Support assay import of cross folder plates

assay/api-src/org/labkey/api/assay/plate/PlateService.java

@@ -162,9 +162,9 @@ static PlateService get()
      * for the standard assay with plate support since other assays types do not store the plate ID with the
      * run.
      */
-    int getRunCountUsingPlate(@NotNull Container c, @NotNull Plate plate);
+    int getRunCountUsingPlate(@NotNull Container c, @NotNull User user, @NotNull Plate plate);
 
-    List<? extends ExpRun> getRunsUsingPlate(@NotNull Container c, @NotNull Plate plate);
+    List<? extends ExpRun> getRunsUsingPlate(@NotNull Container c, @NotNull User user, @NotNull Plate plate);
 
     /**
      * Creates a new plate template.

assay/src/org/labkey/assay/PlateController.java

@@ -645,7 +645,7 @@ public void validateForm(DataViewSnapshotSelectionForm form, Errors errors)
         @Override
         public Object execute(DataViewSnapshotSelectionForm form, BindException errors) throws Exception
         {
-            var results = PlateManager.get().getPlateOperationConfirmationData(getContainer(), form.getIds(false));
+            var results = PlateManager.get().getPlateOperationConfirmationData(getContainer(), getUser(), form.getIds(false));
             return success(results);
         }
     }
@@ -849,7 +849,7 @@ public Object execute(GetPlateForm form, BindException errors) throws Exception
             Plate plate = PlateManager.get().getPlate(cf, form.getRowId());
 
             if (plate != null && Boolean.TRUE.equals(form.getIncludeRunCount()))
-                ((PlateImpl) plate).setRunCount(PlateManager.get().getRunCountUsingPlate(plate.getContainer(), plate));
+                ((PlateImpl) plate).setRunCount(PlateManager.get().getRunCountUsingPlate(plate.getContainer(), getUser(), plate));
 
             return plate;
         }

assay/src/org/labkey/assay/TsvAssayProvider.java

@@ -349,7 +349,7 @@ public void changeDomain(User user, ExpProtocol protocol, GWTDomain<GWTPropertyD
                 Optional<GWTPropertyDescriptor> plateTemplateColumn = update.getFields().stream().filter(field -> field.getName().equals(AssayPlateMetadataService.PLATE_TEMPLATE_COLUMN_NAME)).findFirst();
                 if (plateTemplateColumn.isPresent())
                 {
-                    // Ensure the lookup container is null so it defaults to "Current Folder" to more easily support
+                    // Ensure the lookup container is null, so it defaults to "Current Folder" to more easily support
                     // cross-folder support.
                     GWTPropertyDescriptor plateTemplate = plateTemplateColumn.get();
                     plateTemplate.setLookupContainer(null);

assay/src/org/labkey/assay/plate/AssayPlateMetadataServiceImpl.java

@@ -87,7 +87,7 @@ public void addAssayPlateMetadata(
             if (property != null)
                 plateLsid = Lsid.parse(String.valueOf(run.getProperty(property)));
 
-            Map<Position, Map<String, Object>> plateData = prepareMergedPlateData(plateLsid, plateMetadata, user, protocol, true);
+            Map<Position, Map<String, Object>> plateData = prepareMergedPlateData(container, user, plateLsid, plateMetadata, protocol, true);
             Domain domain = getPlateDataDomain(protocol);
 
             Map<String, PropertyDescriptor> descriptorMap = new CaseInsensitiveHashMap<>();
@@ -158,17 +158,18 @@ public void addAssayPlateMetadata(
      * to metadata properties.
      */
     private Map<Position, Map<String, Object>> prepareMergedPlateData(
+            Container container,
+            User user,
             Lsid plateLsid,
             Map<String, MetadataLayer> plateMetadata,
-            @Nullable User user,
             ExpProtocol protocol,
             boolean ensurePlateDomain           // true to create the plate domain and properties if they don't exist
     ) throws ExperimentException
     {
         _domainDirty = false;
         _propValues.clear();
 
-        Plate plate = PlateService.get().getPlate(protocol.getContainer(), plateLsid);
+        Plate plate = PlateService.get().getPlate(PlateManager.get().getPlateContainerFilter(protocol, container, user), plateLsid);
         if (plate == null)
             throw new ExperimentException("Unable to resolve the plate template for the run");
 
@@ -272,7 +273,7 @@ public List<Map<String, Object>> mergePlateMetadata(
 
         if (plateMetadata != null)
         {
-            Map<Position, Map<String, Object>> plateData = prepareMergedPlateData(plateLsid, plateMetadata, null, protocol, false);
+            Map<Position, Map<String, Object>> plateData = prepareMergedPlateData(container, user, plateLsid, plateMetadata, protocol, false);
             for (Map<String, Object> row : mergedRows)
             {
                 PositionImpl well = new PositionImpl(null, String.valueOf(row.get(AssayResultDomainKind.WELL_LOCATION_COLUMN_NAME)));
@@ -287,12 +288,12 @@ public List<Map<String, Object>> mergePlateMetadata(
         if (AssayPlateMetadataService.isExperimentalAppPlateEnabled())
         {
             // include metadata that may have been applied directly to the plate
-            Plate plate = PlateService.get().getPlate(protocol.getContainer(), plateLsid);
+            Plate plate = PlateService.get().getPlate(PlateManager.get().getPlateContainerFilter(protocol, container, user), plateLsid);
             if (plate == null)
                 throw new ExperimentException("Unable to resolve the plate for the run");
 
             // if there are metadata fields configured for this plate
-            if (!PlateManager.get().getFields(container, plate.getRowId()).isEmpty())
+            if (!plate.getCustomFields().isEmpty())
             {
                 // create the map of well locations to the well
                 Map<Position, Well> positionToWell = new HashMap<>();
@@ -310,7 +311,7 @@ public List<Map<String, Object>> mergePlateMetadata(
 
                     if (positionToWell.containsKey(well))
                     {
-                        for (WellCustomField customField : PlateManager.get().getWellCustomFields(container, user, plate.getRowId(), positionToWell.get(well).getRowId()))
+                        for (WellCustomField customField : PlateManager.get().getWellCustomFields(user, plate, positionToWell.get(well).getRowId()))
                         {
                             row.put(customField.getName(), customField.getValue());
                         }
@@ -493,7 +494,7 @@ public OntologyManager.UpdateableTableImportHelper getImportHelper(
         if (property != null)
             plateLsid = Lsid.parse(String.valueOf(run.getProperty(property)));
 
-        Plate plate = PlateService.get().getPlate(protocol.getContainer(), plateLsid);
+        Plate plate = PlateService.get().getPlate(PlateManager.get().getPlateContainerFilter(protocol, container, user), plateLsid);
         if (plate == null)
             throw new ExperimentException(String.format("Unable to resolve the plate : %s for the run", plateLsid));
 

assay/src/org/labkey/assay/plate/PlateManager.java

@@ -320,9 +320,9 @@ public List<Plate> getPlateTemplates(Container container)
     }
 
     @Override
-    public List<? extends ExpRun> getRunsUsingPlate(@NotNull Container c, @NotNull Plate plate)
+    public List<? extends ExpRun> getRunsUsingPlate(@NotNull Container c, @NotNull User user, @NotNull Plate plate)
     {
-        SqlSelector se = selectRunUsingPlate(c, plate);
+        SqlSelector se = selectRunUsingPlate(c, user, plate);
         if (se == null)
             return emptyList();
 
@@ -331,20 +331,17 @@ public List<? extends ExpRun> getRunsUsingPlate(@NotNull Container c, @NotNull P
     }
 
     @Override
-    public int getRunCountUsingPlate(@NotNull Container c, @NotNull Plate plate)
+    public int getRunCountUsingPlate(@NotNull Container c, @NotNull User user, @NotNull Plate plate)
     {
-        SqlSelector se = selectRunUsingPlate(c, plate);
+        SqlSelector se = selectRunUsingPlate(c, user, plate);
         if (se == null)
             return 0;
 
         return (int) se.getRowCount();
     }
 
-    private @Nullable SqlSelector selectRunUsingPlate(@NotNull Container c, @NotNull Plate plate)
+    private @Nullable SqlSelector selectRunUsingPlate(@NotNull Container c, @NotNull User user, @NotNull Plate plate)
     {
-        if (plate == null)
-            return null;
-
         // first, get the list of GPAT protocols in the container
         AssayProvider gpat = AssayService.get().getProvider(TsvAssayProvider.NAME);
         if (gpat == null)
@@ -369,12 +366,14 @@ public int getRunCountUsingPlate(@NotNull Container c, @NotNull Plate plate)
         List<Integer> plateTemplatePropIds = plateTemplateProps.stream().map(PropertyDescriptor::getPropertyId).toList();
 
         // query for runs with that property that point to the plate by LSID
+        ContainerFilter cf = getPlateContainerFilter(null, c, user);
         SQLFragment sql = new SQLFragment()
                 .append("SELECT r.rowId\n")
                 .append("FROM ").append(ExperimentService.get().getTinfoExperimentRun(), "r").append("\n")
                 .append("INNER JOIN ").append(OntologyManager.getTinfoObject(), "o").append(" ON o.objectUri = r.lsid\n")
                 .append("INNER JOIN ").append(OntologyManager.getTinfoObjectProperty(), "op").append(" ON op.objectId = o.objectId\n")
-                .append("WHERE r.container = ?\n").add(c.getId())
+                .append("WHERE ")
+                .append(cf.getSQLFragment(AssayDbSchema.getInstance().getSchema(), new SQLFragment("r.container"))).append("\n")
                 .append("AND op.propertyId ").appendInClause(plateTemplatePropIds, AssayDbSchema.getInstance().getSchema().getSqlDialect()).append("\n")
                 .append("AND op.stringvalue = ?").add(plate.getLSID());
 
@@ -416,6 +415,16 @@ public Plate createPlateTemplate(Container container, String templateType, int r
         return PlateCache.getPlate(cf, lsid);
     }
 
+    /**
+     * Helper to create container filters to support assay import using cross folder
+     * plates
+     */
+    public ContainerFilter getPlateContainerFilter(@Nullable ExpProtocol protocol, Container container, User user)
+    {
+        ContainerFilter defaultCf = ContainerFilter.Type.Current.create(protocol != null ? protocol.getContainer() : container, user);
+        return QueryService.get().getProductContainerFilterForLookups(container, user, defaultCf);
+    }
+
     @Override
     public @Nullable Plate getPlate(Container container, Lsid lsid)
     {
@@ -1234,6 +1243,7 @@ public PlateType getPlateType(@NotNull Plate plate)
 
     public @NotNull Map<String, List<Map<String, Integer>>> getPlateOperationConfirmationData(
         @NotNull Container container,
+        @NotNull User user,
         @NotNull Set<Integer> plateRowIds
     )
     {
@@ -1247,7 +1257,7 @@ public PlateType getPlateType(@NotNull Plate plate)
         // TODO: This is really expensive. Find a way to consolidate this check into a single query.
         permittedIds.forEach(plateRowId -> {
             Plate plate = getPlate(container, plateRowId);
-            if (plate == null || getRunCountUsingPlate(container, plate) > 0)
+            if (plate == null || getRunCountUsingPlate(container, user, plate) > 0)
                 notPermittedIds.add(plateRowId);
         });
         permittedIds.removeAll(notPermittedIds);
@@ -1510,18 +1520,16 @@ private List<DomainProperty> _getFields(Container container, User user, Integer
         return fields;
     }
 
-    public List<WellCustomField> getWellCustomFields(Container container, User user, Integer plateId, Integer wellId)
+    public List<WellCustomField> getWellCustomFields(User user, Plate plate, Integer wellId)
     {
-        Plate plate = requirePlate(container, plateId, "Failed to get well custom fields.");
-
         Well well = plate.getWell(wellId);
         if (well == null)
             throw new IllegalArgumentException("Failed to get well custom fields. Well id \"" + wellId   + "\" not found.");
 
-        List<WellCustomField> fields = _getFields(container, user, plateId).stream().map(WellCustomField::new).toList();
+        List<WellCustomField> fields = _getFields(plate.getContainer(), user, plate.getRowId()).stream().map(WellCustomField::new).toList();
 
         // need to get the well values associated with each custom field
-        Map<String, Object> properties = OntologyManager.getProperties(container, well.getLsid());
+        Map<String, Object> properties = OntologyManager.getProperties(plate.getContainer(), well.getLsid());
         for (WellCustomField field : fields)
             field.setValue(properties.get(field.getPropertyURI()));
 

assay/src/org/labkey/assay/plate/query/PlateTable.java

@@ -228,7 +228,7 @@ protected Map<String, Object> updateRow(User user, Container container, Map<Stri
             if (plate == null)
                 return Collections.emptyMap();
 
-            int runsInUse = PlateManager.get().getRunCountUsingPlate(container, plate);
+            int runsInUse = PlateManager.get().getRunCountUsingPlate(container, user, plate);
             if (runsInUse > 0)
                 throw new QueryUpdateServiceException(String.format("%s is used by %d runs and cannot be updated", plate.isTemplate() ? "Plate template" : "Plate", runsInUse));
 
@@ -254,7 +254,7 @@ protected Map<String, Object> deleteRow(User user, Container container, Map<Stri
             if (plate == null)
                 return Collections.emptyMap();
 
-            int runsInUse = PlateManager.get().getRunCountUsingPlate(container, plate);
+            int runsInUse = PlateManager.get().getRunCountUsingPlate(container, user, plate);
             if (runsInUse > 0)
                 throw new QueryUpdateServiceException(String.format("%s is used by %d runs and cannot be deleted", plate.isTemplate() ? "Plate template" : "Plate", runsInUse));
 

assay/src/org/labkey/assay/plate/query/WellTable.java

@@ -262,7 +262,7 @@ protected Map<String, Object> updateRow(User user, Container container, Map<Stri
                 Plate plate = PlateManager.get().getPlate(container, (Integer)oldRow.get("plateId"));
                 if (plate != null)
                 {
-                    int runsInUse = PlateManager.get().getRunCountUsingPlate(container, plate);
+                    int runsInUse = PlateManager.get().getRunCountUsingPlate(container, user, plate);
                     if (runsInUse > 0)
                         throw new QueryUpdateServiceException(String.format("This %s is used by %d runs and its wells cannot be modified.", plate.isTemplate() ? "Plate template" : "Plate", runsInUse));
                 }

assay/src/org/labkey/assay/plate/view/plateTemplateList.jsp

@@ -47,7 +47,7 @@
     Map<Plate, Integer> plateTemplateRunCount = new HashMap<>();
     for (Plate template : plateTemplates)
     {
-        int count = PlateService.get().getRunCountUsingPlate(c, template);
+        int count = PlateService.get().getRunCountUsingPlate(c, getUser(), template);
         plateTemplateRunCount.put(template, count);
     }
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