GH Issue 1640: Use a new key for provided amounts and flag old values in the sample timeline audit log

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

@@ -53,6 +53,8 @@ public interface AuditHandler
 {
     String PROVIDED_DATA_PREFIX = ":::provided:::";
     String DELTA_PROVIDED_DATA_PREFIX = ":::delta_provided:::";
+    // GH Issue 1640: values under PROVIDED_DATA_PREFIX were written before the large-import fix and may be wrong, so user-entered amounts now use this prefix
+    String USER_PROVIDED_DATA_PREFIX = ":::user_provided:::";
 
     void addSummaryAuditEvent(User user, Container c, TableInfo table, QueryService.AuditAction action, Integer dataRowCount, @Nullable AuditBehaviorType auditBehaviorType, @Nullable String userComment);
 

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

@@ -166,6 +166,7 @@
 import org.labkey.experiment.samples.DataClassFolderWriter;
 import org.labkey.experiment.samples.SampleStatusFolderImporter;
 import org.labkey.experiment.samples.SampleTimelineAuditProvider;
+import org.labkey.experiment.samples.SampleTimelineMetadataDisplayColumn;
 import org.labkey.experiment.samples.SampleTypeFolderImporter;
 import org.labkey.experiment.samples.SampleTypeFolderWriter;
 import org.labkey.experiment.security.DataClassDesignerRole;
@@ -1170,6 +1171,7 @@ public Collection<String> getSummary(Container c)
             LsidUtils.TestCase.class,
             PropertyController.TestCase.class,
             Quantity.TestCase.class,
+            SampleTimelineMetadataDisplayColumn.TestCase.class,
             Unit.TestCase.class
         );
     }

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

@@ -49,7 +49,7 @@
 import java.util.List;
 import java.util.Map;
 
-import static org.labkey.api.audit.AuditHandler.PROVIDED_DATA_PREFIX;
+import static org.labkey.api.audit.AuditHandler.USER_PROVIDED_DATA_PREFIX;
 import static org.labkey.api.exp.query.ExpMaterialTable.Column.StoredAmount;
 import static org.labkey.api.exp.query.ExpMaterialTable.Column.Units;
 
@@ -60,7 +60,7 @@
 public class SampleProvidedAmountAuditTestCase extends Assert
 {
     private static final int ROW_COUNT = 2500; // spans three audit batches
-    private static final String PROVIDED_AMOUNT_KEY = PROVIDED_DATA_PREFIX + StoredAmount.label();
+    private static final String PROVIDED_AMOUNT_KEY = USER_PROVIDED_DATA_PREFIX + StoredAmount.label();
 
     private static Container _c;
     private static User _user;

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

@@ -136,6 +136,7 @@
 import static java.util.Collections.emptyMap;
 import static org.labkey.api.audit.AuditHandler.DELTA_PROVIDED_DATA_PREFIX;
 import static org.labkey.api.audit.AuditHandler.PROVIDED_DATA_PREFIX;
+import static org.labkey.api.audit.AuditHandler.USER_PROVIDED_DATA_PREFIX;
 import static org.labkey.api.data.TableSelector.ALL_COLUMNS;
 import static org.labkey.api.dataiterator.DataIteratorUtil.DUPLICATE_COLUMN_IN_DATA_ERROR;
 import static org.labkey.api.dataiterator.DetailedAuditLogDataIterator.AuditConfigs;
@@ -379,14 +380,19 @@ protected Map<String, Object> extractProvidedAmountsAndUnits(@NotNull Map<String
         Map<String, Object> result = new HashMap<>();
         String unitsStr = "";
         String prefix;
+        String metadataPrefix;
         if (dataRow.containsKey(DELTA_PROVIDED_DATA_PREFIX + StoredAmount.name()))
+        {
             prefix = DELTA_PROVIDED_DATA_PREFIX;
+            metadataPrefix = DELTA_PROVIDED_DATA_PREFIX;
+        }
         else
         {
             // with no sample type display unit, no conversion will happen
             if (_sampleType == null || _sampleType.getMetricUnit() == null)
                 return null;
             prefix = PROVIDED_DATA_PREFIX;
+            metadataPrefix = USER_PROVIDED_DATA_PREFIX;
         }
         Object amountVal = dataRow.get(prefix + StoredAmount.name());
         if (amountVal == null)
@@ -395,7 +401,7 @@ protected Map<String, Object> extractProvidedAmountsAndUnits(@NotNull Map<String
         if (dataRow.get(prefix + Units.name()) != null)
             unitsStr = " " + dataRow.get(prefix + Units.name()).toString();
 
-        result.put(prefix + StoredAmount.label(), amountVal + unitsStr);
+        result.put(metadataPrefix + StoredAmount.label(), amountVal + unitsStr);
 
         return result;
     }

experiment/src/org/labkey/experiment/samples/SampleTimelineAuditProvider.java

@@ -140,6 +140,10 @@ else if (COLUMN_NAME_USER_COMMENT.equalsIgnoreCase(col.getName()))
                 {
                     col.setLabel("Reason");
                 }
+                else if (METADATA_COLUMN_NAME.equalsIgnoreCase(col.getName()))
+                {
+                    col.setDisplayColumnFactory(SampleTimelineMetadataDisplayColumn::new);
+                }
             }
         };
         table.setTitleColumn(SAMPLE_NAME_COLUMN_NAME);

experiment/src/org/labkey/experiment/samples/SampleTimelineMetadataDisplayColumn.java

@@ -0,0 +1,104 @@
+/*
+ * Copyright (c) 2026 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.labkey.experiment.samples;
+
+import org.apache.commons.lang3.StringUtils;
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
+import org.junit.Assert;
+import org.junit.Test;
+import org.labkey.api.audit.AbstractAuditTypeProvider;
+import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.DataColumn;
+import org.labkey.api.data.RenderContext;
+
+import java.util.Map;
+
+import static org.labkey.api.audit.AuditHandler.DELTA_PROVIDED_DATA_PREFIX;
+import static org.labkey.api.audit.AuditHandler.PROVIDED_DATA_PREFIX;
+import static org.labkey.api.audit.AuditHandler.USER_PROVIDED_DATA_PREFIX;
+import static org.labkey.api.audit.SampleTimelineAuditEvent.SAMPLE_TIMELINE_EVENT_TYPE;
+import static org.labkey.api.exp.query.ExpMaterialTable.Column.StoredAmount;
+
+/** GH Issue 1640: flags metadata that has a provided amount recorded before the large-import fix, which may be wrong. */
+public class SampleTimelineMetadataDisplayColumn extends DataColumn
+{
+    private static final String LEGACY_PROVIDED_AMOUNT_KEY = PROVIDED_DATA_PREFIX + StoredAmount.label();
+    private static final String WARNING_STYLE = "background-color:#fcf8e3";
+    private static final String WARNING_TITLE = "Provided Amount May Be Inaccurate";
+    private static final String WARNING_MESSAGE = "This provided amount value may be inaccurate if recorded during an import or update of more than 1,000 samples. To confirm the provided amount, check the original import file or source data. The stored sample amount is not affected.";
+
+    public SampleTimelineMetadataDisplayColumn(ColumnInfo col)
+    {
+        super(col);
+    }
+
+    static boolean containsLegacyProvidedAmount(@Nullable Object metadata)
+    {
+        return metadata instanceof String str
+                && AbstractAuditTypeProvider.decodeFromDataMap(str).containsKey(LEGACY_PROVIDED_AMOUNT_KEY);
+    }
+
+    private boolean hasLegacyProvidedAmount(RenderContext ctx)
+    {
+        return containsLegacyProvidedAmount(getValue(ctx));
+    }
+
+    @Override
+    public @NotNull String getCssStyle(RenderContext ctx)
+    {
+        String style = super.getCssStyle(ctx);
+        if (!hasLegacyProvidedAmount(ctx))
+            return style;
+        return StringUtils.isEmpty(style) ? WARNING_STYLE : style + ";" + WARNING_STYLE;
+    }
+
+    @Override
+    protected String getHoverContent(RenderContext ctx)
+    {
+        return hasLegacyProvidedAmount(ctx) ? WARNING_MESSAGE : super.getHoverContent(ctx);
+    }
+
+    @Override
+    protected String getHoverTitle(RenderContext ctx)
+    {
+        return hasLegacyProvidedAmount(ctx) ? WARNING_TITLE : super.getHoverTitle(ctx);
+    }
+
+    public static class TestCase extends Assert
+    {
+        private static String metadata(String key, String value)
+        {
+            return AbstractAuditTypeProvider.encodeForDataMap(Map.of(key, value, SAMPLE_TIMELINE_EVENT_TYPE, "INSERT"));
+        }
+
+        @Test
+        public void testLegacyProvidedAmountIsFlagged()
+        {
+            assertTrue(containsLegacyProvidedAmount(metadata(PROVIDED_DATA_PREFIX + StoredAmount.label(), "2 L")));
+        }
+
+        @Test
+        public void testOtherMetadataIsNotFlagged()
+        {
+            assertFalse(containsLegacyProvidedAmount(metadata(USER_PROVIDED_DATA_PREFIX + StoredAmount.label(), "2 L")));
+            assertFalse(containsLegacyProvidedAmount(metadata(DELTA_PROVIDED_DATA_PREFIX + StoredAmount.label(), "-1 mL")));
+            assertFalse(containsLegacyProvidedAmount(AbstractAuditTypeProvider.encodeForDataMap(Map.of(SAMPLE_TIMELINE_EVENT_TYPE, "INSERT"))));
+            assertFalse(containsLegacyProvidedAmount(""));
+            assertFalse(containsLegacyProvidedAmount(null));
+        }
+    }
+}