Improve generics for plate code

Author: labkey-jeckels

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

@@ -156,7 +156,7 @@ static PlateService get()
      */
     @Nullable Plate getPlate(ContainerFilter cf, Long plateSetId, Object plateIdentifier);
 
-    @NotNull List<Plate> getPlates(Container container);
+    @NotNull List<? extends Plate> getPlates(Container container);
 
     /**
      * Gets the plate set by ID

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

@@ -26,7 +26,7 @@ public interface PlateSet extends Identifiable
 
     boolean isTemplate();
 
-    List<Plate> getPlates();
+    List<? extends Plate> getPlates();
 
     PlateSetType getType();
 

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

@@ -112,6 +112,45 @@ public class PlateController extends SpringActionController
     private static final SpringActionController.DefaultActionResolver _actionResolver = new DefaultActionResolver(PlateController.class);
     private static final Logger LOG = LogHelper.getLogger(PlateController.class, "Controller for plate related actions");
 
+    record SubmittedGroup(int rowId, String type, String name, List<PlatePosition> positions, Map<String, Object> properties)
+    {
+        public static SubmittedGroup from(JSONObject g)
+        {
+            int rowId = g.optInt("rowId", -1);
+            String type = g.getString("type");
+            String name = g.getString("name");
+            JSONArray posArr = g.optJSONArray("positions");
+            List<PlatePosition> positions = new ArrayList<>();
+            if (posArr != null)
+            {
+                for (int j = 0; j < posArr.length(); j++)
+                {
+                    JSONObject p = posArr.getJSONObject(j);
+                    positions.add(PlatePosition.from(p));
+                }
+            }
+            JSONObject propsObj = g.optJSONObject("properties");
+            Map<String, Object> props = new HashMap<>();
+            if (propsObj != null)
+            {
+                for (String key : propsObj.keySet())
+                {
+                    Object val = propsObj.get(key);
+                    props.put(key, val == JSONObject.NULL ? null : val);
+                }
+            }
+            return new SubmittedGroup(rowId, type, name, positions, props);
+        }
+    }
+
+    record PlatePosition(int row, int col)
+    {
+        public static PlatePosition from(JSONObject p)
+        {
+            return new PlatePosition(p.getInt("row"), p.getInt("col"));
+        }
+    }
+
     public PlateController()
     {
         setActionResolver(_actionResolver);
@@ -165,7 +204,7 @@ public static class PlateListAction extends SimpleViewAction<ReturnUrlForm>
         public ModelAndView getView(ReturnUrlForm form, BindException errors)
         {
             setHelpTopic("editPlateTemplate");
-            List<Plate> plateTemplates = PlateService.get().getPlates(getContainer())
+            List<? extends Plate> plateTemplates = PlateService.get().getPlates(getContainer())
                     .stream()
                     .filter(p -> !TsvPlateLayoutHandler.TYPE.equalsIgnoreCase(p.getAssayType()))
                     .toList();
@@ -180,6 +219,7 @@ public void addNavTrail(NavTree root)
         }           
     }
 
+    /** Delete soon! */
     @RequiresAnyOf({InsertPermission.class, DesignAssayPermission.class})
     public static class DesignerServiceAction extends GWTServiceAction
     {
@@ -417,7 +457,7 @@ public Object execute(SaveTemplateForm form, BindException errors) throws Except
             }
 
             boolean updateExisting = false;
-            Plate plate;
+            PlateImpl plate;
             if (rowId > 0)
             {
                 plate = PlateManager.get().getPlate(getContainer(), rowId);
@@ -447,42 +487,16 @@ public Object execute(SaveTemplateForm form, BindException errors) throws Except
             plate.setProperties(plateProperties);
 
             // Parse groups from JSON
-            List<Map<String, Object>> submittedGroups = new ArrayList<>();
+            List<SubmittedGroup> submittedGroups = new ArrayList<>();
             Set<Integer> submittedGroupIds = new HashSet<>();
             if (groupsJson != null)
             {
                 for (int i = 0; i < groupsJson.length(); i++)
                 {
-                    JSONObject g = groupsJson.getJSONObject(i);
-                    Map<String, Object> gm = new HashMap<>();
-                    gm.put("rowId", g.optInt("rowId", -1));
-                    gm.put("type", g.getString("type"));
-                    gm.put("name", g.getString("name"));
-                    JSONArray posArr = g.optJSONArray("positions");
-                    List<int[]> positions = new ArrayList<>();
-                    if (posArr != null)
-                    {
-                        for (int j = 0; j < posArr.length(); j++)
-                        {
-                            JSONObject p = posArr.getJSONObject(j);
-                            positions.add(new int[]{p.getInt("row"), p.getInt("col")});
-                        }
-                    }
-                    gm.put("positions", positions);
-                    JSONObject propsObj = g.optJSONObject("properties");
-                    Map<String, Object> props = new HashMap<>();
-                    if (propsObj != null)
-                    {
-                        for (String key : propsObj.keySet())
-                        {
-                            Object val = propsObj.get(key);
-                            props.put(key, val == JSONObject.NULL ? null : val);
-                        }
-                    }
-                    gm.put("properties", props);
-                    submittedGroups.add(gm);
-                    if ((int) gm.get("rowId") > 0)
-                        submittedGroupIds.add((int) gm.get("rowId"));
+                    SubmittedGroup g = SubmittedGroup.from(groupsJson.getJSONObject(i));
+                    submittedGroups.add(g);
+                    if (g.rowId > 0)
+                        submittedGroupIds.add(g.rowId);
                 }
             }
 
@@ -491,14 +505,14 @@ public Object execute(SaveTemplateForm form, BindException errors) throws Except
             for (WellGroup existingGroup : existingWellGroups)
             {
                 if (existingGroup.getRowId() != null && !submittedGroupIds.contains(existingGroup.getRowId()))
-                    ((PlateImpl) plate).markWellGroupForDeletion(existingGroup);
+                    plate.markWellGroupForDeletion(existingGroup);
             }
 
             // Update or create well groups
-            for (Map<String, Object> gm : submittedGroups)
+            for (SubmittedGroup gm : submittedGroups)
             {
-                int gRowId = (int) gm.get("rowId");
-                String groupTypeName = (String) gm.get("type");
+                int gRowId = gm.rowId();
+                String groupTypeName = gm.type();
                 WellGroup.Type groupType;
                 try
                 {
@@ -508,14 +522,12 @@ public Object execute(SaveTemplateForm form, BindException errors) throws Except
                 {
                     throw new ApiUsageException("Unknown well group type: '" + groupTypeName + "'");
                 }
-                @SuppressWarnings("unchecked")
-                List<int[]> posList = (List<int[]>) gm.get("positions");
+                List<PlatePosition> posList = gm.positions();
                 List<Position> positions = new ArrayList<>();
-                for (int[] p : posList)
-                    positions.add(plate.getPosition(p[0], p[1]));
+                for (PlatePosition p : posList)
+                    positions.add(plate.getPosition(p.row, p.col));
 
-                @SuppressWarnings("unchecked")
-                Map<String, Object> props = (Map<String, Object>) gm.get("properties");
+                Map<String, Object> props = gm.properties();
 
                 WellGroupImpl group;
                 if (updateExisting && gRowId > 0)
@@ -524,15 +536,15 @@ public Object execute(SaveTemplateForm form, BindException errors) throws Except
                     if (existing == null)
                         throw new Exception("Well group " + gRowId + " was not found.");
                     if (existing.getType() != groupType)
-                        throw new Exception("Well group type cannot be changed: " + gm.get("name"));
-                    existing.setName((String) gm.get("name"));
+                        throw new Exception("Well group type cannot be changed: " + gm.name());
+                    existing.setName(gm.name);
                     existing.setPositions(positions);
-                    ((PlateImpl) plate).storeWellGroup(existing);
+                    plate.storeWellGroup(existing);
                     group = existing;
                 }
                 else
                 {
-                    group = (WellGroupImpl) plate.addWellGroup((String) gm.get("name"), groupType, positions);
+                    group = plate.addWellGroup(gm.name, groupType, positions);
                 }
                 group.setProperties(props);
             }
@@ -579,6 +591,7 @@ public void addNavTrail(NavTree root)
         }
     }
 
+    /** Delete soon! */
     @RequiresAnyOf({InsertPermission.class, DesignAssayPermission.class})
     public class DesignerGwtAction extends SimpleViewAction<DesignerForm>
     {
@@ -664,7 +677,7 @@ public static class CopyTemplateBean
         private HtmlString _treeHtml;
         private Plate _plate;
         private String _selectedDestination;
-        private List<Plate> _destinationTemplates;
+        private List<? extends Plate> _destinationTemplates;
 
         public CopyTemplateBean(final Container container, final User user, final Integer plateId, final String selectedDestination)
         {
@@ -1083,7 +1096,7 @@ public Object execute(CreatePlateForm form, BindException errors) throws Excepti
                 PlateImpl newPlate = new PlateImpl(getContainer(), form.getName(), form.getBarcode(), form.getAssayType(), _plateType);
                 if (form.getData() == null && form.getTemplateId() != null && TsvPlateLayoutHandler.TYPE.equalsIgnoreCase(newPlate.getAssayType()))
                 {
-                    newPlate = (PlateImpl) PlateManager.get().copyPlate(
+                    newPlate = PlateManager.get().copyPlate(
                         getContainer(),
                         getUser(),
                         form.getTemplateId(),
@@ -1104,7 +1117,7 @@ public Object execute(CreatePlateForm form, BindException errors) throws Excepti
                     if (form.isTemplate() && data == null)
                         data = PlateManager.get().prepareEmptyPlateTemplateData(getContainer(), _plateType);
 
-                    newPlate = (PlateImpl) PlateManager.get().createAndSavePlate(getContainer(), getUser(), newPlate, form.getPlateSetId(), data);
+                    newPlate = PlateManager.get().createAndSavePlate(getContainer(), getUser(), newPlate, form.getPlateSetId(), data);
                 }
 
                 return success(newPlate);

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

@@ -238,7 +238,7 @@ public Map<String, Object> apply(Map<String, Object> row)
         });
     }
 
-    private List<Plate> getPlatesForPlateSet(
+    private List<? extends Plate> getPlatesForPlateSet(
         Container container,
         User user,
         Long plateSetId,
@@ -270,7 +270,7 @@ public DataIteratorBuilder parsePlateData(
     ) throws ExperimentException
     {
         // get the ordered list of plates for the plate set
-        List<Plate> plates = getPlatesForPlateSet(container, user, plateSetId, protocol);
+        List<? extends Plate> plates = getPlatesForPlateSet(container, user, plateSetId, protocol);
         if (plates.isEmpty())
             throw new ExperimentException("No plates were found for the plate set (" + plateSetId + ").");
         PlateSet plateSet = plates.get(0).getPlateSet();
@@ -297,7 +297,7 @@ private List<Map<String, Object>> _parsePlateData(
         AssayProvider provider,
         ExpProtocol protocol,
         PlateSet plateSet,
-        List<Plate> plates,
+        List<? extends Plate> plates,
         FileLike dataFile,
         DataLoaderSettings settings
     ) throws ExperimentException
@@ -356,7 +356,7 @@ public DataIteratorBuilder mergeReRunData(
     ) throws ExperimentException
     {
         Long plateSetId = getPlateSetId(context, provider, protocol);
-        List<Plate> plates = getPlatesForPlateSet(container, user, plateSetId, protocol);
+        List<? extends Plate> plates = getPlatesForPlateSet(container, user, plateSetId, protocol);
         if (plates.isEmpty())
             throw new ExperimentException("No plates were found for the plate set (" + plateSetId + ").");
 
@@ -540,7 +540,7 @@ private boolean isGridFormat(List<Map<String, Object>> data)
     private List<Map<String, Object>> parsePlateRows(
         AssayProvider provider,
         ExpProtocol protocol,
-        List<Plate> plates,
+        List<? extends Plate> plates,
         List<Map<String, Object>> data
     ) throws ExperimentException
     {
@@ -604,7 +604,7 @@ private List<Map<String, Object>> parsePlateRows(
     }
 
     // Resolves a pre-calculated "plateIdField" to a plate rowId and furnishes new "data" rows with the plate rowId.
-    private List<Map<String, Object>> resolvePlateIdentifier(List<Plate> plates, List<Map<String, Object>> data, String plateIdField)
+    private List<Map<String, Object>> resolvePlateIdentifier(List<? extends Plate> plates, List<Map<String, Object>> data, String plateIdField)
     {
         var newData = new ArrayList<Map<String, Object>>();
         var plateIdentifiers = new HashMap<Object, Long>();
@@ -664,7 +664,7 @@ public PlateGridInfo(PlateUtils.GridInfo info, PlateSet plateSet, Set<String> me
 
             // locate the plate in the plate set this grid is associated with plus an optional
             // measure name
-            List<Plate> plates = PlateManager.get().getPlatesForPlateSet(plateSet);
+            List<? extends Plate> plates = PlateManager.get().getPlatesForPlateSet(plateSet);
             List<String> annotations = getAnnotations();
 
             // if the plate set only has one plate, then treat a single annotation as the measure
@@ -694,7 +694,7 @@ public PlateGridInfo(PlateUtils.GridInfo info, PlateSet plateSet, Set<String> me
             }
         }
 
-        private @NotNull Plate getPlateForId(String annotation, List<Plate> platesetPlates) throws ExperimentException
+        private @NotNull Plate getPlateForId(String annotation, List<? extends Plate> platesetPlates) throws ExperimentException
         {
             Plate plate = platesetPlates.stream().filter(p -> p.isIdentifierMatch(annotation)).findFirst().orElse(null);
             if (plate == null)
@@ -734,7 +734,7 @@ private List<Map<String, Object>> parsePlateGrids(
         AssayProvider provider,
         ExpProtocol protocol,
         PlateSet plateSet,
-        List<Plate> plates,
+        List<? extends Plate> plates,
         FileLike dataFile
     ) throws ExperimentException
     {
@@ -1754,7 +1754,7 @@ public void testGridAnnotations() throws Exception
             );
 
             PlateSet plateSet = PlateManager.get().createPlateSet(container, user, new PlateSetImpl(), plates, null, null);
-            List<Plate> plateSetPlates = PlateManager.get().getPlatesForPlateSet(plateSet);
+            List<? extends Plate> plateSetPlates = PlateManager.get().getPlatesForPlateSet(plateSet);
             assertEquals("Expected two plates to be created.", 2, plateSetPlates.size());
             Plate plate = plateSetPlates.get(0);