaluate(res, node);

org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/NarrativeGeneratorTests.java

@@ -11,6 +11,7 @@ import org.hl7.fhir.dstu2.utils.NarrativeGenerator;
 import org.hl7.fhir.dstu2.utils.SimpleWorkerContext;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
@@ -40,9 +41,9 @@ public class NarrativeGeneratorTests {
 
   private void process(String path) throws IOException, EOperationOutcome, FHIRException {
     XmlParser p = new XmlParser();
-    DomainResource r = (DomainResource) p.parse(new FileInputStream(path));
+    DomainResource r = (DomainResource) p.parse(ManagedFileAccess.inStream(path));
     gen.generate(r);
-    FileOutputStream s = new FileOutputStream(Utilities.path("[tmp]", "gen.xml"));
+    FileOutputStream s = ManagedFileAccess.outStream(Utilities.path("[tmp]", "gen.xml"));
     new XmlParser().compose(s, r, true);
     s.close();
   }

org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/ProfileUtilitiesTests.java

@@ -24,8 +24,9 @@ import org.hl7.fhir.dstu2.utils.SimpleWorkerContext;
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
-import org.hl7.fhir.utilities.CSFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.CSFile;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 
@@ -85,11 +86,11 @@ public class ProfileUtilitiesTests {
     for (ProfileComparison outcome : comp.getComparisons()) {
       if (outcome.getSubset() != null)
         new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(
-            new FileOutputStream(Utilities.path("[tmp]", "intersection-" + outcome.getId() + ".xml")),
+            ManagedFileAccess.outStream(Utilities.path("[tmp]", "intersection-" + outcome.getId() + ".xml")),
             outcome.getSubset());
       if (outcome.getSuperset() != null)
         new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(
-            new FileOutputStream(Utilities.path("[tmp]", "union-" + outcome.getId() + ".xml")), outcome.getSuperset());
+            ManagedFileAccess.outStream(Utilities.path("[tmp]", "union-" + outcome.getId() + ".xml")), outcome.getSuperset());
 
       System.out.println("\r\n" + outcome.getId() + ": Comparison of " + outcome.getLeft().getUrl() + " and "
           + outcome.getRight().getUrl());
@@ -115,9 +116,9 @@ public class ProfileUtilitiesTests {
     System.out.println("Compare " + fn1 + " to " + fn2);
     System.out.println("  .. load");
     StructureDefinition left = (StructureDefinition) new XmlParser()
-        .parse(new FileInputStream(Utilities.path(root, fn1)));
+        .parse(ManagedFileAccess.inStream(Utilities.path(root, fn1)));
     StructureDefinition right = (StructureDefinition) new XmlParser()
-        .parse(new FileInputStream(Utilities.path(root, fn2)));
+        .parse(ManagedFileAccess.inStream(Utilities.path(root, fn2)));
     System.out.println(" .. compare");
     comp.compareProfiles(left, right);
 
@@ -918,16 +919,16 @@ public class ProfileUtilitiesTests {
 //    focus.setDifferential(null);
     String f1 = Utilities.path("c:", "temp", "base.xml");
     String f2 = Utilities.path("c:", "temp", "derived.xml");
-    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f1), base);
+    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f1), base);
     ;
-    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f2), focus);
+    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f2), focus);
     ;
     String diff = Utilities.path(System.getenv("ProgramFiles(X86)"), "WinMerge", "WinMergeU.exe");
     List<String> command = new ArrayList<String>();
     command.add("\"" + diff + "\" \"" + f1 + "\" \"" + f2 + "\"");
 
     ProcessBuilder builder = new ProcessBuilder(command);
-    builder.directory(new CSFile(Utilities.path("[tmp]")));
+    builder.directory(ManagedFileAccess.csfile(Utilities.path("[tmp]")));
     builder.start();
 
   }

org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/QuestionnaireBuilderTester.java

@@ -2,27 +2,29 @@ package org.hl7.fhir.dstu2.test;
 
 import java.io.File;
 import java.io.FileInputStream;
+import java.io.IOException;
 
 import org.hl7.fhir.dstu2.formats.XmlParser;
 import org.hl7.fhir.dstu2.model.StructureDefinition;
 import org.hl7.fhir.dstu2.utils.QuestionnaireBuilder;
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class QuestionnaireBuilderTester {
 
   private static final String TEST_PROFILE_DIR = "C:\\work\\org.hl7.fhir\\build\\publish";
 //	private static final String TEST_DEST = Utilities.path("[tmp]", "questionnaires\\");
 
-  public static void main(String[] args) {
+  public static void main(String[] args) throws IOException {
     QuestionnaireBuilder b = new QuestionnaireBuilder(null);
-    for (String f : new File(TEST_PROFILE_DIR).list()) {
+    for (String f : ManagedFileAccess.file(TEST_PROFILE_DIR).list()) {
       if (f.endsWith(".profile.xml") && !f.contains("type-")) {
         System.out.println("process " + f);
         try {
           StructureDefinition p = (StructureDefinition) new XmlParser()
-              .parse(new FileInputStream(TEST_PROFILE_DIR + "\\" + f));
+              .parse(ManagedFileAccess.inStream(TEST_PROFILE_DIR + "\\" + f));
 //					Questionnaire q = b.buildQuestionnaire(p);
-//					new XmlComposer().compose(new FileOutputStream(TEST_DEST+f), q, true);
+//					new XmlComposer().compose(ManagedFileAccess.outStream(TEST_DEST+f), q, true);
           throw new FHIRException("test");
         } catch (Exception e) {
           e.printStackTrace();

org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/ResourceTest.java

@@ -40,6 +40,7 @@ import org.hl7.fhir.dstu2.formats.JsonParser;
 import org.hl7.fhir.dstu2.formats.XmlParser;
 import org.hl7.fhir.dstu2.model.Resource;
 import org.hl7.fhir.exceptions.FHIRFormatError;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class ResourceTest {
 
@@ -61,18 +62,18 @@ public class ResourceTest {
       p = new JsonParser();
     else
       p = new XmlParser(false);
-    Resource rf = p.parse(new FileInputStream(source));
+    Resource rf = p.parse(ManagedFileAccess.inStream(source));
 
-    FileOutputStream out = new FileOutputStream(source.getAbsoluteFile() + ".out.json");
+    FileOutputStream out = ManagedFileAccess.outStream(source.getAbsoluteFile() + ".out.json");
     JsonParser json1 = new JsonParser();
     json1.setOutputStyle(OutputStyle.PRETTY);
     json1.compose(out, rf);
     out.close();
 
     JsonParser json = new JsonParser();
-    rf = json.parse(new FileInputStream(source.getAbsoluteFile() + ".out.json"));
+    rf = json.parse(ManagedFileAccess.inStream(source.getAbsoluteFile() + ".out.json"));
 
-    out = new FileOutputStream(source.getAbsoluteFile() + ".out.xml");
+    out = ManagedFileAccess.outStream(source.getAbsoluteFile() + ".out.xml");
     XmlParser atom = new XmlParser();
     atom.setOutputStyle(OutputStyle.PRETTY);
     atom.compose(out, rf, true);

org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/SingleTest.java

@@ -30,6 +30,8 @@ package org.hl7.fhir.dstu2.test;
 
 import java.io.File;
 
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
+
 public class SingleTest {
 
   /**
@@ -38,7 +40,7 @@ public class SingleTest {
   public static void main(String[] args) {
     try {
       ResourceTest r = new ResourceTest();
-      r.setSource(new File("C:\\work\\org.hl7.fhir\\build\\publish\\patient-example.xml"));
+      r.setSource(ManagedFileAccess.file("C:\\work\\org.hl7.fhir\\build\\publish\\patient-example.xml"));
       r.test();
       System.out.println("Completed OK");
     } catch (Exception e) {

org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/TestingUtilities.java

@@ -13,9 +13,10 @@ import javax.xml.parsers.DocumentBuilderFactory;
 
 import org.apache.commons.codec.binary.Base64;
 import org.hl7.fhir.dstu2.utils.IWorkerContext;
-import org.hl7.fhir.utilities.CSFile;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.CSFile;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 import org.w3c.dom.NamedNodeMap;
@@ -41,7 +42,7 @@ public class TestingUtilities {
       command.add("\"" + diff + "\" \"" + f1 + "\" \"" + f2 + "\"");
 
       ProcessBuilder builder = new ProcessBuilder(command);
-      builder.directory(new CSFile(Utilities.path("[tmp]")));
+      builder.directory(ManagedFileAccess.csfile(Utilities.path("[tmp]")));
       builder.start();
 
     }
@@ -154,7 +155,7 @@ public class TestingUtilities {
 
     factory.setNamespaceAware(true);
     DocumentBuilder builder = factory.newDocumentBuilder();
-    return builder.parse(new FileInputStream(fn));
+    return builder.parse(ManagedFileAccess.inStream(fn));
   }
 
   public static String checkJsonIsSame(String f1, String f2)
@@ -166,7 +167,7 @@ public class TestingUtilities {
       command.add("\"" + diff + "\" \"" + f1 + "\" \"" + f2 + "\"");
 
       ProcessBuilder builder = new ProcessBuilder(command);
-      builder.directory(new CSFile(Utilities.path("[tmp]")));
+      builder.directory(ManagedFileAccess.csfile(Utilities.path("[tmp]")));
       builder.start();
 
     }

org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/ToolsHelper.java

@@ -55,10 +55,11 @@ import org.hl7.fhir.dstu2.model.Resource;
 import org.hl7.fhir.dstu2.utils.SimpleWorkerContext;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
-import org.hl7.fhir.utilities.CSFile;
-import org.hl7.fhir.utilities.CSFileInputStream;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.CSFile;
+import org.hl7.fhir.utilities.filesystem.CSFileInputStream;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.xmlpull.v1.XmlPullParser;
 import org.xmlpull.v1.XmlPullParserException;
 import org.xmlpull.v1.XmlPullParserFactory;
@@ -103,7 +104,7 @@ public class ToolsHelper {
   private void executeExamples(String[] args) throws IOException {
     try {
       @SuppressWarnings("unchecked")
-      List<String> lines = FileUtils.readLines(new File(args[1]), "UTF-8");
+      List<String> lines = FileUtils.readLines(ManagedFileAccess.file(args[1]), "UTF-8");
       String srcDir = lines.get(0);
       lines.remove(0);
       processExamples(srcDir, lines);
@@ -179,7 +180,7 @@ public class ToolsHelper {
 //    } else 
     if (definitions.startsWith("https:") || definitions.startsWith("http:")) {
       defn = loadFromUrl(definitions);
-    } else if (new File(definitions).exists()) {
+    } else if (ManagedFileAccess.file(definitions).exists()) {
       defn = loadFromFile(definitions);
     } else
       throw new FHIRException("Unable to find FHIR validation Pack (source = " + definitions + ")");
@@ -193,7 +194,7 @@ public class ToolsHelper {
   }
 
   private byte[] loadFromFile(String src) throws IOException {
-    FileInputStream in = new FileInputStream(src);
+    FileInputStream in = ManagedFileAccess.inStream(src);
     byte[] b = new byte[in.available()];
     in.read(b);
     in.close();
@@ -220,10 +221,10 @@ public class ToolsHelper {
 
   public void executeFragments(String[] args) throws IOException {
     try {
-      File source = new CSFile(args[1]);
+      File source = ManagedFileAccess.csfile(args[1]);
       if (!source.exists())
         throw new FHIRException("Source File \"" + source.getAbsolutePath() + "\" not found");
-      XmlPullParser xpp = loadXml(new FileInputStream(source));
+      XmlPullParser xpp = loadXml(ManagedFileAccess.inStream(source));
       nextNoWhitespace(xpp);
       if (!xpp.getName().equals("tests"))
         throw new FHIRFormatError("Unable to parse file - starts with " + xpp.getName());
@@ -269,8 +270,8 @@ public class ToolsHelper {
 
   public void executeRoundTrip(String[] args) throws IOException, FHIRException {
     FileInputStream in;
-    File source = new CSFile(args[1]);
+    File source = ManagedFileAccess.csfile(args[1]);
-    File dest = new CSFile(args[2]);
+    File dest = ManagedFileAccess.csfile(args[2]);
     if (args.length >= 4) {
       Utilities.copyFile(args[1], args[3]);
     }
@@ -288,17 +289,17 @@ public class ToolsHelper {
     json.close();
     TextFile.stringToFile(new String(json.toByteArray()), Utilities.changeFileExt(dest.getAbsolutePath(), ".json"));
     rf = pj.parse(new ByteArrayInputStream(json.toByteArray()));
-    FileOutputStream s = new FileOutputStream(dest);
+    FileOutputStream s = ManagedFileAccess.outStream(dest);
     new XmlParser().compose(s, rf, true);
     s.close();
   }
 
   public String executeJson(String[] args) throws IOException, FHIRException {
     FileInputStream in;
-    File source = new CSFile(args[1]);
+    File source = ManagedFileAccess.csfile(args[1]);
-    File dest = new CSFile(args[2]);
+    File dest = ManagedFileAccess.csfile(args[2]);
-    File destc = new CSFile(Utilities.changeFileExt(args[2], ".canonical.json"));
+    File destc = ManagedFileAccess.csfile(Utilities.changeFileExt(args[2], ".canonical.json"));
-    File destt = new CSFile(args[2] + ".tmp");
+    File destt = ManagedFileAccess.csfile(args[2] + ".tmp");
 
     if (!source.exists())
       throw new FHIRException("Source File \"" + source.getAbsolutePath() + "\" not found");
@@ -307,16 +308,16 @@ public class ToolsHelper {
     Resource rf = p.parse(in);
     JsonParser json = new JsonParser();
     json.setOutputStyle(OutputStyle.PRETTY);
-    FileOutputStream s = new FileOutputStream(dest);
+    FileOutputStream s = ManagedFileAccess.outStream(dest);
     json.compose(s, rf);
     s.close();
     json.setOutputStyle(OutputStyle.CANONICAL);
-    s = new FileOutputStream(destc);
+    s = ManagedFileAccess.outStream(destc);
     json.compose(s, rf);
     s.close();
     json.setSuppressXhtml("Snipped for Brevity");
     json.setOutputStyle(OutputStyle.PRETTY);
-    s = new FileOutputStream(destt);
+    s = ManagedFileAccess.outStream(destt);
     json.compose(s, rf);
     s.close();
     return TextFile.fileToString(destt.getAbsolutePath());
@@ -324,8 +325,8 @@ public class ToolsHelper {
 
   public void executeCanonicalXml(String[] args) throws FHIRException, IOException {
     FileInputStream in;
-    File source = new CSFile(args[1]);
+    File source = ManagedFileAccess.csfile(args[1]);
-    File dest = new CSFile(args[2]);
+    File dest = ManagedFileAccess.csfile(args[2]);
 
     if (!source.exists())
       throw new FHIRException("Source File \"" + source.getAbsolutePath() + "\" not found");
@@ -334,7 +335,7 @@ public class ToolsHelper {
     Resource rf = p.parse(in);
     XmlParser cxml = new XmlParser();
     cxml.setOutputStyle(OutputStyle.NORMAL);
-    cxml.compose(new FileOutputStream(dest), rf);
+    cxml.compose(ManagedFileAccess.outStream(dest), rf);
   }
 
   private void executeVersion(String[] args) throws IOException {
@@ -347,7 +348,7 @@ public class ToolsHelper {
         String filename = rootDir + n + ".xml";
         // 1. produce canonical XML
         CSFileInputStream source = new CSFileInputStream(filename);
-        FileOutputStream dest = new FileOutputStream(Utilities.changeFileExt(filename, ".canonical.xml"));
+        FileOutputStream dest = ManagedFileAccess.outStream(Utilities.changeFileExt(filename, ".canonical.xml"));
         XmlParser p = new XmlParser();
         Resource r = p.parse(source);
         XmlParser cxml = new XmlParser();
@@ -356,14 +357,14 @@ public class ToolsHelper {
 
         // 2. produce JSON
         source = new CSFileInputStream(filename);
-        dest = new FileOutputStream(Utilities.changeFileExt(filename, ".json"));
+        dest = ManagedFileAccess.outStream(Utilities.changeFileExt(filename, ".json"));
         r = p.parse(source);
         JsonParser json = new JsonParser();
         json.setOutputStyle(OutputStyle.PRETTY);
         json.compose(dest, r);
         json = new JsonParser();
         json.setOutputStyle(OutputStyle.CANONICAL);
-        dest = new FileOutputStream(Utilities.changeFileExt(filename, ".canonical.json"));
+        dest = ManagedFileAccess.outStream(Utilities.changeFileExt(filename, ".canonical.json"));
         json.compose(dest, r);
       } catch (Exception e) {
         e.printStackTrace();
@@ -383,23 +384,23 @@ public class ToolsHelper {
         String tmp = tmpDir + n.replace(File.separator, "-") + ".tmp";
         String dest = tmpDir + n.replace(File.separator, "-") + ".java.xml";
 
-        FileInputStream in = new FileInputStream(source);
+        FileInputStream in = ManagedFileAccess.inStream(source);
         XmlParser xp = new XmlParser();
         Resource r = xp.parse(in);
         System.err.print(".");
         JsonParser jp = new JsonParser();
-        FileOutputStream out = new FileOutputStream(tmp);
+        FileOutputStream out = ManagedFileAccess.outStream(tmp);
         jp.setOutputStyle(OutputStyle.PRETTY);
         jp.compose(out, r);
         out.close();
         r = null;
         System.err.print(".");
 
-        in = new FileInputStream(tmp);
+        in = ManagedFileAccess.inStream(tmp);
         System.err.print(",");
         r = jp.parse(in);
         System.err.print(".");
-        out = new FileOutputStream(dest);
+        out = ManagedFileAccess.outStream(dest);
         new XmlParser().compose(out, r, true);
         System.err.println("!");
         out.close();
@@ -415,7 +416,7 @@ public class ToolsHelper {
   private void executeTest(String[] args) throws Throwable {
     try {
       @SuppressWarnings("unchecked")
-      List<String> lines = FileUtils.readLines(new File(args[1]), "UTF-8");
+      List<String> lines = FileUtils.readLines(ManagedFileAccess.file(args[1]), "UTF-8");
       String srcDir = lines.get(0);
       lines.remove(0);
       String dstDir = lines.get(0).trim();

org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/metamodel/Tester.java

@@ -40,6 +40,7 @@ import org.hl7.fhir.dstu2016may.utils.IWorkerContext;
 import org.hl7.fhir.dstu2016may.utils.SimpleWorkerContext;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 import com.google.gson.JsonArray;
 import com.google.gson.JsonElement;
@@ -52,21 +53,21 @@ public class Tester {
         .fromPack(Utilities.path("C:\\work\\org.hl7.fhir\\build\\publish", "validation-min.xml.zip"));
     int t = 0;
     int ok = 0;
-    for (String f : new File("C:\\work\\org.hl7.fhir\\build\\publish").list()) {
+    for (String f : ManagedFileAccess.file("C:\\work\\org.hl7.fhir\\build\\publish").list()) {
       if (f.endsWith(".xml") && !f.endsWith(".canonical.xml") && !f.contains("profile") && !f.contains("questionnaire")
-          && new File("C:\\work\\org.hl7.fhir\\build\\publish\\" + Utilities.changeFileExt(f, ".ttl")).exists()) {
+          && ManagedFileAccess.file("C:\\work\\org.hl7.fhir\\build\\publish\\" + Utilities.changeFileExt(f, ".ttl")).exists()) {
 //				if (f.equals("account-questionnaire.xml")) {
         System.out.print("convert " + f);
-//				Manager.convert(context, new FileInputStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+f), FhirFormat.XML, 
+//				Manager.convert(context, ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+f), FhirFormat.XML, 
-//						new FileOutputStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.json")), FhirFormat.JSON, OutputStyle.PRETTY);
+//						ManagedFileAccess.outStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.json")), FhirFormat.JSON, OutputStyle.PRETTY);
 //				String src = normalise(TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.json")));
 //				String tgt = normalise(TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".json")));
-        Element e = Manager.parse(context, new FileInputStream("C:\\work\\org.hl7.fhir\\build\\publish\\" + f),
+        Element e = Manager.parse(context, ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\build\\publish\\" + f),
             FhirFormat.XML);
         Manager.compose(context, e,
-            new FileOutputStream("C:\\work\\org.hl7.fhir\\build\\publish\\" + Utilities.changeFileExt(f, ".mm.ttl")),
+            ManagedFileAccess.outStream("C:\\work\\org.hl7.fhir\\build\\publish\\" + Utilities.changeFileExt(f, ".mm.ttl")),
             FhirFormat.TURTLE, OutputStyle.PRETTY, null);
-        Manager.compose(context, e, new FileOutputStream(Utilities.path("[tmp]", "resource.xml")), FhirFormat.XML,
+        Manager.compose(context, e, ManagedFileAccess.outStream(Utilities.path("[tmp]", "resource.xml")), FhirFormat.XML,
             OutputStyle.PRETTY, null);
         String src = TextFile
             .fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\" + Utilities.changeFileExt(f, ".mm.ttl"));

org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/terminologies/ICPC2Importer.java

@@ -49,6 +49,7 @@ import org.hl7.fhir.dstu2016may.model.Enumerations.ConformanceResourceStatus;
 import org.hl7.fhir.dstu2016may.model.Identifier;
 import org.hl7.fhir.dstu2016may.model.ValueSet;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -118,7 +119,7 @@ public class ICPC2Importer {
     DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
     factory.setNamespaceAware(false);
     DocumentBuilder builder = factory.newDocumentBuilder();
-    Document doc = builder.parse(new FileInputStream(sourceFileName));
+    Document doc = builder.parse(ManagedFileAccess.inStream(sourceFileName));
 
     ValueSet vs = new ValueSet();
     vs.setUrl("http://hl7.org/fhir/sid/icpc2/vs");
@@ -167,8 +168,8 @@ public class ICPC2Importer {
 
     XmlParser xml = new XmlParser();
     xml.setOutputStyle(OutputStyle.PRETTY);
-    xml.compose(new FileOutputStream(targetFileNameVS), vs);
+    xml.compose(ManagedFileAccess.outStream(targetFileNameVS), vs);
-    xml.compose(new FileOutputStream(targetFileNameCS), cs);
+    xml.compose(ManagedFileAccess.outStream(targetFileNameCS), cs);
   }
 
   private void processClass(Element cls, Map<String, ConceptDefinitionComponent> concepts, CodeSystem define) {

org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/terminologies/LoincToDEConvertor.java

@@ -54,6 +54,7 @@ import org.hl7.fhir.dstu2016may.model.Meta;
 import org.hl7.fhir.dstu2016may.utils.ToolingExtensions;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -165,12 +166,12 @@ public class LoincToDEConvertor {
     factory.setNamespaceAware(true);
     DocumentBuilder builder = factory.newDocumentBuilder();
 
-    xml = builder.parse(new FileInputStream(definitions));
+    xml = builder.parse(ManagedFileAccess.inStream(definitions));
   }
 
   private void saveBundle() throws FHIRFormatError, IOException, XmlPullParserException {
     XmlParser xml = new XmlParser();
-    FileOutputStream s = new FileOutputStream(dest);
+    FileOutputStream s = ManagedFileAccess.outStream(dest);
     xml.compose(s, bundle, true);
     s.close();
   }

org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/terminologies/ValueSetExpansionCache.java

@@ -75,6 +75,7 @@ import org.hl7.fhir.dstu2016may.utils.IWorkerContext;
 import org.hl7.fhir.dstu2016may.utils.ToolingExtensions;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
 
 public class ValueSetExpansionCache implements ValueSetExpanderFactory {
@@ -91,7 +92,7 @@ public class ValueSetExpansionCache implements ValueSetExpanderFactory {
         // well, we'll see if the designated server can expand it, and if it can, we'll
         // cache it locally
         vso = context.expandVS(source, false);
-        FileOutputStream s = new FileOutputStream(Utilities.path(cacheFolder, makeFile(source.getUrl())));
+        FileOutputStream s = ManagedFileAccess.outStream(Utilities.path(cacheFolder, makeFile(source.getUrl())));
         context.newXmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, vso.getValueset());
         s.close();
       }
@@ -125,10 +126,10 @@ public class ValueSetExpansionCache implements ValueSetExpanderFactory {
   }
 
   private void loadCache() throws FHIRFormatError, IOException {
-    File[] files = new File(cacheFolder).listFiles();
+    File[] files = ManagedFileAccess.file(cacheFolder).listFiles();
     for (File f : files) {
       if (f.getName().endsWith(".xml")) {
-        final FileInputStream is = new FileInputStream(f);
+        final FileInputStream is = ManagedFileAccess.inStream(f);
         try {
           Resource r = context.newXmlParser().setOutputStyle(OutputStyle.PRETTY).parse(is);
           if (r instanceof OperationOutcome) {

org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/utils/BatchLoader.java

@@ -47,6 +47,7 @@ import org.hl7.fhir.dstu2016may.model.Resource;
 import org.hl7.fhir.dstu2016may.utils.client.FHIRToolingClient;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class BatchLoader {
 
@@ -66,7 +67,7 @@ public class BatchLoader {
         throw new FHIRException("Unimplemented file type " + file);
       } else if (file.endsWith(".zip")) {
         LoadZipFile(server, file, p, size, 0, -1);
-      } else if (new File(file).isDirectory()) {
+      } else if (ManagedFileAccess.file(file).isDirectory()) {
         LoadDirectory(server, file, p, size);
       } else
         throw new FHIRException("Unknown file type " + file);
@@ -99,7 +100,7 @@ public class BatchLoader {
     Bundle b = new Bundle();
     b.setType(BundleType.COLLECTION);
     b.setId(UUID.randomUUID().toString().toLowerCase());
-    ZipInputStream zip = new ZipInputStream(new FileInputStream(file));
+    ZipInputStream zip = new ZipInputStream(ManagedFileAccess.inStream(file));
     ZipEntry entry;
     while ((entry = zip.getNextEntry()) != null) {
       try {

org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/utils/SimpleWorkerContext.java

@@ -71,9 +71,10 @@ import org.hl7.fhir.dstu2016may.utils.client.FHIRToolingClient;
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
-import org.hl7.fhir.utilities.CSFileInputStream;
 import org.hl7.fhir.utilities.OIDUtils;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.CSFileInputStream;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 
@@ -425,7 +426,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
   }
 
   public void loadFromFolder(String folder) throws FileNotFoundException, Exception {
-    for (String n : new File(folder).list()) {
+    for (String n : ManagedFileAccess.file(folder).list()) {
       if (n.endsWith(".json"))
         loadFromFile(Utilities.path(folder, n), new JsonParser());
       else if (n.endsWith(".xml"))
@@ -436,11 +437,11 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
   private void loadFromFile(String filename, IParser p) throws FileNotFoundException, Exception {
     Resource r;
     try {
-      r = p.parse(new FileInputStream(filename));
+      r = p.parse(ManagedFileAccess.inStream(filename));
       if (r.getResourceType() == ResourceType.Bundle) {
         for (BundleEntryComponent e : ((Bundle) r).getEntry()) {
           seeResource(null, e.getResource());
-        }
+        } 
       } else {
         seeResource(null, r);
       }

org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/utils/Transformer.java

@@ -32,6 +32,7 @@ package org.hl7.fhir.dstu2016may.utils;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -45,6 +46,7 @@ import org.hl7.fhir.dstu2016may.model.Bundle;
 import org.hl7.fhir.dstu2016may.model.StructureMap;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class Transformer {
 
@@ -117,7 +119,7 @@ public class Transformer {
         loadMaps(folder);
       }
       System.out.println("  .. load source from " + source);
-      Element e = Manager.parse(context, new FileInputStream(source), FhirFormat.XML);
+      Element e = Manager.parse(context, ManagedFileAccess.inStream(source), FhirFormat.XML);
 
       Bundle bundle = new Bundle();
       StructureMap map = scu.getLibrary().get(mapUri);
@@ -125,7 +127,7 @@ public class Transformer {
         throw new Error("Unable to find map " + mapUri + " (Known Maps = "
             + Utilities.listCanonicalUrls(scu.getLibrary().keySet()) + ")");
       scu.transform(null, e, map, bundle);
-      new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(output), bundle);
+      new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(output), bundle);
       return true;
     } catch (Exception e) {
       e.printStackTrace();
@@ -134,8 +136,8 @@ public class Transformer {
     }
   }
 
-  private void loadMaps(String folder) {
+  private void loadMaps(String folder) throws IOException {
-    for (String f : new File(folder).list()) {
+    for (String f : ManagedFileAccess.file(folder).list()) {
       try {
         StructureMap map = scu.parse(TextFile.fileToString(Utilities.path(folder, f)));
         scu.getLibrary().put(map.getUrl(), map);

org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/utils/Translations.java

@@ -38,7 +38,7 @@ import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 
-import org.hl7.fhir.utilities.CSFileInputStream;
+import org.hl7.fhir.utilities.filesystem.CSFileInputStream;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;

org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/utils/Unbundler.java

@@ -42,6 +42,7 @@ import org.hl7.fhir.dstu2016may.model.Bundle;
 import org.hl7.fhir.dstu2016may.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.dstu2016may.model.Resource;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class Unbundler {
 
@@ -51,7 +52,7 @@ public class Unbundler {
 
   private static void unbundle(String src) throws FHIRFormatError, FileNotFoundException, IOException {
     String folder = Utilities.getDirectoryForFile(src);
-    Bundle bnd = (Bundle) new JsonParser().parse(new FileInputStream(src));
+    Bundle bnd = (Bundle) new JsonParser().parse(ManagedFileAccess.inStream(src));
     for (BundleEntryComponent be : bnd.getEntry()) {
       Resource r = be.getResource();
       if (r != null) {
@@ -61,7 +62,7 @@ public class Unbundler {
         }
         if (!StringUtils.isBlank(r.getId())) {
           String tgt = Utilities.path(folder, r.fhirType() + "-" + r.getId() + ".json");
-          new JsonParser().compose(new FileOutputStream(tgt), r);
+          new JsonParser().compose(ManagedFileAccess.outStream(tgt), r);
         }
       }
     }

org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/FluentPathTests.java

@@ -25,6 +25,7 @@ import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.exceptions.PathEngineException;
 import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
@@ -46,35 +47,35 @@ public class FluentPathTests {
   private Patient patient() throws FHIRFormatError, FileNotFoundException, IOException {
     if (patient == null)
       patient = (Patient) new JsonParser()
-          .parse(new FileInputStream("C:/work/org.hl7.fhir.2016May/build/publish/patient-example.json"));
+          .parse(ManagedFileAccess.inStream("C:/work/org.hl7.fhir.2016May/build/publish/patient-example.json"));
     return patient;
   }
 
   private Appointment appointment() throws FHIRFormatError, FileNotFoundException, IOException {
     if (appointment == null)
       appointment = (Appointment) new JsonParser()
-          .parse(new FileInputStream("C:/work/org.hl7.fhir.2016May/build/publish/appointment-example-request.json"));
+          .parse(ManagedFileAccess.inStream("C:/work/org.hl7.fhir.2016May/build/publish/appointment-example-request.json"));
     return appointment;
   }
 
   private Questionnaire questionnaire() throws FHIRFormatError, FileNotFoundException, IOException {
     if (questionnaire == null)
       questionnaire = (Questionnaire) new JsonParser()
-          .parse(new FileInputStream("C:/work/org.hl7.fhir.2016May/build/publish/questionnaire-example.json"));
+          .parse(ManagedFileAccess.inStream("C:/work/org.hl7.fhir.2016May/build/publish/questionnaire-example.json"));
     return questionnaire;
   }
 
   private ValueSet valueset() throws FHIRFormatError, FileNotFoundException, IOException {
     if (valueset == null)
       valueset = (ValueSet) new JsonParser()
-          .parse(new FileInputStream("C:/work/org.hl7.fhir.2016May/build/publish/valueset-example-expansion.json"));
+          .parse(ManagedFileAccess.inStream("C:/work/org.hl7.fhir.2016May/build/publish/valueset-example-expansion.json"));
     return valueset;
   }
 
   private Observation observation() throws FHIRFormatError, FileNotFoundException, IOException {
     if (observation == null)
       observation = (Observation) new JsonParser()
-          .parse(new FileInputStream("C:/work/org.hl7.fhir.2016May/build/publish/observation-example.json"));
+          .parse(ManagedFileAccess.inStream("C:/work/org.hl7.fhir.2016May/build/publish/observation-example.json"));
     return observation;
   }
 
@@ -929,7 +930,7 @@ public class FluentPathTests {
   @Test
   public void testQuestionnaire() throws FileNotFoundException, IOException, FHIRException {
     Questionnaire q = (Questionnaire) new JsonParser()
-        .parse(new FileInputStream("C:/work/org.hl7.fhir.2016May/build/publish/questionnaire-example-gcs.json"));
+        .parse(ManagedFileAccess.inStream("C:/work/org.hl7.fhir.2016May/build/publish/questionnaire-example-gcs.json"));
     for (QuestionnaireItemComponent qi : q.getItem()) {
       testQItem(qi);
     }
@@ -943,7 +944,7 @@ public class FluentPathTests {
   @Test
   public void testExtensionDefinitions() throws FileNotFoundException, IOException, FHIRException {
     Bundle b = (Bundle) new JsonParser()
-        .parse(new FileInputStream("C:/work/org.hl7.fhir.2016May/build/publish/extension-definitions.json"));
+        .parse(ManagedFileAccess.inStream("C:/work/org.hl7.fhir.2016May/build/publish/extension-definitions.json"));
     for (BundleEntryComponent be : b.getEntry()) {
       testStructureDefinition((StructureDefinition) be.getResource());
     }

org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/NarrativeGeneratorTests.java

@@ -7,6 +7,7 @@ import org.hl7.fhir.dstu2016may.utils.NarrativeGenerator;
 import org.hl7.fhir.dstu2016may.utils.SimpleWorkerContext;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
@@ -41,9 +42,9 @@ public class NarrativeGeneratorTests {
   private void process(String path)
       throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
     XmlParser p = new XmlParser();
-    DomainResource r = (DomainResource) p.parse(new FileInputStream(path));
+    DomainResource r = (DomainResource) p.parse(ManagedFileAccess.inStream(path));
     gen.generate(r);
-    FileOutputStream s = new FileOutputStream(Utilities.path("[tmp]", "gen.xml"));
+    FileOutputStream s = ManagedFileAccess.outStream(Utilities.path("[tmp]", "gen.xml"));
     new XmlParser().compose(s, r, true);
     s.close();
   }

org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/ParserTests.java

@@ -12,7 +12,7 @@ import org.hl7.fhir.dstu2016may.metamodel.Manager.FhirFormat;
 import org.hl7.fhir.dstu2016may.model.Resource;
 import org.hl7.fhir.dstu2016may.utils.SimpleWorkerContext;
 import org.hl7.fhir.utilities.Utilities;
-
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
@@ -32,7 +32,7 @@ public class ParserTests {
   @Test
   public void testAll() throws Exception {
     String examples = Utilities.path(root, "examples");
-    for (String fn : new File(examples).list()) {
+    for (String fn : ManagedFileAccess.file(examples).list()) {
       if (fn.endsWith(".xml")) {
         testRoundTrip(Utilities.path(examples, fn), fn);
       }
@@ -41,50 +41,50 @@ public class ParserTests {
 
   private void testRoundTrip(String filename, String name) throws Exception {
     System.out.println(name);
-    Resource r = new org.hl7.fhir.dstu2016may.formats.XmlParser().parse(new FileInputStream(filename));
+    Resource r = new org.hl7.fhir.dstu2016may.formats.XmlParser().parse(ManagedFileAccess.inStream(filename));
     String fn = makeTempFilename();
     new org.hl7.fhir.dstu2016may.formats.XmlParser().setOutputStyle(OutputStyle.PRETTY)
-        .compose(new FileOutputStream(fn), r);
+        .compose(ManagedFileAccess.outStream(fn), r);
     String msg = TestingUtilities.checkXMLIsSame(filename, fn);
     Assertions.assertNull(msg, name + ": " + msg);
     String j1 = makeTempFilename();
     new org.hl7.fhir.dstu2016may.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY)
-        .compose(new FileOutputStream(j1), r);
+        .compose(ManagedFileAccess.outStream(j1), r);
 
     if (TestingUtilities.context == null) {
       TestingUtilities.context = SimpleWorkerContext.fromPack(Utilities.path(root, "validation-min.xml.zip"));
     }
 
-    Element re = Manager.parse(TestingUtilities.context, new FileInputStream(filename), FhirFormat.XML);
+    Element re = Manager.parse(TestingUtilities.context, ManagedFileAccess.inStream(filename), FhirFormat.XML);
     fn = makeTempFilename();
-    Manager.compose(TestingUtilities.context, re, new FileOutputStream(fn), FhirFormat.XML, OutputStyle.PRETTY, null);
+    Manager.compose(TestingUtilities.context, re, ManagedFileAccess.outStream(fn), FhirFormat.XML, OutputStyle.PRETTY, null);
     msg = TestingUtilities.checkXMLIsSame(filename, fn);
     Assertions.assertNull(msg, name + ": " + msg);
     String j2 = makeTempFilename();
-    Manager.compose(TestingUtilities.context, re, new FileOutputStream(j2), FhirFormat.JSON, OutputStyle.PRETTY, null);
+    Manager.compose(TestingUtilities.context, re, ManagedFileAccess.outStream(j2), FhirFormat.JSON, OutputStyle.PRETTY, null);
 
     msg = TestingUtilities.checkJsonIsSame(j1, j2);
     Assertions.assertNull(msg, name + ": " + msg);
 
     // ok, we've produced equivalent JSON by both methods.
     // now, we're going to reverse the process
-    r = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(new FileInputStream(j2)); // crossover too
+    r = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(ManagedFileAccess.inStream(j2)); // crossover too
     fn = makeTempFilename();
     new org.hl7.fhir.dstu2016may.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY)
-        .compose(new FileOutputStream(fn), r);
+        .compose(ManagedFileAccess.outStream(fn), r);
     msg = TestingUtilities.checkJsonIsSame(j2, fn);
     Assertions.assertNull(msg, name + ": " + msg);
     String x1 = makeTempFilename();
     new org.hl7.fhir.dstu2016may.formats.XmlParser().setOutputStyle(OutputStyle.PRETTY)
-        .compose(new FileOutputStream(x1), r);
+        .compose(ManagedFileAccess.outStream(x1), r);
 
-    re = Manager.parse(TestingUtilities.context, new FileInputStream(j1), FhirFormat.JSON);
+    re = Manager.parse(TestingUtilities.context, ManagedFileAccess.inStream(j1), FhirFormat.JSON);
     fn = makeTempFilename();
-    Manager.compose(TestingUtilities.context, re, new FileOutputStream(fn), FhirFormat.JSON, OutputStyle.PRETTY, null);
+    Manager.compose(TestingUtilities.context, re, ManagedFileAccess.outStream(fn), FhirFormat.JSON, OutputStyle.PRETTY, null);
     msg = TestingUtilities.checkJsonIsSame(j1, fn);
     Assertions.assertNull(msg, name + ": " + msg);
     String x2 = makeTempFilename();
-    Manager.compose(TestingUtilities.context, re, new FileOutputStream(x2), FhirFormat.XML, OutputStyle.PRETTY, null);
+    Manager.compose(TestingUtilities.context, re, ManagedFileAccess.outStream(x2), FhirFormat.XML, OutputStyle.PRETTY, null);
 
     msg = TestingUtilities.checkXMLIsSame(x1, x2);
     Assertions.assertNull(msg, name + ": " + msg);

org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/QuestionnaireBuilderTester.java

@@ -2,27 +2,29 @@ package org.hl7.fhir.dstu2016may.test;
 
 import java.io.File;
 import java.io.FileInputStream;
+import java.io.IOException;
 
 import org.hl7.fhir.dstu2016may.formats.XmlParser;
 import org.hl7.fhir.dstu2016may.model.StructureDefinition;
 import org.hl7.fhir.dstu2016may.utils.QuestionnaireBuilder;
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class QuestionnaireBuilderTester {
 
   private static final String TEST_PROFILE_DIR = "C:\\work\\org.hl7.fhir\\build\\publish";
 //	private static final String TEST_DEST = Utilities.path("[tmp]", "questionnaires\\");
 
-  public static void main(String[] args) {
+  public static void main(String[] args) throws IOException {
     QuestionnaireBuilder b = new QuestionnaireBuilder(null);
-    for (String f : new File(TEST_PROFILE_DIR).list()) {
+    for (String f : ManagedFileAccess.file(TEST_PROFILE_DIR).list()) {
       if (f.endsWith(".profile.xml") && !f.contains("type-")) {
         System.out.println("process " + f);
         try {
           StructureDefinition p = (StructureDefinition) new XmlParser()
-              .parse(new FileInputStream(TEST_PROFILE_DIR + "\\" + f));
+              .parse(ManagedFileAccess.inStream(TEST_PROFILE_DIR + "\\" + f));
 //					Questionnaire q = b.buildQuestionnaire(p);
-//					new XmlComposer().compose(new FileOutputStream(TEST_DEST+f), q, true);
+//					new XmlComposer().compose(ManagedFileAccess.outStream(TEST_DEST+f), q, true);
           throw new FHIRException("test");
         } catch (Exception e) {
           e.printStackTrace();

org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/ResourceTest.java

@@ -40,6 +40,7 @@ import org.hl7.fhir.dstu2016may.formats.JsonParser;
 import org.hl7.fhir.dstu2016may.formats.XmlParser;
 import org.hl7.fhir.dstu2016may.model.Resource;
 import org.hl7.fhir.exceptions.FHIRFormatError;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class ResourceTest {
 
@@ -61,18 +62,18 @@ public class ResourceTest {
       p = new JsonParser();
     else
       p = new XmlParser(false);
-    Resource rf = p.parse(new FileInputStream(source));
+    Resource rf = p.parse(ManagedFileAccess.inStream(source));
 
-    FileOutputStream out = new FileOutputStream(source.getAbsoluteFile() + ".out.json");
+    FileOutputStream out = ManagedFileAccess.outStream(source.getAbsoluteFile() + ".out.json");
     JsonParser json1 = new JsonParser();
     json1.setOutputStyle(OutputStyle.PRETTY);
     json1.compose(out, rf);
     out.close();
 
     JsonParser json = new JsonParser();
-    rf = json.parse(new FileInputStream(source.getAbsoluteFile() + ".out.json"));
+    rf = json.parse(ManagedFileAccess.inStream(source.getAbsoluteFile() + ".out.json"));
 
-    out = new FileOutputStream(source.getAbsoluteFile() + ".out.xml");
+    out = ManagedFileAccess.outStream(source.getAbsoluteFile() + ".out.xml");
     XmlParser atom = new XmlParser();
     atom.setOutputStyle(OutputStyle.PRETTY);
     atom.compose(out, rf, true);

org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/RoundTripTest.java

@@ -16,6 +16,7 @@ import org.hl7.fhir.dstu2016may.metamodel.Manager.FhirFormat;
 import org.hl7.fhir.dstu2016may.model.Resource;
 import org.hl7.fhir.dstu2016may.utils.SimpleWorkerContext;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.params.ParameterizedTest;
@@ -29,7 +30,7 @@ public class RoundTripTest {
   public static Stream<Arguments> getFiles() throws IOException {
     List<Arguments> params = new ArrayList();
     String examples = Utilities.path(root, "examples");
-    for (File f : new File(examples).listFiles()) {
+    for (File f : ManagedFileAccess.file(examples).listFiles()) {
       if (f.getName().endsWith(".xml")) {
         params.add(Arguments.of(f));
       }
@@ -48,50 +49,50 @@ public class RoundTripTest {
   @SuppressWarnings("deprecation")
   public void test(File file) throws Exception {
     System.out.println(file.getName());
-    Resource r = new org.hl7.fhir.dstu2016may.formats.XmlParser().parse(new FileInputStream(file));
+    Resource r = new org.hl7.fhir.dstu2016may.formats.XmlParser().parse(ManagedFileAccess.inStream(file));
     String fn = makeTempFilename();
     new org.hl7.fhir.dstu2016may.formats.XmlParser().setOutputStyle(OutputStyle.PRETTY)
-        .compose(new FileOutputStream(fn), r);
+        .compose(ManagedFileAccess.outStream(fn), r);
     String msg = TestingUtilities.checkXMLIsSame(file.getAbsolutePath(), fn);
     Assertions.assertTrue(msg == null, file.getName() + ": " + msg);
     String j1 = makeTempFilename();
     new org.hl7.fhir.dstu2016may.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY)
-        .compose(new FileOutputStream(j1), r);
+        .compose(ManagedFileAccess.outStream(j1), r);
 
     if (TestingUtilities.context == null) {
       TestingUtilities.context = SimpleWorkerContext.fromPack(Utilities.path(root, "validation-min.xml.zip"));
     }
 
-    Element re = Manager.parse(TestingUtilities.context, new FileInputStream(file), FhirFormat.XML);
+    Element re = Manager.parse(TestingUtilities.context, ManagedFileAccess.inStream(file), FhirFormat.XML);
     fn = makeTempFilename();
-    Manager.compose(TestingUtilities.context, re, new FileOutputStream(fn), FhirFormat.XML, OutputStyle.PRETTY, null);
+    Manager.compose(TestingUtilities.context, re, ManagedFileAccess.outStream(fn), FhirFormat.XML, OutputStyle.PRETTY, null);
     msg = TestingUtilities.checkXMLIsSame(file.getAbsolutePath(), fn);
     Assertions.assertTrue(msg == null, file.getName() + ": " + msg);
     String j2 = makeTempFilename();
-    Manager.compose(TestingUtilities.context, re, new FileOutputStream(j2), FhirFormat.JSON, OutputStyle.PRETTY, null);
+    Manager.compose(TestingUtilities.context, re, ManagedFileAccess.outStream(j2), FhirFormat.JSON, OutputStyle.PRETTY, null);
 
     msg = TestingUtilities.checkJsonIsSame(j1, j2);
     Assertions.assertTrue(msg == null, file.getName() + ": " + msg);
 
     // ok, we've produced equivalent JSON by both methods.
     // now, we're going to reverse the process
-    r = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(new FileInputStream(j2)); // crossover too
+    r = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(ManagedFileAccess.inStream(j2)); // crossover too
     fn = makeTempFilename();
     new org.hl7.fhir.dstu2016may.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY)
-        .compose(new FileOutputStream(fn), r);
+        .compose(ManagedFileAccess.outStream(fn), r);
     msg = TestingUtilities.checkJsonIsSame(j2, fn);
     Assertions.assertTrue(msg == null, file.getName() + ": " + msg);
     String x1 = makeTempFilename();
     new org.hl7.fhir.dstu2016may.formats.XmlParser().setOutputStyle(OutputStyle.PRETTY)
-        .compose(new FileOutputStream(x1), r);
+        .compose(ManagedFileAccess.outStream(x1), r);
 
-    re = Manager.parse(TestingUtilities.context, new FileInputStream(j1), FhirFormat.JSON);
+    re = Manager.parse(TestingUtilities.context, ManagedFileAccess.inStream(j1), FhirFormat.JSON);
     fn = makeTempFilename();
-    Manager.compose(TestingUtilities.context, re, new FileOutputStream(fn), FhirFormat.JSON, OutputStyle.PRETTY, null);
+    Manager.compose(TestingUtilities.context, re, ManagedFileAccess.outStream(fn), FhirFormat.JSON, OutputStyle.PRETTY, null);
     msg = TestingUtilities.checkJsonIsSame(j1, fn);
     Assertions.assertTrue(msg == null, file.getName() + ": " + msg);
     String x2 = makeTempFilename();
-    Manager.compose(TestingUtilities.context, re, new FileOutputStream(x2), FhirFormat.XML, OutputStyle.PRETTY, null);
+    Manager.compose(TestingUtilities.context, re, ManagedFileAccess.outStream(x2), FhirFormat.XML, OutputStyle.PRETTY, null);
 
     msg = TestingUtilities.checkXMLIsSame(x1, x2);
     Assertions.assertTrue(msg == null, file.getName() + ": " + msg);

org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/SingleTest.java

@@ -30,6 +30,8 @@ package org.hl7.fhir.dstu2016may.test;
 
 import java.io.File;
 
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
+
 public class SingleTest {
 
   /**
@@ -38,7 +40,7 @@ public class SingleTest {
   public static void main(String[] args) {
     try {
       ResourceTest r = new ResourceTest();
-      r.setSource(new File("C:\\work\\org.hl7.fhir\\build\\publish\\patient-example.xml"));
+      r.setSource(ManagedFileAccess.file("C:\\work\\org.hl7.fhir\\build\\publish\\patient-example.xml"));
       r.test();
       System.out.println("Completed OK");
     } catch (Exception e) {

org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/StructureMapTests.java

@@ -21,6 +21,7 @@ import org.hl7.fhir.dstu2016may.utils.StructureMapUtilities;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 
@@ -86,16 +87,16 @@ public class StructureMapTests {
 
     StructureMapUtilities scu = new StructureMapUtilities(TestingUtilities.context, maps, null);
 
-    for (String f : new File("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\CDA").list()) {
+    for (String f : ManagedFileAccess.file("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\CDA").list()) {
       try {
         StructureDefinition sd = (StructureDefinition) new XmlParser()
-            .parse(new FileInputStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\CDA\\" + f));
+            .parse(ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\CDA\\" + f));
         ((SimpleWorkerContext) TestingUtilities.context).seeResource(sd.getUrl(), sd);
       } catch (Exception e) {
       }
     }
 
-    for (String f : new File("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\maps").list()) {
+    for (String f : ManagedFileAccess.file("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\maps").list()) {
       try {
         StructureMap map = scu.parse(TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\maps\\" + f));
         maps.put(map.getUrl(), map);
@@ -104,17 +105,17 @@ public class StructureMapTests {
     }
 
     Element cda = Manager.parse(TestingUtilities.context,
-        new FileInputStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\Example\\ccd.xml"), FhirFormat.XML);
+        ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\Example\\ccd.xml"), FhirFormat.XML);
     Manager.compose(TestingUtilities.context, cda,
-        new FileOutputStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\Example\\ccd.out.json"), FhirFormat.JSON,
+        ManagedFileAccess.outStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\Example\\ccd.out.json"), FhirFormat.JSON,
         OutputStyle.PRETTY, null);
     Manager.compose(TestingUtilities.context, cda,
-        new FileOutputStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\Example\\ccd.out.xml"), FhirFormat.XML,
+        ManagedFileAccess.outStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\Example\\ccd.out.xml"), FhirFormat.XML,
         OutputStyle.PRETTY, null);
     Bundle bundle = new Bundle();
     scu.transform(null, cda, maps.get("http://hl7.org/fhir/StructureMap/cda"), bundle);
     new XmlParser().setOutputStyle(OutputStyle.PRETTY)
-        .compose(new FileOutputStream(Utilities.path("[tmp]", "bundle.xml")), bundle);
+        .compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "bundle.xml")), bundle);
   }
 
 }

org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/TestingUtilities.java

@@ -13,9 +13,10 @@ import javax.xml.parsers.DocumentBuilderFactory;
 
 import org.apache.commons.codec.binary.Base64;
 import org.hl7.fhir.dstu2016may.utils.SimpleWorkerContext;
-import org.hl7.fhir.utilities.CSFile;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.CSFile;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 import org.w3c.dom.NamedNodeMap;
@@ -41,7 +42,7 @@ public class TestingUtilities {
       command.add("\"" + diff + "\" \"" + f1 + "\" \"" + f2 + "\"");
 
       ProcessBuilder builder = new ProcessBuilder(command);
-      builder.directory(new CSFile(Utilities.path("[tmp]")));
+      builder.directory(ManagedFileAccess.csfile(Utilities.path("[tmp]")));
       builder.start();
 
     }
@@ -154,7 +155,7 @@ public class TestingUtilities {
 
     factory.setNamespaceAware(true);
     DocumentBuilder builder = factory.newDocumentBuilder();
-    return builder.parse(new FileInputStream(fn));
+    return builder.parse(ManagedFileAccess.inStream(fn));
   }
 
   public static String checkJsonIsSame(String f1, String f2)
@@ -166,7 +167,7 @@ public class TestingUtilities {
       command.add("\"" + diff + "\" \"" + f1 + "\" \"" + f2 + "\"");
 
       ProcessBuilder builder = new ProcessBuilder(command);
-      builder.directory(new CSFile(Utilities.path("[tmp]")));
+      builder.directory(ManagedFileAccess.csfile(Utilities.path("[tmp]")));
       builder.start();
 
     }

org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/ToolsHelper.java

@@ -57,10 +57,11 @@ import org.hl7.fhir.dstu2016may.model.Resource;
 import org.hl7.fhir.dstu2016may.utils.SimpleWorkerContext;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
-import org.hl7.fhir.utilities.CSFile;
-import org.hl7.fhir.utilities.CSFileInputStream;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.CSFile;
+import org.hl7.fhir.utilities.filesystem.CSFileInputStream;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.xmlpull.v1.XmlPullParser;
 import org.xmlpull.v1.XmlPullParserException;
 import org.xmlpull.v1.XmlPullParserFactory;
@@ -105,7 +106,7 @@ public class ToolsHelper {
   private void executeExamples(String[] args) throws IOException {
     try {
       @SuppressWarnings("unchecked")
-      List<String> lines = FileUtils.readLines(new File(args[1]), "UTF-8");
+      List<String> lines = FileUtils.readLines(ManagedFileAccess.file(args[1]), "UTF-8");
       String srcDir = lines.get(0);
       lines.remove(0);
       processExamples(srcDir, lines);
@@ -183,7 +184,7 @@ public class ToolsHelper {
     // } else
     if (definitions.startsWith("https:") || definitions.startsWith("http:")) {
       defn = loadFromUrl(definitions);
-    } else if (new File(definitions).exists()) {
+    } else if (ManagedFileAccess.file(definitions).exists()) {
       defn = loadFromFile(definitions);
     } else
       throw new FHIRException("Unable to find FHIR validation Pack (source = " + definitions + ")");
@@ -197,7 +198,7 @@ public class ToolsHelper {
   }
 
   private byte[] loadFromFile(String src) throws IOException {
-    FileInputStream in = new FileInputStream(src);
+    FileInputStream in = ManagedFileAccess.inStream(src);
     byte[] b = new byte[in.available()];
     in.read(b);
     in.close();
@@ -224,10 +225,10 @@ public class ToolsHelper {
 
   public void executeFragments(String[] args) throws IOException {
     try {
-      File source = new CSFile(args[1]);
+      File source = ManagedFileAccess.csfile(args[1]);
       if (!source.exists())
         throw new FHIRException("Source File \"" + source.getAbsolutePath() + "\" not found");
-      XmlPullParser xpp = loadXml(new FileInputStream(source));
+      XmlPullParser xpp = loadXml(ManagedFileAccess.inStream(source));
       nextNoWhitespace(xpp);
       if (!xpp.getName().equals("tests"))
         throw new FHIRFormatError("Unable to parse file - starts with " + xpp.getName());
@@ -273,8 +274,8 @@ public class ToolsHelper {
 
   public void executeRoundTrip(String[] args) throws IOException, FHIRException {
     FileInputStream in;
-    File source = new CSFile(args[1]);
+    File source = ManagedFileAccess.csfile(args[1]);
-    File dest = new CSFile(args[2]);
+    File dest = ManagedFileAccess.csfile(args[2]);
     if (args.length >= 4) {
       Utilities.copyFile(args[1], args[3]);
     }
@@ -292,18 +293,18 @@ public class ToolsHelper {
     json.close();
     TextFile.stringToFile(new String(json.toByteArray()), Utilities.changeFileExt(dest.getAbsolutePath(), ".json"));
     rf = pj.parse(new ByteArrayInputStream(json.toByteArray()));
-    FileOutputStream s = new FileOutputStream(dest);
+    FileOutputStream s = ManagedFileAccess.outStream(dest);
     new XmlParser().compose(s, rf, true);
     s.close();
   }
 
   public String executeJson(String[] args) throws IOException, FHIRException {
     FileInputStream in;
-    File source = new CSFile(args[1]);
+    File source = ManagedFileAccess.csfile(args[1]);
-    File dest = new CSFile(args[2]);
+    File dest = ManagedFileAccess.csfile(args[2]);
-    File destc = new CSFile(Utilities.changeFileExt(args[2], ".canonical.json"));
+    File destc = ManagedFileAccess.csfile(Utilities.changeFileExt(args[2], ".canonical.json"));
-    File destt = new CSFile(args[2] + ".tmp");
+    File destt = ManagedFileAccess.csfile(args[2] + ".tmp");
-    File destr = new CSFile(Utilities.changeFileExt(args[2], ".ttl"));
+    File destr = ManagedFileAccess.csfile(Utilities.changeFileExt(args[2], ".ttl"));
 
     if (!source.exists())
       throw new FHIRException("Source File \"" + source.getAbsolutePath() + "\" not found");
@@ -312,21 +313,21 @@ public class ToolsHelper {
     Resource rf = p.parse(in);
     JsonParser json = new JsonParser();
     json.setOutputStyle(OutputStyle.PRETTY);
-    FileOutputStream s = new FileOutputStream(dest);
+    FileOutputStream s = ManagedFileAccess.outStream(dest);
     json.compose(s, rf);
     s.close();
     json.setOutputStyle(OutputStyle.CANONICAL);
-    s = new FileOutputStream(destc);
+    s = ManagedFileAccess.outStream(destc);
     json.compose(s, rf);
     s.close();
     json.setSuppressXhtml("Snipped for Brevity");
     json.setOutputStyle(OutputStyle.PRETTY);
-    s = new FileOutputStream(destt);
+    s = ManagedFileAccess.outStream(destt);
     json.compose(s, rf);
     s.close();
 
     RdfParserBase rdf = new RdfParser();
-    s = new FileOutputStream(destr);
+    s = ManagedFileAccess.outStream(destr);
     rdf.compose(s, rf);
     s.close();
 
@@ -335,8 +336,8 @@ public class ToolsHelper {
 
   public void executeCanonicalXml(String[] args) throws FHIRException, IOException {
     FileInputStream in;
-    File source = new CSFile(args[1]);
+    File source = ManagedFileAccess.csfile(args[1]);
-    File dest = new CSFile(args[2]);
+    File dest = ManagedFileAccess.csfile(args[2]);
 
     if (!source.exists())
       throw new FHIRException("Source File \"" + source.getAbsolutePath() + "\" not found");
@@ -345,7 +346,7 @@ public class ToolsHelper {
     Resource rf = p.parse(in);
     XmlParser cxml = new XmlParser();
     cxml.setOutputStyle(OutputStyle.NORMAL);
-    cxml.compose(new FileOutputStream(dest), rf);
+    cxml.compose(ManagedFileAccess.outStream(dest), rf);
   }
 
   private void executeVersion(String[] args) throws IOException {
@@ -358,7 +359,7 @@ public class ToolsHelper {
         String filename = rootDir + n + ".xml";
         // 1. produce canonical XML
         CSFileInputStream source = new CSFileInputStream(filename);
-        FileOutputStream dest = new FileOutputStream(Utilities.changeFileExt(filename, ".canonical.xml"));
+        FileOutputStream dest = ManagedFileAccess.outStream(Utilities.changeFileExt(filename, ".canonical.xml"));
         XmlParser p = new XmlParser();
         Resource r = p.parse(source);
         XmlParser cxml = new XmlParser();
@@ -367,18 +368,18 @@ public class ToolsHelper {
 
         // 2. produce JSON
         source = new CSFileInputStream(filename);
-        dest = new FileOutputStream(Utilities.changeFileExt(filename, ".json"));
+        dest = ManagedFileAccess.outStream(Utilities.changeFileExt(filename, ".json"));
         r = p.parse(source);
         JsonParser json = new JsonParser();
         json.setOutputStyle(OutputStyle.PRETTY);
         json.compose(dest, r);
         json = new JsonParser();
         json.setOutputStyle(OutputStyle.CANONICAL);
-        dest = new FileOutputStream(Utilities.changeFileExt(filename, ".canonical.json"));
+        dest = ManagedFileAccess.outStream(Utilities.changeFileExt(filename, ".canonical.json"));
         json.compose(dest, r);
 
         // 2. produce JSON
-        dest = new FileOutputStream(Utilities.changeFileExt(filename, ".ttl"));
+        dest = ManagedFileAccess.outStream(Utilities.changeFileExt(filename, ".ttl"));
         RdfParserBase rdf = new RdfParser();
         rdf.compose(dest, r);
       } catch (Exception e) {
@@ -399,23 +400,23 @@ public class ToolsHelper {
         String tmp = tmpDir + n.replace(File.separator, "-") + ".tmp";
         String dest = tmpDir + n.replace(File.separator, "-") + ".java.xml";
 
-        FileInputStream in = new FileInputStream(source);
+        FileInputStream in = ManagedFileAccess.inStream(source);
         XmlParser xp = new XmlParser();
         Resource r = xp.parse(in);
         System.err.print(".");
         JsonParser jp = new JsonParser();
-        FileOutputStream out = new FileOutputStream(tmp);
+        FileOutputStream out = ManagedFileAccess.outStream(tmp);
         jp.setOutputStyle(OutputStyle.PRETTY);
         jp.compose(out, r);
         out.close();
         r = null;
         System.err.print(".");
 
-        in = new FileInputStream(tmp);
+        in = ManagedFileAccess.inStream(tmp);
         System.err.print(",");
         r = jp.parse(in);
         System.err.print(".");
-        out = new FileOutputStream(dest);
+        out = ManagedFileAccess.outStream(dest);
         new XmlParser().compose(out, r, true);
         System.err.println("!");
         out.close();
@@ -431,7 +432,7 @@ public class ToolsHelper {
   private void executeTest(String[] args) throws Throwable {
     try {
       @SuppressWarnings("unchecked")
-      List<String> lines = FileUtils.readLines(new File(args[1]), "UTF-8");
+      List<String> lines = FileUtils.readLines(ManagedFileAccess.file(args[1]), "UTF-8");
       String srcDir = lines.get(0);
       lines.remove(0);
       String dstDir = lines.get(0).trim();

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/context/BaseWorkerContext.java

@@ -94,6 +94,7 @@ import org.hl7.fhir.exceptions.TerminologyServiceException;
 import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.i18n.I18nBase;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
@@ -323,7 +324,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
       String cacheFn = null;
       if (cache != null) {
         cacheFn = Utilities.path(cache, determineCacheId(vs, heirarchical) + ".json");
-        if (new File(cacheFn).exists()) {
+        if (ManagedFileAccess.file(cacheFn).exists()) {
           return loadFromCache(vs.copy(), cacheFn);
         }
       }
@@ -335,8 +336,8 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
           .expand(vs, expProfile.setExcludeNested(!heirarchical));
         if (vse.getValueset() != null) {
           if (cache != null) {
-            FileOutputStream s = new FileOutputStream(cacheFn);
+            FileOutputStream s = ManagedFileAccess.outStream(cacheFn);
-            newJsonParser().compose(new FileOutputStream(cacheFn), vse.getValueset());
+            newJsonParser().compose(ManagedFileAccess.outStream(cacheFn), vse.getValueset());
             s.close();
           }
         }
@@ -368,7 +369,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
   private ValueSetExpansionOutcome loadFromCache(ValueSet vs, String cacheFn)
     throws FileNotFoundException, Exception {
     JsonParser parser = new JsonParser();
-    Resource r = parser.parse(new FileInputStream(cacheFn));
+    Resource r = parser.parse(ManagedFileAccess.inStream(cacheFn));
     if (r instanceof OperationOutcome) {
       return new ValueSetExpansionOutcome(
         ((OperationOutcome) r).getIssue().get(0).getDetails().getText(),
@@ -382,7 +383,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
 
   private void saveToCache(Resource res, String cacheFn) throws FileNotFoundException, Exception {
     JsonParser parser = new JsonParser();
-    parser.compose(new FileOutputStream(cacheFn), res);
+    parser.compose(ManagedFileAccess.outStream(cacheFn), res);
   }
 
   private String determineCacheId(ValueSet vs, boolean heirarchical) throws Exception {
@@ -715,7 +716,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     if (fn == null) {
       return null;
     }
-    if (!(new File(fn).exists())) {
+    if (!(ManagedFileAccess.file(fn).exists())) {
       return null;
     }
     String cnt = TextFile.fileToString(fn);

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/context/SimpleWorkerContext.java

@@ -86,9 +86,10 @@ import org.hl7.fhir.dstu3.utils.validation.IResourceValidator;
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
-import org.hl7.fhir.utilities.CSFileInputStream;
 import org.hl7.fhir.utilities.OIDUtils;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.CSFileInputStream;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.npm.NpmPackage;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
@@ -676,7 +677,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
 
 
   public void loadFromFolder(String folder) throws FileNotFoundException, Exception {
-    for (String n : new File(folder).list()) {
+    for (String n : ManagedFileAccess.file(folder).list()) {
       if (n.endsWith(".json")) 
         loadFromFile(Utilities.path(folder, n), new JsonParser());
       else if (n.endsWith(".xml")) 
@@ -687,7 +688,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
   private void loadFromFile(String filename, IParser p) throws FileNotFoundException, Exception {
   	Resource r; 
   	try {
-  		r = p.parse(new FileInputStream(filename));
+  		r = p.parse(ManagedFileAccess.inStream(filename));
       if (r.getResourceType() == ResourceType.Bundle) {
         for (BundleEntryComponent e : ((Bundle) r).getEntry()) {
           seeResource(null, e.getResource());

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/elementmodel/Tester.java

@@ -1,37 +1,38 @@
 package org.hl7.fhir.dstu3.elementmodel;
 
-/*
+/*
-  Copyright (c) 2011+, HL7, Inc.
+  Copyright (c) 2011+, HL7, Inc.
-  All rights reserved.
+  All rights reserved.
-  
+  
-  Redistribution and use in source and binary forms, with or without modification, 
+  Redistribution and use in source and binary forms, with or without modification, 
-  are permitted provided that the following conditions are met:
+  are permitted provided that the following conditions are met:
-    
+    
-   * Redistributions of source code must retain the above copyright notice, this 
+   * Redistributions of source code must retain the above copyright notice, this 
-     list of conditions and the following disclaimer.
+     list of conditions and the following disclaimer.
-   * Redistributions in binary form must reproduce the above copyright notice, 
+   * Redistributions in binary form must reproduce the above copyright notice, 
-     this list of conditions and the following disclaimer in the documentation 
+     this list of conditions and the following disclaimer in the documentation 
-     and/or other materials provided with the distribution.
+     and/or other materials provided with the distribution.
-   * Neither the name of HL7 nor the names of its contributors may be used to 
+   * Neither the name of HL7 nor the names of its contributors may be used to 
-     endorse or promote products derived from this software without specific 
+     endorse or promote products derived from this software without specific 
-     prior written permission.
+     prior written permission.
-  
+  
-  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
-  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
+  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
-  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
+  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
-  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
+  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
-  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
+  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
-  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
+  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
-  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
-  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
-  POSSIBILITY OF SUCH DAMAGE.
+  POSSIBILITY OF SUCH DAMAGE.
-  
+  
- */
+ */
 
 
 
 import java.io.File;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.util.Map.Entry;
@@ -53,17 +54,17 @@ public class Tester {
 		IWorkerContext context = SimpleWorkerContext.fromPack(Utilities.path("C:\\work\\org.hl7.fhir\\build\\publish", "validation-min.xml.zip"));
 		int t = 0;
 		int ok = 0;
-		for (String f : new File("C:\\work\\org.hl7.fhir\\build\\publish").list()) {
+		for (String f : ManagedFileAccess.file("C:\\work\\org.hl7.fhir\\build\\publish").list()) {
-			if (f.endsWith(".xml") && !f.endsWith(".canonical.xml") && !f.contains("profile") && !f.contains("questionnaire") && new File("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".ttl")).exists()) {
+			if (f.endsWith(".xml") && !f.endsWith(".canonical.xml") && !f.contains("profile") && !f.contains("questionnaire") && ManagedFileAccess.file("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".ttl")).exists()) {
 //				if (f.equals("account-questionnaire.xml")) {
 				System.out.print("convert "+f);
-//				Manager.convert(context, new FileInputStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+f), FhirFormat.XML, 
+//				Manager.convert(context, ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+f), FhirFormat.XML, 
-//						new FileOutputStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.json")), FhirFormat.JSON, OutputStyle.PRETTY);
+//						ManagedFileAccess.outStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.json")), FhirFormat.JSON, OutputStyle.PRETTY);
 //				String src = normalise(TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.json")));
 //				String tgt = normalise(TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".json")));
-				Element e = Manager.parse(context, new FileInputStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+f), FhirFormat.XML);
+				Element e = Manager.parse(context, ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+f), FhirFormat.XML);
-				Manager.compose(context, e, new FileOutputStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.ttl")), FhirFormat.TURTLE, OutputStyle.PRETTY, null);
+				Manager.compose(context, e, ManagedFileAccess.outStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.ttl")), FhirFormat.TURTLE, OutputStyle.PRETTY, null);
-        Manager.compose(context, e, new FileOutputStream(Utilities.path("[tmp]", "resource.xml")), FhirFormat.XML, OutputStyle.PRETTY, null);
+        Manager.compose(context, e, ManagedFileAccess.outStream(Utilities.path("[tmp]", "resource.xml")), FhirFormat.XML, OutputStyle.PRETTY, null);
 				String src = TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.ttl"));
 				String tgt = TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".ttl"));
 				t++;

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/terminologies/LoincToDEConvertor.java

@@ -1,33 +1,33 @@
 package org.hl7.fhir.dstu3.terminologies;
 
-/*
+/*
-  Copyright (c) 2011+, HL7, Inc.
+  Copyright (c) 2011+, HL7, Inc.
-  All rights reserved.
+  All rights reserved.
-  
+  
-  Redistribution and use in source and binary forms, with or without modification, 
+  Redistribution and use in source and binary forms, with or without modification, 
-  are permitted provided that the following conditions are met:
+  are permitted provided that the following conditions are met:
-    
+    
-   * Redistributions of source code must retain the above copyright notice, this 
+   * Redistributions of source code must retain the above copyright notice, this 
-     list of conditions and the following disclaimer.
+     list of conditions and the following disclaimer.
-   * Redistributions in binary form must reproduce the above copyright notice, 
+   * Redistributions in binary form must reproduce the above copyright notice, 
-     this list of conditions and the following disclaimer in the documentation 
+     this list of conditions and the following disclaimer in the documentation 
-     and/or other materials provided with the distribution.
+     and/or other materials provided with the distribution.
-   * Neither the name of HL7 nor the names of its contributors may be used to 
+   * Neither the name of HL7 nor the names of its contributors may be used to 
-     endorse or promote products derived from this software without specific 
+     endorse or promote products derived from this software without specific 
-     prior written permission.
+     prior written permission.
-  
+  
-  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
-  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
+  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
-  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
+  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
-  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
+  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
-  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
+  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
-  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
+  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
-  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
-  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
-  POSSIBILITY OF SUCH DAMAGE.
+  POSSIBILITY OF SUCH DAMAGE.
-  
+  
- */
+ */
 
 
 
@@ -56,6 +56,7 @@ import org.hl7.fhir.dstu3.model.Meta;
 import org.hl7.fhir.dstu3.utils.ToolingExtensions;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -157,12 +158,12 @@ public class LoincToDEConvertor {
 		factory.setNamespaceAware(true);
 		DocumentBuilder builder = factory.newDocumentBuilder();
 
-		xml = builder.parse(new FileInputStream(definitions)); 
+		xml = builder.parse(ManagedFileAccess.inStream(definitions)); 
 	}
 
 	private void saveBundle() throws FHIRFormatError, IOException, XmlPullParserException {
 		XmlParser xml = new XmlParser();
-		FileOutputStream s = new FileOutputStream(dest);
+		FileOutputStream s = ManagedFileAccess.outStream(dest);
     xml.compose(s, bundle, true);
     s.close();
 	}

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/terminologies/ValueSetExpansionCache.java

@@ -1,33 +1,33 @@
 package org.hl7.fhir.dstu3.terminologies;
 
-/*
+/*
-  Copyright (c) 2011+, HL7, Inc.
+  Copyright (c) 2011+, HL7, Inc.
-  All rights reserved.
+  All rights reserved.
-  
+  
-  Redistribution and use in source and binary forms, with or without modification, 
+  Redistribution and use in source and binary forms, with or without modification, 
-  are permitted provided that the following conditions are met:
+  are permitted provided that the following conditions are met:
-    
+    
-   * Redistributions of source code must retain the above copyright notice, this 
+   * Redistributions of source code must retain the above copyright notice, this 
-     list of conditions and the following disclaimer.
+     list of conditions and the following disclaimer.
-   * Redistributions in binary form must reproduce the above copyright notice, 
+   * Redistributions in binary form must reproduce the above copyright notice, 
-     this list of conditions and the following disclaimer in the documentation 
+     this list of conditions and the following disclaimer in the documentation 
-     and/or other materials provided with the distribution.
+     and/or other materials provided with the distribution.
-   * Neither the name of HL7 nor the names of its contributors may be used to 
+   * Neither the name of HL7 nor the names of its contributors may be used to 
-     endorse or promote products derived from this software without specific 
+     endorse or promote products derived from this software without specific 
-     prior written permission.
+     prior written permission.
-  
+  
-  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
-  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
+  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
-  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
+  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
-  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
+  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
-  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
+  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
-  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
+  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
-  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
-  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
-  POSSIBILITY OF SUCH DAMAGE.
+  POSSIBILITY OF SUCH DAMAGE.
-  
+  
- */
+ */
 
 
 
@@ -79,6 +79,7 @@ import org.hl7.fhir.dstu3.terminologies.ValueSetExpander.ValueSetExpansionOutcom
 import org.hl7.fhir.dstu3.utils.ToolingExtensions;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
 
 public class ValueSetExpansionCache implements ValueSetExpanderFactory {
@@ -96,7 +97,7 @@ public class ValueSetExpansionCache implements ValueSetExpanderFactory {
 	  	  // well, we'll see if the designated server can expand it, and if it can, we'll cache it locally
 	  		vso = context.expandVS(source, false, profile == null || !profile.getExcludeNested());
 	  		if (cacheFolder != null) {
-	  		FileOutputStream s = new FileOutputStream(Utilities.path(cacheFolder, makeFile(source.getUrl())));
+	  		FileOutputStream s = ManagedFileAccess.outStream(Utilities.path(cacheFolder, makeFile(source.getUrl())));
 	  		context.newXmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, vso.getValueset());
 	  		s.close();
 	  	}
@@ -136,10 +137,10 @@ public class ValueSetExpansionCache implements ValueSetExpanderFactory {
   }
   
 	private void loadCache() throws FHIRFormatError, IOException {
-	  File[] files = new File(cacheFolder).listFiles();
+	  File[] files = ManagedFileAccess.file(cacheFolder).listFiles();
     for (File f : files) {
       if (f.getName().endsWith(".xml")) {
-        final FileInputStream is = new FileInputStream(f);
+        final FileInputStream is = ManagedFileAccess.inStream(f);
         try {	   
         Resource r = context.newXmlParser().setOutputStyle(OutputStyle.PRETTY).parse(is);
         if (r instanceof OperationOutcome) {

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/BatchLoader.java

@@ -1,33 +1,33 @@
 package org.hl7.fhir.dstu3.utils;
 
-/*
+/*
-  Copyright (c) 2011+, HL7, Inc.
+  Copyright (c) 2011+, HL7, Inc.
-  All rights reserved.
+  All rights reserved.
-  
+  
-  Redistribution and use in source and binary forms, with or without modification, 
+  Redistribution and use in source and binary forms, with or without modification, 
-  are permitted provided that the following conditions are met:
+  are permitted provided that the following conditions are met:
-    
+    
-   * Redistributions of source code must retain the above copyright notice, this 
+   * Redistributions of source code must retain the above copyright notice, this 
-     list of conditions and the following disclaimer.
+     list of conditions and the following disclaimer.
-   * Redistributions in binary form must reproduce the above copyright notice, 
+   * Redistributions in binary form must reproduce the above copyright notice, 
-     this list of conditions and the following disclaimer in the documentation 
+     this list of conditions and the following disclaimer in the documentation 
-     and/or other materials provided with the distribution.
+     and/or other materials provided with the distribution.
-   * Neither the name of HL7 nor the names of its contributors may be used to 
+   * Neither the name of HL7 nor the names of its contributors may be used to 
-     endorse or promote products derived from this software without specific 
+     endorse or promote products derived from this software without specific 
-     prior written permission.
+     prior written permission.
-  
+  
-  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
-  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
+  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
-  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
+  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
-  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
+  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
-  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
+  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
-  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
+  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
-  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
-  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
-  POSSIBILITY OF SUCH DAMAGE.
+  POSSIBILITY OF SUCH DAMAGE.
-  
+  
- */
+ */
 
 
 
@@ -52,6 +52,7 @@ import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.IniFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class BatchLoader {
 
@@ -68,7 +69,7 @@ public class BatchLoader {
         throw new FHIRException("Unimplemented file type "+file);
 //      } else if (file.endsWith(".zip")) {
 //        LoadZipFile(server, file, p, size, 0, -1);
-      } else if (new File(file).isDirectory()) {
+      } else if (ManagedFileAccess.file(file).isDirectory()) {
         LoadDirectory(server, file, size);
       } else 
         throw new FHIRException("Unknown file type "+file);
@@ -81,7 +82,7 @@ public class BatchLoader {
     System.out.println("Done");
     
     IniFile ini = new IniFile(Utilities.path(folder, "batch-load-progress.ini"));
-    for (File f : new File(folder).listFiles()) {
+    for (File f : ManagedFileAccess.file(folder).listFiles()) {
       if (f.getName().endsWith(".json") || f.getName().endsWith(".xml")) {
         if (!ini.getBooleanProperty("finished", f.getName())) {
           sendFile(client, f, size, ini);
@@ -145,7 +146,7 @@ public class BatchLoader {
 //    Bundle b = new Bundle();
 //    b.setType(BundleType.COLLECTION);
 //    b.setId(UUID.randomUUID().toString().toLowerCase());
-//    ZipInputStream zip = new ZipInputStream(new FileInputStream(file));
+//    ZipInputStream zip = new ZipInputStream(ManagedFileAccess.inStream(file));
 //    ZipEntry entry;
 //    while((entry = zip.getNextEntry())!=null)
 //    {

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/R3TEchnicalCorrectionProcessor.java

@@ -19,6 +19,7 @@ import org.hl7.fhir.dstu3.model.DomainResource;
 import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class R3TEchnicalCorrectionProcessor {
 
@@ -31,10 +32,10 @@ public class R3TEchnicalCorrectionProcessor {
     System.out.println("Loading resources from "+src);
     List<Resource> resources = new ArrayList<>();
     Map<String, Resource> definitions = new HashMap<>();
-    for (File f : new File(src).listFiles()) {
+    for (File f : ManagedFileAccess.file(src).listFiles()) {
       if (f.getName().endsWith(".xml") && !(f.getName().endsWith("warnings.xml") || f.getName().endsWith(".diff.xml"))) {
         try {
-          Resource r = new XmlParser().parse(new FileInputStream(f));
+          Resource r = new XmlParser().parse(ManagedFileAccess.inStream(f));
           if (f.getName().contains("canonical")) {
             resources.add(r);
           }
@@ -43,17 +44,17 @@ public class R3TEchnicalCorrectionProcessor {
             definitions.put(f.getName(), r);
           }
           r.setUserData("path", f.getName().substring(0, f.getName().indexOf(".")));
-//          FileUtils.copyFile(f, new File(f.getAbsolutePath()+"1"));
+//          FileUtils.copyFile(f, ManagedFileAccess.file(f.getAbsolutePath()+"1"));
-//          FileUtils.copyFile(f, new File(f.getAbsolutePath()+"2"));
+//          FileUtils.copyFile(f, ManagedFileAccess.file(f.getAbsolutePath()+"2"));
         } catch (Exception e) {
           System.out.println("Unable to load "+f.getName()+": "+e.getMessage());
         }
       }
       if (f.getName().endsWith(".json") && !(f.getName().endsWith("schema.json") || f.getName().endsWith(".diff.json"))) {
         try {
-//          new JsonParser().parse(new FileInputStream(f));
+//          new JsonParser().parse(ManagedFileAccess.inStream(f));
-//          FileUtils.copyFile(f, new File(f.getAbsolutePath()+"1"));
+//          FileUtils.copyFile(f, ManagedFileAccess.file(f.getAbsolutePath()+"1"));
-//          FileUtils.copyFile(f, new File(f.getAbsolutePath()+"2"));
+//          FileUtils.copyFile(f, ManagedFileAccess.file(f.getAbsolutePath()+"2"));
         } catch (Exception e) {
           System.out.println("Unable to load "+f.getName()+": "+e.getMessage());
         }
@@ -79,15 +80,15 @@ public class R3TEchnicalCorrectionProcessor {
 
   private void produceDefinitionsXml(Map<String, Resource> definitions, String dest) throws IOException {
     for (String n : definitions.keySet()) {
-      File f = new File(Utilities.path(dest, "definitions.xml", n));
+      File f = ManagedFileAccess.file(Utilities.path(dest, "definitions.xml", n));
-      new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f), definitions.get(n));     
+      new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), definitions.get(n));     
     }
   }
 
   private void produceDefinitionsJson(Map<String, Resource> definitions, String dest) throws IOException {
     for (String n : definitions.keySet()) {
-      File f = new File(Utilities.path(dest, "definitions.json", Utilities.changeFileExt(n, ".json")));
+      File f = ManagedFileAccess.file(Utilities.path(dest, "definitions.json", Utilities.changeFileExt(n, ".json")));
-      new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f), definitions.get(n));     
+      new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), definitions.get(n));     
     }
   }
 
@@ -97,8 +98,8 @@ public class R3TEchnicalCorrectionProcessor {
       if (!r.getId().equals(r.getUserString("path"))) {
         n = n+"("+r.getId()+")";
       }
-      File f = new File(Utilities.path(dest, "examples-json", n+".json"));
+      File f = ManagedFileAccess.file(Utilities.path(dest, "examples-json", n+".json"));
-      new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
+      new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), r);
     }
     
   }
@@ -109,8 +110,8 @@ public class R3TEchnicalCorrectionProcessor {
       if (!r.getId().equals(r.getUserString("path"))) {
         n = n+"("+r.getId()+")";
       }
-      File f = new File(Utilities.path(dest, "examples", n+".xml"));
+      File f = ManagedFileAccess.file(Utilities.path(dest, "examples", n+".xml"));
-      new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
+      new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), r);
     }
   }
 
@@ -119,9 +120,9 @@ public class R3TEchnicalCorrectionProcessor {
     String corePath = Utilities.path(root, "hl7.fhir.r3.core", "package");
     String examplesPath = Utilities.path(root, "hl7.fhir.r3.examples", "package");
     String elementsPath = Utilities.path(root, "hl7.fhir.r3.elements", "package");
-    int coreTotal = new File(corePath).list().length-1;
+    int coreTotal = ManagedFileAccess.file(corePath).list().length-1;
-    int examplesTotal = new File(examplesPath).list().length-1;
+    int examplesTotal = ManagedFileAccess.file(examplesPath).list().length-1;
-    int elementsTotal = new File(elementsPath).list().length-1;
+    int elementsTotal = ManagedFileAccess.file(elementsPath).list().length-1;
         
     int coreCount = 0;
     int examplesCount = 0;
@@ -131,17 +132,17 @@ public class R3TEchnicalCorrectionProcessor {
       FileOutputStream dst = null;
         if (n.startsWith("DataElement-")) {
           elementsCount++;
-          dst = new FileOutputStream(Utilities.path(elementsPath, n));
+          dst = ManagedFileAccess.outStream(Utilities.path(elementsPath, n));
           new JsonParser().setOutputStyle(OutputStyle.NORMAL).compose(dst, r);
         } else {
-          dst = new FileOutputStream(Utilities.path(examplesPath, n));
+          dst = ManagedFileAccess.outStream(Utilities.path(examplesPath, n));
           new JsonParser().setOutputStyle(OutputStyle.NORMAL).compose(dst, r);
           examplesCount++;
           if (isCoreResource(r.fhirType())) {
             coreCount++;
             DomainResource dr = (DomainResource) r;
             dr.setText(null);
-            new JsonParser().setOutputStyle(OutputStyle.NORMAL).compose(new FileOutputStream(Utilities.path(corePath, n)), r);
+            new JsonParser().setOutputStyle(OutputStyle.NORMAL).compose(ManagedFileAccess.outStream(Utilities.path(corePath, n)), r);
           }
         }
     }

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/Translations.java

@@ -40,7 +40,7 @@ import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 
-import org.hl7.fhir.utilities.CSFileInputStream;
+import org.hl7.fhir.utilities.filesystem.CSFileInputStream;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/Unbundler.java

@@ -1,33 +1,33 @@
 package org.hl7.fhir.dstu3.utils;
 
-/*
+/*
-  Copyright (c) 2011+, HL7, Inc.
+  Copyright (c) 2011+, HL7, Inc.
-  All rights reserved.
+  All rights reserved.
-  
+  
-  Redistribution and use in source and binary forms, with or without modification, 
+  Redistribution and use in source and binary forms, with or without modification, 
-  are permitted provided that the following conditions are met:
+  are permitted provided that the following conditions are met:
-    
+    
-   * Redistributions of source code must retain the above copyright notice, this 
+   * Redistributions of source code must retain the above copyright notice, this 
-     list of conditions and the following disclaimer.
+     list of conditions and the following disclaimer.
-   * Redistributions in binary form must reproduce the above copyright notice, 
+   * Redistributions in binary form must reproduce the above copyright notice, 
-     this list of conditions and the following disclaimer in the documentation 
+     this list of conditions and the following disclaimer in the documentation 
-     and/or other materials provided with the distribution.
+     and/or other materials provided with the distribution.
-   * Neither the name of HL7 nor the names of its contributors may be used to 
+   * Neither the name of HL7 nor the names of its contributors may be used to 
-     endorse or promote products derived from this software without specific 
+     endorse or promote products derived from this software without specific 
-     prior written permission.
+     prior written permission.
-  
+  
-  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
-  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
+  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
-  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
+  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
-  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
+  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
-  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
+  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
-  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
+  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
-  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
-  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
-  POSSIBILITY OF SUCH DAMAGE.
+  POSSIBILITY OF SUCH DAMAGE.
-  
+  
- */
+ */
 
 
 
@@ -42,6 +42,7 @@ import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class Unbundler {
 
@@ -51,12 +52,12 @@ public class Unbundler {
 
   private static void unbundle(String src) throws FHIRFormatError, FileNotFoundException, IOException {
     String folder = Utilities.getDirectoryForFile(src);
-    Bundle bnd = (Bundle) new JsonParser().parse(new FileInputStream(src));
+    Bundle bnd = (Bundle) new JsonParser().parse(ManagedFileAccess.inStream(src));
     for (BundleEntryComponent be : bnd.getEntry()) {
       Resource r = be.getResource();
       if (r != null) {
         String tgt = Utilities.path(folder, r.fhirType()+"-"+r.getId()+".json");
-        new JsonParser().compose(new FileOutputStream(tgt), r);
+        new JsonParser().compose(ManagedFileAccess.outStream(tgt), r);
       }
     }
   }

org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/FluentPathTests.java

@@ -19,6 +19,7 @@ import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.dstu3.test.support.TestingUtilities;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeAll;
@@ -59,7 +60,7 @@ public class FluentPathTests {
       if (Utilities.noString(input))
         fp.check(null, null, node);
       else {
-        res = new XmlParser().parse(new FileInputStream(Utilities.path("C:\\work\\org.hl7.fhir\\build\\publish", input)));
+        res = new XmlParser().parse(ManagedFileAccess.inStream(Utilities.path("C:\\work\\org.hl7.fhir\\build\\publish", input)));
         fp.check(res, res.getResourceType().toString(), res.getResourceType().toString(), node);
       }
       outcome = fp.evaluate(res, node);

org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/NarrativeGeneratorTests.java

@@ -12,6 +12,7 @@ import org.hl7.fhir.dstu3.utils.EOperationOutcome;
 import org.hl7.fhir.dstu3.utils.NarrativeGenerator;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Disabled;
@@ -41,9 +42,9 @@ public class NarrativeGeneratorTests {
 
   private void process(String path) throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
     XmlParser p = new XmlParser();
-    DomainResource r = (DomainResource) p.parse(new FileInputStream(path));
+    DomainResource r = (DomainResource) p.parse(ManagedFileAccess.inStream(path));
     gen.generate(r);
-    FileOutputStream s = new FileOutputStream(Utilities.path("[tmp]", "gen.xml"));
+    FileOutputStream s = ManagedFileAccess.outStream(Utilities.path("[tmp]", "gen.xml"));
     new XmlParser().compose(s, r, true);
     s.close();
 

org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/ProfileUtilitiesTests.java

@@ -26,8 +26,9 @@ import org.hl7.fhir.dstu3.utils.EOperationOutcome;
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
-import org.hl7.fhir.utilities.CSFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.CSFile;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 
@@ -45,8 +46,8 @@ public class ProfileUtilitiesTests {
   public static void main(String[] args) throws EOperationOutcome, Exception {
     // new ProfileUtilitiesTests().execute(args);
     new ProfileUtilitiesTests("C:\\work\\org.hl7.fhir\\build\\publish").testSnapshotGeneration();
-    //    StructureDefinition p = (StructureDefinition) new XmlParser().parse(new FileInputStream("C:\\work\\org.hl7.fhir\\build\\publish\\lipid-report-cholesterol.profile.xml"));
+    //    StructureDefinition p = (StructureDefinition) new XmlParser().parse(ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\build\\publish\\lipid-report-cholesterol.profile.xml"));
-    //    new ProfileUtilities(context, messages, null).generateSchematrons(new FileOutputStream(Utilities.path("[tmp]", "test.sch"), p);
+    //    new ProfileUtilities(context, messages, null).generateSchematrons(ManagedFileAccess.outStream(Utilities.path("[tmp]", "test.sch"), p);
   }
   
   public void execute(String[] args) throws FileNotFoundException, IOException, FHIRException {
@@ -76,9 +77,9 @@ public class ProfileUtilitiesTests {
     System.out.println("processing output");
     for (ProfileComparison outcome : comp.getComparisons()) { 
       if (outcome.getSubset() != null)
-        new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "intersection-"+outcome.getId()+".xml")), outcome.getSubset());
+        new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "intersection-"+outcome.getId()+".xml")), outcome.getSubset());
       if (outcome.getSuperset() != null)
-        new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "union-"+outcome.getId()+".xml")), outcome.getSuperset());
+        new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "union-"+outcome.getId()+".xml")), outcome.getSuperset());
     
       System.out.println("\r\n"+outcome.getId()+": Comparison of "+outcome.getLeft().getUrl()+" and "+outcome.getRight().getUrl());
       for (ValidationMessage vm : outcome.getMessages())
@@ -101,8 +102,8 @@ public class ProfileUtilitiesTests {
   private void compare(String fn1, String fn2) throws FHIRFormatError, FileNotFoundException, IOException, DefinitionException {
     System.out.println("Compare "+fn1+" to "+fn2);
     System.out.println("  .. load");
-    StructureDefinition left = (StructureDefinition) new XmlParser().parse(new FileInputStream(Utilities.path(root, fn1)));
+    StructureDefinition left = (StructureDefinition) new XmlParser().parse(ManagedFileAccess.inStream(Utilities.path(root, fn1)));
-    StructureDefinition right = (StructureDefinition) new XmlParser().parse(new FileInputStream(Utilities.path(root, fn2)));
+    StructureDefinition right = (StructureDefinition) new XmlParser().parse(ManagedFileAccess.inStream(Utilities.path(root, fn2)));
     System.out.println(" .. compare");
     comp.compareProfiles(left, right);
     
@@ -893,14 +894,14 @@ public class ProfileUtilitiesTests {
 //    focus.setDifferential(null);
     String f1 = Utilities.path("c:", "temp", "base.xml");
     String f2 = Utilities.path("c:", "temp", "derived.xml");
-    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f1), base);;
+    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f1), base);;
-    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f2), focus);;
+    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f2), focus);;
     String diff = Utilities.path(System.getenv("ProgramFiles(X86)"), "WinMerge", "WinMergeU.exe");
     List<String> command = new ArrayList<String>();
     command.add("\"" + diff + "\" \"" + f1 + "\" \"" + f2 + "\"");
 
     ProcessBuilder builder = new ProcessBuilder(command);
-    builder.directory(new CSFile(Utilities.path("[tmp]")));
+    builder.directory(ManagedFileAccess.csfile(Utilities.path("[tmp]")));
     builder.start();
 
   }

org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/QuestionnaireBuilderTester.java

@@ -1,7 +1,9 @@
 package org.hl7.fhir.dstu3.test;
 
 import java.io.File;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import java.io.FileInputStream;
+import java.io.IOException;
 
 import org.hl7.fhir.dstu3.formats.XmlParser;
 import org.hl7.fhir.dstu3.model.StructureDefinition;
@@ -13,15 +15,15 @@ public class QuestionnaireBuilderTester {
 	private static final String TEST_PROFILE_DIR = "C:\\work\\org.hl7.fhir\\build\\publish";
 //	private static final String TEST_DEST = Utilities.path("[tmp]", "questionnaires\\");
 
-	public static void main(String[] args) {
+	public static void main(String[] args) throws IOException {
 		QuestionnaireBuilder b = new QuestionnaireBuilder(null);
-		for (String f : new File(TEST_PROFILE_DIR).list()) {
+		for (String f : ManagedFileAccess.file(TEST_PROFILE_DIR).list()) {
 			if (f.endsWith(".profile.xml") && !f.contains("type-")) {
 				System.out.println("process "+f);
 				try {
-					StructureDefinition p = (StructureDefinition) new XmlParser().parse(new FileInputStream(TEST_PROFILE_DIR+"\\"+f));
+					StructureDefinition p = (StructureDefinition) new XmlParser().parse(ManagedFileAccess.inStream(TEST_PROFILE_DIR+"\\"+f));
 //					Questionnaire q = b.buildQuestionnaire(p);
-//					new XmlComposer().compose(new FileOutputStream(TEST_DEST+f), q, true);
+//					new XmlComposer().compose(ManagedFileAccess.outStream(TEST_DEST+f), q, true);
 					  throw new FHIRException("test");
         } catch (Exception e) {
 	        e.printStackTrace();

org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/ResourceRoundTripTests.java

@@ -14,6 +14,7 @@ import org.hl7.fhir.dstu3.test.support.TestingUtilities;
 import org.hl7.fhir.dstu3.utils.EOperationOutcome;
 import org.hl7.fhir.dstu3.utils.NarrativeGenerator;
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 
@@ -24,9 +25,9 @@ public class ResourceRoundTripTests {
   public void test() throws FileNotFoundException, IOException, FHIRException, EOperationOutcome {
     if (TestingUtilities.context == null)
       TestingUtilities.context = SimpleWorkerContext.fromPack("C:\\work\\org.hl7.fhir\\build\\publish\\definitions.xml.zip");
-    Resource res = new XmlParser().parse(new FileInputStream("C:\\work\\org.hl7.fhir\\build\\tests\\resources\\unicode.xml"));
+    Resource res = new XmlParser().parse(ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\build\\tests\\resources\\unicode.xml"));
     new NarrativeGenerator("", "", TestingUtilities.context).generate((DomainResource) res);
-    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream("C:\\work\\org.hl7.fhir\\build\\tests\\resources\\unicode.out.xml"), res);
+    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream("C:\\work\\org.hl7.fhir\\build\\tests\\resources\\unicode.out.xml"), res);
   }
 
 }

org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/ResourceTest.java

@@ -45,6 +45,7 @@ import org.hl7.fhir.dstu3.formats.XmlParser;
 import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.dstu3.test.support.TestingUtilities;
 import org.hl7.fhir.exceptions.FHIRFormatError;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 
 public class ResourceTest {
 
@@ -66,18 +67,18 @@ public class ResourceTest {
       p = new JsonParser();
     else
       p = new XmlParser(false);
-    Resource rf = p.parse(new FileInputStream(source));
+    Resource rf = p.parse(ManagedFileAccess.inStream(source));
 
-    FileOutputStream out = new FileOutputStream(source.getAbsoluteFile()+".out.json");
+    FileOutputStream out = ManagedFileAccess.outStream(source.getAbsoluteFile()+".out.json");
     JsonParser json1 = new JsonParser();
     json1.setOutputStyle(OutputStyle.PRETTY);
     json1.compose(out, rf);
     out.close();
 
     JsonParser json = new JsonParser();
-    rf = json.parse(new FileInputStream(source.getAbsoluteFile()+".out.json"));
+    rf = json.parse(ManagedFileAccess.inStream(source.getAbsoluteFile()+".out.json"));
     
-    out = new FileOutputStream(source.getAbsoluteFile()+".out.xml");
+    out = ManagedFileAccess.outStream(source.getAbsoluteFile()+".out.xml");
     XmlParser atom = new XmlParser(); 
     atom.setOutputStyle(OutputStyle.PRETTY);
     atom.compose(out, rf, true);
@@ -89,9 +90,9 @@ public class ResourceTest {
   public Element testEM() throws Exception {
     if (TestingUtilities.context == null)
       TestingUtilities.context = SimpleWorkerContext.fromPack("C:\\work\\org.hl7.fhir\\build\\publish\\definitions.xml.zip");
-  	Element resource = Manager.parse(TestingUtilities.context, new FileInputStream(source), isJson() ? FhirFormat.JSON : FhirFormat.XML);
+  	Element resource = Manager.parse(TestingUtilities.context, ManagedFileAccess.inStream(source), isJson() ? FhirFormat.JSON : FhirFormat.XML);
-  	Manager.compose(TestingUtilities.context, resource, new FileOutputStream(source.getAbsoluteFile()+".out.json"), FhirFormat.JSON, OutputStyle.PRETTY, null);
+  	Manager.compose(TestingUtilities.context, resource, ManagedFileAccess.outStream(source.getAbsoluteFile()+".out.json"), FhirFormat.JSON, OutputStyle.PRETTY, null);
-  	Manager.compose(TestingUtilities.context, resource, new FileOutputStream(source.getAbsoluteFile()+".out.json"), FhirFormat.XML, OutputStyle.PRETTY, null);
+  	Manager.compose(TestingUtilities.context, resource, ManagedFileAccess.outStream(source.getAbsoluteFile()+".out.json"), FhirFormat.XML, OutputStyle.PRETTY, null);
   	return resource;
   }
 

org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/SingleTest.java

@@ -30,6 +30,7 @@ package org.hl7.fhir.dstu3.test;
 
 import java.io.File;
 
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.junit.jupiter.api.Disabled;
 
 @Disabled
@@ -41,7 +42,7 @@ public class SingleTest {
   public static void main(String[] args) {
     try {
       ResourceTest r = new ResourceTest();
-      r.setSource(new File("C:\\work\\org.hl7.fhir\\fhir-test-cases\\r3\\ActivityDefinition-referralPrimaryCareMentalHealth.json"));
+      r.setSource(ManagedFileAccess.file("C:\\work\\org.hl7.fhir\\fhir-test-cases\\r3\\ActivityDefinition-referralPrimaryCareMentalHealth.json"));
       r.test();
       System.out.println("Completed OK");
     } catch (Exception e) {

org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/SnapShotGenerationTests.java

@@ -37,6 +37,7 @@ import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.exceptions.PathEngineException;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.params.ParameterizedTest;
@@ -89,7 +90,7 @@ public class SnapShotGenerationTests {
     context.fixtures.put(op.getResponseId(), output);
     context.snapshots.put(output.getUrl(), output);
 
-    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(Utilities.path("[tmp]"), op.getResponseId() + ".xml")), output);
+    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(Utilities.path("[tmp]"), op.getResponseId() + ".xml")), output);
     //ok, now the asserts:
     for (int i = 1; i < test.getAction().size(); i++) {
       SetupActionAssertComponent a = test.getAction().get(i).getAssert();