[bot] Fast-forward for 25.11.0

announcements/src/org/labkey/announcements/AnnouncementModule.java

@@ -31,13 +31,19 @@
 import org.labkey.api.announcements.CommSchema;
 import org.labkey.api.announcements.api.AnnouncementService;
 import org.labkey.api.attachments.AttachmentService;
+import org.labkey.api.attachments.AttachmentType;
 import org.labkey.api.audit.AuditLogService;
 import org.labkey.api.audit.provider.MessageAuditProvider;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
+import org.labkey.api.data.DbSchema;
 import org.labkey.api.data.SqlExecutor;
+import org.labkey.api.data.TableInfo;
 import org.labkey.api.message.digest.DailyMessageDigest;
 import org.labkey.api.message.settings.MessageConfigService;
+import org.labkey.api.migration.DatabaseMigrationConfiguration;
+import org.labkey.api.migration.DatabaseMigrationService;
+import org.labkey.api.migration.DefaultMigrationSchemaHandler;
 import org.labkey.api.module.DefaultModule;
 import org.labkey.api.module.ModuleContext;
 import org.labkey.api.rss.RSSService;
@@ -53,6 +59,7 @@
 import org.labkey.api.view.ViewContext;
 import org.labkey.api.view.WebPartFactory;
 import org.labkey.api.view.WebPartView;
+import org.labkey.api.wiki.WikiService;
 
 import java.util.ArrayList;
 import java.util.Collection;
@@ -165,6 +172,42 @@ public void doStartup(ModuleContext moduleContext)
         {
             fsr.addFactories(new NotificationSettingsWriterFactory(), new NotificationSettingsImporterFactory());
         }
+
+        // AnnouncementModule owns the schema, so it registers the schema handler... even though it's mostly about wiki
+        DatabaseMigrationService.get().registerSchemaHandler(new DefaultMigrationSchemaHandler(CommSchema.getInstance().getSchema())
+        {
+            @Override
+            public void beforeSchema()
+            {
+                new SqlExecutor(getSchema()).execute("ALTER TABLE comm.Pages DROP CONSTRAINT FK_Pages_PageVersions");
+                new SqlExecutor(getSchema()).execute("ALTER TABLE comm.Pages DROP CONSTRAINT FK_Pages_Parent");
+            }
+
+            @Override
+            public List<TableInfo> getTablesToCopy()
+            {
+                List<TableInfo> tablesToCopy = super.getTablesToCopy();
+                tablesToCopy.add(CommSchema.getInstance().getTableInfoPages());
+                tablesToCopy.add(CommSchema.getInstance().getTableInfoPageVersions());
+
+                return tablesToCopy;
+            }
+
+            @Override
+            public void afterSchema(DatabaseMigrationConfiguration configuration, DbSchema sourceSchema, DbSchema targetSchema)
+            {
+                new SqlExecutor(getSchema()).execute("ALTER TABLE comm.Pages ADD CONSTRAINT FK_Pages_PageVersions FOREIGN KEY (PageVersionId) REFERENCES comm.PageVersions (RowId)");
+                new SqlExecutor(getSchema()).execute("ALTER TABLE comm.Pages ADD CONSTRAINT FK_Pages_Parent FOREIGN KEY (Parent) REFERENCES comm.Pages (RowId)");
+            }
+
+            @Override
+            public @NotNull Collection<AttachmentType> getAttachmentTypes()
+            {
+                // It's theoretically possible to deploy Announcement without Wiki, so conditionalize
+                WikiService ws = WikiService.get();
+                return ws != null ? List.of(AnnouncementType.get(), ws.getAttachmentType()) : List.of(AnnouncementType.get());
+            }
+        });
     }
 
 

announcements/src/org/labkey/announcements/model/AnnouncementType.java

@@ -16,6 +16,7 @@
 package org.labkey.announcements.model;
 
 import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.announcements.CommSchema;
 import org.labkey.api.attachments.AttachmentType;
 import org.labkey.api.data.SQLFragment;
@@ -40,8 +41,8 @@ public static AttachmentType get()
     }
 
     @Override
-    public void addWhereSql(SQLFragment sql, String parentColumn, String documentNameColumn)
+    public @Nullable SQLFragment getSelectParentEntityIdsSql()
     {
-        sql.append(parentColumn).append(" IN (SELECT EntityId FROM ").append(CommSchema.getInstance().getTableInfoAnnouncements(), "ann").append(")");
+        return new SQLFragment("SELECT EntityId FROM ").append(CommSchema.getInstance().getTableInfoAnnouncements(), "ann");
     }
 }

api/src/org/labkey/api/ApiModule.java

@@ -31,7 +31,6 @@
 import org.labkey.api.attachments.AttachmentService;
 import org.labkey.api.attachments.ImageServlet;
 import org.labkey.api.attachments.LookAndFeelResourceType;
-import org.labkey.api.attachments.SecureDocumentType;
 import org.labkey.api.audit.query.AbstractAuditDomainKind;
 import org.labkey.api.cache.BlockingCache;
 import org.labkey.api.collections.ArrayListMap;
@@ -222,7 +221,6 @@ protected void init()
         AttachmentService.get().registerAttachmentType(LookAndFeelResourceType.get());
         AttachmentService.get().registerAttachmentType(AuthenticationLogoType.get());
         AttachmentService.get().registerAttachmentType(AvatarType.get());
-        AttachmentService.get().registerAttachmentType(SecureDocumentType.get());
 
         PropertyManager.registerEncryptionMigrationHandler();
         AuthenticationManager.registerEncryptionMigrationHandler();

api/src/org/labkey/api/assay/transform/AnalysisScript.java

@@ -40,13 +40,13 @@ private AnalysisScript(File script, List<String> operations)
 
     private AnalysisScript(File script)
     {
-        try
+        if (!script.exists())
         {
-            _script = FileSystemLike.wrapFile(script.getParentFile(), script);
+            _script = new FileSystemLike.Builder(script).build().getRoot();
         }
-        catch (IOException e)
+        else
         {
-            throw UnexpectedException.wrap(e);
+            _script = FileSystemLike.wrapFile(script);
         }
     }
 

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

@@ -133,6 +133,11 @@ static AttachmentService get()
 
     void registerAttachmentType(AttachmentType type);
 
+    /**
+     * Returns a collection of all registered AttachmentTypes
+     **/
+    Collection<AttachmentType> getAttachmentTypes();
+
     HttpView<?> getAdminView(ActionURL currentUrl);
 
     HttpView<?> getFindAttachmentParentsView();

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

@@ -16,14 +16,17 @@
 package org.labkey.api.attachments;
 
 import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.SQLFragment;
 
 /**
  * Tags {@link Attachment} objects based on their intended use and what they're attached to. Does not
- * necessarily indicate that they are a file of a particular type/format.
+ * indicate that they are a file of a particular type/format.
  */
 public interface AttachmentType
 {
+    SQLFragment NO_ENTITY_IDS = new SQLFragment("SELECT NULL AS EntityId WHERE 1 = 0");
+
     AttachmentType UNKNOWN = new AttachmentType()
     {
         @NotNull
@@ -43,10 +46,29 @@ public void addWhereSql(SQLFragment sql, String parentColumn, String documentNam
     @NotNull String getUniqueName();
 
     /**
-     * Append to the where clause of a query that wants to select attachments of the implementing type
+     * Append to the where clause of a query that wants to select attachments of the implementing type from the
+     * core.Documents table
      * @param sql Implementers MUST append a valid where clause to this SQLFragment
      * @param parentColumn Column identifier for use in where clause. Usually represents 'core.Documents.Parent'
      * @param documentNameColumn Column identifier for use in where clause. Usually represents 'core.Documents.DocumentName'
      */
-    void addWhereSql(SQLFragment sql, String parentColumn, String documentNameColumn);
+    default void addWhereSql(SQLFragment sql, String parentColumn, String documentNameColumn)
+    {
+        SQLFragment selectSql = getSelectParentEntityIdsSql();
+        if (selectSql == null)
+            throw new IllegalStateException("Must override either addWhereSql() or getSelectParentEntityIdsSql()");
+        sql.append(parentColumn).append(" IN (").append(selectSql).append(")");
+    }
+
+    /**
+     * Return a SQLFragment that selects all the EntityIds that might be attachment parents from the table(s) that
+     * provide attachments of this type, without involving the core.Documents table. For example,
+     * {@code SELECT EntityId FROM comm.Announcements}. Return null if this is not-yet-implemented or inappropriate.
+     * For example, some attachments' parents are container IDs. If the method determines that no parents exist, then
+     * return a valid query that selects no rows, for example, {@code NO_ENTITY_IDS}.
+     */
+    default @Nullable SQLFragment getSelectParentEntityIdsSql()
+    {
+        return null;
+    }
 }

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/collections/ArrayListValuedTreeMap.java

@@ -0,0 +1,22 @@
+package org.labkey.api.collections;
+
+import org.apache.commons.collections4.multimap.AbstractListValuedMap;
+
+import java.util.ArrayList;
+import java.util.Comparator;
+import java.util.List;
+import java.util.TreeMap;
+
+public class ArrayListValuedTreeMap<K, V> extends AbstractListValuedMap<K, V>
+{
+    public ArrayListValuedTreeMap(Comparator<? super K> comparator)
+    {
+        super(new TreeMap<>(comparator));
+    }
+
+    @Override
+    protected List<V> createCollection()
+    {
+        return new ArrayList<>();
+    }
+}

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;