Plate cache updates and DB serialization clean up. (#5162)

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

@@ -40,9 +40,11 @@ public interface Plate extends PropertySet, Identifiable
 
     boolean isTemplate();
 
-    @NotNull PlateType getPlateTypeObject();
+    @NotNull PlateType getPlateType();
 
-    @Nullable PlateSet getPlateSetObject();
+    @Nullable PlateSet getPlateSet();
+
+    @NotNull String getPlateId();
 
     /**
      * Returns an existing well, or creates a new well if one

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

@@ -130,6 +130,14 @@ static PlateService get()
      */
     @Nullable Plate getPlate(Container container, int rowId);
 
+    /**
+     * Gets a plate instance object by plate id.
+     * @param container The plate's container.
+     * @param plateId The plate id of the plate.
+     * @return The requested plate, or null if no plate exists with the specified plate id.
+     */
+    @Nullable Plate getPlate(Container container, String plateId);
+
     /**
      * Gets a plate instance object by row id.
      * @param cf The container filter to find the plate
@@ -146,6 +154,14 @@ static PlateService get()
      */
     @Nullable Plate getPlate(ContainerFilter cf, Lsid lsid);
 
+    /**
+     * Gets a plate instance object by plate id.
+     * @param cf The container filter to find the plate
+     * @param plateId The plate id of the plate.
+     * @return The requested plate, or null if no plate exists with the specified plate id.
+     */
+    @Nullable Plate getPlate(ContainerFilter cf, String plateId);
+
     /**
      * Gets all plate templates for the specified container. Plate templates are Plate instances
      * which have their template field set to TRUE.

assay/src/org/labkey/assay/AssayDomainServiceImpl.java

@@ -26,7 +26,6 @@
 import org.labkey.api.assay.AssayDomainService;
 import org.labkey.api.assay.AssayProvider;
 import org.labkey.api.assay.AssayQCService;
-import org.labkey.api.assay.AssaySchema;
 import org.labkey.api.assay.AssayService;
 import org.labkey.api.assay.DetectionMethodAssayProvider;
 import org.labkey.api.assay.plate.Plate;
@@ -58,9 +57,7 @@
 import org.labkey.api.gwt.client.model.GWTContainer;
 import org.labkey.api.gwt.client.model.GWTDomain;
 import org.labkey.api.gwt.client.model.GWTPropertyDescriptor;
-import org.labkey.api.query.QueryChangeListener;
 import org.labkey.api.query.QueryService;
-import org.labkey.api.query.SchemaKey;
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.security.SecurityPolicy;
 import org.labkey.api.security.User;
@@ -484,7 +481,7 @@ public GWTProtocol saveChanges(GWTProtocol assay, boolean replaceIfExisting) thr
                     if (provider instanceof PlateBasedAssayProvider && assay.getSelectedPlateTemplate() != null)
                     {
                         PlateBasedAssayProvider plateProvider = (PlateBasedAssayProvider)provider;
-                        Plate plate = PlateManager.get().getPlate(getContainer(), assay.getSelectedPlateTemplate());
+                        Plate plate = PlateManager.get().getPlateByName(getContainer(), assay.getSelectedPlateTemplate());
                         if (plate != null)
                             plateProvider.setPlate(getContainer(), protocol, plate);
                         else

assay/src/org/labkey/assay/AssayUpgradeCode.java

@@ -205,7 +205,7 @@ private static Plate getPlate(ExpProtocol protocol)
     {
         // resolve plate by the legacy deprecated plate name method
         ObjectProperty prop = protocol.getObjectProperties().get(protocol.getLSID() + AbstractPlateBasedAssayProvider.PLATE_TEMPLATE_SUFFIX);
-        return prop != null ? PlateManager.get().getPlate(protocol.getContainer(), prop.getStringValue()) : null;
+        return prop != null ? PlateManager.get().getPlateByName(protocol.getContainer(), prop.getStringValue()) : null;
     }
 
     /**

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

@@ -282,6 +282,9 @@ public static class CopyTemplateBean
 
         public CopyTemplateBean(final Container container, final User user, final Integer plateId, final String selectedDestination)
         {
+            if (plateId == null)
+                throw new IllegalArgumentException("Plate ID cannot be null");
+
             _plate = PlateService.get().getPlate(container, plateId);
             if (_plate == null)
                 throw new IllegalStateException("Could not resolve the plate with ID : " + plateId);

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

@@ -46,7 +46,7 @@
 import org.labkey.api.security.User;
 import org.labkey.api.util.JsonUtil;
 import org.labkey.assay.TSVProtocolSchema;
-import org.labkey.assay.plate.model.Well;
+import org.labkey.assay.plate.model.WellBean;
 import org.labkey.assay.query.AssayDbSchema;
 
 import java.io.File;
@@ -297,11 +297,11 @@ public List<Map<String, Object>> mergePlateMetadata(
             if (!plate.getCustomFields().isEmpty())
             {
                 // create the map of well locations to the well
-                Map<Position, Well> positionToWell = new HashMap<>();
+                Map<Position, WellBean> positionToWell = new HashMap<>();
 
                 SimpleFilter filter = SimpleFilter.createContainerFilter(plate.getContainer());
                 filter.addCondition(FieldKey.fromParts("PlateId"), plate.getRowId());
-                for (Well well : new TableSelector(AssayDbSchema.getInstance().getTableInfoWell(), filter, null).getArrayList(Well.class))
+                for (WellBean well : new TableSelector(AssayDbSchema.getInstance().getTableInfoWell(), filter, null).getArrayList(WellBean.class))
                     positionToWell.put(new PositionImpl(plate.getContainer(), well.getRow(), well.getCol()), well);
 
                 for (Map<String, Object> row : mergedRows)
@@ -502,7 +502,7 @@ public OntologyManager.UpdateableTableImportHelper getImportHelper(
 
         SimpleFilter filter = SimpleFilter.createContainerFilter(plate.getContainer());
         filter.addCondition(FieldKey.fromParts("PlateId"), plate.getRowId());
-        for (Well well : new TableSelector(AssayDbSchema.getInstance().getTableInfoWell(), filter, null).getArrayList(Well.class))
+        for (WellBean well : new TableSelector(AssayDbSchema.getInstance().getTableInfoWell(), filter, null).getArrayList(WellBean.class))
             positionToWellLsid.put(new PositionImpl(plate.getContainer(), well.getRow(), well.getCol()), Lsid.parse(well.getLsid()));
 
         return new PlateMetadataImportHelper(plate.getContainer(), data, Collections.unmodifiableMap(positionToWellLsid));

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

@@ -16,6 +16,7 @@
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.exp.Lsid;
 import org.labkey.api.query.FieldKey;
+import org.labkey.assay.plate.model.PlateBean;
 import org.labkey.assay.query.AssayDbSchema;
 
 import java.util.ArrayList;
@@ -46,13 +47,14 @@ public Plate load(@NotNull String key, @Nullable Object argument)
             SimpleFilter filter = SimpleFilter.createContainerFilter(cacheKey._container);
             filter.addCondition(FieldKey.fromParts(cacheKey._type.name()), cacheKey._identifier);
 
-            List<PlateImpl> plates = new TableSelector(AssayDbSchema.getInstance().getTableInfoPlate(), filter, null).getArrayList(PlateImpl.class);
+            List<PlateBean> plates = new TableSelector(AssayDbSchema.getInstance().getTableInfoPlate(), filter, null).getArrayList(PlateBean.class);
             assert plates.size() <= 1;
 
             if (plates.size() == 1)
             {
-                PlateImpl plate = plates.get(0);
-                PlateManager.get().populatePlate(plate);
+                PlateBean bean = plates.get(0);
+
+                Plate plate = PlateManager.get().populatePlate(bean);
                 LOG.info(String.format("Caching plate \"%s\" for folder %s", plate.getName(), cacheKey._container.getPath()));
 
                 // add all cache keys for this plate
@@ -66,8 +68,8 @@ private void addCacheKeys(PlateCacheKey cacheKey, Plate plate)
         {
             if (plate != null)
             {
-                if (plate.getName() == null)
-                    throw new IllegalArgumentException("Plate cannot be cached, name is null");
+                if (plate.getPlateId() == null)
+                    throw new IllegalArgumentException("Plate cannot be cached, plateId is null");
                 if (plate.getRowId() == null)
                     throw new IllegalArgumentException("Plate cannot be cached, rowId is null");
                 if (plate.getLSID() == null)
@@ -78,8 +80,8 @@ private void addCacheKeys(PlateCacheKey cacheKey, Plate plate)
                     PLATE_CACHE.put(PlateCacheKey.getCacheKey(plate.getContainer(), plate.getRowId()), plate);
                 if (cacheKey._type != PlateCacheKey.Type.lsid)
                     PLATE_CACHE.put(PlateCacheKey.getCacheKey(plate.getContainer(), Lsid.parse(plate.getLSID())), plate);
-                if (cacheKey._type != PlateCacheKey.Type.name)
-                    PLATE_CACHE.put(PlateCacheKey.getCacheKey(plate.getContainer(), plate.getName()), plate);
+                if (cacheKey._type != PlateCacheKey.Type.plateId)
+                    PLATE_CACHE.put(PlateCacheKey.getCacheKey(plate.getContainer(), plate.getPlateId()), plate);
 
                 _containerPlateMap.computeIfAbsent(cacheKey._container, k -> new ArrayList<>()).add(plate);
             }
@@ -110,6 +112,14 @@ private void addCacheKeys(PlateCacheKey cacheKey, Plate plate)
         return c != null ? PLATE_CACHE.get(PlateCacheKey.getCacheKey(c, lsid)) : null;
     }
 
+    public static @Nullable Plate getPlate(ContainerFilter cf, String plateId)
+    {
+        SimpleFilter filter = new SimpleFilter(FieldKey.fromParts("plateId"), plateId);
+        Container c = getContainerWithIdentifier(cf, filter);
+
+        return c != null ? PLATE_CACHE.get(PlateCacheKey.getCacheKey(c, plateId)) : null;
+    }
+
     private static @Nullable Container getContainerWithIdentifier(ContainerFilter cf, SimpleFilter filter)
     {
         filter.addClause(cf.createFilterClause(AssayDbSchema.getInstance().getSchema(), FieldKey.fromParts("Container")));
@@ -127,9 +137,9 @@ private void addCacheKeys(PlateCacheKey cacheKey, Plate plate)
         return null;
     }
 
-    public static @Nullable Plate getPlate(Container c, String name)
+    public static @Nullable Plate getPlate(Container c, String plateId)
     {
-        Plate plate = PLATE_CACHE.get(PlateCacheKey.getCacheKey(c, name));
+        Plate plate = PLATE_CACHE.get(PlateCacheKey.getCacheKey(c, plateId));
         return plate != null ? plate.copy() : null;
     }
 
@@ -185,14 +195,14 @@ public static void uncache(Container c, Plate plate)
     {
         LOG.info(String.format("Un-caching plate \"%s\" for folder %s", plate.getName(), c.getPath()));
 
-        if (plate.getName() == null)
-            throw new IllegalArgumentException("Plate cannot be uncached, name is null");
+        if (plate.getPlateId() == null)
+            throw new IllegalArgumentException("Plate cannot be uncached, plateId is null");
         if (plate.getRowId() == null)
             throw new IllegalArgumentException("Plate cannot be uncached, rowId is null");
         if (plate.getLSID() == null)
             throw new IllegalArgumentException("Plate cannot be uncached, LSID is null");
 
-        PLATE_CACHE.remove(PlateCacheKey.getCacheKey(c, plate.getName()));
+        PLATE_CACHE.remove(PlateCacheKey.getCacheKey(c, plate.getPlateId()));
         PLATE_CACHE.remove(PlateCacheKey.getCacheKey(c, plate.getRowId()));
         PLATE_CACHE.remove(PlateCacheKey.getCacheKey(c, Lsid.parse(plate.getLSID())));
 
@@ -210,7 +220,7 @@ private static class PlateCacheKey
         enum Type
         {
             rowId,
-            name,
+            plateId,
             lsid,
         }
         private Type _type;
@@ -226,14 +236,14 @@ enum Type
             _identifier = json.get("identifier");
         }
 
-        public static String getCacheKey(Container c, String name)
+        public static String getCacheKey(Container c, String plateId)
         {
-            return _getCacheKey(c, Type.name, name);
+            return _getCacheKey(c, Type.plateId, plateId);
         }
 
-        public static String getCacheKey(Container c, Integer plateId)
+        public static String getCacheKey(Container c, Integer rowId)
         {
-            return _getCacheKey(c, Type.rowId, plateId);
+            return _getCacheKey(c, Type.rowId, rowId);
         }
 
         public static String getCacheKey(Container c, Lsid lsid)

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

@@ -177,7 +177,7 @@ public int saveChanges(GWTPlate gwtPlate, boolean replaceIfExisting) throws Exce
             else
             {
                 // check another plate of the same name doesn't already exist
-                Plate other = PlateManager.get().getPlate(getContainer(), gwtPlate.getName());
+                Plate other = PlateManager.get().getPlateByName(getContainer(), gwtPlate.getName());
                 if (other != null)
                 {
                     if (!replaceIfExisting)

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

@@ -73,7 +73,7 @@ public static WebdavResource createDocument(@NotNull Plate plate)
 
         StringBuilder body = new StringBuilder();
 
-        PlateType plateType = plate.getPlateTypeObject();
+        PlateType plateType = plate.getPlateType();
         if (plateType != null)
             append(body, plateType.getDescription());