Merge pull request #1542 from griidc/release/6.56.0

Release/6.56.0
griidc · Mar 5, 2024 · 1602331 · 1602331
2 parents a4a4887 + 07352bc
commit 1602331
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Showing 10 changed files with 124 additions and 57 deletions.
diff --git a/assets/static/js/datasetReview.js b/assets/static/js/datasetReview.js
@@ -427,7 +427,7 @@ $(document).ready(function(){
     });
     buildKeywordLists();
 
-    $("form :input").not("input.keywordinput").on('keydown', function(event) {
+    $("form :input").not("input.keywordinput,textarea").on('keydown', function(event) {
         if (event.which == 13) {
             return false;
         }

diff --git a/assets/static/js/submissionKeywords.js b/assets/static/js/submissionKeywords.js
@@ -23,6 +23,8 @@ $(() => {
       gcmdKeywords = JSON.parse(xhr.responseText);
     }
 
+    const toast = $('#toast').dxToast({}).dxToast('instance');
+
     const treeList = $('#treelist').dxTreeView({
       items: anzsrcKeywords,
       dataStructure: 'plain',
@@ -140,6 +142,17 @@ $(() => {
       searchPanel: { visible: true },
     }).dxTreeView('instance');
 
+    function copyToClipboard(text)
+    {
+      navigator.clipboard.writeText(text);
+      toast.option({
+        message: "Keyword copied to clipboard!",
+        type: "info",
+        displayTime: 3000,
+      });
+      toast.show();
+    }
+
     const keywordList = $('#selectedList').dxList({
       dataSource: selectedAnzsrcKeywords,
       allowItemDeleting: false,
@@ -157,6 +170,11 @@ $(() => {
           keywordList.reload();
           keywordList.repaint();
         });
+        $(item.element).find('.dx-tag-remove-button[item=' + item.itemData.id + ']')
+          .parents('.dx-list-item')
+          .on('dblclick', (event) => {
+            copyToClipboard(item.itemData.displayPath);
+          });
       },
       onItemDeleted(item) {
         var keywordListArray = [];
@@ -191,6 +209,11 @@ $(() => {
           keywordListGcmd.reload();
           keywordListGcmd.repaint();
         });
+        $(item.element).find('.dx-tag-remove-button[item=' + item.itemData.id + ']')
+          .parents('.dx-list-item')
+          .on('dblclick', (event) => {
+            copyToClipboard(item.itemData.displayPath);
+          });
       },
       onItemDeleted(item) {
         var keywordListArray = [];

diff --git a/src/Command/GetGoMRIStatisticsCommand.php b/src/Command/GetGoMRIStatisticsCommand.php
@@ -3,53 +3,47 @@
 namespace App\Command;
 
 use App\Entity\Dataset;
-use App\Entity\DIF;
 use App\Entity\DatasetSubmission;
+use App\Entity\DIF;
+use App\Repository\LogActionItemRepository;
 use Doctrine\ORM\EntityManagerInterface;
 use Symfony\Component\Console\Command\Command;
 use Symfony\Component\Console\Input\InputArgument;
 use Symfony\Component\Console\Input\InputInterface;
-use Symfony\Component\Console\Input\InputOption;
 use Symfony\Component\Console\Output\OutputInterface;
 use Symfony\Component\Console\Style\SymfonyStyle;
-use Symfony\Component\Messenger\MessageBusInterface;
-use DateTime;
 
 class GetGoMRIStatisticsCommand extends Command
 {
     protected static $defaultName = 'pelagos:get-gomri-statistics';
     protected static $defaultDescription = 'Produce GoMRI report artifacts.';
 
-    /**
-     * A Doctrine ORM EntityManager instance.
-     *
-     * @var EntityManagerInterface $entityManager
-     */
-    protected $entityManager;
-
     /**
      * Class constructor for dependency injection.
-     *
-     * @param EntityManagerInterface $entityManager A Doctrine EntityManager.
      */
     public function __construct(
-        EntityManagerInterface $entityManager,
+        private EntityManagerInterface $entityManager,
+        private LogActionItemRepository $logActionItemRepository,
     ) {
-        $this->entityManager = $entityManager;
         parent::__construct();
     }
 
     protected function configure(): void
     {
         $this
             ->setDescription(self::$defaultDescription)
+            ->addArgument('start', InputArgument::OPTIONAL, 'Starting date for DL count')
+            ->addArgument('end', InputArgument::OPTIONAL, 'Ending date for DL count')
         ;
     }
 
     protected function execute(InputInterface $input, OutputInterface $output): int
     {
         $io = new SymfonyStyle($input, $output);
 
+        $startEpoch = strtotime($input->getArgument('start'));
+        $endEpoch = strtotime($input->getArgument('end'));
+
         $datasets = $this->entityManager->getRepository(Dataset::class)->findAll();
 
         $datasetCount = 0;
@@ -61,21 +55,20 @@ protected function execute(InputInterface $input, OutputInterface $output): int
         $totalDatasetSubmittedSince2021Count = 0;
 
         foreach ($datasets as $dataset) {
-            /** @var Dataset $dataset */
-            if ($dataset->getDif()->getStatus() === DIF::STATUS_UNSUBMITTED) {
+            if (DIF::STATUS_UNSUBMITTED === $dataset->getDif()->getStatus()) {
                 continue;
             }
-            $datasetCount++;
+            ++$datasetCount;
             $udi = $dataset->getUdi();
             $datasetSubmission = $dataset->getDatasetSubmission();
-            if ($dataset->getResearchGroup()->getFundingCycle()->getFundingOrganization()->getShortName() === 'GoMRI') {
-                $gomriDatasetCount++;
+            if ('GoMRI' === $dataset->getResearchGroup()->getFundingCycle()->getFundingOrganization()->getShortName()) {
+                ++$gomriDatasetCount;
                 if ($datasetSubmission instanceof DatasetSubmission) {
-                    if ($datasetSubmission->getSubmissionTimeStamp()->format('U') >= DateTime::createFromFormat('d/m/Y', '01/01/2021', new \DateTimeZone('America/Chicago'))->format('U')) {
-                        $totalGomriDatasetSubmittedSince2021Count++;
+                    if ($datasetSubmission->getSubmissionTimeStamp()->format('U') >= \DateTime::createFromFormat('d/m/Y', '01/01/2021', new \DateTimeZone('America/Chicago'))->format('U')) {
+                        ++$totalGomriDatasetSubmittedSince2021Count;
                     }
                     if ($datasetSubmission->isDatasetFileInColdStorage()) {
-                        $gomriDatasetColdStorageCount++;
+                        ++$gomriDatasetColdStorageCount;
                         $gomriColdStorageDatasetTotalSize += $datasetSubmission->getColdStorageTotalUnpackedSize() ?? 0;
                     } else {
                         $gomriDatasetTotalSize += $datasetSubmission->getFileset()?->getFileSize() ?? 0;
@@ -84,19 +77,40 @@ protected function execute(InputInterface $input, OutputInterface $output): int
             }
 
             if ($datasetSubmission instanceof DatasetSubmission) {
-                if ($datasetSubmission->getSubmissionTimeStamp()->format('U') >= DateTime::createFromFormat('d/m/Y', '01/01/2021', new \DateTimeZone('America/Chicago'))->format('U')) {
-                    $totalDatasetSubmittedSince2021Count++;
+                if ($datasetSubmission->getSubmissionTimeStamp()->format('U') >= \DateTime::createFromFormat('d/m/Y', '01/01/2021', new \DateTimeZone('America/Chicago'))->format('U')) {
+                    ++$totalDatasetSubmittedSince2021Count;
                 }
             }
         }
 
         $io->writeln("Total GRIIDC Dataset Count: $datasetCount");
         $io->writeln("Total number of GoMRI Datasets: $gomriDatasetCount");
-        $io->writeln("Total Size of GoMRI Datasets: " . round(($gomriDatasetTotalSize + $gomriColdStorageDatasetTotalSize) / 1000000000000, 1) . ' TB');
+        $io->writeln('Total Size of GoMRI Datasets: ' . round(($gomriDatasetTotalSize + $gomriColdStorageDatasetTotalSize) / 1000000000000, 1) . ' TB');
         $io->writeln("Number of GoMRI Datasets in cold storage: $gomriDatasetColdStorageCount");
-        $io->writeln("Total size of GoMRI Datasets in cold storage: " . round($gomriColdStorageDatasetTotalSize / 1000000000000, 1) . ' TB');
-        $io->writeln("Total number of GoMRI datasets submitted since 2021-01-01 until current date " . $totalGomriDatasetSubmittedSince2021Count);
-        $io->writeln("Total number of datasets (all data including GoMRI) submitted since 2021-01-01 until current date " . $totalDatasetSubmittedSince2021Count);
+        $io->writeln('Total size of GoMRI Datasets in cold storage: ' . round($gomriColdStorageDatasetTotalSize / 1000000000000, 1) . ' TB');
+        $io->writeln('Total number of GoMRI datasets submitted since 2021-01-01 until current date ' . $totalGomriDatasetSubmittedSince2021Count);
+        $io->writeln('Total number of datasets (all data including GoMRI) submitted since 2021-01-01 until current date ' . $totalDatasetSubmittedSince2021Count);
+
+        if (false != $startEpoch and false != $endEpoch) { // false on strtotime fail
+            $startDateTime = new \DateTime();
+            // will assume DST-aware central time if not specified.
+            $startDateTime->setTimezone(new \DateTimeZone('America/Chicago'));
+            $startDateTime->setTimestamp($startEpoch);
+            $dbFormatStartTime = $startDateTime->format('Y-m-d H:i:sO');
+
+            $endDateTime = new \DateTime();
+            $endDateTime->setTimezone(new \DateTimeZone('America/Chicago'));
+            $endDateTime->setTimestamp($endEpoch);
+            $dbFormatEndTime = $endDateTime->format('Y-m-d H:i:sO');
+
+            $io->writeln("Total GoMRI Downloads from $dbFormatStartTime to $dbFormatEndTime: "
+                . $this->logActionItemRepository->countDownloads(
+                    $startDateTime,
+                    $endDateTime
+                ));
+        } else {
+            $io->writeln('Total GoMRI Downloads: ' . $this->logActionItemRepository->countDownloads());
+        }
 
         return 0;
     }

diff --git a/src/Entity/Password.php b/src/Entity/Password.php
@@ -242,4 +242,12 @@ public function getHashAlgorithm()
     {
         return $this->passwordHashAlgorithm;
     }
+
+    /**
+     * Return base64 encoded salted password hash.
+     */
+    public function getSSHAPassword(): string
+    {
+        return "{SSHA}" . base64_encode(pack('H*', bin2hex($this->getPasswordHash()) . bin2hex($this->getSalt())));
+    }
 }
diff --git a/src/Repository/LogActionItemRepository.php b/src/Repository/LogActionItemRepository.php
@@ -2,12 +2,12 @@
 
 namespace App\Repository;
 
-use Doctrine\Bundle\DoctrineBundle\Repository\ServiceEntityRepository;
-use Doctrine\Persistence\ManagerRegistry;
-use Doctrine\ORM\Query;
 use App\Entity\Dataset;
 use App\Entity\LogActionItem;
 use App\Util\FundingOrgFilter;
+use Doctrine\Bundle\DoctrineBundle\Repository\ServiceEntityRepository;
+use Doctrine\ORM\Query;
+use Doctrine\Persistence\ManagerRegistry;
 
 /**
  * LogActionItem Entity Repository class.
@@ -23,9 +23,6 @@ class LogActionItemRepository extends ServiceEntityRepository
 
     /**
      * Constructor.
-     *
-     * @param ManagerRegistry  $registry         The Registry Manager.
-     * @param FundingOrgFilter $fundingOrgFilter Utility to filter by funding organization.
      */
     public function __construct(ManagerRegistry $registry, FundingOrgFilter $fundingOrgFilter)
     {
@@ -35,20 +32,31 @@ public function __construct(ManagerRegistry $registry, FundingOrgFilter $funding
     }
 
     /**
-     * Sum of all dataset file sizes.
+     * Count of downloads, optional date range and also filter aware.
      *
-     * @return integer Size of data in bytes.
+     * @return int the count of the datasets downloaded, per FAIR guidelines
      */
-    public function countDownloads(): int
+    public function countDownloads(\DateTime $start = null, \DateTime $stop = null): int
     {
         $qb = $this->createQueryBuilder('log')
-            ->select('log.creationTimeStamp, log.subjectEntityId')
-            ->where('log.subjectEntityName = ?1')
-            ->andWhere('log.actionName = ?2')
-            ->orderBy('log.subjectEntityId', 'ASC')
-            ->addOrderBy('log.creationTimeStamp', 'ASC')
-            ->setParameter(1, 'Pelagos\Entity\Dataset')
-            ->setParameter(2, 'File Download');
+        ->select('log.creationTimeStamp, log.subjectEntityId')
+        ->where('log.subjectEntityName = :entityName')
+        ->andWhere('log.actionName = :actionName')
+        ->orderBy('log.subjectEntityId', 'ASC')
+        ->addOrderBy('log.creationTimeStamp', 'ASC')
+        ->setParameter('entityName', 'Pelagos\Entity\Dataset')
+        ->setParameter('actionName', 'File Download');
+
+        if ($start instanceof \DateTime and $stop instanceof \DateTime) {
+            $dbFormatStartTime = $start->format('Y-m-d H:i:sO');
+            $dbFormatEndTime = $stop->format('Y-m-d H:i:sO');
+
+            $qb
+            ->andWhere('log.creationTimeStamp >= :start')
+            ->andWhere('log.creationTimeStamp <= :stop')
+            ->setParameter('start', $dbFormatStartTime)
+            ->setParameter('stop', $dbFormatEndTime);
+        }
 
         if ($this->fundingOrgFilter->isActive()) {
             $researchGroupIds = $this->fundingOrgFilter->getResearchGroupsIdArray();
@@ -72,9 +80,9 @@ public function countDownloads(): int
             $dateTime = $timeStamp['creationTimeStamp'];
             $epochTime = (int) $dateTime->format('U');
 
-            if ($key === array_key_first($downloads) or ($epochTime - $currentTimeStamp) > 30 or $currentId <> $id) {
+            if ($key === array_key_first($downloads) or ($epochTime - $currentTimeStamp) > 30 or $currentId != $id) {
                 $currentTimeStamp = $epochTime;
-                $downloadCount++;
+                ++$downloadCount;
             }
 
             $currentId = $id;

diff --git a/src/Util/Ldap/Ldap.php b/src/Util/Ldap/Ldap.php
@@ -69,12 +69,17 @@ public function addPerson(Person $person)
      *
      * @return void
      */
-    public function updatePerson(Person $person)
+    public function updatePerson(Person $person, bool $recreate = true)
     {
         $uidNumber = $person->getAccount()->getUidNumber();
         if ($this->checkIfUidNumberAvailable($uidNumber, $person->getAccount()->getUserName())) {
             $ldapPerson = $this->buildLdapPerson($person);
-            $this->ldapClient->modify($ldapPerson['dn'], $ldapPerson['entry']);
+            if ($recreate) {
+                $this->ldapClient->delete($ldapPerson['dn']);
+                $this->ldapClient->add($ldapPerson['dn'], $ldapPerson['entry']);
+            } else {
+                $this->ldapClient->modify($ldapPerson['dn'], $ldapPerson['entry']);
+            }
         } else {
             throw new UidNumberInUseInLDAPException("This UID number ($uidNumber) is already in use in LDAP .");
         }
@@ -117,9 +122,7 @@ protected function buildLdapPerson(Person $person)
             ),
         );
 
-        if ($person->getAccount()->getPasswordEntity()->getClearTextPassword() != null) {
-            $ldapPerson['entry']['userPassword'] = $person->getAccount()->getPasswordEntity()->getClearTextPassword();
-        }
+        $ldapPerson['entry']['userPassword'] = $person->getAccount()->getPasswordEntity()->getSSHAPassword();
 
         $accessor = PropertyAccess::createPropertyAccessor();
 

diff --git a/src/Util/POSIXifyAccount.php b/src/Util/POSIXifyAccount.php
@@ -103,7 +103,6 @@ public function POSIXifyAccount(Account $account)
 
         // Update LDAP with this modified Account (via Person).
         $this->ldap->updatePerson($account->getPerson());
-
         // Persist changes.
         $this->entityHandler->update($account);
     }

diff --git a/templates/Dataland/v2/collection-period-card.html.twig b/templates/Dataland/v2/collection-period-card.html.twig
@@ -47,10 +47,10 @@
                 </div>
                 <div class="card-body">
                     <div class="card-body">
-                        <p class="card-text text-dark whitespace-nowrap text-nowrap">
-                            {{ begin }}
+                        <p class="card-text text-dark text-wrap">
+                            <span class="whitespace-nowrap">{{ begin }}</span>
                             to
-                            {{ end }}
+                            <span  class="whitespace-nowrap">{{ end }}</span>
                         </p>
                     </div>
                 </div>

diff --git a/templates/DatasetSubmission/standard-keywords.html.twig b/templates/DatasetSubmission/standard-keywords.html.twig
@@ -1,3 +1,5 @@
+    <div id="toast"></div>
+
     <div id="keyword-items">
         {% set keywords = [] %}
         {% for keyword in form.keywords %}

diff --git a/tests/unit/Entity/PasswordTest.php b/tests/unit/Entity/PasswordTest.php
@@ -136,6 +136,16 @@ public function testGetHash()
         $this->assertNotNull($this->password->getPasswordHash());
     }
 
+    /**
+     * Test that the SSHA hash can be returned.
+     *
+     * @return void
+     */
+    public function testGetSSHAHash()
+    {
+        $this->assertNotNull($this->password->getSSHAPassword());
+    }
+
     /**
      * Test that the hash alrorithm can be retrieved from the Password entity.
      *