[bot] Merge 26.3 to develop

api/src/org/labkey/api/action/QueryViewAction.java

@@ -16,6 +16,7 @@
 
 package org.labkey.api.action;
 
+import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.ColumnHeaderType;
 import org.labkey.api.data.ExcelWriter;
@@ -135,7 +136,9 @@ protected ModelAndView getHtmlView(Form form, BindException errors) throws Excep
     /**
      * Correctly configures the QueryView to use the QueryViewAction for export purposes
      * @param dataRegion null as a convenience when only a single QueryView is being used
+     * @throws NotFoundException if passed a dataRegion name that doesn't exist
      */
+    @NotNull
     protected final ViewType createInitializedQueryView(Form form, BindException errors, boolean forExport, @Nullable String dataRegion) throws Exception
     {
         ViewType result = createQueryView(form, errors, forExport, dataRegion);
@@ -164,6 +167,7 @@ protected final ViewType createInitializedQueryView(Form form, BindException err
      * Create the specially configured query view.
      * @param dataRegion null as a convenience when only a single QueryView is being used
      */
+    @Nullable
     protected abstract ViewType createQueryView(Form form, BindException errors, boolean forExport, @Nullable String dataRegion) throws Exception;
 
     public static class QueryExportForm extends QueryForm

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

@@ -23,6 +23,7 @@
 import org.labkey.api.util.ContainerContext;
 import org.labkey.api.util.DOM;
 import org.labkey.api.util.GUID;
+import org.labkey.api.util.HtmlString;
 import org.labkey.api.util.JavaScriptFragment;
 import org.labkey.api.util.StringExpression;
 import org.labkey.api.view.ActionURL;
@@ -38,6 +39,7 @@
 
 import static org.labkey.api.util.DOM.SPAN;
 import static org.labkey.api.util.DOM.id;
+import static org.labkey.api.util.DOM.Attribute.style;
 
 /**
  * Uses LABKEY.Ext.CalloutTip to provide additional details, summoned via AJAX
@@ -106,7 +108,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
             props.put("target", divId);
 
             SPAN(
-                id(divId),
+                id(divId).at(style, "display:inline-flex;flex-wrap:nowrap"),
                 (DOM.Renderable) ret -> {
                     super.renderGridCellContents(ctx, out);
                     return ret;

api/src/org/labkey/api/dataiterator/SimpleTranslator.java

@@ -485,28 +485,24 @@ protected class DerivationScopedConvertColumn extends SimpleConvertColumn
         final int derivationDataColInd;
         final int index;
         final boolean isDerivation;
-        final String presentDerivationWarning;
-        final String presentNonDerivationWarning;
 
         final SimpleConvertColumn _convertCol;
 
-        public DerivationScopedConvertColumn(int index, SimpleConvertColumn convertCol, int derivationDataColInd, boolean isDerivation, @Nullable String presentDerivationWarning, @Nullable String presentNonDerivationWarning)
+        public DerivationScopedConvertColumn(int index, SimpleConvertColumn convertCol, int derivationDataColInd, boolean isDerivation)
         {
             super(convertCol.fieldName, convertCol.index, convertCol.type, convertCol.defaultUnit);
             _convertCol = convertCol;
             this.index = index;
             this.derivationDataColInd = derivationDataColInd;
             this.isDerivation = isDerivation;
-            this.presentDerivationWarning = presentDerivationWarning;
-            this.presentNonDerivationWarning = presentNonDerivationWarning;
         }
 
         @Override
         protected Object convert(Object o)
         {
             Object thisValue =  _convertCol.convert(o);
 
-            return getDerivationData(thisValue, derivationDataColInd, isDerivation, presentDerivationWarning, presentNonDerivationWarning);
+            return getDerivationData(thisValue, derivationDataColInd, isDerivation);
 
         }
     }
@@ -519,48 +515,33 @@ protected class DerivationScopedColumn implements Supplier
         final int index;
         final boolean isDerivation;
 
-        final String presentDerivationWarning;
-        final String presentNonDerivationWarning;
-
-        public DerivationScopedColumn(int index, int derivationDataColInd, boolean isDerivation, @Nullable String presentDerivationWarning, @Nullable String presentNonDerivationWarning)
+        public DerivationScopedColumn(int index, int derivationDataColInd, boolean isDerivation)
         {
             this.index = index;
             this.derivationDataColInd = derivationDataColInd;
             this.isDerivation = isDerivation;
-            this.presentDerivationWarning = presentDerivationWarning;
-            this.presentNonDerivationWarning = presentNonDerivationWarning;
         }
 
         @Override
         public Object get()
         {
             Object thisValue =  _data.get(index);
-            return getDerivationData(thisValue, derivationDataColInd, isDerivation, presentDerivationWarning, presentNonDerivationWarning);
+            return getDerivationData(thisValue, derivationDataColInd, isDerivation);
         }
     }
 
     /**
      * @param thisValue the original field value
      * @param derivationDataColInd the col index for the field used to determine if a record is child or parent
      * @param isDerivationField if this field is a child only field
-     * @param presentDerivationWarning the warning msg to log if a child field is present for a parent record
-     * @param presentNonDerivationWarning the warning msg to log if a parent field is present for a child record
      */
-    private Object getDerivationData(Object thisValue, int derivationDataColInd, boolean isDerivationField, @Nullable String presentDerivationWarning, @Nullable String presentNonDerivationWarning)
+    private Object getDerivationData(Object thisValue, int derivationDataColInd, boolean isDerivationField)
     {
         Object derivationData = derivationDataColInd < 0 ? null : _data.get(derivationDataColInd);
         if ((isDerivationField && derivationData != null)
                 || (!isDerivationField && derivationData == null))
             return thisValue;
 
-        if (thisValue != null)
-        {
-            if (isDerivationField && presentDerivationWarning != null)
-                LOG.warn(presentDerivationWarning);
-            else if (!isDerivationField && presentNonDerivationWarning != null)
-                LOG.warn(presentNonDerivationWarning);
-        }
-
         return null;
     }
 

api/webapp/WEB-INF/web.xml

@@ -58,6 +58,11 @@
         <url-pattern>*.post</url-pattern>
     </filter-mapping>
 
+    <!-- Ensure that we never use GET parameters for session IDs -->
+    <session-config>
+        <tracking-mode>COOKIE</tracking-mode>
+    </session-config>
+
     <welcome-file-list>
         <welcome-file>/</welcome-file>
     </welcome-file-list>

audit/src/org/labkey/audit/AuditModule.java

@@ -19,6 +19,13 @@
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.audit.AuditLogService;
 import org.labkey.api.audit.provider.SiteSettingsAuditProvider;
+import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.JdbcType;
+import org.labkey.api.data.SQLFragment;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.data.WrappedColumn;
+import org.labkey.api.migration.DatabaseMigrationService;
+import org.labkey.api.migration.MigrationTableHandler;
 import org.labkey.api.module.DefaultModule;
 import org.labkey.api.module.ModuleContext;
 import org.labkey.api.view.WebPartFactory;
@@ -27,6 +34,7 @@
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Set;
+import java.util.TreeSet;
 
 public class AuditModule extends DefaultModule
 {
@@ -89,4 +97,57 @@ public Set<String> getProvisionedSchemaNames()
     {
         return Collections.singleton(AuditSchema.SCHEMA_NAME);
     }
+
+    private final Set<String> _registeredMigrationTables = new TreeSet<>(String.CASE_INSENSITIVE_ORDER);
+
+    @Override
+    public void registerMigrationHandlers(@NotNull DatabaseMigrationService service)
+    {
+        service.registerSchemaContributor(AuditSchema.SCHEMA_NAME, schema ->
+            schema.getTableNames().stream()
+                .map(schema::getTable)
+                .filter(table -> table != null && _registeredMigrationTables.add(table.getSelectName()))
+                .forEach(table -> service.registerTableHandler(new MigrationTableHandler()
+                {
+                    @Override
+                    public TableInfo getTableInfo()
+                    {
+                        return table;
+                    }
+
+                    @Override
+                    public ColumnInfo handleColumn(ColumnInfo col)
+                    {
+                        if ("hasdetails".equalsIgnoreCase(col.getName()))
+                            return new HasDetailsCastColumn(col);
+                        return col;
+                    }
+                })));
+    }
+
+    // Some legacy source databases store the DatasetAuditDomain "HasDetails" column as varchar
+    // while the target was provisioned as boolean. CAST to BIT in the source SELECT and report
+    // BOOLEAN as the JdbcType so the migration's INSERT parameter binds cleanly into the
+    // target's boolean column (otherwise the parameter inherits the source column's VARCHAR
+    // type and PG rejects the bound value).
+    private static final class HasDetailsCastColumn extends WrappedColumn
+    {
+        private HasDetailsCastColumn(ColumnInfo col)
+        {
+            super(col, col.getName());
+        }
+
+        @Override
+        @NotNull
+        public JdbcType getJdbcType()
+        {
+            return JdbcType.BOOLEAN;
+        }
+
+        @Override
+        public SQLFragment getValueSql(String tableAlias)
+        {
+            return new SQLFragment("CAST(").append(super.getValueSql(tableAlias)).append(" AS BIT)");
+        }
+    }
 }

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

@@ -1607,9 +1607,6 @@ private boolean rowExists(String name)
 
     static class _SamplesCoerceDataIterator extends SimpleTranslator
     {
-        private static final String INVALID_ALIQUOT_PROPERTY = "An aliquot-specific property [%1$s] value has been ignored for a non-aliquot sample.";
-        private static final String INVALID_NON_ALIQUOT_PROPERTY = "A sample property [%1$s] value has been ignored for an aliquot.";
-
         private final ExpSampleTypeImpl _sampleType;
         private final Unit _sampleTypeBaseUnit;
 
@@ -1664,14 +1661,12 @@ else if (amountImportAliasSet.contains(from.getName()))
                     String name = to.getName();
                     boolean isScopedField = scopedFields.containsKey(name);
 
-                    String ignoredAliquotPropValue = String.format(INVALID_ALIQUOT_PROPERTY, name);
-                    String ignoredMetaPropValue = String.format(INVALID_NON_ALIQUOT_PROPERTY, name);
                     if (to.getPropertyType() == PropertyType.ATTACHMENT || to.getPropertyType() == PropertyType.FILE_LINK)
                     {
                         if (isScopedField)
                         {
                             ColumnInfo clone = new BaseColumnInfo(to);
-                            addColumn(clone, new DerivationScopedColumn(i, aliquotedFromDataColInd, scopedFields.get(name), ignoredAliquotPropValue, ignoredMetaPropValue));
+                            addColumn(clone, new DerivationScopedColumn(i, aliquotedFromDataColInd, scopedFields.get(name)));
                         }
                         else
                             addColumn(to, i);
@@ -1683,7 +1678,7 @@ else if (to.isMultiValued() || to.getFk() instanceof MultiValuedForeignKey)
                         {
                             var col = new BaseColumnInfo(getInput().getColumnInfo(i));
                             col.setName(name);
-                            addColumn(col, new DerivationScopedColumn(i, aliquotedFromDataColInd, scopedFields.get(name), ignoredAliquotPropValue, ignoredMetaPropValue));
+                            addColumn(col, new DerivationScopedColumn(i, aliquotedFromDataColInd, scopedFields.get(name)));
                         }
                         else
                             addColumn(to.getName(), i);
@@ -1754,7 +1749,7 @@ private void _addConvertColumn(String name, int fromIndex, JdbcType toType, @Nul
         private void _addConvertColumn(ColumnInfo col, int fromIndex, int derivationDataColInd, boolean isAliquotField)
         {
             SimpleConvertColumn c = createConvertColumn(col, fromIndex, RemapMissingBehavior.Error);
-            c = new DerivationScopedConvertColumn(fromIndex, c, derivationDataColInd, isAliquotField, String.format(INVALID_ALIQUOT_PROPERTY, col.getName()), String.format(INVALID_NON_ALIQUOT_PROPERTY, col.getName()));
+            c = new DerivationScopedConvertColumn(fromIndex, c, derivationDataColInd, isAliquotField);
 
             addColumn(col, c);
         }