import org.apache.commons.logging.LogFactory;
import org.vamsas.client.simpleclient.VamsasArchive;
import org.vamsas.client.simpleclient.VamsasArchiveReader;
+import org.vamsas.objects.core.Alignment;
import org.vamsas.objects.core.ApplicationData;
import org.vamsas.objects.core.Entry;
+import org.vamsas.objects.core.Instance;
import org.vamsas.objects.core.Provenance;
import org.vamsas.objects.core.VAMSAS;
import org.vamsas.objects.core.VamsasDocument;
}
// Merge appDataReferences require transfer of jar entries, perhaps with a renaming of the entry.
// Merge appDatas require eventually unique URNS
+ // TODO: merging global appdata from different documents where same app has written them causes conflict
- public static Hashtable hashOfAppDatas(Hashtable ht, ApplicationData[] appdatas) {
+ public static Hashtable hashOfAppDatas(Hashtable ht, Instance[] appdatas) {
if (ht==null)
ht = new Hashtable();
for (int i=0, j=appdatas.length; i<j; i++) {
* @param entry application data to be copied from source archive
*/
public static void addAppDataEntry(VamsasArchive darc, VamsasDocument dest, VamsasArchiveReader sarc, ApplicationData entry) {
-
- // check uniqueness of entry.urn amongst dest.ApplicationData[].urn
+ // TODO: fix instances
+ // check uniqueness of instance's[] entry.urn amongst dest.ApplicationData[].getInstances[].urn
// check uniqueness of entry.user[].urn amongst dest.ApplicationData[].user[].urn
// check uniqueness of entry.user
// entry.getAppDataChoice().getData() or getDataReference is unique
for (int i=0, j=dest.getApplicationDataCount(); i<j; i++) {
ApplicationData o = dest.getApplicationData()[i];
// ensure new urn is really unique
- String urn = entry.getUrn();
+ //String urn = entry.getUrn();
int v = 1;
- while (o.getUrn().equals(urn)) {
- urn = entry.getUrn()+v++;
- }
+ //while (o.getUrn().equals(urn)) {
+ // urn = entry.getUrn()+v++;
+ // }
// uniqueness of urn
// check each user ApplicationData
// uniqueness (again)
VamsasArchive varc = new VamsasArchive(newarch, true);
VamsasDocument docroot;
docroot = new VamsasDocument();
- docroot.setProvenance(ProvenanceStuff.newProvenance("ArchiveWriter", "Created new Vamsas Document"));
+ docroot.setProvenance(ProvenanceStuff.newProvenance("ArchiveWriter", "user", "Created new Vamsas Document"));
while (++argpos<argv.length) {
File archive = new File(argv[argpos]);
InputStream istream;
if ((istream = vdoc.getVamsasXmlStream())!=null) {
// make a new vamsas document from the vamsas.xml entry
VAMSAS root = VAMSAS.unmarshal(new InputStreamReader(istream)); // TODO: verify only one VAMSAS element per vamsas.xml entry.
- docroot.getProvenance().addEntry(ProvenanceStuff.newProvenanceEntry("user", "added vamsas.xml from "+argv[argpos-1]));
+ docroot.getProvenance().addEntry(ProvenanceStuff.newProvenanceEntry("ArchiveWriter", "user", "added vamsas.xml from "+argv[argpos-1]));
docroot.addVAMSAS(root);
}
}