Merge pull request #1334 from hapifhir/gg-202206-npm-install

Gg 202206 npm install

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

@@ -258,8 +258,11 @@ public class FTPClient {
   private void attemptUpload(String source, String resolvedPath) throws IOException {
     final long startTime = System.nanoTime();
     FileInputStream localStream = new FileInputStream(source);
-    clientImpl.storeFile(resolvedPath, localStream);
+    try {
-    localStream.close();
+      clientImpl.storeFile(resolvedPath, localStream);
+    } finally {
+      localStream.close();
+    }
     this.storeFileTimeNanos += System.nanoTime() - startTime;
   }
 

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

@@ -90,11 +90,16 @@ public class TextFile {
 	
 	
   public static void stringToFile(String content, File file) throws IOException {
-    OutputStreamWriter sw = new OutputStreamWriter(new FileOutputStream(file), "UTF-8");
+    FileOutputStream fs = new FileOutputStream(file);
-    sw.write('\ufeff');  // Unicode BOM, translates to UTF-8 with the configured outputstreamwriter
+    try {
-    sw.write(content);
+      OutputStreamWriter sw = new OutputStreamWriter(fs, "UTF-8");
-    sw.flush();
+      sw.write('\ufeff');  // Unicode BOM, translates to UTF-8 with the configured outputstreamwriter
-    sw.close();
+      sw.write(content);
+      sw.flush();
+      sw.close();
+    } finally {
+      fs.close();
+    }
   }
   
   public static void stringToStream(String content, OutputStream stream, boolean bom) throws IOException {
@@ -124,7 +129,8 @@ public class TextFile {
   }
 
   public static void stringToFile(String content, File file, boolean bom) throws IOException  {
-    OutputStreamWriter sw = new OutputStreamWriter(new FileOutputStream(file), "UTF-8");
+    FileOutputStream fs = new FileOutputStream(file);
+    OutputStreamWriter sw = new OutputStreamWriter(fs, "UTF-8");
     if (bom)
       sw.write('\ufeff');  // Unicode BOM, translates to UTF-8 with the configured outputstreamwriter
     sw.write(content);

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

@@ -628,6 +628,15 @@ public class Utilities {
     return PathBuilder.getPathBuilder().buildPath(args);
   }
 
+  public static String path(File f, String... args) throws IOException {
+    String[] a = new String[args.length+1];
+    a[0] = f.getAbsolutePath();
+    for (int i = 0; i < args.length; i++) {
+      a[i+1] = args[i];
+    }
+    return PathBuilder.getPathBuilder().buildPath(a);
+  }
+
   /**
    * Composes a path string using by concatenating the passed arguments.
    *

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

@@ -91,11 +91,11 @@ public class XsltUtilities {
     return res.getOutputStream().toString();
   }
 
-  public static void saxonTransform(String xsltDir, String source, String xslt, String dest, URIResolver alt) throws FileNotFoundException, TransformerException {
+  public static void saxonTransform(String xsltDir, String source, String xslt, String dest, URIResolver alt) throws TransformerException, IOException {
     saxonTransform(xsltDir, source, xslt, dest, alt, null);
   }
 
-  public static void saxonTransform(String xsltDir, String source, String xslt, String dest, URIResolver alt, Map<String, String> params) throws FileNotFoundException, TransformerException {
+  public static void saxonTransform(String xsltDir, String source, String xslt, String dest, URIResolver alt, Map<String, String> params) throws TransformerException, IOException {
     TransformerFactoryImpl f = new net.sf.saxon.TransformerFactoryImpl();
     f.setAttribute("http://saxon.sf.net/feature/version-warning", Boolean.FALSE);
     StreamSource xsrc = new StreamSource(new FileInputStream(xslt));
@@ -108,12 +108,19 @@ public class XsltUtilities {
     }
 
     t.setURIResolver(new MyURIResolver(xsltDir, alt));
-    StreamSource src = new StreamSource(new FileInputStream(source));
+    FileInputStream fso = new FileInputStream(source);
-    StreamResult res = new StreamResult(new FileOutputStream(dest));
+    FileOutputStream fsr = new FileOutputStream(dest);
-    t.transform(src, res);
+    try {
+      StreamSource src = new StreamSource(fso);
+      StreamResult res = new StreamResult(fsr);
+      t.transform(src, res);
+    } finally {
+      fso.close();
+      fsr.close();
+    }
   }
 
-  public static void transform(String xsltDir, String source, String xslt, String dest, URIResolver alt) throws FileNotFoundException, TransformerException {
+  public static void transform(String xsltDir, String source, String xslt, String dest, URIResolver alt) throws TransformerException, IOException {
 
     TransformerFactory f = TransformerFactory.newInstance();
     StreamSource xsrc = new StreamSource(new FileInputStream(xslt));
@@ -121,9 +128,16 @@ public class XsltUtilities {
     Transformer t = f.newTransformer(xsrc);
 
     t.setURIResolver(new MyURIResolver(xsltDir, alt));
-    StreamSource src = new StreamSource(new FileInputStream(source));
+    FileInputStream fss = new FileInputStream(source);
-    StreamResult res = new StreamResult(new FileOutputStream(dest));
+    FileOutputStream fsr = new FileOutputStream(dest);
-    t.transform(src, res);
+    try {
+      StreamSource src = new StreamSource(fss);
+      StreamResult res = new StreamResult(fsr);
+      t.transform(src, res);
+    } finally {
+      fss.close();
+      fsr.close();
+    }
 
   }
 

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

@@ -49,7 +49,12 @@ public class JsonLangFileProducer extends LanguageFileProducer {
 
     @Override
     public void finish() throws IOException {
-      JsonParser.compose(json, new FileOutputStream(getFileName(id, baseLang)));
+      FileOutputStream fs = new FileOutputStream(getFileName(id, baseLang));
+      try {
+        JsonParser.compose(json, fs);
+      } finally {
+        fs.close();
+      }
     }
   }
 

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java

@@ -109,7 +109,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
   public static final String PACKAGE_VERSION_REGEX_OPT = "^[A-Za-z][A-Za-z0-9\\_\\-]*(\\.[A-Za-z0-9\\_\\-]+)+(\\#[A-Za-z0-9\\-\\_]+(\\.[A-Za-z0-9\\-\\_]+)*)?$";
   private static final Logger ourLog = LoggerFactory.getLogger(FilesystemPackageCacheManager.class);
   private static final String CACHE_VERSION = "3"; // second version - see wiki page
-  private String cacheFolder;
+  private File cacheFolder;
   private boolean progress = true;
   private List<NpmPackage> temporaryPackages = new ArrayList<>();
   private boolean buildLoaded = false;
@@ -134,7 +134,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
    * @throws IOException
    */
   public FilesystemPackageCacheManager(String customFolder) throws IOException {
-    this.cacheFolder = customFolder;
+    this.cacheFolder = new File(customFolder);
     init(FilesystemPackageCacheMode.CUSTOM);  
   }
   
@@ -144,27 +144,33 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
 
     switch (mode) {
     case SYSTEM:
-      cacheFolder = Utilities.path("var", "lib", ".fhir", "packages");
+      cacheFolder = new File(Utilities.path("var", "lib", ".fhir", "packages"));
       break;
     case USER:
-      cacheFolder = Utilities.path(System.getProperty("user.home"), ".fhir", "packages");
+      cacheFolder = new File(Utilities.path(System.getProperty("user.home"), ".fhir", "packages"));
       break;
     case TESTING:
-      cacheFolder = Utilities.path("[tmp]", ".fhir", "packages");
+      cacheFolder = new File(Utilities.path("[tmp]", ".fhir", "packages"));
       break;
     case CUSTOM:
-      if (!new File(cacheFolder).exists()) {
+      if (!cacheFolder.exists()) {
         throw new FHIRException("The folder ''"+cacheFolder+"' could not be found");
       }
     default:
       break;    
     }
 
-    if (!(new File(cacheFolder).exists()))
+    if (!(cacheFolder.exists()))
-      Utilities.createDirectory(cacheFolder);
+      Utilities.createDirectory(cacheFolder.getAbsolutePath());
     if (!(new File(Utilities.path(cacheFolder, "packages.ini")).exists()))
       TextFile.stringToFile("[cache]\r\nversion=" + CACHE_VERSION + "\r\n\r\n[urls]\r\n\r\n[local]\r\n\r\n", Utilities.path(cacheFolder, "packages.ini"), false);
     createIniFile();
+    for (File f : cacheFolder.listFiles()) {
+      if (f.isDirectory() && Utilities.isValidUUID(f.getName())) {
+        Utilities.clearDirectory(f.getAbsolutePath());
+        f.delete();
+      }
+    }
   }
 
   public boolean isMinimalMemory() {
@@ -187,14 +193,19 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
     if (files != null) {
       for (File f : files) {
         if (f.getName().endsWith(".tgz")) {
-          temporaryPackages.add(NpmPackage.fromPackage(new FileInputStream(f)));
+          FileInputStream fs = new FileInputStream(f);
+          try {
+            temporaryPackages.add(NpmPackage.fromPackage(fs));
+          } finally {
+            fs.close();
+          }
         }
       }
     }
   }
 
   public String getFolder() {
-    return cacheFolder;
+    return cacheFolder.getAbsolutePath();
   }
 
   private NpmPackage loadPackageInfo(String path) throws IOException {
@@ -203,7 +214,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
   }
 
   private void clearCache() throws IOException {
-    for (File f : new File(cacheFolder).listFiles()) {
+    for (File f : cacheFolder.listFiles()) {
       if (f.isDirectory()) {
         new CacheLock(f.getName()).doWithLock(() -> {
           Utilities.clearDirectory(f.getAbsolutePath());
@@ -303,7 +314,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
   }
 
   public String getLatestVersionFromCache(String id) throws IOException {
-    for (String f : Utilities.reverseSorted(new File(cacheFolder).list())) {
+    for (String f : Utilities.reverseSorted(cacheFolder.list())) {
       File cf = new File(Utilities.path(cacheFolder, f));
       if (cf.isDirectory()) {
         if (f.startsWith(id + "#")) {
@@ -391,7 +402,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
     }
     String foundPackage = null;
     String foundVersion = null;
-    for (String f : Utilities.reverseSorted(new File(cacheFolder).list())) {
+    for (String f : Utilities.reverseSorted(cacheFolder.list())) {
       File cf = new File(Utilities.path(cacheFolder, f));
       if (cf.isDirectory()) {
         if (f.equals(id + "#" + version) || (Utilities.noString(version) && f.startsWith(id + "#"))) {
@@ -860,7 +871,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
 
   public List<String> listPackages() {
     List<String> res = new ArrayList<>();
-    for (File f : new File(cacheFolder).listFiles()) {
+    for (File f : cacheFolder.listFiles()) {
       if (f.isDirectory() && f.getName().contains("#")) {
         res.add(f.getName());
       }
@@ -1016,7 +1027,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
       }
     }
 
-    for (String f : Utilities.sorted(new File(cacheFolder).list())) {
+    for (String f : Utilities.sorted(cacheFolder.list())) {
       if (f.equals(id + "#" + version) || (Utilities.noString(version) && f.startsWith(id + "#"))) {
         return true;
       }

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

@@ -447,8 +447,7 @@ public class NpmPackage {
   }
   
   public static NpmPackage extractFromTgz(InputStream tgz, String desc, String tempDir, boolean minimal) throws IOException {
-    String dest =  Utilities.path(tempDir, "package");
+    Utilities.createDirectory(tempDir);
-    Utilities.createDirectory(dest);
 
     int size = 0;
     
@@ -463,21 +462,18 @@ public class NpmPackage {
 
       while ((entry = (TarArchiveEntry) tarIn.getNextEntry()) != null) {
         String n = entry.getName();
-        if (n.startsWith("package/")) {
-          n = n.substring(8);
-        }
         if (n.contains("..")) {
           throw new RuntimeException("Entry with an illegal name: " + n);
         }
         if (entry.isDirectory()) {
           if (!Utilities.noString(n)) {
             String dir = n.substring(0, n.length()-1);
-            Utilities.createDirectory(Utilities.path(dest, dir));
+            Utilities.createDirectory(Utilities.path(tempDir, dir));
           }
         } else {
           int count;
           byte data[] = new byte[BUFFER_SIZE];
-          String filename = Utilities.path(dest, n);
+          String filename = Utilities.path(tempDir, n);
           String folder = Utilities.getDirectoryForFile(filename);
           Utilities.createDirectory(folder);
           FileOutputStream fos = new FileOutputStream(filename);

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/PackageHacker.java

@@ -37,7 +37,13 @@ public class PackageHacker {
     if (!f.exists())
       throw new Error("Unable to find "+f.getAbsolutePath());
     
-    NpmPackage pck = NpmPackage.fromPackage(new FileInputStream(f));
+    NpmPackage pck = null;
+    FileInputStream fs = new FileInputStream(f);
+    try {
+      pck = NpmPackage.fromPackage(fs);
+    } finally {
+      fs.close();
+    }
     System.out.println("Altering Package "+f.getAbsolutePath());
     System.out.println(nice(pck.getNpm()));
     
@@ -51,7 +57,12 @@ public class PackageHacker {
     int r = System.in.read();
     if (r == 'y') {
       f.renameTo(new File(Utilities.changeFileExt(name, ".tgz.bak")));
-      pck.save(new FileOutputStream(f));
+      FileOutputStream fso = new FileOutputStream(f);
+      try {
+        pck.save(fso);
+      } finally {
+        fso.close();
+      }
     }   
   }
 

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/PackageScanner.java

@@ -68,7 +68,6 @@ public class PackageScanner {
           }
         }
       }
-      System.out.println("!");
     }
   }
 

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/ResourceRenamer.java

@@ -30,7 +30,12 @@ public class ResourceRenamer {
       String rt = r.asString("resourceType");
       String id = r.asString("id");
       String nn = Utilities.path(Utilities.getDirectoryForFile(f.getAbsolutePath()), rt+"-"+id+".json");
-      JsonParser.compose(r, new FileOutputStream(nn), true); 
+      FileOutputStream fs = new FileOutputStream(nn);
+      try {
+        JsonParser.compose(r, fs, true);
+      } finally {
+        fs.close();
+      }
     } 
   }
 

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/HierarchicalTableGenerator.java

@@ -1008,9 +1008,13 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
         }
         newFile.createNewFile();
         FileOutputStream stream = new FileOutputStream(file);
-        genImage(indents, hasChildren, lineColor, stream);
+        try {
-        if (outputTracker!=null)
+          genImage(indents, hasChildren, lineColor, stream);
-          outputTracker.add(file);
+          if (outputTracker!=null)
+            outputTracker.add(file);
+        } finally {
+          stream.close();
+        }
       }
       return b.toString();
     }

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xls/XLSXmlNormaliser.java

@@ -117,7 +117,12 @@ public class XLSXmlNormaliser {
     if (!hasComment)
       root.appendChild(xml.createComment("canonicalized"));
     try {
-      saveXml(new FileOutputStream(dest));
+      FileOutputStream fs = new FileOutputStream(dest);
+      try {
+        saveXml(fs);
+      } finally {
+        fs.close();
+      }
       String s = TextFile.fileToString(dest);
       s = s.replaceAll("\r\n","\n");
       s = replaceSignificantEoln(s);

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xml/XMLUtil.java

@@ -55,6 +55,7 @@ import javax.xml.transform.stream.StreamResult;
 
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.npm.NpmPackage;
 import org.w3c.dom.Attr;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -458,14 +459,24 @@ public class XMLUtil {
     DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
     factory.setNamespaceAware(false);
     DocumentBuilder builder = factory.newDocumentBuilder();
-    return builder.parse(new FileInputStream(filename));
+    FileInputStream fs = new FileInputStream(filename);
+    try {
+      return builder.parse(fs);
+    } finally {
+      fs.close();
+    }  
   }
 
   public static Document parseFileToDom(String filename, boolean ns) throws ParserConfigurationException, SAXException, IOException  {
     DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
     factory.setNamespaceAware(ns);
     DocumentBuilder builder = factory.newDocumentBuilder();
-    return builder.parse(new FileInputStream(filename));
+    FileInputStream fs = new FileInputStream(filename);
+    try {
+      return builder.parse(fs);
+    } finally {
+      fs.close();
+    }
   }
 
   public static Element getLastChild(Element e) {

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xml/XmlEscaper.java

@@ -27,7 +27,12 @@ public class XmlEscaper {
   }
   
   public static void convert(String source, String target) throws IOException {
-    convertAndClose(new FileInputStream(source), new FileOutputStream(target));
+    FileOutputStream fs = new FileOutputStream(target);
+    try {
+      convertAndClose(new FileInputStream(source), fs);
+    } finally {
+      fs.close();
+    }
   }
   
   public static void convertAndClose(InputStream source, OutputStream target) throws IOException {

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xml/XmlGenerator.java

@@ -74,7 +74,11 @@ public class XmlGenerator {
   
 	public void generate(Element element, File file) throws IOException, FHIRException  {
 		OutputStream stream = new FileOutputStream(file);
-		generate(element, stream);
+		try {
+		  generate(element, stream);
+    } finally {
+      stream.close();
+    }
 	}	
 	
 	public void generate(Element element, OutputStream stream) throws IOException, FHIRException  {