Merge pull request #1055 from griidc/release/6.10.0

Release/6.10.0
griidc · Nov 23, 2021 · 15b27a6 · 15b27a6
2 parents 20ff4f5 + 85ceecf
commit 15b27a6
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Showing 8 changed files with 43 additions and 55 deletions.
diff --git a/assets/static/js/dataset-submission.js b/assets/static/js/dataset-submission.js
@@ -180,6 +180,8 @@ $(function() {
         submitHandler: function(form) {
             formHash = $("#regForm").serialize();
             $("#regForm").prop("unsavedChanges", false);
+            $("#submitButton").button("disable");
+            pelagosUI.loadingSpinner.showSpinner();
             form.submit();
         },
     });

diff --git a/assets/static/js/datasetReview.js b/assets/static/js/datasetReview.js
@@ -88,10 +88,12 @@ $(document).ready(function(){
         },
         ignore: ".ignore,.prototype",
         submitHandler: function (form) {
+            $("#acceptDatasetBtn, #endReviewBtn, #requestRevisionsBtn").button("disable");
+            pelagosUI.loadingSpinner.showSpinner();
             form.submit();
         }
     });
-
+    
     // load qTip descriptions
     $("img.info").not("#contact-prototype img.info").each(function() {
         $(this).qtip({

diff --git a/src/Controller/UI/DatasetReviewController.php b/src/Controller/UI/DatasetReviewController.php
@@ -436,7 +436,8 @@ private function createEntity(Entity $entity)
      */
     public function postAction(Request $request, int $id = null, MessageBusInterface $messageBus)
     {
-        $datasetSubmission = $this->entityHandler->get(DatasetSubmission::class, $id);
+        $entityManager = $this->getDoctrine()->getManager();
+        $datasetSubmission = $entityManager->getRepository(DatasetSubmission::class)->find($id);
 
         if (!$this->isGranted('IS_AUTHENTICATED_FULLY')) {
             return $this->redirect(
@@ -475,35 +476,9 @@ public function postAction(Request $request, int $id = null, MessageBusInterface
             if ($fileset instanceof Fileset) {
                 foreach ($fileset->getNewFiles() as $file) {
                     $file->setStatus(File::FILE_IN_QUEUE);
-                    $this->entityHandler->update($file);
                 }
             }
 
-            $this->entityHandler->update($datasetSubmission->getDatasetSubmissionReview());
-            $this->entityHandler->update($datasetSubmission);
-
-            foreach ($datasetSubmission->getDistributionPoints() as $distributionPoint) {
-                $this->entityHandler->update($distributionPoint);
-            }
-
-            foreach ($datasetSubmission->getDatasetContacts() as $datasetContact) {
-                $this->entityHandler->update($datasetContact);
-            }
-
-            foreach ($datasetSubmission->getMetadataContacts() as $metadataContact) {
-                $this->entityHandler->update($metadataContact);
-            }
-
-            foreach ($datasetSubmission->getDatasetLinks() as $datasetLink) {
-                $this->entityHandler->update($datasetLink);
-            }
-
-            // update MDAPP logs after action is executed.
-            $this->entityEventDispatcher->dispatch(
-                $datasetSubmission,
-                $eventName
-            );
-
             $reviewedBy = $datasetSubmission->getDatasetSubmissionReview()->getReviewEndedBy()->getFirstName();
 
             //when request revisions is clicked, do not display the changes made in review for the dataset-submission
@@ -532,10 +507,18 @@ public function postAction(Request $request, int $id = null, MessageBusInterface
                     }
                     $datasetSubmission = $datasetSubmission->getDataset()->getDatasetSubmission();
                     $datasetSubmission->setFileset($newFileset);
-                    $this->entityHandler->update($datasetSubmission);
+                    $entityManager->persist($newFileset);
                 }
             }
 
+            $entityManager->flush();
+
+            // update MDAPP logs after action is executed.
+            $this->entityEventDispatcher->dispatch(
+                $datasetSubmission,
+                $eventName
+            );
+
             $datasetSubmissionFilerMessage = new DatasetSubmissionFiler($datasetSubmission->getId());
             $messageBus->dispatch($datasetSubmissionFilerMessage);
 

diff --git a/src/Controller/UI/DatasetSubmissionController.php b/src/Controller/UI/DatasetSubmissionController.php
@@ -207,7 +207,8 @@ public function defaultAction(Request $request, EntityManagerInterface $entityMa
      */
     public function postAction(Request $request, int $id = null, MessageBusInterface $messageBus)
     {
-        $datasetSubmission = $this->entityHandler->get(DatasetSubmission::class, $id);
+        $entityManager = $this->getDoctrine()->getManager();
+        $datasetSubmission = $entityManager->getRepository(DatasetSubmission::class)->find($id);
 
         if (!$this->isGranted('IS_AUTHENTICATED_FULLY')) {
             return $this->redirect(
@@ -248,24 +249,10 @@ public function postAction(Request $request, int $id = null, MessageBusInterface
             if ($fileset instanceof Fileset) {
                 foreach ($fileset->getNewFiles() as $file) {
                     $file->setStatus(File::FILE_IN_QUEUE);
-                    $this->entityHandler->update($file);
                 }
             }
 
-            $this->entityHandler->update($datasetSubmission);
-
-            foreach ($datasetSubmission->getDistributionPoints() as $distributionPoint) {
-                $this->entityHandler->update($distributionPoint);
-            }
-            foreach ($datasetSubmission->getDatasetContacts() as $datasetContact) {
-                $this->entityHandler->update($datasetContact);
-            }
-            foreach ($datasetSubmission->getMetadataContacts() as $metadataContact) {
-                $this->entityHandler->update($metadataContact);
-            }
-            foreach ($datasetSubmission->getDatasetLinks() as $datasetLink) {
-                $this->entityHandler->update($datasetLink);
-            }
+            $entityManager->flush();
 
             $this->entityEventDispatcher->dispatch(
                 $datasetSubmission,

diff --git a/src/Entity/Fileset.php b/src/Entity/Fileset.php
@@ -393,4 +393,16 @@ public function getNumberOfFiles(): int
     {
         return count($this->getProcessedAndNewFiles());
     }
+
+    /**
+     * Returns the number of errored files in the fileset.
+     *
+     * @return integer
+     */
+    public function getNumberOfErroredFiles(): int
+    {
+        return count($this->files->filter(function (File $file) {
+            return $file->getStatus() === File::FILE_ERROR;
+        }));
+    }
 }
diff --git a/src/MessageHandler/ProcessFileHandler.php b/src/MessageHandler/ProcessFileHandler.php
@@ -107,12 +107,16 @@ public function __invoke(ProcessFile $processFile)
         );
 
         $filePath = $file->getPhysicalFilePath();
-        $fileStream = fopen($filePath, 'r');
-        try {
+        @$fileStream = fopen($filePath, 'r');
+
+        if ($fileStream === false) {
+            $file->setDescription("Unreadable Queued File:" . error_get_last()['message']);
+            $file->setStatus(File::FILE_ERROR);
+            $this->entityManager->flush();
+            return;
+        } else {
             $fileHash = StreamInfo::calculateHash(array('fileStream' => $fileStream));
             $file->setFileSha256Hash($fileHash);
-        } catch (\Exception $e) {
-            $this->logger->warning(sprintf('Unable to hash file. Message: %s', $e->getMessage()));
         }
 
         try {
@@ -123,11 +127,12 @@ public function __invoke(ProcessFile $processFile)
             $file->setPhysicalFilePath($newFileDestination);
         } catch (\Exception $exception) {
             $this->logger->error(sprintf('Unable to add file to datastore. Message: "%s"', $exception->getMessage()), $loggingContext);
+            $file->setDescription("Error writing to store:" . $exception->getMessage());
             $file->setStatus(File::FILE_ERROR);
             $this->entityManager->flush();
             return;
         }
-        
+
         try {
             unlink($filePath);
             rmdir(dirname($filePath));

diff --git a/templates/DatasetMonitoring/projects.html.twig b/templates/DatasetMonitoring/projects.html.twig
@@ -3,11 +3,6 @@
     {% if instName | default %}
         <span class="header-inst-name">({{instName}})</span>
     {% endif %}
-    {% if not pdf | default %}
-        <span class="awesome-icon awesome-icon-pdf" data-url="/html2pdf?url={{ url(app.request.get('_route'), {'id': id, 'renderer': 'html2pdf'}) }}&format=Letter&orientation=landscape&margin=1cm&download=true&filename={{pdfFilename}}">
-            <i class="fas fa-file-pdf"  style="color: red"></i>
-        </span>
-    {% endif %}
 </div>
 {% for ResearchGroup in researchGroups %}
 <div class="project" project="{{ResearchGroup.id}}">

diff --git a/templates/Email/data-repository-managers.dataset-files-processed.email.twig b/templates/Email/data-repository-managers.dataset-files-processed.email.twig
@@ -12,6 +12,7 @@
      {% if datasetSubmission.fileset is defined and datasetSubmission.fileset is not null %}
         Number of Files: {{ datasetSubmission.fileset.numberOfFiles }} <br>
         Total File Size:  {{ datasetSubmission.fileset.fileSize|formatBytes }}<br>
+        Files with error: {{ datasetSubmission.fileset.numberOfErroredFiles }}<br>
      {% else %}
          N/A<br>
      {% endif %}
@@ -44,6 +45,7 @@
     {% if datasetSubmission.fileset is defined and datasetSubmission.fileset is not null %}
         Number of Files: {{ datasetSubmission.fileset.numberOfFiles }}
         Total File Size:  {{ datasetSubmission.fileset.fileSize|formatBytes }}
+        Files with error: {{ datasetSubmission.fileset.numberOfErroredFiles }}
     {% else %}
         N/A
     {% endif %}