--- /dev/null
+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;
+ }
+}