@BeforeClass
public static void setUpBeforeClass() throws Exception {
setEnv();
// read configuration
Configuration configuration = Configuration.getInstance();
// and initialize the db connections
NdexDatabase db =
NdexDatabase.createNdexDatabase(
configuration.getHostURI(),
configuration.getDBURL(),
configuration.getDBUser(),
configuration.getDBPasswd(),
10);
String user = "******";
XgmmlParser parser =
new XgmmlParser(
"/home/chenjing/Dropbox/Network_test_files/pdmap130712.xgmml", user, db, "pdmap13", "");
parser.parseFile();
// XbelParser
// parser = new XbelParser("/home/chenjing/working/ndex/networks/selventa_full.xbel", user);
// parser.parseFile();
db.close();
}
/*
* private method to invoke the xbel network exporter
*/
private void exportNetwork() throws Exception {
this.taskStatus = Status.PROCESSING;
this.startTask();
String exportFilename =
this.resolveFilename(
Configuration.getInstance().getNdexRoot() + "/exported-networks/",
this.XBEL_FILE_EXTENSION);
ODatabaseDocumentTx db = null;
try {
db = NdexDatabase.getInstance().getAConnection();
NdexTaskModelService modelService = new NdexJVMDataModelService(db);
XbelNetworkExporter exporter =
new XbelNetworkExporter(
this.getTask().getTaskOwnerId().toString(),
this.networkId,
modelService,
exportFilename);
exporter.exportNetwork();
this.taskStatus = Status.COMPLETED;
this.updateTaskStatus(this.taskStatus);
} finally {
if (db != null) db.close();
}
}
private void createNetworkCache() throws NdexException {
String networkIdStr = this.getTask().getResource();
try (NetworkDAO dao = new NetworkDAO(NdexDatabase.getInstance().getAConnection())) {
Long taskCommitId = (Long) getTask().getAttribute(TaskAttribute.readOnlyCommitId);
String fullpath =
Configuration.getInstance().getNdexNetworkCachePath() + taskCommitId + ".gz";
ODocument d = dao.getNetworkDocByUUIDString(networkIdStr);
d.reload();
Long actId = d.field(NdexClasses.Network_P_readOnlyCommitId);
if (!actId.equals(taskCommitId)) {
// stop task
getTask()
.setMessage(
"Network cache not created. readOnlyCommitId="
+ actId
+ " in db, but in task we have commitId="
+ taskCommitId);
return;
}
// create cache.
Network n = dao.getNetworkById(UUID.fromString(networkIdStr));
try (GZIPOutputStream w = new GZIPOutputStream(new FileOutputStream(fullpath), 16384)) {
// String s = mapper.writeValueAsString( original);
ObjectMapper mapper = new ObjectMapper();
mapper.writeValue(w, n);
} catch (FileNotFoundException e) {
throw new NdexException("Can't create network cache file in server: " + fullpath);
} catch (IOException e) {
throw new NdexException(
"IO Error when writing cache file: " + fullpath + ". Cause: " + e.getMessage());
}
// check again.
d.reload();
actId = d.field(NdexClasses.Network_P_readOnlyCommitId);
if (!actId.equals(taskCommitId)) {
// stop task
getTask()
.setMessage(
"Network cache not created. Second check found network readOnlyCommitId is"
+ actId
+ ", task has commitId "
+ taskCommitId);
return;
}
d.field(NdexClasses.Network_P_cacheId, taskCommitId).save();
logger.info("Cache " + actId + " created.");
dao.commit();
}
}
