Fix bug in Package installation

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/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() {
@@ -199,7 +205,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
   }
 
   public String getFolder() {
-    return cacheFolder;
+    return cacheFolder.getAbsolutePath();
   }
 
   private NpmPackage loadPackageInfo(String path) throws IOException {
@@ -208,7 +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());
@@ -308,7 +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 + "#")) {
@@ -396,7 +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 + "#"))) {
@@ -865,7 +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());
       }
@@ -1021,7 +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);