Merge 25.12 to develop

labkey-teamcity · labkey-teamcity · commit 340c4abfce91 · 2025-12-10T15:21:55.000Z
diff --git a/api/src/org/labkey/api/data/SQLParameterException.java b/api/src/org/labkey/api/data/SQLParameterException.java
@@ -0,0 +1,29 @@
+/*
+ * Copyright (c) 2011 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.api.data;
+
+import org.labkey.api.util.SkipMothershipLogging;
+
+/**
+ * Signals there was a problem with a SQL parameter, such as a conversion problem.
+ */
+public class SQLParameterException extends SQLGenerationException implements SkipMothershipLogging
+{
+    public SQLParameterException(String message)
+    {
+        super(message);
+    }
+}
diff --git a/api/src/org/labkey/api/data/SqlExecutingSelector.java b/api/src/org/labkey/api/data/SqlExecutingSelector.java
@@ -567,7 +567,9 @@ public void handleSqlException(SQLException e, @Nullable Connection conn)
             if (null != _sql)
                 ExceptionUtil.decorateException(e, ExceptionUtil.ExceptionInfo.DialectSQL, _sql.toDebugString(), false);
 
-            throw getExceptionFramework().translate(getScope(), "ExecutingSelector", e);
+            RuntimeException translated = getExceptionFramework().translate(getScope(), "ExecutingSelector", e);
+            ExceptionUtil.copyDecorations(e, translated);
+            throw translated;
         }
     }
 }
diff --git a/api/src/org/labkey/api/data/Table.java b/api/src/org/labkey/api/data/Table.java
@@ -19,6 +19,7 @@
 import org.apache.commons.beanutils.BeanUtils;
 import org.apache.commons.beanutils.PropertyUtils;
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Strings;
 import org.apache.logging.log4j.Level;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
@@ -50,6 +51,7 @@
 import org.labkey.api.query.RuntimeValidationException;
 import org.labkey.api.security.User;
 import org.labkey.api.util.BaseScanner;
+import org.labkey.api.util.ExceptionUtil;
 import org.labkey.api.util.GUID;
 import org.labkey.api.util.JunitUtil;
 import org.labkey.api.util.MemTracker;
@@ -571,7 +573,7 @@ Object getObject(ResultSet rs) throws SQLException
     // Standard SQLException catch block: log exception, query SQL, and params
     static void logException(@Nullable SQLFragment sql, @Nullable Connection conn, SQLException e, Level logLevel)
     {
-        if (SqlDialect.isCancelException(e))
+        if (SqlDialect.isCancelException(e) || ExceptionUtil.isIgnorable(e))
         {
             return;
         }
@@ -585,7 +587,7 @@ static void logException(@Nullable SQLFragment sql, @Nullable Connection conn, S
             String trim = sql.getSQL().trim();
 
             // Treat a ConstraintException during INSERT/UPDATE as a WARNING. Treat all other SQLExceptions as an ERROR.
-            if (RuntimeSQLException.isConstraintException(e) && (StringUtils.startsWithIgnoreCase(trim, "INSERT") || StringUtils.startsWithIgnoreCase(trim, "UPDATE")))
+            if (RuntimeSQLException.isConstraintException(e) && (Strings.CI.startsWith(trim, "INSERT") || Strings.CI.startsWith(trim, "UPDATE")))
             {
                 // Log this ConstraintException if log Level is WARN (the default) or lower. Skip logging for callers that request just ERRORs.
                 if (Level.WARN.isMoreSpecificThan(logLevel))
@@ -1409,7 +1411,7 @@ public void testSelect() throws SQLException
             //noinspection EmptyTryBlock,UnusedDeclaration
             try (ResultSet rs = new TableSelector(tinfo).getResultSet()){}
 
-            Map[] maps = new TableSelector(tinfo).getMapArray();
+            Map<?, ?>[] maps = new TableSelector(tinfo).getMapArray();
             assertNotNull(maps);
 
             Principal[] principals = new TableSelector(tinfo).getArray(Principal.class);
@@ -1739,7 +1741,7 @@ public static ParameterMapStatement deleteStatement(Connection conn, TableInfo t
         //
 
         Domain domain = tableDelete.getDomain();
-        DomainKind domainKind = tableDelete.getDomainKind();
+        DomainKind<?> domainKind = tableDelete.getDomainKind();
         if (null != domain && null != domainKind && StringUtils.isEmpty(domainKind.getStorageSchemaName()))
         {
             if (!d.isPostgreSQL() && !d.isSqlServer())
diff --git a/api/src/org/labkey/api/data/TableSelector.java b/api/src/org/labkey/api/data/TableSelector.java
@@ -396,7 +396,7 @@ public Results getResultsAsync(final boolean cache, final boolean scrollable, Ht
     }
 
     /**
-     * Setting this options asks the TableSelector to add additional display columns to the generated SQL, as well
+     * Setting this option asks the TableSelector to add additional display columns to the generated SQL, as well
 
      * as forcing the results to be sorted.
      * @return this
diff --git a/api/src/org/labkey/api/util/ExceptionUtil.java b/api/src/org/labkey/api/util/ExceptionUtil.java
@@ -106,6 +106,14 @@ public class ExceptionUtil
      */
     private static final Map<String, ExceptionTally> EXCEPTION_TALLIES = Collections.synchronizedMap(new HashMap<>());
 
+    public static void copyDecorations(Throwable source, Throwable target)
+    {
+        for (Map.Entry<Enum<?>, String> entry : getExceptionDecorations(source).entrySet())
+        {
+            decorateException(target, entry.getKey(), entry.getValue(), false);
+        }
+    }
+
     private static class ExceptionTally
     {
         /** Total number of times the exception has happened */
diff --git a/api/src/org/labkey/api/util/SkipMothershipLogging.java b/api/src/org/labkey/api/util/SkipMothershipLogging.java
@@ -16,13 +16,9 @@
 
 package org.labkey.api.util;
 
-/*
-* User: adam
-* Date: Aug 10, 2009
-* Time: 2:03:50 PM
-*/
-
-// Exceptions implement this interface to tell mothership not to log them
+/**
+ * Exceptions implement this interface as a tag to tell mothership not to log them
+ */
 public interface SkipMothershipLogging
 {
 }
diff --git a/core/src/org/labkey/core/dialect/PostgreSql92Dialect.java b/core/src/org/labkey/core/dialect/PostgreSql92Dialect.java
@@ -48,7 +48,6 @@
 abstract class PostgreSql92Dialect extends BasePostgreSqlDialect
 {
     public static final String PRODUCT_NAME = "PostgreSQL";
-    public static final String RECOMMENDED = PRODUCT_NAME + " 17.x is the recommended version.";
 
     // This has been the standard PostgreSQL identifier max byte length for many years. However, this could change in
     // the future plus servers can be compiled with a different limit, so we query this setting on first connection to
diff --git a/core/src/org/labkey/core/dialect/PostgreSqlDialectFactory.java b/core/src/org/labkey/core/dialect/PostgreSqlDialectFactory.java
@@ -116,7 +116,7 @@ else if (psv.isDeprecated())
 
     public static String getStandardWarningMessage(String warning, String databaseProductVersion)
     {
-        return "LabKey Server " + warning + " " + PostgreSql92Dialect.PRODUCT_NAME + " version " + databaseProductVersion + ". " + PostgreSql92Dialect.RECOMMENDED;
+        return "LabKey Server " + warning + " " + PostgreSql92Dialect.PRODUCT_NAME + " version " + databaseProductVersion + ". " + PostgreSqlVersion.RECOMMENDED;
     }
 
     @Override
diff --git a/core/src/org/labkey/core/dialect/PostgreSqlVersion.java b/core/src/org/labkey/core/dialect/PostgreSqlVersion.java
@@ -10,20 +10,24 @@
 import java.util.function.Supplier;
 import java.util.stream.Collectors;
 
+import static org.labkey.core.dialect.PostgreSql92Dialect.PRODUCT_NAME;
+
 /**
  * Enum that specifies the versions of PostgreSQL that LabKey supports plus their properties
  */
 public enum PostgreSqlVersion
 {
     POSTGRESQL_UNSUPPORTED(-1, true, false, null),
-    POSTGRESQL_13(130, false, true, PostgreSql_13_Dialect::new),
+    POSTGRESQL_13(130, true, true, PostgreSql_13_Dialect::new),
     POSTGRESQL_14(140, false, true, PostgreSql_14_Dialect::new),
     POSTGRESQL_15(150, false, true, PostgreSql_15_Dialect::new),
     POSTGRESQL_16(160, false, true, PostgreSql_16_Dialect::new),
     POSTGRESQL_17(170, false, true, PostgreSql_17_Dialect::new),
-    POSTGRESQL_18(180, false, false, PostgreSql_18_Dialect::new),
+    POSTGRESQL_18(180, false, true, PostgreSql_18_Dialect::new),
     POSTGRESQL_FUTURE(Integer.MAX_VALUE, true, false, PostgreSql_18_Dialect::new);
 
+    public static final String RECOMMENDED = PRODUCT_NAME + " 18.x is the recommended version.";
+
     private final int _version;
     private final boolean _deprecated;
     private final boolean _tested;
diff --git a/query/src/org/labkey/query/QueryServiceImpl.java b/query/src/org/labkey/query/QueryServiceImpl.java
@@ -23,6 +23,7 @@
 import org.apache.commons.collections4.MultiValuedMap;
 import org.apache.commons.collections4.SetValuedMap;
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Strings;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.apache.xmlbeans.XmlError;
@@ -65,7 +66,7 @@
 import org.labkey.api.data.ResultsImpl;
 import org.labkey.api.data.RuntimeSQLException;
 import org.labkey.api.data.SQLFragment;
-import org.labkey.api.data.SQLGenerationException;
+import org.labkey.api.data.SQLParameterException;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.Sort;
 import org.labkey.api.data.SqlSelector;
@@ -120,6 +121,7 @@
 import org.labkey.api.util.CSRFUtil;
 import org.labkey.api.util.ConfigurationException;
 import org.labkey.api.util.ContainerContext;
+import org.labkey.api.util.ExceptionUtil;
 import org.labkey.api.util.GUID;
 import org.labkey.api.util.JunitUtil;
 import org.labkey.api.util.Pair;
@@ -1360,7 +1362,7 @@ public MultiValuedMap<Path, ModuleCustomViewDef> load(Stream<? extends Resource>
         {
             // Note: Can't use standard filter (getFilter(suffix)) below since we must allow ".qview.xml"
             return unmodifiable(resources
-                    .filter(resource -> StringUtils.endsWithIgnoreCase(resource.getName(), CustomViewXmlReader.XML_FILE_EXTENSION))
+                    .filter(resource -> Strings.CI.endsWith(resource.getName(), CustomViewXmlReader.XML_FILE_EXTENSION))
                     .map(ModuleCustomViewDef::new)
                     .collect(LabKeyCollectors.toMultiValuedMap(def -> def.getPath().getParent(), def -> def)));
         }
@@ -2683,7 +2685,9 @@ public void bindNamedParameters(SQLFragment frag, @Nullable Map<String, Object>
             }
             catch (ConversionException e)
             {
-                throw new RuntimeSQLException(new SQLGenerationException(ConvertHelper.getStandardConversionErrorMessage(value, p.getName(), p.getJdbcType().getJavaClass())));
+                SQLParameterException paramException = new SQLParameterException(ConvertHelper.getStandardConversionErrorMessage(value, p.getName(), p.getJdbcType().getJavaClass()));
+                ExceptionUtil.decorateException(paramException, ExceptionUtil.ExceptionInfo.SkipMothershipLogging, "true", true);
+                throw new RuntimeSQLException(paramException);
             }
         }
     }
diff --git a/study/resources/schemas/dbscripts/postgresql/study-25.004-25.005.sql b/study/resources/schemas/dbscripts/postgresql/study-25.004-25.005.sql
@@ -0,0 +1 @@
+ALTER TABLE study.uploadlog DROP CONSTRAINT UQ_UploadLog_FilePath;
diff --git a/study/resources/schemas/dbscripts/sqlserver/study-25.004-25.005.sql b/study/resources/schemas/dbscripts/sqlserver/study-25.004-25.005.sql
@@ -0,0 +1 @@
+ALTER TABLE study.uploadlog DROP CONSTRAINT UQ_UploadLog_FilePath;
diff --git a/study/src/org/labkey/study/StudyModule.java b/study/src/org/labkey/study/StudyModule.java
@@ -42,8 +42,6 @@
 import org.labkey.api.exp.PropertyType;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.exp.property.PropertyService;
-import org.labkey.api.files.FileContentService;
-import org.labkey.api.files.TableUpdaterFileListener;
 import org.labkey.api.message.digest.ReportAndDatasetChangeDigestProvider;
 import org.labkey.api.migration.DatabaseMigrationService;
 import org.labkey.api.migration.DefaultMigrationSchemaHandler;
@@ -228,7 +226,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 25.003;
+        return 25.005;
     }
 
     @Override
@@ -391,8 +389,6 @@ protected void startupAfterSpringConfig(ModuleContext moduleContext)
             folderRegistry.addFactories(new StudyWriterFactory(), new StudyImporterFactory());
         }
 
-        FileContentService.get().addFileListener(new TableUpdaterFileListener(StudySchema.getInstance().getTableInfoUploadLog(), "FilePath", TableUpdaterFileListener.Type.filePath, "RowId"));
-
         DatasetDefinition.cleanupOrphanedDatasetDomains();
 
         OptionalFeatureService.get().addExperimentalFeatureFlag(StudyQuerySchema.EXPERIMENTAL_STUDY_SUBSCHEMAS, "Use sub-schemas in Study",
diff --git a/study/src/org/labkey/study/assay/StudyPublishManager.java b/study/src/org/labkey/study/assay/StudyPublishManager.java
diff --git a/study/src/org/labkey/study/controllers/StudyController.java b/study/src/org/labkey/study/controllers/StudyController.java
diff --git a/study/src/org/labkey/study/dataset/DatasetSnapshotProvider.java b/study/src/org/labkey/study/dataset/DatasetSnapshotProvider.java
diff --git a/study/src/org/labkey/study/model/DatasetDefinition.java b/study/src/org/labkey/study/model/DatasetDefinition.java
diff --git a/study/src/org/labkey/study/model/StudyManager.java b/study/src/org/labkey/study/model/StudyManager.java
diff --git a/study/src/org/labkey/study/model/UploadLog.java b/study/src/org/labkey/study/model/UploadLog.java

Original file line number	Diff line number	Diff line change
`@@ -567,7 +567,9 @@ public void handleSqlException(SQLException e, @Nullable Connection conn)`
`567`	`567`	`if (null != _sql)`
`568`	`568`	`ExceptionUtil.decorateException(e, ExceptionUtil.ExceptionInfo.DialectSQL, _sql.toDebugString(), false);`
`569`	`569`
`570`		`- throw getExceptionFramework().translate(getScope(), "ExecutingSelector", e);`
	`570`	`+ RuntimeException translated = getExceptionFramework().translate(getScope(), "ExecutingSelector", e);`
	`571`	`+ ExceptionUtil.copyDecorations(e, translated);`
	`572`	`+ throw translated;`
`571`	`573`	`}`
`572`	`574`	`}`
`573`	`575`	`}`
Original file line number	Diff line number	Diff line change
`@@ -396,7 +396,7 @@ public Results getResultsAsync(final boolean cache, final boolean scrollable, Ht`
`396`	`396`	`}`
`397`	`397`
`398`	`398`	`/**`
`399`		`- * Setting this options asks the TableSelector to add additional display columns to the generated SQL, as well`
	`399`	`+ * Setting this option asks the TableSelector to add additional display columns to the generated SQL, as well`
`400`	`400`
`401`	`401`	`* as forcing the results to be sorted.`
`402`	`402`	`* @return this`
Original file line number	Diff line number	Diff line change
`@@ -48,7 +48,6 @@`
`48`	`48`	`abstract class PostgreSql92Dialect extends BasePostgreSqlDialect`
`49`	`49`	`{`
`50`	`50`	`public static final String PRODUCT_NAME = "PostgreSQL";`
`51`		`- public static final String RECOMMENDED = PRODUCT_NAME + " 17.x is the recommended version.";`
`52`	`51`
`53`	`52`	`// This has been the standard PostgreSQL identifier max byte length for many years. However, this could change in`
`54`	`53`	`// the future plus servers can be compiled with a different limit, so we query this setting on first connection to`
Original file line number	Diff line number	Diff line change
`@@ -116,7 +116,7 @@ else if (psv.isDeprecated())`
`116`	`116`
`117`	`117`	`public static String getStandardWarningMessage(String warning, String databaseProductVersion)`
`118`	`118`	`{`
`119`		`- return "LabKey Server " + warning + " " + PostgreSql92Dialect.PRODUCT_NAME + " version " + databaseProductVersion + ". " + PostgreSql92Dialect.RECOMMENDED;`
	`119`	`+ return "LabKey Server " + warning + " " + PostgreSql92Dialect.PRODUCT_NAME + " version " + databaseProductVersion + ". " + PostgreSqlVersion.RECOMMENDED;`
`120`	`120`	`}`
`121`	`121`
`122`	`122`	`@Override`