private void extractTable(InputStream stream, String entryName) throws Exception {
CyTableReader reader =
(CyTableReader) csvCyReaderFactory.createTaskIterator(stream, entryName).next();
reader.run(taskMonitor);
// Assume one table per entry
CyTable table = reader.getTables()[0];
Matcher matcher = NETWORK_TABLE_PATTERN.matcher(entryName);
if (matcher.matches()) {
String networkName = SessionUtil.unescape(matcher.group(2));
Long oldNetId = getOldNetworkId(networkName);
if (oldNetId == null) {
throw new NullPointerException(
"Cannot extract table. Network SUID is null for entry: " + entryName);
}
String namespace = SessionUtil.unescape(matcher.group(3));
Class<?> type = Class.forName(SessionUtil.unescape(matcher.group(4)));
String title = SessionUtil.unescape(matcher.group(5));
table.setTitle(title);
CyTableMetadataBuilder builder =
new CyTableMetadataBuilder().setCyTable(table).setNamespace(namespace).setType(type);
Set<CyTableMetadataBuilder> builders = networkTableMap.get(oldNetId);
if (builders == null) {
builders = new HashSet<CyTableMetadataBuilder>();
networkTableMap.put(oldNetId, builders);
}
builders.add(builder);
String filename = matcher.group(1);
filenameTableMap.put(filename, table);
builderFilenameMap.put(builder, filename);
return;
}
matcher = GLOBAL_TABLE_PATTERN.matcher(entryName);
if (matcher.matches()) {
String title = SessionUtil.unescape(matcher.group(3));
table.setTitle(title);
CyTableMetadataBuilder builder =
new CyTableMetadataBuilder().setCyTable(table).setNetwork(null);
tableMetadata.add(builder.build());
String filename = matcher.group(1);
filenameTableMap.put(filename, table);
builderFilenameMap.put(builder, filename);
// Look for SUID-type columns--only global tables now
suidUpdater.addTable(table);
}
}
@SuppressWarnings("unchecked")
private final void mergeNetworkTable(CyNetwork network, CyTableMetadataBuilder builder) {
final Class<? extends CyIdentifiable> type =
(Class<? extends CyIdentifiable>) builder.getType();
final String namespace = builder.getNamespace();
final CyTable src = builder.getTable();
final CyTable tgt = networkTableMgr.getTable(network, type, namespace);
if (tgt == null) {
// Just use the source table
networkTableMgr.setTable(network, type, namespace, src);
builder.setCyTable(src);
suidUpdater.addTable(src);
} else {
mergeTables(src, tgt, type);
builder.setCyTable(tgt);
suidUpdater.addTable(tgt);
}
}
private void updateSUIDColumns() {
suidUpdater.updateSUIDColumns();
}
@Override
protected void init(TaskMonitor tm) throws Exception {
super.init(tm);
suidUpdater.init();
}