private int executeCountQuery(String tableId, String countQuery) throws SynapseException {
String jobToken =
synapseAdmin.queryTableEntityBundleAsyncStart(countQuery, 0L, 1L, true, 1, tableId);
QueryResultBundle qrb = null;
long backoff = 100L;
for (int i = 0; i < 100; i++) {
try {
qrb = synapseAdmin.queryTableEntityBundleAsyncGet(jobToken, tableId);
break;
} catch (SynapseResultNotReadyException e) {
// keep waiting
try {
Thread.sleep(backoff);
} catch (InterruptedException ie) {
// continue
}
backoff *= 2L;
}
}
if (qrb == null) throw new RuntimeException("Query failed to return");
List<Row> rows = qrb.getQueryResult().getQueryResults().getRows();
if (rows.size() != 1)
throw new RuntimeException(
"Expected one row for count query result but found " + rows.size());
Row row = rows.get(0);
List<String> rowValues = row.getValues();
if (rowValues.size() != 1)
throw new RuntimeException(
"Expected one column for count query result but found " + rows.size());
return Integer.parseInt(rowValues.get(0));
}
/**
* Note: There are two types of scoring, that in which each submission is scored alone and that in
* which the entire set of submissions is rescored whenever a new one arrives.
*
* @throws SynapseException
* @throws JSONObjectAdapterException
*/
public void execute() throws SynapseException, IOException, JSONObjectAdapterException {
long startTime = System.currentTimeMillis();
long total = Integer.MAX_VALUE;
int started = 0;
for (int offset = 0; offset < total; offset += PAGE_SIZE) {
PaginatedResults<SubmissionBundle> submissionPGs = null;
submissionPGs =
synapseAdmin.getAllSubmissionBundlesByStatus(
evaluation.getId(), SubmissionStatusEnum.RECEIVED, offset, PAGE_SIZE);
total = (int) submissionPGs.getTotalNumberOfResults();
List<SubmissionBundle> page = submissionPGs.getResults();
for (int i = 0; i < page.size(); i++) {
SubmissionBundle bundle = page.get(i);
Submission sub = bundle.getSubmission();
FileHandle fileHandle = getFileHandleFromEntityBundle(sub.getEntityBundleJSON());
SubmissionStatus status = bundle.getSubmissionStatus();
// Retrieve and run COUNT_QUERY. If > 0 then execute Docker image
String tableId = readStringAnnotation(status, TABLE_ID_ANNOTATION_NAME);
String countQuery = readStringAnnotation(status, COUNT_QUERY_ANNOTATION_NAME);
if (tableId != null && countQuery != null) {
int count = executeCountQuery(tableId, countQuery);
if (count == 0) {
System.out.println("Count query returned 0: " + countQuery);
continue; // nothing to process, so skip this submission
}
}
// if no tableId or no countQuery then run the image
// it's then the image's job to put this information in the annotations
try {
String dockerReference = getDockerReferenceFromFileHandle(fileHandle);
if (readStringAnnotation(status, DOCKER_REPOSITORY_ANNOTATION_NAME) == null)
addAnnotation(status, DOCKER_REPOSITORY_ANNOTATION_NAME, dockerReference, false);
status.setStatus(SubmissionStatusEnum.EVALUATION_IN_PROGRESS);
status = synapseAdmin.updateSubmissionStatus(status);
// we run the image if either (1) there are new rows to process of (2) it hasn't been run
// before
runOneImage(fileHandle, sub.getId());
// make sure that the Docker reference is in an annotation so it can be displayed
started++;
} catch (Exception e) {
status = synapseAdmin.getSubmissionStatus(sub.getId());
if (status.getStatus() != SubmissionStatusEnum.RECEIVED) {
status.setStatus(SubmissionStatusEnum.RECEIVED);
status = synapseAdmin.updateSubmissionStatus(status);
}
// TODO send failure notification to submitter
e.printStackTrace();
}
}
}
long delta = System.currentTimeMillis() - startTime;
System.out.println("Started " + started + " jobs. Elapsed time: " + formatInterval(delta));
}
public void setUp() throws SynapseException, UnsupportedEncodingException {
evaluation = synapseAdmin.getEvaluation(getProperty("EVALUATION_ID"));
}
public TableTrigger() throws SynapseException {
synapseAdmin = createSynapseClient();
String adminUserName = getProperty("ADMIN_USERNAME");
String adminPassword = getProperty("ADMIN_PASSWORD");
synapseAdmin.login(adminUserName, adminPassword);
}
private void sendMessage(String userId, String subject, String body) throws SynapseException {
MessageToUser messageMetadata = new MessageToUser();
messageMetadata.setRecipients(Collections.singleton(userId));
messageMetadata.setSubject(subject);
synapseAdmin.sendStringMessage(messageMetadata, body);
}