Merge branch 'main' into dicom_archive_siteproject_main

Author: ridz1208

.eslintignore

@@ -2,6 +2,7 @@ node_modules/*
 vendor/*
 project/*
 babel.config.js
+webpack.config.ts
 
 # compiled js ignored since it is run on the jsx directory
 modules/*/js/*

CHANGELOG.md

@@ -167,6 +167,7 @@ the `Data` key instead of `$InstrumentName` (PR #7857)
 - Fixed broken DB calls in `assign_missing_instruments` and `instruments` (PR #8162)
 - Add support for PHP 8.1 (PR #7989)
 - Fix Project tab of Configuration module to give correct errors, and prevent saving without Alias (PR #8349)
+- Fix BVL feedback summary in instruments (PR #8889)
 ### Modules
 #### API
 - Ability to use PSCID instead of the CandID in the candidates API (PR #8138)

SQL/0000-00-03-ConfigTables.sql

@@ -211,7 +211,6 @@ INSERT INTO Config (ConfigID, Value) SELECT ID, "365" FROM ConfigSettings WHERE
 
 INSERT INTO Config (ConfigID, Value) SELECT ID, "/data/%PROJECTNAME%/data/" FROM ConfigSettings WHERE Name="imagePath";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "%LORISROOT%" FROM ConfigSettings WHERE Name="base";
-INSERT INTO Config (ConfigID, Value) SELECT ID, "%LORISROOT%" FROM ConfigSettings WHERE Name="DownloadPath";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "tools/logs/" FROM ConfigSettings WHERE Name="log";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "/data/%PROJECTNAME%/bin/mri/" FROM ConfigSettings WHERE Name="MRICodePath";
 INSERT INTO Config (ConfigID, Value) SELECT ID, "/data/incoming/" FROM ConfigSettings WHERE Name="MRIUploadIncomingPath";

docs/wiki/01_STUDY_PARAMETERS_SETUP/01_Study_Variables/04_Subprojects.md renamed to docs/wiki/01_STUDY_PARAMETERS_SETUP/01_Study_Variables/04_Cohorts.md

@@ -1,15 +1,15 @@
 # Code customization
 ## The project/ directory
 
-The `project/` directory is designed to house project-specific code and some data such as documents.  This includes instrument forms, instrument table schemas, and any customizations to other pages or modules in the Loris codebase.  
+The `project/` directory is designed to house project-specific code and some data such as documents.  This includes instrument forms, instrument table schemas, and any customizations to other pages or modules in the Loris codebase.
 The `project/` folder and its subdirectories are created by the install script, which also installs the `_config.xml_` file there.
 
-[[Instrument forms|Behavioural-Database]] (_.linst_ or php) should be stored under `project/instruments/` and their table schemas (.sql) should be stored under `project/tables_sql/` 
+[[Instrument forms|Behavioural-Database]] (_.linst_ or php) should be stored under `project/instruments/` and their table schemas (.sql) should be stored under `project/tables_sql/`
 
 ## Backing up `project/`
 
 * Important: Commit your project/ directory and its contents to a separate private repo - e.g. on GitHub
-* Equally Important: Exclude all data and the _config.xml_ file (which contains a database credential) stored under project/ from commits/backups to your online repo (such as on GitHub).  Back up this data and the config file elsewhere on another server, using a cronjob. 
+* Equally Important: Exclude all data and the _config.xml_ file (which contains a database credential) stored under project/ from commits/backups to your online repo (such as on GitHub).  Back up this data and the config file elsewhere on another server, using a cronjob.
 
 ## Tracking changes
 
@@ -25,5 +25,29 @@ i.e. `/var/www/loris/project/libraries/_filename.class.inc` will override `/var/
 
 ## Module override
 
-For projects wishing to customize existing modules, the recommended best practice is to copy _all_ module code from `$lorisroot/modules/_module_name_/*` to a new `project/modules/` subdirectory (project/modules/_module_name_/* ) and modify code there.  
-This will use the `project/` override functionality of Loris.  These changes should be added and committed to your project-specific private repo. 
+For projects wishing to customize existing modules, the recommended best practice is to copy _all_ module code from `$lorisroot/modules/_module_name_/*` to a new `project/modules/` subdirectory (project/modules/_module_name_/* ) and modify code there.
+This will use the `project/` override functionality of Loris.  These changes should be added and committed to your project-specific private repo.
+
+
+## Manage additional dependencies
+
+### Additional composer dependencies
+
+In case your project requires additional composer dependencies or different dependency version requirements, you can create a `composer.json` file in `project/` folder by running `composer init`. Any existing or new dependencies in this file will be merged with the main composer dependencies in `vendor/` after `composer update` has been run. For any change in the `project/composer.json` file, run `composer update` again in the root folder.
+
+### Additional npm dependencies
+
+To add new npm packages to your project, you can create a `package.json` file in `project/` by running `npm init`. Any dependencies in this file will be automatically installed under `project/` when make or npm ci/npm install is run from loris root.
+
+## Webpack compilation
+
+Modules overriden js files will automatically compile and replace the file they intend to modify. On the other hand, new js files will need to be registered in order to be compiled with `npm run compile`. To register, for example, a new React components located in `project/modules/_new_module_name_/jsx/_react_component_.js` you can create `project/webpack-project.config.js` with the following template:
+
+```
+const entry = {
+  '_new_module_name_': [
+    '_react_component_',
+  ],
+};
+module.exports = entry;
+```

docs/wiki/99_Developers/Code_Customization.md

@@ -928,3 +928,8 @@ legend {
 .highlighted {
     animation: highlight ease 3s;
 }
+
+select[multiple].input-sm.resizable {
+    height: 100px;
+    resize: both;
+}

htdocs/bootstrap/css/custom-css.css

@@ -65,7 +65,7 @@ class CandidateListIndex extends Component {
    * Called by React when the component has been rendered on the page.
    */
   componentDidMount() {
-    fetch('options',
+    fetch(loris.BaseURL+'/candidate_list/options',
       {credentials: 'same-origin'}).then(
       (resp) => resp.json()
     ).then(

modules/candidate_list/jsx/candidateListIndex.js

@@ -80,14 +80,16 @@ class Run extends \LORIS\Http\Endpoint
                 $rowsBinary,
                 bool $end
             ) use (&$values, &$db, &$runid) {
-                $values[] = join(
-                    ',',
-                    [$runid, $candid, $db->quote(json_encode($rowsArray))]
-                );
+                $values[] = "SELECT "
+                .  $runid . ","
+                . "c.ID, "
+                . $db->quote(json_encode($rowsArray))
+                . " FROM candidate c"
+                . "            WHERE c.CandID=" . intval($candid);
                 if ((count($values) >= 2000 || $end) && count($values) > 0) {
                     $insertstmt = "INSERT INTO dataquery_run_results
-    					    (RunID, CandID, RowData) VALUES "
-                    . " (" . join('),(', $values) . ')';
+                                         (RunID, CandidateID, RowData) "
+                    . join(' UNION ', $values);
                     $q          = $db->prepare($insertstmt);
                     $q->execute([]);
                     $values = [];

modules/dataquery/php/endpoints/queries/query/run.class.inc

@@ -53,6 +53,9 @@ const ResponsiveViewer : FunctionComponent<CProps> = ({
   const layers = React.Children.toArray(children).map(provision);
 
   const domain = window.EEGLabSeriesProviderStore[chunksURL]?.getState().bounds.domain;
+  // Data not loaded yet
+  if (!domain) return null;
+
   const amplitude = [0, 1];
   const eventScale = [
     scaleLinear()

modules/electrophysiology_browser/jsx/react-series-data-viewer/src/series/components/ResponsiveViewer.tsx

@@ -535,6 +535,9 @@ function testSessionsProjectPermissions()
      */
     function testSessionsNavigation()
     {
+        $this->markTestSkipped(
+            'rewrite later'
+        );
         $this->safeGet($this->url . "/electrophysiology_browser/sessions/999999");
         $link = self::$nextLink;
         $this->safeClick(WebDriverBy::cssSelector($link));

modules/electrophysiology_browser/jsx/react-series-data-viewer/tsconfig.json

@@ -46,6 +46,11 @@ export default function ElectrophysiologyUploader(props) {
     });
   };
 
+  const refreshForm = () => {
+    setData({});
+    fetchData();
+  };
+
   if (!isLoaded) {
     return <Loader />;
   }
@@ -74,6 +79,7 @@ export default function ElectrophysiologyUploader(props) {
         <TabPane TabId={tabList[1].id}>
           <UploadForm
             uploadURL={`${props.DataURL}/upload`}
+            refreshPage={refreshForm}
           />
         </TabPane>
       </Tabs>

modules/electrophysiology_browser/test/electrophysiologyBrowserTest.php

@@ -46,6 +46,14 @@ export default function UploadForm(props) {
       newFormData.pscid = ids[0];
       newFormData.candID = ids[1];
       newFormData.visit = ids[2];
+
+      // Clear possible error messages from previous file selection
+      setErrorMessage({
+        eegFile: null,
+        candID: null,
+        pscid: null,
+        visit: null,
+      });
     }
 
     setFormData(newFormData);
@@ -149,6 +157,10 @@ export default function UploadForm(props) {
           title: 'Upload Successful!',
           text: text,
           type: 'success',
+        }).then((result) => {
+          if (result.value) {
+            this.props.refreshPage();
+          }
         });
 
         resetForm();

modules/electrophysiology_uploader/jsx/ElectrophysiologyUploader.js

@@ -146,7 +146,7 @@ class ExaminerIndex extends Component {
 
     switch (column) {
     case 'Examiner':
-      if (this.state.data.useCertification) {
+      if (this.state.data.fieldOptions.useCertification) {
         const url = loris.BaseURL + '/examiner/editExaminer/?identifier=' +
                     row.ID;
         result = <td><a href={url}>{cell}</a></td>;

modules/electrophysiology_uploader/jsx/UploadForm.js

@@ -170,7 +170,7 @@ class ImagingBrowserIndex extends Component {
       {label: 'Entity Type', show: false, filter: {
         name: 'entityType',
         type: 'multiselect',
-        option: options.entityType,
+        options: options.entityType,
       }},
     ];
     /**

modules/examiner/jsx/examinerIndex.js

@@ -96,6 +96,7 @@ class Imaging_Uploader extends \NDB_Menu_Filter_Form
             'Visit_label' => 's.Visit_label',
             'IsPhantom'   => 'mu.IsPhantom',
         ];
+        $this->order_by     ="UploadDate DESC";
     }
      /**
       * Sets up the menu filter items for the imaging uploader

modules/imaging_browser/jsx/imagingBrowserIndex.js

@@ -371,6 +371,7 @@ class InstrumentQueryEngine implements \LORIS\Data\Query\QueryEngine
                         $candData[$dict->getName()] = [];
                     }
                     $sid = $loadedInstrument->getSessionID();
+
                     switch ($dict->fieldname) {
                     case 'Administration':
                     case 'Data_entry':
@@ -383,16 +384,39 @@ class InstrumentQueryEngine implements \LORIS\Data\Query\QueryEngine
                         ];
                         break;
                     default:
-                        $candData[$dict->getName()][$sid->__toString()] = [
-                            'VisitLabel' => $loadedInstrument->getVisitLabel(),
-                            'SessionID'  => $sid->__toString(),
-                            'value'      => $loadedInstrument
-                        ->getDictionaryValue($dict),
-                        ];
+                        if ($dict->getCardinality()->__toString() == "many") {
+                            $candData[$dict->getName()][$sid->__toString()] = [
+                                'keytype'    => $dict->getName() . " response",
+                                'VisitLabel' => $loadedInstrument->getVisitLabel(),
+                                'SessionID'  => $sid->__toString(),
+                                'values'     => [],
+                            ];
+                            $i = 1;
+
+                            // Line length work-arounds
+                            $candData =& $candData[$dict->getName()];
+                            $vals     =& $candData[$sid->__toString()]['values'];
+
+                            $values = explode(
+                                '{@}',
+                                $loadedInstrument->getDictionaryValue($dict)
+                            );
+                            foreach ($values as $value) {
+                                $vals["Response $i"] = $value;
+                                $i++;
+                            }
+                        } else {
+                            $candData[$dict->getName()][$sid->__toString()] = [
+                                'VisitLabel' => $loadedInstrument->getVisitLabel(),
+                                'SessionID'  => $sid->__toString(),
+                                'value'      =>
+                            $loadedInstrument->getDictionaryValue($dict),
+                            ];
+                        }
                     }
                 }
+                yield "$iCandID" => $candData;
             }
-            yield "$iCandID" => $candData;
         }
     }
 }

modules/imaging_uploader/php/imaging_uploader.class.inc

@@ -984,19 +984,23 @@ class Edit extends \NDB_Page implements ETagCalculator
     ) {
         $db      = $this->loris->getDatabaseConnection();
         $baseurl = \NDB_Factory::singleton()->settings()->getBaseURL();
+        $study   = \NDB_Factory::singleton()->config()->getSetting('title');
 
-        $title = $db->pSelectOne(
-            "SELECT title FROM issues
+        $emailItems = $db->pselectRow(
+            "SELECT `title`,`priority`,`status` FROM issues
             WHERE issueID=:issueID",
             ['issueID' => $issueID]
         );
 
         $msg_data            = [];
+        $msg_data['study']   = $study;
         $msg_data['url']     = $baseurl .
             "/issue_tracker/issue/" . $issueID;
         $msg_data['issueID'] = $issueID;
         $msg_data['currentUser'] = $user->getUsername();
-        $msg_data['title']       = $title;
+        $msg_data['title']       = $emailItems['title'] ?? null;
+        $msg_data['priority']    = $emailItems['priority'] ?? null;
+        $msg_data['status']      = $emailItems['status'] ?? null;
         $msg_data['comment']     = $values['comment'];
 
         if (isset($changed_assignee) && $new_assignee_tag == 'false') {

modules/instruments/php/instrumentqueryengine.class.inc

@@ -52,25 +52,25 @@ class MriUploadServerProcess extends AbstractServerProcess
     private $_sourceLocation;
 
     /**
-     * Root of the MRI files directory.
+     * The value of MRICodePath config setting.
      *
      * @var string
      */
     private $_mriCodePath;
 
     /**
-     * Path of the environment file (relative to $_mriCodePath).
+     * The value of MriConfigFile config setting.
      *
      * @var string
      */
-    private $_environmentFile;
+    private $_prodFile;
 
     /**
-     * Path of the prod file (relative to $_mriCodePath/dicom-archive/.loris-mri).
+     * The value of EnvironmentFile config setting.
      *
      * @var string
      */
-    private $_prodFile;
+    private $_environmentFile;
 
     /**
      * Builds a new MriUploadServerProcess
@@ -99,7 +99,7 @@ class MriUploadServerProcess extends AbstractServerProcess
         $config =& \NDB_Config::singleton();
         if (is_null($config)) {
             throw new \RuntimeException(
-                "Cannot construct MriUploadTask: unable to instantiate 
+                "Cannot construct MriUploadTask: unable to instantiate
                  configuration object"
             );
         }

modules/issue_tracker/php/edit.class.inc

@@ -72,14 +72,14 @@ class ServerProcessesMonitor
      * whatever is stored in the database for that process, the information
      * stored in the database is updated to reflect the current process state.
      *
-     * @param array  $idsToMonitor IDs of the server processes to monitor.
-     *                             If null, then the state of all the processes
-     *                             stored in the database is returned.
-     * @param string $userid       only the processes run by the user with name
-     *                             $userid are considered. If null, then the userid
-     *                             check is not performed.
-     * @param string $type         the type of server processes to retrieve. If null
-     *                             then all types are considered.
+     * @param array       $idsToMonitor IDs of the server processes to monitor.
+     *                                  If null, then the state of all the processes
+     *                                  stored in the database is returned.
+     * @param string|null $userid       Only the processes run by the user with name
+     *                                  $userid are considered. If null, then the
+     *                                  userid check is not performed.
+     * @param string|null $type         The type of server processes to retrieve. If
+     *                                  null then all types are considered.
      *
      * @return array (associative) of the current state of the processes.
      * @throws \DatabaseException if connection to the database cannot be
@@ -93,7 +93,7 @@ class ServerProcessesMonitor
         //------------------------------------------------------
         $db = $this->getDatabaseProvider()->getDatabase();
 
-        $query = "SELECT id, pid, type, userid, stdout_file, stderr_file, 
+        $query = "SELECT id, pid, type, userid, stdout_file, stderr_file,
                          exit_code_file, exit_code, start_time, end_time,
                          exit_text
                   FROM server_processes

modules/server_processes_manager/php/mriuploadserverprocess.class.inc

@@ -814,6 +814,7 @@ class Edit_User extends \NDB_Form
             'Sites',
             $siteOptions,
             [
+                'class'    => 'form-control input-sm resizable',
                 'multiple' => 'multiple',
                 'required' => true,
             ]
@@ -833,6 +834,7 @@ class Edit_User extends \NDB_Form
             'Projects',
             $projectOptions,
             [
+                'class'    => 'form-control input-sm resizable',
                 'multiple' => 'multiple',
                 'required' => true,
             ]

modules/server_processes_manager/php/serverprocessesmonitor.class.inc

@@ -14,7 +14,7 @@ const getPath = (p) => {
 
   if (
     pathParts[0] === 'modules' &&
-    fs.existsSync(path.join(__dirname, 'project', 'modules', pathParts[1]))
+    fs.existsSync(path.join(__dirname, 'project', ...pathParts))
   ) {
     return path.join('project', p);
   }