Add audit detail change for dataclass lineage events

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

@@ -13,21 +13,23 @@
 import org.labkey.api.exp.api.ExpMaterial;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.gwt.client.AuditBehaviorType;
-import org.labkey.api.query.QueryKey;
 import org.labkey.api.query.QueryService;
 import org.labkey.api.security.User;
 import org.labkey.api.util.Pair;
 
+import java.io.IOException;
 import java.text.NumberFormat;
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.Date;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
 import java.util.Set;
+import java.util.stream.Collectors;
 
 
 public interface AuditHandler
@@ -104,7 +106,7 @@ static Pair<Map<String, Object>, Map<String, Object>> getOldAndNewRecordForMerge
             }
             String lcName = nameFromAlias.toLowerCase();
             // Preserve casing of inputs so we can show the names properly
-            boolean isExpInput = false;
+            boolean isExpInput = false; // TODO: extract lineage handling out of this generic method
             String encodedInputColumn = ExperimentService.getEncodedLineageKey(lcName);
             if (encodedInputColumn != null)
             {
@@ -172,6 +174,21 @@ else if (!Objects.equals(oldValue, newValue) || isExtraAuditField)
                     }
                     else
                     {
+                        if (isExpInput && oldValue != null && newValue != null)
+                        {
+                            // For parent inputs, the order of the values does not matter, so compare as sets
+                            try
+                            {
+                                Set<String> oldSet = Arrays.stream(ExperimentService.getParentValues(oldValue.toString())).collect(Collectors.toSet());
+                                Set<String> newSet = Arrays.stream(ExperimentService.getParentValues(newValue.toString())).collect(Collectors.toSet());
+                                if (oldSet.equals(newSet) && !isExtraAuditField)
+                                    continue;
+                            }
+                            catch (IOException ignore)
+                            {
+                            }
+                        }
+
                         originalRow.put(nameFromAlias, oldValue);
                         modifiedRow.put(nameFromAlias, newValue);
                     }

api/src/org/labkey/api/data/NameGenerator.java

@@ -745,26 +745,16 @@ public static Stream<String> parentNames(Object value, String parentColName, TSV
             // using TabLoader instead of just splitting on the comma.
             boolean likelyAlreadyQuoted = valueStr.contains(",") || valueStr.contains("\n") || valueStr.contains("\r") || (valueStr.startsWith("\"") && valueStr.endsWith("\""));
             String quotedStr = likelyAlreadyQuoted ? valueStr : tsvWriter.quoteValue(valueStr); // if value contains comma, no need to quote again
-            try (TabLoader tabLoader = new TabLoader(quotedStr))
-            {
-                tabLoader.setDelimiterCharacter(',');
-                tabLoader.setUnescapeBackslashes(false);
-                // Issue 50924: LKSM: Importing samples using naming expression referencing parent inputs with # result in error
-                tabLoader.setIncludeComments(true);
-                // Issue 51056 Samples with single double quotes in the name will not resolve if added as parent samples.
-                tabLoader.setParseEnclosedQuotes(true);
-                try
-                {
-                    String[][] parsedValues = tabLoader.getFirstNLines(1);
-                    values = Arrays.stream(parsedValues[0]);
-                }
-                catch (IOException e)
-                {
-                    if (errors != null)
-                        errors.addRowError(new ValidationException("Unable to parse parent names from " + value, parentColName));
-                    else
-                        throw new IllegalStateException("Unable to parse parent names from " + valueStr, e);
-                }
+            try
+            {
+                values = Arrays.stream(ExperimentService.getParentValues(quotedStr));
+            }
+            catch (IOException e)
+            {
+                if (errors != null)
+                    errors.addRowError(new ValidationException("Unable to parse parent names from " + value, parentColName));
+                else
+                    throw new IllegalStateException("Unable to parse parent names from " + valueStr, e);
             }
         }
         else if (value instanceof Collection<?> coll)

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

@@ -75,6 +75,7 @@
 import org.labkey.api.query.QueryViewProvider;
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.query.ValidationException;
+import org.labkey.api.reader.TabLoader;
 import org.labkey.api.security.User;
 import org.labkey.api.services.ServiceRegistry;
 import org.labkey.api.util.Pair;
@@ -521,6 +522,23 @@ static boolean isInputOutputColumn(String columnName)
         return null;
     }
 
+    static @NotNull String[] getParentValues(String valueStr) throws IOException
+    {
+        if (StringUtils.isEmpty(valueStr.trim()))
+            return new String[0];
+        try (TabLoader tabLoader = new TabLoader(valueStr))
+        {
+            tabLoader.setDelimiterCharacter(',');
+            tabLoader.setUnescapeBackslashes(false);
+            // Issue 50924: LKSM: Importing samples using naming expression referencing parent inputs with # result in error
+            tabLoader.setIncludeComments(true);
+            // Issue 51056 Samples with single double quotes in the name will not resolve if added as parent samples.
+            tabLoader.setParseEnclosedQuotes(true);
+            String[][] parsedValues = tabLoader.getFirstNLines(1);
+            return parsedValues[0];
+        }
+    }
+
     static Pair<String, String> parseInputOutputAlias(String columnName)
     {
         if (!isInputOutputColumn(columnName))
@@ -593,33 +611,6 @@ static void validateParentAlias(Map<String, String> aliasMap, Set<String> reserv
      * ignoring any sample children derived from ExpData children.
      */
     Set<ExpMaterial> getRelatedChildSamples(Container c, User user, ExpData start);
-
-    /**
-     * Find the ExpData objects, if any, that are parents of the <code>start</code> ExpMaterial.
-     */
-    @NotNull
-    Set<ExpData> getParentDatas(Container c, User user, ExpMaterial start);
-
-    /**
-     * Find the ExpMaterial objects, if any, that are parents of the <code>start</code> ExpMaterial.
-     */
-    @NotNull
-    Set<ExpMaterial> getParentMaterials(Container c, User user, ExpMaterial start);
-
-    /**
-     * Find all parent ExpData that are parents of the <code>start</code> ExpMaterial,
-     * stopping at the first parent generation (no grandparents.)
-     */
-    @NotNull
-    Set<ExpData> getNearestParentDatas(Container c, User user, ExpMaterial start);
-
-    /**
-     * Find all parent ExpMaterial that are parents of the <code>start</code> ExpMaterial,
-     * stopping at the first parent generation (no grandparents.)
-     */
-    @NotNull
-    Set<ExpMaterial> getNearestParentMaterials(Container c, User user, ExpMaterial start);
-
     /**
      * Get the lineage for the seed Identifiable object.  Typically, the seed object is a ExpMaterial,
      * a ExpData (in a DataClass), or an ExpRun.

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

@@ -20,6 +20,7 @@
 import org.apache.commons.collections4.MapUtils;
 import org.apache.commons.collections4.ListUtils;
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Strings;
 import org.apache.logging.log4j.Level;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -1231,12 +1232,66 @@ public List<Map<String, Object>> insertRows(User user, Container container, List
             return super._insertRowsUsingDIB(user, container, rows, getDataIteratorContext(errors, InsertOption.INSERT, configParameters), extraScriptContext);
         }
 
+        @Override
+        public Map<Integer, Map<String, Object>> getExistingRows(User user, Container container, Map<Integer, Map<String, Object>> keys, boolean verifyNoCrossFolderData, boolean verifyExisting, @Nullable Set<String> columns) throws SQLException, QueryUpdateServiceException, InvalidKeyException
+        {
+            Map<Integer, Map<String, Object>> dataRows = super.getExistingRows(user, container, keys, verifyNoCrossFolderData, verifyExisting, columns);
+            boolean hasParentInput = false;
+            if (_dataClass != null && columns != null && !columns.isEmpty())
+            {
+                try
+                {
+                    Map<String, String> importAliases = _dataClass.getImportAliases();
+                    for (String col : columns)
+                    {
+                        if (ExperimentService.isInputOutputColumn(col) || Strings.CI.equals("parent",col) || importAliases.containsKey(col))
+                        {
+                            hasParentInput = true;
+                            break;
+                        }
+                    }
+                }
+                catch (IOException ignored)
+                {
+                }
+            }
+
+            if (!hasParentInput)
+                return dataRows;
+
+            Set<String> lsids = new HashSet<>();
+            for (Map<String, Object> dataRow : dataRows.values())
+                lsids.add((String) dataRow.get("lsid"));
+            List<ExpDataImpl> seeds = ExperimentServiceImpl.get().getExpDatasByLSID(lsids);
+
+            ExperimentServiceImpl.get().addRowsParentsFields(new HashSet<>(seeds), dataRows, user, container);
+
+            return dataRows;
+        }
+
         @Override
         protected Map<String, Object> getRow(User user, Container container, Map<String, Object> keys) throws InvalidKeyException, SQLException
         {
             return getRow(user, container, keys, false);
         }
 
+        @Override
+        public List<Map<String, Object>> getRows(User user, Container container, List<Map<String, Object>> keys)
+                throws SQLException
+        {
+            if (!hasPermission(user, ReadPermission.class))
+                throw new UnauthorizedException("You do not have permission to read data from this table.");
+
+            List<Map<String, Object>> result = new ArrayList<>(keys.size());
+            for (Map<String, Object> row : keys)
+            {
+                Map<String, Object> materialMap = getDataMap(row, user, container, true, false);
+                if (materialMap != null)
+                    result.add(materialMap);
+            }
+            return result;
+        }
+
         /* This class overrides getRow() in order to support getRow() using "rowid" or "lsid" */
         @Override
         protected Map<String, Object> getRow(User user, Container container, Map<String, Object> keys, boolean allowCrossContainer) throws InvalidKeyException, SQLException
@@ -1246,15 +1301,11 @@ protected Map<String, Object> getRow(User user, Container container, Map<String,
             Long rowId = (Long)JdbcType.BIGINT.convert(keys.get(Column.RowId.name()));
             String lsid = (String)JdbcType.VARCHAR.convert(keys.get(Column.LSID.name()));
             String name = (String)JdbcType.VARCHAR.convert(keys.get(Name.name()));
-            Long classId = (Long)JdbcType.BIGINT.convert(keys.get(Column.ClassId.name()));
-
-            if (classId == null)
-                classId = _dataClass.getRowId();
 
             if (null == rowId && null == lsid && null == name)
                 throw new InvalidKeyException("Value must be supplied for key field 'rowid' or 'lsid' or 'name'", keys);
 
-            return _select(container, rowId, lsid, name, classId, allowCrossContainer);
+            return getDataMap(keys, user, container, allowCrossContainer, true);
         }
 
         @Override
@@ -1263,9 +1314,17 @@ protected Map<String, Object> _select(Container container, Object[] keys) throws
             throw new IllegalStateException();
         }
 
-        protected Map<String, Object> _select(Container container, Long rowId, String lsid, String name, Long classId, boolean allowCrossContainer) throws SQLException
+        @Nullable protected Map<String, Object> getDataMap(Map<String, Object> keys, User user, Container container, boolean allowCrossContainer, boolean addInputs) throws SQLException
         {
-            if (null == rowId && null == lsid && (null == name || null == classId))
+            Long rowId = (Long)JdbcType.BIGINT.convert(keys.get(Column.RowId.name()));
+            String lsid = (String)JdbcType.VARCHAR.convert(keys.get(Column.LSID.name()));
+            String name = (String)JdbcType.VARCHAR.convert(keys.get(Name.name()));
+            Long classId = (Long)JdbcType.BIGINT.convert(keys.get(Column.ClassId.name()));
+
+            if (classId == null)
+                classId = _dataClass.getRowId();
+
+            if (null == rowId && null == lsid && null == name)
                 return null;
 
             // Issue 52886: Use queryTable here, not raw database table, so the rows are from the user schema with names
@@ -1284,13 +1343,31 @@ else if (null != lsid)
             TableInfo queryTable = getQueryTable();
             TableSelector selector = new TableSelector(queryTable, filter, null);
 
+            Map<String, Object> dataRow = null;
             try (var results = selector.getResults()) {
                 if (results.next())
                 {
-                    return FieldKeyRowMap.toNameMap(results.getFieldKeyRowMap());
+                    dataRow = FieldKeyRowMap.toNameMap(results.getFieldKeyRowMap());
                 }
             }
-            return null;
+
+            if (!addInputs)
+                return dataRow;
+
+            ExperimentService experimentService = ExperimentService.get();
+            ExpData seed = null;
+            if (lsid != null && (rowId == null || rowId <= 0))
+                seed = experimentService.getExpData(lsid);
+            else if (rowId != null && rowId > 0)
+                seed = experimentService.getExpData(_dataClass, rowId);
+            else if (name != null)
+                seed = experimentService.getExpData(_dataClass, name);
+            if (null == seed)
+                return dataRow;
+
+            ExperimentServiceImpl.get().addParentsFields(seed, dataRow, user, container);
+
+            return dataRow;
         }
 
         @Override