X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fvamsas%2Fclient%2Fsimpleclient%2FVamsasArchiveReader.java;fp=src%2Forg%2Fvamsas%2Fclient%2Fsimpleclient%2FVamsasArchiveReader.java;h=3ca12880d946d7e14f5920a25d9504d1d7f95604;hb=8c0230fceb94cba911790b1622b030d02eb0e7ac;hp=0000000000000000000000000000000000000000;hpb=5fb0ffd7883f1723b9461a318c107b64a24de3f3;p=vamsas.git

diff --git a/src/org/vamsas/client/simpleclient/VamsasArchiveReader.java b/src/org/vamsas/client/simpleclient/VamsasArchiveReader.java
new file mode 100644
index 0000000..3ca1288
--- /dev/null
+++ b/src/org/vamsas/client/simpleclient/VamsasArchiveReader.java
@@ -0,0 +1,125 @@
+package org.vamsas.client.simpleclient;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Iterator;
+import java.util.jar.JarEntry;
+import java.util.jar.JarFile;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+/**
+ * Basic methods for accessing an existing Vamsas Archive, 
+ * and Jar entry names for creating new vamsas archives.
+ * 
+ * @author jimp
+ *
+ */
+public class VamsasArchiveReader {
+  JarFile jfile;
+  public VamsasArchiveReader(File vamsasfile) {
+    jfile=null;
+    if (vamsasfile.exists()) {
+      try {
+        jfile=new JarFile(vamsasfile);
+      }
+      catch (Exception e) {
+        jfile=null;
+      }
+    }
+    
+  }
+  
+  /**
+   * name of the jarEntry containing a well formatted vamsas XML Document
+   */
+  
+  final public static String VAMSASDOC="vamsasDocument.xml";
+  
+  /**
+   * name of the jarEntry containing a root VAMSAS element, and containing a 
+   * random sequence of VAMSAS DataSet elements 
+   */
+  
+  final public static String VAMSASXML="vamsas.xml";
+  
+  /**
+   * 
+   * @return JarEntry for VamsasArchiveReader.VAMSASDOC
+   */
+  protected JarEntry getVamsasDocumentEntry() {
+    if (jfile!=null)
+      return jfile.getJarEntry(VAMSASDOC);
+    return null;
+  }
+  /**
+   * 
+   * @return JarEntry for VamsasArchiveReader.VAMSASXML
+   */
+  protected JarEntry getVamsasXmlEntry() {
+    if (jfile!=null)
+      return jfile.getJarEntry(VAMSASXML);
+    return null;
+  }
+  /**
+   * Test for valid vamsas document archive
+   * @return true if getVamsasDocumentStream will return a stream likely to contain valid XML
+   */
+  public boolean isValid() {
+    if (jfile!=null)
+      // TODO: check if VAMSASDOC is well formed, follows www.vamsas.ac.uk/schemas/vamsasDocument.xsd, and all appData references are resolvable - preferably as jar entries
+      return (getVamsasDocumentEntry()!=null);
+    return false;   
+  }
+
+  /**
+   * get the VamsasDocument input stream, if it exists.
+   * @return null or valid input stream
+   */
+  public InputStream getVamsasDocumentStream() {
+    InputStream vdoc;
+    if (jfile==null || !isValid())
+      return null;
+    try {
+      vdoc = jfile.getInputStream(getVamsasDocumentEntry());
+    } catch (IOException e) {
+      e.printStackTrace(System.err);
+      vdoc=null;
+    }
+    return vdoc;
+  }
+  
+  /**
+   * get the VamsasXML input stream, if it exists.
+   * Note: Deprecated beyond our prealpha testing.
+   * @return null or valid input stream.
+   */
+  
+  public InputStream getVamsasXmlStream() {
+    JarEntry xmle=getVamsasXmlEntry();
+    InputStream vdoc;
+    if (xmle==null)
+      return null;
+    try {
+      vdoc = jfile.getInputStream(xmle);
+    } catch (IOException e) {
+      e.printStackTrace(System.err);
+      vdoc=null;
+    }
+    return vdoc;
+  }
+  
+  /**
+   * silently close the jar file.
+   *
+   */
+  public void close() {
+    if (jfile!=null) {
+      try {
+        jfile.close();
+      } catch (IOException e) {
+        e.printStackTrace(System.err);
+      }
+    }
+  }
+}