Merge branch 'master' into 2020-02-11-new-schedule

README.md

@@ -108,15 +108,16 @@ such as the OS you're using, your PHP and Apache versions, etc.
 
 ## Contributing
 
-The [LORIS team](http://loris.ca) at the Montreal Neurological Institute (MNI) is very happy to get code contributions and features from the global LORIS community.
 
-### Contributing Code
+We are very happy to get code contributions and features from the global LORIS community. 
+
+
 If you would like to contribute to LORIS development, please consult our [Contributing Guide](./CONTRIBUTING.md).
 
 ## Powered by MCIN
 
-LORIS is made by staff developers at the McGill Centre for Integrative Neuroscience ([MCIN.ca](www.mcin.ca)), led by Alan Evans and Samir Das at the Montreal Neurological Institute.
+LORIS is made by staff developers at the [McGill Centre for Integrative Neuroscience](http://www.mcin.ca), led by Alan Evans and Samir Das at The Neuro (Montreal Neurological Institute-Hospital).
 
-See [LORIS.ca](www.loris.ca) for our current team, the history of LORIS, and our **Technical Papers**.
+Visit [the LORIS website](https://loris.ca) for the history of LORIS and our **Technical Papers**.
 
 The original (pre-GitHub) LORIS development team from 1999-2010 included: Dario Vins, Alex Zijdenbos, Jonathan Harlap, Matt Charlet, Andrew Corderey, Sebastian Muehlboeck, and Samir Das.

htdocs/bootstrap/css/custom-css.css

@@ -23,6 +23,7 @@ Note: other colors are currenly inherited from Bootstrap default color palette
     border-top-right-radius: 0;
     border-top-left-radius: 0;
     background-color: white;
+    border: 1px solid #064785;
 }
 
 .navbar-nav > li > .dropdown-menu > li > a,
@@ -34,6 +35,18 @@ Note: other colors are currenly inherited from Bootstrap default color palette
 .navbar-nav > li > .dropdown-menu > li > a:hover {
     color: #E89A0C;
 }
+/* For mobile and tablet, repeat the above styling */
+@media (max-width: 991px) {
+  .navbar-default .navbar-nav .open .dropdown-menu >li>a,
+  .navbar-default .navbar-nav .open .dropdown-menu >li>a:focus {
+    color: #064785;
+    background-color: white;
+  }
+  .navbar-default .navbar-nav .open .dropdown-menu>li>a:hover {
+    color: #E89A0C;
+    background-color: white;
+  }
+}
 
 .navbar-brand {
     padding: 16px 15px;
@@ -53,9 +66,11 @@ Note: other colors are currenly inherited from Bootstrap default color palette
 }
 
 /* Show submenu when hovering on menu item */
-.dropdown:hover .dropdown-menu {
+/* If hover functionality exists and window size larger than tablet */
+@media (hover: hover) and (min-width: 992px) {
+  .dropdown:hover .dropdown-menu {
     display: block;
-    border: 1px solid #064785;
+  }
 }
 
 /* Loris logo */
@@ -73,30 +88,46 @@ Note: other colors are currenly inherited from Bootstrap default color palette
     border-top-left-radius: 5px;
     border-top-right-radius: 5px;
 }
-
-.navbar-default .navbar-nav > li:hover > a,
-.navbar-default .navbar-nav > li > a:hover,
-.navbar-default .navbar-nav > li > a:focus,
-.navbar-default .navbar-nav > li > a:active {
-    color: #064785;
-    background-color: white;
+/* Styling for clicking on menu items */
+.navbar-default .navbar-nav > li.dropdown > a:focus,
+.navbar-default .navbar-nav > li.dropdown > a:active {
+    background-color: transparent;
 }
-
-.navbar-default .navbar-right > li.dropdown:hover > a,
-.navbar-default .navbar-right > li.dropdown > a:hover,
-.navbar-default .navbar-right > li.dropdown > a:focus,
-.navbar-default .navbar-right > li.dropdown > a:active {
+/* Styling for opened submenu dropdowns - order matters */
+.navbar-default .navbar-nav > li.open > a,
+.navbar-default .navbar-nav > li.open > a:focus,
+.navbar-default .navbar-nav > li.open > a:active {
     color: #064785;
     background-color: white;
 }
+@media (hover: hover) {
+  /* Styling for hovering over menu items - order matters */
+  .navbar-default .navbar-nav > li.dropdown:hover > a,
+  .navbar-default .navbar-nav > li.dropdown > a:hover {
+      color: #064785;
+      background-color: white;
+  }
+}
+/* Styling for chevron icon to toggle collapsible navigation bar */
+.navbar-default .navbar-toggle:hover,
+.navbar-default .navbar-toggle:focus {
+    background-color: #064785;
+}
 
-/* Submenu items*/
+/* Submenu items */
 .dropdown-menu {
     padding: 5px 1px;
     border-top-color: transparent !important;
     box-shadow: 6px 8px 8px 1px rgba(0,0,0,0.175);
 }
 
+/* For mobile and tablet, submenu items */
+@media (max-width: 991px) {
+  .dropdown-menu {
+      padding: 0px;
+      border-top-color: transparent !important;
+  }
+}
 .dropdown-menu > .active > a,
 .dropdown-menu > .active > a:hover {
     color: #246EB6;
@@ -112,6 +143,8 @@ Note: other colors are currenly inherited from Bootstrap default color palette
     cursor: pointer;
 }
 
+/* Styling for right hand side of nav bar */
+
 /* Question mark */
 .nav > li > a > img {
     padding-bottom: 3px;
@@ -122,10 +155,21 @@ Note: other colors are currenly inherited from Bootstrap default color palette
     padding: 5px 8px;
 }
 
-.navbar-default .navbar-right > li:hover > a,
-.navbar-default .navbar-right > li > a:hover,
+/* Styling for clicking on menu items */
 .navbar-default .navbar-right > li > a:focus,
-.navbar-default .navbar-right > li > a:active{
+.navbar-default .navbar-right > li > a:active {
+  background-color: transparent;
+}
+/* Styling for clicking on Question mark - order matters */
+.navbar-default .navbar-right > li > a.help-open,
+.navbar-default .navbar-right > li > a.help-open:focus,
+.navbar-default .navbar-right > li > a.help-open:active {
+    color: white;
+    background-color: #246EB6;
+}
+/* Styling for hovering over menu items - order matters */
+.navbar-default .navbar-right > li:hover > a,
+.navbar-default .navbar-right > li > a:hover {
     color: white;
     background-color: #246EB6;
 }

htdocs/css/simple-sidebar.css

@@ -119,7 +119,7 @@
 
     #sidebar-wrapper {
         left: 0;
-        color: white;
+        color: #064785;
     }
 
     .wrapper.active {

htdocs/js/helpHandler.js

@@ -7,6 +7,11 @@ $(document).ready(function() {
     $('.wrapper').toggleClass('active');
   });
   $('.help-button').click(function(e) {
+    if ($(this).hasClass('help-open')) {
+      $(this).removeClass('help-open');
+    } else {
+      $(this).addClass('help-open');
+    }
     let helpContent = $('div.help-content');
     if (helpContent.length) {
       helpContent.toggle();
@@ -68,6 +73,7 @@ $(document).ready(function() {
       $(div).addClass('visible');
       btn.addEventListener('click', function(e) {
         $(div).hide();
+        $('.help-button').removeClass('help-open');
         e.preventDefault();
       });
       e.preventDefault();

htdocs/main.css

@@ -33,7 +33,6 @@ html, body {
 #page {
     min-height: 100vh;
     position: relative;
-    padding-top: 50px;
 }
 
 

modules/candidate_profile/help/candidate_profile.md

@@ -0,0 +1,7 @@
+# Candidate Profile
+
+This module allows you to see a summary of a candidate's information
+across all modules. 
+
+Click on the visit link in the "Candidate Info" card in order to access
+that visit for the candidate.

modules/candidate_profile/php/candidate_profile.class.inc

@@ -130,7 +130,7 @@ class Candidate_Profile extends \NDB_Page
             return new \LORIS\BreadcrumbTrail(
                 new \LORIS\Breadcrumb(
                     'Access Profile',
-                    '/candidate_list'
+                    '/candidate_list/?betaprofile=1'
                 ),
             );
         }
@@ -140,11 +140,11 @@ class Candidate_Profile extends \NDB_Page
         return new \LORIS\BreadcrumbTrail(
             new \LORIS\Breadcrumb(
                 'Access Profile',
-                '/candidate_list'
+                '/candidate_list/?betaprofile=1'
             ),
             new \LORIS\Breadcrumb(
                 "Candidate Dashboard $candid / $pscid",
-                "/$candid"
+                "/candidate_profile/$candid"
             )
         );
     }

modules/electrophysiology_browser/php/sessions.class.inc

@@ -36,6 +36,7 @@ class Sessions extends \NDB_Page
 
     public $skipTemplate = true; // stops from looking for a smarty template
     protected $timepoint;
+    protected $sessionID;
 
     /**
      * Determine whether the user has permission to view this page
@@ -82,6 +83,7 @@ class Sessions extends \NDB_Page
             $this->timepoint = \NDB_Factory::singleton()->timepoint(
                 $session_id
             );
+            $this->sessionID = $session_id;
         } catch(\LorisException $e) {
             return (new \LORIS\Middleware\PageDecorationMiddleware($user))
                 ->process(
@@ -126,19 +128,18 @@ class Sessions extends \NDB_Page
             ));
         }
 
-        return $this->getSessionData($session_id, $outputType);
+        return $this->getSessionData($outputType);
     }
 
 
     /**
      * Get the session data information.
      *
-     * @param int    $sessionID  ID of the session to display
      * @param string $outputType output type to be displayed
      *
      * @return ResponseInterface The JSON response
      */
-    function getSessionData($sessionID, $outputType)
+    function getSessionData($outputType)
     {
         $db = \NDB_Factory::singleton()->database();
 
@@ -161,10 +162,10 @@ class Sessions extends \NDB_Page
         $sessions            = array_column($sessions, 'SessionID');
         $response['patient'] = $this->getSubjectData($outputType);
         $response['database']    = array_values(
-            $this->getFilesData($sessionID, $outputType)
+            $this->getFilesData($outputType)
         );
         $response['sessions']    = $sessions;
-        $currentIndex            = array_search($sessionID, $sessions);
+        $currentIndex            = array_search($this->sessionID, $sessions);
         $response['nextSession'] = $sessions[$currentIndex+1] ?? '';
         $response['prevSession'] = $sessions[$currentIndex-1] ?? '';
 
@@ -204,18 +205,17 @@ class Sessions extends \NDB_Page
     /**
      * Get the list of electrophysiology recordings with their recording information.
      *
-     * @param int    $sessionID  ID of the electrophysiology session
      * @param string $outputType output type to be displayed
      *
      * @return array with the file collection
      */
-    function getFilesData(int $sessionID, string $outputType)
+    function getFilesData(string $outputType)
     {
         $db = \NDB_Factory::singleton()->database();
 
         $fileCollection = array();
         $params         = array();
-        $params['SID']  = $sessionID;
+        $params['SID']  = $this->sessionID;
         $query          = 'SELECT 
                          pf.PhysiologicalFileID, 
                          pf.FilePath 
@@ -458,4 +458,23 @@ class Sessions extends \NDB_Page
         return $depends;
     }
 
+    /**
+     * Generate a breadcrumb trail for this page.
+     *
+     * @return \LORIS\BreadcrumbTrail
+     */
+    public function getBreadcrumbs(): \LORIS\BreadcrumbTrail
+    {
+        return new \LORIS\BreadcrumbTrail(
+            new \LORIS\Breadcrumb(
+                'Electrophysiology Browser',
+                '/electrophysiology_browser'
+            ),
+            new \LORIS\Breadcrumb(
+                'View Session',
+                "/electrophysiology_browser/sessions/$this->sessionID"
+            )
+        );
+    }
+
 }

modules/issue_tracker/test/issue_tracker_test_plan.md

@@ -1,5 +1,5 @@
 Issue Tracker Filter Form [Automation Testing]
-1. User can access the page iff they have issue tracker reporter or developer permission
+1. A user can access the module only if they have one or more of the `issue_tracker_reporter` or `issue_tracker_developer` permissions.
 2. User can see data from other sites iff they have access_all_profiles permission
 3. Test that all filters work. Nothing should be filtered at first loading.
 4. Test that all tabs (with filters) work and redirect to the correct table. My issues should be missing assignee filter and closed issues should be missing status filter. 
@@ -14,7 +14,8 @@ Issue Tracker Create New Issue [Manual Testing]
 4. Submit invalid and valid PSCID and visit label pairs. Error messages should respond accordingly. Not that you cannot submit PSCIDs from other sites unless you have access all profiles permission
 5. Submit just a visit label - this should give an error message.
 6. Check that all values are propagated and saved correctly.
-7. Check that watching logging is working - turn it off and on for your current user, and for other watchers on the issue
+7. Add an attachment to the new issue and make sure that it is successfully uploaded.
+8. Check that watching logging is working - turn it off and on for your current user, and for other watchers on the issue
 
 Issue Tracker Edit Existing Issue [Manual Testing]
 1. User can access the page if they have (developer or reporter permission) and (they have either access_all_profiles or are a member of the site of the issue or the site has no issue).
@@ -24,7 +25,10 @@ Issue Tracker Edit Existing Issue [Manual Testing]
 5. Submit just a visit label - this should give an error message.
 6. Check that all values are propagated and saved correctly.
 7. Check that watching logging is working - turn it off and on for your current user, and for other watchers on the issue
-
+8. Check that an attachment can be adding to an existing issue.
+9. Test if users assigned to issues can upload attachments.
+10. Test if users can delete their own uploaded attachments.
+11. Test if user assigned to issue cannot delete attachments of issue owner.
 
 Permissions [Automation Testing]
 1. Remove access all profile permission.

modules/mri_violations/php/mri_protocol_check_violations.class.inc

@@ -86,6 +86,7 @@ class Mri_Protocol_Check_Violations extends \NDB_Menu_Filter
             'ValidRange',
             'ValidRegex',
             'SeriesUID',
+            'TarchiveID'
         );
         $this->tpl_data['hiddenHeaders'] = json_encode(['TarchiveID']);
         $this->validFilters = array(

modules/publication/jsx/projectFields.js

@@ -129,10 +129,10 @@ class ProjectFormFields extends React.Component {
     // Create download link & edit fields for existing files
     if (this.props.files) {
       this.props.files.forEach(function(f) {
-        let downloadURL = loris.BaseURL + '/publication/ajax/FileDownload.php?File=' + encodeURIComponent(f.URL);
+        let downloadURL = loris.BaseURL + '/publication/ajax/FileDownload.php?File=' + encodeURIComponent(f.Filename);
         let link = (
           <span>
-            <a href={downloadURL}>{f.URL}</a>
+            <a href={downloadURL}>{f.Filename}</a>
             &nbsp;&nbsp;
             <span
               className="glyphicon glyphicon-remove"

modules/publication/jsx/viewProject.js

@@ -131,8 +131,8 @@ class ViewProject extends React.Component {
     let files = this.state.files;
     let toReturn = [];
     files.forEach(function(f) {
-      let download = loris.BaseURL + '/publication/ajax/FileDownload.php?File=' + f.URL;
-      let link = <a href={download}>{f.URL}</a>;
+      let download = loris.BaseURL + '/publication/ajax/FileDownload.php?File=' + f.Filename;
+      let link = <a href={download}>{f.Filename}</a>;
       let uploadType = this.state.uploadTypes[f.PublicationUploadTypeID];
       toReturn.push(
           <StaticElement