Sample color display - grid column renderer, sample detail header, storage box view, etc.

api/src/org/labkey/api/audit/SampleTimelineAuditEvent.java

@@ -20,6 +20,7 @@
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.data.Container;
+import org.labkey.api.exp.api.DataColor;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.qc.DataState;
 import org.labkey.api.qc.SampleStatusService;
@@ -278,7 +279,11 @@ private String getColorLabel(Map<String, String> row, Container container)
     {
         String value = row.get(ExpMaterialColor.name());
         if (!StringUtils.isBlank(value))
-            return ExperimentService.get().getDataColorLabel(container, Long.parseLong(value));
+        {
+            DataColor dataColor = ExperimentService.get().getDataColor(container, Long.parseLong(value));
+            if (dataColor != null)
+                return dataColor.getLabel();
+        }
         return null;
     }
 }

experiment/src/org/labkey/experiment/api/DataColor.java → api/src/org/labkey/api/exp/api/DataColor.java

@@ -3,7 +3,7 @@
  *
  * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
  */
-package org.labkey.experiment.api;
+package org.labkey.api.exp.api;
 
 import org.labkey.api.data.Container;
 import org.labkey.api.data.Entity;

api/src/org/labkey/api/exp/api/ExperimentService.java

@@ -133,8 +133,6 @@ public interface ExperimentService extends ExperimentRunTypeSource
 
     String EXPERIMENTAL_FEATURE_ALLOW_ROW_ID_MERGE = "org.labkey.experiment.api.SampleTypeUpdateServiceDI#ALLOW_ROW_ID_SAMPLE_MERGE";
 
-    String EXPERIMENTAL_SAMPLE_COLORS = "org.labkey.api.exp.api.ExperimentService#SAMPLE_COLORS";
-
     int SIMPLE_PROTOCOL_FIRST_STEP_SEQUENCE = 1;
     int SIMPLE_PROTOCOL_CORE_STEP_SEQUENCE = 10;
     int SIMPLE_PROTOCOL_EXTRA_STEP_SEQUENCE = 15;
@@ -1160,7 +1158,11 @@ List<? extends ExpProtocol> getExpProtocolsWithParameterValue(
 
     @NotNull Set<Long> getActiveDataTypeColors(@NotNull Container container, DataTypeForExclusion dataType, long dataTypeId);
 
-    @Nullable String getDataColorLabel(@NotNull Container container, long colorRowId);
+    @NotNull List<DataColor> getActiveProjectColors(@NotNull Container container);
+
+    @NotNull List<DataColor> getAllProjectColors(@NotNull Container container);
+
+    @Nullable DataColor getDataColor(@NotNull Container container, long colorRowId);
 
     boolean ensureDataColorExclusions(long dataTypeId, DataTypeForExclusion dataType, @Nullable Collection<Long> disabledColorRowIds, @NotNull Container container, User user);
 

experiment/src/org/labkey/experiment/ExpDataIterators.java

@@ -119,7 +119,7 @@
 import org.labkey.experiment.api.ExpMaterialTableImpl;
 import org.labkey.experiment.api.ExpRunItemTableImpl;
 import org.labkey.experiment.api.ExpSampleTypeImpl;
-import org.labkey.experiment.api.DataColor;
+import org.labkey.api.exp.api.DataColor;
 import org.labkey.experiment.api.DataColorManager;
 import org.labkey.experiment.api.ExperimentServiceImpl;
 import org.labkey.experiment.api.SampleTypeServiceImpl;

experiment/src/org/labkey/experiment/ExperimentModule.java

@@ -299,8 +299,6 @@ protected void init()
                 "Support for querying lineage of experiment objects", false, true);
         OptionalFeatureService.get().addExperimentalFeatureFlag(ExperimentService.EXPERIMENTAL_FEATURE_ALLOW_ROW_ID_MERGE, "Allow RowId to be accepted when merging samples or data class data",
                 "If the incoming data includes a RowId column we will allow the column but ignore it's values.", false, true);
-        OptionalFeatureService.get().addExperimentalFeatureFlag(ExperimentService.EXPERIMENTAL_SAMPLE_COLORS, "Sample Colors",
-                "Enable assigning custom colors to individual samples, with an app-level color palette configurable per sample type.", false, true);
 
         RoleManager.registerPermission(new DesignVocabularyPermission(), true);
         RoleManager.registerRole(new SampleTypeDesignerRole());
@@ -1241,7 +1239,6 @@ public JSONObject getPageContextJson(ContainerUser context)
     {
         JSONObject json = super.getPageContextJson(context);
         json.put(SAMPLE_FILES_TABLE, OptionalFeatureService.get().isFeatureEnabled(SAMPLE_FILES_TABLE));
-        json.put("SampleColors", OptionalFeatureService.get().isFeatureEnabled(ExperimentService.EXPERIMENTAL_SAMPLE_COLORS));
         return json;
     }
 }

experiment/src/org/labkey/experiment/api/DataColorManager.java

@@ -15,6 +15,7 @@
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.Sort;
 import org.labkey.api.data.TableSelector;
+import org.labkey.api.exp.api.DataColor;
 
 import java.util.ArrayList;
 import java.util.Collections;
@@ -91,12 +92,6 @@ public List<DataColor> getColors(Container container)
         return CACHE.get(container)._colors;
     }
 
-    @NotNull
-    public List<DataColor> getActiveColors(Container container)
-    {
-        return getColors(container).stream().filter(c -> !c.isArchived()).toList();
-    }
-
     @NotNull
     public List<DataColor> getAllProjectColors(Container container)
     {

experiment/src/org/labkey/experiment/api/DataColorTable.java

@@ -26,6 +26,7 @@
 import org.labkey.api.data.SqlSelector;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
+import org.labkey.api.exp.api.DataColor;
 import org.labkey.api.exp.api.ExpMaterial;
 import org.labkey.api.exp.api.ExpSampleType;
 import org.labkey.api.exp.api.ExperimentService;

experiment/src/org/labkey/experiment/api/ExpMaterialTableImpl.java

@@ -118,7 +118,6 @@
 import org.labkey.api.security.permissions.Permission;
 import org.labkey.api.security.permissions.ReadPermission;
 import org.labkey.api.security.permissions.UpdatePermission;
-import org.labkey.api.settings.OptionalFeatureService;
 import org.labkey.api.test.TestWhen;
 import org.labkey.api.util.ContextListener;
 import org.labkey.api.util.GUID;
@@ -774,8 +773,6 @@ private static boolean isStatusEnabled(Container c)
 
     private boolean colorsEnabled(Container c)
     {
-        if (!OptionalFeatureService.get().isFeatureEnabled(ExperimentService.EXPERIMENTAL_SAMPLE_COLORS))
-            return false;
         if (_ss != null)
             return !ExperimentService.get().getActiveDataTypeColors(c, ExperimentService.DataTypeForExclusion.SampleType, _ss.getRowId()).isEmpty();
         return !DataColorManager.getInstance().getActiveProjectColors(c).isEmpty();
@@ -867,6 +864,9 @@ protected void populateColumns()
         addColumn(SampleSet);
         addColumn(MaterialExpDate);
         defaultCols.add(MaterialExpDate.fieldKey());
+        addColumn(ExpMaterialColor);
+        if (colorsEnabled(getContainer()))
+            defaultCols.add(ExpMaterialColor.fieldKey());
         addContainerColumn(Folder, null);
         if (getContainer().hasProductFolders())
             defaultCols.add(Folder.fieldKey());
@@ -886,9 +886,6 @@ protected void populateColumns()
         addColumn(SampleState);
         if (isStatusEnabled(getContainer()))
             defaultCols.add(SampleState.fieldKey());
-        addColumn(ExpMaterialColor);
-        if (colorsEnabled(getContainer()))
-            defaultCols.add(ExpMaterialColor.fieldKey());
 
         // TODO is this a real Domain???
         if (st != null && !"urn:lsid:labkey.com:SampleSource:Default".equals(st.getDomain().getTypeURI()))

experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java

@@ -123,6 +123,7 @@
 import org.labkey.api.exp.XarSource;
 import org.labkey.api.exp.api.ColumnExporter;
 import org.labkey.api.exp.api.DataClassDomainKindProperties;
+import org.labkey.api.exp.api.DataColor;
 import org.labkey.api.exp.api.DataType;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.exp.api.ExpDataClass;
@@ -9184,11 +9185,10 @@ public String getDisabledDataTypeAuditMsg(DataTypeForExclusion type, List<Long>
     }
 
     @Override
-    public @Nullable String getDataColorLabel(@NotNull Container container, long colorRowId)
+    public @Nullable DataColor getDataColor(@NotNull Container container, long colorRowId)
     {
-        return DataColorManager.getInstance().getAllProjectColors(container).stream()
+        return getAllProjectColors(container).stream()
                 .filter(c -> c.getRowId() == colorRowId)
-                .map(DataColor::getLabel)
                 .findFirst()
                 .orElse(null);
     }
@@ -9203,6 +9203,18 @@ public String getDisabledDataTypeAuditMsg(DataTypeForExclusion type, List<Long>
                 .collect(toSet());
     }
 
+    @Override
+    public @NotNull List<DataColor> getActiveProjectColors(@NotNull Container container)
+    {
+        return DataColorManager.getInstance().getActiveProjectColors(container);
+    }
+
+    @Override
+    public @NotNull List<DataColor> getAllProjectColors(@NotNull Container container)
+    {
+        return DataColorManager.getInstance().getAllProjectColors(container);
+    }
+
     // Applies a reconciled set of exclusion changes to exp.DataTypeColorExclusion in one transaction: one key column is
     // held fixed (fixedColumn = fixedValue), the other varies. Rows in toAdd are inserted; rows in toRemove are deleted.
     // Shared by ensureDataColorExclusions (fixes DataTypeRowId, varies ColorRowId) and updateColorDataTypeExclusions

experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java

@@ -7743,6 +7743,7 @@ private SQLFragment getOrderedRowsSql()
                 sampleColumns.addAll(Arrays.asList(
                         "S.Name AS SampleID",
                         "S.MaterialExpDate AS ExpirationDate",
+                        "S.ExpMaterialColor",
                         "S.SampleSet as SampleType",
                         "S.SampleState",
                         "S.isAliquot",
@@ -7755,6 +7756,7 @@ private SQLFragment getOrderedRowsSql()
                 sampleColumns.addAll(Arrays.asList(
                         "S.Name AS SampleID",
                         "S.MaterialExpDate AS ExpirationDate",
+                        "S.ExpMaterialColor",
                         "S.LabelColor",
                         "S.SampleSet",
                         "S.SampleState",

list/src/org/labkey/list/model/ListTable.java

@@ -104,9 +104,10 @@ public class ListTable extends FilteredTable<ListQuerySchema> implements Updatea
     {
         defaultPicklistVisibleColumns.add(FieldKey.fromParts(PICKLIST_SAMPLE_ID, "Name"));
         defaultPicklistVisibleColumns.add(FieldKey.fromParts(PICKLIST_SAMPLE_ID, "MaterialExpDate"));
+        defaultPicklistVisibleColumns.add(FieldKey.fromParts(PICKLIST_SAMPLE_ID, "ExpMaterialColor"));
         defaultPicklistVisibleColumns.add(FieldKey.fromParts(PICKLIST_SAMPLE_ID, "LabelColor"));
-        defaultPicklistVisibleColumns.add(FieldKey.fromParts(PICKLIST_SAMPLE_ID, "Folder"));
         defaultPicklistVisibleColumns.add(FieldKey.fromParts(PICKLIST_SAMPLE_ID, "SampleSet"));
+        defaultPicklistVisibleColumns.add(FieldKey.fromParts(PICKLIST_SAMPLE_ID, "Folder"));
         defaultPicklistVisibleColumns.add(FieldKey.fromParts(PICKLIST_SAMPLE_ID, "SampleState"));
         defaultPicklistVisibleColumns.add(FieldKey.fromParts(PICKLIST_SAMPLE_ID, "StoredAmount"));
         defaultPicklistVisibleColumns.add(FieldKey.fromParts(PICKLIST_SAMPLE_ID, "Units"));