/** Test the bulk expire method */
public void testExpire() throws Exception {
initializeData();
LocalDate date = new LocalDate(new Date());
testFindExpired();
flushAndClear();
screen1NotExpired = genericEntityDao.reloadEntity(screen1NotExpired);
screen2Expired = genericEntityDao.reloadEntity(screen2Expired);
screen3Expired = genericEntityDao.reloadEntity(screen3Expired);
screen4Default = genericEntityDao.reloadEntity(screen4Default);
screen5RnaiExpired = genericEntityDao.reloadEntity(screen5RnaiExpired);
screen6ExpiredNoResults = genericEntityDao.reloadEntity(screen6ExpiredNoResults);
screen7ExpiredDropped = genericEntityDao.reloadEntity(screen7ExpiredDropped);
screen8ExpiredTransferred = genericEntityDao.reloadEntity(screen8ExpiredTransferred);
screen9ExpiredMaxDatePassed = genericEntityDao.reloadEntity(screen9ExpiredMaxDatePassed);
List<Pair<Screen, AdministrativeActivity>> results =
screenDataSharingLevelUpdater.expireScreenDataSharingLevels(
date, admin, ScreenType.SMALL_MOLECULE);
// TODO: Do some checking of the activities as well.
Set<Screen> screens = Sets.newLinkedHashSet();
for (Pair<Screen, AdministrativeActivity> result : results) {
screens.add(result.getFirst());
}
log.info("screens: " + screens);
screen1NotExpired = genericEntityDao.reloadEntity(screen1NotExpired);
screen2Expired = genericEntityDao.reloadEntity(screen2Expired);
screen3Expired = genericEntityDao.reloadEntity(screen3Expired);
screen4Default = genericEntityDao.reloadEntity(screen4Default);
screen5RnaiExpired = genericEntityDao.reloadEntity(screen5RnaiExpired);
assertTrue("screen2Expired should be expired", screens.contains(screen2Expired));
assertTrue(
"screen2Expired should be shared",
screen2Expired.getDataSharingLevel() == ScreenDataSharingLevel.MUTUAL_SCREENS);
assertTrue("screen3Expired should be expired", screens.contains(screen3Expired));
assertTrue(
"screen3Expired should be shared",
screen3Expired.getDataSharingLevel() == ScreenDataSharingLevel.MUTUAL_SCREENS);
assertFalse("screen4Default should not be expired", screens.contains(screen4Default));
assertTrue(
"screen4Default should not be shared",
screen4Default.getDataSharingLevel() != ScreenDataSharingLevel.MUTUAL_SCREENS);
assertFalse("screen1NotExpired should be expired", screens.contains(screen1NotExpired));
assertTrue(
"screen1NotExpired should not be shared",
screen1NotExpired.getDataSharingLevel() != ScreenDataSharingLevel.MUTUAL_SCREENS);
assertFalse(
"screen5RnaiExpired should NOT be expired (unless setting the screenType=RNAi)",
screens.contains(screen5RnaiExpired));
assertTrue(
"screen5RnaiExpired NOT should be shared",
screen5RnaiExpired.getDataSharingLevel() != ScreenDataSharingLevel.MUTUAL_SCREENS);
assertTrue(
"screen9ExpiredMaxDatePassed should be expired",
screens.contains(screen9ExpiredMaxDatePassed));
assertTrue(
"screen9ExpiredMaxDatePassed should be shared",
screen9ExpiredMaxDatePassed.getDataSharingLevel() == ScreenDataSharingLevel.MUTUAL_SCREENS);
// TODO: Do some checking of the activities as well.
// RNAi
results =
screenDataSharingLevelUpdater.expireScreenDataSharingLevels(date, admin, ScreenType.RNAI);
screen5RnaiExpired = genericEntityDao.reloadEntity(screen5RnaiExpired);
assertFalse(results.isEmpty());
assertTrue("should only return the 1 RNAI screen: " + results, results.size() == 1);
assertTrue(
"screen5RnaiExpired should be expired (setting the screenType=RNAi)",
results.get(0).getFirst().equals((screen5RnaiExpired)));
assertTrue(
"screen5RnaiExpired should be shared",
screen5RnaiExpired.getDataSharingLevel() == ScreenDataSharingLevel.MUTUAL_SCREENS);
}
public void testAdjustDataPrivacyExpirationByActivities() throws Exception {
initializeData();
// as of [#2175] expiration services to become notification services only
// the DPED will be set separately from the ScreenResultImport (the old way).
// It will now be set by batch process, SCREEN_ACTIVITY_DATA_PRIVACY_EXPIRATION_AGE_DAYS from
// the last ScreeningActivity date for a screen:
// Meaning:
// DPED will be set in one step (this test)
// DPED will be used in separate step to find and expire screens (next test)
// 1. create some screens
Screen screen1NoActivities = createScreen("SDSL TEST1");
Screen screen2HasActivity = createScreen("SDSL TEST2");
Screen screen5TransferredHasActivity = createScreen("SDSL TEST5");
screen5TransferredHasActivity.createStatusItem(
new LocalDate(), ScreenStatus.TRANSFERRED_TO_BROAD_INSTITUTE);
Screen screen3RnaiHasActivity = createScreen("SDSL TEST RNAI", ScreenType.RNAI);
Screen screen4HasNoLibraryScreeningActivity =
createScreen("screen4HasNoLibraryScreeningActivity");
Screen screen6MinMaxSet = createScreen("screen6MinMaxSet");
// 2. add some activities
LocalDate newActivityDate = new LocalDate();
screen2HasActivity.createLibraryScreening(admin, leadScreener, newActivityDate);
screen2HasActivity.createLibraryScreening(admin, leadScreener, newActivityDate);
screen2HasActivity.createLibraryScreening(admin, leadScreener, newActivityDate);
screen2HasActivity.createLibraryScreening(admin, leadScreener, newActivityDate);
// create a screening for user provided plates
LibraryScreening ls =
screen2HasActivity.createLibraryScreening(
admin, leadScreener, newActivityDate.plusDays(100));
ls.setForExternalLibraryPlates(true);
// create a non-library-screening activity too
screen2HasActivity.createCherryPickRequest(admin, leadScreener, newActivityDate.plusDays(100));
screen4HasNoLibraryScreeningActivity.createCherryPickRequest(
admin, leadScreener, newActivityDate.plusDays(100));
screen3RnaiHasActivity.createLibraryScreening(admin, leadScreener, newActivityDate);
screen5TransferredHasActivity.createLibraryScreening(admin, leadScreener, newActivityDate);
screen5TransferredHasActivity.createLibraryScreening(admin, leadScreener, newActivityDate);
screen5TransferredHasActivity.createLibraryScreening(admin, leadScreener, newActivityDate);
screen5TransferredHasActivity.createLibraryScreening(admin, leadScreener, newActivityDate);
// create a screening for user provided plates
ls =
screen5TransferredHasActivity.createLibraryScreening(
admin, leadScreener, newActivityDate.plusDays(100));
ls.setForExternalLibraryPlates(true);
// 3. add some results
screen2HasActivity.createScreenResult();
screen5TransferredHasActivity.createScreenResult();
screen4HasNoLibraryScreeningActivity.createScreenResult();
LocalDate maxAllowedDataPrivacyExpirationDate = newActivityDate.minusDays(10);
LocalDate minAllowedDataPrivacyExpirationDate = newActivityDate.minusDays(20);
screen6MinMaxSet.setMinAllowedDataPrivacyExpirationDate(minAllowedDataPrivacyExpirationDate);
screen6MinMaxSet.setMaxAllowedDataPrivacyExpirationDate(maxAllowedDataPrivacyExpirationDate);
screen6MinMaxSet.createLibraryScreening(admin, leadScreener, newActivityDate);
screen6MinMaxSet.createScreenResult();
genericEntityDao.persistEntity(screen1NoActivities);
genericEntityDao.persistEntity(screen2HasActivity);
genericEntityDao.persistEntity(screen3RnaiHasActivity);
genericEntityDao.persistEntity(screen4HasNoLibraryScreeningActivity);
genericEntityDao.persistEntity(screen5TransferredHasActivity);
genericEntityDao.persistEntity(screen6MinMaxSet);
flushAndClear();
// 4. find the ones with "old" activities (activity age >
// SCREEN_ACTIVITY_DATA_PRIVACY_EXPIRATION_AGE_DAYS)
int ageToExpireFromActivityDateInDays = 760;
ScreenDataSharingLevelUpdater.DataPrivacyAdjustment adjustment =
screenDataSharingLevelUpdater.adjustDataPrivacyExpirationByActivities(
ageToExpireFromActivityDateInDays, admin, ScreenType.SMALL_MOLECULE);
flushAndClear();
screen1NoActivities = genericEntityDao.reloadEntity(screen1NoActivities);
screen2HasActivity = genericEntityDao.reloadEntity(screen2HasActivity);
screen3RnaiHasActivity = genericEntityDao.reloadEntity(screen3RnaiHasActivity);
screen4HasNoLibraryScreeningActivity =
genericEntityDao.reloadEntity(screen4HasNoLibraryScreeningActivity);
screen5TransferredHasActivity = genericEntityDao.reloadEntity(screen5TransferredHasActivity);
screen6MinMaxSet = genericEntityDao.reloadEntity(screen6MinMaxSet);
boolean containsFirst = false,
containsSecond = false,
containsThird = false,
containsFourth = false,
containsFifth = false,
containsSixth = false;
for (Pair<Screen, AdministrativeActivity> result : adjustment.screensAdjusted) {
log.info("entry: " + result.getSecond());
if (result.getFirst().equals(screen1NoActivities)) containsFirst = true;
if (result.getFirst().equals(screen2HasActivity)) containsSecond = true;
if (result.getFirst().equals(screen3RnaiHasActivity)) containsThird = true;
if (result.getFirst().equals(screen4HasNoLibraryScreeningActivity)) containsFourth = true;
if (result.getFirst().equals(screen5TransferredHasActivity)) containsFifth = true;
if (result.getFirst().equals(screen6MinMaxSet)) containsSixth = true;
}
// TODO: update test for this
assertTrue(
"no screens should not be allowed", adjustment.screenPrivacyAdjustmentNotAllowed.isEmpty());
assertFalse(
"the sixth screen should adjusted to allowed",
adjustment.screensAdjustedToAllowed.isEmpty());
assertFalse("screen1NoActivities should not have been adjusted", containsFirst);
assertTrue("screen2HasActivity should have been adjusted", containsSecond);
assertFalse("screen3RnaiHasActivity should not have been adjusted", containsThird);
assertFalse(
"screen4HasNoLibraryScreeningActivity should not have been adjusted", containsFourth);
assertFalse("screen5TransferredHasActivity should not have been adjusted", containsFifth);
assertFalse("screen6MinMaxSet should not have been adjusted", containsSixth);
assertEquals(
"new screen2HasActivity dataPrivacyExpirationDate() wrong: ",
newActivityDate.plusDays(ageToExpireFromActivityDateInDays),
screen2HasActivity.getDataPrivacyExpirationDate());
}
