add saving packages

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

@@ -0,0 +1,52 @@
+package org.hl7.fhir.convertors.misc;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.Map.Entry;
+
+import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.cache.NpmPackage;
+
+import com.google.gson.JsonElement;
+import com.google.gson.JsonObject;
+
+
+public class XMLPackageConvertor {
+
+  public static void main(String[] args) throws FileNotFoundException, IOException {
+   new XMLPackageConvertor().process(new File("C:\\web\\hl7.org\\fhir"));
+  }
+
+  private void process(File folder) throws FileNotFoundException, IOException {
+    for (File f : folder.listFiles()) {
+      if (f.isDirectory()) {
+        process(f);
+      } else {
+        if (f.getName().endsWith(".tgz")) {
+          System.out.println("Package "+f.getAbsolutePath());
+          NpmPackage p = NpmPackage.fromPackage(new FileInputStream(f));
+          if (p.getNpm().has("dependencies")) {
+            JsonObject dep = p.getNpm().getAsJsonObject("dependencies");
+            if (dep.entrySet().isEmpty()) {
+              System.out.println("  Dependencies: none");
+            } else {
+              System.out.println("  Dependencies:");
+              for (Entry<String, JsonElement> e : dep.entrySet()) {
+                System.out.println("    "+e.getKey()+": "+e.getValue().getAsString());
+              }
+            }
+          } else {
+            System.out.println("  Dependencies: n/a");
+          }
+        }
+      }
+        
+      
+    }
+    
+  }
+
+}

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

@@ -29,6 +29,8 @@ import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.OutputStream;
+import java.nio.charset.Charset;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
@@ -40,7 +42,9 @@ import java.util.zip.ZipInputStream;
 
 import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
 import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
+import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream;
 import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
+import org.apache.commons.compress.compressors.gzip.GzipCompressorOutputStream;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.exceptions.FHIRException;
@@ -51,6 +55,8 @@ import org.hl7.fhir.utilities.cache.PackageCacheManager.PackageEntry;
 import org.hl7.fhir.utilities.cache.PackageGenerator.PackageType;
 import org.hl7.fhir.utilities.json.JsonTrackingParser;
 
+import com.google.gson.GsonBuilder;
+import com.google.gson.JsonArray;
 import com.google.gson.JsonElement;
 import com.google.gson.JsonObject;
 
@@ -463,4 +469,57 @@ import com.google.gson.JsonObject;
         FileUtils.copyDirectory(new File(path), new File(dir));      
     }
 
+    public void save(OutputStream stream) throws IOException {
+      TarArchiveOutputStream tar;
+      ByteArrayOutputStream OutputStream;
+      BufferedOutputStream bufferedOutputStream;
+      GzipCompressorOutputStream gzipOutputStream;
+
+      OutputStream = new ByteArrayOutputStream();
+      bufferedOutputStream = new BufferedOutputStream(OutputStream);
+      gzipOutputStream = new GzipCompressorOutputStream(bufferedOutputStream);
+      tar = new TarArchiveOutputStream(gzipOutputStream);
+
+      NpmPackageIndexBuilder indexer = new NpmPackageIndexBuilder();
+      indexer.start();
+
+      for (String s : content.keySet()) {
+        byte[] b = content.get(s);
+        if (s.startsWith("package/")) { 
+          indexer.seeFile(tail(s), b);
+        }
+        if (!s.endsWith(".index.json") && !s.equals("package/package.json")) {
+          TarArchiveEntry entry = new TarArchiveEntry(s);
+          entry.setSize(b.length);
+          tar.putArchiveEntry(entry);
+          tar.write(b);
+          tar.closeArchiveEntry();
+        }
+      }
+      byte[] cnt = new GsonBuilder().setPrettyPrinting().create().toJson(npm).getBytes(Charset.forName("UTF-8"));
+      TarArchiveEntry entry = new TarArchiveEntry("package/package.json");
+      entry.setSize(cnt.length);
+      tar.putArchiveEntry(entry);
+      tar.write(cnt);
+      tar.closeArchiveEntry();
+      
+      cnt = indexer.build().getBytes(Charset.forName("UTF-8"));
+      entry = new TarArchiveEntry("package/.index.json");
+      entry.setSize(cnt.length);
+      tar.putArchiveEntry(entry);
+      tar.write(cnt);
+      tar.closeArchiveEntry();
+
+      tar.finish();
+      tar.close();
+      gzipOutputStream.close();
+      bufferedOutputStream.close();
+      OutputStream.close();
+      byte[] b = OutputStream.toByteArray();
+      stream.write(b);
+    }
+
+    private String tail(String s) {
+      return s.substring(s.lastIndexOf("/")+1);
+    }
   }

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

@@ -529,19 +529,14 @@ public class PackageCacheManager {
       
     int i = 0;
     int c = 0;
+    int size = 0;
     for (Entry<String, byte[]> e : npm.getContent().entrySet()) {
-//      if (e.getValue() == null) {
-//        thorw 
-//        File f = new File(Utilities.path(packRoot, e.name));
-//        if (!f.mkdir()) 
-//          throw new IOException("Unable to create directory '%s', during extraction of archive contents: "+ f.getAbsolutePath());
-//      } else {
       String fn = Utilities.path(packRoot, e.getKey());
       String dir = Utilities.getDirectoryForFile(fn);
       if (!(new File(dir).exists()))
         Utilities.createDirectory(dir);
       TextFile.bytesToFile(e.getValue(), fn);
-//    }
+      size = size + e.getValue().length;
       i++;
       if (progress && i % 50 == 0) {
         c++;
@@ -563,6 +558,7 @@ public class PackageCacheManager {
     IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
     ini.setTimeStampFormat("yyyyMMddhhmmss");
     ini.setTimestampProperty("packages", id+"#"+version, Timestamp.from(Instant.now()), null);
+    ini.setIntegerProperty("package-sizes", id+"#"+version, size, null);
     ini.save();
     if (progress)
       System.out.println(" done.");

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

@@ -0,0 +1,65 @@
+package org.hl7.fhir.utilities.cache;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.Map;
+
+import org.hl7.fhir.utilities.Utilities;
+
+import com.google.gson.GsonBuilder;
+import com.google.gson.JsonArray;
+import com.google.gson.JsonObject;
+
+/**
+ * intenral use only - set the file name to edit in main(), and fill out the edit routine
+ * 
+ * @author grahame
+ *
+ */
+public class PackageHacker {
+
+  public static void main(String[] args) throws FileNotFoundException, IOException {
+  }
+
+  private void edit(String name) throws FileNotFoundException, IOException {
+    File f = new File(name);
+    if (!f.exists())
+      throw new Error("Unable to find "+f.getAbsolutePath());
+    
+    NpmPackage pck = NpmPackage.fromPackage(new FileInputStream(f));
+    System.out.println("Altering Package "+f.getAbsolutePath());
+    System.out.println(nice(pck.getNpm()));
+    
+    change(pck.getNpm(), pck.getContent());
+    
+    System.out.println("Revised Package");
+    System.out.println("=======================");
+    System.out.println(nice(pck.getNpm()));
+    System.out.println("=======================");
+    System.out.print("save? y/n: ");
+    int r = System.in.read();
+    if (r == 'y') {
+      f.renameTo(new File(Utilities.changeFileExt(name, ".tgz.bak")));
+      pck.save(new FileOutputStream(f));
+    }   
+    
+  }
+
+  private String nice(JsonObject json) {
+    return new GsonBuilder().setPrettyPrinting().create().toJson(json);
+  }
+
+  private void change(JsonObject npm, Map<String, byte[]> content) {
+    JsonArray fhirVersions = new JsonArray();
+    fhirVersions.add("1.9.0");
+    npm.add("fhirVersions", fhirVersions);
+    JsonObject dependencies = new JsonObject();
+    dependencies.addProperty("hl7.fhir.r3.core", "3.0.2");
+    npm.remove("dependencies");
+//    npm.add("dependencies", dependencies);
+  }
+
+}