private Screen createScreen(String title, ScreenType type) {
log.info("leads" + leadScreener);
Screen screen =
new Screen(
null,
Integer.toString(screen_number_counter++),
leadScreener,
labHead,
type,
StudyType.IN_VITRO,
ProjectPhase.PRIMARY_SCREEN,
title);
screen.addCollaborator(collaborator);
screen.createStatusItem(new LocalDate(), ScreenStatus.ACCEPTED);
genericEntityDao.persistEntity(screen);
return screen;
}
public void testFindNewPublishedPrivate() throws Exception {
initializeData();
Screen screen1NotPublished = createScreen("SDSL TEST1 Not Published");
genericEntityDao.persistEntity(screen1NotPublished);
Screen screen2Published = createScreen("SDSL TEST2 Published");
screen2Published.createScreenResult();
Publication publication = new Publication();
publication.setAuthors("Test Authors");
publication.setJournal("Test Journal");
publication.setTitle("Test Publication Title");
screen2Published.addPublication(publication);
genericEntityDao.persistEntity(screen2Published);
Screen screen3Mutual = createScreen("SDSL screen3Mutual");
screen3Mutual.createScreenResult();
screen3Mutual.setDataSharingLevel(ScreenDataSharingLevel.MUTUAL_SCREENS);
publication = new Publication();
publication.setAuthors("Test Authors x");
publication.setJournal("Test Journal x");
publication.setTitle("Test Publication Title x");
screen3Mutual.addPublication(publication);
genericEntityDao.persistEntity(screen3Mutual);
Screen screen4Private = createScreen("SDSL private");
screen4Private.createScreenResult();
screen4Private.setDataSharingLevel(ScreenDataSharingLevel.PRIVATE);
publication = new Publication();
publication.setAuthors("Test Authors x");
publication.setJournal("Test Journal x");
publication.setTitle("Test Publication Title x");
screen4Private.addPublication(publication);
genericEntityDao.persistEntity(screen4Private);
Screen screenPrivatePublishedTransferred =
createScreen("SDSL screenPrivatePublishedTransferred");
screenPrivatePublishedTransferred.createScreenResult();
screenPrivatePublishedTransferred.setDataSharingLevel(ScreenDataSharingLevel.PRIVATE);
publication = new Publication();
publication.setAuthors("Test Authors x");
publication.setJournal("Test Journal x");
publication.setTitle("Test Publication Title x");
screenPrivatePublishedTransferred.createStatusItem(
new LocalDate(), ScreenStatus.TRANSFERRED_TO_BROAD_INSTITUTE);
screenPrivatePublishedTransferred.addPublication(publication);
genericEntityDao.persistEntity(screenPrivatePublishedTransferred);
Screen screen4Public = createScreen("SDSL screen4Public");
screen4Public.createScreenResult();
screen4Public.setDataSharingLevel(ScreenDataSharingLevel.SHARED);
publication = new Publication();
publication.setAuthors("Test Authors xx");
publication.setJournal("Test Journal xx");
publication.setTitle("Test Publication Title xx");
screen4Public.addPublication(publication);
genericEntityDao.persistEntity(screen4Public);
flushAndClear();
screen2Published = genericEntityDao.reloadEntity(screen2Published);
screen3Mutual = genericEntityDao.reloadEntity(screen3Mutual);
screen4Private = genericEntityDao.reloadEntity(screen4Private);
Set<Screen> publishedScreens =
Sets.newHashSet(
screenDataSharingLevelUpdater.findNewPublishedPrivate(
ScreenType.SMALL_MOLECULE)); // TODO: Test RNAi as well
assertNotNull(publishedScreens);
assertEquals(
Sets.newHashSet(screen2Published, screen3Mutual, screen4Private), publishedScreens);
}
public void testFindExpired() throws Exception {
initializeData();
LocalDate date = new LocalDate(new Date());
screen1NotExpired = createScreen("SDSL TEST1");
screen1NotExpired.setDataPrivacyExpirationDate(date.plusYears(2));
genericEntityDao.persistEntity(screen1NotExpired);
screen2Expired = createScreen("SDSL TEST2");
screen2Expired.createScreenResult();
screen2Expired.setDataPrivacyExpirationDate(date);
genericEntityDao.persistEntity(screen2Expired);
screen3Expired = createScreen("SDSL TEST3");
screen3Expired.createScreenResult();
screen3Expired.setDataPrivacyExpirationDate(date.minusYears(1));
genericEntityDao.persistEntity(screen3Expired);
screen9ExpiredMaxDatePassed = createScreen("screen9ExpiredMaxDatePassed");
screen9ExpiredMaxDatePassed.createScreenResult();
screen9ExpiredMaxDatePassed.setMinAllowedDataPrivacyExpirationDate(date.minusYears(2));
screen9ExpiredMaxDatePassed.setMaxAllowedDataPrivacyExpirationDate(date.minusYears(2));
screen9ExpiredMaxDatePassed.setDataPrivacyExpirationDate(date.minusYears(2));
genericEntityDao.persistEntity(screen9ExpiredMaxDatePassed);
screen4Default = createScreen("SDSL TEST4");
genericEntityDao.persistEntity(screen4Default);
screen5RnaiExpired = createScreen("Test RNAI expired", ScreenType.RNAI);
screen5RnaiExpired.setDataPrivacyExpirationDate(date.minusYears(1));
screen5RnaiExpired.createScreenResult();
genericEntityDao.persistEntity(screen5RnaiExpired);
screen6ExpiredNoResults = createScreen("test expired no results", ScreenType.RNAI);
screen6ExpiredNoResults.setDataPrivacyExpirationDate(date.minusYears(1));
genericEntityDao.persistEntity(screen6ExpiredNoResults);
screen7ExpiredDropped = createScreen("test expired dropped technical");
screen7ExpiredDropped.setDataPrivacyExpirationDate(date.minusYears(1));
screen7ExpiredDropped.createScreenResult();
screen7ExpiredDropped.createStatusItem(new LocalDate(), ScreenStatus.DROPPED_TECHNICAL);
genericEntityDao.persistEntity(screen7ExpiredDropped);
screen8ExpiredTransferred = createScreen("test expired transferred");
screen8ExpiredTransferred.setDataPrivacyExpirationDate(date.minusYears(1));
screen8ExpiredTransferred.createScreenResult();
screen8ExpiredTransferred.createStatusItem(
new LocalDate(), ScreenStatus.TRANSFERRED_TO_BROAD_INSTITUTE);
genericEntityDao.persistEntity(screen8ExpiredTransferred);
flushAndClear();
// startNewTransaction();
List<Screen> allScreens = genericEntityDao.findAllEntitiesOfType(Screen.class);
for (Screen screen : allScreens) {
log.info(
"allScreens: "
+ screen.getTitle()
+ " , expires: "
+ screen.getDataPrivacyExpirationDate());
}
List<Screen> screens =
screenDataSharingLevelUpdater.findNewExpiredNotNotified(date, ScreenType.SMALL_MOLECULE);
for (Screen screen : screens) {
log.info(
"expiredScreens: "
+ screen.getTitle()
+ " , expires: "
+ screen.getDataPrivacyExpirationDate());
}
assertFalse("no expired screens", screens.isEmpty());
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);
assertTrue("screen2Expired should be expired: ", screens.contains(screen2Expired));
assertTrue("screen3Expired should be expired: ", screens.contains(screen3Expired));
assertTrue(
"screen9ExpiredMaxDatePassed should be expired: ",
screens.contains(screen9ExpiredMaxDatePassed));
assertFalse("screen4Default should not be expired", screens.contains(screen4Default));
assertFalse("screen1NotExpired should not be expired", screens.contains(screen1NotExpired));
assertFalse(
"screen5RnaiExpired should NOT be expired (unless setting screenType=RNAi)",
screens.contains(screen5RnaiExpired));
assertFalse(
"screen6ExpiredNoResults should not be expired", screens.contains(screen6ExpiredNoResults));
assertFalse(
"screen7ExpiredDropped should not be expired", screens.contains(screen7ExpiredDropped));
assertFalse(
"screen8ExpiredTransferred should not be expired",
screens.contains(screen8ExpiredTransferred));
// just a little test here to see if we get a null or an empty list, find none
screens =
screenDataSharingLevelUpdater.findNewExpiredNotNotified(
date.minusYears(20), ScreenType.SMALL_MOLECULE);
log.info("empty result: " + screens);
assertNotNull(screens);
assertTrue(screens.isEmpty());
screens = screenDataSharingLevelUpdater.findNewExpiredNotNotified(date, ScreenType.RNAI);
assertFalse("no expired screens", screens.isEmpty());
assertTrue(
"only the RNAi screen should be returned (no Small Molecule): " + screens,
screens.size() == 1);
assertTrue(
"screen5RnaiExpired should NOT be expired (unless setting screenType=RNAi)",
screens.contains(screen5RnaiExpired));
}
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());
}