X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Forg%2Fvamsas%2Fclient%2Fsimpleclient%2FSimpleDocBinding.java;fp=src%2Forg%2Fvamsas%2Fclient%2Fsimpleclient%2FSimpleDocBinding.java;h=c0c80849d4f8e9c0fd6781a2637d7d6ab8350f2f;hb=e15b38a5b95e0aa5b11707728abb539c073fe27c;hp=0000000000000000000000000000000000000000;hpb=bfd813ba38e1d432d49a311422ade5ba33203a43;p=vamsas.git

diff --git a/src/org/vamsas/client/simpleclient/SimpleDocBinding.java b/src/org/vamsas/client/simpleclient/SimpleDocBinding.java
new file mode 100644
index 0000000..c0c8084
--- /dev/null
+++ b/src/org/vamsas/client/simpleclient/SimpleDocBinding.java
@@ -0,0 +1,138 @@
+package org.vamsas.client.simpleclient;
+
+import java.io.BufferedInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.Vector;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.vamsas.client.Vobject;
+import org.vamsas.client.VorbaIdFactory;
+import org.vamsas.client.VorbaXmlBinder;
+import org.vamsas.objects.core.VAMSAS;
+import org.vamsas.objects.core.VamsasDocument;
+import org.vamsas.objects.utils.AppDataReference;
+import org.vamsas.objects.utils.DocumentStuff;
+import org.vamsas.objects.utils.ProvenanceStuff;
+import org.vamsas.objects.utils.document.VersionEntries;
+
+/**
+ * Base class for SimpleClient Vamsas Document Object Manipulation
+ * holds static vamsasDocument from XML routines and
+ * state objects for a particular unmarshalled Document instance.
+ * @author jimp
+ */
+  
+
+public class SimpleDocBinding {
+
+  protected VorbaIdFactory vorba;
+  protected static Log log = LogFactory.getLog(SimpleDocBinding.class);
+
+  /**
+   * @return Returns the vorba.
+   */
+  public VorbaIdFactory getVorba() {
+    return vorba;
+  }
+
+  /**
+   * @param vorba The vorba to set.
+   */
+  public void setVorba(VorbaIdFactory vorba) {
+    this.vorba = vorba;
+  }
+
+  /**
+   * Uses VorbaXmlBinder to retrieve the VamsasDocument from the given stream
+   */
+  public VamsasDocument getVamsasDocument(VamsasArchiveReader oReader) throws IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+    if (oReader!=null) {
+      // check the factory
+      if (vorba==null) {
+        log.error("Invalid SimpleDocument construction - no VorbaIdFactory defined!");
+        return null;
+      }
+  
+      if (oReader.isValid()) {
+        // Read vamsasDocument.xsd instance
+        InputStreamReader vdoc = new InputStreamReader(oReader.getVamsasDocumentStream());
+        Object unmarsh[] = VorbaXmlBinder.getVamsasObjects(vdoc, vorba, new VamsasDocument());
+        if (unmarsh==null)
+          log.fatal("Couldn't unmarshall document!");
+        
+        Vobject vobjs = (Vobject) unmarsh[0];
+        if (vobjs!=null) { 
+          VamsasDocument doc=(VamsasDocument) vobjs;
+          if (doc!=null)
+            return doc;
+        }
+        log.debug("Found no VamsasDocument object in properly formatted Vamsas Archive.");
+      } else {        
+        // deprecated data handler (vamsas.xsd instance)
+        InputStream vxmlis = oReader.getVamsasXmlStream();
+        if (vxmlis!=null) { // Might be an old vamsas file.
+          BufferedInputStream ixml = new BufferedInputStream(oReader.getVamsasXmlStream());
+          InputStreamReader vxml = new InputStreamReader(ixml);
+          Object unmarsh[] = VorbaXmlBinder.getVamsasObjects(vxml, vorba, new VAMSAS());
+          
+          if (unmarsh==null)
+            log.fatal("Couldn't unmarshall document!");
+          
+          VAMSAS root[]= new VAMSAS[] { null};
+          root[0] = (VAMSAS) unmarsh[0]; 
+          
+          if (root[0]==null) {
+            log.debug("Found no VAMSAS object in VamsasXML stream.");
+          } else {
+            log.debug("Making new VamsasDocument from VamsasXML stream.");
+            VamsasDocument doc = DocumentStuff.newVamsasDocument(root, 
+                ProvenanceStuff.newProvenance(
+                    vorba.getUserHandle().getFullName(), 
+                    "Vamsas Document constructed from vamsas.xml"), VersionEntries.ALPHA_VERSION);
+            // VAMSAS: decide on 'system' operations provenance form
+            // LATER: implement classes for translating Vorba properties into provenance user fields.
+            // VAMSAS: decide on machine readable info embedding in provenance should be done
+            root[0]=null;
+            root=null;
+            return doc;
+          }
+        }
+      }
+    }
+    // otherwise - there was no valid original document to read.
+    return null;    
+  }
+
+  /**
+   * Extract all jarEntries in an archive referenced by the vamsas document
+   * LATER: a family of methods for finding extraneous jarEntries , and invalid appDataReferences
+   * @param doc
+   * @param oReader
+   * @return array of the subset of JarEntry names that are referenced in doc 
+   */
+  public Vector getReferencedEntries(VamsasDocument doc, VamsasArchiveReader oReader) {
+    if (oReader==null)
+     return null;
+    if (doc==null) {
+     try { doc = getVamsasDocument(oReader); } 
+     catch (Exception e) { log.warn("Failed to get document from "+oReader.jfile.getName()); };
+    }
+    Vector docrefs = AppDataReference.getAppDataReferences(doc);
+    if (docrefs==null)
+      return null;
+    Vector entries = oReader.getExtraEntries();
+    if (entries!=null && docrefs.size()>0) {
+      int i=0, j=entries.size();
+      do {
+        if (!docrefs.contains(entries.get(i))) {
+            entries.remove(i);
+            j--;
+        } else
+          i++;
+      } while (i<j);
+    }
+    return entries;
+  }
+}