+++ /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;
- }
-}