/**
* If this test is run by itself, it leaves the database in a state that is convenient for testing
* from the command line.
*/
@Rollback(value = false)
public void testThatSetsUpForCommandLineTest() throws Exception {
initializeData();
int daysToNofify = 60;
int daysToExpire =
790; // 2 years, 2months (technically, a month is variable, using 30 days for all
// calculations)
LocalDate today = new LocalDate();
LocalDate activityDateToExpireToday = today.minusDays(daysToExpire);
LocalDate activityDateToNotifyToday = today.minusDays(daysToExpire).plusDays(daysToNofify);
Screen screen1ToExpireTodayAfterAdjust =
createScreen("is testing for expiration (760 days after lab activity) today");
screen1ToExpireTodayAfterAdjust.createScreenResult();
screen1ToExpireTodayAfterAdjust.createLibraryScreening(
admin, leadScreener, activityDateToExpireToday);
Screen screen2ToNotifyTodayAfterAdjust =
createScreen("is testing for notification (60 days before expiration) today");
screen2ToNotifyTodayAfterAdjust.createScreenResult();
screen2ToNotifyTodayAfterAdjust.createLibraryScreening(
admin, leadScreener, activityDateToNotifyToday);
Screen screen3AjustementOverridden =
createScreen("is testing for max/min DPED override - Adjustment to the allowed value");
screen3AjustementOverridden.createScreenResult();
screen3AjustementOverridden.createLibraryScreening(
admin, leadScreener, activityDateToExpireToday);
screen3AjustementOverridden.setDataPrivacyExpirationDate(today.plusDays(2));
screen3AjustementOverridden.setMinAllowedDataPrivacyExpirationDate(today.plusDays(1));
Screen screen3aAjustementOverridden =
createScreen("is testing for max/min DPED override - adjustment not allowed - overridden");
screen3aAjustementOverridden.createScreenResult();
screen3aAjustementOverridden.createLibraryScreening(
admin, leadScreener, activityDateToExpireToday);
screen3aAjustementOverridden.setMinAllowedDataPrivacyExpirationDate(today.plusDays(1));
screen3aAjustementOverridden.setDataPrivacyExpirationDate(today.plusDays(1));
Screen screen4Published = createScreen("is testing a published Screen");
screen4Published.createScreenResult();
screen4Published.createLibraryScreening(admin, leadScreener, activityDateToNotifyToday);
screen4Published.addPublication(new Publication());
genericEntityDao.persistEntity(screen1ToExpireTodayAfterAdjust);
genericEntityDao.persistEntity(screen2ToNotifyTodayAfterAdjust);
genericEntityDao.persistEntity(screen3AjustementOverridden);
genericEntityDao.persistEntity(screen3aAjustementOverridden);
genericEntityDao.persistEntity(screen4Published);
genericEntityDao.flush();
}
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());
}