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); }