Add CenterID class to LORIS (#7359)

This adds a new CenterID class and updates it throughout LORIS.

Author: driusan

modules/api/php/endpoints/candidate/visit/visit.class.inc

@@ -198,6 +198,7 @@ class Visit extends Endpoint implements \LORIS\Middleware\ETagCalculator
             'Project',
         ];
         $diff           = array_diff($requiredfields, array_keys($visitinfo));
+
         if (!empty($diff)) {
             return new \LORIS\Http\Response\JSON\BadRequest(
                 'Field(s) missing: ' . implode(', ', $diff)
@@ -226,13 +227,19 @@ class Visit extends Endpoint implements \LORIS\Middleware\ETagCalculator
 
         $centerid = array_search($visitinfo['Site'], \Utility::getSiteList());
 
-        if (!in_array($centerid, $user->getCenterIDs())) {
+        if ($centerid === false
+            || !in_array(new \CenterID("$centerid"), $user->getCenterIDs())
+        ) {
             return new \LORIS\Http\Response\JSON\Forbidden(
-                "You can't create  or modify candidates visit for the site " .
+                "You can't create or modify candidates visit for the site " .
                 $centerid
             );
         }
 
+        // \Utility::getSiteList key was a string. Now that the
+        // validation is done, convert to an object.
+        $centerid = new \CenterID("$centerid");
+
         $subprojectid = array_search(
             $visitinfo['Battery'],
             \Utility::getSubprojectList()

modules/api/php/endpoints/candidates.class.inc

@@ -187,7 +187,7 @@ class Candidates extends Endpoint implements \LORIS\Middleware\ETagCalculator
         $usersites = $user->getSiteNames();
         if (!in_array($data['Candidate']['Site'], $usersites)) {
             return new \LORIS\Http\Response\JSON\Forbidden(
-                'You are not affiliated with the candidate`s site'
+                "You are not affiliated with the candidate's site"
             );
         }
 
@@ -209,7 +209,7 @@ class Candidates extends Endpoint implements \LORIS\Middleware\ETagCalculator
 
         try {
             $candid = \Candidate::createNew(
-                $centerid,
+                new \CenterID("$centerid"),
                 $data['Candidate']['DoB'],
                 $data['Candidate']['EDC'],
                 $sex,

modules/api/php/models/candidatesrow.class.inc

@@ -31,7 +31,7 @@ class CandidatesRow implements \LORIS\Data\DataInstance,
     private $_edc;
     private $_dob;
     private $_sex;
-    private $_centerid;
+    private \CenterID $_centerid;
 
     /**
      * Create a new CandidatesRow.
@@ -50,7 +50,7 @@ class CandidatesRow implements \LORIS\Data\DataInstance,
         $this->_edc      = $row['EDC'] ?? null;
         $this->_dob      = $row['DoB'] ?? null;
         $this->_sex      = $row['Sex'] ?? null;
-        $this->_centerid = $row['CenterID'] ?? null;
+        $this->_centerid = new \CenterID($row['CenterID']);
     }
 
     /**
@@ -78,14 +78,14 @@ class CandidatesRow implements \LORIS\Data\DataInstance,
      * Returns the CenterID for this row, for filters such as
      * \LORIS\Data\Filters\UserSiteMatch to match against.
      *
-     * @return integer The CenterID
+     * @return \CenterID The CenterID
      */
-    public function getCenterID(): int
+    public function getCenterID(): \CenterID
     {
         if ($this->_centerid === null) {
             throw new \Exception('CenterID is null');
         }
-        return intval($this->_centerid);
+        return $this->_centerid;
     }
 
     /**

modules/api/php/models/projectimagesrow.class.inc

@@ -28,7 +28,7 @@ class ProjectImagesRow implements \LORIS\Data\DataInstance,
     private $_entitytype;
     private $_visitlabel;
     private $_visitdate;
-    private $_centerid;
+    private \CenterID $_centerid;
     private $_centername;
     private $_filename;
     private $_inserttime;
@@ -48,7 +48,7 @@ class ProjectImagesRow implements \LORIS\Data\DataInstance,
         $this->_entitytype = $row['Entity_type'] ?? null;
         $this->_visitlabel = $row['Visit'] ?? null;
         $this->_visitdate  = $row['Visit_date'] ?? null;
-        $this->_centerid   = $row['CenterID'] ?? null;
+        $this->_centerid   = new \CenterID($row['CenterID']);
         $this->_centername = $row['Site'] ?? null;
         $this->_filename   = $row['File'] ?? null;
         $this->_inserttime = $row['InsertTime'] ?? null;
@@ -89,11 +89,11 @@ class ProjectImagesRow implements \LORIS\Data\DataInstance,
      * Returns the CenterID for this row, for filters such as
      * \LORIS\Data\Filters\UserSiteMatch to match again.
      *
-     * @return integer The CenterID
+     * @return \CenterID
      */
-    public function getCenterID(): int
+    public function getCenterID(): \CenterID
     {
-        return intval($this->_centerid);
+        return $this->_centerid;
     }
 
     /**

modules/candidate_list/php/candidatelistrow.class.inc

@@ -29,7 +29,7 @@ class CandidateListRow implements \LORIS\Data\DataInstance,
     \LORIS\StudyEntities\SiteHaver
 {
     protected $DBRow;
-    protected $CenterID;
+    protected \CenterID $CenterID;
     protected $ProjectID;
 
     /**
@@ -38,10 +38,10 @@ class CandidateListRow implements \LORIS\Data\DataInstance,
      * @param array      $row The row (in the same format as
      *                        \Database::pselectRow
      *                        returns.)
-     * @param integer    $cid The centerID affiliated with this row.
+     * @param \CenterID  $cid The centerID affiliated with this row.
      * @param \ProjectID $pid The projectID affiliated with this row.
      */
-    public function __construct(array $row, int $cid, \ProjectID $pid)
+    public function __construct(array $row, \CenterID $cid, \ProjectID $pid)
     {
         $this->DBRow     = $row;
         $this->CenterID  = $cid;
@@ -62,9 +62,9 @@ class CandidateListRow implements \LORIS\Data\DataInstance,
      * Returns the CenterID for this row, for filters such as
      * \LORIS\Data\Filters\UserSiteMatch to match again.
      *
-     * @return integer The CenterID
+     * @return \CenterID
      */
-    public function getCenterID(): int
+    public function getCenterID(): \CenterID
     {
         return $this->CenterID;
     }

modules/candidate_list/php/candidatelistrowprovisioner.class.inc

@@ -95,7 +95,7 @@ class CandidateListRowProvisioner extends \LORIS\Data\Provisioners\DBRowProvisio
         // user's sites, but for now this maintains the previous
         // behaviour of requiring the registration site to match
         // one of the user's sites.
-        $cid = (int) $row['RegistrationCenterID'];
+        $cid = new \CenterID($row['RegistrationCenterID']);
         $pid = new \ProjectID($row['RegistrationProjectID']);
         unset($row['RegistrationCenterID']);
         unset($row['RegistrationProjectID']);

modules/create_timepoint/php/timepoint.class.inc

@@ -183,7 +183,7 @@ class Timepoint extends \NDB_Page implements ETagCalculator
         if ($num_sites == 1) {
             $site = \Site::singleton($user_list_of_sites[0]);
         } else if ($num_sites > 1) {
-            $site = \Site::singleton(intval($values['psc']));
+            $site = \Site::singleton(new \CenterID(($values['psc'])));
         }
 
         // Project
@@ -255,7 +255,8 @@ class Timepoint extends \NDB_Page implements ETagCalculator
             null : $values['psc'];
 
         // validate site entered
-        $site = (int) $values['psc'];
+        $site = !empty($values['psc']) ? new \CenterID($values['psc']) : null;
+
         $user_list_of_sites = $user->getCenterIDs();
         $num_sites          = count($user_list_of_sites);
         $conflict           = [];

modules/dicom_archive/php/dicomarchiveanonymizer.class.inc

@@ -50,18 +50,11 @@ class DICOMArchiveAnonymizer implements Mapper
             $config = \NDB_Config::singleton()->getSetting("imaging_modules");
         }
 
-        if (!$resource instanceof \LORIS\StudyEntities\SiteHaver) {
-            throw new \LorisException(
-                "Mapper requires a resource type with getCenterID"
-            );
-        }
         $newrow = json_decode(json_encode($resource), true);
         if (!is_array($newrow)) {
             throw new \Exception("Error converting DataInstance to array");
         }
 
-        $cid = $resource->getCenterID();
-
         // escape any forward slashes
         $pNameRegex      = preg_replace(
             '/\//',
@@ -103,6 +96,12 @@ class DICOMArchiveAnonymizer implements Mapper
         if (!preg_match("/$pIDRegex/", $newrow['patientID'] ?? '')) {
             $newrow['patientID'] = 'INVALID - HIDDEN';
         }
-        return new DICOMArchiveRow($newrow, $cid);
+
+        if (!$resource instanceof \LORIS\StudyEntities\SiteHaver) {
+            return new DICOMArchiveRowWithoutSession($newrow);
+        } else {
+            $cid = $resource->getCenterID();
+            return new DICOMArchiveRowWithSession($newrow, $cid);
+        }
     }
 }

modules/dicom_archive/php/dicomarchiverowprovisioner.class.inc

@@ -72,8 +72,12 @@ class DicomArchiveRowProvisioner extends \LORIS\Data\Provisioners\DBRowProvision
      */
     public function getInstance($row) : \LORIS\Data\DataInstance
     {
-            $cid = (int) $row['CenterID'];
+        if ($row['CenterID'] !== null) {
+            $cid = new \CenterID($row['CenterID']);
             unset($row['CenterID']);
-            return new DICOMArchiveRow($row, $cid);
+            return new DICOMArchiveRowWithSession($row, $cid);
+        }
+        unset($row['CenterID']);
+        return new DICOMArchiveRowWithoutSession($row);
     }
 }

modules/dicom_archive/php/dicomarchiverowwithoutsession.class.inc

@@ -0,0 +1,55 @@
+<?php
+/**
+ * This class implements a data Instance which represents a single
+ * row in the dicom archive menu table.
+ *
+ * PHP Version 7
+ *
+ * @category   Behavioural
+ * @package    Main
+ * @subpackage Imaging
+ * @author     Dave MacFarlane <david.macfarlane2@mcgill.ca>
+ * @license    http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
+ * @link       https://www.github.com/aces/Loris/
+ */
+
+namespace LORIS\dicom_archive;
+
+/**
+ * A DICOMArchiveRow represents a row in the DICOM Archive menu table.
+ *
+ * @category   Behavioural
+ * @package    Main
+ * @subpackage Imaging
+ * @author     Dave MacFarlane <david.macfarlane2@mcgill.ca>
+ * @license    http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
+ * @link       https://www.github.com/aces/Loris/
+ */
+class DICOMArchiveRowWithoutSession implements \LORIS\Data\DataInstance
+{
+    protected $DBRow;
+
+    /**
+     * Create a new DICOMArchiveRow without a session.
+     *
+     * Session-less DICOMArchiveRows do not have CenterIDs to be filtered
+     * by.
+     *
+     * @param array $row The row (in the same format as \Database::pselectRow
+     *                   returns)
+     */
+    public function __construct(array $row)
+    {
+        $this->DBRow = $row;
+    }
+
+    /**
+     * Implements \LORIS\Data\DataInstance interface for this row.
+     *
+     * @return array which can be serialized by json_encode()
+     */
+    public function jsonSerialize() : array
+    {
+        return $this->DBRow;
+    }
+}