Refactor Plate cache

api/src/org/labkey/api/assay/plate/AssayPlateMetadataService.java

@@ -25,6 +25,7 @@ public interface AssayPlateMetadataService
 {
     String PLATE_TEMPLATE_COLUMN_NAME = "PlateTemplate";
     Map<AssayDataType, AssayPlateMetadataService> _handlers = new HashMap<>();
+    String EXPERIMENTAL_APP_PLATE_SUPPORT = "experimental-app-plate-support";
 
     static void registerService(AssayDataType dataType, AssayPlateMetadataService handler)
     {
@@ -38,7 +39,7 @@ static void registerService(AssayDataType dataType, AssayPlateMetadataService ha
 
     static boolean isExperimentalAppPlateEnabled()
     {
-        return ExperimentalFeatureService.get().isFeatureEnabled("experimental-app-plate-support");
+        return ExperimentalFeatureService.get().isFeatureEnabled(EXPERIMENTAL_APP_PLATE_SUPPORT);
     }
 
     @Nullable

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

@@ -16,6 +16,7 @@
 
 package org.labkey.api.assay.plate;
 
+import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.exp.Identifiable;
 import org.labkey.api.study.PropertySet;
@@ -43,6 +44,8 @@ public interface Plate extends PropertySet, Identifiable
 
     Well getWell(int rowId);
 
+    List<Well> getWells();
+
     WellGroup getWellGroup(WellGroup.Type type, String wellGroupName);
 
     @Nullable WellGroup getWellGroup(int rowId);
@@ -71,4 +74,17 @@ public interface Plate extends PropertySet, Identifiable
 
     @Override
     @Nullable ActionURL detailsURL();
+
+    /**
+     * The list of metadata fields that are configured for this plate
+     */
+    @NotNull List<PlateCustomField> getCustomFields();
+
+    Plate copy();
+
+    /**
+     * Returns the domain ID for the plate metadata domain.
+     */
+    @Nullable
+    Integer getMetadataDomainId();
 }

assay/src/org/labkey/assay/plate/model/PlateCustomField.java → assay/api-src/org/labkey/api/assay/plate/PlateCustomField.java

@@ -1,4 +1,4 @@
-package org.labkey.assay.plate.model;
+package org.labkey.api.assay.plate;
 
 import com.fasterxml.jackson.annotation.JsonInclude;
 import org.labkey.api.exp.property.DomainProperty;

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

@@ -25,6 +25,8 @@
 import org.labkey.api.data.statistics.StatsService;
 import org.labkey.api.exp.Lsid;
 import org.labkey.api.exp.api.ExpRun;
+import org.labkey.api.exp.property.Domain;
+import org.labkey.api.query.ValidationException;
 import org.labkey.api.security.User;
 import org.labkey.api.services.ServiceRegistry;
 import org.labkey.api.view.ActionURL;
@@ -236,6 +238,11 @@ static PlateService get()
      */
     TableInfo getPlateTableInfo();
 
+    /**
+     * Create the plate metadata domain for this container.
+     */
+    @NotNull Domain ensurePlateMetadataDomain(Container container, User user) throws ValidationException;
+
     /**
      * A PlateDetailsResolver implementation provides a URL where a detailed, plate-type specific
      * UI can be found.

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

@@ -78,6 +78,12 @@ public int getColumn()
         return _column;
     }
 
+    // needed for DB serialization
+    public int getCol()
+    {
+        return getColumn();
+    }
+
     @Override
     public int getRow()
     {
@@ -143,11 +149,6 @@ public void setCol(int column)
         setColumn(column);
     }
 
-    public int getCol()
-    {
-        return getColumn();
-    }
-
     public Integer getPlateId()
     {
         return _plateId;

assay/src/org/labkey/assay/plate/model/WellCustomField.java → assay/api-src/org/labkey/api/assay/plate/WellCustomField.java

@@ -1,4 +1,4 @@
-package org.labkey.assay.plate.model;
+package org.labkey.api.assay.plate;
 
 import org.labkey.api.exp.property.DomainProperty;
 

assay/src/org/labkey/assay/AssayModule.java

@@ -54,6 +54,7 @@
 import org.labkey.api.security.User;
 import org.labkey.api.security.permissions.ReadPermission;
 import org.labkey.api.security.roles.RoleManager;
+import org.labkey.api.settings.AdminConsole;
 import org.labkey.api.util.ContextListener;
 import org.labkey.api.util.JspTestCase;
 import org.labkey.api.util.PageFlowUtil;
@@ -89,6 +90,7 @@
 
 import static org.labkey.api.assay.DefaultDataTransformer.LEGACY_SESSION_COOKIE_NAME_REPLACEMENT;
 import static org.labkey.api.assay.DefaultDataTransformer.LEGACY_SESSION_ID_REPLACEMENT;
+import static org.labkey.api.assay.plate.AssayPlateMetadataService.EXPERIMENTAL_APP_PLATE_SUPPORT;
 
 public class AssayModule extends SpringModule
 {
@@ -246,6 +248,9 @@ public void moduleStartupComplete(ServletContext servletContext)
         });
 
         ExperimentService.get().addExperimentListener(new AssayExperimentListener());
+
+        AdminConsole.addExperimentalFeatureFlag(new AdminConsole.ExperimentalFeatureFlag(EXPERIMENTAL_APP_PLATE_SUPPORT,
+                "Plate samples in Biologics", "Plate samples in Biologics for import and analysis.", false, true));
     }
 
     @Override

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

@@ -30,10 +30,12 @@
 import org.labkey.api.action.SimpleViewAction;
 import org.labkey.api.action.SpringActionController;
 import org.labkey.api.assay.plate.Plate;
+import org.labkey.api.assay.plate.PlateCustomField;
 import org.labkey.api.assay.plate.PlateService;
 import org.labkey.api.assay.security.DesignAssayPermission;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
+import org.labkey.api.exp.property.Domain;
 import org.labkey.api.gwt.client.model.GWTPropertyDescriptor;
 import org.labkey.api.gwt.server.BaseRemoteService;
 import org.labkey.api.security.RequiresAnyOf;
@@ -57,9 +59,7 @@
 import org.labkey.assay.plate.PlateDataServiceImpl;
 import org.labkey.assay.plate.PlateManager;
 import org.labkey.assay.plate.PlateUrls;
-import org.labkey.assay.plate.model.PlateCustomField;
 import org.labkey.assay.plate.model.PlateType;
-import org.labkey.assay.plate.model.WellCustomField;
 import org.labkey.assay.view.AssayGWTView;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
@@ -734,12 +734,12 @@ public Object execute(CustomFieldsForm form, BindException errors) throws Except
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class GetFieldsAction extends MutatingApiAction<CustomFieldsForm>
+    public class GetFieldsAction extends ReadOnlyApiAction<CustomFieldsForm>
     {
         @Override
         public Object execute(CustomFieldsForm form, BindException errors) throws Exception
         {
-            return success(PlateManager.get().getFields(getContainer(), getUser(), form.getPlateId()));
+            return success(PlateManager.get().getFields(getContainer(), form.getPlateId()));
         }
     }
 
@@ -753,39 +753,50 @@ public Object execute(CustomFieldsForm form, BindException errors) throws Except
         }
     }
 
-    public static class SetFieldsForm extends CustomFieldsForm
+    /**
+     * Returns the Domain ID for the plate metadata configured for this container. If the domain has
+     * not been created then null will be returned.
+     */
+    @RequiresPermission(ReadPermission.class)
+    public class GetPlateMetadataDomainAction extends ReadOnlyApiAction<Object>
     {
-        private Integer _wellId;
-        private List<WellCustomField> _wellFields;
-
-        public Integer getWellId()
+        @Override
+        public Object execute(Object form, BindException errors) throws Exception
         {
-            return _wellId;
+            Domain domain = PlateManager.get().getPlateMetadataDomain(getContainer(), getUser());
+            return success(domain != null ? domain.getTypeId() : null);
         }
+    }
 
-        public void setWellId(Integer wellId)
-        {
-            _wellId = wellId;
-        }
+    public static class GetPlateForm
+    {
+        private Integer _rowId;
 
-        public List<WellCustomField> getWellFields()
+        public Integer getRowId()
         {
-            return _wellFields;
+            return _rowId;
         }
 
-        public void setWellFields(List<WellCustomField> wellFields)
+        public void setRowId(Integer rowId)
         {
-            _wellFields = wellFields;
+            _rowId = rowId;
         }
     }
 
-    @RequiresPermission(UpdatePermission.class)
-    public class SetFieldsAction extends MutatingApiAction<SetFieldsForm>
+    @RequiresPermission(ReadPermission.class)
+    public static class GetPlateAction extends ReadOnlyApiAction<GetPlateForm>
     {
         @Override
-        public Object execute(SetFieldsForm form, BindException errors) throws Exception
+        public void validateForm(GetPlateForm form, Errors errors)
+        {
+            if (form.getRowId() == null)
+                errors.reject(ERROR_GENERIC, "Plate \"rowId\" is required.");
+        }
+
+        @Override
+        public Object execute(GetPlateForm form, BindException errors) throws Exception
         {
-            return success(PlateManager.get().setFields(getContainer(), getUser(), form.getPlateId(), form.getWellId(), form.getWellFields()));
+            return PlateManager.get().getPlate(getContainer(), form.getRowId());
         }
     }
 }

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

@@ -44,7 +44,7 @@
 import org.labkey.api.security.User;
 import org.labkey.assay.TSVProtocolSchema;
 import org.labkey.assay.plate.model.Well;
-import org.labkey.assay.plate.model.WellCustomField;
+import org.labkey.api.assay.plate.WellCustomField;
 import org.labkey.assay.query.AssayDbSchema;
 
 import java.io.File;
@@ -283,7 +283,7 @@ public List<Map<String, Object>> mergePlateMetadata(
                 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, user, plate.getRowId()).isEmpty())
+            if (!PlateManager.get().getFields(container, plate.getRowId()).isEmpty())
             {
                 // create the map of well locations to the well
                 Map<Position, Well> positionToWell = new HashMap<>();