Merge branch 'develop'

Indicia-Team · Sep 25, 2024 · 211620c · 211620c
2 parents df5638d + f6aaa93
commit 211620c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,38 @@
+# Version 9.4.0
+*2024-09-23*
+
+* Adds features to trigger reports that allow them to directly send emails, e.g. for replying to
+  partially complete reports of Asian Hornets.
+* Adds fields to the `groups` entity (for iRecord Activities) for the following:
+  * Controlling if blogs are enabled and, if so, whether any member can post a blog or only admins.
+    See https://github.com/BiologicalRecordsCentre/iRecord/issues/1703.
+  * Defining if a group is a container for other groups, e.g. a project divided by years. See
+    https://github.com/BiologicalRecordsCentre/iRecord/issues/1678.
+  * Defining if a group is contained by another group.
+* Update the `library/groups/find_group_by_url` report to include information about container and
+  contained groups. See https://github.com/BiologicalRecordsCentre/iRecord/issues/1678.
+* Bugfixes for the new bulk edit tool. See https://github.com/BiologicalRecordsCentre/iRecord/issues/1673.
+* Updated download field formats to support sensitive record download requirements. See
+  https://github.com/BiologicalRecordsCentre/iRecord/issues/1714 and the columns documentation at
+  https://indicia-docs.readthedocs.io/en/latest/site-building/iform/helpers/elasticsearch-report-helper.html#elasticsearchreporthelper-datagrid.
+* Bugfix for the handling of the current common name when AddSynonym operations are processed by
+  the UKSI History processor. See https://github.com/Indicia-Team/warehouse/pull/522.
+* Update the `library/groups/group_list` report to include a full text search parameter and also so
+  that setting the parameter `userFilterMode=joinable` excludes groups you are already a member of.
+* The Elasticsearch special field handler for "sitename" now supports additional options -
+  `obscureifsensitive` - shows a warning message instead of the site name if sensitive and
+  `showifsensitive` - displays the full site name for sensitive records (only if the user has
+  access to full precision sensitive data).
+* In Elasticsearch, sensitive or private records have their site names replaced by '!' to
+  distinguish them from records where there is no site name given. See
+  https://github.com/BiologicalRecordsCentre/iRecord/issues/1714.
+
+# Version 9.3.0
+*2024-08-19*
+
+* Adds `search_code` to parameters of Rest endpoint, `services/rest/taxa/search`
+  and includes it in the response.
+
 # Version 9.2.0
 *2024-06-17*
 

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# Indicia Warehouse [![Build Status](https://travis-ci.com/Indicia-Team/warehouse.svg?branch=master)](https://travis-ci.com/Indicia-Team/warehouse)
+# Indicia Warehouse
 
 This is the repository for the Indicia Warehouse, the server-side component of Indicia, the online wildlife recording
 toolkit. Indicia accelerates development of wildlife recording websites and mobile applications. Documentation is

diff --git a/application/config/version.php b/application/config/version.php
@@ -29,14 +29,14 @@
  *
  * @var string
  */
-$config['version'] = '9.3.3';
+$config['version'] = '9.4.0';
 
 /**
  * Version release date.
  *
  * @var string
  */
-$config['release_date'] = '2024-09-02';
+$config['release_date'] = '2024-09-25';
 
 /**
  * Link to the code repository downloads page.

diff --git a/application/controllers/attribute_by_survey.php b/application/controllers/attribute_by_survey.php
@@ -20,7 +20,7 @@
  */
 
 /**
- * Controller providing the ability to configure the list of attributes joined to a survey.
+ * Controller for relationship between custom attributes and surveys.
  */
 class Attribute_By_Survey_Controller extends Indicia_Controller {
   private $_survey = NULL;
@@ -83,8 +83,10 @@ public function edit($id) {
   }
 
   /**
-   * Handle the layout_update action, which uses $_POST data to find a list of commands
-   * for re-ordering the controls.
+   * Handle the layout_update action.
+   *
+   * Which uses $_POST data to find a list of commands for re-ordering the
+   * controls.
    */
   public function layout_update() {
     // Get the survey id from the segments in the URI.
@@ -223,8 +225,13 @@ protected function editViewName() {
   }
 
   /**
-   * Setup the values to be loaded into the edit view. For this class, we need to explode the
-   * items out of the validation_rules field, which our base class can do.
+   * Setup the values to be loaded into the edit view.
+   *
+   * For this class, we need to explode the items out of the validation_rules
+   * field, which our base class can do.
+   *
+   * @return array
+   *   Key value pairs of data for the edit view.
    */
   protected function getModelValues() {
     $r = parent::getModelValues();
@@ -308,8 +315,12 @@ protected function prepareOtherViewData(array $values) {
     return $otherData;
   }
 
+  /**
+   * Override save handler to format validation rules correctly.
+   */
   public function save() {
-    // Build the validation_rules field from the set of controls that are associated with it.
+    // Build the validation_rules field from the set of controls that are
+    // associated with it.
     $rules = [];
     $ruleNames = ([
       'required',
@@ -340,12 +351,20 @@ public function save() {
     parent::save();
   }
 
+  /**
+   * Determine the page to return to after saving.
+   *
+   * @return string
+   *   Path to the page to return to.
+   */
   protected function get_return_page() {
-    $surveyPostKey = $this->type.'_attributes_website:restrict_to_survey_id';
+    $surveyPostKey = $this->type . '_attributes_website:restrict_to_survey_id';
     if (isset($_POST[$surveyPostKey])) {
-      return 'attribute_by_survey/'.$_POST[$surveyPostKey].'?type='.$this->type;
-    } else {
-      // If $_POST data not available, then just return to the survey list. Shouldn't really happen.
+      return 'attribute_by_survey/' . $_POST[$surveyPostKey] . '?type=' . $this->type;
+    }
+    else {
+      // If $_POST data not available, then just return to the survey list.
+      // Shouldn't really happen.
       return 'survey';
     }
   }
@@ -356,7 +375,8 @@ protected function get_return_page() {
   protected function defineEditBreadcrumbs() {
     $this->page_breadcrumbs[] = html::anchor('survey', 'Survey datasets');
     $survey = ORM::Factory('survey', $this->model->restrict_to_survey_id);
-    $this->page_breadcrumbs[] = html::anchor('/attribute_by_survey/'.$this->model->restrict_to_survey_id.'?type='.$this->type, 'Attributes for '.$survey->title);
+    $this->page_breadcrumbs[] = html::anchor(
+      "/attribute_by_survey/$survey->id?type=$this->type", "Attributes for $survey->title");
     $this->page_breadcrumbs[] = $this->model->caption();
   }
 
@@ -371,8 +391,10 @@ protected function page_authorised() {
         $this->_website_id = $survey->website_id;
       }
       return in_array($this->_website_id, $this->auth_filter['values']);
-    } else
+    }
+    else {
       return true;
+    }
   }
 
   /**
@@ -385,5 +407,4 @@ protected function getSurvey() {
     return $this->_survey;
   }
 
-
-}
+}
diff --git a/application/controllers/forgotten_password.php b/application/controllers/forgotten_password.php
@@ -26,6 +26,9 @@
  */
 class Forgotten_Password_Controller extends Indicia_Controller {
 
+  /**
+   * Set up the main controller page.
+   */
   public function index() {
 
     if ($this->auth->logged_in()) {
@@ -59,10 +62,25 @@ public function index() {
     }
   }
 
+  /**
+   * Return true if the user can login to the warehouse.
+   *
+   * User's only have login rughts if they have site editor role or higher, or
+   * core admin.
+   *
+   * @param ORM $user
+   *   User object.
+   *
+   * @return bool
+   *   True if the user is allowed to login.
+   */
   public function check_can_login($user) {
-    if (is_null($user->core_role_id) && ORM::factory('users_website')
-      ->where('user_id', $user->id)->where('site_role_id IS NOT ', NULL)->find_all() === 0) {
-      $this->template->content->error_message = $_POST['UserID'] . ' does not have permission to log on to this website';
+    if (is_null($user->core_role_id)
+        && ORM::factory('users_website')
+        ->where('user_id', $user->id)
+        ->where('site_role_id IS NOT ', NULL)
+        ->find_all() === 0) {
+      $this->template->content->error_message = "$_POST[UserID] does not have permission to log on to this website";
       return FALSE;
     }
     return TRUE;

diff --git a/application/controllers/location_comment.php b/application/controllers/location_comment.php
@@ -65,6 +65,9 @@ protected function getDefaults() {
    *
    * After saving a comment you are returned to the location entry which has
    * the comment.
+   *
+   * @return string
+   *   Page path to return to.
    */
   protected function get_return_page() {
     if (array_key_exists('location_comment:location_id', $_POST)) {

diff --git a/application/controllers/logout.php b/application/controllers/logout.php
@@ -19,19 +19,17 @@
  * @link https://github.com/indicia-team/warehouse
  */
 
-/*
+/**
  *  Provides application support for logging users out.
  */
 class Logout_Controller extends Indicia_Controller {
 
-  /*
-  *  description:  Logs the current user out of the application. Destroys the current session
-  *  parameters:   None expected.
-  */
-  public function index()
-  {
+  /**
+   *  Logs the current user out of the application. Destroys the current session.
+   */
+  public function index() {
     $this->auth->logout(TRUE);
     url::redirect();
   }
 
-}
+}
diff --git a/application/controllers/scheduled_tasks.php b/application/controllers/scheduled_tasks.php
@@ -149,7 +149,7 @@ protected function checkTriggers() {
       $params = json_decode($trigger->params_json, TRUE);
       $reportEngine = new ReportEngine();
       // Get parameter for last run specific to this trigger.
-      $params['date'] = variable::get("trigger_last_run-$trigger->id", $this->lastRunDate);
+      $params['date'] = variable::get("trigger_last_run-$trigger->id", $this->lastRunDate, FALSE);
       $currentTime = time();
       try {
         $data = $reportEngine->requestReport($trigger->trigger_template_file . '.xml', 'local', 'xml', $params);
@@ -239,6 +239,13 @@ protected function checkTriggers() {
           ],
           $digestMode
         );
+        $this->doTriggerImmediateEmails(
+          $trigger->name,
+          [
+            'headings' => $parsedData['headingData'],
+            'data' => $parsedData['websiteRecordData'],
+          ]
+        );
       }
       // Remember when this specific trigger last ran.
       variable::set("trigger_last_run-$trigger->id", date('c', $currentTime));
@@ -354,6 +361,101 @@ private function doDirectTriggerNotifications($triggerName, array $data, $digest
     }
   }
 
+  /**
+   * Send emails for trigger reports that directly define an email to send.
+   *
+   * These emails can be sent directly, bypassing the notifications system and
+   * therefore can be sent to anyone not just registered users. E.g. a thank
+   * you email to anonymous recorders.
+   *
+   * @param string $triggerName
+   *   Name of the trigger which fired.
+   * @param array $data
+   *   Info regarding the trigger report columns and associated retrieved data.
+   */
+  private function doTriggerImmediateEmails($triggerName, array $data) {
+    if (count($data['data']) === 0 || !in_array('email_to', $data['headings'])) {
+      return;
+    }
+    $emailConfig = Kohana::config('email');
+    if (!isset($emailConfig['address'])) {
+      self::msg('Email address not provided in email configuration', 'error');
+      return;
+    }
+    $colIndexes = [];
+    $sysCols = ['email_to', 'email_subject', 'email_body', 'email_name'];
+    foreach ($sysCols as $col) {
+      if (($colIdx = array_search($col, $data['headings'])) !== FALSE) {
+        $colIndexes[$col] = $colIdx;
+      }
+    }
+    $defaultSubject = empty(kohana::config('email.notification_subject'))
+      ? kohana::lang('misc.notification_subject')
+      : kohana::config('email.notification_subject');
+    $emails = [];
+    foreach ($data['data'] as $records) {
+      foreach ($records as $record) {
+        if (!empty($record[$colIndexes['email_to']])) {
+          $to = $record[$colIndexes['email_to']];
+          $name = empty($colIndexes['email_name']) || empty($record[$colIndexes['email_name']])
+            ? $to
+            : $record[$colIndexes['email_name']];
+          if (!isset($emails["$to $name"])) {
+            $emails["$to $name"] = [];
+          }
+
+          $subject = empty($colIndexes['email_subject']) || empty($record[$colIndexes['email_subject']])
+            ? $defaultSubject
+            : $record[$colIndexes['email_subject']];
+          if (empty($colIndexes['email_body']) || empty($record[$colIndexes['email_body']])) {
+            // Email body not provided, so construct it from the other columns.
+            $body = '';
+            foreach ($data['headings'] as $idx => $colTitle) {
+              // Skip the functional email columns.
+              if (!in_array($colTitle, $sysCols)) {
+                $body[] = '<h2>' . htmlspecialchars($colTitle) . '</h2>';
+                $body[] = '<p>' . htmlspecialchars($record[$idx]) . '</p>';
+              }
+            }
+          }
+          else {
+            $body = $record[$colIndexes['email_body']];
+          }
+          // Aggregate emails per email address, so we don't send multiple.
+          $emails["$to $name"][] = [
+            'to' => $to,
+            'name' => $name,
+            'subject' => $subject,
+            'body' => $body,
+          ];
+        }
+      }
+    }
+    $swift = email::connect();
+    // Now send the emails as a digest so each recipient only gets one email.
+    foreach ($emails as $infoList) {
+      // If a single email for this recipient we can use the subject, otherwise
+      // we use a generic subject and put each email subject in as a subtitle.
+      $subject = count($infoList) === 1 ? $infoList[0]['subject'] : $defaultSubject;
+      $emailContent = '';
+      foreach ($infoList as $infoItem) {
+        if (count($infoList) > 1) {
+          $emailContent .= '<h1>' . htmlspecialchars($infoItem['subject']) . '</h1>';
+        }
+        $emailContent .= '<div>' . $infoItem['body'] . '</div>';
+      }
+      $message = new Swift_Message(
+        $subject,
+        "<html>$emailContent</html>",
+        'text/html'
+      );
+      $recipients = new Swift_RecipientList();
+      $recipients->addTo($infoList[0]['to'], $infoList[0]['name']);
+      // Send the email.
+      $swift->send($message, $recipients, $emailConfig['address']);
+    }
+  }
+
   /**
    * Create email digests for trigger notifications.
    *

diff --git a/application/controllers/taxa_taxon_list.php b/application/controllers/taxa_taxon_list.php
@@ -31,9 +31,9 @@ public function __construct() {
     $this->columns = [
       'taxon' => '',
       'authority' => '',
-      'taxon_group' => 'Taxon Group',
+      'taxon_group' => 'Taxon group',
       'language' => '',
-      'taxonomic_sort_order' => 'Sort Order',
+      'taxonomic_sort_order' => 'Sort order',
     ];
     $this->pagetitle = "Species";
   }

diff --git a/application/i18n/en_GB/form_error_messages.php b/application/i18n/en_GB/form_error_messages.php
@@ -75,7 +75,7 @@
     'default' => 'Invalid input.',
   ],
   'centroid_sref_system' => [
-    'required' => 'The centorid spatial reference system must be supplied.',
+    'required' => 'The centroid spatial reference system must be supplied.',
     'default' => 'Invalid input.',
   ],
   'external_key' => [