Preocess prefix declarations early on.

For now, we only use the prefixes declared in a schema to resolve the
imports, which can be done after a SchemaDefinition has been completed
converted.

But at some point, we will likely need to have those prefix declarations
while we are still in the process of converting the SchemaDefinition
(e.g. to resolve the values of the `class_uri` or `slot_uri` slots,
which we currently do not support but that we will have to support
soon).

So instead of using the generic ObjectConverter to convert
SchemaDefinition, we use a specialised derived class in which we
proactively look for the `prefixes` slot and process (convert) it
immediately at the beginning of the conversion, before processing any
other slot. This will ensure that all prefix declarations are known to
the ConverterContext when all the other slots are processed in turn.

Author: gouttegd

core/src/main/java/org/incenp/linkml/core/ConverterContext.java

@@ -282,7 +282,7 @@ public void finalizeAssignments() throws LinkMLRuntimeException {
      */
     public static ConverterContext getLinkMLContext() {
         ConverterContext ctx = new ConverterContext();
-        ctx.addConverter(SchemaDefinition.class);
+        ctx.addConverter(SchemaDefinition.class, new SchemaDefinitionConverter());
         ctx.addConverter(TypeDefinition.class);
         ctx.addConverter(EnumDefinition.class);
         ctx.addConverter(SlotDefinition.class);

core/src/main/java/org/incenp/linkml/core/ObjectConverter.java

@@ -63,6 +63,21 @@ public ObjectConverter(Class<?> klass) {
         }
     }
 
+    /**
+     * Gets the specified slot.
+     * <p>
+     * This is mostly intended for the benefit of derived classes, so that they do
+     * not have to call {@link Slot#getSlot(Class, String)} themselves (which would
+     * be a duplication of the job done in the constructor of this class).
+     * 
+     * @param name The name of the slot.
+     * @return The corresponding slot, or <code>null</code> if the class for which
+     *         this object is a converter does not have any slot with that name.
+     */
+    protected Slot getSlot(String name) {
+        return slots.get(name);
+    }
+
     /**
      * Indicates whether this converter converts raw objects into “identifiable
      * objects”.

core/src/main/java/org/incenp/linkml/core/SchemaDefinitionConverter.java

@@ -0,0 +1,61 @@
+/*
+ * LinkML-Java - LinkML library for Java
+ * Copyright © 2026 Damien Goutte-Gattat
+ * 
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package org.incenp.linkml.core;
+
+import java.util.Map;
+
+import org.incenp.linkml.model.SchemaDefinition;
+
+/**
+ * A converter object specifically intended to convert {@link SchemaDefinition}
+ * objects.
+ * <p>
+ * We need a subclass for {@link SchemaDefinition} objects because we want to
+ * ensure that prefix declarations are processed early on when converting the
+ * schema object, so that they can be made available to the converter context as
+ * soon as possible.
+ * <p>
+ * We cannot rely on the fact that the <code>prefixes</code> block is typically
+ * somewhere near the beginning of a LinkML schema, because (1) there is no
+ * guarantee of that (the LinkML spec does not mandate an order for any of the
+ * keys that make up the SchemaDefinition class), and (2) in any case since the
+ * YAML object has been transformed into a Map, we have no guarantee that we
+ * iterate over the keys in the same order than they appear in the source file.
+ */
+public class SchemaDefinitionConverter extends ObjectConverter {
+
+    private final static String PREFIXES_KEY = "prefixes";
+
+    public SchemaDefinitionConverter() {
+        super(SchemaDefinition.class);
+    }
+
+    @Override
+    public void convertTo(Map<String, Object> rawMap, Object dest, ConverterContext ctx) throws LinkMLRuntimeException {
+        // Pre-process the prefixes slot before everything else
+        Object prefixes = rawMap.remove(PREFIXES_KEY);
+        if ( prefixes != null ) {
+            Slot slot = getSlot(PREFIXES_KEY);
+            convertSlot(prefixes, slot, dest, ctx);
+            ctx.addPrefixes(((SchemaDefinition) dest).getPrefixes());
+        }
+
+        super.convertTo(rawMap, dest, ctx);
+    }
+}

core/src/main/java/org/incenp/linkml/core/SchemaDocument.java

@@ -115,10 +115,6 @@ private SchemaDefinition parseSchema(ISchemaSource source, ObjectMapper mapper,
             throw new InvalidSchemaException(INVALID_LINKML, e);
         }
 
-        if ( schema.getPrefixes() != null ) {
-            ctx.addPrefixes(schema.getPrefixes());
-        }
-
         importedSources.add(source);
         if ( schema.getImports() != null ) {
             for ( String importName : schema.getImports() ) {