From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 3 Nov 2005 14:10:01 +0000 (+0000)
Subject: Vamsas Archive Reader and simple test class.
X-Git-Tag: Release_0.2~433
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8c0230fceb94cba911790b1622b030d02eb0e7ac;hp=5fb0ffd7883f1723b9461a318c107b64a24de3f3;p=vamsas.git

Vamsas Archive Reader and simple test class.


git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@87 be28352e-c001-0410-b1a7-c7978e42abec
---

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);
+      }
+    }
+  }
+}
diff --git a/src/org/vamsas/test/simpleclient/ArchiveReader.java b/src/org/vamsas/test/simpleclient/ArchiveReader.java
new file mode 100644
index 0000000..2156c51
--- /dev/null
+++ b/src/org/vamsas/test/simpleclient/ArchiveReader.java
@@ -0,0 +1,72 @@
+package org.vamsas.test.simpleclient;
+
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.Vector;
+
+import org.vamsas.client.simpleclient.VamsasArchiveReader;
+import org.vamsas.objects.core.VAMSAS;
+import org.vamsas.objects.core.VamsasDocument;
+
+public class ArchiveReader {
+  public static boolean reportDocument(VamsasDocument document) {
+    if (document!=null) {
+      System.out.print("Vamsas Document version '"+document.getVersion()+"'");
+      System.out.print("Document contains "+document.getVAMSASCount()+" VAMSAS Elements and "+document.getApplicationDataCount()+" elements.\n");
+      return true;
+    } else {
+      System.out.print("Document Object is null");
+    }
+    return false;
+  }
+  
+  public static boolean rootReport(VAMSAS[] roots) {
+    if (roots!=null) {
+      for (int i=0; i<roots.length; i++) {
+        VAMSAS r = roots[i];
+        System.out.print("Vamsas Root "+i+" (id="
+            +((r.getId()!=null) ? r.getId():"<none>")
+            +") contains "+r.getDataSetCount()+" DataSets, "
+            + r.getTreeCount()+" Global trees");
+      }
+      return true;
+    }
+    return false;
+  }
+  
+  public static void main(String args[]) {
+    
+    try {
+      File av = new File(args[0]);
+      VamsasArchiveReader var = new VamsasArchiveReader(av);
+      VAMSAS roots[]=null;
+      if (var.isValid()) {
+        InputStreamReader vdoc = new InputStreamReader(var.getVamsasDocumentStream());
+        VamsasDocument doc = VamsasDocument.unmarshal(vdoc);
+        if (reportDocument(doc)) {
+          roots = doc.getVAMSAS();
+        }
+      } else {
+        InputStream vxmlis = var.getVamsasXmlStream();
+        
+        if (vxmlis!=null) { // Might be an old vamsas file.
+          BufferedInputStream ixml = new BufferedInputStream(var.getVamsasXmlStream());
+          InputStreamReader vxml = new InputStreamReader(ixml);
+          VAMSAS root;
+          // unmarshal seems to always close the stream (should check this)
+          if ((root = VAMSAS.unmarshal(vxml))!=null) {
+            System.out.println("Read a root.");
+            roots = new VAMSAS[1];
+            roots[0] = root;
+          }
+        }
+      }
+      if (!rootReport(roots))
+        System.err.print(args[0]+" is not a valid vamsas archive.");
+    } catch (Exception e) {
+      e.printStackTrace(System.err);
+    }
+  }
+}