From b1e5bbad1aa35380453c052389762981f8bd7225 Mon Sep 17 00:00:00 2001
From: mokaddem <sami.mokaddem@circl.lu>
Date: Tue, 24 Aug 2021 10:48:53 +0200
Subject: [PATCH 01/16] new: [tag] Started integration of tag plugin with
 custom helpers - WiP

---
 composer.json                                 |  1 +
 src/Application.php                           |  1 +
 src/Model/Table/IndividualsTable.php          |  4 +
 src/View/Helper/BootstrapHelper.php           | 22 +++--
 src/View/Helper/TagHelper.php                 | 98 +++++++++++++++++++
 src/View/Helper/TextColourHelper.php          | 21 ++++
 templates/Individuals/view.php                |  4 +
 .../SingleViews/Fields/tagsField.php          | 16 +++
 templates/layout/default.php                  |  1 -
 webroot/css/main.css                          | 19 ++++
 webroot/js/bootstrap-helper.js                | 11 ++-
 webroot/js/main.js                            | 54 ++++++++++
 12 files changed, 243 insertions(+), 9 deletions(-)
 create mode 100644 src/View/Helper/TagHelper.php
 create mode 100644 src/View/Helper/TextColourHelper.php
 create mode 100644 templates/element/genericElements/SingleViews/Fields/tagsField.php

diff --git a/composer.json b/composer.json
index f0b35aa..13f42e8 100644
--- a/composer.json
+++ b/composer.json
@@ -11,6 +11,7 @@
         "cakephp/cakephp": "^4.0",
         "cakephp/migrations": "^3.0",
         "cakephp/plugin-installer": "^1.2",
+        "dereuromark/cakephp-tags": "^1.2",
         "erusev/parsedown": "^1.7",
         "mobiledetect/mobiledetectlib": "^2.8"
     },
diff --git a/src/Application.php b/src/Application.php
index 2da0df1..c6529bd 100644
--- a/src/Application.php
+++ b/src/Application.php
@@ -59,6 +59,7 @@ class Application extends BaseApplication implements AuthenticationServiceProvid
             $this->addPlugin('DebugKit');
         }
         $this->addPlugin('Authentication');
+        $this->addPlugin('Tags');
         // Load more plugins here
     }
 
diff --git a/src/Model/Table/IndividualsTable.php b/src/Model/Table/IndividualsTable.php
index d6893f7..81d4c65 100644
--- a/src/Model/Table/IndividualsTable.php
+++ b/src/Model/Table/IndividualsTable.php
@@ -14,6 +14,10 @@ class IndividualsTable extends AppTable
     {
         parent::initialize($config);
         $this->addBehavior('UUID');
+        $this->addBehavior('Tags.Tag', [
+            'taggedCounter' => false,
+            'strategy' => 'array',
+        ]);
         $this->hasMany(
             'Alignments',
             [
diff --git a/src/View/Helper/BootstrapHelper.php b/src/View/Helper/BootstrapHelper.php
index 05ce6fe..83cd7f1 100644
--- a/src/View/Helper/BootstrapHelper.php
+++ b/src/View/Helper/BootstrapHelper.php
@@ -670,6 +670,7 @@ class BoostrapButton extends BootstrapGeneric {
         'class' => [],
         'type' => 'button',
         'nodeType' => 'button',
+        'title' => '',
         'params' => [],
         'badge' => false
     ];
@@ -678,7 +679,7 @@ class BoostrapButton extends BootstrapGeneric {
 
     function __construct($options) {
         $this->allowedOptionValues = [
-            'variant' => BootstrapGeneric::$variants,
+            'variant' => array_merge(BootstrapGeneric::$variants, ['link', 'text']),
             'size' => ['', 'sm', 'lg'],
             'type' => ['button', 'submit', 'reset']
         ];
@@ -701,11 +702,15 @@ class BoostrapButton extends BootstrapGeneric {
             $this->bsClasses[] = "btn-{$this->options['variant']}";
         }
         if (!empty($this->options['size'])) {
-            $this->bsClasses[] = "btn-$this->options['size']";
+            $this->bsClasses[] = "btn-{$this->options['size']}";
         }
         if ($this->options['block']) {
             $this->bsClasses[] = 'btn-block';
         }
+        if ($this->options['variant'] == 'text') {
+            $this->bsClasses[] = 'p-0';
+            $this->bsClasses[] = 'lh-1';
+        }
     }
 
     public function button()
@@ -718,7 +723,8 @@ class BoostrapButton extends BootstrapGeneric {
         $html = $this->openNode($this->options['nodeType'], array_merge($this->options['params'], [
             'class' => array_merge($this->options['class'], $this->bsClasses),
             'role' => "alert",
-            'type' => $this->options['type']
+            'type' => $this->options['type'],
+            'title' => h($this->options['title']),
         ]));
 
         $html .= $this->genIcon();
@@ -734,7 +740,8 @@ class BoostrapButton extends BootstrapGeneric {
     private function genIcon()
     {
         return $this->genNode('span', [
-            'class' => ['mr-1', "fa fa-{$this->options['icon']}"],
+            // 'class' => ['mr-1', "fa fa-{$this->options['icon']}"],
+            'class' => ['', "fa fa-{$this->options['icon']}"],
         ]);
     }
 
@@ -749,7 +756,8 @@ class BoostrapBadge extends BootstrapGeneric {
         'text' => '',
         'variant' => 'primary',
         'pill' => false,
-        'title' => ''
+        'title' => '',
+        'class' => [],
     ];
 
     function __construct($options) {
@@ -773,11 +781,11 @@ class BoostrapBadge extends BootstrapGeneric {
     private function genBadge()
     {
         $html = $this->genNode('span', [
-            'class' => [
+            'class' => array_merge($this->options['class'], [
                 'badge',
                 "badge-{$this->options['variant']}",
                 $this->options['pill'] ? 'badge-pill' : '',
-            ],
+            ]),
             'title' => $this->options['title']
         ], h($this->options['text']));
         return $html;
diff --git a/src/View/Helper/TagHelper.php b/src/View/Helper/TagHelper.php
new file mode 100644
index 0000000..2cca055
--- /dev/null
+++ b/src/View/Helper/TagHelper.php
@@ -0,0 +1,98 @@
+<?php
+
+namespace App\View\Helper;
+
+use Cake\View\Helper;
+use Cake\Utility\Hash;
+
+class TagHelper extends Helper
+{
+    public $helpers = [
+        'Bootstrap',
+        'TextColour',
+        'FontAwesome',
+        'Tags.Tag',
+    ];
+
+    protected $_defaultConfig = [
+        'default_colour' => '#983965',
+    ];
+
+    public function control(array $options = [])
+    {
+        return $this->Tag->control($options);
+    }
+
+    public function picker(array $options = [])
+    {
+        $optionsHtml = '';
+        foreach ($options['allTags'] as $i => $tag) {
+            $optionsHtml .= $this->Bootstrap->genNode('option', [
+                'value' => h($tag['text']),
+                'data-colour' => h($tag['colour']),
+            ], h($tag['text']));
+        }
+        $html = $this->Bootstrap->genNode('select', [
+            'class' => ['tag-input', 'd-none'],
+            'multiple' => '',
+        ], $optionsHtml);
+        $html .= $this->Bootstrap->button([
+            'size' => 'sm',
+            'icon' => 'plus',
+            'variant' => 'secondary',
+            'class' => ['badge'],
+            'params' => [
+                'onclick' => 'createTagPicker(this)',
+            ]
+        ]);
+        return $html;
+    }
+
+    public function tags(array $options = [])
+    {
+        $tags = !empty($options['tags']) ? $options['tags'] : [];
+        $html = '<div class="tag-container my-1">';
+        $html .= '<div class="tag-list d-inline-block">';
+        foreach ($tags as $tag) {
+            if (is_array($tag)) {
+                $html .= $this->tag($tag);
+            } else {
+                $html .= $this->tag([
+                    'name' => $tag
+                ]);
+            }
+        }
+        $html .= '</div>';
+        
+        if (!empty($options['picker'])) {
+            $html .= $this->picker($options);
+        }
+        $html .= '</div>';
+        return $html;
+    }
+
+    public function tag(array $tag)
+    {
+        $tag['colour'] = !empty($tag['colour']) ? $tag['colour'] : $this->getConfig()['default_colour'];
+        $textColour = $this->TextColour->getTextColour(h($tag['colour']));
+        $deleteButton = $this->Bootstrap->button([
+            'size' => 'sm',
+            'icon' => 'times',
+            'class' => ['ml-1', 'border-0', "text-${textColour}"],
+            'variant' => 'text',
+            'title' => __('Delete tag'),
+        ]);
+        
+        $html = $this->Bootstrap->genNode('span', [
+            'class' => [
+                'tag',
+                'badge',
+                'mx-1',
+                'align-middle',
+            ],
+            'title' => h($tag['name']),
+            'style' => sprintf('color:%s; background-color:%s', $textColour, h($tag['colour'])),
+        ], h($tag['name']) . $deleteButton);
+        return $html;
+    }
+}
diff --git a/src/View/Helper/TextColourHelper.php b/src/View/Helper/TextColourHelper.php
new file mode 100644
index 0000000..c484486
--- /dev/null
+++ b/src/View/Helper/TextColourHelper.php
@@ -0,0 +1,21 @@
+<?php
+namespace App\View\Helper;
+
+use Cake\View\Helper;
+
+// This helper helps determining the brightness of a colour (initially only used for the tagging) in order to decide
+// what text colour to use against the background (black or white)
+class TextColourHelper extends Helper {
+
+    public function getTextColour($RGB) {
+        $r = hexdec(substr($RGB, 1, 2));
+        $g = hexdec(substr($RGB, 3, 2));
+        $b = hexdec(substr($RGB, 5, 2));
+        $average = ((2 * $r) + $b + (3 * $g))/6;
+        if ($average < 127) {
+            return 'white';
+        } else {
+            return 'black';
+        }
+    }
+}
\ No newline at end of file
diff --git a/templates/Individuals/view.php b/templates/Individuals/view.php
index 6c4d6a8..3eeddbc 100644
--- a/templates/Individuals/view.php
+++ b/templates/Individuals/view.php
@@ -28,6 +28,10 @@ echo $this->element(
                 'key' => __('Position'),
                 'path' => 'position'
             ],
+            [
+                'key' => __('Tags'),
+                'type' => 'tags',
+            ],
             [
                 'key' => __('Alignments'),
                 'type' => 'alignment',
diff --git a/templates/element/genericElements/SingleViews/Fields/tagsField.php b/templates/element/genericElements/SingleViews/Fields/tagsField.php
new file mode 100644
index 0000000..a8b9f88
--- /dev/null
+++ b/templates/element/genericElements/SingleViews/Fields/tagsField.php
@@ -0,0 +1,16 @@
+<?php
+// $tags = Cake\Utility\Hash::extract($data, $field['path']);
+$tagList = Cake\Utility\Hash::get($data, 'tag_list');
+$tagList = ['tlp:red'];
+$allTags = [
+    ['id' => 'tlp:red', 'text' => 'tlp:red', 'colour' => 'red'],
+    ['id' => 'tlp:green', 'text' => 'tlp:green', 'colour' => 'green'],
+    ['id' => 'tlp:amber', 'text' => 'tlp:amber', 'colour' => '#983965'],
+    ['id' => 'tlp:white', 'text' => 'tlp:white', 'colour' => 'white'],
+];
+$this->loadHelper('Tag');
+echo $this->Tag->tags([
+    'allTags' => $allTags,
+    'tags' => $tagList,
+    'picker' => true,
+]);
\ No newline at end of file
diff --git a/templates/layout/default.php b/templates/layout/default.php
index 1e2cbde..d97b800 100644
--- a/templates/layout/default.php
+++ b/templates/layout/default.php
@@ -86,6 +86,5 @@ $cakeDescription = 'Cerebrate';
 </body>
 <script>
     const darkMode = (<?= empty($darkMode) ? 'false' : 'true' ?>)
-    $.fn.select2.defaults.set('theme', 'bootstrap4');
 </script>
 </html>
diff --git a/webroot/css/main.css b/webroot/css/main.css
index bcf6c0e..de19e15 100644
--- a/webroot/css/main.css
+++ b/webroot/css/main.css
@@ -115,6 +115,13 @@
 .text-black {color:black;}
 .text-white {color:white;}
 
+.lh-1 {
+    line-height: 1;
+}
+.lh-2 {
+    line-height: 1.5;
+}
+
 .link-unstyled, .link-unstyled:link, .link-unstyled:hover {
   color: inherit;
   text-decoration: inherit;
@@ -145,3 +152,15 @@ input[type="checkbox"]:disabled.change-cursor {
     border-bottom-left-radius: 0;
     border-bottom-right-radius: 0;
 }
+
+.select2-selection__choice { /* Our app do not have the same font size */
+    padding-left: 1.5em !important;
+}
+.picker-container .select2-selection {
+    border-top-right-radius: 0 !important;
+    border-bottom-right-radius: 0 !important;
+}
+.picker-container .picker-action .btn:first-child {
+    border-top-left-radius: 0 !important;
+    border-bottom-left-radius: 0 !important;
+}
\ No newline at end of file
diff --git a/webroot/js/bootstrap-helper.js b/webroot/js/bootstrap-helper.js
index 61bca3f..2fc230a 100644
--- a/webroot/js/bootstrap-helper.js
+++ b/webroot/js/bootstrap-helper.js
@@ -1108,4 +1108,13 @@ class HtmlHelper {
         }
         return $table
     }
-}
\ No newline at end of file
+
+    static tag(options={}) {
+        const $tag = $('<span/>')
+            .addClass(['tag', 'badge', 'border'])
+            .css({color: getTextColour(options.colour), 'background-color': options.colour})
+            .text(options.text)
+
+        return $tag
+    }
+}
diff --git a/webroot/js/main.js b/webroot/js/main.js
index d950781..9ff0797 100644
--- a/webroot/js/main.js
+++ b/webroot/js/main.js
@@ -99,6 +99,60 @@ function syntaxHighlightJson(json, indent) {
     });
 }
 
+function getTextColour(hex) {
+    if (hex === undefined || hex.length == 0) {
+        return 'black'
+    }
+    hex = hex.slice(1)
+    var r = parseInt(hex.substring(0,2), 16)
+    var g = parseInt(hex.substring(2,4), 16)
+    var b = parseInt(hex.substring(4,6), 16)
+    var avg = ((2 * r) + b + (3 * g))/6
+    if (avg < 128) {
+        return 'white'
+    } else {
+        return 'black'
+    }
+}
+
+function createTagPicker(clicked) {
+
+    function templateTag(state) {
+        if (!state.id) {
+            return state.text;
+        }
+        if (state.colour === undefined) {
+            state.colour = $(state.element).data('colour')
+        }
+        return HtmlHelper.tag(state)
+    }
+
+    const $clicked = $(clicked)
+    const $container = $clicked.closest('.tag-container')
+    $('.picker-container').remove()
+    const $pickerContainer = $('<div></div>').addClass(['picker-container', 'd-flex'])
+    const $select = $container.find('select.tag-input').removeClass('d-none').addClass('flex-grow-1')
+    const $saveButton = $('<button></button>').addClass(['btn btn-primary btn-sm', 'align-self-start'])
+        .append($('<span></span>').text('Save').prepend($('<i></i>').addClass('fa fa-save mr-1')))
+    const $cancelButton = $('<button></button>').addClass(['btn btn-secondary btn-sm', 'align-self-start'])
+        .append($('<span></span>').text('Cancel').prepend($('<i></i>').addClass('fa fa-times mr-1')))
+        .click(function() {
+            $select.appendTo($container)
+            $pickerContainer.remove()
+        })
+    const $buttons = $('<span></span>').addClass(['picker-action', 'btn-group']).append($saveButton, $cancelButton)
+    $select.prependTo($pickerContainer)
+    $pickerContainer.append($buttons)
+    $container.parent().append($pickerContainer)
+    $select.select2({
+        placeholder: 'Pick a tag',
+        tags: true,
+        templateResult: templateTag,
+        templateSelection: templateTag,
+    })
+}
+
+
 var UI
 $(document).ready(() => {
     if (typeof UIFactory !== "undefined") {

From 8b659fb6afec2285a5b0255a028fbc1ca9ff28b2 Mon Sep 17 00:00:00 2001
From: mokaddem <sami.mokaddem@circl.lu>
Date: Thu, 26 Aug 2021 12:06:12 +0200
Subject: [PATCH 02/16] chg: [tag] Continuation of integrating tagging plugin -
 WiP - Tagging / Untagging

---
 src/Controller/Component/CRUDComponent.php    | 154 ++++++++++++++++++
 src/Controller/IndividualsController.php      |  27 +++
 src/View/Helper/TagHelper.php                 |  84 ++++++----
 templates/Individuals/add.php                 |   6 +-
 .../genericElements/Form/Fields/tagsField.php |  19 +++
 .../SingleViews/Fields/tagsField.php          |   5 +-
 templates/genericTemplates/tag.php            |  13 ++
 templates/genericTemplates/tagForm.php        |  24 +++
 webroot/js/bootstrap-helper.js                |  25 ++-
 webroot/js/main.js                            |  70 +++++++-
 10 files changed, 382 insertions(+), 45 deletions(-)
 create mode 100644 templates/element/genericElements/Form/Fields/tagsField.php
 create mode 100644 templates/genericTemplates/tag.php
 create mode 100644 templates/genericTemplates/tagForm.php

diff --git a/src/Controller/Component/CRUDComponent.php b/src/Controller/Component/CRUDComponent.php
index 14f4c4f..2f32bcd 100644
--- a/src/Controller/Component/CRUDComponent.php
+++ b/src/Controller/Component/CRUDComponent.php
@@ -243,6 +243,9 @@ class CRUDComponent extends Component
             throw new NotFoundException(__('Invalid {0}.', $this->ObjectAlias));
         }
         $this->getMetaTemplates();
+        if ($this->taggingSupported()) {
+            $params['contain'][] = 'Tags';
+        }
         $data = $this->Table->get($id, isset($params['get']) ? $params['get'] : []);
         $data = $this->getMetaFields($id, $data);
         if (!empty($params['fields'])) {
@@ -350,6 +353,10 @@ class CRUDComponent extends Component
             throw new NotFoundException(__('Invalid {0}.', $this->ObjectAlias));
         }
 
+        if ($this->taggingSupported()) {
+            $params['contain'][] = 'Tags';
+        }
+
         $data = $this->Table->get($id, $params);
         $data = $this->attachMetaData($id, $data);
         if (isset($params['afterFind'])) {
@@ -404,6 +411,148 @@ class CRUDComponent extends Component
         $this->Controller->render('/genericTemplates/delete');
     }
 
+    public function tag($id=false): void
+    {
+        if (!$this->taggingSupported()) {
+            throw new Exception("Table {$this->TableAlias} does not support tagging");
+        }
+        if ($this->request->is('get')) {
+            if(!empty($id)) {
+                $params = [
+                    'contain' => 'Tags',
+                ];
+                $entity = $this->Table->get($id, $params);
+                $this->Controller->set('id', $entity->id);
+                $this->Controller->set('data', $entity);
+                $this->Controller->set('bulkEnabled', false);
+            } else {
+                $this->Controller->set('bulkEnabled', true);
+            }
+        } else if ($this->request->is('post') || $this->request->is('delete')) {
+            $ids = $this->getIdsOrFail($id);
+            $isBulk = count($ids) > 1;
+            $bulkSuccesses = 0;
+            foreach ($ids as $id) {
+                $params = [
+                    'contain' => 'Tags',
+                ];
+                $entity = $this->Table->get($id, $params);
+                // patching will mirror tag in the DB, however, we only want to add tags
+                $input = $this->request->getData();
+                $tagsToAdd = explode(',', $input['tag_list']);
+                $entity->tag_list = $entity->tag_list;
+                $input['tag_list'] = implode(',', array_merge($tagsToAdd, $entity->tag_list));
+                $patchEntityParams = [
+                    'fields' => ['tags'],
+                ];
+                $entity = $this->Table->patchEntity($entity, $input, $patchEntityParams);
+                $savedData = $this->Table->save($entity);
+                $success = true;
+                if ($success) {
+                    $bulkSuccesses++;
+                }
+            }
+            $message = $this->getMessageBasedOnResult(
+                $bulkSuccesses == count($ids),
+                $isBulk,
+                __('{0} tagged.', $this->ObjectAlias),
+                __('All {0} have been tagged.', Inflector::pluralize($this->ObjectAlias)),
+                __('Could not tag {0}.', $this->ObjectAlias),
+                __('{0} / {1} {2} have been tagged.',
+                    $bulkSuccesses,
+                    count($ids),
+                    Inflector::pluralize($this->ObjectAlias)
+                )
+            );
+            $this->setResponseForController('tag', $bulkSuccesses, $message, $savedData);
+        }
+        $this->Controller->viewBuilder()->setLayout('ajax');
+        $this->Controller->render('/genericTemplates/tagForm');
+    }
+
+    public function untag($id=false): void
+    {
+        if (!$this->taggingSupported()) {
+            throw new Exception("Table {$this->TableAlias} does not support tagging");
+        }
+        if ($this->request->is('get')) {
+            if(!empty($id)) {
+                $params = [
+                    'contain' => 'Tags',
+                ];
+                $entity = $this->Table->get($id, $params);
+                $this->Controller->set('id', $entity->id);
+                $this->Controller->set('data', $entity);
+                $this->Controller->set('bulkEnabled', false);
+            } else {
+                $this->Controller->set('bulkEnabled', true);
+            }
+        } else if ($this->request->is('post') || $this->request->is('delete')) {
+            $ids = $this->getIdsOrFail($id);
+            $isBulk = count($ids) > 1;
+            $bulkSuccesses = 0;
+            foreach ($ids as $id) {
+                $params = [
+                    'contain' => 'Tags',
+                ];
+                $entity = $this->Table->get($id, $params);
+                // patching will mirror tag in the DB, however, we only want to remove tags
+                $input = $this->request->getData();
+                $tagsToRemove = explode(',', $input['tag_list']);
+                $entity->tag_list = $entity->tag_list;
+                $input['tag_list'] = implode(',', array_filter($entity->tag_list, function ($existingTag) use ($tagsToRemove) {
+                    return !in_array($existingTag, $tagsToRemove);
+                }));
+                $patchEntityParams = [
+                    'fields' => ['tags'],
+                ];
+                $entity = $this->Table->patchEntity($entity, $input, $patchEntityParams);
+                $savedData = $this->Table->save($entity);
+                $success = true;
+                if ($success) {
+                    $bulkSuccesses++;
+                }
+            }
+            $message = $this->getMessageBasedOnResult(
+                $bulkSuccesses == count($ids),
+                $isBulk,
+                __('{0} untagged.', $this->ObjectAlias),
+                __('All {0} have been untagged.', Inflector::pluralize($this->ObjectAlias)),
+                __('Could not untag {0}.', $this->ObjectAlias),
+                __('{0} / {1} {2} have been untagged.',
+                    $bulkSuccesses,
+                    count($ids),
+                    Inflector::pluralize($this->ObjectAlias)
+                )
+            );
+            $this->setResponseForController('tag', $bulkSuccesses, $message, $entity);
+        }
+        $this->Controller->viewBuilder()->setLayout('ajax');
+        $this->Controller->render('/genericTemplates/tagForm');
+    }
+
+    public function viewTags(int $id, array $params = []): void
+    {
+        if (!$this->taggingSupported()) {
+            throw new Exception("Table {$this->TableAlias} does not support tagging");
+        }
+        if (empty($id)) {
+            throw new NotFoundException(__('Invalid {0}.', $this->ObjectAlias));
+        }
+
+        $params['contain'][] = 'Tags';
+        $data = $this->Table->get($id, $params);
+        if (isset($params['afterFind'])) {
+            $data = $params['afterFind']($data);
+        }
+        if ($this->Controller->ParamHandler->isRest()) {
+            $this->Controller->restResponsePayload = $this->RestResponse->viewData($data, 'json');
+        }
+        $this->Controller->set('entity', $data);
+        $this->Controller->viewBuilder()->setLayout('ajax');
+        $this->Controller->render('/genericTemplates/tag');
+    }
+
     public function setResponseForController($action, $success, $message, $data=[], $errors=null)
     {
         if ($success) {
@@ -683,6 +832,11 @@ class CRUDComponent extends Component
         return $prefixedConditions;
     }
 
+    public function taggingSupported()
+    {
+        return $this->Table->behaviors()->has('Tag');
+    }
+
     public function toggle(int $id, string $fieldName = 'enabled', array $params = []): void
     {
         if (empty($id)) {
diff --git a/src/Controller/IndividualsController.php b/src/Controller/IndividualsController.php
index e3445eb..13e37c8 100644
--- a/src/Controller/IndividualsController.php
+++ b/src/Controller/IndividualsController.php
@@ -72,4 +72,31 @@ class IndividualsController extends AppController
         }
         $this->set('metaGroup', 'ContactDB');
     }
+
+    public function tag($id)
+    {
+        $this->CRUD->tag($id);
+        $responsePayload = $this->CRUD->getResponsePayload();
+        if (!empty($responsePayload)) {
+            return $responsePayload;
+        }
+    }
+
+    public function untag($id)
+    {
+        $this->CRUD->untag($id);
+        $responsePayload = $this->CRUD->getResponsePayload();
+        if (!empty($responsePayload)) {
+            return $responsePayload;
+        }
+    }
+
+    public function viewTags($id)
+    {
+        $this->CRUD->viewTags($id);
+        $responsePayload = $this->CRUD->getResponsePayload();
+        if (!empty($responsePayload)) {
+            return $responsePayload;
+        }
+    }
 }
diff --git a/src/View/Helper/TagHelper.php b/src/View/Helper/TagHelper.php
index 2cca055..9e38f1c 100644
--- a/src/View/Helper/TagHelper.php
+++ b/src/View/Helper/TagHelper.php
@@ -11,31 +11,38 @@ class TagHelper extends Helper
         'Bootstrap',
         'TextColour',
         'FontAwesome',
+        'Form',
+        'Url',
         'Tags.Tag',
     ];
 
-    protected $_defaultConfig = [
-        'default_colour' => '#983965',
+    protected $defaultConfig = [
+        'default_colour' => '#924da6',
+        'picker' => false,
+        'editable' => false,
     ];
 
     public function control(array $options = [])
     {
-        return $this->Tag->control($options);
-    }
-
-    public function picker(array $options = [])
-    {
-        $optionsHtml = '';
-        foreach ($options['allTags'] as $i => $tag) {
-            $optionsHtml .= $this->Bootstrap->genNode('option', [
+        $field = 'tag_list';
+        $values = !empty($options['allTags']) ? array_map(function($tag) {
+            return [
+                'text' => h($tag['text']),
                 'value' => h($tag['text']),
                 'data-colour' => h($tag['colour']),
-            ], h($tag['text']));
-        }
-        $html = $this->Bootstrap->genNode('select', [
-            'class' => ['tag-input', 'd-none'],
-            'multiple' => '',
-        ], $optionsHtml);
+            ];
+        }, $options['allTags']) : [];
+        $selectConfig = [
+            'multiple' => true,
+            // 'value' => $options['tags'],
+            'class' => ['tag-input', 'd-none']
+        ];
+        return $this->Form->select($field, $values, $selectConfig);
+    }
+
+    protected function picker(array $options = [])
+    {
+        $html =  $this->Tag->control($options);
         $html .= $this->Bootstrap->button([
             'size' => 'sm',
             'icon' => 'plus',
@@ -50,8 +57,10 @@ class TagHelper extends Helper
 
     public function tags(array $options = [])
     {
+        $this->_config = array_merge($this->defaultConfig, $options);
         $tags = !empty($options['tags']) ? $options['tags'] : [];
-        $html = '<div class="tag-container my-1">';
+        $html = '<div class="tag-container-wrapper">';
+        $html .= '<div class="tag-container my-1">';
         $html .= '<div class="tag-list d-inline-block">';
         foreach ($tags as $tag) {
             if (is_array($tag)) {
@@ -64,25 +73,44 @@ class TagHelper extends Helper
         }
         $html .= '</div>';
         
-        if (!empty($options['picker'])) {
+        if (!empty($this->getConfig('picker'))) {
             $html .= $this->picker($options);
         }
         $html .= '</div>';
+        $html .= '</div>';
         return $html;
     }
 
-    public function tag(array $tag)
+    public function tag(array $tag, array $options = [])
     {
-        $tag['colour'] = !empty($tag['colour']) ? $tag['colour'] : $this->getConfig()['default_colour'];
+        if (empty($this->_config)) {
+            $this->_config = array_merge($this->defaultConfig, $options);
+        }
+        $tag['colour'] = !empty($tag['colour']) ? $tag['colour'] : $this->getConfig('default_colour');
         $textColour = $this->TextColour->getTextColour(h($tag['colour']));
-        $deleteButton = $this->Bootstrap->button([
-            'size' => 'sm',
-            'icon' => 'times',
-            'class' => ['ml-1', 'border-0', "text-${textColour}"],
-            'variant' => 'text',
-            'title' => __('Delete tag'),
-        ]);
-        
+
+        if (!empty($this->getConfig('editable'))) {
+            $deleteButton = $this->Bootstrap->button([
+                'size' => 'sm',
+                'icon' => 'times',
+                'class' => ['ml-1', 'border-0', "text-${textColour}"],
+                'variant' => 'text',
+                'title' => __('Delete tag'),
+                'params' => [
+                    'onclick' => sprintf('deleteTag(\'%s\', \'%s\', this)',
+                        $this->Url->build([
+                            'controller' => $this->getView()->getName(),
+                            'action' => 'untag',
+                            $this->getView()->get('entity')['id']
+                        ]),
+                        h($tag['name'])
+                    ),
+                ],
+            ]);
+        } else {
+            $deleteButton = '';
+        }
+
         $html = $this->Bootstrap->genNode('span', [
             'class' => [
                 'tag',
diff --git a/templates/Individuals/add.php b/templates/Individuals/add.php
index 1941ad3..935c2de 100644
--- a/templates/Individuals/add.php
+++ b/templates/Individuals/add.php
@@ -20,7 +20,11 @@
                 ),
                 array(
                     'field' => 'position'
-                )
+                ),
+                array(
+                    'field' => 'tag_list',
+                    'type' => 'tags'
+                ),
             ),
             'metaTemplates' => empty($metaTemplates) ? [] : $metaTemplates,
             'submit' => array(
diff --git a/templates/element/genericElements/Form/Fields/tagsField.php b/templates/element/genericElements/Form/Fields/tagsField.php
new file mode 100644
index 0000000..fdc99f1
--- /dev/null
+++ b/templates/element/genericElements/Form/Fields/tagsField.php
@@ -0,0 +1,19 @@
+<?php
+    $allTags = [
+        ['id' => 'tlp:red', 'text' => 'tlp:red', 'colour' => 'red'],
+        ['id' => 'tlp:green', 'text' => 'tlp:green', 'colour' => 'green'],
+        ['id' => 'tlp:amber', 'text' => 'tlp:amber', 'colour' => '#983965'],
+        ['id' => 'tlp:white', 'text' => 'tlp:white', 'colour' => 'white'],
+    ];
+    $tagsHtml = $this->Tag->tags([
+        'allTags' => $allTags,
+        'tags' => $entity['tag_list'],
+        'picker' => true,
+    ]);
+?>
+<div class="form-group row">
+    <div class="col-sm-2 col-form-label"><?= __('Tags') ?></div>
+    <div class="col-sm-10">
+        <?= $tagsHtml ?>
+    </div>
+</div>
\ No newline at end of file
diff --git a/templates/element/genericElements/SingleViews/Fields/tagsField.php b/templates/element/genericElements/SingleViews/Fields/tagsField.php
index a8b9f88..564ee3e 100644
--- a/templates/element/genericElements/SingleViews/Fields/tagsField.php
+++ b/templates/element/genericElements/SingleViews/Fields/tagsField.php
@@ -1,16 +1,15 @@
 <?php
 // $tags = Cake\Utility\Hash::extract($data, $field['path']);
 $tagList = Cake\Utility\Hash::get($data, 'tag_list');
-$tagList = ['tlp:red'];
 $allTags = [
     ['id' => 'tlp:red', 'text' => 'tlp:red', 'colour' => 'red'],
     ['id' => 'tlp:green', 'text' => 'tlp:green', 'colour' => 'green'],
     ['id' => 'tlp:amber', 'text' => 'tlp:amber', 'colour' => '#983965'],
     ['id' => 'tlp:white', 'text' => 'tlp:white', 'colour' => 'white'],
 ];
-$this->loadHelper('Tag');
 echo $this->Tag->tags([
     'allTags' => $allTags,
     'tags' => $tagList,
     'picker' => true,
-]);
\ No newline at end of file
+    'editable' => true,
+]);
diff --git a/templates/genericTemplates/tag.php b/templates/genericTemplates/tag.php
new file mode 100644
index 0000000..4f97df8
--- /dev/null
+++ b/templates/genericTemplates/tag.php
@@ -0,0 +1,13 @@
+<?php
+    $allTags = [
+        ['id' => 'tlp:red', 'text' => 'tlp:red', 'colour' => 'red'],
+        ['id' => 'tlp:green', 'text' => 'tlp:green', 'colour' => 'green'],
+        ['id' => 'tlp:amber', 'text' => 'tlp:amber', 'colour' => '#983965'],
+        ['id' => 'tlp:white', 'text' => 'tlp:white', 'colour' => 'white'],
+    ];
+    echo $this->Tag->tags([
+        'allTags' => $allTags,
+        'tags' => $entity->tag_list,
+        'picker' => true,
+        'editable' => true,
+    ]);
diff --git a/templates/genericTemplates/tagForm.php b/templates/genericTemplates/tagForm.php
new file mode 100644
index 0000000..be5ebba
--- /dev/null
+++ b/templates/genericTemplates/tagForm.php
@@ -0,0 +1,24 @@
+<?php
+$form = $this->element('genericElements/Form/genericForm', [
+    'entity' => null,
+    'ajax' => false,
+    'raw' => true,
+    'data' => [
+        'fields' => [
+            [
+                'type' => 'text',
+                'field' => 'ids',
+                'default' => !empty($id) ? json_encode([$id]) : ''
+            ],
+            [
+                'type' => 'text',
+                'field' => 'tag_list',
+            ],
+        ],
+        'submit' => [
+            'action' => $this->request->getParam('action')
+        ]
+    ]
+]);
+$formHTML = sprintf('<div class="d-none">%s</div>', $form);
+echo $formHTML;
diff --git a/webroot/js/bootstrap-helper.js b/webroot/js/bootstrap-helper.js
index 2fc230a..48be80c 100644
--- a/webroot/js/bootstrap-helper.js
+++ b/webroot/js/bootstrap-helper.js
@@ -217,8 +217,9 @@ class UIFactory {
         return AJAXApi.quickFetchURL(url, {
             statusNode: $statusNode[0],
         }).then((theHTML) => {
-            $container.replaceWith(theHTML)
-            return $container
+            var $tmp = $(theHTML);
+            $container.replaceWith($tmp)
+            return $tmp;
         }).finally(() => {
             otherStatusNodes.forEach(overlay => {
                 overlay.hide()
@@ -267,9 +268,9 @@ class Toaster {
      * @property {string=('primary'|'secondary'|'success'|'danger'|'warning'|'info'|'light'|'dark'|'white'|'transparent')} variant - The variant of the toast
      * @property {boolean} autohide    - If the toast show be hidden after some time defined by the delay
      * @property {number}  delay        - The number of milliseconds the toast should stay visible before being hidden
-     * @property {string}  titleHtml    - The raw HTML title's content of the toast
-     * @property {string}  mutedHtml    - The raw HTML muted's content of the toast
-     * @property {string}  bodyHtml     - The raw HTML body's content of the toast
+     * @property {(jQuery|string)}  titleHtml    - The raw HTML title's content of the toast
+     * @property {(jQuery|string)}  mutedHtml    - The raw HTML muted's content of the toast
+     * @property {(jQuery|string)}  bodyHtml     - The raw HTML body's content of the toast
      * @property {boolean} closeButton - If the toast's title should include a close button
      */
     static defaultOptions = {
@@ -860,7 +861,8 @@ class OverlayFactory {
         spinnerVariant: '',
         spinnerSmall: false,
         spinnerType: 'border',
-        fallbackBoostrapVariant: ''
+        fallbackBoostrapVariant: '',
+        wrapperCSSDisplay: '',
     }
 
     static overlayWrapper = '<div aria-busy="true" class="position-relative"/>'
@@ -875,6 +877,14 @@ class OverlayFactory {
      /** Create the HTML of the overlay */
     buildOverlay() {
         this.$overlayWrapper = $(OverlayFactory.overlayWrapper)
+        if (this.options.wrapperCSSDisplay) {
+            this.$overlayWrapper.css('display', this.options.wrapperCSSDisplay)
+        }
+        if (this.$node[0]) {
+            const boundingRect = this.$node[0].getBoundingClientRect()
+            this.$overlayWrapper.css('min-height', boundingRect.height)
+            this.$overlayWrapper.css('min-width', boundingRect.width)
+        }
         this.$overlayContainer = $(OverlayFactory.overlayContainer)
         this.$overlayBg = $(OverlayFactory.overlayBg)
             .addClass([`bg-${this.options.variant}`, (this.options.rounded ? 'rounded' : '')])
@@ -940,7 +950,8 @@ class OverlayFactory {
         }
         if (this.$node.is('input[type="checkbox"]') || this.$node.css('border-radius') !== '0px') {
             this.options.rounded = true
-        } 
+        }
+        this.options.wrapperCSSDisplay = this.$node.css('display')
         let classes = this.$node.attr('class')
         if (classes !== undefined) {
             classes = classes.split(' ')
diff --git a/webroot/js/main.js b/webroot/js/main.js
index 9ff0797..7c5cd73 100644
--- a/webroot/js/main.js
+++ b/webroot/js/main.js
@@ -127,18 +127,26 @@ function createTagPicker(clicked) {
         return HtmlHelper.tag(state)
     }
 
+    function closePicker($select, $container) {
+        $select.appendTo($container)
+        $container.parent().find('.picker-container').remove()
+    }
+
     const $clicked = $(clicked)
     const $container = $clicked.closest('.tag-container')
-    $('.picker-container').remove()
+    const $select = $container.parent().find('select.tag-input').removeClass('d-none').addClass('flex-grow-1')
+    closePicker($select, $container)
     const $pickerContainer = $('<div></div>').addClass(['picker-container', 'd-flex'])
-    const $select = $container.find('select.tag-input').removeClass('d-none').addClass('flex-grow-1')
-    const $saveButton = $('<button></button>').addClass(['btn btn-primary btn-sm', 'align-self-start'])
+    const $saveButton = $('<button></button>').addClass(['btn btn-primary btn-sm', 'align-self-start']).attr('type', 'button')
         .append($('<span></span>').text('Save').prepend($('<i></i>').addClass('fa fa-save mr-1')))
-    const $cancelButton = $('<button></button>').addClass(['btn btn-secondary btn-sm', 'align-self-start'])
+        .click(function() {
+            const tags = $select.select2('data').map(tag => tag.text)
+            addTags(tags, $(this))
+        })
+    const $cancelButton = $('<button></button>').addClass(['btn btn-secondary btn-sm', 'align-self-start']).attr('type', 'button')
         .append($('<span></span>').text('Cancel').prepend($('<i></i>').addClass('fa fa-times mr-1')))
         .click(function() {
-            $select.appendTo($container)
-            $pickerContainer.remove()
+            closePicker($select, $container)
         })
     const $buttons = $('<span></span>').addClass(['picker-action', 'btn-group']).append($saveButton, $cancelButton)
     $select.prependTo($pickerContainer)
@@ -152,6 +160,56 @@ function createTagPicker(clicked) {
     })
 }
 
+function deleteTag(url, tag, clicked) {
+    const data = {
+        tag_list: tag
+    }
+    const $statusNode = $(clicked).closest('.tag')
+    const APIOptions = {
+        statusNode: $statusNode,
+        skipFeedback: true,
+    }
+    return AJAXApi.quickFetchAndPostForm(url, data, APIOptions).then((result) => {
+        let $container = $statusNode.closest('.tag-container-wrapper')
+        refreshTagList(result, $container).then(($tagContainer) => {
+            $container = $tagContainer // old container might not exist anymore since it was replaced after the refresh
+        })
+        const theToast = UI.toast({
+            variant: 'success',
+            title: 'Tag deleted',
+            bodyHtml: $('<div/>').append(
+                $('<span/>').text('Cancel untag operation.'),
+                $('<button/>').addClass(['btn', 'btn-primary', 'btn-sm', 'ml-3']).text('Restore tag').click(function() {
+                    addTags([tag], $container.find('.tag-container')).then(() => {
+                        theToast.removeToast()
+                    })
+                }),
+            ),
+        })
+    }).catch((e) => {})
+}
+
+function addTags(tags, $statusNode) {
+    const url = '/individuals/tag/2'
+    const data = {
+        tag_list: tags
+    }
+    const APIOptions = {
+        statusNode: $statusNode
+    }
+    return AJAXApi.quickFetchAndPostForm(url, data, APIOptions).then((result) => {
+        const $container = $statusNode.closest('.tag-container-wrapper')
+        refreshTagList(result, $container)
+    }).catch((e) => {})
+}
+
+function refreshTagList(result, $container) {
+    const controllerName = result.url.split('/')[1]
+    const entityId = result.data.id
+    const url = `/${controllerName}/viewTags/${entityId}`
+    return UI.reload(url, $container)
+}
+
 
 var UI
 $(document).ready(() => {

From 29595c6e22d13b8f9de30356849e2cb412060bd9 Mon Sep 17 00:00:00 2001
From: mokaddem <sami.mokaddem@circl.lu>
Date: Thu, 26 Aug 2021 16:12:55 +0200
Subject: [PATCH 03/16] chg: [tag] Continuation of integrating tagging plugin -
 WiP - Can tag/untag any model

---
 src/Controller/Component/CRUDComponent.php    | 20 +++++++++++---
 src/Controller/IndividualsController.php      |  1 +
 src/View/Helper/TagHelper.php                 | 27 +++++++++++--------
 .../genericElements/Form/Fields/tagsField.php |  8 +-----
 .../SingleViews/Fields/tagsField.php          | 10 ++-----
 templates/genericTemplates/tag.php            |  8 +-----
 webroot/js/bootstrap-helper.js                |  3 +++
 webroot/js/main.js                            | 15 ++++++-----
 8 files changed, 49 insertions(+), 43 deletions(-)

diff --git a/src/Controller/Component/CRUDComponent.php b/src/Controller/Component/CRUDComponent.php
index 2f32bcd..0342a67 100644
--- a/src/Controller/Component/CRUDComponent.php
+++ b/src/Controller/Component/CRUDComponent.php
@@ -7,6 +7,7 @@ use Cake\Error\Debugger;
 use Cake\Utility\Hash;
 use Cake\Utility\Inflector;
 use Cake\View\ViewBuilder;
+use Cake\ORM\TableRegistry;
 use Cake\Http\Exception\MethodNotAllowedException;
 use Cake\Http\Exception\NotFoundException;
 
@@ -355,6 +356,7 @@ class CRUDComponent extends Component
 
         if ($this->taggingSupported()) {
             $params['contain'][] = 'Tags';
+            $this->setAllTags();
         }
 
         $data = $this->Table->get($id, $params);
@@ -417,6 +419,7 @@ class CRUDComponent extends Component
             throw new Exception("Table {$this->TableAlias} does not support tagging");
         }
         if ($this->request->is('get')) {
+            $this->setAllTags();
             if(!empty($id)) {
                 $params = [
                     'contain' => 'Tags',
@@ -455,9 +458,9 @@ class CRUDComponent extends Component
             $message = $this->getMessageBasedOnResult(
                 $bulkSuccesses == count($ids),
                 $isBulk,
-                __('{0} tagged.', $this->ObjectAlias),
+                __('{0} tagged with `{1}`.', $this->ObjectAlias, $input['tag_list']),
                 __('All {0} have been tagged.', Inflector::pluralize($this->ObjectAlias)),
-                __('Could not tag {0}.', $this->ObjectAlias),
+                __('Could not tag {0} with `{1}`.', $this->ObjectAlias, $input['tag_list']),
                 __('{0} / {1} {2} have been tagged.',
                     $bulkSuccesses,
                     count($ids),
@@ -476,6 +479,7 @@ class CRUDComponent extends Component
             throw new Exception("Table {$this->TableAlias} does not support tagging");
         }
         if ($this->request->is('get')) {
+            $this->setAllTags();
             if(!empty($id)) {
                 $params = [
                     'contain' => 'Tags',
@@ -516,9 +520,9 @@ class CRUDComponent extends Component
             $message = $this->getMessageBasedOnResult(
                 $bulkSuccesses == count($ids),
                 $isBulk,
-                __('{0} untagged.', $this->ObjectAlias),
+                __('{0} untagged with `{1}`.', $this->ObjectAlias, implode(', ', $tagsToRemove)),
                 __('All {0} have been untagged.', Inflector::pluralize($this->ObjectAlias)),
-                __('Could not untag {0}.', $this->ObjectAlias),
+                __('Could not untag {0} with `{1}`.', $this->ObjectAlias, $input['tag_list']),
                 __('{0} / {1} {2} have been untagged.',
                     $bulkSuccesses,
                     count($ids),
@@ -549,6 +553,7 @@ class CRUDComponent extends Component
             $this->Controller->restResponsePayload = $this->RestResponse->viewData($data, 'json');
         }
         $this->Controller->set('entity', $data);
+        $this->setAllTags();
         $this->Controller->viewBuilder()->setLayout('ajax');
         $this->Controller->render('/genericTemplates/tag');
     }
@@ -837,6 +842,13 @@ class CRUDComponent extends Component
         return $this->Table->behaviors()->has('Tag');
     }
 
+    public function setAllTags()
+    {
+        $this->Tags = TableRegistry::getTableLocator()->get('Tags.Tags');
+        $allTags = $this->Tags->find()->all()->toList();
+        $this->Controller->set('allTags', $allTags);
+    }
+
     public function toggle(int $id, string $fieldName = 'enabled', array $params = []): void
     {
         if (empty($id)) {
diff --git a/src/Controller/IndividualsController.php b/src/Controller/IndividualsController.php
index 13e37c8..046824f 100644
--- a/src/Controller/IndividualsController.php
+++ b/src/Controller/IndividualsController.php
@@ -9,6 +9,7 @@ use Cake\Database\Expression\QueryExpression;
 use Cake\Http\Exception\NotFoundException;
 use Cake\Http\Exception\MethodNotAllowedException;
 use Cake\Http\Exception\ForbiddenException;
+use Cake\ORM\TableRegistry;
 
 class IndividualsController extends AppController
 {
diff --git a/src/View/Helper/TagHelper.php b/src/View/Helper/TagHelper.php
index 9e38f1c..9b0449b 100644
--- a/src/View/Helper/TagHelper.php
+++ b/src/View/Helper/TagHelper.php
@@ -27,15 +27,20 @@ class TagHelper extends Helper
         $field = 'tag_list';
         $values = !empty($options['allTags']) ? array_map(function($tag) {
             return [
-                'text' => h($tag['text']),
-                'value' => h($tag['text']),
+                'text' => h($tag['label']),
+                'value' => h($tag['label']),
                 'data-colour' => h($tag['colour']),
+                'data-text-colour' => h($tag['text_colour']),
             ];
         }, $options['allTags']) : [];
         $selectConfig = [
             'multiple' => true,
-            // 'value' => $options['tags'],
-            'class' => ['tag-input', 'd-none']
+            'class' => ['tag-input', 'd-none'],
+            'data-url' => $this->Url->build([
+                'controller' => $this->getView()->getName(),
+                'action' => 'tag',
+                $this->getView()->get('entity')['id']
+            ]),
         ];
         return $this->Form->select($field, $values, $selectConfig);
     }
@@ -63,11 +68,11 @@ class TagHelper extends Helper
         $html .= '<div class="tag-container my-1">';
         $html .= '<div class="tag-list d-inline-block">';
         foreach ($tags as $tag) {
-            if (is_array($tag)) {
+            if (is_object($tag)) {
                 $html .= $this->tag($tag);
             } else {
                 $html .= $this->tag([
-                    'name' => $tag
+                    'label' => $tag
                 ]);
             }
         }
@@ -81,13 +86,13 @@ class TagHelper extends Helper
         return $html;
     }
 
-    public function tag(array $tag, array $options = [])
+    public function tag($tag, array $options = [])
     {
         if (empty($this->_config)) {
             $this->_config = array_merge($this->defaultConfig, $options);
         }
         $tag['colour'] = !empty($tag['colour']) ? $tag['colour'] : $this->getConfig('default_colour');
-        $textColour = $this->TextColour->getTextColour(h($tag['colour']));
+        $textColour = !empty($tag['text_colour']) ? $tag['text_colour'] : $this->TextColour->getTextColour(h($tag['colour']));;
 
         if (!empty($this->getConfig('editable'))) {
             $deleteButton = $this->Bootstrap->button([
@@ -103,7 +108,7 @@ class TagHelper extends Helper
                             'action' => 'untag',
                             $this->getView()->get('entity')['id']
                         ]),
-                        h($tag['name'])
+                        h($tag['label'])
                     ),
                 ],
             ]);
@@ -118,9 +123,9 @@ class TagHelper extends Helper
                 'mx-1',
                 'align-middle',
             ],
-            'title' => h($tag['name']),
+            'title' => h($tag['label']),
             'style' => sprintf('color:%s; background-color:%s', $textColour, h($tag['colour'])),
-        ], h($tag['name']) . $deleteButton);
+        ], h($tag['label']) . $deleteButton);
         return $html;
     }
 }
diff --git a/templates/element/genericElements/Form/Fields/tagsField.php b/templates/element/genericElements/Form/Fields/tagsField.php
index fdc99f1..ba35700 100644
--- a/templates/element/genericElements/Form/Fields/tagsField.php
+++ b/templates/element/genericElements/Form/Fields/tagsField.php
@@ -1,13 +1,7 @@
 <?php
-    $allTags = [
-        ['id' => 'tlp:red', 'text' => 'tlp:red', 'colour' => 'red'],
-        ['id' => 'tlp:green', 'text' => 'tlp:green', 'colour' => 'green'],
-        ['id' => 'tlp:amber', 'text' => 'tlp:amber', 'colour' => '#983965'],
-        ['id' => 'tlp:white', 'text' => 'tlp:white', 'colour' => 'white'],
-    ];
     $tagsHtml = $this->Tag->tags([
         'allTags' => $allTags,
-        'tags' => $entity['tag_list'],
+        'tags' => $entity['tags'],
         'picker' => true,
     ]);
 ?>
diff --git a/templates/element/genericElements/SingleViews/Fields/tagsField.php b/templates/element/genericElements/SingleViews/Fields/tagsField.php
index 564ee3e..16f7a71 100644
--- a/templates/element/genericElements/SingleViews/Fields/tagsField.php
+++ b/templates/element/genericElements/SingleViews/Fields/tagsField.php
@@ -1,15 +1,9 @@
 <?php
 // $tags = Cake\Utility\Hash::extract($data, $field['path']);
-$tagList = Cake\Utility\Hash::get($data, 'tag_list');
-$allTags = [
-    ['id' => 'tlp:red', 'text' => 'tlp:red', 'colour' => 'red'],
-    ['id' => 'tlp:green', 'text' => 'tlp:green', 'colour' => 'green'],
-    ['id' => 'tlp:amber', 'text' => 'tlp:amber', 'colour' => '#983965'],
-    ['id' => 'tlp:white', 'text' => 'tlp:white', 'colour' => 'white'],
-];
+$tags = Cake\Utility\Hash::get($data, 'tags');
 echo $this->Tag->tags([
     'allTags' => $allTags,
-    'tags' => $tagList,
+    'tags' => $tags,
     'picker' => true,
     'editable' => true,
 ]);
diff --git a/templates/genericTemplates/tag.php b/templates/genericTemplates/tag.php
index 4f97df8..c1bc69b 100644
--- a/templates/genericTemplates/tag.php
+++ b/templates/genericTemplates/tag.php
@@ -1,13 +1,7 @@
 <?php
-    $allTags = [
-        ['id' => 'tlp:red', 'text' => 'tlp:red', 'colour' => 'red'],
-        ['id' => 'tlp:green', 'text' => 'tlp:green', 'colour' => 'green'],
-        ['id' => 'tlp:amber', 'text' => 'tlp:amber', 'colour' => '#983965'],
-        ['id' => 'tlp:white', 'text' => 'tlp:white', 'colour' => 'white'],
-    ];
     echo $this->Tag->tags([
         'allTags' => $allTags,
-        'tags' => $entity->tag_list,
+        'tags' => $entity->tags,
         'picker' => true,
         'editable' => true,
     ]);
diff --git a/webroot/js/bootstrap-helper.js b/webroot/js/bootstrap-helper.js
index 48be80c..cc740d3 100644
--- a/webroot/js/bootstrap-helper.js
+++ b/webroot/js/bootstrap-helper.js
@@ -1121,6 +1121,9 @@ class HtmlHelper {
     }
 
     static tag(options={}) {
+        if (!options.colour) {
+            options.colour = '#924da6'
+        }
         const $tag = $('<span/>')
             .addClass(['tag', 'badge', 'border'])
             .css({color: getTextColour(options.colour), 'background-color': options.colour})
diff --git a/webroot/js/main.js b/webroot/js/main.js
index 7c5cd73..57e7560 100644
--- a/webroot/js/main.js
+++ b/webroot/js/main.js
@@ -119,7 +119,7 @@ function createTagPicker(clicked) {
 
     function templateTag(state) {
         if (!state.id) {
-            return state.text;
+            return state.label;
         }
         if (state.colour === undefined) {
             state.colour = $(state.element).data('colour')
@@ -141,7 +141,7 @@ function createTagPicker(clicked) {
         .append($('<span></span>').text('Save').prepend($('<i></i>').addClass('fa fa-save mr-1')))
         .click(function() {
             const tags = $select.select2('data').map(tag => tag.text)
-            addTags(tags, $(this))
+            addTags($select.data('url'), tags, $(this))
         })
     const $cancelButton = $('<button></button>').addClass(['btn btn-secondary btn-sm', 'align-self-start']).attr('type', 'button')
         .append($('<span></span>').text('Cancel').prepend($('<i></i>').addClass('fa fa-times mr-1')))
@@ -176,11 +176,15 @@ function deleteTag(url, tag, clicked) {
         })
         const theToast = UI.toast({
             variant: 'success',
-            title: 'Tag deleted',
+            title: result.message,
             bodyHtml: $('<div/>').append(
                 $('<span/>').text('Cancel untag operation.'),
                 $('<button/>').addClass(['btn', 'btn-primary', 'btn-sm', 'ml-3']).text('Restore tag').click(function() {
-                    addTags([tag], $container.find('.tag-container')).then(() => {
+                    const split = url.split('/')
+                    const controllerName = split[1]
+                    const id = split[3]
+                    const urlRetag = `/${controllerName}/tag/${id}`
+                    addTags(urlRetag, [tag], $container.find('.tag-container')).then(() => {
                         theToast.removeToast()
                     })
                 }),
@@ -189,8 +193,7 @@ function deleteTag(url, tag, clicked) {
     }).catch((e) => {})
 }
 
-function addTags(tags, $statusNode) {
-    const url = '/individuals/tag/2'
+function addTags(url, tags, $statusNode) {
     const data = {
         tag_list: tags
     }

From a4535ea42e9abc4b9a5a2d311a01a4a9329e5bee Mon Sep 17 00:00:00 2001
From: mokaddem <sami.mokaddem@circl.lu>
Date: Mon, 30 Aug 2021 15:11:21 +0200
Subject: [PATCH 04/16] chg: [tag] Continuation of integrating tagging plugin -
 WiP - Filtering - CRUD of tags

---
 src/Controller/Component/CRUDComponent.php    | 35 +++++++-
 src/Controller/IndividualsController.php      |  9 ++-
 src/Controller/TagsController.php             | 80 +++++++++++++++++++
 src/Model/Table/IndividualsTable.php          |  1 +
 src/View/Helper/TagHelper.php                 | 42 ++++++----
 templates/Individuals/index.php               |  8 +-
 templates/Tags/add.php                        | 22 +++++
 templates/Tags/index.php                      | 79 ++++++++++++++++++
 templates/Tags/view.php                       | 32 ++++++++
 .../genericElements/Form/Fields/tagsField.php |  6 +-
 .../genericElements/IndexTable/Fields/tag.php |  6 ++
 .../IndexTable/Fields/tags.php                | 18 +----
 .../SingleViews/Fields/tagField.php           |  3 +
 .../SingleViews/Fields/tagsField.php          |  3 +-
 templates/genericTemplates/filters.php        | 37 ++++++++-
 templates/genericTemplates/tag.php            |  3 +-
 webroot/css/main.css                          |  4 +
 webroot/js/main.js                            | 77 +++++++++++-------
 18 files changed, 388 insertions(+), 77 deletions(-)
 create mode 100644 src/Controller/TagsController.php
 create mode 100644 templates/Tags/add.php
 create mode 100644 templates/Tags/index.php
 create mode 100644 templates/Tags/view.php
 create mode 100644 templates/element/genericElements/IndexTable/Fields/tag.php
 create mode 100644 templates/element/genericElements/SingleViews/Fields/tagField.php

diff --git a/src/Controller/Component/CRUDComponent.php b/src/Controller/Component/CRUDComponent.php
index 0342a67..97a0c37 100644
--- a/src/Controller/Component/CRUDComponent.php
+++ b/src/Controller/Component/CRUDComponent.php
@@ -35,6 +35,9 @@ class CRUDComponent extends Component
             $options['filters'][] = 'quickFilter';
         }
         $options['filters'][] = 'filteringLabel';
+        if ($this->taggingSupported()) {
+            $options['filters'][] = 'filteringTags';
+        }
 
         $optionFilters = empty($options['filters']) ? [] : $options['filters'];
         foreach ($optionFilters as $i => $filter) {
@@ -50,6 +53,9 @@ class CRUDComponent extends Component
         if (!empty($options['contain'])) {
             $query->contain($options['contain']);
         }
+        if ($this->taggingSupported()) {
+            $query->contain('Tags');
+        }
         if (!empty($options['fields'])) {
             $query->select($options['fields']);
         }
@@ -73,15 +79,17 @@ class CRUDComponent extends Component
                     $data = $this->Table->{$options['afterFind']}($data);
                 }
             }
-            if (!empty($options['contextFilters'])) {
-                $this->setFilteringContext($options['contextFilters'], $params);
-            }
+            $this->setFilteringContext($options['contextFilters'] ?? [], $params);
             $this->Controller->set('data', $data);
         }
     }
 
     public function filtering(): void
     {
+        if ($this->taggingSupported()) {
+            $this->Controller->set('taggingEnabled', true);
+            $this->setAllTags();
+        }
         $filters = !empty($this->Controller->filters) ? $this->Controller->filters : [];
         $this->Controller->set('filters', $filters);
         $this->Controller->viewBuilder()->setLayout('ajax');
@@ -246,8 +254,9 @@ class CRUDComponent extends Component
         $this->getMetaTemplates();
         if ($this->taggingSupported()) {
             $params['contain'][] = 'Tags';
+            $this->setAllTags();
         }
-        $data = $this->Table->get($id, isset($params['get']) ? $params['get'] : []);
+        $data = $this->Table->get($id, isset($params['get']) ? $params['get'] : $params);
         $data = $this->getMetaFields($id, $data);
         if (!empty($params['fields'])) {
             $this->Controller->set('fields', $params['fields']);
@@ -676,6 +685,8 @@ class CRUDComponent extends Component
     {
         $filteringLabel = !empty($params['filteringLabel']) ? $params['filteringLabel'] : '';
         unset($params['filteringLabel']);
+        $filteringTags = !empty($params['filteringTags']) && $this->taggingSupported() ? $params['filteringTags'] : '';
+        unset($params['filteringTags']);
         $customFilteringFunction = '';
         $chosenFilter = '';
         if (!empty($options['contextFilters']['custom'])) {
@@ -719,10 +730,26 @@ class CRUDComponent extends Component
                 }
             }
         }
+
+        if ($this->taggingSupported() && !empty($filteringTags)) {
+            $activeFilters['filteringTags'] = $filteringTags;
+            $query = $this->setTagFilters($query, $filteringTags);
+        }
+
         $this->Controller->set('activeFilters', $activeFilters);
         return $query;
     }
 
+    protected function setTagFilters($query, $tags)
+    {
+        $modelAlias = $this->Table->getAlias();
+        $subQuery = $this->Table->find('tagged', [
+            'label' => $tags,
+            'forceAnd' => true
+        ])->select($modelAlias . '.id');
+        return $query = $query->where([$modelAlias . '.id IN' => $subQuery]);
+    }
+
     protected function setNestedRelatedCondition($query, $filterParts, $filterValue)
     {
         $modelName = $filterParts[0];
diff --git a/src/Controller/IndividualsController.php b/src/Controller/IndividualsController.php
index 046824f..71e4a0f 100644
--- a/src/Controller/IndividualsController.php
+++ b/src/Controller/IndividualsController.php
@@ -13,10 +13,12 @@ use Cake\ORM\TableRegistry;
 
 class IndividualsController extends AppController
 {
+    public $filters = ['uuid', 'email', 'first_name', 'last_name', 'position', 'Organisations.id', 'Alignments.type'];
+
     public function index()
     {
         $this->CRUD->index([
-            'filters' => ['uuid', 'email', 'first_name', 'last_name', 'position', 'Organisations.id', 'Alignments.type'],
+            'filters' => $this->filters,
             'quickFilters' => ['uuid', 'email', 'first_name', 'last_name', 'position'],
             'contextFilters' => [
                 'fields' => [
@@ -33,6 +35,11 @@ class IndividualsController extends AppController
         $this->set('metaGroup', 'ContactDB');
     }
 
+    public function filtering()
+    {
+        $this->CRUD->filtering();
+    }
+
     public function add()
     {
         $this->CRUD->add();
diff --git a/src/Controller/TagsController.php b/src/Controller/TagsController.php
new file mode 100644
index 0000000..57481e0
--- /dev/null
+++ b/src/Controller/TagsController.php
@@ -0,0 +1,80 @@
+<?php
+
+namespace App\Controller;
+
+use App\Controller\AppController;
+use Cake\Utility\Hash;
+use Cake\Utility\Inflector;
+use Cake\Utility\Text;
+use Cake\Database\Expression\QueryExpression;
+use Cake\Http\Exception\NotFoundException;
+use Cake\Http\Exception\MethodNotAllowedException;
+use Cake\Http\Exception\ForbiddenException;
+use Cake\ORM\TableRegistry;
+
+class TagsController extends AppController
+{
+
+    public function initialize(): void
+    {
+        parent::initialize();
+        $this->Table = TableRegistry::getTableLocator()->get('Tags.Tags');
+        $this->CRUD->Table = $this->Table;
+        $this->CRUD->TableAlias = $this->CRUD->Table->getAlias();
+        $this->CRUD->ObjectAlias = Inflector::singularize($this->CRUD->TableAlias);
+    }
+
+    public function index()
+    {
+        $this->CRUD->index([
+            'filters' => ['label', 'colour'],
+            'quickFilters' => [['label' => true], 'colour']
+        ]);
+        $responsePayload = $this->CRUD->getResponsePayload();
+        if (!empty($responsePayload)) {
+            return $responsePayload;
+        }
+        $this->set('metaGroup', $this->isAdmin ? 'Administration' : 'Cerebrate');
+    }
+
+    public function add()
+    {
+        $this->CRUD->add();
+        $responsePayload = $this->CRUD->getResponsePayload();
+        if (!empty($responsePayload)) {
+            return $responsePayload;
+        }
+        $this->set('metaGroup', $this->isAdmin ? 'Administration' : 'Cerebrate');
+    }
+
+    public function view($id)
+    {
+        $this->CRUD->view($id);
+        $responsePayload = $this->CRUD->getResponsePayload();
+        if (!empty($responsePayload)) {
+            return $responsePayload;
+        }
+        $this->set('metaGroup', $this->isAdmin ? 'Administration' : 'Cerebrate');
+    }
+
+    public function edit($id)
+    {
+        $this->CRUD->edit($id);
+        $responsePayload = $this->CRUD->getResponsePayload();
+        if (!empty($responsePayload)) {
+            return $responsePayload;
+        }
+        $this->set('metaGroup', $this->isAdmin ? 'Administration' : 'Cerebrate');
+        $this->render('add');
+    }
+
+    public function delete($id)
+    {
+        $this->CRUD->delete($id);
+        $responsePayload = $this->CRUD->getResponsePayload();
+        if (!empty($responsePayload)) {
+            return $responsePayload;
+        }
+        $this->set('metaGroup', $this->isAdmin ? 'Administration' : 'Cerebrate');
+    }
+}
diff --git a/src/Model/Table/IndividualsTable.php b/src/Model/Table/IndividualsTable.php
index 81d4c65..5693321 100644
--- a/src/Model/Table/IndividualsTable.php
+++ b/src/Model/Table/IndividualsTable.php
@@ -17,6 +17,7 @@ class IndividualsTable extends AppTable
         $this->addBehavior('Tags.Tag', [
             'taggedCounter' => false,
             'strategy' => 'array',
+            'finderField' => 'label',
         ]);
         $this->hasMany(
             'Alignments',
diff --git a/src/View/Helper/TagHelper.php b/src/View/Helper/TagHelper.php
index 9b0449b..f601650 100644
--- a/src/View/Helper/TagHelper.php
+++ b/src/View/Helper/TagHelper.php
@@ -33,14 +33,20 @@ class TagHelper extends Helper
                 'data-text-colour' => h($tag['text_colour']),
             ];
         }, $options['allTags']) : [];
-        $selectConfig = [
-            'multiple' => true,
-            'class' => ['tag-input', 'd-none'],
-            'data-url' => $this->Url->build([
+        $classes = ['tag-input', 'flex-grow-1'];
+        $url = '';
+        if (!empty($this->getConfig('editable'))) {
+            $url = $this->Url->build([
                 'controller' => $this->getView()->getName(),
                 'action' => 'tag',
                 $this->getView()->get('entity')['id']
-            ]),
+            ]);
+            $classes[] = 'd-none';
+        }
+        $selectConfig = [
+            'multiple' => true,
+            'class' => $classes,
+            'data-url' => $url,
         ];
         return $this->Form->select($field, $values, $selectConfig);
     }
@@ -48,24 +54,26 @@ class TagHelper extends Helper
     protected function picker(array $options = [])
     {
         $html =  $this->Tag->control($options);
-        $html .= $this->Bootstrap->button([
-            'size' => 'sm',
-            'icon' => 'plus',
-            'variant' => 'secondary',
-            'class' => ['badge'],
-            'params' => [
-                'onclick' => 'createTagPicker(this)',
-            ]
-        ]);
+        if (!empty($this->getConfig('editable'))) {
+            $html .= $this->Bootstrap->button([
+                'size' => 'sm',
+                'icon' => 'plus',
+                'variant' => 'secondary',
+                'class' => ['badge'],
+                'params' => [
+                    'onclick' => 'createTagPicker(this)',
+                ]
+            ]);
+        }
+        $html .= '<script>$(document).ready(function() { initSelect2Pickers() })</script>';
         return $html;
     }
 
-    public function tags(array $options = [])
+    public function tags(array $tags = [], array $options = [])
     {
         $this->_config = array_merge($this->defaultConfig, $options);
-        $tags = !empty($options['tags']) ? $options['tags'] : [];
         $html = '<div class="tag-container-wrapper">';
-        $html .= '<div class="tag-container my-1">';
+        $html .= '<div class="tag-container my-1 d-flex">';
         $html .= '<div class="tag-list d-inline-block">';
         foreach ($tags as $tag) {
             if (is_object($tag)) {
diff --git a/templates/Individuals/index.php b/templates/Individuals/index.php
index 91520e1..4930899 100644
--- a/templates/Individuals/index.php
+++ b/templates/Individuals/index.php
@@ -23,7 +23,8 @@ echo $this->element('genericElements/IndexTable/index_table', [
                     'button' => __('Filter'),
                     'placeholder' => __('Enter value to search'),
                     'data' => '',
-                    'searchKey' => 'value'
+                    'searchKey' => 'value',
+                    'allowFilering' => true
                 ]
             ]
         ],
@@ -54,6 +55,11 @@ echo $this->element('genericElements/IndexTable/index_table', [
                 'element' => 'alignments',
                 'scope' => $alignmentScope
             ],
+            [
+                'name' => __('Tags'),
+                'data_path' => 'tags',
+                'element' => 'tags',
+            ],
             [
                 'name' => __('UUID'),
                 'sort' => 'uuid',
diff --git a/templates/Tags/add.php b/templates/Tags/add.php
new file mode 100644
index 0000000..412dc1c
--- /dev/null
+++ b/templates/Tags/add.php
@@ -0,0 +1,22 @@
+<?php
+    echo $this->element('genericElements/Form/genericForm', array(
+        'data' => array(
+            'description' => __('Individuals are natural persons. They are meant to describe the basic information about an individual that may or may not be a user of this community. Users in genral require an individual object to identify the person behind them - however, no user account is required to store information about an individual. Individuals can have affiliations to organisations and broods as well as cryptographic keys, using which their messages can be verified and which can be used to securely contact them.'),
+            'model' => 'Organisations',
+            'fields' => array(
+                array(
+                    'field' => 'label'
+                ),
+                array(
+                    'field' => 'colour',
+                    'type' => 'color',
+                ),
+            ),
+            'metaTemplates' => empty($metaTemplates) ? [] : $metaTemplates,
+            'submit' => array(
+                'action' => $this->request->getParam('action')
+            )
+        )
+    ));
+?>
+</div>
diff --git a/templates/Tags/index.php b/templates/Tags/index.php
new file mode 100644
index 0000000..a826fb1
--- /dev/null
+++ b/templates/Tags/index.php
@@ -0,0 +1,79 @@
+<?php
+echo $this->element('genericElements/IndexTable/index_table', [
+    'data' => [
+        'data' => $data,
+        'top_bar' => [
+            'children' => [
+                [
+                    'type' => 'simple',
+                    'children' => [
+                        'data' => [
+                            'type' => 'simple',
+                            'text' => __('Add tag'),
+                            'popover_url' => '/tags/add'
+                        ]
+                    ]
+                ],
+                [
+                    'type' => 'context_filters',
+                    'context_filters' => $filteringContexts
+                ],
+                [
+                    'type' => 'search',
+                    'button' => __('Filter'),
+                    'placeholder' => __('Enter value to search'),
+                    'data' => '',
+                    'searchKey' => 'value'
+                ]
+            ]
+        ],
+        'fields' => [
+            [
+                'name' => '#',
+                'sort' => 'id',
+                'data_path' => 'id',
+            ],
+            [
+                'name' => __('Label'),
+                'sort' => 'label',
+                'element' => 'tag'
+            ],
+            [
+                'name' => __('Counter'),
+                'sort' => 'couter',
+                'data_path' => 'counter',
+            ],
+            [
+                'name' => __('Colour'),
+                'sort' => 'colour',
+                'data_path' => 'colour',
+            ],
+            [
+                'name' => __('Created'),
+                'sort' => 'created',
+                'data_path' => 'created',
+            ],
+        ],
+        'title' => __('Tag index'),
+        'description' => __('The list of all tags existing on this instance'),
+        'actions' => [
+            [
+                'url' => '/tags/view',
+                'url_params_data_paths' => ['id'],
+                'icon' => 'eye'
+            ],
+            [
+                'open_modal' => '/tags/edit/[onclick_params_data_path]',
+                'modal_params_data_path' => 'id',
+                'icon' => 'edit'
+            ],
+            [
+                'open_modal' => '/tags/delete/[onclick_params_data_path]',
+                'modal_params_data_path' => 'id',
+                'icon' => 'trash'
+            ],
+        ]
+    ]
+]);
+echo '</div>';
+?>
diff --git a/templates/Tags/view.php b/templates/Tags/view.php
new file mode 100644
index 0000000..00ce41a
--- /dev/null
+++ b/templates/Tags/view.php
@@ -0,0 +1,32 @@
+<?php
+echo $this->element(
+    '/genericElements/SingleViews/single_view',
+    [
+        'data' => $entity,
+        'fields' => [
+            [
+                'key' => __('ID'),
+                'path' => 'id'
+            ],
+            [
+                'key' => __('Label'),
+                'path' => '',
+                'type' => 'tag',
+            ],
+            [
+                'key' => __('Counter'),
+                'path' => 'counter',
+                'type' => 'json',
+            ],
+            [
+                'key' => __('Colour'),
+                'path' => 'colour',
+            ],
+            [
+                'key' => __('Created'),
+                'path' => 'created',
+            ],
+        ],
+        'children' => []
+    ]
+);
diff --git a/templates/element/genericElements/Form/Fields/tagsField.php b/templates/element/genericElements/Form/Fields/tagsField.php
index ba35700..4d67db8 100644
--- a/templates/element/genericElements/Form/Fields/tagsField.php
+++ b/templates/element/genericElements/Form/Fields/tagsField.php
@@ -1,8 +1,8 @@
 <?php
-    $tagsHtml = $this->Tag->tags([
-        'allTags' => $allTags,
-        'tags' => $entity['tags'],
+    $tagsHtml = $this->Tag->tags($entity['tags'], [
+        'allTags' => [],
         'picker' => true,
+        'editable' => true,
     ]);
 ?>
 <div class="form-group row">
diff --git a/templates/element/genericElements/IndexTable/Fields/tag.php b/templates/element/genericElements/IndexTable/Fields/tag.php
new file mode 100644
index 0000000..fbb270a
--- /dev/null
+++ b/templates/element/genericElements/IndexTable/Fields/tag.php
@@ -0,0 +1,6 @@
+<?php
+    $tag = $row;
+    echo $this->Tag->tag($tag, [
+    ]);
+
+?>
diff --git a/templates/element/genericElements/IndexTable/Fields/tags.php b/templates/element/genericElements/IndexTable/Fields/tags.php
index b3dd0d8..a5eb311 100644
--- a/templates/element/genericElements/IndexTable/Fields/tags.php
+++ b/templates/element/genericElements/IndexTable/Fields/tags.php
@@ -1,17 +1,5 @@
 <?php
     $tags = $this->Hash->extract($row, $field['data_path']);
-    if (!empty($tags)) {
-        if (empty($tags[0])) {
-            $tags = array($tags);
-        }
-        echo $this->element(
-            'ajaxTags',
-            array(
-                'attributeId' => 0,
-                'tags' => $tags,
-                'tagAccess' => false,
-                'static_tags_only' => 1
-            )
-        );
-    }
-?>
+    echo $this->Tag->tags($tags, [
+        'tags'
+    ]);
diff --git a/templates/element/genericElements/SingleViews/Fields/tagField.php b/templates/element/genericElements/SingleViews/Fields/tagField.php
new file mode 100644
index 0000000..523c9a6
--- /dev/null
+++ b/templates/element/genericElements/SingleViews/Fields/tagField.php
@@ -0,0 +1,3 @@
+<?php
+echo $this->Tag->tag($data, [
+]);
diff --git a/templates/element/genericElements/SingleViews/Fields/tagsField.php b/templates/element/genericElements/SingleViews/Fields/tagsField.php
index 16f7a71..414da50 100644
--- a/templates/element/genericElements/SingleViews/Fields/tagsField.php
+++ b/templates/element/genericElements/SingleViews/Fields/tagsField.php
@@ -1,9 +1,8 @@
 <?php
 // $tags = Cake\Utility\Hash::extract($data, $field['path']);
 $tags = Cake\Utility\Hash::get($data, 'tags');
-echo $this->Tag->tags([
+echo $this->Tag->tags($tags, [
     'allTags' => $allTags,
-    'tags' => $tags,
     'picker' => true,
     'editable' => true,
 ]);
diff --git a/templates/genericTemplates/filters.php b/templates/genericTemplates/filters.php
index b3b0c91..6713b7b 100644
--- a/templates/genericTemplates/filters.php
+++ b/templates/genericTemplates/filters.php
@@ -15,7 +15,7 @@ $filteringForm = $this->Bootstrap->table(
         [
             'labelHtml' => sprintf('%s %s',
                 __('Value'),
-                sprintf('<sup class="fa fa-info" title="%s"><sup>', __('Supports strict match and LIKE match with the `%` character.&#10;Example: `%.com`'))
+                sprintf('<sup class="fa fa-info" title="%s"><sup>', __('Supports strict matches and LIKE matches with the `%` character.&#10;Example: `%.com`'))
             )
         ],
         __('Action')
@@ -23,12 +23,28 @@ $filteringForm = $this->Bootstrap->table(
     'items' => []
 ]);
 
+if ($taggingEnabled) {
+    $helpText = $this->Bootstrap->genNode('sup', [
+        'class' => ['ml-1 fa fa-info'],
+        'title' => __('Supports negation matches (with the `!` character) and LIKE matches (with the `%` character).&#10;Example: `!exportable`, `%able`'),
+    ]);
+    $filteringTags = $this->Bootstrap->genNode('h5', [], __('Tags') . $helpText);
+    $filteringTags .= $this->Tag->tags([], [
+        'allTags' => $allTags,
+        'picker' => true,
+        'editable' => false,
+    ]);
+} else {
+    $filteringTags = '';
+}
+$modalBody = sprintf('%s%s', $filteringForm, $filteringTags);
+
 
 echo $this->Bootstrap->modal([
     'title' => __('Filtering options for {0}', Inflector::singularize($this->request->getParam('controller'))),
     'size' => 'lg',
     'type' => 'confirm',
-    'bodyHtml' => $filteringForm,
+    'bodyHtml' => $modalBody,
     'confirmText' => __('Filter'),
     'confirmFunction' => 'filterIndex'
 ]);
@@ -54,7 +70,9 @@ echo $this->Bootstrap->modal([
             }
             activeFilters[fullFilter] = rowData['value']
         })
-        const searchParam = (new URLSearchParams(activeFilters)).toString();
+        $select = modalObject.$modal.find('select.tag-input')
+        activeFilters['filteringTags'] = $select.select2('data').map(tag => tag.text)
+        const searchParam = jQuery.param(activeFilters);
         const url = `/${controller}/${action}?${searchParam}`
 
         const randomValue = getRandomValue()
@@ -70,6 +88,8 @@ echo $this->Bootstrap->modal([
         addControlRow($filteringTable)
         const randomValue = getRandomValue()
         const activeFilters = $(`#toggleFilterButton-${randomValue}`).data('activeFilters')
+        const tags = activeFilters['filteringTags'] !== undefined ? Object.assign({}, activeFilters)['filteringTags'] : []
+        delete activeFilters['filteringTags']
         for (let [field, value] of Object.entries(activeFilters)) {
             const fieldParts = field.split(' ')
             let operator = '='
@@ -81,6 +101,17 @@ echo $this->Bootstrap->modal([
             }
             addFilteringRow($filteringTable, field, value, operator)
         }
+        $select = $filteringTable.closest('.modal-body').find('select.tag-input')
+        let passedTags = []
+        tags.forEach(tagname => {
+            if (!$select.find("option[value='" + tagname + "']")) {
+                passedTags.push(new Option(tagname, tagname, true, true))
+            }
+        })
+        $select
+            .append(passedTags)
+            .val(tags)
+            .trigger('change')
     }
 
     function addControlRow($filteringTable) {
diff --git a/templates/genericTemplates/tag.php b/templates/genericTemplates/tag.php
index c1bc69b..41e84d3 100644
--- a/templates/genericTemplates/tag.php
+++ b/templates/genericTemplates/tag.php
@@ -1,7 +1,6 @@
 <?php
-    echo $this->Tag->tags([
+    echo $this->Tag->tags($entity->tags, [
         'allTags' => $allTags,
-        'tags' => $entity->tags,
         'picker' => true,
         'editable' => true,
     ]);
diff --git a/webroot/css/main.css b/webroot/css/main.css
index de19e15..f1f2d47 100644
--- a/webroot/css/main.css
+++ b/webroot/css/main.css
@@ -163,4 +163,8 @@ input[type="checkbox"]:disabled.change-cursor {
 .picker-container .picker-action .btn:first-child {
     border-top-left-radius: 0 !important;
     border-bottom-left-radius: 0 !important;
+}
+
+.tag {
+    filter: drop-shadow(2px 2px 2px rgba(0, 0, 0, 0.5));
 }
\ No newline at end of file
diff --git a/webroot/js/main.js b/webroot/js/main.js
index 57e7560..20602a3 100644
--- a/webroot/js/main.js
+++ b/webroot/js/main.js
@@ -117,47 +117,37 @@ function getTextColour(hex) {
 
 function createTagPicker(clicked) {
 
-    function templateTag(state) {
-        if (!state.id) {
-            return state.label;
-        }
-        if (state.colour === undefined) {
-            state.colour = $(state.element).data('colour')
-        }
-        return HtmlHelper.tag(state)
-    }
-
     function closePicker($select, $container) {
         $select.appendTo($container)
         $container.parent().find('.picker-container').remove()
     }
 
-    const $clicked = $(clicked)
-    const $container = $clicked.closest('.tag-container')
-    const $select = $container.parent().find('select.tag-input').removeClass('d-none').addClass('flex-grow-1')
-    closePicker($select, $container)
-    const $pickerContainer = $('<div></div>').addClass(['picker-container', 'd-flex'])
-    const $saveButton = $('<button></button>').addClass(['btn btn-primary btn-sm', 'align-self-start']).attr('type', 'button')
+    function getEditableButtons($select, $container) {
+        const $saveButton = $('<button></button>').addClass(['btn btn-primary btn-sm', 'align-self-start']).attr('type', 'button')
         .append($('<span></span>').text('Save').prepend($('<i></i>').addClass('fa fa-save mr-1')))
         .click(function() {
             const tags = $select.select2('data').map(tag => tag.text)
             addTags($select.data('url'), tags, $(this))
         })
-    const $cancelButton = $('<button></button>').addClass(['btn btn-secondary btn-sm', 'align-self-start']).attr('type', 'button')
-        .append($('<span></span>').text('Cancel').prepend($('<i></i>').addClass('fa fa-times mr-1')))
-        .click(function() {
-            closePicker($select, $container)
-        })
-    const $buttons = $('<span></span>').addClass(['picker-action', 'btn-group']).append($saveButton, $cancelButton)
+        const $cancelButton = $('<button></button>').addClass(['btn btn-secondary btn-sm', 'align-self-start']).attr('type', 'button')
+            .append($('<span></span>').text('Cancel').prepend($('<i></i>').addClass('fa fa-times mr-1')))
+            .click(function() {
+                closePicker($select, $container)
+            })
+        const $buttons = $('<span></span>').addClass(['picker-action', 'btn-group']).append($saveButton, $cancelButton)
+        return $buttons
+    }
+
+    const $clicked = $(clicked)
+    const $container = $clicked.closest('.tag-container')
+    const $select = $container.parent().find('select.tag-input').removeClass('d-none')//.addClass('flex-grow-1')
+    closePicker($select, $container)
+    const $pickerContainer = $('<div></div>').addClass(['picker-container', 'd-flex'])
+    
     $select.prependTo($pickerContainer)
-    $pickerContainer.append($buttons)
+    $pickerContainer.append(getEditableButtons($select, $container))
     $container.parent().append($pickerContainer)
-    $select.select2({
-        placeholder: 'Pick a tag',
-        tags: true,
-        templateResult: templateTag,
-        templateSelection: templateTag,
-    })
+    initSelect2Picker($select)
 }
 
 function deleteTag(url, tag, clicked) {
@@ -213,6 +203,35 @@ function refreshTagList(result, $container) {
     return UI.reload(url, $container)
 }
 
+function initSelect2Pickers() {
+    $('select.tag-input').each(function() {
+        if (!$(this).hasClass("select2-hidden-accessible")) {
+            initSelect2Picker($(this))
+        }
+    })
+}
+
+function initSelect2Picker($select) {
+
+    function templateTag(state) {
+        if (!state.id) {
+            return state.label;
+        }
+        if (state.colour === undefined) {
+            state.colour = $(state.element).data('colour')
+        }
+        return HtmlHelper.tag(state)
+    }
+
+    $select.select2({
+        placeholder: 'Pick a tag',
+        tags: true,
+        width: '100%',
+        templateResult: templateTag,
+        templateSelection: templateTag,
+    })
+}
+
 
 var UI
 $(document).ready(() => {

From e8358104062dd2b51e8db9ee100a8329d6b2fb9a Mon Sep 17 00:00:00 2001
From: mokaddem <sami.mokaddem@circl.lu>
Date: Tue, 31 Aug 2021 11:19:15 +0200
Subject: [PATCH 05/16] fix: [genericTemplates:filters] Custom tags (such as
 negated and like) are correctly parsed and added to the picker

---
 templates/genericTemplates/filters.php |  5 ++++-
 webroot/js/main.js                     | 17 ++++++++++++++---
 2 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/templates/genericTemplates/filters.php b/templates/genericTemplates/filters.php
index 6713b7b..3be1b09 100644
--- a/templates/genericTemplates/filters.php
+++ b/templates/genericTemplates/filters.php
@@ -104,7 +104,10 @@ echo $this->Bootstrap->modal([
         $select = $filteringTable.closest('.modal-body').find('select.tag-input')
         let passedTags = []
         tags.forEach(tagname => {
-            if (!$select.find("option[value='" + tagname + "']")) {
+            const existingOption = $select.find('option').filter(function() {
+                return $(this).val() === tagname
+            })
+            if (existingOption.length == 0) {
                 passedTags.push(new Option(tagname, tagname, true, true))
             }
         })
diff --git a/webroot/js/main.js b/webroot/js/main.js
index 20602a3..465969d 100644
--- a/webroot/js/main.js
+++ b/webroot/js/main.js
@@ -213,13 +213,24 @@ function initSelect2Pickers() {
 
 function initSelect2Picker($select) {
 
-    function templateTag(state) {
+    function templateTag(state, $select) {
         if (!state.id) {
             return state.label;
         }
         if (state.colour === undefined) {
             state.colour = $(state.element).data('colour')
         }
+        if ($select !== undefined && state.text[0] === '!') {
+            // fetch corresponding tag and set colors?
+            // const baseTag = state.text.slice(1)
+            // const existingBaseTag = $select.find('option').filter(function() {
+            //     return $(this).val() === baseTag
+            // })
+            // if (existingBaseTag.length > 0) {
+            //     state.colour = existingBaseTag.data('colour')
+            //     state.text = baseTag
+            // }
+        }
         return HtmlHelper.tag(state)
     }
 
@@ -227,8 +238,8 @@ function initSelect2Picker($select) {
         placeholder: 'Pick a tag',
         tags: true,
         width: '100%',
-        templateResult: templateTag,
-        templateSelection: templateTag,
+        templateResult: (state) => templateTag(state),
+        templateSelection: (state) => templateTag(state, $select),
     })
 }
 

From 61255e2837097e80221fb138d5197e4daff7823d Mon Sep 17 00:00:00 2001
From: mokaddem <sami.mokaddem@circl.lu>
Date: Tue, 31 Aug 2021 15:21:28 +0200
Subject: [PATCH 06/16] chg: [tags] Improved UI and added missing files

---
 src/Controller/Component/CRUDComponent.php |  18 +-
 src/Controller/OrganisationsController.php |  27 +++
 src/Model/Behavior/TagBehavior.php         | 212 +++++++++++++++++++++
 src/Model/Entity/Tag.php                   |  43 +++++
 src/Model/Entity/Tagged.php                |  14 ++
 src/Model/Table/IndividualsTable.php       |   6 +-
 src/Model/Table/OrganisationsTable.php     |   1 +
 src/Model/Table/TaggedTable.php            |  34 ++++
 src/Model/Table/TagsTable.php              |  28 +++
 src/View/Helper/TagHelper.php              |   3 +-
 templates/Organisations/view.php           |   4 +
 webroot/js/main.js                         |  15 +-
 12 files changed, 383 insertions(+), 22 deletions(-)
 create mode 100644 src/Model/Behavior/TagBehavior.php
 create mode 100644 src/Model/Entity/Tag.php
 create mode 100644 src/Model/Entity/Tagged.php
 create mode 100644 src/Model/Table/TaggedTable.php
 create mode 100644 src/Model/Table/TagsTable.php

diff --git a/src/Controller/Component/CRUDComponent.php b/src/Controller/Component/CRUDComponent.php
index 97a0c37..51cdbfc 100644
--- a/src/Controller/Component/CRUDComponent.php
+++ b/src/Controller/Component/CRUDComponent.php
@@ -449,11 +449,10 @@ class CRUDComponent extends Component
                     'contain' => 'Tags',
                 ];
                 $entity = $this->Table->get($id, $params);
-                // patching will mirror tag in the DB, however, we only want to add tags
                 $input = $this->request->getData();
-                $tagsToAdd = explode(',', $input['tag_list']);
-                $entity->tag_list = $entity->tag_list;
-                $input['tag_list'] = implode(',', array_merge($tagsToAdd, $entity->tag_list));
+                $tagsToAdd = json_decode($input['tag_list']);
+                // patching will mirror tag in the DB, however, we only want to add tags
+                $input['tags'] = array_merge($tagsToAdd, $entity->tags);
                 $patchEntityParams = [
                     'fields' => ['tags'],
                 ];
@@ -509,13 +508,12 @@ class CRUDComponent extends Component
                     'contain' => 'Tags',
                 ];
                 $entity = $this->Table->get($id, $params);
-                // patching will mirror tag in the DB, however, we only want to remove tags
                 $input = $this->request->getData();
-                $tagsToRemove = explode(',', $input['tag_list']);
-                $entity->tag_list = $entity->tag_list;
-                $input['tag_list'] = implode(',', array_filter($entity->tag_list, function ($existingTag) use ($tagsToRemove) {
-                    return !in_array($existingTag, $tagsToRemove);
-                }));
+                $tagsToRemove = json_decode($input['tag_list']);
+                // patching will mirror tag in the DB, however, we only want to remove tags
+                $input['tags'] = array_filter($entity->tags, function ($existingTag) use ($tagsToRemove) {
+                    return !in_array($existingTag->label, $tagsToRemove);
+                });
                 $patchEntityParams = [
                     'fields' => ['tags'],
                 ];
diff --git a/src/Controller/OrganisationsController.php b/src/Controller/OrganisationsController.php
index 8e8cba8..d381595 100644
--- a/src/Controller/OrganisationsController.php
+++ b/src/Controller/OrganisationsController.php
@@ -112,4 +112,31 @@ class OrganisationsController extends AppController
         }
         $this->set('metaGroup', 'ContactDB');
     }
+
+    public function tag($id)
+    {
+        $this->CRUD->tag($id);
+        $responsePayload = $this->CRUD->getResponsePayload();
+        if (!empty($responsePayload)) {
+            return $responsePayload;
+        }
+    }
+
+    public function untag($id)
+    {
+        $this->CRUD->untag($id);
+        $responsePayload = $this->CRUD->getResponsePayload();
+        if (!empty($responsePayload)) {
+            return $responsePayload;
+        }
+    }
+
+    public function viewTags($id)
+    {
+        $this->CRUD->viewTags($id);
+        $responsePayload = $this->CRUD->getResponsePayload();
+        if (!empty($responsePayload)) {
+            return $responsePayload;
+        }
+    }
 }
diff --git a/src/Model/Behavior/TagBehavior.php b/src/Model/Behavior/TagBehavior.php
new file mode 100644
index 0000000..63dd57d
--- /dev/null
+++ b/src/Model/Behavior/TagBehavior.php
@@ -0,0 +1,212 @@
+<?php
+
+namespace App\Model\Behavior;
+
+use Cake\ORM\Behavior;
+use Cake\ORM\Entity;
+use Cake\ORM\Query;
+use Cake\ORM\Table;
+
+class TagBehavior extends Behavior
+{
+
+    protected $_defaultConfig = [
+        'tagsAssoc' => [
+            'className' => 'Tags',
+            // 'joinTable' => 'tagged', // uncomment me!
+            'joinTable' => 'tags_tagged', // remove me!
+            'foreignKey' => 'fk_id',
+            'targetForeignKey' => 'tag_id',
+            'propertyName' => 'tags',
+        ],
+        'tagsCounter' => ['counter'],
+        'taggedAssoc' => [
+            'className' => 'Tagged',
+            'foreignKey' => 'fk_id'
+        ],
+        'implementedEvents' => [
+            'Model.beforeMarshal' => 'beforeMarshal',
+            'Model.beforeFind' => 'beforeFind',
+            'Model.beforeSave' => 'beforeSave',
+        ],
+        'implementedMethods' => [
+            'normalizeTags' => 'normalizeTags',
+        ],
+        'implementedFinders' => [
+            'tagged' => 'findByTag',
+            'untagged' => 'findUntagged',
+        ],
+    ];
+
+    public function initialize(array $config): void {
+        $this->bindAssociations();
+        $this->attachCounters();
+    }
+
+    public function bindAssociations() {
+        $config = $this->getConfig();
+        $tagsAssoc = $config['tagsAssoc'];
+        $taggedAssoc = $config['taggedAssoc'];
+        
+        $table = $this->_table;
+        $tableAlias = $this->_table->getAlias();
+        
+        $assocConditions = ['Tagged.fk_model' => $tableAlias];
+
+        if (!$table->hasAssociation('Tagged')) {
+            $table->hasMany('Tagged', array_merge(
+                $taggedAssoc,
+                [
+                    'conditions' => $assocConditions
+                ]
+            ));
+        }
+
+        if (!$table->hasAssociation('Tags')) {
+            $table->belongsToMany('Tags', array_merge(
+                $tagsAssoc,
+                [
+                    'through' => $table->Tagged->getTarget(),
+                    'conditions' => $assocConditions,
+                ]
+            ));
+        }
+
+        if (!$table->Tags->hasAssociation($tableAlias)) {
+            $table->Tags->belongsToMany($tableAlias, array_merge(
+                $tagsAssoc,
+                [
+                    'className' => get_class($table),
+                ]
+            ));
+        }
+
+        if (!$table->Tagged->hasAssociation($tableAlias)) {
+            $table->Tagged->belongsTo($tableAlias, [
+                'className' => get_class($table),
+                'foreignKey' => $tagsAssoc['foreignKey'],
+                'conditions' => $assocConditions,
+                'joinType' => 'INNER',
+            ]);
+        }
+
+        if (!$table->Tagged->hasAssociation($tableAlias . 'Tags')) {
+            $table->Tagged->belongsTo($tableAlias . 'Tags', [
+                'className' => $tagsAssoc['className'],
+                'foreignKey' => $tagsAssoc['targetForeignKey'],
+                'conditions' => $assocConditions,
+                'joinType' => 'INNER',
+            ]);
+        }
+    }
+
+    public function attachCounters() {
+        $config = $this->getConfig();
+        $taggedTable = $this->_table->Tagged;
+
+        if (!$taggedTable->hasBehavior('CounterCache')) {
+            $taggedTable->addBehavior('CounterCache', [
+                'Tags' => $config['tagsCounter']
+            ]);
+        }
+    }
+
+    public function beforeMarshal($event, $data, $options) {
+        $property = $this->getConfig('tagsAssoc.propertyName');
+        $options['accessibleFields'][$property] = true;
+        $options['associated']['Tags']['accessibleFields']['id'] = true;
+
+        if (isset($data['tags'])) {
+            if (!empty($data['tags'])) {
+                $data[$property] = $this->normalizeTags($data['tags']);
+            }
+        }
+    }
+
+    public function beforeSave($event, $entity, $options)
+    {
+        if (empty($entity->tags)) {
+            return;
+        }
+        foreach ($entity->tags as $k => $tag) {
+            if (!$tag->isNew()) {
+                continue;
+            }
+
+            $existingTag = $this->getExistingTag($tag->label);
+            if (!$existing) {
+                continue;
+            }
+
+            $joinData = $tag->_joinData;
+            $tag = $existing;
+            $tag->_joinData = $joinData;
+            $entity->tags[$k] = $tag;
+        }
+    }
+
+    public function normalizeTags($tags) {
+
+        $result = [];
+
+        $modelAlias = $this->_table->getAlias();
+
+        $common = [
+            '_joinData' => [
+                'fk_model' => $modelAlias
+            ]
+        ];
+
+        $tagsTable = $this->_table->Tags;
+        $displayField = $tagsTable->getDisplayField();
+
+        $tagIdentifiers = [];
+        foreach ($tags as $tag) {
+            if (empty($tag)) {
+                continue;
+            }
+            if (is_object($tag)) {
+                $result[] = $tag->toArray();
+            }
+            $tagIdentifier = $this->getTagIdentifier($tag);
+            if (isset($tagIdentifiers[$tagIdentifier])) {
+                continue;
+            }
+            $tagIdentifiers[$tagIdentifier] = true;
+
+            $existingTag = $this->getExistingTag($tagIdentifier);
+            if ($existingTag) {
+                $result[] = array_merge($common, ['id' => $existingTag->id]);
+                continue;
+            }
+
+            $result[] = array_merge(
+                $common,
+                [
+                    'label' => $tagIdentifier,
+                ]
+            );
+        }
+
+        return $result;
+    }
+
+    protected function getTagIdentifier($tag)
+    {
+        if (is_object($tag)) {
+            return $tag->label;
+        } else {
+            return trim($tag);
+        }
+    }
+
+    protected function getExistingTag($tagName)
+    {
+        $tagsTable = $this->_table->Tags->getTarget();
+        $query = $tagsTable->find()->where([
+            'Tags.label' => $tagName
+        ])
+        ->select('Tags.id');
+        return $query->first();
+    }
+}
\ No newline at end of file
diff --git a/src/Model/Entity/Tag.php b/src/Model/Entity/Tag.php
new file mode 100644
index 0000000..19802f0
--- /dev/null
+++ b/src/Model/Entity/Tag.php
@@ -0,0 +1,43 @@
+<?php
+
+namespace App\Model\Entity;
+
+use App\Model\Entity\AppModel;
+
+class Tag extends AppModel {
+
+    protected $_accessible = [
+        'id' => false,
+        'counter' => false,
+        '*' => true,
+    ];
+
+    protected $_accessibleOnNew = [
+        'label' => true,
+        'colour' => true,
+    ];
+
+    protected $_virtual = ['text_colour'];
+
+    protected function _getTextColour()
+    {
+        $textColour = null;
+        if (!empty($this->colour)) {
+            $textColour = $this->getTextColour($this->colour);
+        }
+        return $textColour;
+    }
+
+    protected function getTextColour($RGB) {
+        $r = hexdec(substr($RGB, 1, 2));
+        $g = hexdec(substr($RGB, 3, 2));
+        $b = hexdec(substr($RGB, 5, 2));
+        $average = ((2 * $r) + $b + (3 * $g))/6;
+        if ($average < 127) {
+            return 'white';
+        } else {
+            return 'black';
+        }
+    }
+
+}
diff --git a/src/Model/Entity/Tagged.php b/src/Model/Entity/Tagged.php
new file mode 100644
index 0000000..eac3b44
--- /dev/null
+++ b/src/Model/Entity/Tagged.php
@@ -0,0 +1,14 @@
+<?php
+
+namespace App\Model\Entity;
+
+use Cake\ORM\Entity;
+
+class Tagged extends AppModel {
+
+    protected $_accessible = [
+        'id' => false,
+        '*' => true,
+    ];
+
+}
diff --git a/src/Model/Table/IndividualsTable.php b/src/Model/Table/IndividualsTable.php
index 5693321..3a621b3 100644
--- a/src/Model/Table/IndividualsTable.php
+++ b/src/Model/Table/IndividualsTable.php
@@ -14,11 +14,7 @@ class IndividualsTable extends AppTable
     {
         parent::initialize($config);
         $this->addBehavior('UUID');
-        $this->addBehavior('Tags.Tag', [
-            'taggedCounter' => false,
-            'strategy' => 'array',
-            'finderField' => 'label',
-        ]);
+        $this->addBehavior('Tag');
         $this->hasMany(
             'Alignments',
             [
diff --git a/src/Model/Table/OrganisationsTable.php b/src/Model/Table/OrganisationsTable.php
index 8587864..a43b7e9 100644
--- a/src/Model/Table/OrganisationsTable.php
+++ b/src/Model/Table/OrganisationsTable.php
@@ -18,6 +18,7 @@ class OrganisationsTable extends AppTable
     public function initialize(array $config): void
     {
         parent::initialize($config);
+        $this->addBehavior('Tag');
         $this->hasMany(
             'Alignments',
             [
diff --git a/src/Model/Table/TaggedTable.php b/src/Model/Table/TaggedTable.php
new file mode 100644
index 0000000..289cbbc
--- /dev/null
+++ b/src/Model/Table/TaggedTable.php
@@ -0,0 +1,34 @@
+<?php
+
+namespace App\Model\Table;
+
+use App\Model\Table\AppTable;
+use Cake\Validation\Validator;
+
+class TaggedTable extends AppTable
+{
+    protected $_accessible = [
+        'id' => false
+    ];
+
+    public function initialize(array $config): void
+    {
+        // $this->setTable('tagged');
+        $this->setTable('tags_tagged');
+        $this->belongsTo('Tags', [
+            'className' => 'Tags',
+            'foreignKey' => 'tag_id',
+            'propertyName' => 'tag',
+        ]);
+        $this->addBehavior('Timestamp');
+    }
+
+    public function validationDefault(Validator $validator): Validator
+    {
+        $validator
+            ->notBlank('fk_model')
+            ->notBlank('fk_id')
+            ->notBlank('tag_id');
+        return $validator;
+    }
+}
diff --git a/src/Model/Table/TagsTable.php b/src/Model/Table/TagsTable.php
new file mode 100644
index 0000000..6a885dc
--- /dev/null
+++ b/src/Model/Table/TagsTable.php
@@ -0,0 +1,28 @@
+<?php
+
+namespace App\Model\Table;
+
+use App\Model\Table\AppTable;
+use Cake\Validation\Validator;
+
+class TagsTable extends AppTable
+{
+    protected $_accessible = [
+        'id' => false
+    ];
+
+    public function initialize(array $config): void
+    {
+        // $this->setTable('tags');
+        $this->setTable('tags_tags');
+        $this->setDisplayField('label'); // Change to name?
+        $this->addBehavior('Timestamp');
+    }
+
+    public function validationDefault(Validator $validator): Validator
+    {
+        $validator
+            ->notBlank('label');
+        return $validator;
+    }
+}
diff --git a/src/View/Helper/TagHelper.php b/src/View/Helper/TagHelper.php
index f601650..c027e98 100644
--- a/src/View/Helper/TagHelper.php
+++ b/src/View/Helper/TagHelper.php
@@ -64,8 +64,9 @@ class TagHelper extends Helper
                     'onclick' => 'createTagPicker(this)',
                 ]
             ]);
+        } else {
+            $html .= '<script>$(document).ready(function() { initSelect2Pickers() })</script>';
         }
-        $html .= '<script>$(document).ready(function() { initSelect2Pickers() })</script>';
         return $html;
     }
 
diff --git a/templates/Organisations/view.php b/templates/Organisations/view.php
index 323571e..0652a8c 100644
--- a/templates/Organisations/view.php
+++ b/templates/Organisations/view.php
@@ -37,6 +37,10 @@ echo $this->element(
                 'key' => __('Contacts'),
                 'path' => 'contacts'
             ],
+            [
+                'key' => __('Tags'),
+                'type' => 'tags',
+            ],
             [
                 'key' => __('Alignments'),
                 'type' => 'alignment',
diff --git a/webroot/js/main.js b/webroot/js/main.js
index 465969d..eca62cc 100644
--- a/webroot/js/main.js
+++ b/webroot/js/main.js
@@ -124,13 +124,13 @@ function createTagPicker(clicked) {
 
     function getEditableButtons($select, $container) {
         const $saveButton = $('<button></button>').addClass(['btn btn-primary btn-sm', 'align-self-start']).attr('type', 'button')
-        .append($('<span></span>').text('Save').prepend($('<i></i>').addClass('fa fa-save mr-1')))
+        .append($('<span></span>').text('Save').addClass('text-nowrap').prepend($('<i></i>').addClass('fa fa-save mr-1')))
         .click(function() {
             const tags = $select.select2('data').map(tag => tag.text)
             addTags($select.data('url'), tags, $(this))
         })
         const $cancelButton = $('<button></button>').addClass(['btn btn-secondary btn-sm', 'align-self-start']).attr('type', 'button')
-            .append($('<span></span>').text('Cancel').prepend($('<i></i>').addClass('fa fa-times mr-1')))
+            .append($('<span></span>').text('Cancel').addClass('text-nowrap').prepend($('<i></i>').addClass('fa fa-times mr-1')))
             .click(function() {
                 closePicker($select, $container)
             })
@@ -150,9 +150,12 @@ function createTagPicker(clicked) {
     initSelect2Picker($select)
 }
 
-function deleteTag(url, tag, clicked) {
+function deleteTag(url, tags, clicked) {
+    if (!Array.isArray(tags)) {
+        tags = [tags];
+    }
     const data = {
-        tag_list: tag
+        tag_list: JSON.stringify(tags)
     }
     const $statusNode = $(clicked).closest('.tag')
     const APIOptions = {
@@ -174,7 +177,7 @@ function deleteTag(url, tag, clicked) {
                     const controllerName = split[1]
                     const id = split[3]
                     const urlRetag = `/${controllerName}/tag/${id}`
-                    addTags(urlRetag, [tag], $container.find('.tag-container')).then(() => {
+                    addTags(urlRetag, tags, $container.find('.tag-container')).then(() => {
                         theToast.removeToast()
                     })
                 }),
@@ -185,7 +188,7 @@ function deleteTag(url, tag, clicked) {
 
 function addTags(url, tags, $statusNode) {
     const data = {
-        tag_list: tags
+        tag_list: JSON.stringify(tags)
     }
     const APIOptions = {
         statusNode: $statusNode

From eed5b9226a6ae88788aeb941376ce0320dc4990b Mon Sep 17 00:00:00 2001
From: mokaddem <sami.mokaddem@circl.lu>
Date: Wed, 1 Sep 2021 16:12:56 +0200
Subject: [PATCH 07/16] chg: [behavior:tags] Custom finder and small
 improvements

---
 src/Controller/Component/CRUDComponent.php |   2 +-
 src/Model/Behavior/TagBehavior.php         | 149 ++++++++++++++++++++-
 templates/genericTemplates/filters.php     |   2 +-
 webroot/js/bootstrap-helper.js             |   2 +-
 webroot/js/main.js                         |  16 +--
 5 files changed, 158 insertions(+), 13 deletions(-)

diff --git a/src/Controller/Component/CRUDComponent.php b/src/Controller/Component/CRUDComponent.php
index 51cdbfc..75f02ba 100644
--- a/src/Controller/Component/CRUDComponent.php
+++ b/src/Controller/Component/CRUDComponent.php
@@ -745,7 +745,7 @@ class CRUDComponent extends Component
             'label' => $tags,
             'forceAnd' => true
         ])->select($modelAlias . '.id');
-        return $query = $query->where([$modelAlias . '.id IN' => $subQuery]);
+        return $query->where([$modelAlias . '.id IN' => $subQuery]);
     }
 
     protected function setNestedRelatedCondition($query, $filterParts, $filterValue)
diff --git a/src/Model/Behavior/TagBehavior.php b/src/Model/Behavior/TagBehavior.php
index 63dd57d..437e74c 100644
--- a/src/Model/Behavior/TagBehavior.php
+++ b/src/Model/Behavior/TagBehavior.php
@@ -11,6 +11,7 @@ class TagBehavior extends Behavior
 {
 
     protected $_defaultConfig = [
+        'finderField' => 'label',
         'tagsAssoc' => [
             'className' => 'Tags',
             // 'joinTable' => 'tagged', // uncomment me!
@@ -148,9 +149,7 @@ class TagBehavior extends Behavior
     public function normalizeTags($tags) {
 
         $result = [];
-
         $modelAlias = $this->_table->getAlias();
-
         $common = [
             '_joinData' => [
                 'fk_model' => $modelAlias
@@ -209,4 +208,150 @@ class TagBehavior extends Behavior
         ->select('Tags.id');
         return $query->first();
     }
+
+    public function findByTag(Query $query, array $options) {
+        $finderField = $optionsKey = $this->getConfig('finderField');
+        if (!$finderField) {
+            $finderField = $optionsKey = 'label';
+        }
+
+        if (!isset($options[$optionsKey])) {
+            throw new RuntimeException(__('Expected key `{0}` not present in find(\'tagged\') options argument.', $optionsKey));
+        }
+        $isAndOperator = isset($options['OperatorAND']) ? $options['OperatorAND'] : true;
+        $filterValue = $options[$optionsKey];
+        if (!$filterValue) {
+            return $query;
+        }
+
+        $filterValue = $this->dissectArgs($filterValue);
+        if (!empty($filterValue['NOT']) || !empty($filterValue['LIKE'])) {
+            return $this->findByComplexQueryConditions($query, $filterValue, $finderField, $isAndOperator);
+        }
+
+        $subQuery = $this->buildQuerySnippet($filterValue, $finderField, $isAndOperator);
+        if (is_string($subQuery)) {
+            $query->matching('Tags', function ($q) use ($finderField, $subQuery) {
+                $key = 'Tags.' . $finderField;
+                return $q->where([
+                    $key => $subQuery,
+                ]);
+            });
+            return $query;
+        }
+
+        $modelAlias = $this->_table->getAlias();
+        return $query->where([$modelAlias . '.id IN' => $subQuery]);
+    }
+
+    public function findUntagged(Query $query, array $options) {
+        $modelAlias = $this->_table->getAlias();
+        $foreignKey = $this->getConfig('tagsAssoc.foreignKey');
+        $conditions = ['fk_model' => $modelAlias];
+        $this->_table->hasOne('NoTags', [
+            'className' => $this->getConfig('taggedAssoc.className'),
+            'foreignKey' => $foreignKey,
+            'conditions' => $conditions
+        ]);
+        $query = $query->contain(['NoTags'])->where(['NoTags.id IS' => null]);
+        return $query;
+    }
+
+    protected function dissectArgs($filterValue): array
+    {
+        if (!is_array($filterValue)) {
+            return $filterValue;
+        }
+        $dissected = [
+            'AND' => [],
+            'NOT' => [],
+            'LIKE' => [],
+        ];
+        foreach ($filterValue as $value) {
+            if (substr($value, 0, 1) == '!') {
+                $dissected['NOT'][] = substr($value, 1);
+            }
+            else if (strpos($value, '%') != false) {
+                $dissected['LIKE'][] = $value;
+            } else {
+                $dissected['AND'][] = $value;
+            }
+        }
+        if (empty($dissected['NOT']) && empty($dissected['LIKE'])) {
+            return $dissected['AND'];
+        }
+        return $dissected;
+    }
+
+    protected function buildQuerySnippet($filterValue, string $finderField, bool $OperatorAND=true)
+    {
+        if (!is_array($filterValue)) {
+            return $filterValue;
+        }
+        $key = 'Tags.' . $finderField;
+        $foreignKey = $this->getConfig('tagsAssoc.foreignKey');
+        $conditions = [
+            $key . ' IN' => $filterValue,
+        ];
+
+        $query = $this->_table->Tagged->find();
+        if ($OperatorAND) {
+            $query->contain(['Tags'])
+                ->group('Tagged.' . $foreignKey)
+                ->having('COUNT(*) = ' . count($filterValue))
+                ->select('Tagged.' . $foreignKey)
+                ->where($conditions);
+        } else {
+            $query->contain(['Tags'])
+                ->select('Tagged.' . $foreignKey)
+                ->where($conditions);
+        }
+        return $query;
+    }
+
+    protected function findByComplexQueryConditions($query, $filterValue, string $finderField, bool $OperatorAND=true)
+    {
+        $key = 'Tags.' . $finderField;
+        $taggedAlias = 'Tagged';
+        $foreignKey = $this->getConfig('tagsAssoc.foreignKey');
+        
+        if (!empty($filterValue['AND'])) {
+            $subQuery = $this->buildQuerySnippet($filterValue['AND'], $finderField, $OperatorAND);
+            $modelAlias = $this->_table->getAlias();
+            $query->where([$modelAlias . '.id IN' => $subQuery]);
+        }
+
+        if (!empty($filterValue['NOT'])) {
+            $subQuery = $this->buildQuerySnippet($filterValue['NOT'], $finderField, false);
+            $modelAlias = $this->_table->getAlias();
+            $query->where([$modelAlias . '.id NOT IN' => $subQuery]);
+        }
+
+        if (!empty($filterValue['LIKE'])) {
+            $conditions = ['OR' => []];
+            foreach($filterValue['LIKE'] as $likeValue) {
+                $conditions['OR'][] = [
+                    $key . ' LIKE' => $likeValue,
+                ];
+            }
+            $subQuery = $this->buildQuerySnippet($filterValue['NOT'], $finderField, $OperatorAND);
+            if ($OperatorAND) {
+                $subQuery = $this->_table->Tagged->find()
+                    ->contain(['Tags'])
+                    ->group('Tagged.' . $foreignKey)
+                    ->having('COUNT(*) >= ' . count($filterValue['LIKE']))
+                    ->select('Tagged.' . $foreignKey)
+                    ->where($conditions);
+            } else {
+                $subQuery = $this->_table->Tagged->find()
+                    ->contain(['Tags'])
+                    ->select('Tagged.' . $foreignKey)
+                    ->where($conditions);
+            }
+            $modelAlias = $this->_table->getAlias();
+            $query->where([$modelAlias . '.id IN' => $subQuery]);
+        }
+
+        return $query;
+    }
 }
\ No newline at end of file
diff --git a/templates/genericTemplates/filters.php b/templates/genericTemplates/filters.php
index 3be1b09..9a7c49a 100644
--- a/templates/genericTemplates/filters.php
+++ b/templates/genericTemplates/filters.php
@@ -87,7 +87,7 @@ echo $this->Bootstrap->modal([
         $filteringTable.find('tbody').empty()
         addControlRow($filteringTable)
         const randomValue = getRandomValue()
-        const activeFilters = $(`#toggleFilterButton-${randomValue}`).data('activeFilters')
+        const activeFilters = Object.assign({}, $(`#toggleFilterButton-${randomValue}`).data('activeFilters'))
         const tags = activeFilters['filteringTags'] !== undefined ? Object.assign({}, activeFilters)['filteringTags'] : []
         delete activeFilters['filteringTags']
         for (let [field, value] of Object.entries(activeFilters)) {
diff --git a/webroot/js/bootstrap-helper.js b/webroot/js/bootstrap-helper.js
index cc740d3..39cc6ce 100644
--- a/webroot/js/bootstrap-helper.js
+++ b/webroot/js/bootstrap-helper.js
@@ -1125,7 +1125,7 @@ class HtmlHelper {
             options.colour = '#924da6'
         }
         const $tag = $('<span/>')
-            .addClass(['tag', 'badge', 'border'])
+            .addClass(['tag', 'badge', 'align-text-top'])
             .css({color: getTextColour(options.colour), 'background-color': options.colour})
             .text(options.text)
 
diff --git a/webroot/js/main.js b/webroot/js/main.js
index eca62cc..3acc35f 100644
--- a/webroot/js/main.js
+++ b/webroot/js/main.js
@@ -162,14 +162,14 @@ function deleteTag(url, tags, clicked) {
         statusNode: $statusNode,
         skipFeedback: true,
     }
-    return AJAXApi.quickFetchAndPostForm(url, data, APIOptions).then((result) => {
+    return AJAXApi.quickFetchAndPostForm(url, data, APIOptions).then((apiResult) => {
         let $container = $statusNode.closest('.tag-container-wrapper')
-        refreshTagList(result, $container).then(($tagContainer) => {
+        refreshTagList(apiResult, $container).then(($tagContainer) => {
             $container = $tagContainer // old container might not exist anymore since it was replaced after the refresh
         })
         const theToast = UI.toast({
             variant: 'success',
-            title: result.message,
+            title: apiResult.message,
             bodyHtml: $('<div/>').append(
                 $('<span/>').text('Cancel untag operation.'),
                 $('<button/>').addClass(['btn', 'btn-primary', 'btn-sm', 'ml-3']).text('Restore tag').click(function() {
@@ -193,15 +193,15 @@ function addTags(url, tags, $statusNode) {
     const APIOptions = {
         statusNode: $statusNode
     }
-    return AJAXApi.quickFetchAndPostForm(url, data, APIOptions).then((result) => {
+    return AJAXApi.quickFetchAndPostForm(url, data, APIOptions).then((apiResult) => {
         const $container = $statusNode.closest('.tag-container-wrapper')
-        refreshTagList(result, $container)
+        refreshTagList(apiResult, $container)
     }).catch((e) => {})
 }
 
-function refreshTagList(result, $container) {
-    const controllerName = result.url.split('/')[1]
-    const entityId = result.data.id
+function refreshTagList(apiResult, $container) {
+    const controllerName = apiResult.url.split('/')[1]
+    const entityId = apiResult.data.id
     const url = `/${controllerName}/viewTags/${entityId}`
     return UI.reload(url, $container)
 }

From a14dc2e8fe85e3ebc8bd4791503c50c092cb9401 Mon Sep 17 00:00:00 2001
From: mokaddem <sami.mokaddem@circl.lu>
Date: Thu, 2 Sep 2021 11:30:09 +0200
Subject: [PATCH 08/16] chg: [tags] Transformed feature into a pluging - WiP

---
 composer.json                                 |   5 +-
 plugins/Tags/config/routes.php                |  20 ++++
 plugins/Tags/src/Controller/AppController.php |  23 ++++
 .../Tags/src/Controller/TagsController.php    | 111 ++++++++++++++++++
 .../Tags/src}/Model/Behavior/TagBehavior.php  |  10 +-
 .../Tags/src}/Model/Entity/Tag.php            |   0
 .../Tags/src}/Model/Entity/Tagged.php         |   0
 .../Tags/src}/Model/Table/TaggedTable.php     |   5 +-
 .../Tags/src}/Model/Table/TagsTable.php       |   3 +-
 plugins/Tags/src/Plugin.php                   |  41 +++++++
 src/Application.php                           |   5 +-
 src/Controller/AppController.php              |   3 +-
 src/Controller/TagsController.php             |  80 -------------
 src/Model/Table/IndividualsTable.php          |   2 +-
 src/Model/Table/OrganisationsTable.php        |   2 +-
 15 files changed, 213 insertions(+), 97 deletions(-)
 create mode 100644 plugins/Tags/config/routes.php
 create mode 100644 plugins/Tags/src/Controller/AppController.php
 create mode 100644 plugins/Tags/src/Controller/TagsController.php
 rename {src => plugins/Tags/src}/Model/Behavior/TagBehavior.php (98%)
 rename {src => plugins/Tags/src}/Model/Entity/Tag.php (100%)
 rename {src => plugins/Tags/src}/Model/Entity/Tagged.php (100%)
 rename {src => plugins/Tags/src}/Model/Table/TaggedTable.php (86%)
 rename {src => plugins/Tags/src}/Model/Table/TagsTable.php (89%)
 create mode 100644 plugins/Tags/src/Plugin.php
 delete mode 100644 src/Controller/TagsController.php

diff --git a/composer.json b/composer.json
index 13f42e8..c233ebd 100644
--- a/composer.json
+++ b/composer.json
@@ -11,7 +11,6 @@
         "cakephp/cakephp": "^4.0",
         "cakephp/migrations": "^3.0",
         "cakephp/plugin-installer": "^1.2",
-        "dereuromark/cakephp-tags": "^1.2",
         "erusev/parsedown": "^1.7",
         "mobiledetect/mobiledetectlib": "^2.8"
     },
@@ -30,12 +29,14 @@
     },
     "autoload": {
         "psr-4": {
-            "App\\": "src/"
+            "App\\": "src/",
+            "Tags\\": "plugins/Tags/src/"
         }
     },
     "autoload-dev": {
         "psr-4": {
             "App\\Test\\": "tests/",
+            "Tags\\Test\\": "plugins/Tags/tests/",
             "Cake\\Test\\": "vendor/cakephp/cakephp/tests/"
         }
     },
diff --git a/plugins/Tags/config/routes.php b/plugins/Tags/config/routes.php
new file mode 100644
index 0000000..3fab36a
--- /dev/null
+++ b/plugins/Tags/config/routes.php
@@ -0,0 +1,20 @@
+<?php
+use Cake\Routing\Route\DashedRoute;
+use Cake\Routing\RouteBuilder;
+
+$routes->plugin(
+    'Tags',
+    ['path' => '/tags'],
+    function ($routes) {
+        $routes->setRouteClass(DashedRoute::class);
+
+        $routes->connect(
+            '/{action}/*',
+            ['controller' => 'Tags']
+        );
+
+        // $routes->get('/', ['controller' => 'Tags']);
+        // $routes->get('/{id}', ['controller' => 'Tags', 'action' => 'view']);
+        // $routes->put('/{id}', ['controller' => 'Tags', 'action' => 'edit']);
+    }
+);
\ No newline at end of file
diff --git a/plugins/Tags/src/Controller/AppController.php b/plugins/Tags/src/Controller/AppController.php
new file mode 100644
index 0000000..28c7ae4
--- /dev/null
+++ b/plugins/Tags/src/Controller/AppController.php
@@ -0,0 +1,23 @@
+<?php
+
+namespace Tags\Controller;
+
+use App\Controller\AppController as BaseController;
+
+class AppController extends BaseController
+{
+    public function initialize(): void
+    {
+        parent::initialize();
+        // $this->loadComponent('RequestHandler');
+        // $this->loadComponent('ParamHandler', [
+        //     'request' => $this->request
+        // ]);
+        // $this->loadComponent('CRUD', [
+        //     'request' => $this->request,
+        //     'table' => $this->{$this->modelClass},
+        //     'MetaFields' => $this->MetaFields,
+        //     'MetaTemplates' => $this->MetaTemplates
+        // ]);
+    }
+}
\ No newline at end of file
diff --git a/plugins/Tags/src/Controller/TagsController.php b/plugins/Tags/src/Controller/TagsController.php
new file mode 100644
index 0000000..ab75bc9
--- /dev/null
+++ b/plugins/Tags/src/Controller/TagsController.php
@@ -0,0 +1,111 @@
+<?php
+
+namespace Tags\Controller;
+
+use Tags\Controller\AppController;
+use Cake\Utility\Hash;
+use Cake\Utility\Inflector;
+use Cake\Utility\Text;
+use Cake\Database\Expression\QueryExpression;
+use Cake\Http\Exception\NotFoundException;
+use Cake\Http\Exception\MethodNotAllowedException;
+use Cake\Http\Exception\ForbiddenException;
+use Cake\ORM\TableRegistry;
+
+class TagsController extends AppController
+{
+
+    public function index()
+    {
+        $this->CRUD->index([
+            'filters' => ['label', 'colour'],
+            'quickFilters' => [['label' => true], 'colour']
+        ]);
+        $responsePayload = $this->CRUD->getResponsePayload();
+        if (!empty($responsePayload)) {
+            return $responsePayload;
+        }
+    }
+
+    public function add()
+    {
+        $this->CRUD->add();
+        $responsePayload = $this->CRUD->getResponsePayload();
+        if (!empty($responsePayload)) {
+            return $responsePayload;
+        }
+    }
+
+    public function view($id)
+    {
+        $this->CRUD->view($id);
+        $responsePayload = $this->CRUD->getResponsePayload();
+        if (!empty($responsePayload)) {
+            return $responsePayload;
+        }
+    }
+
+    public function edit($id)
+    {
+        $this->CRUD->edit($id);
+        $responsePayload = $this->CRUD->getResponsePayload();
+        if (!empty($responsePayload)) {
+            return $responsePayload;
+        }
+        $this->render('add');
+    }
+
+    public function delete($id)
+    {
+        $this->CRUD->delete($id);
+        $responsePayload = $this->CRUD->getResponsePayload();
+        if (!empty($responsePayload)) {
+            return $responsePayload;
+        }
+    }
+
+    // public function tag($model, $id)
+    // {
+    //     $controller = $this->getControllerBeingTagged($model);
+    //     $controller->CRUD->tag($id);
+    //     $responsePayload = $controller->CRUD->getResponsePayload();
+    //     if (!empty($responsePayload)) {
+    //         return $responsePayload;
+    //     }
+    //     return $controller->getResponse();
+    // }
+
+    // public function untag($model, $id)
+    // {
+    //     $controller = $this->getControllerBeingTagged($model);
+    //     $controller->CRUD->untag($id);
+    //     $responsePayload = $controller->CRUD->getResponsePayload();
+    //     if (!empty($responsePayload)) {
+    //         return $responsePayload;
+    //     }
+    //     return $controller->getResponse();
+    // }
+
+    // public function viewTags($model, $id)
+    // {
+    //     $controller = $this->getControllerBeingTagged($model);
+    //     $controller->CRUD->viewTags($id);
+    //     $responsePayload = $controller->CRUD->getResponsePayload();
+    //     if (!empty($responsePayload)) {
+    //         return $responsePayload;
+    //     }
+    //     return $controller->getResponse();
+    // }
+
+    // private function getControllerBeingTagged($model)
+    // {
+    //     $modelName = Inflector::camelize($model);
+    //     $controllerName = "\\App\\Controller\\{$modelName}Controller";
+    //     if (!class_exists($controllerName)) {
+    //         throw new MethodNotAllowedException(__('Model `{0}` does not exists', $model));
+    //     }
+    //     $controller = new $controllerName;
+    //     // Make sure that the request is correctly assigned to this controller
+    //     return $controller;
+    // }
+}
diff --git a/src/Model/Behavior/TagBehavior.php b/plugins/Tags/src/Model/Behavior/TagBehavior.php
similarity index 98%
rename from src/Model/Behavior/TagBehavior.php
rename to plugins/Tags/src/Model/Behavior/TagBehavior.php
index 437e74c..3db1b67 100644
--- a/src/Model/Behavior/TagBehavior.php
+++ b/plugins/Tags/src/Model/Behavior/TagBehavior.php
@@ -1,6 +1,6 @@
 <?php
 
-namespace App\Model\Behavior;
+namespace Tags\Model\Behavior;
 
 use Cake\ORM\Behavior;
 use Cake\ORM\Entity;
@@ -9,20 +9,18 @@ use Cake\ORM\Table;
 
 class TagBehavior extends Behavior
 {
-
     protected $_defaultConfig = [
         'finderField' => 'label',
         'tagsAssoc' => [
-            'className' => 'Tags',
-            // 'joinTable' => 'tagged', // uncomment me!
-            'joinTable' => 'tags_tagged', // remove me!
+            'className' => 'Tags.Tags',
+            'joinTable' => 'tags_tagged',
             'foreignKey' => 'fk_id',
             'targetForeignKey' => 'tag_id',
             'propertyName' => 'tags',
         ],
         'tagsCounter' => ['counter'],
         'taggedAssoc' => [
-            'className' => 'Tagged',
+            'className' => 'Tags.Tagged',
             'foreignKey' => 'fk_id'
         ],
         'implementedEvents' => [
diff --git a/src/Model/Entity/Tag.php b/plugins/Tags/src/Model/Entity/Tag.php
similarity index 100%
rename from src/Model/Entity/Tag.php
rename to plugins/Tags/src/Model/Entity/Tag.php
diff --git a/src/Model/Entity/Tagged.php b/plugins/Tags/src/Model/Entity/Tagged.php
similarity index 100%
rename from src/Model/Entity/Tagged.php
rename to plugins/Tags/src/Model/Entity/Tagged.php
diff --git a/src/Model/Table/TaggedTable.php b/plugins/Tags/src/Model/Table/TaggedTable.php
similarity index 86%
rename from src/Model/Table/TaggedTable.php
rename to plugins/Tags/src/Model/Table/TaggedTable.php
index 289cbbc..f6604d2 100644
--- a/src/Model/Table/TaggedTable.php
+++ b/plugins/Tags/src/Model/Table/TaggedTable.php
@@ -1,6 +1,6 @@
 <?php
 
-namespace App\Model\Table;
+namespace Tags\Model\Table;
 
 use App\Model\Table\AppTable;
 use Cake\Validation\Validator;
@@ -13,10 +13,9 @@ class TaggedTable extends AppTable
 
     public function initialize(array $config): void
     {
-        // $this->setTable('tagged');
         $this->setTable('tags_tagged');
         $this->belongsTo('Tags', [
-            'className' => 'Tags',
+            'className' => 'Tags.Tags',
             'foreignKey' => 'tag_id',
             'propertyName' => 'tag',
         ]);
diff --git a/src/Model/Table/TagsTable.php b/plugins/Tags/src/Model/Table/TagsTable.php
similarity index 89%
rename from src/Model/Table/TagsTable.php
rename to plugins/Tags/src/Model/Table/TagsTable.php
index 6a885dc..2149134 100644
--- a/src/Model/Table/TagsTable.php
+++ b/plugins/Tags/src/Model/Table/TagsTable.php
@@ -1,6 +1,6 @@
 <?php
 
-namespace App\Model\Table;
+namespace Tags\Model\Table;
 
 use App\Model\Table\AppTable;
 use Cake\Validation\Validator;
@@ -13,7 +13,6 @@ class TagsTable extends AppTable
 
     public function initialize(array $config): void
     {
-        // $this->setTable('tags');
         $this->setTable('tags_tags');
         $this->setDisplayField('label'); // Change to name?
         $this->addBehavior('Timestamp');
diff --git a/plugins/Tags/src/Plugin.php b/plugins/Tags/src/Plugin.php
new file mode 100644
index 0000000..84c8702
--- /dev/null
+++ b/plugins/Tags/src/Plugin.php
@@ -0,0 +1,41 @@
+<?php
+
+namespace Tags;
+
+use Cake\Core\BasePlugin;
+use Cake\Core\PluginApplicationInterface;
+use Cake\Console\CommandCollection;
+use Cake\Http\MiddlewareQueue;
+
+class Plugin extends BasePlugin
+{
+    public function middleware(MiddlewareQueue $middleware): MiddlewareQueue
+    {
+        // Add middleware here.
+        $middleware = parent::middleware($middleware);
+
+        return $middleware;
+    }
+
+    public function console(CommandCollection $commands): CommandCollection
+    {
+        // Add console commands here.
+        $commands = parent::console($commands);
+
+        return $commands;
+    }
+
+    public function bootstrap(PluginApplicationInterface $app): void
+    {
+        // Add constants, load configuration defaults.
+        // By default will load `config/bootstrap.php` in the plugin.
+        parent::bootstrap($app);
+    }
+
+    public function routes($routes): void
+    {
+        // Add routes.
+        // By default will load `config/routes.php` in the plugin.
+        parent::routes($routes);
+    }
+}
diff --git a/src/Application.php b/src/Application.php
index c6529bd..2a8a88b 100644
--- a/src/Application.php
+++ b/src/Application.php
@@ -29,6 +29,9 @@ use Authentication\AuthenticationServiceInterface;
 use Authentication\AuthenticationServiceProviderInterface;
 use Authentication\Middleware\AuthenticationMiddleware;
 use Psr\Http\Message\ServerRequestInterface;
+
+use Tags\Plugin as TagsPlugin;
+
 /**
  * Application setup class.
  *
@@ -59,7 +62,7 @@ class Application extends BaseApplication implements AuthenticationServiceProvid
             $this->addPlugin('DebugKit');
         }
         $this->addPlugin('Authentication');
-        $this->addPlugin('Tags');
+        $this->addPlugin('Tags', ['routes' => true]);
         // Load more plugins here
     }
 
diff --git a/src/Controller/AppController.php b/src/Controller/AppController.php
index 498b0ae..ee1c1b1 100644
--- a/src/Controller/AppController.php
+++ b/src/Controller/AppController.php
@@ -63,9 +63,10 @@ class AppController extends Controller
         ]);
         $this->loadModel('MetaFields');
         $this->loadModel('MetaTemplates');
+        $table = $this->getTableLocator()->get($this->modelClass);
         $this->loadComponent('CRUD', [
             'request' => $this->request,
-            'table' => $this->{$this->modelClass},
+            'table' => $table,
             'MetaFields' => $this->MetaFields,
             'MetaTemplates' => $this->MetaTemplates
         ]);
diff --git a/src/Controller/TagsController.php b/src/Controller/TagsController.php
deleted file mode 100644
index 57481e0..0000000
--- a/src/Controller/TagsController.php
+++ /dev/null
@@ -1,80 +0,0 @@
-<?php
-
-namespace App\Controller;
-
-use App\Controller\AppController;
-use Cake\Utility\Hash;
-use Cake\Utility\Inflector;
-use Cake\Utility\Text;
-use Cake\Database\Expression\QueryExpression;
-use Cake\Http\Exception\NotFoundException;
-use Cake\Http\Exception\MethodNotAllowedException;
-use Cake\Http\Exception\ForbiddenException;
-use Cake\ORM\TableRegistry;
-
-class TagsController extends AppController
-{
-
-    public function initialize(): void
-    {
-        parent::initialize();
-        $this->Table = TableRegistry::getTableLocator()->get('Tags.Tags');
-        $this->CRUD->Table = $this->Table;
-        $this->CRUD->TableAlias = $this->CRUD->Table->getAlias();
-        $this->CRUD->ObjectAlias = Inflector::singularize($this->CRUD->TableAlias);
-    }
-
-    public function index()
-    {
-        $this->CRUD->index([
-            'filters' => ['label', 'colour'],
-            'quickFilters' => [['label' => true], 'colour']
-        ]);
-        $responsePayload = $this->CRUD->getResponsePayload();
-        if (!empty($responsePayload)) {
-            return $responsePayload;
-        }
-        $this->set('metaGroup', $this->isAdmin ? 'Administration' : 'Cerebrate');
-    }
-
-    public function add()
-    {
-        $this->CRUD->add();
-        $responsePayload = $this->CRUD->getResponsePayload();
-        if (!empty($responsePayload)) {
-            return $responsePayload;
-        }
-        $this->set('metaGroup', $this->isAdmin ? 'Administration' : 'Cerebrate');
-    }
-
-    public function view($id)
-    {
-        $this->CRUD->view($id);
-        $responsePayload = $this->CRUD->getResponsePayload();
-        if (!empty($responsePayload)) {
-            return $responsePayload;
-        }
-        $this->set('metaGroup', $this->isAdmin ? 'Administration' : 'Cerebrate');
-    }
-
-    public function edit($id)
-    {
-        $this->CRUD->edit($id);
-        $responsePayload = $this->CRUD->getResponsePayload();
-        if (!empty($responsePayload)) {
-            return $responsePayload;
-        }
-        $this->set('metaGroup', $this->isAdmin ? 'Administration' : 'Cerebrate');
-        $this->render('add');
-    }
-
-    public function delete($id)
-    {
-        $this->CRUD->delete($id);
-        $responsePayload = $this->CRUD->getResponsePayload();
-        if (!empty($responsePayload)) {
-            return $responsePayload;
-        }
-        $this->set('metaGroup', $this->isAdmin ? 'Administration' : 'Cerebrate');
-    }
-}
diff --git a/src/Model/Table/IndividualsTable.php b/src/Model/Table/IndividualsTable.php
index 3a621b3..f8c41f1 100644
--- a/src/Model/Table/IndividualsTable.php
+++ b/src/Model/Table/IndividualsTable.php
@@ -14,7 +14,7 @@ class IndividualsTable extends AppTable
     {
         parent::initialize($config);
         $this->addBehavior('UUID');
-        $this->addBehavior('Tag');
+        $this->addBehavior('Tags.Tag');
         $this->hasMany(
             'Alignments',
             [
diff --git a/src/Model/Table/OrganisationsTable.php b/src/Model/Table/OrganisationsTable.php
index a43b7e9..2ac2b66 100644
--- a/src/Model/Table/OrganisationsTable.php
+++ b/src/Model/Table/OrganisationsTable.php
@@ -18,7 +18,7 @@ class OrganisationsTable extends AppTable
     public function initialize(array $config): void
     {
         parent::initialize($config);
-        $this->addBehavior('Tag');
+        $this->addBehavior('Tags.Tag');
         $this->hasMany(
             'Alignments',
             [

From 6a9fc98382d3a71765f683b85e83b7467be89f99 Mon Sep 17 00:00:00 2001
From: mokaddem <sami.mokaddem@circl.lu>
Date: Thu, 2 Sep 2021 11:52:47 +0200
Subject: [PATCH 09/16] chg: [tags] Moved tag helper as plugin tag helper

---
 plugins/Tags/src/Controller/AppController.php       | 10 ----------
 {src => plugins/Tags/src}/View/Helper/TagHelper.php |  2 +-
 src/View/AppView.php                                |  1 +
 templates/Organisations/index.php                   |  7 ++++++-
 4 files changed, 8 insertions(+), 12 deletions(-)
 rename {src => plugins/Tags/src}/View/Helper/TagHelper.php (99%)

diff --git a/plugins/Tags/src/Controller/AppController.php b/plugins/Tags/src/Controller/AppController.php
index 28c7ae4..5a0bda8 100644
--- a/plugins/Tags/src/Controller/AppController.php
+++ b/plugins/Tags/src/Controller/AppController.php
@@ -9,15 +9,5 @@ class AppController extends BaseController
     public function initialize(): void
     {
         parent::initialize();
-        // $this->loadComponent('RequestHandler');
-        // $this->loadComponent('ParamHandler', [
-        //     'request' => $this->request
-        // ]);
-        // $this->loadComponent('CRUD', [
-        //     'request' => $this->request,
-        //     'table' => $this->{$this->modelClass},
-        //     'MetaFields' => $this->MetaFields,
-        //     'MetaTemplates' => $this->MetaTemplates
-        // ]);
     }
 }
\ No newline at end of file
diff --git a/src/View/Helper/TagHelper.php b/plugins/Tags/src/View/Helper/TagHelper.php
similarity index 99%
rename from src/View/Helper/TagHelper.php
rename to plugins/Tags/src/View/Helper/TagHelper.php
index c027e98..865c6b9 100644
--- a/src/View/Helper/TagHelper.php
+++ b/plugins/Tags/src/View/Helper/TagHelper.php
@@ -1,6 +1,6 @@
 <?php
 
-namespace App\View\Helper;
+namespace Tags\View\Helper;
 
 use Cake\View\Helper;
 use Cake\Utility\Hash;
diff --git a/src/View/AppView.php b/src/View/AppView.php
index 87b775b..7636a87 100644
--- a/src/View/AppView.php
+++ b/src/View/AppView.php
@@ -43,5 +43,6 @@ class AppView extends View
         $this->loadHelper('PrettyPrint');
         $this->loadHelper('FormFieldMassage');
         $this->loadHelper('Paginator', ['templates' => 'cerebrate-pagination-templates']);
+        $this->loadHelper('Tags.Tag');
     }
 }
diff --git a/templates/Organisations/index.php b/templates/Organisations/index.php
index da638cb..4a98718 100644
--- a/templates/Organisations/index.php
+++ b/templates/Organisations/index.php
@@ -71,7 +71,12 @@ echo $this->element('genericElements/IndexTable/index_table', [
             [
                 'name' => __('Type'),
                 'data_path' => 'type',
-            ]
+            ],
+            [
+                'name' => __('Tags'),
+                'data_path' => 'tags',
+                'element' => 'tags',
+            ],
         ],
         'title' => __('ContactDB Organisation Index'),
         'description' => __('A list of organisations known by your Cerebrate instance. This list can get populated either directly, by adding new organisations or by fetching them from trusted remote sources.'),

From 15e9f5124472a8f5c0ba7047a48ca2320cbf2cc7 Mon Sep 17 00:00:00 2001
From: mokaddem <sami.mokaddem@circl.lu>
Date: Thu, 2 Sep 2021 12:03:07 +0200
Subject: [PATCH 10/16] chg: [tag] Moved CSS and JS parts into the plugin
 folder

---
 plugins/Tags/webroot/css/tagging.css |   3 +
 plugins/Tags/webroot/js/tagging.js   | 142 +++++++++++++++++++++++++++
 templates/layout/default.php         |   4 +
 webroot/css/main.css                 |   4 -
 webroot/js/bootstrap-helper.js       |  11 ---
 webroot/js/main.js                   | 132 -------------------------
 6 files changed, 149 insertions(+), 147 deletions(-)
 create mode 100644 plugins/Tags/webroot/css/tagging.css
 create mode 100644 plugins/Tags/webroot/js/tagging.js

diff --git a/plugins/Tags/webroot/css/tagging.css b/plugins/Tags/webroot/css/tagging.css
new file mode 100644
index 0000000..260b4ce
--- /dev/null
+++ b/plugins/Tags/webroot/css/tagging.css
@@ -0,0 +1,3 @@
+.tag {
+    filter: drop-shadow(2px 2px 2px rgba(0, 0, 0, 0.5));
+}
diff --git a/plugins/Tags/webroot/js/tagging.js b/plugins/Tags/webroot/js/tagging.js
new file mode 100644
index 0000000..355f6a9
--- /dev/null
+++ b/plugins/Tags/webroot/js/tagging.js
@@ -0,0 +1,142 @@
+function createTagPicker(clicked) {
+
+    function closePicker($select, $container) {
+        $select.appendTo($container)
+        $container.parent().find('.picker-container').remove()
+    }
+
+    function getEditableButtons($select, $container) {
+        const $saveButton = $('<button></button>').addClass(['btn btn-primary btn-sm', 'align-self-start']).attr('type', 'button')
+        .append($('<span></span>').text('Save').addClass('text-nowrap').prepend($('<i></i>').addClass('fa fa-save mr-1')))
+        .click(function() {
+            const tags = $select.select2('data').map(tag => tag.text)
+            addTags($select.data('url'), tags, $(this))
+        })
+        const $cancelButton = $('<button></button>').addClass(['btn btn-secondary btn-sm', 'align-self-start']).attr('type', 'button')
+            .append($('<span></span>').text('Cancel').addClass('text-nowrap').prepend($('<i></i>').addClass('fa fa-times mr-1')))
+            .click(function() {
+                closePicker($select, $container)
+            })
+        const $buttons = $('<span></span>').addClass(['picker-action', 'btn-group']).append($saveButton, $cancelButton)
+        return $buttons
+    }
+
+    const $clicked = $(clicked)
+    const $container = $clicked.closest('.tag-container')
+    const $select = $container.parent().find('select.tag-input').removeClass('d-none')
+    closePicker($select, $container)
+    const $pickerContainer = $('<div></div>').addClass(['picker-container', 'd-flex'])
+    
+    $select.prependTo($pickerContainer)
+    $pickerContainer.append(getEditableButtons($select, $container))
+    $container.parent().append($pickerContainer)
+    initSelect2Picker($select)
+}
+
+function deleteTag(url, tags, clicked) {
+    if (!Array.isArray(tags)) {
+        tags = [tags];
+    }
+    const data = {
+        tag_list: JSON.stringify(tags)
+    }
+    const $statusNode = $(clicked).closest('.tag')
+    const APIOptions = {
+        statusNode: $statusNode,
+        skipFeedback: true,
+    }
+    return AJAXApi.quickFetchAndPostForm(url, data, APIOptions).then((apiResult) => {
+        let $container = $statusNode.closest('.tag-container-wrapper')
+        refreshTagList(apiResult, $container).then(($tagContainer) => {
+            $container = $tagContainer // old container might not exist anymore since it was replaced after the refresh
+        })
+        const theToast = UI.toast({
+            variant: 'success',
+            title: apiResult.message,
+            bodyHtml: $('<div/>').append(
+                $('<span/>').text('Cancel untag operation.'),
+                $('<button/>').addClass(['btn', 'btn-primary', 'btn-sm', 'ml-3']).text('Restore tag').click(function() {
+                    const split = url.split('/')
+                    const controllerName = split[1]
+                    const id = split[3]
+                    const urlRetag = `/${controllerName}/tag/${id}`
+                    addTags(urlRetag, tags, $container.find('.tag-container')).then(() => {
+                        theToast.removeToast()
+                    })
+                }),
+            ),
+        })
+    }).catch((e) => {})
+}
+
+function addTags(url, tags, $statusNode) {
+    const data = {
+        tag_list: JSON.stringify(tags)
+    }
+    const APIOptions = {
+        statusNode: $statusNode
+    }
+    return AJAXApi.quickFetchAndPostForm(url, data, APIOptions).then((apiResult) => {
+        const $container = $statusNode.closest('.tag-container-wrapper')
+        refreshTagList(apiResult, $container)
+    }).catch((e) => {})
+}
+
+function refreshTagList(apiResult, $container) {
+    const controllerName = apiResult.url.split('/')[1]
+    const entityId = apiResult.data.id
+    const url = `/${controllerName}/viewTags/${entityId}`
+    return UI.reload(url, $container)
+}
+
+function initSelect2Pickers() {
+    $('select.tag-input').each(function() {
+        if (!$(this).hasClass("select2-hidden-accessible")) {
+            initSelect2Picker($(this))
+        }
+    })
+}
+
+function initSelect2Picker($select) {
+
+    function templateTag(state, $select) {
+        if (!state.id) {
+            return state.label;
+        }
+        if (state.colour === undefined) {
+            state.colour = $(state.element).data('colour')
+        }
+        if ($select !== undefined && state.text[0] === '!') {
+            // fetch corresponding tag and set colors?
+            // const baseTag = state.text.slice(1)
+            // const existingBaseTag = $select.find('option').filter(function() {
+            //     return $(this).val() === baseTag
+            // })
+            // if (existingBaseTag.length > 0) {
+            //     state.colour = existingBaseTag.data('colour')
+            //     state.text = baseTag
+            // }
+        }
+        return buildTag(state)
+    }
+
+    $select.select2({
+        placeholder: 'Pick a tag',
+        tags: true,
+        width: '100%',
+        templateResult: (state) => templateTag(state),
+        templateSelection: (state) => templateTag(state, $select),
+    })
+}
+
+function buildTag(options={}) {
+    if (!options.colour) {
+        options.colour = '#924da6'
+    }
+    const $tag = $('<span/>')
+        .addClass(['tag', 'badge', 'align-text-top'])
+        .css({color: getTextColour(options.colour), 'background-color': options.colour})
+        .text(options.text)
+
+    return $tag
+}
\ No newline at end of file
diff --git a/templates/layout/default.php b/templates/layout/default.php
index d97b800..93bd9eb 100644
--- a/templates/layout/default.php
+++ b/templates/layout/default.php
@@ -60,6 +60,10 @@ $cakeDescription = 'Cerebrate';
     <?= $this->fetch('css') ?>
     <?= $this->fetch('script') ?>
     <?= $this->Html->css('bootstrap-additional.css') ?>
+
+    <?= $this->Html->script('Tags.tagging') ?>
+    <?= $this->Html->css('Tags.tagging') ?>
+
     <?= $this->Html->meta('favicon.ico', '/img/favicon.ico', ['type' => 'icon']); ?>
 </head>
 <body>
diff --git a/webroot/css/main.css b/webroot/css/main.css
index f1f2d47..9466306 100644
--- a/webroot/css/main.css
+++ b/webroot/css/main.css
@@ -164,7 +164,3 @@ input[type="checkbox"]:disabled.change-cursor {
     border-top-left-radius: 0 !important;
     border-bottom-left-radius: 0 !important;
 }
-
-.tag {
-    filter: drop-shadow(2px 2px 2px rgba(0, 0, 0, 0.5));
-}
\ No newline at end of file
diff --git a/webroot/js/bootstrap-helper.js b/webroot/js/bootstrap-helper.js
index 39cc6ce..ce1591f 100644
--- a/webroot/js/bootstrap-helper.js
+++ b/webroot/js/bootstrap-helper.js
@@ -1120,15 +1120,4 @@ class HtmlHelper {
         return $table
     }
 
-    static tag(options={}) {
-        if (!options.colour) {
-            options.colour = '#924da6'
-        }
-        const $tag = $('<span/>')
-            .addClass(['tag', 'badge', 'align-text-top'])
-            .css({color: getTextColour(options.colour), 'background-color': options.colour})
-            .text(options.text)
-
-        return $tag
-    }
 }
diff --git a/webroot/js/main.js b/webroot/js/main.js
index 3acc35f..9097365 100644
--- a/webroot/js/main.js
+++ b/webroot/js/main.js
@@ -115,138 +115,6 @@ function getTextColour(hex) {
     }
 }
 
-function createTagPicker(clicked) {
-
-    function closePicker($select, $container) {
-        $select.appendTo($container)
-        $container.parent().find('.picker-container').remove()
-    }
-
-    function getEditableButtons($select, $container) {
-        const $saveButton = $('<button></button>').addClass(['btn btn-primary btn-sm', 'align-self-start']).attr('type', 'button')
-        .append($('<span></span>').text('Save').addClass('text-nowrap').prepend($('<i></i>').addClass('fa fa-save mr-1')))
-        .click(function() {
-            const tags = $select.select2('data').map(tag => tag.text)
-            addTags($select.data('url'), tags, $(this))
-        })
-        const $cancelButton = $('<button></button>').addClass(['btn btn-secondary btn-sm', 'align-self-start']).attr('type', 'button')
-            .append($('<span></span>').text('Cancel').addClass('text-nowrap').prepend($('<i></i>').addClass('fa fa-times mr-1')))
-            .click(function() {
-                closePicker($select, $container)
-            })
-        const $buttons = $('<span></span>').addClass(['picker-action', 'btn-group']).append($saveButton, $cancelButton)
-        return $buttons
-    }
-
-    const $clicked = $(clicked)
-    const $container = $clicked.closest('.tag-container')
-    const $select = $container.parent().find('select.tag-input').removeClass('d-none')//.addClass('flex-grow-1')
-    closePicker($select, $container)
-    const $pickerContainer = $('<div></div>').addClass(['picker-container', 'd-flex'])
-    
-    $select.prependTo($pickerContainer)
-    $pickerContainer.append(getEditableButtons($select, $container))
-    $container.parent().append($pickerContainer)
-    initSelect2Picker($select)
-}
-
-function deleteTag(url, tags, clicked) {
-    if (!Array.isArray(tags)) {
-        tags = [tags];
-    }
-    const data = {
-        tag_list: JSON.stringify(tags)
-    }
-    const $statusNode = $(clicked).closest('.tag')
-    const APIOptions = {
-        statusNode: $statusNode,
-        skipFeedback: true,
-    }
-    return AJAXApi.quickFetchAndPostForm(url, data, APIOptions).then((apiResult) => {
-        let $container = $statusNode.closest('.tag-container-wrapper')
-        refreshTagList(apiResult, $container).then(($tagContainer) => {
-            $container = $tagContainer // old container might not exist anymore since it was replaced after the refresh
-        })
-        const theToast = UI.toast({
-            variant: 'success',
-            title: apiResult.message,
-            bodyHtml: $('<div/>').append(
-                $('<span/>').text('Cancel untag operation.'),
-                $('<button/>').addClass(['btn', 'btn-primary', 'btn-sm', 'ml-3']).text('Restore tag').click(function() {
-                    const split = url.split('/')
-                    const controllerName = split[1]
-                    const id = split[3]
-                    const urlRetag = `/${controllerName}/tag/${id}`
-                    addTags(urlRetag, tags, $container.find('.tag-container')).then(() => {
-                        theToast.removeToast()
-                    })
-                }),
-            ),
-        })
-    }).catch((e) => {})
-}
-
-function addTags(url, tags, $statusNode) {
-    const data = {
-        tag_list: JSON.stringify(tags)
-    }
-    const APIOptions = {
-        statusNode: $statusNode
-    }
-    return AJAXApi.quickFetchAndPostForm(url, data, APIOptions).then((apiResult) => {
-        const $container = $statusNode.closest('.tag-container-wrapper')
-        refreshTagList(apiResult, $container)
-    }).catch((e) => {})
-}
-
-function refreshTagList(apiResult, $container) {
-    const controllerName = apiResult.url.split('/')[1]
-    const entityId = apiResult.data.id
-    const url = `/${controllerName}/viewTags/${entityId}`
-    return UI.reload(url, $container)
-}
-
-function initSelect2Pickers() {
-    $('select.tag-input').each(function() {
-        if (!$(this).hasClass("select2-hidden-accessible")) {
-            initSelect2Picker($(this))
-        }
-    })
-}
-
-function initSelect2Picker($select) {
-
-    function templateTag(state, $select) {
-        if (!state.id) {
-            return state.label;
-        }
-        if (state.colour === undefined) {
-            state.colour = $(state.element).data('colour')
-        }
-        if ($select !== undefined && state.text[0] === '!') {
-            // fetch corresponding tag and set colors?
-            // const baseTag = state.text.slice(1)
-            // const existingBaseTag = $select.find('option').filter(function() {
-            //     return $(this).val() === baseTag
-            // })
-            // if (existingBaseTag.length > 0) {
-            //     state.colour = existingBaseTag.data('colour')
-            //     state.text = baseTag
-            // }
-        }
-        return HtmlHelper.tag(state)
-    }
-
-    $select.select2({
-        placeholder: 'Pick a tag',
-        tags: true,
-        width: '100%',
-        templateResult: (state) => templateTag(state),
-        templateSelection: (state) => templateTag(state, $select),
-    })
-}
-
-
 var UI
 $(document).ready(() => {
     if (typeof UIFactory !== "undefined") {

From 0458bbc76fabfbaa4aceb0394b3a9f60adeac87f Mon Sep 17 00:00:00 2001
From: mokaddem <sami.mokaddem@circl.lu>
Date: Thu, 2 Sep 2021 18:00:36 +0200
Subject: [PATCH 11/16] chg: [helpers:bootstrap] Prevent toast to hide if it's
 being hovered

---
 webroot/js/bootstrap-helper.js | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/webroot/js/bootstrap-helper.js b/webroot/js/bootstrap-helper.js
index ce1591f..0fff695 100644
--- a/webroot/js/bootstrap-helper.js
+++ b/webroot/js/bootstrap-helper.js
@@ -291,6 +291,7 @@ class Toaster {
     makeToast() {
         if (this.isValid()) {
             this.$toast = Toaster.buildToast(this.options)
+            this.$toast.data('toastObject', this)
             $('#mainToastContainer').append(this.$toast)
         }
     }
@@ -301,6 +302,19 @@ class Toaster {
             var that = this
             this.$toast.toast(this.bsToastOptions)
                 .toast('show')
+                .on('hide.bs.toast', function (evt) {
+                    const $toast = $(this)
+                    const hoveredElements = $(':hover').filter(function() {
+                        return $(this).is($toast)
+                    });
+                    if (hoveredElements.length > 0) {
+                        console.log('Toast hovered. Not hidding')
+                        evt.preventDefault()
+                        setTimeout(() => {
+                            $toast.toast('hide')
+                        }, that.options.delay);
+                    }
+                })
                 .on('hidden.bs.toast', function () {
                     that.removeToast()
                 })
@@ -355,7 +369,10 @@ class Toaster {
                 $toastHeader.append($toastHeaderMuted)
             }
             if (options.closeButton) {
-                var $closeButton = $('<button type="button" class="ml-2 mb-1 close" data-dismiss="toast" aria-label="Close"><span aria-hidden="true">&times;</span></button>')
+                var $closeButton = $('<button type="button" class="ml-2 mb-1 close" aria-label="Close"><span aria-hidden="true">&times;</span></button>')
+                    .click(function() {
+                        $(this).closest('.toast').data('toastObject').removeToast()
+                    })
                 $toastHeader.append($closeButton)
             }
             $toast.append($toastHeader)

From 8df647cdb97f3bd0f491b1b5742023cce10833f8 Mon Sep 17 00:00:00 2001
From: mokaddem <sami.mokaddem@circl.lu>
Date: Fri, 3 Sep 2021 09:47:13 +0200
Subject: [PATCH 12/16] chg: [migration] Added support of plugin migrations

---
 src/Model/Table/InstanceTable.php      | 12 ++++++++++++
 templates/Instance/migration_index.php |  4 ++++
 2 files changed, 16 insertions(+)

diff --git a/src/Model/Table/InstanceTable.php b/src/Model/Table/InstanceTable.php
index 5613e95..dd935b8 100644
--- a/src/Model/Table/InstanceTable.php
+++ b/src/Model/Table/InstanceTable.php
@@ -9,6 +9,8 @@ use Migrations\Migrations;
 
 class InstanceTable extends AppTable
 {
+    protected $activePlugins = ['Tags'];
+    
     public function initialize(array $config): void
     {
         parent::initialize($config);
@@ -23,6 +25,16 @@ class InstanceTable extends AppTable
     {
         $migrations = new Migrations();
         $status = $migrations->status();
+        foreach ($this->activePlugins as $pluginName) {
+            $pluginStatus = $migrations->status([
+                'plugin' => $pluginName
+            ]);
+            $pluginStatus = array_map(function ($entry) use ($pluginName) {
+                $entry['plugin'] = $pluginName;
+                return $entry;
+            }, $pluginStatus);
+            $status = array_merge($status, $pluginStatus);
+        }
         $status = array_reverse($status);
 
         $updateAvailables = array_filter($status, function ($update) {
diff --git a/templates/Instance/migration_index.php b/templates/Instance/migration_index.php
index f2bef2e..022cc28 100644
--- a/templates/Instance/migration_index.php
+++ b/templates/Instance/migration_index.php
@@ -27,6 +27,10 @@ foreach ($status as $i => &$update) {
     } else if ($update['status'] == 'down') {
         $update['_rowVariant'] = 'danger';
     }
+
+    if (!empty($update['plugin'])) {
+        $update['name'] = "{$update['plugin']}.{$update['name']}";
+    }
 }
 
 echo $this->Bootstrap->table([], [

From ea3168b84087b02c77928ba25764936853841a3f Mon Sep 17 00:00:00 2001
From: mokaddem <sami.mokaddem@circl.lu>
Date: Fri, 3 Sep 2021 09:47:36 +0200
Subject: [PATCH 13/16] new: [genericElements:singleView] Added new string
 field to extract without type deduction

---
 .../element/genericElements/SingleViews/Fields/stringField.php | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 templates/element/genericElements/SingleViews/Fields/stringField.php

diff --git a/templates/element/genericElements/SingleViews/Fields/stringField.php b/templates/element/genericElements/SingleViews/Fields/stringField.php
new file mode 100644
index 0000000..fc27aa5
--- /dev/null
+++ b/templates/element/genericElements/SingleViews/Fields/stringField.php
@@ -0,0 +1,3 @@
+<?php
+$value = Cake\Utility\Hash::get($data, $field['path']);
+echo h($value);
\ No newline at end of file

From ded1ae64e74e0f1fa51bfd85eb89a65340be434c Mon Sep 17 00:00:00 2001
From: mokaddem <sami.mokaddem@circl.lu>
Date: Fri, 3 Sep 2021 09:48:49 +0200
Subject: [PATCH 14/16] chg: [tags] Moved templates into the plugin folder

---
 {templates => plugins/Tags/templates}/Tags/add.php   | 0
 {templates => plugins/Tags/templates}/Tags/index.php | 0
 {templates => plugins/Tags/templates}/Tags/view.php  | 2 +-
 3 files changed, 1 insertion(+), 1 deletion(-)
 rename {templates => plugins/Tags/templates}/Tags/add.php (100%)
 rename {templates => plugins/Tags/templates}/Tags/index.php (100%)
 rename {templates => plugins/Tags/templates}/Tags/view.php (95%)

diff --git a/templates/Tags/add.php b/plugins/Tags/templates/Tags/add.php
similarity index 100%
rename from templates/Tags/add.php
rename to plugins/Tags/templates/Tags/add.php
diff --git a/templates/Tags/index.php b/plugins/Tags/templates/Tags/index.php
similarity index 100%
rename from templates/Tags/index.php
rename to plugins/Tags/templates/Tags/index.php
diff --git a/templates/Tags/view.php b/plugins/Tags/templates/Tags/view.php
similarity index 95%
rename from templates/Tags/view.php
rename to plugins/Tags/templates/Tags/view.php
index 00ce41a..0886fc9 100644
--- a/templates/Tags/view.php
+++ b/plugins/Tags/templates/Tags/view.php
@@ -16,7 +16,7 @@ echo $this->element(
             [
                 'key' => __('Counter'),
                 'path' => 'counter',
-                'type' => 'json',
+                'type' => 'string',
             ],
             [
                 'key' => __('Colour'),

From 99c857d5868a6237408d7edba0da7e697f1738e7 Mon Sep 17 00:00:00 2001
From: mokaddem <sami.mokaddem@circl.lu>
Date: Fri, 3 Sep 2021 09:49:20 +0200
Subject: [PATCH 15/16] chg: [aclcomponent] Added ACL entry

---
 src/Controller/AppController.php          |  4 ++++
 src/Controller/Component/ACLComponent.php | 24 +++++++++++++++++++++++
 2 files changed, 28 insertions(+)

diff --git a/src/Controller/AppController.php b/src/Controller/AppController.php
index ee1c1b1..913a633 100644
--- a/src/Controller/AppController.php
+++ b/src/Controller/AppController.php
@@ -127,6 +127,10 @@ class AppController extends Controller
         $this->request->getParam('prefix');
         $this->set('darkMode', !empty(Configure::read('Cerebrate')['ui.dark']));
         $this->set('baseurl', Configure::read('App.fullBaseUrl'));
+
+        if ($this->modelClass == 'Tags.Tags') {
+            $this->set('metaGroup', !empty($this->isAdmin) ? 'Administration' : 'Cerebrate');
+        }
     }
 
     private function authApiUser(): void
diff --git a/src/Controller/Component/ACLComponent.php b/src/Controller/Component/ACLComponent.php
index fc8966c..8e0e25f 100644
--- a/src/Controller/Component/ACLComponent.php
+++ b/src/Controller/Component/ACLComponent.php
@@ -747,6 +747,30 @@ class ACLComponent extends Component
                             'label' => __('List Outbox Processors'),
                             'skipTopMenu' => 1
                         ]
+                    ],
+                    'skipTopMenu' => true,
+                ],
+                'Tags' => [
+                    'label' => __('Tags'),
+                    'url' => '/tags/index',
+                    'children' => [
+                        'index' => [
+                            'url' => '/tags/index',
+                            'label' => __('List Tags'),
+                        ],
+                        'view' => [
+                            'url' => '/tags/view/{{id}}',
+                            'label' => __('View Tags'),
+                            'actions' => ['delete', 'edit', 'view'],
+                            'skipTopMenu' => true,
+                        ],
+                        'delete' => [
+                            'url' => '/tags/delete/{{id}}',
+                            'label' => __('Delete Tag'),
+                            'actions' => ['delete', 'edit', 'view'],
+                            'skipTopMenu' => true,
+                            'popup' => 1
+                        ],
                     ]
                 ],
                 'MetaTemplates' => [

From 6a682905616d001c08c0fcb34c64a48856836fdb Mon Sep 17 00:00:00 2001
From: mokaddem <sami.mokaddem@circl.lu>
Date: Fri, 3 Sep 2021 09:59:49 +0200
Subject: [PATCH 16/16] chg: [plugin:tags] Added migration script

---
 .../Migrations/20210831121348_TagSystem.php   | 89 +++++++++++++++++++
 1 file changed, 89 insertions(+)
 create mode 100644 plugins/Tags/config/Migrations/20210831121348_TagSystem.php

diff --git a/plugins/Tags/config/Migrations/20210831121348_TagSystem.php b/plugins/Tags/config/Migrations/20210831121348_TagSystem.php
new file mode 100644
index 0000000..7b15623
--- /dev/null
+++ b/plugins/Tags/config/Migrations/20210831121348_TagSystem.php
@@ -0,0 +1,89 @@
+<?php
+declare(strict_types=1);
+
+use Migrations\AbstractMigration;
+
+
+class TagSystem extends AbstractMigration
+{
+    public function change() {
+        $tags = $this->table('tags_tags')
+            ->addColumn('namespace', 'string', [
+                'default' => null,
+                'limit' => 255,
+                'null' => true,
+            ])
+            ->addColumn('predicate', 'string', [
+                'default' => null,
+                'limit' => 255,
+                'null' => true,
+            ])
+            ->addColumn('value', 'string', [
+                'default' => null,
+                'limit' => 255,
+                'null' => true,
+            ])
+            ->addColumn('name', 'string', [
+                'default' => null,
+                'limit' => 255,
+                'null' => false,
+            ])
+            ->addColumn('colour', 'string', [
+                'default' => null,
+                'limit' => 7,
+                'null' => false,
+            ])
+            ->addColumn('counter', 'integer', [
+                'default' => 0,
+                'length' => 11,
+                'null' => false,
+                'signed' => false,
+                'comment' => 'Field used by the CounterCache behaviour to count the occurence of tags'
+            ])
+            ->addColumn('created', 'datetime', [
+                'default' => null,
+                'null' => false,
+            ])
+            ->addColumn('modified', 'datetime', [
+                'default' => null,
+                'null' => false,
+            ])
+            ->create();
+
+        $tagged = $this->table('tags_tagged')
+            ->addColumn('tag_id', 'integer', [
+                'default' => null,
+                'null' => false,
+                'signed' => false,
+                'length' => 10,
+            ])
+            ->addColumn('fk_id', 'integer', [
+                'default' => null,
+                'null' => true,
+                'signed' => false,
+                'length' => 10,
+                'comment' => 'The ID of the entity being tagged'
+            ])
+            ->addColumn('fk_model', 'string', [
+                'default' => null,
+                'limit' => 255,
+                'null' => false,
+                'comment' => 'The model name of the entity being tagged'
+            ])
+            ->addColumn('created', 'datetime', [
+                'default' => null,
+                'null' => false,
+            ])
+            ->addColumn('modified', 'datetime', [
+                'default' => null,
+                'null' => false,
+            ])
+            ->create();
+
+        $tags->addIndex(['name'], ['unique' => true])
+            ->update();
+
+        $tagged->addIndex(['tag_id', 'fk_id', 'fk_table'], ['unique' => true])
+            ->update();
+    }
+}
\ No newline at end of file