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[bot] Merge 23.11 to 24.3 #226

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merged 3 commits into from
Aug 16, 2024
+91 −32
Merged

[bot] Merge 23.11 to 24.3 #226

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cb33b9e
Fixed issue where certain subpackages were not getting populated in t…
jallentxbiomed Aug 9, 2024
8cf8758
new feature branch from snapshot (#223)
jallentxbiomed Aug 14, 2024
58ef4b2
Merge 23.11 to 24.3
labkey-teamcity Aug 16, 2024
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19 changes: 12 additions & 7 deletions src/org/labkey/snd/SNDController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1040,14 +1040,19 @@ public ApiResponse execute(SimpleApiJsonForm form, BindException errors)
}

Event savedEvent = SNDService.get().saveEvent(getContainer(), getUser(), event, validateOnly);
response.put("event", savedEvent.toJSON(getContainer(), getUser()));

if (savedEvent.hasErrors())
{
response.put("success", false);
}
else
{
if (savedEvent != null) {
response.put("event", savedEvent.toJSON(getContainer(), getUser()));
if (savedEvent.hasErrors())
{
response.put("success", false);
}
else
{
response.put("success", true);
}
} else {
response.put("event", null);
response.put("success", true);
}
}
Expand Down
92 changes: 68 additions & 24 deletions src/org/labkey/snd/SNDManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2941,6 +2941,52 @@ private void deleteExpObjects(Container c, User u, int eventId)
}
}

public Event deleteEvent(Container c, User u, Event event) {

if (!event.hasErrors()) {
UserSchema schema = getSndUserSchemaAdminRole(c, u);
TableInfo eventTable = getTableInfo(schema, SNDSchema.EVENTS_TABLE_NAME);
QueryUpdateService eventQus = getQueryUpdateService(eventTable);

BatchValidationException errors = new BatchValidationException();

try (DbScope.Transaction tx = eventTable.getSchema().getScope().ensureTransaction())
{
deleteEventDatas(c, u, event.getEventId());
deleteEventNotes(c, u, event.getEventId());
deleteEventsCache(c, u, event.getEventId());
NarrativeAuditProvider.addAuditEntry(c, u, event.getEventId(), event.getSubjectId(), event.getDate(), "", event.getQcState(), "Delete event");

Map<String, Object> row;
List<Map<String, Object>> rows = new ArrayList<>();
row = new HashMap<>();
row.put("EventId", event.getEventId());
rows.add(row);
eventQus.deleteRows(u, c, rows, null, null);

tx.commit();

} catch (QueryUpdateServiceException | BatchValidationException | SQLException | InvalidKeyException e) {

event.setException(new ValidationException(e.getMessage(), ValidationException.SEVERITY.ERROR));

} finally
{
if (errors.hasErrors())
{
event.addBatchValidationExceptions(errors);
}
// Errors, warnings and info are embedded in the event so don't override
else if (!event.hasErrorsWarningsOrInfo())
{
event = getEvent(c, u, event.getEventId(), null, null, true, errors);
}
}
}

return event;
}

/**
* Called from SNDService.saveEvent to update an existing event.
*/
Expand Down Expand Up @@ -3778,7 +3824,7 @@ public Event getEvent(Container c, User u, int eventId, Set<EventNarrativeOption
public Map<Integer, Event> getBulkEvents(Container c, User u, List<Integer> eventIds, Set<EventNarrativeOption> narrativeOptions,
@Nullable Map<Integer, Map<Integer, SuperPackage>> topLevelSuperPkgs, boolean skipPermissionCheck, BatchValidationException errors,
List<GWTPropertyDescriptor> eventExtraFields, List<GWTPropertyDescriptor> eventDataExtraFields,
boolean includeEmptySubPackges) {
boolean includeEmptySubPackages) {

// Events from query - SELECT * FROM Events WHERE EventId IN {eventIds}
TableSelector eventSelector = getTableSelector(c, u, eventIds, SNDSchema.EVENTS_TABLE_NAME, Event.EVENT_ID, null, null);
Expand All @@ -3796,7 +3842,7 @@ public Map<Integer, Event> getBulkEvents(Container c, User u, List<Integer> even
Map<String, String> projectIdRevs = getBulkProjectIdRevs(c, u, events.stream().map(Event::getParentObjectId).collect(Collectors.toList()));

//EventData grouped by EventId
Map<Integer, List<EventData>> eventData = getBulkEventData(c, topLevelSuperPkgs, rawEventData, eventDataExtensibleFields, eventDataExtraFields, includeEmptySubPackges);
Map<Integer, List<EventData>> eventData = getBulkEventData(c, topLevelSuperPkgs, rawEventData, eventDataExtensibleFields, eventDataExtraFields, includeEmptySubPackages);

// Build events from eventData, eventNotes, and project data and group by EventId
Map<Integer, Event> eventsById = events.stream().collect(Collectors.toMap(Event::getEventId, (Event event) -> {
Expand Down Expand Up @@ -4044,17 +4090,14 @@ private Map<Integer, List<EventData>> getBulkEventData(Container c, Map<Integer,

addExtraFieldsToEventData(eventData, eventDataExtraFields, extraFields);

boolean hasEmptySubpackages =
includeEmptySubPackages
&&
!superPackagesByEventDataId.get(eventData.getEventDataId()).getChildPackages().isEmpty();
boolean hasSubpackages = !superPackagesByEventDataId.get(eventData.getEventDataId()).getChildPackages().isEmpty();

Map<Integer, Map<Integer, SuperPackage>> nextLevelSuperPkgs = getNextLevelEventDataSuperPkgs(eventData, childEventData, currentLevelSuperPkgs, includeEmptySubPackages, hasEmptySubpackages);
Map<Integer, Map<Integer, SuperPackage>> nextLevelSuperPkgs = getNextLevelEventDataSuperPkgs(eventData, childEventData, currentLevelSuperPkgs, includeEmptySubPackages, hasSubpackages);

if (nextLevelSuperPkgs != null && !nextLevelSuperPkgs.isEmpty()) {
if (nextLevelSuperPkgs != null && !nextLevelSuperPkgs.get(eventData.getEventId()).isEmpty()) {
// Recursion for next child level of sub packages
Map<Integer, List<EventData>> subEventData = getBulkEventData(c, nextLevelSuperPkgs, currentEventData, eventDataExtensibleFields, eventDataExtraFields, includeEmptySubPackages);
if (subEventData != null) {
if (subEventData != null && subEventData.containsKey(eventData.getEventId())) {
List<EventData> sorted = subEventData.get(eventData.getEventId()).stream().sorted(Comparator.comparing(
(EventData child) -> nextLevelSuperPkgs.get(child.getEventId()).get(child.getEventDataId()).getTreePath()))
.filter(ed -> ed.getParentEventDataId() == null || ed.getParentEventDataId().equals(eventData.getEventDataId()))
Expand Down Expand Up @@ -4138,9 +4181,9 @@ private AttributeData getAttributeData(GWTPropertyDescriptor propertyDescriptor,
*/
private Map<Integer, Map<Integer, SuperPackage>> getNextLevelEventDataSuperPkgs(EventData eventData, Map<Integer,
List<EventData>> childEventData, Map<Integer, Map<Integer, SuperPackage>> currentLevelSuperPkgs,
boolean includeEmptySubPackages, boolean hasChildPackages) {
boolean includeEmptySubPackages, boolean hasSubpackages) {

if (!childEventData.containsKey(eventData.getEventId()) && !hasChildPackages) {
if ((!includeEmptySubPackages && !childEventData.containsKey(eventData.getEventId())) || (includeEmptySubPackages && !hasSubpackages)) {
return null;
}

Expand All @@ -4157,10 +4200,10 @@ private Map<Integer, Map<Integer, SuperPackage>> getNextLevelEventDataSuperPkgs(
));

// Get superPkg for eventData and group by eventId and then by eventId
Map<Integer, Map<Integer, SuperPackage>> nextLevelEventDataSuperPkgs;
List<Integer> eventDataSuperPkgIds;
Map<Integer, Map<Integer, SuperPackage>> nextLevelEventDataSuperPkgs = new HashMap<>();
nextLevelEventDataSuperPkgs.put(eventData.getEventId(), new HashMap<>());

if (!childEventData.isEmpty()) {
if (!childSuperPkgs.isEmpty() && !childEventData.isEmpty()) {
Map<Integer, SuperPackage> children = childSuperPkgs;
nextLevelEventDataSuperPkgs = childEventData.get(eventData.getEventId())
.stream()
Expand All @@ -4174,24 +4217,25 @@ private Map<Integer, Map<Integer, SuperPackage>> getNextLevelEventDataSuperPkgs(
)
)
);
eventDataSuperPkgIds = nextLevelEventDataSuperPkgs.containsKey(eventData.getEventId())
? nextLevelEventDataSuperPkgs.get(eventData.getEventId()).values().stream().map(SuperPackage::getSuperPkgId).toList()
: new ArrayList<>();
}
else
{
nextLevelEventDataSuperPkgs = new HashMap<>();

if (!nextLevelEventDataSuperPkgs.containsKey(eventData.getEventId())) {
nextLevelEventDataSuperPkgs.put(eventData.getEventId(), new HashMap<>());
eventDataSuperPkgIds = new ArrayList<>();
}

AtomicInteger emptyEventDataId = new AtomicInteger(0);

if (includeEmptySubPackages && nextLevelEventDataSuperPkgs.containsKey(eventData.getEventId())) {
if (includeEmptySubPackages) {

List<Integer> eventDataSuperPkgIds = !nextLevelEventDataSuperPkgs.get(eventData.getEventId()).isEmpty()
? nextLevelEventDataSuperPkgs.get(eventData.getEventId()).values().stream().map(SuperPackage::getSuperPkgId).toList()
: new ArrayList<>();

AtomicInteger emptyEventDataId = new AtomicInteger(0);
Map<Integer, Map<Integer, SuperPackage>> eventDataSuperPkgs = nextLevelEventDataSuperPkgs;
childSuperPkgs.values().stream()
.filter(superPkg -> !eventDataSuperPkgIds.contains(superPkg.getSuperPkgId()))
.forEach(spkg -> {
nextLevelEventDataSuperPkgs.get(eventData.getEventId()).put(emptyEventDataId.getAndAdd(1), spkg);
eventDataSuperPkgs.get(eventData.getEventId()).put(emptyEventDataId.getAndAdd(1), spkg);
});
}

Expand Down
12 changes: 11 additions & 1 deletion src/org/labkey/snd/SNDServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -351,7 +351,17 @@ public Event saveEvent(Container c, User u, Event event, boolean validateOnly)
{
if (event.getEventId() != null && SNDManager.get().eventExists(c, u, event.getEventId()))
{
event = SNDManager.get().updateEvent(c, u, event, validateOnly);
if ((event.getEventData() == null || event.getEventData().isEmpty()) &&
(!event.getEventNotesRow(c).containsKey("note") ||
event.getEventNotesRow(c).get("note") == null ||
event.getEventNotesRow(c).get("note").toString().trim().length() == 0))
{
event = SNDManager.get().deleteEvent(c, u, event);
}
else
{
event = SNDManager.get().updateEvent(c, u, event, validateOnly);
}
}
else
{
Expand Down
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