From ae259a6ef8dd3a8b209c1c866ee90bf73056181e Mon Sep 17 00:00:00 2001
From: haszi <haszika80@gmail.com>
Date: Mon, 26 Feb 2024 18:16:21 +0100
Subject: [PATCH 1/2] Fix GH-98

Store IDs of non-chunked elements.
Closes #98.
---
 phpdotnet/phd/Index.php        |  3 +++
 phpdotnet/phd/TestIndex.php    |  8 ++++++++
 tests/index/bug_GH-98.phpt     | 37 ++++++++++++++++++++++++++++++++++
 tests/index/data/bug_GH-98.xml | 28 +++++++++++++++++++++++++
 4 files changed, 76 insertions(+)
 create mode 100644 phpdotnet/phd/TestIndex.php
 create mode 100644 tests/index/bug_GH-98.phpt
 create mode 100644 tests/index/data/bug_GH-98.xml

diff --git a/phpdotnet/phd/Index.php b/phpdotnet/phd/Index.php
index e0d119d3..8f991313 100644
--- a/phpdotnet/phd/Index.php
+++ b/phpdotnet/phd/Index.php
@@ -383,6 +383,9 @@ public function format_chunk($open, $name, $attrs, $props) {
                 $this->chunks[] = $id;
                 $this->currentchunk = $id;
                 $this->storeInfo($name, $id, $id);
+            } else {
+                $this->storeInfo($name, $id, $this->currentchunk, false);
+                $this->appendID();
             }
             return false;
         }
diff --git a/phpdotnet/phd/TestIndex.php b/phpdotnet/phd/TestIndex.php
new file mode 100644
index 00000000..f33a9c87
--- /dev/null
+++ b/phpdotnet/phd/TestIndex.php
@@ -0,0 +1,8 @@
+<?php
+namespace phpdotnet\phd;
+
+class TestIndex extends Index {
+    public function getIndexes(): array {
+        return $this->indexes;
+    }
+}
diff --git a/tests/index/bug_GH-98.phpt b/tests/index/bug_GH-98.phpt
new file mode 100644
index 00000000..ef93dead
--- /dev/null
+++ b/tests/index/bug_GH-98.phpt
@@ -0,0 +1,37 @@
+--TEST--
+Bug GH-98 - Non-chunked section is not linked
+--FILE--
+<?php
+namespace phpdotnet\phd;
+
+require_once __DIR__ . "/../setup.php";
+
+$xml_file = __DIR__ . "/data/bug_GH-98.xml";
+
+Config::init([
+    "index"    => true,
+    "xml_file" => $xml_file,
+]);
+
+$index = new TestIndex;
+$render = new TestRender(new Reader, new Config, null, $index);
+
+$render->run();
+
+$indexes = array_keys($index->getIndexes());
+
+echo "Indexes stored:\n";
+
+var_dump(in_array("non-chunked.element.id", $indexes));
+var_dump(in_array("another.non-chunked.element.id", $indexes));
+var_dump(in_array("chunked.element.id", $indexes));
+var_dump(in_array("another.chunked.element.id", $indexes));
+var_dump(in_array("bug-GH-98", $indexes));
+?>
+--EXPECT--
+Indexes stored:
+bool(true)
+bool(true)
+bool(true)
+bool(true)
+bool(true)
diff --git a/tests/index/data/bug_GH-98.xml b/tests/index/data/bug_GH-98.xml
new file mode 100644
index 00000000..dd1dba21
--- /dev/null
+++ b/tests/index/data/bug_GH-98.xml
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="utf-8"?>
+<chapter xml:id="bug-GH-98">
+
+ <sect1 xmlns="http://docbook.org/ns/docbook" annotations="chunk:false" xml:id="non-chunked.element.id">
+  <para>
+   Content to ensure this elements is indexed
+  </para>
+ </sect1>
+
+ <section xmlns="http://docbook.org/ns/docbook" annotations="chunk:false" xml:id="another.non-chunked.element.id">
+  <para>
+   Content to ensure this elements is indexed too
+  </para>
+ </section>
+
+ <sect1 xmlns="http://docbook.org/ns/docbook" xml:id="chunked.element.id">
+  <para>
+   Content to ensure this elements is indexed as well
+  </para>
+ </sect1>
+
+ <section xmlns="http://docbook.org/ns/docbook" xml:id="another.chunked.element.id">
+  <para>
+   Content to ensure this elements is also indexed
+  </para>
+ </section>
+
+</chapter>

From 3c88dcd14f65fcbf290ed3b190dce0704d095e38 Mon Sep 17 00:00:00 2001
From: haszi <haszika80@gmail.com>
Date: Mon, 26 Feb 2024 20:30:18 +0100
Subject: [PATCH 2/2] Force index and use parsed indexes

---
 phpdotnet/phd/Index.php     | 2 +-
 phpdotnet/phd/TestIndex.php | 4 ++--
 tests/index/bug_GH-98.phpt  | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/phpdotnet/phd/Index.php b/phpdotnet/phd/Index.php
index 8f991313..24be8ab6 100644
--- a/phpdotnet/phd/Index.php
+++ b/phpdotnet/phd/Index.php
@@ -89,7 +89,7 @@ class Index extends Format
     private $currentid;
     private $chunks    = array();
     private $isChunk   = array();
-    private $nfo       = array();
+    protected $nfo       = array();
     private $isSectionChunk = array();
     private $log = '';
     private $previousId = "";
diff --git a/phpdotnet/phd/TestIndex.php b/phpdotnet/phd/TestIndex.php
index f33a9c87..d5586d19 100644
--- a/phpdotnet/phd/TestIndex.php
+++ b/phpdotnet/phd/TestIndex.php
@@ -2,7 +2,7 @@
 namespace phpdotnet\phd;
 
 class TestIndex extends Index {
-    public function getIndexes(): array {
-        return $this->indexes;
+    public function getNfo(): array {
+        return $this->nfo;
     }
 }
diff --git a/tests/index/bug_GH-98.phpt b/tests/index/bug_GH-98.phpt
index ef93dead..dcc9e434 100644
--- a/tests/index/bug_GH-98.phpt
+++ b/tests/index/bug_GH-98.phpt
@@ -9,7 +9,7 @@ require_once __DIR__ . "/../setup.php";
 $xml_file = __DIR__ . "/data/bug_GH-98.xml";
 
 Config::init([
-    "index"    => true,
+    "force_index"    => true,
     "xml_file" => $xml_file,
 ]);
 
@@ -18,7 +18,7 @@ $render = new TestRender(new Reader, new Config, null, $index);
 
 $render->run();
 
-$indexes = array_keys($index->getIndexes());
+$indexes = array_keys($index->getNfo());
 
 echo "Indexes stored:\n";