@After
public void tearDown() throws Exception {
if (accessApproval != null && accessApproval.getId() != null) {
accessApprovalDAO.delete(accessApproval.getId().toString());
}
if (accessApproval2 != null && accessApproval2.getId() != null) {
accessApprovalDAO.delete(accessApproval2.getId().toString());
}
if (accessRequirement != null && accessRequirement.getId() != null) {
accessRequirementDAO.delete(accessRequirement.getId().toString());
}
if (accessRequirement2 != null && accessRequirement2.getId() != null) {
accessRequirementDAO.delete(accessRequirement2.getId().toString());
}
if (node != null && nodeDAO != null) {
nodeDAO.delete(node.getId());
node = null;
}
if (node2 != null && nodeDAO != null) {
nodeDAO.delete(node2.getId());
node2 = null;
}
if (evaluation != null && evaluationDAO != null) {
evaluationDAO.delete(evaluation.getId());
evaluation = null;
}
individualGroup = userGroupDAO.findGroup(TEST_USER_NAME, true);
if (individualGroup != null) {
userGroupDAO.delete(individualGroup.getId());
}
individualGroup2 = userGroupDAO.findGroup(TEST_USER_NAME_2, true);
if (individualGroup2 != null) {
userGroupDAO.delete(individualGroup2.getId());
}
}
/**
* 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));
}
@Test
public void testUnmetARsForEvaluation() throws Exception {
RestrictableObjectDescriptor rod =
AccessRequirementUtilsTest.createRestrictableObjectDescriptor(
evaluation.getId(), RestrictableObjectType.EVALUATION);
// Logic for unmet requirements doesn't reflect ownership at the DAO level. It's factored in at
// the manager level.
// Therefore, the owner see unmet ARs for herself..
List<Long> unmetARIds =
accessRequirementDAO.unmetAccessRequirements(
rod,
Arrays.asList(new Long[] {Long.parseLong(individualGroup.getId())}),
participateAndDownload);
assertEquals(1, unmetARIds.size());
assertEquals(accessRequirement2.getId(), unmetARIds.iterator().next());
// ... just as someone else does, if they haven't signed the ToU
unmetARIds =
accessRequirementDAO.unmetAccessRequirements(
rod,
Arrays.asList(new Long[] {Long.parseLong(individualGroup2.getId())}),
participateAndDownload);
assertEquals(1, unmetARIds.size());
assertEquals(accessRequirement2.getId(), unmetARIds.iterator().next());
// Create a new object
accessApproval2 = newAccessApproval(individualGroup2, accessRequirement2);
// Create it
accessApproval2 = accessApprovalDAO.create(accessApproval2);
String id = accessApproval2.getId().toString();
assertNotNull(id);
// no unmet requirement anymore ...
assertTrue(
accessRequirementDAO
.unmetAccessRequirements(
rod,
Arrays.asList(new Long[] {Long.parseLong(individualGroup2.getId())}),
participateAndDownload)
.isEmpty());
// Get by evaluation Id
Collection<AccessApproval> ars =
accessApprovalDAO.getForAccessRequirementsAndPrincipals(
Arrays.asList(new String[] {accessRequirement2.getId().toString()}),
Arrays.asList(new String[] {individualGroup2.getId().toString()}));
assertEquals(1, ars.size());
assertEquals(accessApproval2, ars.iterator().next());
}
@Before
public void setUp() throws Exception {
individualGroup = userGroupDAO.findGroup(TEST_USER_NAME, true);
if (individualGroup == null) {
individualGroup = new UserGroup();
individualGroup.setName(TEST_USER_NAME);
individualGroup.setIsIndividual(true);
individualGroup.setCreationDate(new Date());
individualGroup.setId(userGroupDAO.create(individualGroup));
}
individualGroup2 = userGroupDAO.findGroup(TEST_USER_NAME, true);
if (individualGroup2 == null) {
individualGroup2 = new UserGroup();
individualGroup2.setName(TEST_USER_NAME_2);
individualGroup2.setIsIndividual(true);
individualGroup2.setCreationDate(new Date());
individualGroup2.setId(userGroupDAO.create(individualGroup2));
}
if (node == null) {
node = NodeTestUtils.createNew("foo", Long.parseLong(individualGroup.getId()));
node.setId(nodeDAO.createNew(node));
}
;
if (node2 == null) {
node2 = NodeTestUtils.createNew("bar", Long.parseLong(individualGroup.getId()));
node2.setId(nodeDAO.createNew(node2));
}
;
accessRequirement =
DBOAccessRequirementDAOImplTest.newEntityAccessRequirement(individualGroup, node, "foo");
accessRequirement = accessRequirementDAO.create(accessRequirement);
Long id = accessRequirement.getId();
assertNotNull(id);
if (evaluation == null) {
evaluation =
DBOAccessRequirementDAOImplTest.createNewEvaluation(
"foo", individualGroup.getId(), idGenerator, node.getId());
evaluation.setId(evaluationDAO.create(evaluation, Long.parseLong(individualGroup.getId())));
}
;
accessRequirement2 =
DBOAccessRequirementDAOImplTest.newMixedAccessRequirement(
individualGroup, node2, evaluation, "bar");
accessRequirement2 = accessRequirementDAO.create(accessRequirement2);
id = accessRequirement2.getId();
assertNotNull(id);
if (participateAndDownload == null) {
participateAndDownload = new ArrayList<ACCESS_TYPE>();
participateAndDownload.add(ACCESS_TYPE.DOWNLOAD);
participateAndDownload.add(ACCESS_TYPE.PARTICIPATE);
}
if (downloadAccessType == null) {
downloadAccessType = new ArrayList<ACCESS_TYPE>();
downloadAccessType.add(ACCESS_TYPE.DOWNLOAD);
}
if (updateAccessType == null) {
updateAccessType = new ArrayList<ACCESS_TYPE>();
updateAccessType.add(ACCESS_TYPE.UPDATE);
}
}