[api/lib] instrument validation

.github/workflows/loristest.yml

@@ -22,6 +22,7 @@ jobs:
       # (see https://github.com/actions/runner-images/blob/releases/ubuntu22/20230305/images/linux/Ubuntu2204-Readme.md)
       # that updated the list of installed apt packages/apt repositories. That issue may disappear in future Ubuntu images.
         run: |
+          sudo apt-get update
           sudo apt install -y imagemagick-6-common libmagickcore-6.q16-7t64 libmagickwand-6.q16-7t64 \
              libprotobuf-dev libprotobuf32t64 libprotoc32t64 protobuf-compiler          
           cd modules/electrophysiology_browser/jsx/react-series-data-viewer/
@@ -268,6 +269,7 @@ jobs:
       # (see https://github.com/actions/runner-images/blob/releases/ubuntu22/20230305/images/linux/Ubuntu2204-Readme.md)
       # that updated the list of installed apt packages/apt repositories. That issue may disappear in future Ubuntu images.
       run: |
+        sudo apt-get update
         sudo apt install -y imagemagick-6-common libmagickcore-6.q16-7t64 libmagickwand-6.q16-7t64 \
              libprotobuf-dev libprotobuf32t64 libprotoc32t64 protobuf-compiler
         cd modules/electrophysiology_browser/jsx/react-series-data-viewer/

htdocs/index.php

@@ -29,6 +29,21 @@
 // See: https://www.php.net/manual/en/session.configuration.php#ini.session.use-strict-mode
 ini_set('session.use_strict_mode', '1');
 
+// TODO: Remove this code once PHP 8.4 becomes the minimal PHP version in LORIS.
+if (version_compare(PHP_VERSION, '8.4', '<')) {
+    // @phan-file-suppress PhanRedefineFunctionInternal
+
+    // phpcs:ignore
+    function array_all(array $array, callable $callable): bool {
+        foreach ($array as $key => $value) {
+            if (!$callable($value, $key)) {
+                return false;
+            }
+        }
+        return true;
+    }
+}
+
 // FIXME: The code in NDB_Client should mostly be replaced by middleware.
 $client = new \NDB_Client;
 $client->initialize();

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

@@ -156,27 +156,19 @@ class Flags extends Endpoint implements \LORIS\Middleware\ETagCalculator
         $this->_instrumentStatus = new \NDB_BVL_InstrumentStatus($loris);
         $this->_instrumentStatus->select($this->_instrument->commentID);
 
-        if (!$this->_instrument->determineDataEntryAllowed()) {
-            return new \LORIS\Http\Response\JSON\Forbidden(
-                'Can not update instruments that are flagged as complete.'
-            );
-        }
-
         $data = json_decode((string) $request->getBody(), true);
-
         if (!is_array($data)) {
             return new \LORIS\Http\Response\JSON\BadRequest(
                 'Invalid request'
             );
         }
-        if (!$this->_instrument->validate($data)) {
-            return new \LORIS\Http\Response\JSON\Forbidden(
-                'Could not update.'
+        if (!array_key_exists('Flags', $data)) {
+            return new \LORIS\Http\Response\JSON\BadRequest(
+                "Invalid request. 'Flags' missing."
             );
         }
 
         try {
-
             $requiredfields = [
                 'Data_entry',
                 'Administration',
@@ -229,22 +221,15 @@ class Flags extends Endpoint implements \LORIS\Middleware\ETagCalculator
         $this->_instrumentStatus = new \NDB_BVL_InstrumentStatus($loris);
         $this->_instrumentStatus->select($this->_instrument->commentID);
 
-        if (!$this->_instrument->determineDataEntryAllowed()) {
-            return new \LORIS\Http\Response\JSON\Forbidden(
-                'Can not update instruments that are flagged as complete.'
-            );
-        }
-
         $data = json_decode((string) $request->getBody(), true);
         if (!is_array($data)) {
             return new \LORIS\Http\Response\JSON\BadRequest(
                 'Invalid request'
             );
         }
-
-        if (!$this->_instrument->validate($data)) {
-            return new \LORIS\Http\Response\JSON\Forbidden(
-                'Could not update.'
+        if (!array_key_exists('Flags', $data)) {
+            return new \LORIS\Http\Response\JSON\BadRequest(
+                "Invalid request. 'Flags' missing."
             );
         }
 

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

@@ -170,41 +170,7 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
      */
     private function _handlePUT(ServerRequestInterface $request) : ResponseInterface
     {
-        if (!$this->_instrument->determineDataEntryAllowed()) {
-            return new \LORIS\Http\Response\JSON\Forbidden(
-                'Can not update instruments that are flagged as complete.'
-            );
-        }
-
-        $data = json_decode((string) $request->getBody(), true);
-        if (!is_array($data)) {
-            return new \LORIS\Http\Response\JSON\BadRequest(
-                'Invalid request'
-            );
-        }
-
-        if (!$this->_instrument->validate($data)) {
-            return new \LORIS\Http\Response\JSON\Forbidden(
-                'Could not update.'
-            );
-        }
-
-        try {
-            $this->_instrument->clearInstrument();
-            $version = $request->getAttribute('LORIS-API-Version');
-            if ($version == 'v0.0.3') {
-                $instrumentname = $this->_instrument->testName;
-                $this->_instrument->_saveValues($data[$instrumentname]);
-            } else {
-                $this->_instrument->_saveValues($data['Data']);
-            }
-            $this->_instrument->score();
-            $this->_instrument->updateRequiredElementsCompletedFlag();
-        } catch (\Throwable $e) {
-            error_log($e->getMessage());
-            return new \LORIS\Http\Response\JSON\InternalServerError();
-        }
-        return (new \LORIS\Http\Response\JSON\NoContent());
+        return $this->_handlePATCHAndPUT($request);
     }
 
     /**
@@ -217,40 +183,86 @@ class Instrument extends Endpoint implements \LORIS\Middleware\ETagCalculator
      */
     private function _handlePATCH(ServerRequestInterface $request): ResponseInterface
     {
+        return $this->_handlePATCHAndPUT($request);
+    }
+
+    /**
+     * Handles a PUT and PATCH request.
+     * Mainly serves as a quick PATCH/PUT selection to validate all (PUT) or
+     * part (PATCH) of the sent payload.
+     *
+     * @param ServerRequestInterface $request The incoming PSR7 request
+     *
+     * @return ResponseInterface The outgoing PSR7 response
+     */
+    private function _handlePATCHAndPUT(
+        ServerRequestInterface $request
+    ): ResponseInterface {
+        $requestType = $request->getMethod();
+        if ($requestType !== "PATCH" && $requestType !== "PUT") {
+            return new \LORIS\Http\Response\JSON\BadRequest(
+                'Invalid request'
+            );
+        }
+        $isRequestPUT = $requestType === "PUT";
+
+        // data entry allowed?
         if (!$this->_instrument->determineDataEntryAllowed()) {
             return new \LORIS\Http\Response\JSON\Forbidden(
                 'Can not update instruments that are flagged as complete.'
             );
         }
 
+        // get payload
         $data = json_decode((string) $request->getBody(), true);
         if (!is_array($data)) {
             return new \LORIS\Http\Response\JSON\BadRequest(
                 'Invalid request'
             );
         }
 
-        if (!$this->_instrument->validate($data)) {
+        // validate given data against the instrument
+        $instrumentName = $this->_instrument->testName;
+        try {
+            $version = $request->getAttribute('LORIS-API-Version');
+
+            // extract data according to LORIS API version
+            $instrumentData = $version == 'v0.0.3'
+                ? ($data[$instrumentName] ?? [])
+                : ($data['Data'] ?? []);
+
+            // validate
+            $this->_instrument->validate(
+                $instrumentData,
+                $isRequestPUT
+            );
+        } catch (\LorisException $th) {
+            return new \LORIS\Http\Response\JSON\BadRequest(
+                "Could not update. {$th->getMessage()}"
+            );
+        } catch (\Throwable $th) {
+            error_log($th->getMessage());
             return new \LORIS\Http\Response\JSON\Forbidden(
-                'Could not update.'
+                "Could not update."
             );
         }
 
+        // update values
         try {
-            $version = $request->getAttribute('LORIS-API-Version');
-            if ($version == 'v0.0.3') {
-                $instrumentname = $this->_instrument->testName;
-                $this->_instrument->_saveValues($data[$instrumentname]);
-            } else {
-                $this->_instrument->_saveValues($data['Data']);
+            // only clear if PUT
+            if ($isRequestPUT) {
+                $this->_instrument->clearInstrument();
             }
+
+            // save/score data
+            $this->_instrument->_saveValues($instrumentData);
             $this->_instrument->score();
             $this->_instrument->updateRequiredElementsCompletedFlag();
         } catch (\Throwable $e) {
             error_log($e->getMessage());
             return new \LORIS\Http\Response\JSON\InternalServerError();
         }
-        return (new \LORIS\Http\Response\JSON\NoContent());
+        return new \LORIS\Http\Response\JSON\NoContent();
     }
 
     /**