Merge remote-tracking branch 'aces/26.0-release' into 26ToMain

driusan · Oct 2, 2024 · 89d3fde · 89d3fde
2 parents ca334d6 + 85645d1
commit 89d3fde
Show file tree

Hide file tree

Showing 18 changed files with 172 additions and 63 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,7 +8,7 @@ core section.***
 - ***When possible please provide the number of the pull request(s) containing the 
 changes in the following format: PR #1234***
 
-## LORIS 26.0 (Release Date: ????-??-??)
+## LORIS 26.0 (Release Date: 2024-06-13)
 ### Core
 #### Features
 - Add OpenID Connect authorization support to LORIS (PR #8255)
@@ -26,7 +26,7 @@ changes in the following format: PR #1234***
 - While proposing a project or editing a project in publications module, prevent indefinite "File to upload" fields from being added if files are browsed then cancelled (PR #9179)
 - Conflict resolver fixed when Test_name is not equal to table name. This is done be replacing the "TableName" variable with "TestName" everywhere in resolved & unresolved conflicts tables as well as modules (PR #9270)
 
-## LORIS 25.0 (Release Date: ????-??-??)
+## LORIS 25.0 (Release Date: 2023-07-17)
 ### Core
 #### Features
 - Added new interface intended to be used for querying module data from PHP (PR #8215) 

diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@ LORIS (Longitudinal Online Research and Imaging System) is a self-hosted web app
 
 * Try the LORIS demo instance at https://demo.loris.ca.
 
-This Readme covers installation of LORIS version <b>25.0</b> on <b>Ubuntu</b>.
+This Readme covers installation of LORIS version <b>26.0</b> on <b>Ubuntu</b>.
 
 ([CentOS Readme also available](docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/01_LORIS_Install/CentOS/README.md)).
 

diff --git a/docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/01_LORIS_Install/CentOS/README.md b/docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/01_LORIS_Install/CentOS/README.md
@@ -10,9 +10,9 @@ For further details on the install process, please see the LORIS GitHub Wiki Cen
 # System Requirements - Install dependencies
 
 Default dependencies installed by CentOS 7.x may not meet the version requirements for LORIS deployment or development:
-* MariaDB 10.3 is supported for LORIS 25.
+* MariaDB 10.3 is supported for LORIS 26.
 
-* PHP 8.1 (or higher) is supported for LORIS 25.
+* PHP 8.2 (or higher) is supported for LORIS 26.
 
 In addition to the above, the following packages should be installed with `yum` and may also differ from the packages referenced in the main (Ubuntu) [LORIS Readme](../../../../../README.md). Detailed command examples are provided below (`sudo` privilege may be required depending on your system).
  * Apache 2.4 or higher  

diff --git a/modules/api/php/endpoints/candidate/visit/image/qc.class.inc b/modules/api/php/endpoints/candidate/visit/image/qc.class.inc
@@ -166,7 +166,7 @@ class Qc extends Endpoint implements \LORIS\Middleware\ETagCalculator
             );
         }
 
-        $inputqcstatus = $data['QCStatus'] ?? null;
+        $inputqcstatus = $data['QC'] ?? null;
         $inputselected = $data['Selected'] ?? null;
 
         // TODO :: This is (and was) not checking or handling Caveats

diff --git a/modules/candidate_parameters/jsx/DiagnosisEvolution.js b/modules/candidate_parameters/jsx/DiagnosisEvolution.js
@@ -61,6 +61,7 @@ class DiagnosisEvolution extends Component {
   formattedDiagnosisEvolution() {
     const dxEvolution = this.state.data.diagnosisEvolution;
     let formattedDxEvolution = [];
+    try {
     dxEvolution.map((record) => {
       let formattedDiagnosis = [];
       Object.entries(JSON.parse(record.Diagnosis)).map((entry, index) => {
@@ -94,6 +95,9 @@ class DiagnosisEvolution extends Component {
         ]
       );
     });
+    } catch (error) {
+        console.error('Error parsing JSON:', error);
+    }
     return formattedDxEvolution;
   }
 

diff --git a/modules/electrophysiology_uploader/README.md b/modules/electrophysiology_uploader/README.md
@@ -2,7 +2,13 @@
 
 ## Purpose
 
-The electrophysiology uploader is intended to allow users to upload and browse electrophysiology files.
+The electrophysiology uploader is intended to allow users to upload electrophysiology files.
+
+**LORIS 26 Beta Note:** Files uploaded in this module will not be viewable 
+in 
+the Electrophysiology Browser module.
+This feature is under construction for the next release. Please get in 
+touch with the LORIS team to configure this for your project.
 
 
 ## Intended Users
@@ -26,6 +32,7 @@ EEG recordings can be re-uploaded multiple times. Previous upload attempts will
 Permission `electrophysiology_browser_view_allsites` or `electrophysiology_browser_view_site`
 is necessary to have access to the module and gives the user the ability to 
 upload and browse all recordings uploaded to the database.
+Permission `monitor_eeg_uploads` is necessary to receive EEG upload notifications.
 
 #### Filesystem Permission
 
@@ -49,3 +56,6 @@ EEGUploadIncomingPath - This setting determines where on the filesystem the
         `EEGUploadIncomingPath` following a successful archival and insertion 
         through the LORIS-MRI pipeline. 
 
+### Caveat
+
+Archive extraction and EEG insertion have to be performed manually at the moment.
diff --git a/modules/electrophysiology_uploader/jsx/ElectrophysiologyUploader.js b/modules/electrophysiology_uploader/jsx/ElectrophysiologyUploader.js
@@ -56,19 +56,28 @@ export default function ElectrophysiologyUploader(props) {
   ];
 
   return (
-    <Tabs tabs={tabList} defaultTab='browse' updateURL={true}>
-      <TabPane TabId={tabList[0].id}>
-        <UploadViewer
-          data={data.Data}
-          fieldOptions={data.fieldOptions}
-        />
-      </TabPane>
-      <TabPane TabId={tabList[1].id}>
-        <UploadForm
-          uploadURL={`${props.DataURL}/upload`}
-        />
-      </TabPane>
-    </Tabs>
+    <>
+      <div className="alert alert-warning" role="alert">
+        <strong>LORIS 26 Beta Note:</strong> Files uploaded in this module
+         will not be viewable in the Electrophysiology Browser
+         module. This feature is under construction for the next release.
+         Please get in touch with the LORIS team to configure this for your
+         project.
+      </div>
+      <Tabs tabs={tabList} defaultTab='browse' updateURL={true}>
+        <TabPane TabId={tabList[0].id}>
+          <UploadViewer
+            data={data.Data}
+            fieldOptions={data.fieldOptions}
+          />
+        </TabPane>
+        <TabPane TabId={tabList[1].id}>
+          <UploadForm
+            uploadURL={`${props.DataURL}/upload`}
+          />
+        </TabPane>
+      </Tabs>
+    </>
   );
 }
 

diff --git a/modules/imaging_uploader/php/imaging_uploader.class.inc b/modules/imaging_uploader/php/imaging_uploader.class.inc
@@ -125,7 +125,7 @@ class Imaging_Uploader extends \NDB_Menu_Filter_Form
             $upload_max_size = \Utility::getMaxUploadSize();
             $error_message   = "Please make sure files are not larger than " .
                                 $upload_max_size;
-            http_response_code(400);
+            http_response_code(413);
             $errors = [
                 'IsPhantom'  => [],
                 'candID'     => [],

diff --git a/modules/media/test/MediaTest.php b/modules/media/test/MediaTest.php
@@ -61,8 +61,41 @@ function testLoadsWithPermissionRead()
             "An error occured while loading the page.",
             $bodyText
         );
+        $bodyText = $this->safeFindElement(
+            WebDriverBy::cssSelector("#dynamictable > thead > tr")
+        )->getText();
+        $this->assertStringNotContainsString("Edit Metadata", $bodyText);
+
+        $this->resetPermissions();
+    }
+    /**
+     * Tests that the page does not load if the user does not have correct
+     * permissions
+     *
+     * @return void
+     */
+    function testLoadsWithPermissionWrite()
+    {
+        $this->setupPermissions(["media_write"]);
+        $this->safeGet($this->url . "/media/");
+        $bodyText = $this->safeFindElement(
+            WebDriverBy::cssSelector("body")
+        )->getText();
+        $this->assertStringNotContainsString(
+            "You do not have access to this page.",
+            $bodyText
+        );
+        $this->assertStringNotContainsString(
+            "An error occured while loading the page.",
+            $bodyText
+        );
+        $bodyText = $this->safeFindElement(
+            WebDriverBy::cssSelector("#dynamictable > thead > tr")
+        )->getText();
+        $this->assertStringContainsString("Edit Metadata", $bodyText);
         $this->resetPermissions();
     }
+    /**
     /**
      * Tests that the page does not load if the user does not have correct
      * permissions
@@ -185,5 +218,45 @@ function _testFilter($element,$table,$records,$value)
             );
         $this->assertEquals("", $inputText);
     }
+    /**
+     * Testing Browse tab and coulumn clicking
+     *
+     * @return void
+     */
+    function testBrowseTab()
+    {
+        $this->safeGet($this->url . "/media/");
+
+        $this->checkColumn(2, "DCC090_V1_bmi.txt");
+        $this->checkColumn(3, "DCC090");
+        $this->checkColumn(4, "V1");
+        $this->checkColumn(5, "");
+        $this->checkColumn(6, "");
+        $this->checkColumn(7, "Data Coordinating Center");
+        $this->checkColumn(8, "Pumpernickel");
+    }
+    /**
+     * Test Browse tab and coulumn clicking-middleware
+     *
+     * @param int    $columnNumber columnNumber
+     * @param string $expectedText expectedText
+     *
+     * @return void
+     */
+    function checkColumn($columnNumber, $expectedText)
+    {
+        $this->safeClick(
+            WebDriverBy::cssSelector(
+                "#dynamictable > thead > tr > th:nth-child($columnNumber)"
+            )
+        );
+        $bodyText = $this->safeFindElement(
+            WebDriverBy::cssSelector(
+                "#dynamictable > tbody > tr:nth-child(1)".
+                " > td:nth-child($columnNumber)"
+            )
+        )->getText();
+            $this->assertEquals($expectedText, $bodyText);
+    }
 }
 
diff --git a/modules/media/test/TestPlan.md b/modules/media/test/TestPlan.md
@@ -4,7 +4,7 @@
 
 Media module allows users to upload, browse and edit media files associated with a specific timepoint in Loris.
 
-### 🔒 Permissions 
+### 🔒 Permissions [Automation Testing]
 
 In order to use the media module the user might need one or both of the following permissions:
 
@@ -60,7 +60,7 @@ is selected, the file name should should start with [PSCID]\_[Visit Label]\_[Ins
   7. Once the file finished uploading, a modal containing a success message should appear with an 'OK' button.
   8. Click on the 👉 **OK** button and the page should refresh to the browse tab. Make sure the file you just uploaded is shown in the data table.
 
-**Test file browsing** 
+**Test file browsing** [Automation Testing]
   1. After a couple of files are uploaded, make sure they are properly displayed in the data table
   2. Make sure that information in the data table corresponds to the information in the database (media table)
   3. Click on 👉  **column headers** to make sure sorting functionality is working as expected (Ascending/Descending)

diff --git a/modules/mri_violations/php/mri_violations.class.inc b/modules/mri_violations/php/mri_violations.class.inc
@@ -148,7 +148,11 @@ class Mri_Violations extends \DataFrameworkMenu
             );
         default:
             return (new Provisioner())
-                ->filter(new UserCenterMatchOrNull())
+                ->filter(
+                    new UserCenterMatchOrNullOrAnyPermission(
+                        $this->allSitePermissionNames(),
+                    )
+                )
                 ->filter(new UserProjectMatchOrNull());
         }
     }

diff --git a/modules/statistics/php/charts.class.inc b/modules/statistics/php/charts.class.inc
@@ -127,7 +127,7 @@ class Charts extends \NDB_Page
 
             $recruitmentBySiteData[] = [
                 "label" => $siteName,
-                "total" => intval($data[$siteID]) ?? 0,
+                "total" => intval($data[$siteID] ?? 0),
             ];
         }
         return new \LORIS\Http\Response\JsonResponse($recruitmentBySiteData);

diff --git a/modules/statistics/php/statistics_dd_site.class.inc b/modules/statistics/php/statistics_dd_site.class.inc
@@ -112,7 +112,7 @@ class Statistics_DD_Site extends statistics_site
     function _getResults(
         ?\CenterID $centerID,
         ?\ProjectID $projectID,
-        $instrument
+        string $instrument
     ) {
         $this->_checkCriteria($centerID, $projectID);
         $DB = $this->loris->getDatabaseConnection();

diff --git a/modules/statistics/php/statistics_mri_site.class.inc b/modules/statistics/php/statistics_mri_site.class.inc
@@ -79,7 +79,7 @@ class Statistics_Mri_Site extends Statistics_Site
     function _completeCount(
         ?\CenterID $centerID,
         ?\ProjectID $projectID,
-        $issue
+        string $issue
     ): ?string {
         return null;
     }
@@ -96,7 +96,7 @@ class Statistics_Mri_Site extends Statistics_Site
     function _getResults(
         ?\CenterID $centerID,
         ?\ProjectID $projectID,
-        $issue
+        string $issue
     ) {
         $this->_checkCriteria($centerID, $projectID);
         $DB = $this->loris->getDatabaseConnection();

diff --git a/modules/statistics/php/statistics_site.class.inc b/modules/statistics/php/statistics_site.class.inc
@@ -193,18 +193,20 @@ class Statistics_Site extends \NDB_Menu
         $this->_checkCriteria($centerID, $projectID);
         $DB    = $this->loris->getDatabaseConnection();
         $count = $DB->pselectOne(
-            "SELECT count(s.CandID)  FROM session s,
-                candidate c, flag f, {$instrument} i
-                WHERE s.ID=f.SessionID AND f.CommentID=i.CommentID
-                AND s.CandID=c.CandID
-                AND s.Active='Y'
-                AND s.CenterID <> '1'
-                $this->query_criteria
-                AND f.Data_entry='Complete'
-                AND s.Current_stage <> 'Recycling Bin'
-                AND f.Administration='All'
-                AND i.CommentID NOT LIKE 'DDE%'",
-            $this->query_vars
+            "SELECT COUNT(DISTINCT s.CandID)  FROM 
+                flag f
+                    JOIN session s ON (s.ID=f.SessionID)
+                    JOIN candidate c ON (c.CandID=s.CandID)
+                WHERE 
+                    s.Active='Y' AND s.CenterID <> '1'
+                    AND c.Active='Y'
+                    $this->query_criteria
+                    AND f.Data_entry='Complete'
+                    AND s.Current_stage <> 'Recycling Bin'
+                    AND f.Administration='All'
+                    AND f.CommentID NOT LIKE 'DDE%'
+                    AND f.Test_name=:instrument",
+            ['instrument' => $instrument, ...$this->query_vars]
         );
         return $count;
     }
@@ -218,24 +220,31 @@ class Statistics_Site extends \NDB_Menu
      *
      * @return array
      */
-    function _getResults(?\CenterID $centerID, ?\ProjectID $projectID, $instrument)
-    {
+    function _getResults(
+        ?\CenterID $centerID,
+        ?\ProjectID $projectID,
+        string $instrument
+    ) {
         $this->_checkCriteria($centerID, $projectID);
         $DB     = $this->loris->getDatabaseConnection();
         $result = $DB->pselect(
-            "SELECT s.CandID, f.SessionID, i.CommentID, c.PSCID,
+            "SELECT DISTINCT s.CandID,
+                f.SessionID,
+                f.CommentID,
+                c.PSCID,
                 s.Visit_label
-                FROM session s, candidate c, flag  f,
-                {$instrument} i
-                WHERE s.ID=f.SessionID AND f.CommentID=i.CommentID
-                AND s.CandID=c.CandID
-                AND s.Active='Y'
-                AND s.CenterID <> '1'
-                AND s.Current_stage <> 'Recycling Bin'
-                $this->query_criteria
-                AND (f.Data_entry is NULL OR f.Data_entry<>'Complete')
-                AND i.CommentID NOT LIKE 'DDE%' ORDER BY s.Visit_label, c.PSCID",
-            $this->query_vars
+                FROM flag f
+                    JOIN session s ON (s.ID=f.SessionID)
+                    JOIN candidate c ON (c.CandID=s.CandID)
+                WHERE s.Active='Y' AND c.Active='Y'
+                    AND s.CenterID <> '1'
+                    AND s.Current_stage <> 'Recycling Bin'
+                    $this->query_criteria
+                    AND f.Test_name=:instrument
+                    AND (f.Data_entry is NULL OR f.Data_entry<>'Complete')
+                    AND f.CommentID NOT LIKE 'DDE%'
+                ORDER BY s.Visit_label, c.PSCID",
+            ['instrument'=>$instrument, ...$this->query_vars]
         );
         return iterator_to_array($result);
     }