From 6dabff149dd9cdfc236b37ed31e939b52924db88 Mon Sep 17 00:00:00 2001
From: n-peugnet <n.peugnet@free.fr>
Date: Thu, 28 Nov 2019 18:55:41 +0100
Subject: [PATCH 01/13] feat: first add of index with HashIndex

---
 src/JamesMoss/Flywheel/Config.php             |   5 +-
 src/JamesMoss/Flywheel/Index/HashIndex.php    |  52 ++++++
 .../Flywheel/Index/IndexInterface.php         |  46 ++++++
 src/JamesMoss/Flywheel/Index/StoredIndex.php  | 154 ++++++++++++++++++
 src/JamesMoss/Flywheel/Repository.php         |  53 ++++--
 .../Flywheel/Index/HashIndexTest.php          | 124 ++++++++++++++
 test/JamesMoss/Flywheel/TestBase.php          |  10 +-
 7 files changed, 431 insertions(+), 13 deletions(-)
 create mode 100644 src/JamesMoss/Flywheel/Index/HashIndex.php
 create mode 100644 src/JamesMoss/Flywheel/Index/IndexInterface.php
 create mode 100644 src/JamesMoss/Flywheel/Index/StoredIndex.php
 create mode 100644 test/JamesMoss/Flywheel/Index/HashIndexTest.php

diff --git a/src/JamesMoss/Flywheel/Config.php b/src/JamesMoss/Flywheel/Config.php
index 333686d..2f01f21 100644
--- a/src/JamesMoss/Flywheel/Config.php
+++ b/src/JamesMoss/Flywheel/Config.php
@@ -48,12 +48,13 @@ public function getPath()
      * Gets a specific option from the config
      *
      * @param string $name The name of the option to return.
+     * @param mixed $default The default value to use.
      *
      * @return mixed The value of the option if it exists or null if it doesnt.
      */
-    public function getOption($name)
+    public function getOption($name, $default = null)
     {
-        return isset($this->options[$name]) ? $this->options[$name] : null;
+        return isset($this->options[$name]) ? $this->options[$name] : $default;
     }
 
     public function hasAPC()
diff --git a/src/JamesMoss/Flywheel/Index/HashIndex.php b/src/JamesMoss/Flywheel/Index/HashIndex.php
new file mode 100644
index 0000000..d970301
--- /dev/null
+++ b/src/JamesMoss/Flywheel/Index/HashIndex.php
@@ -0,0 +1,52 @@
+<?php
+
+namespace JamesMoss\Flywheel\Index;
+
+use JamesMoss\Flywheel\Index\StoredIndex;
+use stdClass;
+
+class HashIndex extends StoredIndex
+{
+
+    /**
+     * @inheritdoc
+     */
+    protected function getEntries($value)
+    {
+        if (!isset($this->data->$value)) {
+            return array();
+        }
+        return array_keys(get_object_vars($this->data->$value));
+    }
+
+    /**
+     * @inheritdoc
+     */
+    protected function addEntry($id, $value)
+    {
+        if (!isset($this->data->$value)) {
+            $this->data->$value = new stdClass();
+        }
+        $this->data->$value->$id = 1;
+    }
+
+    /**
+     * @inheritdoc
+     */
+    protected function removeEntry($id, $value)
+    {
+        if(!isset($this->data->$value)) {
+            return;
+        }
+        unset($this->data->$value->$id);
+        if (count(get_object_vars($this->data->$value)) === 0) {
+            unset($this->data->$value);
+        }
+    }
+
+    protected function updateEntry($id, $new, $old)
+    {
+        $this->removeEntry($id, $old);
+        $this->addEntry($id, $new);
+    }
+}
diff --git a/src/JamesMoss/Flywheel/Index/IndexInterface.php b/src/JamesMoss/Flywheel/Index/IndexInterface.php
new file mode 100644
index 0000000..52690dd
--- /dev/null
+++ b/src/JamesMoss/Flywheel/Index/IndexInterface.php
@@ -0,0 +1,46 @@
+<?php
+
+namespace JamesMoss\Flywheel\Index;
+
+interface IndexInterface
+{
+    /**
+     * Get documents from the index.
+     *
+     * @param mixed $value the value we are looking for.
+     *
+     * @return array<int,string> a list of documents ids.
+     */
+    public function get($value);
+
+    /**
+     * Add a document to the index.
+     *
+     * @param string $id the id of this document.
+     * @param mixed $value the value of this document for the indexed field.
+     *
+     * @return void
+     */
+    public function add($id, $value);
+
+    /**
+     * Remove a document from the index.
+     *
+     * @param string $id the id of this document.
+     * @param mixed $value the value of this document for the indexed field.
+     *
+     * @return void
+     */
+    public function remove($id, $value);
+
+    /**
+     * Update a document in the index.
+     *
+     * @param string $id the id of this document.
+     * @param mixed $new the new value of this document for the indexed field.
+     * @param mixed $old the old value of this document for the indexed field.
+     *
+     * @return void
+     */
+    public function update($id, $new, $old);
+}
diff --git a/src/JamesMoss/Flywheel/Index/StoredIndex.php b/src/JamesMoss/Flywheel/Index/StoredIndex.php
new file mode 100644
index 0000000..3214889
--- /dev/null
+++ b/src/JamesMoss/Flywheel/Index/StoredIndex.php
@@ -0,0 +1,154 @@
+<?php
+
+namespace JamesMoss\Flywheel\Index;
+
+use JamesMoss\Flywheel\Index\IndexInterface;
+use JamesMoss\Flywheel\Formatter\FormatInterface;
+use JamesMoss\Flywheel\Repository;
+use stdClass;
+
+abstract class StoredIndex implements IndexInterface
+{
+    /** @var mixed $data                content of the index */
+    protected $data = null;
+
+    /** @var string $field              name of the indexed field */
+    protected $field;
+
+    /** @var FormatInterface $formatter used to store data */
+    protected $formatter;
+
+    /** @var Repository $repository     repository of the index */
+    protected $repository;
+
+    /** @var string $path               where the data is stored */
+    protected $path;
+
+    /**
+     * Constructor
+     *
+     * @param string $field the field to index.
+     * @param string $path the directory where to store the index file.
+     * @param FormatInterface $formatter the formatter used to store the data.
+     * @param Repository $repository the repository of this index.
+     */
+    public function __construct($field, $path, $formatter, $repository) {
+        $this->field = $field;
+        $this->formatter = $formatter;
+        $this->repository = $repository;
+        $this->path = $path . DIRECTORY_SEPARATOR . "$field." . $formatter->getFileExtension();
+    }
+
+    /**
+     * @inheritdoc
+     */
+    public function get($value)
+    {
+        $this->needsData();
+        return $this->getEntries($value);
+    }
+
+    /**
+     * @inheritdoc
+     */
+    public function add($id, $value)
+    {
+        $this->needsData();
+        $this->addEntry($id, $value);
+        $this->flush();
+    }
+
+    /**
+     * @inheritdoc
+     */
+    public function remove($id, $value)
+    {
+        $this->needsData();
+        $this->removeEntry($id, $value);
+        $this->flush();
+    }
+
+    /**
+     * @inheritdoc
+     */
+    public function update($id, $new, $old)
+    {
+        if ($new === $old) {
+            return;
+        }
+        $this->needsData();
+        $this->updateEntry($id, $new, $old);
+        $this->flush();
+    }
+
+    protected function needsData()
+    {
+        if (isset($this->data)) {
+            return;
+        }
+        $this->data = new stdClass();
+        if (file_exists($this->path)) {
+            $fp       = fopen($this->path, 'r');
+            $contents = fread($fp, filesize($this->path));
+            fclose($fp);
+            $this->data = $this->formatter->decode($contents);
+        } else {
+            $field = $this->field;
+            foreach ($this->repository->findAll() as $doc) {
+                if (empty($doc->$field)) {
+                    continue;
+                }
+                $this->addEntry($doc->getId(), $doc->$field);
+            }
+            $this->flush();
+        }
+    }
+
+    protected function flush()
+    {
+        $contents = $this->formatter->encode(get_object_vars($this->data));
+        $fp = fopen($this->path, 'w');
+        if(!flock($fp, LOCK_EX)) {
+            return false;
+        }
+        $result = fwrite($fp, $contents);
+        flock($fp, LOCK_UN);
+        fclose($fp);
+
+        return $result !== false;
+    }
+
+    /**
+     * Get entries from the index
+     *
+     * @param string $value
+     *
+     * @return array<int,string> array of ids
+     */
+    abstract protected function getEntries($value);
+
+    /**
+     * Adds an entry in the index
+     *
+     * @param string $id
+     * @param string $value
+     */
+    abstract protected function addEntry($id, $value);
+
+    /**
+     * Removes an entry from the index
+     *
+     * @param string $id
+     * @param string $value
+     */
+    abstract protected function removeEntry($id, $value);
+
+    /**
+     * Removes an entry from the index
+     *
+     * @param string $id
+     * @param string $value
+     */
+    abstract protected function updateEntry($id, $new, $old);
+
+}
diff --git a/src/JamesMoss/Flywheel/Repository.php b/src/JamesMoss/Flywheel/Repository.php
index c4463d4..0287d3a 100644
--- a/src/JamesMoss/Flywheel/Repository.php
+++ b/src/JamesMoss/Flywheel/Repository.php
@@ -2,6 +2,9 @@
 
 namespace JamesMoss\Flywheel;
 
+use JamesMoss\Flywheel\Formatter\JSON;
+use JamesMoss\Flywheel\Index\IndexInterface;
+
 /**
  * Repository
  *
@@ -15,6 +18,9 @@ class Repository
     protected $formatter;
     protected $queryClass;
     protected $documentClass;
+    protected $indexDir;
+    /** @var array<string,IndexInterface> $indexes */
+    protected $indexes;
 
     /**
      * Constructor
@@ -30,17 +36,28 @@ public function __construct($name, Config $config)
         $this->formatter     = $config->getOption('formatter');
         $this->queryClass    = $config->getOption('query_class');
         $this->documentClass = $config->getOption('document_class');
+        $this->indexes       = $config->getOption('indexes', array());
+        $this->indexDir      = $this->path . DIRECTORY_SEPARATOR . 'index';
+        array_walk($this->indexes, function(&$class, $field) {
+            $class = new $class($field, $this->indexDir, new JSON(), $this);
+        });
 
         // Ensure the repo name is valid
         $this->validateName($this->name);
+        $this->ensureDirectory($this->path);
+        $this->ensureDirectory($this->indexDir);
+    }
 
-        // Ensure directory exists and we can write there
-        if (!is_dir($this->path)) {
-            if (!@mkdir($this->path, 0777, true)) {
-                throw new \RuntimeException(sprintf('`%s` doesn\'t exist and can\'t be created.', $this->path));
+    /**
+     * Ensure directory exists and we can write there
+     */
+    protected function ensureDirectory($path) {
+        if (!is_dir($path)) {
+            if (!@mkdir($path, 0777, true)) {
+                throw new \RuntimeException(sprintf('`%s` doesn\'t exist and can\'t be created.', $path));
             }
-        } else if (!is_writable($this->path)) {
-            throw new \RuntimeException(sprintf('`%s` is not writable.', $this->path));
+        } else if (!is_writable($path)) {
+            throw new \RuntimeException(sprintf('`%s` is not writable.', $path));
         }
     }
 
@@ -79,7 +96,7 @@ public function query()
     /**
      * Returns all the documents within this repo.
      *
-     * @return array An array of Documents.
+     * @return array<int,Document> An array of Documents.
      */
     public function findAll()
     {
@@ -141,7 +158,7 @@ public function findById($id)
      *
      * @param Document $document The document to store
      *
-     * @return bool True if stored, otherwise false
+     * @return string|false True if stored, otherwise false
      */
     public function store(DocumentInterface $document)
     {
@@ -155,6 +172,18 @@ public function store(DocumentInterface $document)
         if (!$this->validateId($id)) {
             throw new \Exception(sprintf('`%s` is not a valid document ID.', $id));
         }
+        $previous = $this->findById($id);
+        foreach ($this->indexes as $field => $index) {
+            $setPrev = $previous ? isset($previous->$field) : false;
+            $setActu = isset($document->$field);
+            if (!$setPrev && $setActu) {
+                $index->add($document->getId(), $document->$field);
+            } elseif ($setPrev && !$setActu) {
+                $index->remove($document->getId(), $previous->$field);
+            } elseif ($setPrev && $setActu) {
+                $index->update($document->getId(), $document->$field, $previous->$field);
+            }
+        }
 
         $path = $this->getPathForDocument($id);
         $data = get_object_vars($document);
@@ -189,9 +218,13 @@ public function update(DocumentInterface $document)
 
         // If the ID has changed we need to delete the old document.
         if($document->getId() !== $document->getInitialId()) {
-            if(file_exists($oldPath)) {
-                unlink($oldPath);
+            $previous = $this->findById($document->getInitialId());
+            foreach ($this->indexes as $field => $index) {
+                if(isset($previous->$field)) {
+                    $index->remove($previous->getId(), $previous->$field);
+                }
             }
+            unlink($oldPath);
         }
 
         return $this->store($document);
diff --git a/test/JamesMoss/Flywheel/Index/HashIndexTest.php b/test/JamesMoss/Flywheel/Index/HashIndexTest.php
new file mode 100644
index 0000000..eea60ae
--- /dev/null
+++ b/test/JamesMoss/Flywheel/Index/HashIndexTest.php
@@ -0,0 +1,124 @@
+<?php
+
+namespace JamesMoss\Flywheel\Index;
+
+use JamesMoss\Flywheel\Config;
+use JamesMoss\Flywheel\Document;
+use JamesMoss\Flywheel\Formatter\JSON;
+use JamesMoss\Flywheel\Index\HashIndex;
+use JamesMoss\Flywheel\Repository;
+use JamesMoss\Flywheel\TestBase;
+
+class HashIndexTest extends TestBase
+{
+    const REPO_DIR = '/tmp/flywheel';
+    const REPO_NAME = '_index_test';
+
+    /** @var Repository $repo */
+    private $repo;
+
+    /** @var HashIndex $index */
+    private $index;
+
+    protected function setUp()
+    {
+        parent::setUp();
+        if (!is_dir(self::REPO_DIR)) {
+            mkdir(self::REPO_DIR);
+        }
+        $config = new Config(self::REPO_DIR, array(
+            'indexes' => array(
+                'col1' => "JamesMoss\Flywheel\Index\HashIndex",
+            )
+        ));
+        $this->repo = new Repository(self::REPO_NAME, $config);
+        $this->index = new HashIndex('col1', $this->repo->getPath() . DIRECTORY_SEPARATOR . 'index', new JSON(), $this->repo);
+    }
+
+    protected function tearDown()
+    {
+        parent::tearDown();
+        $this->recurseRmdir(self::REPO_DIR . DIRECTORY_SEPARATOR . self::REPO_NAME);
+    }
+
+    public function testAddEntry()
+    {
+        $id = 'testdoc123';
+        $this->index->add($id, '123');
+        $this->assertEquals(array($id), $this->index->get('123'));
+    }
+
+    public function testRemoveEntry()
+    {
+        $id = 'testdoc123';
+        $this->index->add($id, '123');
+        $this->assertEquals(array($id), $this->index->get('123'));
+        $this->index->remove($id, '123');
+        $this->assertEquals(array(), $this->index->get('123'));
+    }
+
+    public function testUpdateEntry()
+    {
+        $id = 'testdoc123';
+        $this->index->add($id, '123');
+        $this->assertEquals(array($id), $this->index->get('123'));
+        $this->index->update($id, '456', '123');
+        $this->assertEquals(array(), $this->index->get('123'));
+        $this->assertEquals(array($id), $this->index->get('456'));
+    }
+
+    public function testStoreDocument()
+    {
+        $doc = new Document(array(
+            'col1' => '123',
+        ));
+        $id = 'testdoc123';
+        $doc->setId($id);
+        $this->assertEquals($id, $this->repo->store($doc));
+        $this->assertEquals(array($id), $this->index->get('123'));
+    }
+
+    public function testReStoreDocumentUpdate()
+    {
+        $doc = new Document(array(
+            'col1' => '123',
+        ));
+        $id = 'testdoc123';
+        $doc->setId($id);
+        $this->assertEquals($id, $this->repo->store($doc));
+        $doc->col1 = '456';
+        $this->assertEquals($id, $this->repo->store($doc));
+        $this->assertEquals(array(), $this->index->get('123'));
+        $this->assertEquals(array($id), $this->index->get('456'));
+    }
+
+    public function testReStoreDocumentRemove()
+    {
+        $doc = new Document(array(
+            'col1' => '123',
+        ));
+        $id = 'testdoc123';
+        $doc->setId($id);
+        $this->assertEquals($id, $this->repo->store($doc));
+        unset($doc->col1);
+        $this->assertEquals($id, $this->repo->store($doc));
+        $this->assertEquals(array(), $this->index->get('123'));
+    }
+
+    public function testUpdateDocument()
+    {
+        $doc = new Document(array(
+            'col1' => '123',
+        ));
+        $id = 'testdoc123';
+        $doc->setId($id);
+        $this->assertEquals($id, $this->repo->store($doc));
+        $id = 'testdoc456';
+        $doc->setId($id);
+        $doc->col1 = '456';
+        $this->assertEquals($id, $this->repo->update($doc));
+        $this->assertEquals(array(), $this->index->get('123'));
+        $this->assertEquals(array($id), $this->index->get('456'));
+    }
+
+}
\ No newline at end of file
diff --git a/test/JamesMoss/Flywheel/TestBase.php b/test/JamesMoss/Flywheel/TestBase.php
index c4bb75b..82f4619 100644
--- a/test/JamesMoss/Flywheel/TestBase.php
+++ b/test/JamesMoss/Flywheel/TestBase.php
@@ -7,5 +7,13 @@ class TestBase extends \PHPUnit\Framework\TestCase
     public function normalizeLineendings($content)
     {
         return str_replace("\r\n", "\n", $content);
-    }    
+    }
+
+    public function recurseRmdir($dir) {
+        $files = array_diff(scandir($dir), array('.','..'));
+        foreach ($files as $file) {
+          (is_dir("$dir/$file")) ? $this->recurseRmdir("$dir/$file") : unlink("$dir/$file");
+        }
+        return rmdir($dir);
+    }
 }
\ No newline at end of file

From 5c49aadbfe389e057c81994c98bb48f630d34959 Mon Sep 17 00:00:00 2001
From: n-peugnet <n.peugnet@free.fr>
Date: Fri, 29 Nov 2019 14:04:33 +0100
Subject: [PATCH 02/13] feat: working query executor on fullindex query

---
 src/JamesMoss/Flywheel/Index/HashIndex.php    |  27 +-
 .../Flywheel/Index/IndexInterface.php         |  12 +-
 src/JamesMoss/Flywheel/Index/StoredIndex.php  |  38 ++-
 src/JamesMoss/Flywheel/Predicate.php          |   4 +-
 src/JamesMoss/Flywheel/QueryExecuter.php      |  85 +++++-
 src/JamesMoss/Flywheel/Repository.php         |  45 ++-
 .../Flywheel/Index/HashIndexTest.php          | 101 ++++++-
 test/JamesMoss/Flywheel/QueryExecuterTest.php |  21 +-
 test/JamesMoss/Flywheel/RepositoryTest.php    |  54 +++-
 test/JamesMoss/Flywheel/TestBase.php          |  41 ++-
 .../querytest/countries/.indexes/region.json  | 264 ++++++++++++++++++
 11 files changed, 640 insertions(+), 52 deletions(-)
 create mode 100644 test/JamesMoss/Flywheel/fixtures/datastore/querytest/countries/.indexes/region.json

diff --git a/src/JamesMoss/Flywheel/Index/HashIndex.php b/src/JamesMoss/Flywheel/Index/HashIndex.php
index d970301..9f73435 100644
--- a/src/JamesMoss/Flywheel/Index/HashIndex.php
+++ b/src/JamesMoss/Flywheel/Index/HashIndex.php
@@ -7,16 +7,34 @@
 
 class HashIndex extends StoredIndex
 {
+    protected static $operators = array(
+        '==', '===', '!=', '!=='
+    );
 
     /**
      * @inheritdoc
      */
-    protected function getEntries($value)
+    public function isOperatorCompatible($operator)
+    {
+        return in_array($operator, self::$operators);
+    }
+
+    /**
+     * @inheritdoc
+     */
+    protected function getEntries($value, $operator)
     {
         if (!isset($this->data->$value)) {
             return array();
         }
-        return array_keys(get_object_vars($this->data->$value));
+        $ids = array_keys(get_object_vars($this->data->$value));
+        switch ($operator) {
+            case '==':
+            case '===': return $ids;
+            case '!=':
+            case '!==': return array_diff(get_object_vars($this->data), $ids);
+            default: throw new \InvalidArgumentException('Incompatible operator `'.$operator.'`.');
+        }
     }
 
     /**
@@ -35,7 +53,7 @@ protected function addEntry($id, $value)
      */
     protected function removeEntry($id, $value)
     {
-        if(!isset($this->data->$value)) {
+        if (!isset($this->data->$value)) {
             return;
         }
         unset($this->data->$value->$id);
@@ -44,6 +62,9 @@ protected function removeEntry($id, $value)
         }
     }
 
+    /**
+     * @inheritdoc
+     */
     protected function updateEntry($id, $new, $old)
     {
         $this->removeEntry($id, $old);
diff --git a/src/JamesMoss/Flywheel/Index/IndexInterface.php b/src/JamesMoss/Flywheel/Index/IndexInterface.php
index 52690dd..7481d78 100644
--- a/src/JamesMoss/Flywheel/Index/IndexInterface.php
+++ b/src/JamesMoss/Flywheel/Index/IndexInterface.php
@@ -4,14 +4,24 @@
 
 interface IndexInterface
 {
+    /**
+     * Checks if the given operator is compatible with this index.
+     *
+     * @param string $operator the operator to check.
+     *
+     * @return bool true if it is compatible.
+     */
+    public function isOperatorCompatible($operator);
+
     /**
      * Get documents from the index.
      *
      * @param mixed $value the value we are looking for.
+     * @param string $operator the operator used for comparision.
      *
      * @return array<int,string> a list of documents ids.
      */
-    public function get($value);
+    public function get($value, $operator);
 
     /**
      * Add a document to the index.
diff --git a/src/JamesMoss/Flywheel/Index/StoredIndex.php b/src/JamesMoss/Flywheel/Index/StoredIndex.php
index 3214889..e82312f 100644
--- a/src/JamesMoss/Flywheel/Index/StoredIndex.php
+++ b/src/JamesMoss/Flywheel/Index/StoredIndex.php
@@ -4,6 +4,8 @@
 
 use JamesMoss\Flywheel\Index\IndexInterface;
 use JamesMoss\Flywheel\Formatter\FormatInterface;
+use JamesMoss\Flywheel\Predicate;
+use JamesMoss\Flywheel\QueryExecuter;
 use JamesMoss\Flywheel\Repository;
 use stdClass;
 
@@ -32,7 +34,8 @@ abstract class StoredIndex implements IndexInterface
      * @param FormatInterface $formatter the formatter used to store the data.
      * @param Repository $repository the repository of this index.
      */
-    public function __construct($field, $path, $formatter, $repository) {
+    public function __construct($field, $path, $formatter, $repository)
+    {
         $this->field = $field;
         $this->formatter = $formatter;
         $this->repository = $repository;
@@ -42,10 +45,15 @@ public function __construct($field, $path, $formatter, $repository) {
     /**
      * @inheritdoc
      */
-    public function get($value)
+    abstract public function isOperatorCompatible($operator);
+
+    /**
+     * @inheritdoc
+     */
+    public function get($value, $operator)
     {
         $this->needsData();
-        return $this->getEntries($value);
+        return $this->getEntries($value, $operator);
     }
 
     /**
@@ -81,6 +89,11 @@ public function update($id, $new, $old)
         $this->flush();
     }
 
+    /**
+     * Lazyloading data initializer.
+     *
+     * @return void
+     */
     protected function needsData()
     {
         if (isset($this->data)) {
@@ -94,21 +107,30 @@ protected function needsData()
             $this->data = $this->formatter->decode($contents);
         } else {
             $field = $this->field;
+            $predicate = new Predicate();
+            $qe = new QueryExecuter($this->repository, $predicate->where($field, '=='), array(), array());
             foreach ($this->repository->findAll() as $doc) {
-                if (empty($doc->$field)) {
+                $docVal = $qe->getFieldValue($doc, $field, $found);
+        
+                if (!$found) {
                     continue;
                 }
-                $this->addEntry($doc->getId(), $doc->$field);
+                $this->addEntry($doc->getId(), $docVal);
             }
             $this->flush();
         }
     }
 
+    /**
+     * Write back the data on the filesystem.
+     *
+     * @return bool succeded.
+     */
     protected function flush()
     {
         $contents = $this->formatter->encode(get_object_vars($this->data));
         $fp = fopen($this->path, 'w');
-        if(!flock($fp, LOCK_EX)) {
+        if (!flock($fp, LOCK_EX)) {
             return false;
         }
         $result = fwrite($fp, $contents);
@@ -122,10 +144,11 @@ protected function flush()
      * Get entries from the index
      *
      * @param string $value
+     * @param string $operator
      *
      * @return array<int,string> array of ids
      */
-    abstract protected function getEntries($value);
+    abstract protected function getEntries($value, $operator);
 
     /**
      * Adds an entry in the index
@@ -150,5 +173,4 @@ abstract protected function removeEntry($id, $value);
      * @param string $value
      */
     abstract protected function updateEntry($id, $new, $old);
-
 }
diff --git a/src/JamesMoss/Flywheel/Predicate.php b/src/JamesMoss/Flywheel/Predicate.php
index 7efe0ec..8d75d4c 100644
--- a/src/JamesMoss/Flywheel/Predicate.php
+++ b/src/JamesMoss/Flywheel/Predicate.php
@@ -14,7 +14,7 @@ class Predicate
     const LOGICAL_OR = 'or';
 
     protected $predicates = array();
-    protected $operators = array(
+    protected static $operators = array(
         '>', '>=', '<', '<=', '==', '===', '!=', '!==', 'IN',
     );
 
@@ -63,7 +63,7 @@ protected function addPredicate($type, $field, $operator = null, $value = null)
             throw new \InvalidArgumentException('Field name cannot be empty.');
         }
 
-        if (!in_array($operator, $this->operators)) {
+        if (!in_array($operator, self::$operators)) {
             throw new \InvalidArgumentException('Unknown operator `'.$operator.'`.');
         }
 
diff --git a/src/JamesMoss/Flywheel/QueryExecuter.php b/src/JamesMoss/Flywheel/QueryExecuter.php
index 9d9e296..d3628f5 100644
--- a/src/JamesMoss/Flywheel/QueryExecuter.php
+++ b/src/JamesMoss/Flywheel/QueryExecuter.php
@@ -14,6 +14,7 @@ class QueryExecuter
     protected $predicate;
     protected $limit;
     protected $orderBy;
+    protected $indexes;
 
     /**
      * Constructor
@@ -29,6 +30,7 @@ public function __construct(Repository $repo, Predicate $pred, array $limit, arr
         $this->predicate = $pred;
         $this->limit = $limit;
         $this->orderBy = $orderBy;
+        $this->indexes = $repo->getIndexes();
     }
 
     /**
@@ -38,10 +40,17 @@ public function __construct(Repository $repo, Predicate $pred, array $limit, arr
      */
     public function run()
     {
-        $documents = $this->repo->findAll();
-
+        /** @var array<int,Document> $documents */
+        $documents;
         if ($predicates = $this->predicate->getAll()) {
-            $documents = $this->filter($documents, $predicates);
+            if ($this->isFullIndex($predicates)) {
+                $documents = $this->findByIndex($predicates);
+            } else {
+                $documents = $this->repo->findAll();
+                $documents = $this->filter($documents, $predicates);
+            }
+        } else {
+            $documents = $this->repo->findAll();
         }
 
         if ($this->orderBy) {
@@ -114,6 +123,32 @@ public function matchDocument($doc, $field, $operator, $value)
         return false;
     }
 
+    /**
+     * Checks if the query can be executed with indexes only.
+     *
+     * @param array<int,array> $predicates the array of predicates.
+     *
+     * @return bool true if it can.
+     */
+    protected function isFullIndex($predicates)
+    {
+        foreach ($predicates as $p) {
+            list($type, $field, $operator) = $p;
+            if (!isset($this->indexes[$field]) || !$this->indexes[$field]->isOperatorCompatible($operator)) {
+                return false;
+            }
+        }
+        return true;
+    }
+
+    /**
+     * Filters an array of documents by the predicates.
+     *
+     * @param array<int,Document> $documents the array to filter.
+     * @param array<int,array> $predicates the array of predicates.
+     *
+     * @return array<int,Document> the filtered array of documents.
+     */
     protected function filter($documents, $predicates)
     {
         $result = array();
@@ -162,6 +197,50 @@ protected function filter($documents, $predicates)
         return $result;
     }
 
+    /**
+     * Find an array of documents from the predicates using the indexes.
+     *
+     * @param array<int,array> $predicates the array of predicates.
+     *
+     * @return array<int,Document> the filtered array of documents.
+     */
+    protected function findByIndex($predicates) {
+        $result = array();
+        $ids = array();
+
+        $andPredicates = array_filter($predicates, function($pred) {
+            return $pred[0] !== Predicate::LOGICAL_OR;
+        });
+
+        $orPredicates = array_filter($predicates, function($pred) {
+            return $pred[0] === Predicate::LOGICAL_OR;
+        });
+
+        foreach($andPredicates as $predicate) {
+            if (is_array($predicate[1])) {
+                $ids = $this->findByIndex($predicate[1]);
+            } else {
+                list($type, $field, $operator, $value) = $predicate;
+                $ids = $this->indexes[$field]->get($value, $operator);
+            }
+
+            $result = $ids;
+        }
+
+        foreach($orPredicates as $predicate) {
+            if (is_array($predicate[1])) {
+                $ids = $this->findByIndex($predicate[1]);
+            } else {
+                list($type, $field, $operator, $value) = $predicate;
+                $ids = $this->indexes['$field']->get($value, $operator);
+            }
+
+            $result = array_unique(array_merge($result, $ids), SORT_REGULAR);
+        }
+
+        return $this->repo->findByIds($result);
+    }
+
     /**
      * Sorts an array of documents by multiple fields if needed.
      *
diff --git a/src/JamesMoss/Flywheel/Repository.php b/src/JamesMoss/Flywheel/Repository.php
index 0287d3a..5982b1e 100644
--- a/src/JamesMoss/Flywheel/Repository.php
+++ b/src/JamesMoss/Flywheel/Repository.php
@@ -37,7 +37,7 @@ public function __construct($name, Config $config)
         $this->queryClass    = $config->getOption('query_class');
         $this->documentClass = $config->getOption('document_class');
         $this->indexes       = $config->getOption('indexes', array());
-        $this->indexDir      = $this->path . DIRECTORY_SEPARATOR . 'index';
+        $this->indexDir      = $this->path . DIRECTORY_SEPARATOR . '.indexes';
         array_walk($this->indexes, function(&$class, $field) {
             $class = new $class($field, $this->indexDir, new JSON(), $this);
         });
@@ -81,6 +81,16 @@ public function getPath()
         return $this->path;
     }
 
+    /**
+     * Returns the list of indexes of this repository.
+     *
+     * @return array<string,IndexInterface> The list of indexes.
+     */
+    public function getIndexes()
+    {
+        return $this->indexes;
+    }
+
     /**
      * A factory method that initialises and returns an instance of a Query object.
      *
@@ -127,7 +137,7 @@ public function findAll()
      *
      * @param  string $id The ID of the document to find
      *
-     * @return Document|boolean  The document if it exists, false if not.
+     * @return Document|false The document if it exists, false if not.
      */
     public function findById($id)
     {
@@ -153,6 +163,37 @@ public function findById($id)
         return $doc;
     }
 
+    /**
+     * Returns a list of documents based on their ID.
+     *
+     * @param array<int,string> $ids The IDs array of document to find.
+     *
+     * @return array<int,Document>|false An array of Documents.
+     */
+    public function findByIds($ids)
+    {
+        $ext       = $this->formatter->getFileExtension();
+        $documents = array();
+        foreach ($ids as $id) {
+            if(!file_exists($path = $this->getPathForDocument($id))) {
+                return false;
+            }
+            $fp       = fopen($path, 'r');
+            $contents = fread($fp, filesize($path));
+            fclose($fp);
+
+            $data = $this->formatter->decode($contents);
+
+            if (null !== $data) {
+                $doc = new $this->documentClass((array) $data);
+                $doc->setId($this->getIdFromPath($path, $ext));
+
+                $documents[] = $doc;
+            }
+        }
+        return $documents;
+    }
+
     /**
      * Store a Document in the repository.
      *
diff --git a/test/JamesMoss/Flywheel/Index/HashIndexTest.php b/test/JamesMoss/Flywheel/Index/HashIndexTest.php
index eea60ae..7fbcc35 100644
--- a/test/JamesMoss/Flywheel/Index/HashIndexTest.php
+++ b/test/JamesMoss/Flywheel/Index/HashIndexTest.php
@@ -11,8 +11,9 @@
 
 class HashIndexTest extends TestBase
 {
-    const REPO_DIR = '/tmp/flywheel';
+    const REPO_DIR  = '/tmp/flywheel';
     const REPO_NAME = '_index_test';
+    const REPO_PATH = '/tmp/flywheel/_index_test/';
 
     /** @var Repository $repo */
     private $repo;
@@ -32,39 +33,39 @@ protected function setUp()
             )
         ));
         $this->repo = new Repository(self::REPO_NAME, $config);
-        $this->index = new HashIndex('col1', $this->repo->getPath() . DIRECTORY_SEPARATOR . 'index', new JSON(), $this->repo);
+        $this->index = new HashIndex('col1', self::REPO_PATH . '.indexes', new JSON(), $this->repo);
     }
 
     protected function tearDown()
     {
         parent::tearDown();
-        $this->recurseRmdir(self::REPO_DIR . DIRECTORY_SEPARATOR . self::REPO_NAME);
+        $this->recurseRmdir(self::REPO_PATH);
     }
 
     public function testAddEntry()
     {
         $id = 'testdoc123';
         $this->index->add($id, '123');
-        $this->assertEquals(array($id), $this->index->get('123'));
+        $this->assertEquals(array($id), $this->index->get('123', '=='));
     }
 
     public function testRemoveEntry()
     {
         $id = 'testdoc123';
         $this->index->add($id, '123');
-        $this->assertEquals(array($id), $this->index->get('123'));
+        $this->assertEquals(array($id), $this->index->get('123', '=='));
         $this->index->remove($id, '123');
-        $this->assertEquals(array(), $this->index->get('123'));
+        $this->assertEquals(array(), $this->index->get('123', '=='));
     }
 
     public function testUpdateEntry()
     {
         $id = 'testdoc123';
         $this->index->add($id, '123');
-        $this->assertEquals(array($id), $this->index->get('123'));
+        $this->assertEquals(array($id), $this->index->get('123', '=='));
         $this->index->update($id, '456', '123');
-        $this->assertEquals(array(), $this->index->get('123'));
-        $this->assertEquals(array($id), $this->index->get('456'));
+        $this->assertEquals(array(), $this->index->get('123', '=='));
+        $this->assertEquals(array($id), $this->index->get('456', '=='));
     }
 
     public function testStoreDocument()
@@ -75,7 +76,32 @@ public function testStoreDocument()
         $id = 'testdoc123';
         $doc->setId($id);
         $this->assertEquals($id, $this->repo->store($doc));
-        $this->assertEquals(array($id), $this->index->get('123'));
+        $this->assertEquals(array($id), $this->index->get('123', '=='));
+    }
+
+    public function testReStoreDocumentNochange()
+    {
+        $doc = new Document(array(
+            'col1' => '123',
+        ));
+        $id = 'testdoc123';
+        $doc->setId($id);
+        $this->assertEquals($id, $this->repo->store($doc));
+        $this->assertEquals($id, $this->repo->store($doc));
+        $this->assertEquals(array($id), $this->index->get('123', '=='));
+    }
+
+    public function testReStoreDocumentAdd()
+    {
+        $doc = new Document(array(
+            'col2' => '123',
+        ));
+        $id = 'testdoc123';
+        $doc->setId($id);
+        $this->assertEquals($id, $this->repo->store($doc));
+        $doc->col1 = '456';
+        $this->assertEquals($id, $this->repo->store($doc));
+        $this->assertEquals(array($id), $this->index->get('456', '=='));
     }
 
     public function testReStoreDocumentUpdate()
@@ -88,8 +114,8 @@ public function testReStoreDocumentUpdate()
         $this->assertEquals($id, $this->repo->store($doc));
         $doc->col1 = '456';
         $this->assertEquals($id, $this->repo->store($doc));
-        $this->assertEquals(array(), $this->index->get('123'));
-        $this->assertEquals(array($id), $this->index->get('456'));
+        $this->assertEquals(array(), $this->index->get('123', '=='));
+        $this->assertEquals(array($id), $this->index->get('456', '=='));
     }
 
     public function testReStoreDocumentRemove()
@@ -102,7 +128,7 @@ public function testReStoreDocumentRemove()
         $this->assertEquals($id, $this->repo->store($doc));
         unset($doc->col1);
         $this->assertEquals($id, $this->repo->store($doc));
-        $this->assertEquals(array(), $this->index->get('123'));
+        $this->assertEquals(array(), $this->index->get('123', '=='));
     }
 
     public function testUpdateDocument()
@@ -117,8 +143,53 @@ public function testUpdateDocument()
         $doc->setId($id);
         $doc->col1 = '456';
         $this->assertEquals($id, $this->repo->update($doc));
-        $this->assertEquals(array(), $this->index->get('123'));
-        $this->assertEquals(array($id), $this->index->get('456'));
+        $this->assertEquals(array(), $this->index->get('123', '=='));
+        $this->assertEquals(array($id), $this->index->get('456', '=='));
+    }
+
+    public function testExistingData()
+    {
+        $repo = new Repository(self::REPO_NAME, new Config(
+            self::REPO_DIR
+        ));
+        $doc = new Document(array(
+            'col1' => '123',
+        ));
+        $id = 'testdoc123';
+        $doc->setId($id);
+        $this->assertEquals($id, $repo->store($doc));
+        $this->assertEquals(array($id), $this->index->get('123', '=='));
+    }
+
+    public function testDeepKey()
+    {
+        $id = 'testdoc123456';
+        $doc = new Document(array(
+            'col1' => '123',
+            'col2' => array('4', '5', '6'),
+        ));
+        $doc->setId($id);
+
+        $repo2 = new Repository(self::REPO_NAME, new Config(
+            self::REPO_DIR, array(
+                'indexes' => array(
+                    'col2.0' => "JamesMoss\Flywheel\Index\HashIndex",
+                )
+            )
+        ));
+
+        $this->assertEquals($id, $this->repo->store($doc));
+        $this->assertEquals($id, $repo2->store($doc));
+
+        // test generating index from fs
+        $index1 = new HashIndex('col2.0', self::REPO_PATH . '.indexes', new JSON(), $this->repo);
+        $this->assertEquals(array($id), $index1->get('4', '=='));
+
+        // test generating index on store document
+        $index2 = $repo2->getIndexes()['col2.0'];
+        $this->assertEquals(array($id), $index2->get('4', '=='));
+
+
     }
 
 }
\ No newline at end of file
diff --git a/test/JamesMoss/Flywheel/QueryExecuterTest.php b/test/JamesMoss/Flywheel/QueryExecuterTest.php
index 19d6e1b..47cd456 100644
--- a/test/JamesMoss/Flywheel/QueryExecuterTest.php
+++ b/test/JamesMoss/Flywheel/QueryExecuterTest.php
@@ -193,11 +193,28 @@ public function testOrderingById()
         $this->assertEquals('Djibouti', $result[2]->name);
     }
 
+    public function testFindByIndex()
+    {
+        $pred = $this->getPredicate()
+            ->where('region', '==', 'Europe');
+        $options = array(
+            'indexes' => array(
+                'region' => '\JamesMoss\Flywheel\Index\HashIndex'
+            )
+        );
+        $qe = new QueryExecuter($this->getRepo('countries', $options), $pred, array(), array());
+        $withIndex = $qe->run();
+        $qe = new QueryExecuter($this->getRepo('countries'), $pred, array(), array());
+        $withoutIndex = $qe->run();
+        $this->assertSameSize($withoutIndex, $withIndex);
+        $this->assertEqualsUnordered(get_object_vars($withoutIndex), get_object_vars($withIndex));
+    }
+
 
-    protected function getRepo($repoName)
+    protected function getRepo($repoName, $options = array())
     {
         $path = __DIR__ . '/fixtures/datastore/querytest';
-        $config = new Config($path . '/');
+        $config = new Config($path . '/', $options);
 
         return new Repository($repoName, $config);
     }
diff --git a/test/JamesMoss/Flywheel/RepositoryTest.php b/test/JamesMoss/Flywheel/RepositoryTest.php
index 164a610..49c192a 100644
--- a/test/JamesMoss/Flywheel/RepositoryTest.php
+++ b/test/JamesMoss/Flywheel/RepositoryTest.php
@@ -6,6 +6,10 @@
 
 class RespositoryTest extends TestBase
 {
+    const REPO_DIR  = '/tmp/flywheel';
+    const REPO_NAME = '_pages';
+    const REPO_PATH = '/tmp/flywheel/_pages/';
+
     /** @var Repository $repo */
     private $repo;
 
@@ -13,12 +17,17 @@ class RespositoryTest extends TestBase
     protected function setUp()
     {
         parent::setUp();
-        
-        if (!is_dir('/tmp/flywheel')) {
-            mkdir('/tmp/flywheel');
+        if (!is_dir(self::REPO_DIR)) {
+            mkdir(self::REPO_DIR);
         }
-        $config = new Config('/tmp/flywheel');
-        $this->repo = new Repository('_pages', $config);
+        $config = new Config(self::REPO_DIR);
+        $this->repo = new Repository(self::REPO_NAME, $config);
+    }
+
+    protected function tearDown()
+    {
+        parent::tearDown();
+        $this->recurseRmdir(self::REPO_PATH);
     }
 
     /**
@@ -26,9 +35,10 @@ protected function setUp()
      */
     public function testValidRepoName($name)
     {
-        $config = new Config('/tmp');
+        $config = new Config(self::REPO_DIR);
         $repo = new Repository($name, $config);
         $this->assertSame($name, $repo->getName());
+        $this->recurseRmdir($repo->getPath());
     }
 
     /**
@@ -37,7 +47,7 @@ public function testValidRepoName($name)
      */
     public function testInvalidRepoName($name)
     {
-        $config = new Config('/tmp');
+        $config = new Config(self::REPO_DIR);
         new Repository($name, $config);
     }
 
@@ -107,7 +117,7 @@ public function testStoringDocuments()
             $repo->store($document);
 
             $name = $i . '.json';
-            $this->assertSame($data, (array) json_decode(file_get_contents('/tmp/flywheel/_pages/' . $name)));
+            $this->assertSame($data, (array) json_decode(file_get_contents(self::REPO_PATH . $name)));
         }
     }
 
@@ -116,7 +126,7 @@ public function testDeletingDocuments()
         $repo   = $this->repo;
         $id     = 'delete_test';
         $name   = $id . '.json';
-        $path   = '/tmp/flywheel/_pages/' . $name;
+        $path   = self::REPO_PATH . $name;
 
         file_put_contents($path, '');
 
@@ -138,7 +148,7 @@ public function testRenamingDocumentChangesDocumentID()
 
         $repo->store($doc);
 
-        rename('/tmp/flywheel/_pages/testdoc123.json', '/tmp/flywheel/_pages/newname.json');
+        rename(self::REPO_PATH . 'testdoc123.json', self::REPO_PATH . 'newname.json');
 
         foreach ($repo->findAll() as $document) {
             if ('newname' === $document->getId()) {
@@ -160,12 +170,32 @@ public function testChangingDocumentIDChangesFilename()
         $doc->setId('test1234');
         $repo->store($doc);
 
-        $this->assertTrue(file_exists('/tmp/flywheel/_pages/test1234.json'));
+        $this->assertTrue(file_exists(self::REPO_PATH . 'test1234.json'));
 
         $doc->setId('9876test');
         $repo->update($doc);
 
-        $this->assertFalse(file_exists('/tmp/flywheel/_pages/test1234.json'));
+        $this->assertFalse(file_exists(self::REPO_PATH . 'test1234.json'));
+    }
+
+    public function testFindByIds()
+    {
+        for ($i=0; $i < 10; $i++) {
+            $doc = new Document(array(
+                'test' => $i,
+            ));
+            $doc->setId("doc$i");
+            $this->repo->store($doc);
+        }
+        $docs = $this->repo->findByIds(array('doc1', 'doc3', 'doc4'));
+        $this->assertCount(3, $docs);
+        $this->assertEquals(1, $docs[0]->test);
+        $this->assertEquals(3, $docs[1]->test);
+        $this->assertEquals(4, $docs[2]->test);
+        $docs = $this->repo->findByIds(array('doc1', 'DOC3', 'doc4'));
+        $this->assertFalse($docs);
+        $docs = $this->repo->findByIds(array());
+        $this->assertCount(0, $docs);
     }
 
     // public function testLockingOnWrite()
diff --git a/test/JamesMoss/Flywheel/TestBase.php b/test/JamesMoss/Flywheel/TestBase.php
index 82f4619..0505df9 100644
--- a/test/JamesMoss/Flywheel/TestBase.php
+++ b/test/JamesMoss/Flywheel/TestBase.php
@@ -9,11 +9,44 @@ public function normalizeLineendings($content)
         return str_replace("\r\n", "\n", $content);
     }
 
-    public function recurseRmdir($dir) {
-        $files = array_diff(scandir($dir), array('.','..'));
+    public function recurseRmdir($dir)
+    {
+        $files = array_diff(scandir($dir), array('.', '..'));
         foreach ($files as $file) {
-          (is_dir("$dir/$file")) ? $this->recurseRmdir("$dir/$file") : unlink("$dir/$file");
+            (is_dir("$dir/$file")) ? $this->recurseRmdir("$dir/$file") : unlink("$dir/$file");
         }
         return rmdir($dir);
     }
-}
\ No newline at end of file
+
+    private function arraysEqualsUnordered($a, $b)
+    {
+        // if the indexes don't match, return immediately
+        if (count(array_diff_assoc($a, $b))) {
+            return false;
+        }
+        // we know that the indexes, but maybe not values, match.
+        // compare the values between the two arrays
+        foreach ($a as $k => $v) {
+            if ($v !== $b[$k]) {
+                return false;
+            }
+        }
+        // we have identical indexes, and no unequal values
+        return true;
+    }
+
+    /**
+    * Determine if two associative arrays are similar
+    *
+    * Both arrays must have the same indexes with identical values
+    * without respect to key ordering 
+    * 
+    * @param array $expected
+    * @param array $actual
+    * @return bool
+    */
+    public function assertEqualsUnordered($expected, $actual)
+    {
+        $this->assertTrue($this->arraysEqualsUnordered($expected, $actual));
+    }
+}
diff --git a/test/JamesMoss/Flywheel/fixtures/datastore/querytest/countries/.indexes/region.json b/test/JamesMoss/Flywheel/fixtures/datastore/querytest/countries/.indexes/region.json
new file mode 100644
index 0000000..ed4e178
--- /dev/null
+++ b/test/JamesMoss/Flywheel/fixtures/datastore/querytest/countries/.indexes/region.json
@@ -0,0 +1,264 @@
+{
+    "Europe": {
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+        "Montenegro_479fb34bdbf4aba90d03cca83f64ad4e912cc854": 1,
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+        "Bosnia and Herzegovina_62ac59b7255ce5ff9fee8ac49157bdd9bc4445e2": 1,
+        "Germany_17d53e0e6a68acdf80b78d4f9d868c8736db2cec": 1,
+        "Faroe Islands_1082f89115626b9c431f2176f832b3a7cc60fb2c": 1,
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+        "Romania_d6b897fd145a64fbad36ff7cb1c47a00dcbbe9b6": 1,
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+    },
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+        "Cook Islands_4bacfe2535ecbceb9a04a1b85c3a2e0bc53c64d6": 1,
+        "Christmas Island_c6dfa97a611dbc45bfdc51c69a762488964e6361": 1,
+        "French Polynesia_40f39cdcd3acd771d31e4269e54caeff9b3b5edf": 1,
+        "Pitcairn Islands_0311d743a395837f9490fa8a89013d4b047b366e": 1,
+        "Tokelau_a08c1ca2fca39f1ea2de01c2de009926d07afb4d": 1,
+        "Northern Mariana Islands_28a117f173634e3c574231e0cfb011aabfd2bba8": 1,
+        "Guam_f8aa3a934ee38a6c86d1b092624a9c385267d927": 1,
+        "Kiribati_3f57adf2c06cecd095ff83ab72787889961bbe87": 1,
+        "Marshall Islands_bb130626b42c3cce860334424aef9a144f8231f2": 1,
+        "Tuvalu_9a2248f7c4de37c13c8e2688356857b589f669b4": 1,
+        "American Samoa_ca0b36fec74bc61226adce2b5ce0e8ef6fdca179": 1,
+        "Nauru_f648c72a69c3a9b157c3603ebd4a75141a833e46": 1,
+        "Tonga_e8a1234b8442f09d8965e48d93a16e10fa398baa": 1,
+        "Australia_ceafb51e2b0783d53dd620019dff3aa66708a26f": 1,
+        "Wallis and Futuna_a187509aa2afa6ef9b1abbaed04d4bb5b6124ffb": 1,
+        "Norfolk Island_fedb20736102194ca53af14fae03929409c27b9c": 1,
+        "New Zealand_a2238e91907fa2436a6a50e0fd8cf97ab60ec508": 1,
+        "Niue_c635e30148c3a013261cd3147f9ff8c70b2f9fea": 1,
+        "Solomon Islands_ecae78abec522d0fa00ddb3666aa9db9baf0265f": 1,
+        "Samoa_f5680604ea9e0abbe3833339ee5a793c2c02551d": 1,
+        "Micronesia_5a7d7bc91620c2307f0ad338a4b7d7929bb8af8e": 1,
+        "Cocos (Keeling) Islands_d2dd2d43fef0a1aa180b01e58e8a9c32d7ac165a": 1,
+        "Vanuatu_d16ad2dcc6af8252a554ea5f1722abc518dfa3b1": 1,
+        "New Caledonia_b9967e88983d851428fa745aa72bb8b4e0bec2da": 1
+    },
+    "": {
+        "Bouvet Island_290125ef9fc28ca6df6137e0523169786f3ecfea": 1,
+        "Antarctica_00f33fc530d3e011ee6ab56f206622e221888971": 1,
+        "French Southern and Antarctic Lands_44e46ba30eabfe96165ac52eb27f1318dd7396e4": 1,
+        "Heard Island and McDonald Islands_130447083d0bf6b6914b952751355ad34949129b": 1
+    }
+}
\ No newline at end of file

From e7775eb265e4c873fdfd659f8c89e5fac0109d18 Mon Sep 17 00:00:00 2001
From: n-peugnet <n.peugnet@free.fr>
Date: Sun, 1 Dec 2019 13:47:51 +0100
Subject: [PATCH 03/13] tests: better testFindByIndex

---
 test/JamesMoss/Flywheel/QueryExecuterTest.php | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/test/JamesMoss/Flywheel/QueryExecuterTest.php b/test/JamesMoss/Flywheel/QueryExecuterTest.php
index 47cd456..a17ccc8 100644
--- a/test/JamesMoss/Flywheel/QueryExecuterTest.php
+++ b/test/JamesMoss/Flywheel/QueryExecuterTest.php
@@ -202,12 +202,25 @@ public function testFindByIndex()
                 'region' => '\JamesMoss\Flywheel\Index\HashIndex'
             )
         );
+        $n = 5;
+
         $qe = new QueryExecuter($this->getRepo('countries', $options), $pred, array(), array());
-        $withIndex = $qe->run();
+        $start = microtime(true);
+        for ($i=0; $i < $n; $i++) {
+            $withIndex = $qe->run();
+        }
+        $timeWithIndex = microtime(true) - $start;
+
         $qe = new QueryExecuter($this->getRepo('countries'), $pred, array(), array());
-        $withoutIndex = $qe->run();
+        $start = microtime(true);
+        for ($i=0; $i < $n; $i++) {
+            $withoutIndex = $qe->run();
+        }
+        $timeWithoutIndex = microtime(true) - $start;
+
         $this->assertSameSize($withoutIndex, $withIndex);
         $this->assertEqualsUnordered(get_object_vars($withoutIndex), get_object_vars($withIndex));
+        $this->assertLessThan($timeWithoutIndex, $timeWithIndex);
     }
 
 

From 0afd3552153495f94ed41074f2ced08f8451df6e Mon Sep 17 00:00:00 2001
From: n-peugnet <n.peugnet@free.fr>
Date: Sun, 1 Dec 2019 15:27:18 +0100
Subject: [PATCH 04/13] feat: add option parameter to JSON formatter

to use an ugly json encoding for the indexes
---
 src/JamesMoss/Flywheel/Formatter/JSON.php     |  11 +-
 .../JamesMoss/Flywheel/Formatter/JSONTest.php |   8 +-
 .../querytest/countries/.indexes/region.json  | 265 +-----------------
 3 files changed, 13 insertions(+), 271 deletions(-)

diff --git a/src/JamesMoss/Flywheel/Formatter/JSON.php b/src/JamesMoss/Flywheel/Formatter/JSON.php
index d848aaa..4fe3c16 100644
--- a/src/JamesMoss/Flywheel/Formatter/JSON.php
+++ b/src/JamesMoss/Flywheel/Formatter/JSON.php
@@ -4,6 +4,13 @@
 
 class JSON implements FormatInterface
 {
+    protected $jsonOptions;
+
+    public function __construct($jsonOptions = 0)
+    {
+        $this->jsonOptions = $jsonOptions;
+    }
+
     public function getFileExtension()
     {
         return 'json';
@@ -11,9 +18,7 @@ public function getFileExtension()
 
     public function encode(array $data)
     {
-        $options = defined('JSON_PRETTY_PRINT') ? JSON_PRETTY_PRINT : null;
-
-        return json_encode($data, $options);
+        return json_encode($data, $this->jsonOptions);
     }
 
     public function decode($data)
diff --git a/test/JamesMoss/Flywheel/Formatter/JSONTest.php b/test/JamesMoss/Flywheel/Formatter/JSONTest.php
index 56a132b..2bca33e 100644
--- a/test/JamesMoss/Flywheel/Formatter/JSONTest.php
+++ b/test/JamesMoss/Flywheel/Formatter/JSONTest.php
@@ -14,16 +14,16 @@ public function testFileExtension()
 
     public function testEncoding()
     {
-        $formatter = new JSON;
+        $formatter = new JSON();
+        $formatterPretty = new JSON(JSON_PRETTY_PRINT);
         $data = array(
             'name'     => 'Joe',
             'age'      => 21,
             'employed' => true,
         );
 
-        $options = defined('JSON_PRETTY_PRINT') ? JSON_PRETTY_PRINT : null;
-
-        $this->assertSame(json_encode($data, $options), $formatter->encode($data));
+        $this->assertSame(json_encode($data), $formatter->encode($data));
+        $this->assertSame(json_encode($data, JSON_PRETTY_PRINT), $formatterPretty->encode($data));
     }
 
     public function testDecoding()
diff --git a/test/JamesMoss/Flywheel/fixtures/datastore/querytest/countries/.indexes/region.json b/test/JamesMoss/Flywheel/fixtures/datastore/querytest/countries/.indexes/region.json
index ed4e178..b521fa8 100644
--- a/test/JamesMoss/Flywheel/fixtures/datastore/querytest/countries/.indexes/region.json
+++ b/test/JamesMoss/Flywheel/fixtures/datastore/querytest/countries/.indexes/region.json
@@ -1,264 +1 @@
-{
-    "Europe": {
-        "Isle of Man_76733f338bb21fd91ee8304d05accb9163ee6e52": 1,
-        "Montenegro_479fb34bdbf4aba90d03cca83f64ad4e912cc854": 1,
-        "Hungary_f14e46ce7d094f9326167acc499698128651be85": 1,
-        "Bosnia and Herzegovina_62ac59b7255ce5ff9fee8ac49157bdd9bc4445e2": 1,
-        "Germany_17d53e0e6a68acdf80b78d4f9d868c8736db2cec": 1,
-        "Faroe Islands_1082f89115626b9c431f2176f832b3a7cc60fb2c": 1,
-        "Monaco_35ab1c3de6dac148401654e1ebf5dd935ccefa14": 1,
-        "Romania_d6b897fd145a64fbad36ff7cb1c47a00dcbbe9b6": 1,
-        "Netherlands_fb61c8a8eba24117016597fc7618f38821b16e8f": 1,
-        "Republic of Kosovo_338e718d14c93382811119b87ed77b25aaed8a98": 1,
-        "Russia_6754fe3cd8310d20ed04b8c7b66abebcdb16d88d": 1,
-        "France_e3772ac4b4db87b4a8dbfa59ef43cd1a8ad29515": 1,
-        "Croatia_d7e0453bb4af87006533f4d77ad9546dac533db8": 1,
-        "Estonia_f0a96da3f86a334cbe8d569110d6545277973859": 1,
-        "Vatican City_136f5db5de74430b7c1e66fcd4ef0b6a70ace276": 1,
-        "Greece_4902a456caa9a4eab463ce526c9df0f6180be184": 1,
-        "Belarus_027a12c2fc8568e8b70b07ff536faf288a013670": 1,
-        "Andorra_9d3bd1fb52785a7baeb03b437e7b2ecba54ef34f": 1,
-        "Macedonia_41349e9557e537855ae0f63cc43918fa13a561d3": 1,
-        "Guernsey_180c97abdb80833b91cb32903dced0e8f8b49562": 1,
-        "San Marino_87fd3befcce67042618f49ec496c2b09a49459fa": 1,
-        "Czech Republic_1fef42909247a6c230eeef66277f2b5e0e8f274e": 1,
-        "Svalbard and Jan Mayen_ac99404d12d60aa0c46631720dd7afa750d0e909": 1,
-        "Jersey_ff4636d0caf61d70e7dfa437d80aab75e921e76c": 1,
-        "Norway_988455e67df7cd81d090ea4bacdc05f39fb7caa5": 1,
-        "Portugal_a495190bcc2ef4116725616d321016a7def5bd8f": 1,
-        "Iceland_b3c92eecf0aa1905086059d9f6d3261d8fb19657": 1,
-        "Moldova_9791bc4d7273587d61fef79841bd342381f5e321": 1,
-        "United Kingdom_9769121f10f77079b27eb08e9ffa488cbcc37ed0": 1,
-        "Switzerland_77dcd849e550afec3c83d38fcc8cbc72c058f4db": 1,
-        "Belgium_5cb4c9d828175ed3931ec52305b32f47173a8e04": 1,
-        "Latvia_c5f5bb3b350774d7cda57104c55fb6c82b7ae7d9": 1,
-        "Spain_20a8df9b760336178fca425339ec1c7e542a2463": 1,
-        "Finland_c909b138eba89ecfbd86df4c9d170ac78d4a3820": 1,
-        "Austria_593905b31972f6ffe58325abf98595caf4ebf458": 1,
-        "Liechtenstein_b0ddce0f54c916c106117e280aead4f9c0cbf1df": 1,
-        "Italy_ad79ef0f076d3a686ab9738925f4dd2c7e69d7d1": 1,
-        "Lithuania_74a788cee27d549015a0786732c662e05cdd7567": 1,
-        "Albania_79b9d273ac6d2488109d1ea43e2bdb7977bd2b28": 1,
-        "Malta_1a591a3e91fcb7a47f2c08e9e2e117f39af22078": 1,
-        "Denmark_89da124e04dfe1ad9946cd37d91a119e1d028898": 1,
-        "Luxembourg_5076721c4060feeb69bd2c3dd9bdce115d5c62f3": 1,
-        "Serbia_6d31bf00d7eddc6a617a6b16699f8ba91794e2fd": 1,
-        "Ukraine_c951ec00f123510a00d1e3d9539b11b4631d4096": 1,
-        "Slovenia_d1aa0503612aa4168939b77b59ca74532a11951a": 1,
-        "Sweden_72ddd2b619af6d6a73febf80f7fcad22495498cd": 1,
-        "A\u030aland Islands_065154080d2f7539638e616e64cfcdb36c0577a1": 1,
-        "Ireland_eb2131ece0efe78ee8bb1ae98af6099114a8df09": 1,
-        "Slovakia_b6c149c3e00467fba347629a63ed02fed098d061": 1,
-        "Poland_5ff03b7273b1808e5ba852e230991bbf07da703c": 1,
-        "Bulgaria_5c77726358c5daf98ad9cdccd0882bca0f718b88": 1,
-        "Gibraltar_e51335897c0ef4bb952693d4166902146a1bc812": 1
-    },
-    "Americas": {
-        "Chile_349507e41dd8c71c10c9df6d2444b5e64a285691": 1,
-        "Saint Pierre and Miquelon_70e53283edb6d53accd21aa7731dfe1f66246b84": 1,
-        "Jamaica_5eedd6a16ab862cb5d6b2e194e0bdf8b0161d89a": 1,
-        "Argentina_354bf98925838ca68611b950e2a37ebd11c21640": 1,
-        "Uruguay_66b98924b384b40aea844bf0fe399d5d3832388e": 1,
-        "Bonaire_fd71a444cd1566324317cbc5204af645857b5b72": 1,
-        "Saint Kitts and Nevis_3ad2dd829664a86f29aec0770e244c1717c79255": 1,
-        "Costa Rica_1bf429f94068620b112aca3888b58aecbc2eadee": 1,
-        "Suriname_b17fc6f05c078b63528a6d19c2abe0917e1e8a1b": 1,
-        "Saint Vincent and the Grenadines_3fa9b2dd85d217dd4f6407fbb779928701f9e184": 1,
-        "French Guiana_07090aa7d613105dad9bd80005cd91b8da1c4cb2": 1,
-        "Montserrat_35f005157cfd133875b06f037eeeff3b7494456c": 1,
-        "Trinidad and Tobago_4d206a8103d3d20ac685314dbba1c88f6cfedd85": 1,
-        "South Georgia_618cd353b39276e0dd2215fabbbbb4d21803a69c": 1,
-        "Paraguay_71a45296474d608f35d4b49f3b10384fc738e16f": 1,
-        "Bahamas_1f797564f7843d36ebe5e841e5bd39c98157e22b": 1,
-        "Saint Lucia_673b1cf863c8e2d10109731b098b19ba81aec9fb": 1,
-        "United States Virgin Islands_65f5cb3322400cfd62ba3c8bcffbd7a8d71d0f32": 1,
-        "Turks and Caicos Islands_611bc125b7ad66ad9d5103c6bfd968a775763e6c": 1,
-        "Haiti_a4842f0234d7270b757b60b6f17a1b9f4d560dad": 1,
-        "Falkland Islands_11499959510cbab21e5241a8a6099a3d545b5227": 1,
-        "Puerto Rico_fe23c52dc2441843aa073092188089600dad336c": 1,
-        "Aruba_f3a826101b9a25f3573cb0f1a7505587de8c65c3": 1,
-        "Honduras_5aa588714ab4cbfd615d238fd9778c3a14ca4ba8": 1,
-        "Bermuda_027ed37f00fb38adb089a91f2d52c7b931949168": 1,
-        "Anguilla_5722849f2ccb586368a07473e71e8df1bae7a221": 1,
-        "Curac\u0327ao_9461dd94ebb7643ea4fbbed9dc781497e05a6e7e": 1,
-        "Panama_1e36b31e788231fba03577144de1d23b04a5d324": 1,
-        "United States_768685ca582abd0af2fbb57ca37752aa98c9372b": 1,
-        "Peru_36c57243155b80cf350c59764354b20dde157333": 1,
-        "Nicaragua_4812648c8a890c1818305642f6a01fa134b34401": 1,
-        "Cuba_c484b137e2d18229e4e7e677f1f8cfce6a0ab819": 1,
-        "United States Minor Outlying Islands_ede34a33eb69cc5980a8c2353752463771b7060e": 1,
-        "Guadeloupe_f0f524ff3b9cf7a30a94a59841b9c0d2fd858b56": 1,
-        "British Virgin Islands_1fc1b5b29cefd14d32c7e252ca38633927f0c3ee": 1,
-        "Dominican Republic_8a4bf12e17b2be590b12721ef8d5d0248698b5b6": 1,
-        "Colombia_2f737399606486655401cb27b066f4658424766d": 1,
-        "Saint Martin_854ccc29cc22ef957d1e5ce961f30c1e92677d9c": 1,
-        "Antigua and Barbuda_530670dca74039e859436ac4734296b861556efd": 1,
-        "Belize_42ab0c94a1e3bd6175a15dba215ccf5f10e861e5": 1,
-        "Ecuador_09f199d25132204e99bfb1a89916de24494f19bb": 1,
-        "Dominica_bc1cd4f07d828493332f9c95c491d6fb338afd40": 1,
-        "Greenland_1ba0cfa550295f8b2c5fa44b8236639adc825cf9": 1,
-        "Mexico_41937b20fbe8c71d9c6c3346aff43c001aa25e33": 1,
-        "El Salvador_259a6e935b848823a0c0b76aced2803060b4bd0c": 1,
-        "Guyana_bc88a24030a15bde613c8749ed93d30e0a81fcc2": 1,
-        "Sint Maarten_ad7c3cc73f9cd1c049d3208aac984c49953b94b2": 1,
-        "Guatemala_11760e1aac4396e10d315e93ad3df3e99204dc5e": 1,
-        "Grenada_dbf2a2da6458b242407285e7f1483aeb6cfee9fd": 1,
-        "Martinique_66f1a98a952d50fc3164cde58265772e2ab821c2": 1,
-        "Bolivia_a001af75ee89582f31cb4db6d3dd0b4766c80050": 1,
-        "Barbados_93409af2f208e7545f0f26996e048113edd88652": 1,
-        "Venezuela_9d4ac43d5e24e3d01e448ce01a277ba5971e60f6": 1,
-        "Canada_cd6a7b8768528485a0dbcd459185091e80dc28ad": 1,
-        "Saint Barthe\u0301lemy_f48e864508243ec01f6ac7ff781f13cd5bde0a0f": 1,
-        "Cayman Islands_e9e21c35ab345ef790305554368ebf78279482f2": 1,
-        "Brazil_37497aa5a2272c49714aee1b07e8edf973a95f59": 1
-    },
-    "Africa": {
-        "Guinea_b47b54fd3a460f43ebbcabe5b10c189176f25f25": 1,
-        "Gabon_a06dcd71328fd2b44fa7f84012096e8f318e4b48": 1,
-        "Swaziland_c985df0809c3183c074ef84ac9e902d70ff81992": 1,
-        "Niger_6687e1896dd857dc1587782149127ff073a95696": 1,
-        "Lesotho_93b12bf57f18c13c9ad2f55e33a8e3fd786fc394": 1,
-        "Liberia_1ed5dd9d833f675b7509886681e2164d842f8dad": 1,
-        "Libya_55949d4c16632f1c275d7684a379b8f1717b3904": 1,
-        "Ethiopia_3d91f7631ba813c13a08a208f1255b2e96fb03d0": 1,
-        "Democratic Republic of the Congo_f39d28021812d3e91f4c64c9ac055a20d5bcfd30": 1,
-        "Morocco_32e087f099be121c1211285a1700ff83542193f7": 1,
-        "Cameroon_73a7ddd505f2fc2cead1522e54a794328f228c44": 1,
-        "Cape Verde_8e40809e474f3e0705ddef056618ce3e5043522a": 1,
-        "Botswana_180c89bf50c8b29deb45e49d9dac62fcd5c8bedb": 1,
-        "Seychelles_3d2d7b1c3400e9222f97a999decf652a6c34bdc5": 1,
-        "Co\u0302te d'Ivoire_b2182992301690448db9754c5493729921c28056": 1,
-        "Madagascar_f92bcb6a06d2ec7c0af7c8a338f131bf887c64a0": 1,
-        "Re\u0301union_8e7e261a1ff0a9bbf184ec58b7db9d014d425e65": 1,
-        "British Indian Ocean Territory_9bb835f4f91b31fae3286529520eecae620d718c": 1,
-        "Mayotte_dcc64425eed0e625072cc41ac60a88d4b3d50086": 1,
-        "Egypt_1c39abf68e93e438ae5dca946e2d6a986cccd3a9": 1,
-        "Sa\u0303o Tome\u0301 and Pri\u0301ncipe_655191a80835f37342e045bd71b73188430d3b39": 1,
-        "Central African Republic_dba86789b53e54df0477a589a57298893cd87502": 1,
-        "South Sudan_6981f4026cf83935b630141d375a9455fc18acd7": 1,
-        "Republic of the Congo_b78ae043a4412720001cad4a83c176d09da0437f": 1,
-        "Malawi_0ce65b26dcd3c08e1b329d9efbb6bbbced426f31": 1,
-        "Eritrea_18740af5bcec9573bd3c059e0fc6570353097aab": 1,
-        "Sudan_1193ba31f109ecfdfab76f13cc2b5e44479d5603": 1,
-        "Algeria_bd6acc8626d118aea60331ce33bf000c9d7d1cee": 1,
-        "Zimbabwe_5922f5ceeff38bcfdb993efd6cfd5c472f827fa9": 1,
-        "Ghana_317dbac90743c3e5e82b2ddf122cd076a2226a92": 1,
-        "Nigeria_9742d008c420ec9d44b1794c03b9701c477f93ff": 1,
-        "South Africa_35fda17ff05f63e9061208c2dd2aaaf98790e921": 1,
-        "Burkina Faso_e71b56d92347386fa76239ce33f67aaa2de52207": 1,
-        "Gambia_7c39974f44b2b12933c66a9eba3fe33c8d0805b6": 1,
-        "Saint Helena_03bdca149f934311777f23c15054c37a49e3289b": 1,
-        "Somalia_4dfdf195ecb76a3fa83788deca6fd3b289dd568f": 1,
-        "Equatorial Guinea_80eaf3087b0b041473c6c223f1e09197b649362e": 1,
-        "Tunisia_edf404d0db32652d41a29b428a804405e1d73a9e": 1,
-        "Uganda_e92904bce8026b3c1f8828b0ce882e6b081c7fb6": 1,
-        "Namibia_bfe79debcedda1c1e11f7836c0fc13ad22dffca7": 1,
-        "Kenya_a84f56f2e6a77ecb4b2f89344446dd3ff91b87c4": 1,
-        "Mozambique_a40a9be00a9ae956acd67011c0d96758916f40ea": 1,
-        "Mauritius_26160d23fb07cf8d5dae186eba322e9fc8e27bb4": 1,
-        "Senegal_d8973b8edfe5e3211044e39d5452523b5d69cba9": 1,
-        "Togo_30949d5f4a69766caa7abe5e6fd9993090b1b6b3": 1,
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Africa_35fda17ff05f63e9061208c2dd2aaaf98790e921":1,"Burkina Faso_e71b56d92347386fa76239ce33f67aaa2de52207":1,"Gambia_7c39974f44b2b12933c66a9eba3fe33c8d0805b6":1,"Saint Helena_03bdca149f934311777f23c15054c37a49e3289b":1,"Somalia_4dfdf195ecb76a3fa83788deca6fd3b289dd568f":1,"Equatorial Guinea_80eaf3087b0b041473c6c223f1e09197b649362e":1,"Tunisia_edf404d0db32652d41a29b428a804405e1d73a9e":1,"Uganda_e92904bce8026b3c1f8828b0ce882e6b081c7fb6":1,"Namibia_bfe79debcedda1c1e11f7836c0fc13ad22dffca7":1,"Kenya_a84f56f2e6a77ecb4b2f89344446dd3ff91b87c4":1,"Mozambique_a40a9be00a9ae956acd67011c0d96758916f40ea":1,"Mauritius_26160d23fb07cf8d5dae186eba322e9fc8e27bb4":1,"Senegal_d8973b8edfe5e3211044e39d5452523b5d69cba9":1,"Togo_30949d5f4a69766caa7abe5e6fd9993090b1b6b3":1,"Guinea-Bissau_b07cb9a2b24832a8197cd3dfa67d1d6adfb0cfbb":1,"Western Sahara_fab1a52391201253134c8cc0b956613cad675611":1,"Djibouti_60a8b0c6de6f6abe5999959a5c7352750116fb9c":1,"Mali_daa6a489dbca7a13c480aaa1d0c344957590fdb7":1,"Zambia_dcf25ed56c9566181e0f2d48d8854c04c4ca6b37":1,"Rwanda_7266a1da7e3a6739b245ddfe74b0b682f7da63f8":1,"Burundi_4617585b8749a71bbb21237cab6c2dc9cbe3b86f":1,"Benin_373616e39fb47d9a1a4e87dfd4ea968037435f14":1,"Chad_6c6b1b2b3ecc0e6900000dabf4faae6f8df5ffd1":1,"Angola_a42522a0cdd6e41a1379e6c95d08a9c46a17249c":1,"Comoros_e5bb59a2731998cae2070f6fd4f2e075fd61146f":1,"Tanzania_7e380be8dc28d72571144716e95e598c986bc4d6":1,"Sierra Leone_50df2d658581499ea96e34b53f6280fd7754bd1f":1,"Mauritania_85fa355bdb4f46fa53a20a441623d53d686d4036":1},"Asia":{"Armenia_5f4599daa3415f788c1afc3db145f01b4bd2b438":1,"Tajikistan_279c771ae60c33fc34bde4627bb56ee8eecca33a":1,"Bahrain_3ae11c725c30009d4d3418bc6b30789feed78322":1,"Lebanon_5caa7f811b5aff6eb9993f309c4c045785ee67ec":1,"Malaysia_ff3ea3bec182358766650a6fd2872d9221f7e6cc":1,"Timor-Leste_2d79f6dbae283f57f4092d5370a518c3ef5caec1":1,"Iraq_1aed9ecc6e1be8eaaaddc5ffb6ba3ed84a8b1ae6":1,"North Korea_765b46e79beff128df05b121d344cc7ad23dbac5":1,"Laos_7998be8d446d668c99abca446cb3bd79fce08d2b":1,"Nepal_0e1d589f58b71e2b7d5d8068156d160146820407":1,"Japan_fcf29f6cad3232704b33e962ef5194fad3b6817b":1,"Saudi Arabia_6f49c31192f5681e1053a1d699956998c5d7e97d":1,"Yemen_ac33d641f4c9d9de5b29bb95e7f909066cfca512":1,"Oman_c14c36dffca61b07410f5e3630ba5d99c60ab5d5":1,"Afghanistan_c69153687791fb52c12ce7cca2f4d03a65d9abf8":1,"Myanmar_928b7c48a60ad93b81bc3bee9d274c5f2aed9ad3":1,"Uzbekistan_db800e86e9f303e72e1102efb21d459512902d37":1,"Israel_4c197dfd67f1ed79d11a8b0218cc368bfcce6ccb":1,"India_967ce367d89dccc133d71049f1197d29561b3726":1,"Brunei_130e4a34f1b807a8f3bd24b204c06ec4de4010da":1,"Azerbaijan_213598a7e92217bee3a758f3c69aea09ed940c0e":1,"Bhutan_bb2254a806f43df24753ca390143e2ca8c1e4e80":1,"Qatar_83ef3e6cee83cb88a39814638a94fa1ad33e65a5":1,"United Arab Emirates_d115b8d5acb8386b8012aaf4cbb3812cacd97c8e":1,"Bangladesh_fa6c3752cd00f7f1277fd7e5604ab8d2edaf26b8":1,"Kyrgyzstan_c78791a3f0e109d34ba4eac2afa35ec011439ae3":1,"Palestine_05a15c18a2038b35edcdb52e92f002c65d4fcf32":1,"Syria_3ed104337eb1dfb750107978743cbf25fbe2c2b5":1,"Thailand_a2b7c120c93a01e67dcd4d984d2a781cde2c46df":1,"Cambodia_314ccd964ef6a8e68ac5f9bb89f751a1c2196c56":1,"Turkmenistan_1f8dc1a6076e90fb31efa48a19e2d220b647c81f":1,"Sri Lanka_197042c4de91dae8aeafa9a52dc8c3a59aa41dc0":1,"Cyprus_852addab901cbc5699d190285a009d7a7035fb57":1,"China_d2eaf2aa1512d6596e0a5bae633537c6b8e779a3":1,"Mongolia_f54da380bade5d43098fd1f338cb8257523c508b":1,"Kazakhstan_2f36b6bb1852c24392fb3ee9a2879da24eb0750d":1,"Iran_889224e3fca24a6ab17d01fe47a45bc82244e938":1,"South Korea_04653e650280742f94a5a74ad6530ee09c2dc2be":1,"Vietnam_681101d8f9fa4e5e1fbe8ac5a2c05504c6c4875a":1,"Indonesia_35536a41b209715d9e3ad440431fef2672f20bbe":1,"Singapore_20c0b7bdab70ca2cc9c844a0d74a3af0bbf41c3e":1,"Kuwait_93295b0c76b900da760a8e0f2e9a29a1ba4b0f4c":1,"Georgia_9113c6c0c1f9cb53e3543b53136ba30c51018373":1,"Macao_918c53a2d6129e9e4f42191b60fa11886bd9fa50":1,"Taiwan_094d515b3608fefc6759a36412cee467437417a5":1,"Pakistan_82d220df17cebf5ce4897d780c354dd5e925c209":1,"Philippines_8067364d44f5e37baba7e13ba124e934df410e2a":1,"Jordan_674027e17b0ed64e76cde2005cb8e76fb4cd671a":1,"Turkey_d7153e6702b4ea48c7c0d01affdef0e1b39fd6dc":1,"Maldives_213cb204509284ff2aedeca9290b70a6da307eab":1,"Hong Kong_2f488ffc82ccc67a1616e39fdfc537297f1646c5":1},"Oceania":{"Palau_e5e0b68adfacb66979505bedf6d424070c536eb6":1,"Fiji_bbb7ef7f2ec9557d0895c9da1c5cddd50d15049e":1,"Papua New Guinea_fbaa3c3e9e1bbf9fe813f2d4c038b295ef046512":1,"Cook Islands_4bacfe2535ecbceb9a04a1b85c3a2e0bc53c64d6":1,"Christmas Island_c6dfa97a611dbc45bfdc51c69a762488964e6361":1,"French Polynesia_40f39cdcd3acd771d31e4269e54caeff9b3b5edf":1,"Pitcairn Islands_0311d743a395837f9490fa8a89013d4b047b366e":1,"Tokelau_a08c1ca2fca39f1ea2de01c2de009926d07afb4d":1,"Northern Mariana Islands_28a117f173634e3c574231e0cfb011aabfd2bba8":1,"Guam_f8aa3a934ee38a6c86d1b092624a9c385267d927":1,"Kiribati_3f57adf2c06cecd095ff83ab72787889961bbe87":1,"Marshall Islands_bb130626b42c3cce860334424aef9a144f8231f2":1,"Tuvalu_9a2248f7c4de37c13c8e2688356857b589f669b4":1,"American Samoa_ca0b36fec74bc61226adce2b5ce0e8ef6fdca179":1,"Nauru_f648c72a69c3a9b157c3603ebd4a75141a833e46":1,"Tonga_e8a1234b8442f09d8965e48d93a16e10fa398baa":1,"Australia_ceafb51e2b0783d53dd620019dff3aa66708a26f":1,"Wallis and Futuna_a187509aa2afa6ef9b1abbaed04d4bb5b6124ffb":1,"Norfolk Island_fedb20736102194ca53af14fae03929409c27b9c":1,"New Zealand_a2238e91907fa2436a6a50e0fd8cf97ab60ec508":1,"Niue_c635e30148c3a013261cd3147f9ff8c70b2f9fea":1,"Solomon Islands_ecae78abec522d0fa00ddb3666aa9db9baf0265f":1,"Samoa_f5680604ea9e0abbe3833339ee5a793c2c02551d":1,"Micronesia_5a7d7bc91620c2307f0ad338a4b7d7929bb8af8e":1,"Cocos (Keeling) Islands_d2dd2d43fef0a1aa180b01e58e8a9c32d7ac165a":1,"Vanuatu_d16ad2dcc6af8252a554ea5f1722abc518dfa3b1":1,"New Caledonia_b9967e88983d851428fa745aa72bb8b4e0bec2da":1},"":{"Bouvet Island_290125ef9fc28ca6df6137e0523169786f3ecfea":1,"Antarctica_00f33fc530d3e011ee6ab56f206622e221888971":1,"French Southern and Antarctic Lands_44e46ba30eabfe96165ac52eb27f1318dd7396e4":1,"Heard Island and McDonald Islands_130447083d0bf6b6914b952751355ad34949129b":1}}
\ No newline at end of file

From 15ce9fed9a6eb8d8255d0f77b21b21d5c344d46c Mon Sep 17 00:00:00 2001
From: n-peugnet <n.peugnet@free.fr>
Date: Sun, 1 Dec 2019 16:50:39 +0100
Subject: [PATCH 05/13] refactor: simplify IndexInterface

by removing add and remove functions as only update is required
---
 src/JamesMoss/Flywheel/Index/HashIndex.php    | 18 +++++++---
 .../Flywheel/Index/IndexInterface.php         | 20 -----------
 src/JamesMoss/Flywheel/Index/StoredIndex.php  | 36 -------------------
 src/JamesMoss/Flywheel/Repository.php         |  4 +--
 .../Flywheel/Index/HashIndexTest.php          |  8 ++---
 5 files changed, 20 insertions(+), 66 deletions(-)

diff --git a/src/JamesMoss/Flywheel/Index/HashIndex.php b/src/JamesMoss/Flywheel/Index/HashIndex.php
index 9f73435..92c2ae3 100644
--- a/src/JamesMoss/Flywheel/Index/HashIndex.php
+++ b/src/JamesMoss/Flywheel/Index/HashIndex.php
@@ -38,7 +38,10 @@ protected function getEntries($value, $operator)
     }
 
     /**
-     * @inheritdoc
+     * Adds an entry in the index
+     *
+     * @param string $id
+     * @param string $value
      */
     protected function addEntry($id, $value)
     {
@@ -49,7 +52,10 @@ protected function addEntry($id, $value)
     }
 
     /**
-     * @inheritdoc
+     * Removes an entry from the index
+     *
+     * @param string $id
+     * @param string $value
      */
     protected function removeEntry($id, $value)
     {
@@ -67,7 +73,11 @@ protected function removeEntry($id, $value)
      */
     protected function updateEntry($id, $new, $old)
     {
-        $this->removeEntry($id, $old);
-        $this->addEntry($id, $new);
+        if (!empty($new)) {
+            $this->addEntry($id, $new);
+        }
+        if (!empty($old)) {
+            $this->removeEntry($id, $old);
+        }
     }
 }
diff --git a/src/JamesMoss/Flywheel/Index/IndexInterface.php b/src/JamesMoss/Flywheel/Index/IndexInterface.php
index 7481d78..18c7a46 100644
--- a/src/JamesMoss/Flywheel/Index/IndexInterface.php
+++ b/src/JamesMoss/Flywheel/Index/IndexInterface.php
@@ -23,26 +23,6 @@ public function isOperatorCompatible($operator);
      */
     public function get($value, $operator);
 
-    /**
-     * Add a document to the index.
-     *
-     * @param string $id the id of this document.
-     * @param mixed $value the value of this document for the indexed field.
-     *
-     * @return void
-     */
-    public function add($id, $value);
-
-    /**
-     * Remove a document from the index.
-     *
-     * @param string $id the id of this document.
-     * @param mixed $value the value of this document for the indexed field.
-     *
-     * @return void
-     */
-    public function remove($id, $value);
-
     /**
      * Update a document in the index.
      *
diff --git a/src/JamesMoss/Flywheel/Index/StoredIndex.php b/src/JamesMoss/Flywheel/Index/StoredIndex.php
index e82312f..ceee271 100644
--- a/src/JamesMoss/Flywheel/Index/StoredIndex.php
+++ b/src/JamesMoss/Flywheel/Index/StoredIndex.php
@@ -56,26 +56,6 @@ public function get($value, $operator)
         return $this->getEntries($value, $operator);
     }
 
-    /**
-     * @inheritdoc
-     */
-    public function add($id, $value)
-    {
-        $this->needsData();
-        $this->addEntry($id, $value);
-        $this->flush();
-    }
-
-    /**
-     * @inheritdoc
-     */
-    public function remove($id, $value)
-    {
-        $this->needsData();
-        $this->removeEntry($id, $value);
-        $this->flush();
-    }
-
     /**
      * @inheritdoc
      */
@@ -150,22 +130,6 @@ protected function flush()
      */
     abstract protected function getEntries($value, $operator);
 
-    /**
-     * Adds an entry in the index
-     *
-     * @param string $id
-     * @param string $value
-     */
-    abstract protected function addEntry($id, $value);
-
-    /**
-     * Removes an entry from the index
-     *
-     * @param string $id
-     * @param string $value
-     */
-    abstract protected function removeEntry($id, $value);
-
     /**
      * Removes an entry from the index
      *
diff --git a/src/JamesMoss/Flywheel/Repository.php b/src/JamesMoss/Flywheel/Repository.php
index 5982b1e..c1c277c 100644
--- a/src/JamesMoss/Flywheel/Repository.php
+++ b/src/JamesMoss/Flywheel/Repository.php
@@ -218,9 +218,9 @@ public function store(DocumentInterface $document)
             $setPrev = $previous ? isset($previous->$field) : false;
             $setActu = isset($document->$field);
             if (!$setPrev && $setActu) {
-                $index->add($document->getId(), $document->$field);
+                $index->update($document->getId(), $document->$field, null);
             } elseif ($setPrev && !$setActu) {
-                $index->remove($document->getId(), $previous->$field);
+                $index->update($document->getId(), null, $previous->$field);
             } elseif ($setPrev && $setActu) {
                 $index->update($document->getId(), $document->$field, $previous->$field);
             }
diff --git a/test/JamesMoss/Flywheel/Index/HashIndexTest.php b/test/JamesMoss/Flywheel/Index/HashIndexTest.php
index 7fbcc35..10b437c 100644
--- a/test/JamesMoss/Flywheel/Index/HashIndexTest.php
+++ b/test/JamesMoss/Flywheel/Index/HashIndexTest.php
@@ -45,23 +45,23 @@ protected function tearDown()
     public function testAddEntry()
     {
         $id = 'testdoc123';
-        $this->index->add($id, '123');
+        $this->index->update($id, '123', null);
         $this->assertEquals(array($id), $this->index->get('123', '=='));
     }
 
     public function testRemoveEntry()
     {
         $id = 'testdoc123';
-        $this->index->add($id, '123');
+        $this->index->update($id, '123', null);
         $this->assertEquals(array($id), $this->index->get('123', '=='));
-        $this->index->remove($id, '123');
+        $this->index->update($id, null, '123');
         $this->assertEquals(array(), $this->index->get('123', '=='));
     }
 
     public function testUpdateEntry()
     {
         $id = 'testdoc123';
-        $this->index->add($id, '123');
+        $this->index->update($id, '123', null);
         $this->assertEquals(array($id), $this->index->get('123', '=='));
         $this->index->update($id, '456', '123');
         $this->assertEquals(array(), $this->index->get('123', '=='));

From 2e8d85db8a64b66580be596cd70d71dc1312e3d6 Mon Sep 17 00:00:00 2001
From: n-peugnet <n.peugnet@free.fr>
Date: Sun, 1 Dec 2019 16:54:33 +0100
Subject: [PATCH 06/13] fix: multidimentional key indexes bugs

update and delte functions of the repo were not tested and didn't work
this is now fixed
---
 src/JamesMoss/Flywheel/Repository.php         | 58 +++++++++++++------
 .../Flywheel/Index/HashIndexTest.php          | 19 +++---
 2 files changed, 51 insertions(+), 26 deletions(-)

diff --git a/src/JamesMoss/Flywheel/Repository.php b/src/JamesMoss/Flywheel/Repository.php
index c1c277c..488efd8 100644
--- a/src/JamesMoss/Flywheel/Repository.php
+++ b/src/JamesMoss/Flywheel/Repository.php
@@ -116,7 +116,10 @@ public function findAll()
 
         foreach ($files as $file) {
             $fp       = fopen($file, 'r');
-            $contents = fread($fp, filesize($file));
+            $contents = null;
+            if(($filesize = filesize($file)) > 0) {
+                $contents = fread($fp, $filesize);
+            }
             fclose($fp);
 
             $data = $this->formatter->decode($contents);
@@ -146,7 +149,10 @@ public function findById($id)
         }
 
         $fp       = fopen($path, 'r');
-        $contents = fread($fp, filesize($path));
+        $contents = null;
+        if(($filesize = filesize($path)) > 0) {
+            $contents = fread($fp, $filesize);
+        }
         fclose($fp);
 
         $data = $this->formatter->decode($contents);
@@ -179,7 +185,10 @@ public function findByIds($ids)
                 return false;
             }
             $fp       = fopen($path, 'r');
-            $contents = fread($fp, filesize($path));
+            $contents = null;
+            if(($filesize = filesize($path)) > 0) {
+                $contents = fread($fp, $filesize);
+            }
             fclose($fp);
 
             $data = $this->formatter->decode($contents);
@@ -215,14 +224,16 @@ public function store(DocumentInterface $document)
         }
         $previous = $this->findById($id);
         foreach ($this->indexes as $field => $index) {
-            $setPrev = $previous ? isset($previous->$field) : false;
-            $setActu = isset($document->$field);
-            if (!$setPrev && $setActu) {
-                $index->update($document->getId(), $document->$field, null);
-            } elseif ($setPrev && !$setActu) {
-                $index->update($document->getId(), null, $previous->$field);
-            } elseif ($setPrev && $setActu) {
-                $index->update($document->getId(), $document->$field, $previous->$field);
+            $oldFound = false;
+            $newFound = false;
+            $oldVal = $previous ? $previous->getNestedProperty($field, $oldFound) : null;
+            $newVal = $document->getNestedProperty($field, $newFound);
+            if (!$oldFound && $newFound) {
+                $index->update($document->getId(), $newVal, null);
+            } elseif ($oldFound && !$newFound) {
+                $index->update($document->getId(), null, $oldVal);
+            } elseif ($oldFound && $newFound) {
+                $index->update($document->getId(), $newVal, $oldVal);
             }
         }
 
@@ -243,7 +254,7 @@ public function store(DocumentInterface $document)
      *
      * @param Document $document The document to store
      *
-     * @return bool True if stored, otherwise false
+     * @return string|false the id if stored, otherwise false
      */
     public function update(DocumentInterface $document)
     {
@@ -261,8 +272,9 @@ public function update(DocumentInterface $document)
         if($document->getId() !== $document->getInitialId()) {
             $previous = $this->findById($document->getInitialId());
             foreach ($this->indexes as $field => $index) {
-                if(isset($previous->$field)) {
-                    $index->remove($previous->getId(), $previous->$field);
+                $value = $previous->getNestedProperty($field, $found);
+                if ($found) {
+                    $index->update($previous->getId(), null, $value);
                 }
             }
             unlink($oldPath);
@@ -274,14 +286,24 @@ public function update(DocumentInterface $document)
     /**
      * Delete a document from the repository using its ID.
      *
-     * @param mixed $id The ID of the document (or the document itself) to delete
+     * @param mixed $doc The ID of the document (or the document itself) to delete
      *
      * @return boolean True if deleted, false if not.
      */
-    public function delete($id)
+    public function delete($doc)
     {
-        if ($id instanceof DocumentInterface) {
-            $id = $id->getId();
+        if ($doc instanceof DocumentInterface) {
+            $id = $doc->getId();
+        } else {
+            $id = $doc;
+            $doc = $this->findById($id);
+        }
+        foreach ($this->indexes as $field => $index) {
+            $found = false;
+            $value = $doc ? $doc->getNestedProperty($field, $found) : null;
+            if ($found) {
+                $index->update($id, null, $value);
+            }
         }
 
         $path = $this->getPathForDocument($id);
diff --git a/test/JamesMoss/Flywheel/Index/HashIndexTest.php b/test/JamesMoss/Flywheel/Index/HashIndexTest.php
index 10b437c..81bbe1e 100644
--- a/test/JamesMoss/Flywheel/Index/HashIndexTest.php
+++ b/test/JamesMoss/Flywheel/Index/HashIndexTest.php
@@ -161,11 +161,10 @@ public function testExistingData()
         $this->assertEquals(array($id), $this->index->get('123', '=='));
     }
 
-    public function testDeepKey()
+    public function testMultidimentionalKey()
     {
-        $id = 'testdoc123456';
+        $id = 'testdoc456';
         $doc = new Document(array(
-            'col1' => '123',
             'col2' => array('4', '5', '6'),
         ));
         $doc->setId($id);
@@ -178,18 +177,22 @@ public function testDeepKey()
             )
         ));
 
-        $this->assertEquals($id, $this->repo->store($doc));
-        $this->assertEquals($id, $repo2->store($doc));
-
         // test generating index from fs
+        $this->assertEquals($id, $this->repo->store($doc));
         $index1 = new HashIndex('col2.0', self::REPO_PATH . '.indexes', new JSON(), $this->repo);
         $this->assertEquals(array($id), $index1->get('4', '=='));
+        $this->assertTrue($this->repo->delete($doc));
 
         // test generating index on store document
+        $this->assertEquals($id, $repo2->store($doc));
         $index2 = $repo2->getIndexes()['col2.0'];
         $this->assertEquals(array($id), $index2->get('4', '=='));
-
-
+        $id = 'doc456';
+        $doc->setId($id);
+        $this->assertEquals($id, $repo2->update($doc));
+        $this->assertEquals(array($id), $index2->get('4', '=='));
+        $this->assertTrue($repo2->delete($id));
+        $this->assertEquals(array(), $index2->get('4', '=='));
     }
 
 }
\ No newline at end of file

From a4c0d133ba458c74590acaedb2db435cae5c0b48 Mon Sep 17 00:00:00 2001
From: n-peugnet <n.peugnet@free.fr>
Date: Sun, 1 Dec 2019 18:28:02 +0100
Subject: [PATCH 07/13] feat(HashIndex): working '!=' and '!==' operators

these two operators are not very efficient so i'm not sure to
keep them in the hashindex, but at least they are working
---
 src/JamesMoss/Flywheel/Index/HashIndex.php    | 13 +++--
 .../Flywheel/Index/HashIndexTest.php          | 13 +++++
 test/JamesMoss/Flywheel/QueryExecuterTest.php | 52 ++++++++++---------
 3 files changed, 50 insertions(+), 28 deletions(-)

diff --git a/src/JamesMoss/Flywheel/Index/HashIndex.php b/src/JamesMoss/Flywheel/Index/HashIndex.php
index 92c2ae3..4c72587 100644
--- a/src/JamesMoss/Flywheel/Index/HashIndex.php
+++ b/src/JamesMoss/Flywheel/Index/HashIndex.php
@@ -27,12 +27,11 @@ protected function getEntries($value, $operator)
         if (!isset($this->data->$value)) {
             return array();
         }
-        $ids = array_keys(get_object_vars($this->data->$value));
         switch ($operator) {
             case '==':
-            case '===': return $ids;
+            case '===': return array_keys(get_object_vars($this->data->$value));
             case '!=':
-            case '!==': return array_diff(get_object_vars($this->data), $ids);
+            case '!==': return $this->idsExcept($value);
             default: throw new \InvalidArgumentException('Incompatible operator `'.$operator.'`.');
         }
     }
@@ -80,4 +79,12 @@ protected function updateEntry($id, $new, $old)
             $this->removeEntry($id, $old);
         }
     }
+
+    protected function idsExcept($value) {
+        $data = get_object_vars($this->data);
+        unset($data[$value]);
+        return array_keys(array_reduce($data, function($prev, $val) {
+            return array_merge($prev, get_object_vars($val));
+        }, array()));
+    }
 }
diff --git a/test/JamesMoss/Flywheel/Index/HashIndexTest.php b/test/JamesMoss/Flywheel/Index/HashIndexTest.php
index 81bbe1e..1da0aab 100644
--- a/test/JamesMoss/Flywheel/Index/HashIndexTest.php
+++ b/test/JamesMoss/Flywheel/Index/HashIndexTest.php
@@ -68,6 +68,19 @@ public function testUpdateEntry()
         $this->assertEquals(array($id), $this->index->get('456', '=='));
     }
 
+    public function testGet()
+    {
+        $n = 4;
+        for ($i=1; $i <= $n; $i++) {
+            $id = "doc$i";
+            $this->index->update($id, "val$i", null);
+        }
+        $this->assertEquals(array('doc1'), $this->index->get('val1', '=='));
+        $this->assertEquals(array('doc2'), $this->index->get('val2', '==='));
+        $this->assertEquals(array('doc1', 'doc2', 'doc4'), $this->index->get('val3', '!='));
+        $this->assertEquals(array('doc1', 'doc2', 'doc3'), $this->index->get('val4', '!=='));
+    }
+
     public function testStoreDocument()
     {
         $doc = new Document(array(
diff --git a/test/JamesMoss/Flywheel/QueryExecuterTest.php b/test/JamesMoss/Flywheel/QueryExecuterTest.php
index a17ccc8..dc51ce5 100644
--- a/test/JamesMoss/Flywheel/QueryExecuterTest.php
+++ b/test/JamesMoss/Flywheel/QueryExecuterTest.php
@@ -195,32 +195,34 @@ public function testOrderingById()
 
     public function testFindByIndex()
     {
-        $pred = $this->getPredicate()
-            ->where('region', '==', 'Europe');
-        $options = array(
-            'indexes' => array(
-                'region' => '\JamesMoss\Flywheel\Index\HashIndex'
-            )
-        );
-        $n = 5;
-
-        $qe = new QueryExecuter($this->getRepo('countries', $options), $pred, array(), array());
-        $start = microtime(true);
-        for ($i=0; $i < $n; $i++) {
-            $withIndex = $qe->run();
+        foreach(array('==', '===', '!=', '!==') as $operator) {
+            $pred = $this->getPredicate()
+                ->where('region', $operator, 'Europe');
+            $options = array(
+                'indexes' => array(
+                    'region' => '\JamesMoss\Flywheel\Index\HashIndex'
+                )
+            );
+            $n = 5;
+
+            $qe = new QueryExecuter($this->getRepo('countries', $options), $pred, array(), array());
+            $start = microtime(true);
+            for ($i=0; $i < $n; $i++) {
+                $withIndex = $qe->run();
+            }
+            $timeWithIndex = microtime(true) - $start;
+
+            $qe = new QueryExecuter($this->getRepo('countries'), $pred, array(), array());
+            $start = microtime(true);
+            for ($i=0; $i < $n; $i++) {
+                $withoutIndex = $qe->run();
+            }
+            $timeWithoutIndex = microtime(true) - $start;
+
+            $this->assertSameSize($withoutIndex, $withIndex);
+            $this->assertEqualsUnordered(get_object_vars($withoutIndex), get_object_vars($withIndex));
+            $this->assertLessThan($timeWithoutIndex, $timeWithIndex);
         }
-        $timeWithIndex = microtime(true) - $start;
-
-        $qe = new QueryExecuter($this->getRepo('countries'), $pred, array(), array());
-        $start = microtime(true);
-        for ($i=0; $i < $n; $i++) {
-            $withoutIndex = $qe->run();
-        }
-        $timeWithoutIndex = microtime(true) - $start;
-
-        $this->assertSameSize($withoutIndex, $withIndex);
-        $this->assertEqualsUnordered(get_object_vars($withoutIndex), get_object_vars($withIndex));
-        $this->assertLessThan($timeWithoutIndex, $timeWithIndex);
     }
 
 

From d631398aa564d0c4d42c465189efb3e009913e37 Mon Sep 17 00:00:00 2001
From: n-peugnet <n.peugnet@free.fr>
Date: Mon, 2 Dec 2019 16:35:17 +0100
Subject: [PATCH 08/13] refactor: cleaner IndexInterface

- move $data initialisation into concrete StoredIndex extensions
- add constructor definition to IndexInterface to make sure it is
  compatible with the initialisation in Repository
- completely abstract filesystem from HashIndex (constructor)
---
 src/JamesMoss/Flywheel/Index/HashIndex.php    | 16 ++++++++++
 .../Flywheel/Index/IndexInterface.php         |  8 +++++
 src/JamesMoss/Flywheel/Index/StoredIndex.php  | 30 ++++++++++++-------
 src/JamesMoss/Flywheel/Repository.php         | 23 ++++++++++----
 .../Flywheel/Index/HashIndexTest.php          |  4 +--
 5 files changed, 64 insertions(+), 17 deletions(-)

diff --git a/src/JamesMoss/Flywheel/Index/HashIndex.php b/src/JamesMoss/Flywheel/Index/HashIndex.php
index 4c72587..145b3f4 100644
--- a/src/JamesMoss/Flywheel/Index/HashIndex.php
+++ b/src/JamesMoss/Flywheel/Index/HashIndex.php
@@ -2,6 +2,7 @@
 
 namespace JamesMoss\Flywheel\Index;
 
+use JamesMoss\Flywheel\Formatter\JSON;
 use JamesMoss\Flywheel\Index\StoredIndex;
 use stdClass;
 
@@ -11,6 +12,13 @@ class HashIndex extends StoredIndex
         '==', '===', '!=', '!=='
     );
 
+    /**
+     * @inheritdoc
+     */
+    public function __construct($field, $repository) {
+        $this->construct($field, $repository);
+    }
+
     /**
      * @inheritdoc
      */
@@ -19,6 +27,14 @@ public function isOperatorCompatible($operator)
         return in_array($operator, self::$operators);
     }
 
+    /**
+     * @inheritdoc
+     */
+    protected function initData()
+    {
+        $this->data = new stdClass();
+    }
+
     /**
      * @inheritdoc
      */
diff --git a/src/JamesMoss/Flywheel/Index/IndexInterface.php b/src/JamesMoss/Flywheel/Index/IndexInterface.php
index 18c7a46..8686934 100644
--- a/src/JamesMoss/Flywheel/Index/IndexInterface.php
+++ b/src/JamesMoss/Flywheel/Index/IndexInterface.php
@@ -4,6 +4,14 @@
 
 interface IndexInterface
 {
+    /**
+     * Constructor
+     *
+     * @param string $field the field to index.
+     * @param Repository $repository the repository of this index.
+     */
+    public function __construct($field, $repository);
+
     /**
      * Checks if the given operator is compatible with this index.
      *
diff --git a/src/JamesMoss/Flywheel/Index/StoredIndex.php b/src/JamesMoss/Flywheel/Index/StoredIndex.php
index ceee271..5673f39 100644
--- a/src/JamesMoss/Flywheel/Index/StoredIndex.php
+++ b/src/JamesMoss/Flywheel/Index/StoredIndex.php
@@ -4,10 +4,10 @@
 
 use JamesMoss\Flywheel\Index\IndexInterface;
 use JamesMoss\Flywheel\Formatter\FormatInterface;
+use JamesMoss\Flywheel\Formatter\JSON;
 use JamesMoss\Flywheel\Predicate;
 use JamesMoss\Flywheel\QueryExecuter;
 use JamesMoss\Flywheel\Repository;
-use stdClass;
 
 abstract class StoredIndex implements IndexInterface
 {
@@ -27,21 +27,25 @@ abstract class StoredIndex implements IndexInterface
     protected $path;
 
     /**
-     * Constructor
+     * Protected constructor
      *
      * @param string $field the field to index.
-     * @param string $path the directory where to store the index file.
-     * @param FormatInterface $formatter the formatter used to store the data.
      * @param Repository $repository the repository of this index.
+     * @param FormatInterface $formatter the formatter used to store the data.
      */
-    public function __construct($field, $path, $formatter, $repository)
+    protected function construct($field, $repository, $formatter = null)
     {
         $this->field = $field;
-        $this->formatter = $formatter;
+        $this->formatter = $formatter == null ? new JSON() : $formatter;
         $this->repository = $repository;
-        $this->path = $path . DIRECTORY_SEPARATOR . "$field." . $formatter->getFileExtension();
+        $this->path = $repository->addDirectory('.indexes') . DIRECTORY_SEPARATOR . "$field." . $this->formatter->getFileExtension();
     }
 
+    /**
+     * @inheritdoc
+     */
+    abstract public function __construct($field, $repository);
+
     /**
      * @inheritdoc
      */
@@ -79,7 +83,7 @@ protected function needsData()
         if (isset($this->data)) {
             return;
         }
-        $this->data = new stdClass();
+        $this->initData();
         if (file_exists($this->path)) {
             $fp       = fopen($this->path, 'r');
             $contents = fread($fp, filesize($this->path));
@@ -91,11 +95,10 @@ protected function needsData()
             $qe = new QueryExecuter($this->repository, $predicate->where($field, '=='), array(), array());
             foreach ($this->repository->findAll() as $doc) {
                 $docVal = $qe->getFieldValue($doc, $field, $found);
-        
                 if (!$found) {
                     continue;
                 }
-                $this->addEntry($doc->getId(), $docVal);
+                $this->updateEntry($doc->getId(), $docVal, null);
             }
             $this->flush();
         }
@@ -120,6 +123,13 @@ protected function flush()
         return $result !== false;
     }
 
+    /**
+     * Init the data object
+     *
+     * @return void
+     */
+    abstract protected function initData();
+
     /**
      * Get entries from the index
      *
diff --git a/src/JamesMoss/Flywheel/Repository.php b/src/JamesMoss/Flywheel/Repository.php
index 488efd8..a7a65c3 100644
--- a/src/JamesMoss/Flywheel/Repository.php
+++ b/src/JamesMoss/Flywheel/Repository.php
@@ -2,7 +2,6 @@
 
 namespace JamesMoss\Flywheel;
 
-use JamesMoss\Flywheel\Formatter\JSON;
 use JamesMoss\Flywheel\Index\IndexInterface;
 
 /**
@@ -18,7 +17,6 @@ class Repository
     protected $formatter;
     protected $queryClass;
     protected $documentClass;
-    protected $indexDir;
     /** @var array<string,IndexInterface> $indexes */
     protected $indexes;
 
@@ -37,15 +35,16 @@ public function __construct($name, Config $config)
         $this->queryClass    = $config->getOption('query_class');
         $this->documentClass = $config->getOption('document_class');
         $this->indexes       = $config->getOption('indexes', array());
-        $this->indexDir      = $this->path . DIRECTORY_SEPARATOR . '.indexes';
         array_walk($this->indexes, function(&$class, $field) {
-            $class = new $class($field, $this->indexDir, new JSON(), $this);
+            if (!is_subclass_of($class, '\JamesMoss\Flywheel\Index\IndexInterface')) {
+                throw new \RuntimeException(sprintf('`%s` does not implement IndexInterface.', $class));
+            }
+            $class = new $class($field, $this);
         });
 
         // Ensure the repo name is valid
         $this->validateName($this->name);
         $this->ensureDirectory($this->path);
-        $this->ensureDirectory($this->indexDir);
     }
 
     /**
@@ -61,6 +60,20 @@ protected function ensureDirectory($path) {
         }
     }
 
+    /**
+     * Adds a directory in the repository.
+     *
+     * @param string $name The name of the new directory.
+     *
+     * @return string The path of the directory.
+     */
+    public function addDirectory($name)
+    {
+        $path = $this->path . DIRECTORY_SEPARATOR . $name;
+        $this->ensureDirectory($path);
+        return $path;
+    }
+
     /**
      * Returns the name of this repository
      *
diff --git a/test/JamesMoss/Flywheel/Index/HashIndexTest.php b/test/JamesMoss/Flywheel/Index/HashIndexTest.php
index 1da0aab..c85d327 100644
--- a/test/JamesMoss/Flywheel/Index/HashIndexTest.php
+++ b/test/JamesMoss/Flywheel/Index/HashIndexTest.php
@@ -33,7 +33,7 @@ protected function setUp()
             )
         ));
         $this->repo = new Repository(self::REPO_NAME, $config);
-        $this->index = new HashIndex('col1', self::REPO_PATH . '.indexes', new JSON(), $this->repo);
+        $this->index = new HashIndex('col1', $this->repo);
     }
 
     protected function tearDown()
@@ -192,7 +192,7 @@ public function testMultidimentionalKey()
 
         // test generating index from fs
         $this->assertEquals($id, $this->repo->store($doc));
-        $index1 = new HashIndex('col2.0', self::REPO_PATH . '.indexes', new JSON(), $this->repo);
+        $index1 = new HashIndex('col2.0', $this->repo);
         $this->assertEquals(array($id), $index1->get('4', '=='));
         $this->assertTrue($this->repo->delete($doc));
 

From 7d6f20d29b3e05a42764f46933b1c8b6beb1dd27 Mon Sep 17 00:00:00 2001
From: n-peugnet <n.peugnet@free.fr>
Date: Mon, 2 Dec 2019 17:44:26 +0100
Subject: [PATCH 09/13] fix(HashIndex): bad result with inconsitent data

- removed operators '===' and '!==' as I don't think we can implement
  them with the current HashIndex data structure. (We could maybe write
  the type in the key to implement this)
- change test accordingly
- add inconsistent data test
- simplify index generation from document files
---
 src/JamesMoss/Flywheel/Index/HashIndex.php    | 12 +++---
 src/JamesMoss/Flywheel/Index/StoredIndex.php  |  7 +---
 .../Flywheel/Index/HashIndexTest.php          | 37 ++++++++++++++++++-
 test/JamesMoss/Flywheel/QueryExecuterTest.php |  2 +-
 4 files changed, 42 insertions(+), 16 deletions(-)

diff --git a/src/JamesMoss/Flywheel/Index/HashIndex.php b/src/JamesMoss/Flywheel/Index/HashIndex.php
index 145b3f4..4d8a7a0 100644
--- a/src/JamesMoss/Flywheel/Index/HashIndex.php
+++ b/src/JamesMoss/Flywheel/Index/HashIndex.php
@@ -9,7 +9,7 @@
 class HashIndex extends StoredIndex
 {
     protected static $operators = array(
-        '==', '===', '!=', '!=='
+        '==', '!='
     );
 
     /**
@@ -44,10 +44,8 @@ protected function getEntries($value, $operator)
             return array();
         }
         switch ($operator) {
-            case '==':
-            case '===': return array_keys(get_object_vars($this->data->$value));
-            case '!=':
-            case '!==': return $this->idsExcept($value);
+            case '==': return array_keys(get_object_vars($this->data->$value));
+            case '!=': return $this->idsExcept($value);
             default: throw new \InvalidArgumentException('Incompatible operator `'.$operator.'`.');
         }
     }
@@ -88,10 +86,10 @@ protected function removeEntry($id, $value)
      */
     protected function updateEntry($id, $new, $old)
     {
-        if (!empty($new)) {
+        if ($new !== null) {
             $this->addEntry($id, $new);
         }
-        if (!empty($old)) {
+        if ($old !== null) {
             $this->removeEntry($id, $old);
         }
     }
diff --git a/src/JamesMoss/Flywheel/Index/StoredIndex.php b/src/JamesMoss/Flywheel/Index/StoredIndex.php
index 5673f39..b74af6b 100644
--- a/src/JamesMoss/Flywheel/Index/StoredIndex.php
+++ b/src/JamesMoss/Flywheel/Index/StoredIndex.php
@@ -5,8 +5,6 @@
 use JamesMoss\Flywheel\Index\IndexInterface;
 use JamesMoss\Flywheel\Formatter\FormatInterface;
 use JamesMoss\Flywheel\Formatter\JSON;
-use JamesMoss\Flywheel\Predicate;
-use JamesMoss\Flywheel\QueryExecuter;
 use JamesMoss\Flywheel\Repository;
 
 abstract class StoredIndex implements IndexInterface
@@ -90,11 +88,8 @@ protected function needsData()
             fclose($fp);
             $this->data = $this->formatter->decode($contents);
         } else {
-            $field = $this->field;
-            $predicate = new Predicate();
-            $qe = new QueryExecuter($this->repository, $predicate->where($field, '=='), array(), array());
             foreach ($this->repository->findAll() as $doc) {
-                $docVal = $qe->getFieldValue($doc, $field, $found);
+                $docVal = $doc->getNestedProperty($this->field, $found);
                 if (!$found) {
                     continue;
                 }
diff --git a/test/JamesMoss/Flywheel/Index/HashIndexTest.php b/test/JamesMoss/Flywheel/Index/HashIndexTest.php
index c85d327..90a7094 100644
--- a/test/JamesMoss/Flywheel/Index/HashIndexTest.php
+++ b/test/JamesMoss/Flywheel/Index/HashIndexTest.php
@@ -76,9 +76,7 @@ public function testGet()
             $this->index->update($id, "val$i", null);
         }
         $this->assertEquals(array('doc1'), $this->index->get('val1', '=='));
-        $this->assertEquals(array('doc2'), $this->index->get('val2', '==='));
         $this->assertEquals(array('doc1', 'doc2', 'doc4'), $this->index->get('val3', '!='));
-        $this->assertEquals(array('doc1', 'doc2', 'doc3'), $this->index->get('val4', '!=='));
     }
 
     public function testStoreDocument()
@@ -208,4 +206,39 @@ public function testMultidimentionalKey()
         $this->assertEquals(array(), $index2->get('4', '=='));
     }
 
+    public function testInconsitentData()
+    {
+        $doc1 = new Document(array('col1' => '1'));
+        $doc1->setId('doc1');
+        $doc2 = new Document(array('col2' => '2'));
+        $doc2->setId('doc2');
+        $doc3 = new Document(array('col1' => ''));
+        $doc3->setId('doc3');
+        $doc4 = new Document(array('col2' => '4'));
+        $doc4->setId('doc4');
+        $doc5 = new Document(array('col1' => ''));
+        $doc5->setId('doc5');
+
+        $repo2 = new Repository(self::REPO_NAME, new Config(self::REPO_DIR, array()));
+        $query11 = $this->repo->query()->where('col1', '==', 1)->orderBy('__id');
+        $query12 = $this->repo->query()->where('col1', '!=', 1)->orderBy('__id');
+        $query21 = $repo2->query()->where('col1', '==', 1)->orderBy('__id');
+        $query22 = $repo2->query()->where('col1', '!=', 1)->orderBy('__id');
+
+        // test generating index from document files
+        $this->assertEquals('doc1', $repo2->store($doc1));
+        $this->assertEquals('doc2', $repo2->store($doc2));
+        $this->assertEquals('doc3', $repo2->store($doc3));
+        $this->assertEquals($query21->execute(), $query11->execute());
+        $this->assertEquals($query22->execute(), $query12->execute());
+
+        // test generating index on store document
+        $this->assertEquals('doc4', $this->repo->store($doc4));
+        $this->assertEquals('doc4', $repo2->store($doc4));
+        $this->assertEquals('doc5', $this->repo->store($doc5));
+        $this->assertEquals('doc5', $repo2->store($doc5));
+        $this->assertEquals($query21->execute(), $query11->execute());
+        $this->assertEquals($query22->execute(), $query12->execute());
+    }
+
 }
\ No newline at end of file
diff --git a/test/JamesMoss/Flywheel/QueryExecuterTest.php b/test/JamesMoss/Flywheel/QueryExecuterTest.php
index dc51ce5..659f21d 100644
--- a/test/JamesMoss/Flywheel/QueryExecuterTest.php
+++ b/test/JamesMoss/Flywheel/QueryExecuterTest.php
@@ -195,7 +195,7 @@ public function testOrderingById()
 
     public function testFindByIndex()
     {
-        foreach(array('==', '===', '!=', '!==') as $operator) {
+        foreach(array('==', '!=') as $operator) {
             $pred = $this->getPredicate()
                 ->where('region', $operator, 'Europe');
             $options = array(

From ee3e297ee2c31597e6bd25ffa0baa2e184829648 Mon Sep 17 00:00:00 2001
From: n-peugnet <n.peugnet@free.fr>
Date: Mon, 2 Dec 2019 19:36:32 +0100
Subject: [PATCH 10/13] fix(HashIndex): empty string in index

use an array instead of an stdClass to store the data
---
 src/JamesMoss/Flywheel/Formatter/JSON.php    |  2 +-
 src/JamesMoss/Flywheel/Index/HashIndex.php   | 26 ++++++++++----------
 src/JamesMoss/Flywheel/Index/StoredIndex.php |  2 +-
 3 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/src/JamesMoss/Flywheel/Formatter/JSON.php b/src/JamesMoss/Flywheel/Formatter/JSON.php
index 4fe3c16..fd1c5c8 100644
--- a/src/JamesMoss/Flywheel/Formatter/JSON.php
+++ b/src/JamesMoss/Flywheel/Formatter/JSON.php
@@ -23,6 +23,6 @@ public function encode(array $data)
 
     public function decode($data)
     {
-        return json_decode($data);
+        return json_decode($data, $this->jsonOptions&JSON_OBJECT_AS_ARRAY);
     }
 }
\ No newline at end of file
diff --git a/src/JamesMoss/Flywheel/Index/HashIndex.php b/src/JamesMoss/Flywheel/Index/HashIndex.php
index 4d8a7a0..50095ec 100644
--- a/src/JamesMoss/Flywheel/Index/HashIndex.php
+++ b/src/JamesMoss/Flywheel/Index/HashIndex.php
@@ -16,7 +16,7 @@ class HashIndex extends StoredIndex
      * @inheritdoc
      */
     public function __construct($field, $repository) {
-        $this->construct($field, $repository);
+        $this->construct($field, $repository, new JSON(JSON_OBJECT_AS_ARRAY));
     }
 
     /**
@@ -32,7 +32,7 @@ public function isOperatorCompatible($operator)
      */
     protected function initData()
     {
-        $this->data = new stdClass();
+        $this->data = array();
     }
 
     /**
@@ -40,11 +40,11 @@ protected function initData()
      */
     protected function getEntries($value, $operator)
     {
-        if (!isset($this->data->$value)) {
+        if (!isset($this->data[$value])) {
             return array();
         }
         switch ($operator) {
-            case '==': return array_keys(get_object_vars($this->data->$value));
+            case '==': return array_keys($this->data[$value]);
             case '!=': return $this->idsExcept($value);
             default: throw new \InvalidArgumentException('Incompatible operator `'.$operator.'`.');
         }
@@ -58,10 +58,10 @@ protected function getEntries($value, $operator)
      */
     protected function addEntry($id, $value)
     {
-        if (!isset($this->data->$value)) {
-            $this->data->$value = new stdClass();
+        if (!isset($this->data[$value])) {
+            $this->data[$value] = array();
         }
-        $this->data->$value->$id = 1;
+        $this->data[$value][$id] = 1;
     }
 
     /**
@@ -72,12 +72,12 @@ protected function addEntry($id, $value)
      */
     protected function removeEntry($id, $value)
     {
-        if (!isset($this->data->$value)) {
+        if (!isset($this->data[$value])) {
             return;
         }
-        unset($this->data->$value->$id);
-        if (count(get_object_vars($this->data->$value)) === 0) {
-            unset($this->data->$value);
+        unset($this->data[$value][$id]);
+        if (count($this->data[$value]) === 0) {
+            unset($this->data[$value]);
         }
     }
 
@@ -95,10 +95,10 @@ protected function updateEntry($id, $new, $old)
     }
 
     protected function idsExcept($value) {
-        $data = get_object_vars($this->data);
+        $data = $this->data;
         unset($data[$value]);
         return array_keys(array_reduce($data, function($prev, $val) {
-            return array_merge($prev, get_object_vars($val));
+            return array_merge($prev, $val);
         }, array()));
     }
 }
diff --git a/src/JamesMoss/Flywheel/Index/StoredIndex.php b/src/JamesMoss/Flywheel/Index/StoredIndex.php
index b74af6b..12b56f1 100644
--- a/src/JamesMoss/Flywheel/Index/StoredIndex.php
+++ b/src/JamesMoss/Flywheel/Index/StoredIndex.php
@@ -106,7 +106,7 @@ protected function needsData()
      */
     protected function flush()
     {
-        $contents = $this->formatter->encode(get_object_vars($this->data));
+        $contents = $this->formatter->encode($this->data);
         $fp = fopen($this->path, 'w');
         if (!flock($fp, LOCK_EX)) {
             return false;

From 37aaa9eb0a4814a795307d885f3362e5c2a38865 Mon Sep 17 00:00:00 2001
From: n-peugnet <n.peugnet@free.fr>
Date: Mon, 2 Dec 2019 20:30:39 +0100
Subject: [PATCH 11/13] build: add php 5.3 again

+ fix tests for php5.3
---
 .travis.yml                                     |  2 ++
 composer.json                                   |  2 +-
 composer.lock                                   | 10 ++++++----
 src/JamesMoss/Flywheel/Formatter/JSON.php       |  3 +++
 src/JamesMoss/Flywheel/Repository.php           |  5 +++--
 test/JamesMoss/Flywheel/Index/HashIndexTest.php |  3 ++-
 test/JamesMoss/Flywheel/QueryExecuterTest.php   | 16 +++++++---------
 7 files changed, 24 insertions(+), 17 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 245c4eb..f1f7bf1 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -11,6 +11,8 @@ jobs:
       dist: trusty
     - php: 5.4
       dist: trusty
+    - php: 5.3.29
+      dist: precise
 
 install:
   - if [[ ${TRAVIS_PHP_VERSION:0:3} < "7.1" ]]; then rm composer.lock; fi
diff --git a/composer.json b/composer.json
index 7c9b4ad..5e1d195 100644
--- a/composer.json
+++ b/composer.json
@@ -17,7 +17,7 @@
 	"require-dev": {
 		"mikey179/vfsstream": "^1.6",
 		"mockery/mockery": "1.* || 0.*",
-		"mustangostang/spyc": "^0.6",
+		"mustangostang/spyc": "dev-master#eba310c",
 		"phpunit/phpunit": "7.* || 4.*"
 	},
 	"suggest": {
diff --git a/composer.lock b/composer.lock
index 4fb8d1d..cad2a38 100644
--- a/composer.lock
+++ b/composer.lock
@@ -4,7 +4,7 @@
         "Read more about it at https://getcomposer.org/doc/01-basic-usage.md#composer-lock-the-lock-file",
         "This file is @generated automatically"
     ],
-    "content-hash": "ac5e07039672da7f040f0ff8506869f6",
+    "content-hash": "857529a9f504739efe6a1d43c40bdb5d",
     "packages": [],
     "packages-dev": [
         {
@@ -225,7 +225,7 @@
         },
         {
             "name": "mustangostang/spyc",
-            "version": "0.6.3",
+            "version": "dev-master",
             "source": {
                 "type": "git",
                 "url": "git@github.com:mustangostang/spyc.git",
@@ -1540,7 +1540,7 @@
         },
         {
             "name": "symfony/polyfill-ctype",
-            "version": "v1.13.0",
+            "version": "v1.13.1",
             "source": {
                 "type": "git",
                 "url": "https://github.com/symfony/polyfill-ctype.git",
@@ -1687,7 +1687,9 @@
     ],
     "aliases": [],
     "minimum-stability": "stable",
-    "stability-flags": [],
+    "stability-flags": {
+        "mustangostang/spyc": 20
+    },
     "prefer-stable": false,
     "prefer-lowest": false,
     "platform": {
diff --git a/src/JamesMoss/Flywheel/Formatter/JSON.php b/src/JamesMoss/Flywheel/Formatter/JSON.php
index fd1c5c8..89d9630 100644
--- a/src/JamesMoss/Flywheel/Formatter/JSON.php
+++ b/src/JamesMoss/Flywheel/Formatter/JSON.php
@@ -2,6 +2,9 @@
 
 namespace JamesMoss\Flywheel\Formatter;
 
+defined('JSON_OBJECT_AS_ARRAY') or define('JSON_OBJECT_AS_ARRAY', 1);
+defined('JSON_PRETTY_PRINT') or define('JSON_PRETTY_PRINT', 128);
+
 class JSON implements FormatInterface
 {
     protected $jsonOptions;
diff --git a/src/JamesMoss/Flywheel/Repository.php b/src/JamesMoss/Flywheel/Repository.php
index a7a65c3..bbb8936 100644
--- a/src/JamesMoss/Flywheel/Repository.php
+++ b/src/JamesMoss/Flywheel/Repository.php
@@ -35,11 +35,12 @@ public function __construct($name, Config $config)
         $this->queryClass    = $config->getOption('query_class');
         $this->documentClass = $config->getOption('document_class');
         $this->indexes       = $config->getOption('indexes', array());
-        array_walk($this->indexes, function(&$class, $field) {
+        $self = $this;
+        array_walk($this->indexes, function(&$class, $field) use ($self) {
             if (!is_subclass_of($class, '\JamesMoss\Flywheel\Index\IndexInterface')) {
                 throw new \RuntimeException(sprintf('`%s` does not implement IndexInterface.', $class));
             }
-            $class = new $class($field, $this);
+            $class = new $class($field, $self);
         });
 
         // Ensure the repo name is valid
diff --git a/test/JamesMoss/Flywheel/Index/HashIndexTest.php b/test/JamesMoss/Flywheel/Index/HashIndexTest.php
index 90a7094..4e25ee0 100644
--- a/test/JamesMoss/Flywheel/Index/HashIndexTest.php
+++ b/test/JamesMoss/Flywheel/Index/HashIndexTest.php
@@ -196,7 +196,8 @@ public function testMultidimentionalKey()
 
         // test generating index on store document
         $this->assertEquals($id, $repo2->store($doc));
-        $index2 = $repo2->getIndexes()['col2.0'];
+        $indexes = $repo2->getIndexes();
+        $index2 = $indexes['col2.0'];
         $this->assertEquals(array($id), $index2->get('4', '=='));
         $id = 'doc456';
         $doc->setId($id);
diff --git a/test/JamesMoss/Flywheel/QueryExecuterTest.php b/test/JamesMoss/Flywheel/QueryExecuterTest.php
index 659f21d..30fba9c 100644
--- a/test/JamesMoss/Flywheel/QueryExecuterTest.php
+++ b/test/JamesMoss/Flywheel/QueryExecuterTest.php
@@ -85,15 +85,15 @@ public function testSubPredicates()
                   ->orWhere('language.0', '==', 'English');
             });
 
-        $qe = new QueryExecuter($this->getRepo('countries'), $pred, array(), array());
+        $qe = new QueryExecuter($this->getRepo('countries'), $pred, array(), array('name ASC'));
 
         $result = $qe->run();
 
         $this->assertEquals(3, $result->total());
 
-        $this->assertEquals('Vatican City', $result->first()->name);
+        $this->assertEquals('Gibraltar', $result->first()->name);
         $this->assertEquals('San Marino', $result[1]->name);
-        $this->assertEquals('Gibraltar', $result[2]->name);
+        $this->assertEquals('Vatican City', $result[2]->name);
     }
 
     public function testInOperator()
@@ -103,17 +103,15 @@ public function testInOperator()
             ->andWhere('population', '<', 40000)
             ->andWhere('language.0', 'IN', array('Italian', 'English'));
 
-        $qe = new QueryExecuter($this->getRepo('countries'), $pred, array(), array());
+        $qe = new QueryExecuter($this->getRepo('countries'), $pred, array(), array('name ASC'));
 
         $result = $qe->run();
 
         $this->assertEquals(3, $result->total());
 
-        $this->assertEquals('Vatican City', $result->first()->name);
-        // The two following assertions doesn't work on PHP 5.4 and 5.5
-        // probably because these versions need mockery 0.* instead of 1.*
-        // $this->assertEquals('San Marino', $result[1]->name);
-        // $this->assertEquals('Gibraltar', $result[2]->name);
+        $this->assertEquals('Gibraltar', $result->first()->name);
+        $this->assertEquals('San Marino', $result[1]->name);
+        $this->assertEquals('Vatican City', $result[2]->name);
     }
 
     public function testSimpleOrdering()

From 4590b02993068d4764e3b813ddc98de009c9c518 Mon Sep 17 00:00:00 2001
From: n-peugnet <n.peugnet@free.fr>
Date: Fri, 6 Dec 2019 01:12:23 +0100
Subject: [PATCH 12/13] feat(index): add regenerateIndexes function

+ test regenerate function
+ refactor testFindByIndex
---
 .../Flywheel/Index/IndexInterface.php         |  7 ++
 src/JamesMoss/Flywheel/Index/StoredIndex.php  | 24 ++++---
 src/JamesMoss/Flywheel/Repository.php         |  7 ++
 .../Flywheel/Index/HashIndexTest.php          | 14 ++++
 test/JamesMoss/Flywheel/QueryExecuterTest.php | 67 +++++++++++--------
 5 files changed, 82 insertions(+), 37 deletions(-)

diff --git a/src/JamesMoss/Flywheel/Index/IndexInterface.php b/src/JamesMoss/Flywheel/Index/IndexInterface.php
index 8686934..9097e33 100644
--- a/src/JamesMoss/Flywheel/Index/IndexInterface.php
+++ b/src/JamesMoss/Flywheel/Index/IndexInterface.php
@@ -41,4 +41,11 @@ public function get($value, $operator);
      * @return void
      */
     public function update($id, $new, $old);
+
+    /**
+     * Regenerate the index from the repository's documents.
+     *
+     * @return void;
+     */
+    public function regenerate();
 }
diff --git a/src/JamesMoss/Flywheel/Index/StoredIndex.php b/src/JamesMoss/Flywheel/Index/StoredIndex.php
index 12b56f1..5320c48 100644
--- a/src/JamesMoss/Flywheel/Index/StoredIndex.php
+++ b/src/JamesMoss/Flywheel/Index/StoredIndex.php
@@ -81,22 +81,30 @@ protected function needsData()
         if (isset($this->data)) {
             return;
         }
-        $this->initData();
         if (file_exists($this->path)) {
             $fp       = fopen($this->path, 'r');
             $contents = fread($fp, filesize($this->path));
             fclose($fp);
             $this->data = $this->formatter->decode($contents);
         } else {
-            foreach ($this->repository->findAll() as $doc) {
-                $docVal = $doc->getNestedProperty($this->field, $found);
-                if (!$found) {
-                    continue;
-                }
-                $this->updateEntry($doc->getId(), $docVal, null);
+            $this->regenerate();
+        }
+    }
+
+    /**
+     * @inheritdoc
+     */
+    public function regenerate()
+    {
+        $this->initData();
+        foreach ($this->repository->findAll() as $doc) {
+            $docVal = $doc->getNestedProperty($this->field, $found);
+            if (!$found) {
+                continue;
             }
-            $this->flush();
+            $this->updateEntry($doc->getId(), $docVal, null);
         }
+        $this->flush();
     }
 
     /**
diff --git a/src/JamesMoss/Flywheel/Repository.php b/src/JamesMoss/Flywheel/Repository.php
index bbb8936..244191b 100644
--- a/src/JamesMoss/Flywheel/Repository.php
+++ b/src/JamesMoss/Flywheel/Repository.php
@@ -448,4 +448,11 @@ protected function getIdFromPath($path, $ext)
         return basename($path, '.' . $ext);
     }
 
+    public function regenerateIndexes()
+    {
+        foreach ($this->indexes as $index) {
+            $index->regenerate();
+        }
+    }
+
 }
diff --git a/test/JamesMoss/Flywheel/Index/HashIndexTest.php b/test/JamesMoss/Flywheel/Index/HashIndexTest.php
index 4e25ee0..a1f09ad 100644
--- a/test/JamesMoss/Flywheel/Index/HashIndexTest.php
+++ b/test/JamesMoss/Flywheel/Index/HashIndexTest.php
@@ -242,4 +242,18 @@ public function testInconsitentData()
         $this->assertEquals($query22->execute(), $query12->execute());
     }
 
+    public function testRegenerate()
+    {
+        $id = 'doc1';
+        $doc = new Document(array('col1' => 'val1'));
+        $doc->setId($id);
+        $this->repo->store($doc);
+        $this->assertEquals(array($id), $this->index->get('val1', '=='));
+        $formatter = new JSON();
+        file_put_contents($this->repo->getPathForDocument($id), $formatter->encode(array('col1' => 'val2')));
+        $this->index->regenerate();
+        $this->assertEquals(array(), $this->index->get('val1', '=='));
+        $this->assertEquals(array($id), $this->index->get('val2', '=='));
+    }
+
 }
\ No newline at end of file
diff --git a/test/JamesMoss/Flywheel/QueryExecuterTest.php b/test/JamesMoss/Flywheel/QueryExecuterTest.php
index 30fba9c..6941ba0 100644
--- a/test/JamesMoss/Flywheel/QueryExecuterTest.php
+++ b/test/JamesMoss/Flywheel/QueryExecuterTest.php
@@ -191,36 +191,37 @@ public function testOrderingById()
         $this->assertEquals('Djibouti', $result[2]->name);
     }
 
-    public function testFindByIndex()
-    {
-        foreach(array('==', '!=') as $operator) {
-            $pred = $this->getPredicate()
-                ->where('region', $operator, 'Europe');
-            $options = array(
-                'indexes' => array(
-                    'region' => '\JamesMoss\Flywheel\Index\HashIndex'
-                )
-            );
-            $n = 5;
-
-            $qe = new QueryExecuter($this->getRepo('countries', $options), $pred, array(), array());
-            $start = microtime(true);
-            for ($i=0; $i < $n; $i++) {
-                $withIndex = $qe->run();
-            }
-            $timeWithIndex = microtime(true) - $start;
-
-            $qe = new QueryExecuter($this->getRepo('countries'), $pred, array(), array());
-            $start = microtime(true);
-            for ($i=0; $i < $n; $i++) {
-                $withoutIndex = $qe->run();
-            }
-            $timeWithoutIndex = microtime(true) - $start;
-
-            $this->assertSameSize($withoutIndex, $withIndex);
-            $this->assertEqualsUnordered(get_object_vars($withoutIndex), get_object_vars($withIndex));
-            $this->assertLessThan($timeWithoutIndex, $timeWithIndex);
+    /**
+     * @dataProvider hashIndexOperatorsProvider
+     */
+    public function testFindByIndex($operator)
+    {
+        $pred = $this->getPredicate()
+            ->where('region', $operator, 'Europe');
+        $options = array(
+            'indexes' => array(
+                'region' => '\JamesMoss\Flywheel\Index\HashIndex'
+            )
+        );
+        $n = 5;
+
+        $qe = new QueryExecuter($this->getRepo('countries', $options), $pred, array(), array());
+        $start = microtime(true);
+        for ($i=0; $i < $n; $i++) {
+            $withIndex = $qe->run();
+        }
+        $timeWithIndex = microtime(true) - $start;
+
+        $qe = new QueryExecuter($this->getRepo('countries'), $pred, array(), array());
+        $start = microtime(true);
+        for ($i=0; $i < $n; $i++) {
+            $withoutIndex = $qe->run();
         }
+        $timeWithoutIndex = microtime(true) - $start;
+
+        $this->assertSameSize($withoutIndex, $withIndex);
+        $this->assertEqualsUnordered(get_object_vars($withoutIndex), get_object_vars($withIndex));
+        $this->assertLessThan($timeWithoutIndex, $timeWithIndex);
     }
 
 
@@ -236,4 +237,12 @@ protected function getPredicate()
     {
         return new Predicate();
     }
+
+    public function hashIndexOperatorsProvider()
+    {
+        return array(
+            array('=='),
+            array('!='),
+        );
+    }
 }

From 4c03c7642c9cab422aa88a5b1874413b05a504c0 Mon Sep 17 00:00:00 2001
From: n-peugnet <n.peugnet@free.fr>
Date: Sat, 14 Dec 2019 19:08:01 +0100
Subject: [PATCH 13/13] docs: add indexes section in readme

---
 readme.md | 31 ++++++++++++++++++++++++++++---
 1 file changed, 28 insertions(+), 3 deletions(-)

diff --git a/readme.md b/readme.md
index 8bf1423..8187c60 100644
--- a/readme.md
+++ b/readme.md
@@ -221,11 +221,13 @@ $posts = $repo->query()
 
 ## Config options
 
- - `formatter`. See [Formats](https://github.com/jamesmoss/flywheel#formats) section of this readme. Defaults to an
+ - `formatter`. See [Formats](#formats) section of this readme. Defaults to an
    instance of `JamesMoss\Flywheel\Formatter\JSON`.
  - `query_class`. The name of the class that gets returned from `Repository::query()`. By default, Flywheel detects
     if you have APC or APCu installed and uses `CachedQuery` class if applicable, otherwise it just uses `Query`.
  - `document_class`. The name of the class to use when hydrating documenst from the filesystem. Must implement `JamesMoss\Flywheel\DocumentInterface`. Defaults to `JamesMoss\Flywheel\Document`.
+ - `indexes`. See [Indexes](#indexes) section of this readme. Defaults to an
+   instance of `JamesMoss\Flywheel\Formatter\JSON`.
 
 
 ## Formats
@@ -252,12 +254,35 @@ The following formatter classes are available.
 **Important** If you use the `YAML` or `Markdown` formatters when using the `--no-dev` flag in Composer you'll need
 to manually add `mustangostang\spyc` to your `composer.json`. Flywheel tries to keep it's dependencies to a minimum.
 
-If you write your own formatter it must implement `JamesMoss\Flywheel\Formatter\Format`.
+If you write your own formatter it must implement `JamesMoss\Flywheel\Formatter\FormatInterface`.
+
+## Indexes
+
+To speed up the queries on some specific fields you can add indexes on these fields.
+There are different types of index, each specialized on certain queries:
+
+- `HashIndex` - supports only `==` and `!=` operators.
+
+If a query cannot be executed only on indexes it will fallback to the default behaviour, which is opening all the files of the repository.
+
+**Important** Indexes maintain their own copy of the data so you won't be able to manually edit the files while keeping the consistency of the database anymore.
+
+```php
+use JamesMoss\Flywheel\Index\HashIndex;
+
+$config = new Config('/path/to/writable/directory', array(
+    'indexes' => {
+        'fieldname' => HashIndex::class
+    },
+))
+```
+
+If you write your own index it must implement `JamesMoss\Flywheel\Index\IndexInterface`.
 
 ## Todo
 
 - More caching around `Repository::findAll`.
-- Indexing.
+- More Indexes.
 - HHVM support.
 - Abstract the filesystem, something like Gaufrette or Symfony's Filesystem component?
 - Events system.