NO-JIRA-deprecation-errors-and-more

app/availableplugins/FileConnector/src/Model/Table/FileSourcesTable.php

@@ -166,9 +166,9 @@ public function inventory(
     }
 
     // The first line of a CSV v3 file is our configuration
-    fgetcsv($handle);
+    fgetcsv($handle, escape: '\\');
 
-    while(($data = fgetcsv($handle)) !== false) {
+    while(($data = fgetcsv($handle, escape: '\\')) !== false) {
       // The source key is always the first field in each line, make sure it is not empty
 
       if(!empty($data[0]) && !ctype_space($data[0])) {
@@ -306,9 +306,9 @@ protected function processChangeList(
       }
 
       // Ignore the header line
-      fgetcsv($handle);
+      fgetcsv($handle, escape: '\\');
 
-      while(($data = fgetcsv($handle)) !== false) {
+      while(($data = fgetcsv($handle, escape: '\\')) !== false) {
         // Implode the record back together for string comparison purposes.
         // This may not be the same as the original line due to quotes, etc.
         // $data[0] is the SORID
@@ -327,9 +327,9 @@ protected function processChangeList(
       }
 
       // Ignore the header line
-      fgetcsv($handle);
+      fgetcsv($handle, escape: '\\');
 
-      while(($data = fgetcsv($handle)) !== false) {
+      while(($data = fgetcsv($handle, escape: '\\')) !== false) {
         // $data[0] is the SORID
         if(array_key_exists($data[0], $knownRecords)) {
           $newData = implode(',', $data);
@@ -445,7 +445,7 @@ protected function readFieldConfig(
     }
 
     // The first line is our configuration
-    $cfg = fgetcsv($handle);
+    $cfg = fgetcsv($handle, escape: '\\');
 
     fclose($handle);
 
@@ -700,13 +700,13 @@ public function retrieve(
     // If there is more than one record, we'll return the first one we find.
 
     // The first line of a CSV v3 file is our configuration
-    fgetcsv($handle);
+    fgetcsv($handle, escape: '\\');
 
     // Set null defaults in case we don't find a matching record
     $ret['source_record'] = null;
     $ret['entity_data'] = null;
 
-    while(($data = fgetcsv($handle)) !== false) {
+    while(($data = fgetcsv($handle, escape: '\\')) !== false) {
       if($data[0] == $source_key) {
         // This is our record
 
@@ -809,9 +809,9 @@ public function search(
     }
 
     // The first line of a CSV v3 file is our configuration
-    fgetcsv($handle);
+    fgetcsv($handle, escape: '\\');
 
-    while(($data = fgetcsv($handle)) !== false) {
+    while(($data = fgetcsv($handle, escape: '\\')) !== false) {
       // strtolower, previous behavior was full string only so dupe that
 
       $match = collection($data)

app/plugins/CoreJob/src/Lib/Jobs/SyncJob.php

@@ -238,21 +238,22 @@ protected function fullSync() {
 
   /**
    * Cache the current run context.
-   * 
+   *
+   * @param JobsTable $JobsTable $JobsTable              JobsTable
+   * @param JobHistoryRecordsTable $JobHistoryRecordsTable $JobHistoryRecordsTable JobHistoryRecordsTable
+   * @param Job $job Current Job
+   * @param array $parameters Job Parameters (from the command line)
+   * @param int|null $eisId External Identity Source ID
+   * @return \StdClass
    * @since  COmanage Registry v5.0.0
-   * @param  JobsTable              $JobsTable              JobsTable
-   * @param  JobHistoryRecordsTable $JobHistoryRecordsTable JobHistoryRecordsTable
-   * @param  Job                    $job                    Current Job
-   * @param  array                  $parameters             Job Parameters (from the command line)
-   * @param  int                    $eisId                  External Identity Source ID
    */
 
   protected function getRunContext(
     \App\Model\Table\JobsTable              $JobsTable,
     \App\Model\Table\JobHistoryRecordsTable $JobHistoryRecordsTable,
     \App\Model\Entity\Job                   $job, 
     array                                   $parameters,
-    int                                     $eisId=null
+    ?int                                    $eisId = null
   ): \StdClass {
     // We use $runContext so we don't have to pass a complicated set of parameters around.
 
@@ -451,7 +452,7 @@ public function run(
       );
 
       if($this->runContext->eis->status == SyncModeEnum::Disabled) {
-        throw new \InvalidArgumentException('core_job', 'Sync.error.disabled');
+        throw new \InvalidArgumentException(__d('core_job', 'Sync.error.disabled'));
       }
 
       if(!empty($parameters['source_keys'])) {
@@ -465,7 +466,7 @@ public function run(
           if(count($keys) == 1) {
             $referenceId = $parameters['reference_id'];
           } else {
-            throw new \InvalidArgumentException('core_job', 'Sync.error.reference_id');
+            throw new \InvalidArgumentException(__d('core_job', 'Sync.error.reference_id'));
           }
         }
 
@@ -516,11 +517,11 @@ public function run(
    * 
    * @since  COmanage Registry v5.0.0
    * @param  string $key          Source Key to process
-   * @param  string $referenceId  Reference ID to link to record, if known
+   * @param  string|null $referenceId  Reference ID to link to record, if known
    * @return bool         True if processing should continue, false otherwise
    */
 
-  protected function syncRecord(string $key, string $referenceId=null): bool {
+  protected function syncRecord(string $key, ?string $referenceId=null): bool {
     // comment and status for HistoryRecords
     $c = "unknown";
     $s = JobStatusEnum::Failed;
@@ -577,9 +578,9 @@ protected function syncRecord(string $key, string $referenceId=null): bool {
     if($this->runContext->JobsTable->isCanceled($this->runContext->job->id)) {
       // The Job was already marked Canceled, but we can optionally add a History Record
       $this->runContext->JobHistoryRecordsTable->record(
-        jobId: $job->id,
+        jobId: $this->runContext->job->id,
         recordKey: "",
-        comment:  __d(
+        comment: __d(
           'core_job',
           'Sync.finish_summary.count',
           [$this->runContext->created, $this->runContext->updated, $this->runContext->errors, $this->runContext->count]

app/plugins/CoreServer/src/Model/Table/Oauth2ServersTable.php

@@ -107,18 +107,23 @@ public function exchangeCode(int|string $id, string $code, string $redirectUri,
   /**
    * Obtain an OAuth token.
    *
-   * @param Integer $id          Oauth2Server ID
-   * @param String $grantType   OAuth grant type
-   * @param  String|null  $code        Access code returned by call to /oauth/authorize, for authorization_code grant
-   * @param String|null $redirectUri Callback URL used for initial request, for authorization_code grant
-   * @param Boolean $store       If true, store the retrieved tokens in the Oauth2Server configuration
+   * @param int $id          Oauth2Server ID
+   * @param string $grantType   OAuth grant type
+   * @param  string|null  $code        Access code returned by call to /oauth/authorize, for authorization_code grant
+   * @param string|null $redirectUri Callback URL used for initial request, for authorization_code grant
+   * @param bool $store       If true, store the retrieved tokens in the Oauth2Server configuration
    * @return mixed               Object of data as returned by server, including access and refresh token
    * @throws RuntimeException
    *@since  COmanage Registry v5.2.0
    */
 
-  public function obtainToken(int $id, string $grantType, string $code=null, string $redirectUri=null, bool $store=true): mixed
-  {
+  public function obtainToken(
+    int $id,
+    string $grantType,
+    ?string $code=null,
+    ?string $redirectUri=null,
+    bool $store=true)
+  : mixed {
     // Pull our configuration
     $srvr = $this->get($id);
 

app/src/Command/SetupCommand.php

@@ -192,7 +192,10 @@ public function execute(Arguments $args, ConsoleIo $io)
       )
     ];
 
-    $coTable->People->save($person);
+    // Setup should not trigger provisioning side effects. Save with a provisioning-off hint.
+    $coTable->People->save($person, [
+      'provision' => false,
+    ]);
 
     // Write the salt file if not set in environment and file does not exist.
     if(!env('SECURITY_SALT', null)) {

app/src/Controller/StandardController.php

@@ -721,10 +721,10 @@ public function index() {
    * Populate any auto view variables, as requested via AutoViewVarsTrait.
    *
    * @since  COmanage Registry v5.0.0
-   * @param  object $obj Current object (eg: from edit), if set
+   * @param  object|null $obj Current object (eg: from edit), if set
    */
 
-  protected function populateAutoViewVars(object $obj=null) {
+  protected function populateAutoViewVars(?object $obj=null) {
     /** var Cake\ORM\Table $table */
     $table = $this->getCurrentTable();
 

app/src/Lib/Random/RandomString.php

@@ -98,15 +98,19 @@ public static function generateCode(): string {
    * a token is not expected to be directly visible or handled by a human, but
    * will (eg) be injected into a URL or a message.
    *
+   * @param int $length Length of token
+   * @param string|null $allowedCharset Allowed characters
+   * @param string|null $regex Regex to match characters
+   *
    * @return string Token
    * @throws RandomException
    * @since  COmanage Registry v5.0.0
    */
 
   public static function generateToken(
     int $length = 16,
-    string $allowedCharset = null,
-    string $regex = null, // Permitted
+    ?string $allowedCharset = null,
+    ?string $regex = null, // Permitted
   ): string {
     // Unlike App Keys, tokens don't have restrictions on characters.
 

app/src/Lib/Traits/IndexQueryTrait.php

@@ -156,7 +156,7 @@ public function getIndexQuery(bool $pickerMode = false, array $requestParams = [
     // Initialize the Query Object
     $query = $table->find();
     // Get a pointer to my expression list
-    $newexp = $query->newExpr();
+    $newexp = $query->expr();
     // The searchable attributes can have an AND or an OR conjunction. The first one is used from the filtering block
     // while the second one from the picker vue module.
     $newexp = $newexp->setConjunction($pickerMode ? 'OR' : 'AND');

app/src/Lib/Util/DeliveryUtilities.php

@@ -181,9 +181,9 @@ public static function sendEmailFromTemplate(
         subject:    $template->getMessagePart('subject'),
         body_text:  $template->getMessagePart('body_text'),
         body_html:  $template->getMessagePart('body_html'),
-        cc:         $template->cc,
-        bcc:        $template->bcc,
-        replyTo:    $template->reply_to
+        cc:         $template->cc ?? '',
+        bcc:        $template->bcc ?? '',
+        replyTo:    $template->reply_to ?? ''
       );
     } else {
       self::sendEmailToAddress(
@@ -192,9 +192,9 @@ public static function sendEmailFromTemplate(
         subject:    $template->getMessagePart('subject'),
         body_text:  $template->getMessagePart('body_text'),
         body_html:  $template->getMessagePart('body_html'),
-        cc:         $template->cc,
-        bcc:        $template->bcc,
-        replyTo:    $template->reply_to
+        cc:         $template->cc ?? '',
+        bcc:        $template->bcc ?? '',
+        replyTo:    $template->reply_to ?? ''
       );
 
       return [

app/src/Model/Table/JobsTable.php

@@ -200,7 +200,7 @@ public function assign(Job $job) {
         __d('error',
             'Jobs.status.invalid', 
             [
-              $jobs->id, 
+              $job->id,
               __d('enumeration', 'JobStatusEnum.Queued'),
               __d('enumeration', 'JobStatusEnum.Assigned'),
               __d('enumeration', 'JobStatusEnum.'.$job->status)
@@ -417,7 +417,7 @@ public function finish(Job $job, string $summary="", string $result=JobStatusEnu
       // The new job will be substantially the same as the last one...
 
       $this->register(
-        coId: job->co_id,
+        coId: $job->co_id,
         plugin: $job->plugin,
         parameters: json_decode($job->parameters, true),
         registerSummary: $job->register_summary,
@@ -471,7 +471,7 @@ public function process(Job $job, string $dbcxn='default') {
         __d('error',
             'Jobs.status.invalid', 
             [
-              $jobs->id, 
+              $job->id,
               __d('enumeration', 'JobStatusEnum.Assigned'),
               __d('enumeration', 'JobStatusEnum.InProgress'),
               __d('enumeration', 'JobStatusEnum.'.$job->status)
@@ -687,7 +687,7 @@ public function start(Job $job, string $summary="") {
         __d('error',
             'Jobs.status.invalid',
             [
-              $job->id, 
+              $job->id,
               __d('enumeration', 'JobStatusEnum.Assigned'),
               __d('enumeration', 'JobStatusEnum.InProgress'),
               __d('enumeration', 'JobStatusEnum.'.$job->status)

app/src/Model/Table/PeopleTable.php

@@ -448,12 +448,16 @@ public function implementedEvents(): array {
   public function localAfterSave(\Cake\Event\EventInterface $event, \Cake\Datasource\EntityInterface $entity, \ArrayObject $options): bool {
     $this->recordHistory($entity);
 
-    // XXX implement this eventually?
-    //$provision = (isset($options['provision']) ? $options['provision'] : true);
+    // SetupCommand and other bootstrapping operations must be able to save People without
+    // triggering provisioning side effects
+    $provision = true;
+    if (isset($options['provision'])) {
+      $provision = (bool)$options['provision'];
+    }
 
     if(!$entity->deleted) {
       // If the entity was deleted we handled this in beforeDelete, above
-      $this->reconcileCoMembersGroupMemberships($entity);
+      $this->reconcileCoMembersGroupMemberships($entity, $provision);
     }
 
     return true;

app/src/Model/Table/PluginsTable.php

@@ -321,6 +321,12 @@ public function getPluginSchema(\App\Model\Entity\Plugin $plugin): ?object {
   public function pluginPath(\App\Model\Entity\Plugin $plugin, string $file): string {
     $fileName = $this->paths[$plugin->location]['path'] . DS . $plugin->plugin . DS . $file;
 
+    // "tests/" is optional in deployed environments. Return the computed path
+    // without treating absence as an error so callers can probe as needed.
+    if($file === 'tests' || str_starts_with($file, 'tests' . DS)) {
+      return $fileName;
+    }
+
     if(is_readable($fileName)) {
       // This is the plugin we're looking for
       $this->llog('debug', "Found plugin $plugin->plugin in $plugin->location directory");

app/src/Model/Table/VerificationsTable.php

@@ -265,13 +265,12 @@ public function requestCodeForPetition(
     int     $codeLength,
     ?string  $codeCharset,
     ?string  $codeRegex,
-    int     $verificationId = null
+    ?int     $verificationId = null
   ): int {
     // First generate a new code
     $code = RandomString::generateToken($codeLength, $codeCharset, $codeRegex);
     $expiry = date('Y-m-d H:i:s', time() + ($validity * 60));
 
-    $verification = null;
 
     // If there's already a Verification, pull it, check it, and update it
     if($verificationId) {

app/src/View/Helper/FieldHelper.php

@@ -297,7 +297,7 @@ public function constructSPAField(string $element, string $vueElementName): stri
 
   public function dateField(string $fieldName,
                             string $dateType = DateTypeEnum::Standard,
-                            array  $fieldArgs = null): string
+                            ?array  $fieldArgs = null): string
   {
     // Initialize
     $dateFormat = $dateType === DateTypeEnum::DateOnly ? 'yyyy-MM-dd' : 'yyyy-MM-dd HH:mm:ss';
@@ -422,13 +422,13 @@ public function dateField(string $fieldName,
    * @since  COmanage Registry v5.0.0
    */
   public function formField(string $fieldName,
-                            array  $fieldOptions = null,
-                            string $fieldLabel = null,
+                            ?array  $fieldOptions = null,
+                            ?string $fieldLabel = null,
                             string $fieldPrefix = '',
-                            string $fieldType = null,
-                            array  $fieldSelectOptions = null,
-                            string $fieldNameAlias = null,
-                            bool   $labelIsTextOnly = null): string
+                            ?string $fieldType = null,
+                            ?array  $fieldSelectOptions = null,
+                            ?string $fieldNameAlias = null,
+                            ?bool $labelIsTextOnly = null): string
   {
     $fieldArgs = $fieldOptions ?? [];
     $fieldArgs['label'] = $fieldOptions['label'] ?? false;
@@ -766,7 +766,8 @@ public function restructureFieldArguments(array $fieldArgs) {
       'id',
       'style',
       'checked',
-      'label'
+      'label',
+      'name'
     ];
 
     // Remove the top-level field options that are intended for Cake, and

app/src/View/Helper/TabHelper.php

@@ -295,7 +295,7 @@ public function tabBelongsToModelPath(string $tab, string $modelFullName, int &$
    * @return int
    * @since  COmanage Registry v5.0.0
    */
-  public function getCurrentId(string $tabName = null, bool $isNested = false): int
+  public function getCurrentId(?string $tabName = null, bool $isNested = false): int
   {
     $vv_obj = $this->getView()->get('vv_obj');
     $vv_primary_link = $this->getView()->get('vv_primary_link');