[bot] Merge 25.11 to develop (Conflicts)

api/src/org/labkey/api/attachments/SvgSource.java

@@ -3,6 +3,7 @@
 import org.apache.batik.anim.dom.SVGDOMImplementation;
 import org.apache.batik.transcoder.TranscoderException;
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Strings;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.view.NotFoundException;
 
@@ -19,6 +20,8 @@ public class SvgSource
 {
     private final String _filteredSvg;
 
+    private Float _height = null;
+
     public SvgSource(String svg)
     {
         if (StringUtils.isBlank(svg))
@@ -29,11 +32,19 @@ public SvgSource(String svg)
         if (!svg.contains("xmlns=\"" + SVGDOMImplementation.SVG_NAMESPACE_URI + "\"") && !svg.contains("xmlns='" + SVGDOMImplementation.SVG_NAMESPACE_URI + "'"))
             svg = svg.replace("<svg", "<svg xmlns='" + SVGDOMImplementation.SVG_NAMESPACE_URI + "'");
 
+        int idx = svg.indexOf("height=\"");
+        if (idx != -1)
+        {
+            int heightStart = idx + 8;
+            int end = svg.indexOf("\"",  heightStart);
+            _height = Float.parseFloat(svg.substring(heightStart, end));
+        }
+
         // remove xlink:title to prevent org.apache.batik.transcoder.TranscoderException (issue #16173)
         svg = svg.replaceAll("xlink:title", "title");
 
         // Reject hrefs. See #45819.
-        if (StringUtils.containsIgnoreCase(svg, "xlink:href"))
+        if (Strings.CI.contains(svg, "xlink:href"))
             throw new RuntimeException(new TranscoderException("The security settings do not allow any external resources to be referenced from the document"));
 
         _filteredSvg = svg;
@@ -56,4 +67,9 @@ public Reader getReader()
     {
         return new StringReader(_filteredSvg);
     }
+
+    public Float getHeight()
+    {
+        return _height;
+    }
 }

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

@@ -585,7 +585,8 @@ public static List<Container> findAndCheckContainersMatchingTabs(Container c, Fo
         return containersMatchingTabs;
     }
 
-    private static final Set<Container> containersWithBadFolderTypes = new ConcurrentHashSet<>();
+    private static final Set<Integer> containersWithBadFolderTypes = new ConcurrentHashSet<>();
+    private static final Set<String> badFolderTypes = new ConcurrentHashSet<>();
 
     @NotNull
     public static FolderType getFolderType(Container c)
@@ -602,10 +603,16 @@ public static FolderType getFolderType(Container c)
                 // If we're upgrading then folder types won't be defined yet... don't warn in that case.
                 if (!ModuleLoader.getInstance().isUpgradeInProgress() &&
                     !ModuleLoader.getInstance().isUpgradeRequired() &&
-                    !containersWithBadFolderTypes.contains(c))
+                    containersWithBadFolderTypes.add(c.getRowId()))
                 {
-                    LOG.warn("No such folder type " + name + " for folder " + c.toString());
-                    containersWithBadFolderTypes.add(c);
+                    if (badFolderTypes.add(name))
+                    {
+                        LOG.warn("No such folder type {} for container {}. Additional containers of this folder type will be logged at DEBUG level.", name, c.getPath());
+                    }
+                    else
+                    {
+                        LOG.debug("No such folder type {} for container {}.", name, c.getPath());
+                    }
                 }
 
                 folderType = FolderType.NONE;

api/src/org/labkey/api/migration/DefaultMigrationSchemaHandler.java

@@ -290,7 +290,7 @@ public static void logUnseenAttachmentTypes()
         Set<AttachmentType> unseen = new HashSet<>(AttachmentService.get().getAttachmentTypes());
         unseen.removeAll(SEEN);
 
-        if (SEEN.isEmpty())
+        if (unseen.isEmpty())
             DatabaseMigrationService.LOG.info("All AttachmentTypes have been seen");
         else
             DatabaseMigrationService.LOG.info("These AttachmentTypes have not been seen: {}", unseen.stream().map(type -> type.getClass().getSimpleName()).collect(Collectors.joining(", ")));

api/src/org/labkey/api/pipeline/PipeRoot.java

@@ -70,22 +70,22 @@ public interface PipeRoot extends SecurableResource
     Path resolveToNioPathFromUrl(String url);
 
     /**
-     * @return the file that's at the given relativePath from the pipeline root. Will be null if the relative path
-     * attempts to reference something that's not under the root (such as "../../etc/passwd". When the root
+     * @return the file that's at the given relativePath from the pipeline root. When the root
      * is configured with an alternative file path, we'll check to see if the file exists there. If not, we'll return
      * a path relative to the root's primary path.
+     * @throws org.labkey.api.util.FileUtil.InvalidPathReferenceException if the relative path
+     * attempts to reference something not under the root (such as "../../etc/passwd")
      */
     @Deprecated // prefer resolvePathToFileLike()
-    @Nullable
     File resolvePath(String relativePath);
 
     /**
-     * @return the file that's at the given relativePath from the pipeline root. Will be null if the relative path
-     * attempts to reference something that's not under the root (such as "../../etc/passwd". When the root
+     * @return the file that's at the given relativePath from the pipeline root. When the root
      * is configured with an alternative file path, we'll check to see if the file exists there. If not, we'll return
      * a path relative to the root's primary path.
+     * @throws org.labkey.api.util.FileUtil.InvalidPathReferenceException if the relative path
+     * attempts to reference something not under the root (such as "../../etc/passwd")
      */
-    @Nullable
     FileLike resolvePathToFileLike(String relativePath);
 
     @NotNull

api/src/org/labkey/api/products/ProductRegistry.java

@@ -15,6 +15,7 @@
  */
 package org.labkey.api.products;
 
+import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -219,7 +220,9 @@ public String getPrimaryProductIdForContainer(@NotNull Container container)
     public ProductMenuProvider getPrimaryProductMenuForContainer(@NotNull Container container)
     {
         List<String> productIds = getProductIdsForContainer(container);
+        _logger.debug("Product Ids in container '{}' of type '{}' are {}", container.getPath(), container.getFolderType().getName(), StringUtils.join(productIds));
         List<ProductMenuProvider> providers = getRegisteredProducts().stream().filter(provider -> productIds.contains(provider.getProductId())).toList();
+        _logger.debug("Menu providers: {}", providers.stream().map(ProductMenuProvider::getProductId).collect(Collectors.toList()));
         if (providers.isEmpty())
             return null;
 
@@ -229,16 +232,27 @@ public ProductMenuProvider getPrimaryProductMenuForContainer(@NotNull Container
         // see if there's a provider that matches the folder type (need to check this first so if LabKey LIMS or LKB is the configured product you can still show LKSM folders)
         Optional<ProductMenuProvider> optionalProvider = providers.stream().filter(provider -> provider.getFolderTypeName() != null && provider.getFolderTypeName().equals(container.getFolderType().getName())).findFirst();
         if (optionalProvider.isPresent())
+        {
+            _logger.debug("Found product menu provider for folder type '{}'", container.getFolderType().getName());
             return optionalProvider.get();
+        }
 
         List<String> orderedProducts = getProducts(true, false).stream().filter(Product::isEnabled).map(Product::getProductGroupId).toList();
-        ProductMenuProvider highestProvider = providers.stream().min(Comparator.comparing(provider -> orderedProducts.indexOf(provider.getProductId()))).orElse(null);
+        _logger.debug("Products are {}", _products.keySet());
+        _logger.debug("Ordered products are {}", orderedProducts);
+        ProductMenuProvider highestProvider = providers.stream()
+                .min(Comparator.comparing(provider -> orderedProducts.indexOf(provider.getProductId()))).orElse(null);
+        _logger.debug("Highest product menu provider: {}", highestProvider.getProductId());
         // then see if there's a provider that matches the configured product
         Product product = new ProductConfiguration().getCurrentProduct();
         if (product == null)
+        {
+            _logger.debug("Using highest product menu provider.");
             return highestProvider;
+        }
 
         optionalProvider = providers.stream().filter(provider -> provider.getProductId().equals(product.getProductGroupId())).findFirst();
+        _logger.debug("Product from product group: {}", optionalProvider.isPresent() ? optionalProvider.get() : "null");
         // if neither of those is true (when can this happen?), use the highest provider
         return optionalProvider.orElseGet(() -> highestProvider);
     }

api/src/org/labkey/api/settings/ProductConfiguration.java

@@ -1,18 +1,21 @@
 package org.labkey.api.settings;
 
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.products.Product;
 import org.labkey.api.products.ProductRegistry;
+import org.labkey.api.util.logging.LogHelper;
 
 import java.util.Collection;
 
 public class ProductConfiguration extends AbstractWriteableSettingsGroup implements StartupProperty
 {
     public static final String SCOPE_PRODUCT_CONFIGURATION = "ProductConfiguration";
     public static final String PROPERTY_NAME = "productKey";
+    private static final Logger _logger = LogHelper.getLogger(ProductConfiguration.class, "Product Configuration properties");
 
     @Override
     protected String getGroupName()
@@ -54,6 +57,7 @@ public String getCurrentProductKey()
     public Product getCurrentProduct()
     {
         String productKey = getCurrentProductKey();
+        _logger.debug("Current product key: {}", productKey);
         if (productKey == null)
             return null;
         return ProductRegistry.getProduct(productKey);

api/src/org/labkey/api/util/ExceptionUtil.java

@@ -865,6 +865,21 @@ else if (ex instanceof BadRequestException)
             message = ex.getMessage();
             unhandledException = null;
         }
+        else if (ex instanceof FileUtil.InvalidPathReferenceException ipre)
+        {
+            responseStatus = HttpServletResponse.SC_NOT_FOUND;
+            errorType = ErrorRenderer.ErrorType.notFound;
+            if (ex.getMessage() != null)
+            {
+                message = ex.getMessage();
+                responseStatusMessage = message;
+            }
+            else
+                message = responseStatus + ": Page not Found";
+            unhandledException = null;
+            log.info("InvalidPathReferenceException: {}", ipre.getInput());
+            log.debug("InvalidPathReferenceException", ex);
+        }
         else if (ex instanceof NotFoundException)
         {
             responseStatus = HttpServletResponse.SC_NOT_FOUND;

api/src/org/labkey/api/util/FileUtil.java

@@ -852,11 +852,20 @@ public static File appendPath(File dir, org.labkey.api.util.Path originalPath)
     {
         org.labkey.api.util.Path path = originalPath.normalize();
         if (path == null || (!path.isEmpty() && "..".equals(path.get(0))))
-            throw new InvalidPathException(originalPath.toString(), "Path to parent not allowed");
+            throw new InvalidPathReferenceException(originalPath.toString(), "Path to parent not allowed");
         @SuppressWarnings("SSBasedInspection")
         var ret = new File(dir, path.toString());
-        if (!ret.toPath().normalize().startsWith(dir.toPath().normalize()))
-            throw new InvalidPathException(originalPath.toString(), "Path to parent not allowed");
+        boolean valid;
+        try
+        {
+            valid = ret.toPath().normalize().startsWith(dir.toPath().normalize());
+        }
+        catch (InvalidPathException e)
+        {
+            throw new InvalidPathReferenceException(originalPath.toString(), e.getMessage());
+        }
+        if (!valid)
+            throw new InvalidPathReferenceException(originalPath.toString(), "Path to parent not allowed");
         return ret;
     }
 
@@ -866,7 +875,7 @@ public static FileLike appendPath(FileLike dir, org.labkey.api.util.Path path)
     {
         path = path.normalize();
         if (!path.isEmpty() && "..".equals(path.get(0)))
-            throw new InvalidPathException(path.toString(), "Path to parent not allowed");
+            throw new InvalidPathReferenceException(path.toString(), "Path to parent not allowed");
         return dir.resolveFile(path);
     }
 
@@ -897,7 +906,7 @@ public static File appendName(File dir, String name)
         var ret = new File(dir, name);
 
         if (!ret.toPath().normalize().startsWith(dir.toPath().normalize()))
-            throw new InvalidPathException(name, "Path to parent not allowed");
+            throw new InvalidPathReferenceException(name, "Path to parent not allowed");
         return ret;
     }
 
@@ -908,7 +917,7 @@ public static Path appendName(Path dir, String name)
         var ret = dir.resolve(name);
 
         if (!ret.normalize().startsWith(dir.normalize()))
-            throw new InvalidPathException(name, "Path to parent not allowed");
+            throw new InvalidPathReferenceException(name, "Path to parent not allowed");
         return ret;
     }
 
@@ -919,11 +928,24 @@ public static void legalPathPartThrow(String name)
     {
         int invalidCharacterIndex = StringUtils.indexOfAny(name, '/', File.separatorChar);
         if (invalidCharacterIndex >= 0)
-            throw new InvalidPathException(name, "Invalid file or directory name", invalidCharacterIndex);
+            throw new InvalidPathReferenceException(name, "Invalid file or directory name", invalidCharacterIndex);
         if (".".equals(name) || "..".equals(name))
-            throw new InvalidPathException(name, "Invalid file or directory name");
+            throw new InvalidPathReferenceException(name, "Invalid file or directory name");
     }
 
+    /** Our own subclass for bogus paths that we can special-case in ExceptionUtil in terms of HTTP response codes and logging */
+    public static class InvalidPathReferenceException extends InvalidPathException
+    {
+        public InvalidPathReferenceException(String path, String reason)
+        {
+            super(path, reason);
+        }
+
+        public InvalidPathReferenceException(String name, String reason, int index)
+        {
+            super(name, reason, index);
+        }
+    }
 
     public static String decodeSpaces(@NotNull String str)
     {

assay/package.json

@@ -12,7 +12,7 @@
     "clean": "rimraf resources/web/assay/gen && rimraf resources/views/gen && rimraf resources/web/gen"
   },
   "dependencies": {
-    "@labkey/components": "6.70.2"
+    "@labkey/components": "6.70.8"
   },
   "devDependencies": {
     "@labkey/build": "8.7.0",

assay/src/org/labkey/assay/AssayResultMigrationSchemaHandler.java

@@ -12,18 +12,15 @@
 import org.labkey.api.data.SimpleFilter.SQLClause;
 import org.labkey.api.data.SqlSelector;
 import org.labkey.api.data.TableInfo;
-import org.labkey.api.data.TableSelector;
 import org.labkey.api.migration.AssaySkipContainers;
 import org.labkey.api.migration.DatabaseMigrationService.DataFilter;
 import org.labkey.api.migration.DefaultMigrationSchemaHandler;
 import org.labkey.api.migration.ExperimentDeleteService;
 import org.labkey.api.util.GUID;
-import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.api.util.logging.LogHelper;
 import org.labkey.assay.plate.PlateReplicateStatsDomainKind;
 
 import java.util.Collection;
-import java.util.Collections;
 import java.util.Set;
 
 class AssayResultMigrationSchemaHandler extends DefaultMigrationSchemaHandler
@@ -38,7 +35,7 @@ public AssayResultMigrationSchemaHandler()
     private boolean skipTable(TableInfo sourceTable)
     {
         // For now, we're ignoring this table since it's empty in our first migration client's database
-        return Strings.CI.endsWith(sourceTable.getName(), PlateReplicateStatsDomainKind.ASSAY_PLATE_REPLICATE);
+        return Strings.CI.endsWith(sourceTable.getName(), PlateReplicateStatsDomainKind.NAME);
     }
 
     @Override
@@ -63,8 +60,8 @@ public FilterClause getContainerClause(TableInfo sourceTable, Set<GUID> containe
     @Override
     public void addDomainDataFilterClause(OrClause orClause, DataFilter filter, TableInfo sourceTable, Set<String> selectColumnNames)
     {
-        // No filtering on assay results for now; just add the passed in containers. Note that these will be filtered
-        // if AssaySkipContainers is configured.
+        // No row-by-row filtering on assay results for now; just add the passed in containers. Note that these will be
+        // filtered by container if AssaySkipContainers is configured.
         orClause.addClause(getContainerClause(sourceTable, filter.containers()));
     }
 
@@ -92,9 +89,6 @@ public void afterTable(TableInfo sourceTable, TableInfo targetTable, SimpleFilte
                 // Delete exp.Data, exp.Object, etc. rows associated with the rows that weren't copied
                 ExperimentDeleteService.get().deleteDataRows(notCopiedObjectIds);
             }
-
-            // TODO: Temp!
-            LOG.info("   " + StringUtilsLabKey.pluralize(new TableSelector(sourceTable, Collections.singleton("DataId")).stream(Integer.class).distinct().count(), "distinct DataId"));
         }
     }
 }