Feature/codecheck status

CodecheckPlugin.php

@@ -115,15 +115,18 @@ public function validatePublicationHook(string $hookName, array $args): bool
 
     public function addCodecheckStatusLocalizations($hookName, $args) {
         $templateMgr = $args[0];
+
+        $localeKeys = array_combine(
+            Constants::CODECHECK_STATUSES,
+            array_map(fn($status) => __($status), Constants::CODECHECK_STATUSES)
+        );
+
+        $localeKeys[Constants::CODECHECK_STATUS_PENDING] = __(Constants::CODECHECK_STATUS_PENDING);
+
         $templateMgr->addJavaScript(
             'codecheck-locale-status',
             'pkp.localeKeys = pkp.localeKeys || {};' .
-            'Object.assign(pkp.localeKeys, ' . json_encode(
-                array_combine(
-                    Constants::CODECHECK_STATUSES,
-                    array_map(fn($status) => __($status), Constants::CODECHECK_STATUSES)
-                )
-            ) . ');',
+            'Object.assign(pkp.localeKeys, ' . json_encode($localeKeys) . ');',
             ['inline' => true, 'contexts' => ['backend']]
         );
         return false;

api/v1/CodecheckApiHandler.php

@@ -611,14 +611,16 @@ private function reserveIdentifierWithApi(
         array $repositories
     ): array
     {
+        $updateInformation = $this->plugin->getSetting($this->request->getContext()->getId(), Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_FIELDS);
         // Add the new issue to the CODECHECK GtiHub Register
         $issue = $codecheckGithubRegisterApiClient->addIssue(
             $identifier,
             $issueLabels,
             $articleTitle,
             $authorString,
             $codecheckers,
-            $repositories
+            $repositories,
+            $updateInformation
         );
 
         return $issue;
@@ -640,8 +642,9 @@ private function reserveIdentifierWithNewIssueUrl(
         array $repositories
     ): string
     {
-        $journalName = $this->request->getContext()?->getLocalizedName() ?? 'Unknwon Journal';
-
+        $context = $this->request->getContext();
+        $journalName = $context?->getLocalizedName() ?? 'Unknwon Journal';
+        $updateInformation = $this->plugin->getSetting($context->getId(), Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_FIELDS);
         $codecheckIssue = new CodecheckGithubRegisterIssue(
             $githubRegisterOrganization,
             $githubRegisterRepository,
@@ -652,7 +655,8 @@ private function reserveIdentifierWithNewIssueUrl(
             $authorString,
             $this->codecheckMetadataHandler->getSubmissionId(),
             $codecheckers,
-            $repositories
+            $repositories,
+            $updateInformation
         );
 
         return $codecheckIssue->getNewIssueUrl();
@@ -972,15 +976,6 @@ public function getCurrentStatus(): void
 
         $statusRecord = CodecheckStatusHandler::getCurrentStatusData($submissionId);
 
-        if($statusRecord == null) {
-            JsonResponse::staticResponse([
-                'success' => false,
-                'error' => "There doesn't exist any Status in the OJS Databse for this submission Id yet.",
-                'statusRecord' => null,
-                'allStatuses' => Constants::CODECHECK_STATUSES,
-            ], 500);
-        }
-
         JsonResponse::staticResponse([
             'success' => true,
             'statusRecord' => $statusRecord,
@@ -990,14 +985,18 @@ public function getCurrentStatus(): void
 
     public function getStatusHistory(): void
     {
+        CodecheckLogger::debug("Get Status History");
         $submissionId = (int) $this->codecheckMetadataHandler->getSubmissionId();
 
         $statusHistory = CodecheckStatusHandler::getStatusDataHistory($submissionId);
 
-        if($statusHistory == null) {
+        CodecheckLogger::debug(print_r($statusHistory, true));
+
+        if(empty($statusHistory)) {
             JsonResponse::staticResponse([
                 'success' => false,
-                'statusHistory' => $statusHistory,
+                'error' => "Currently there is no recorded CODECHECK status history for this submission ID in the OJS database.",
+                'statusHistory' => null,
             ], 400);
         }
 
@@ -1038,13 +1037,13 @@ public function updateStatus(): void
             }
             $statusUpdate = CodecheckStatusHandler::automaticStatusUpdate($submissionMetadata);
 
-            if($statusUpdate == null) {
+            if(empty($statusUpdate)) {
                 JsonResponse::staticResponse([
                     'success' => false,
                     'statusRecord' => $statusUpdate,
                     'allStatuses' => Constants::CODECHECK_STATUSES,
                     'error' => "Status doesn't need to be automatically updated."
-                ], 200);
+                ], 400);
             } else {
                 JsonResponse::staticResponse([
                     'success' => true,

classes/CodecheckRegister/CodecheckGithubRegisterApiClient.php

@@ -204,7 +204,8 @@ public function addIssue(
         string $paperTitle,
         string $authorString,
         array $codecheckers,
-        array $repositories
+        array $repositories,
+        array $updateInformation
     ): array {
         $this->client->authenticate($this->githubPAT, null, Client::AUTH_ACCESS_TOKEN);
 
@@ -218,7 +219,8 @@ public function addIssue(
             $authorString,
             $this->submissionID,
             $codecheckers,
-            $repositories
+            $repositories,
+            $updateInformation
         );
 
         try {
@@ -272,7 +274,8 @@ public function updateIssue(
             $authorString,
             $this->submissionID,
             $codecheckers,
-            $repositories
+            $repositories,
+            $updateInformation
         );
 
         $issueContents = [];

classes/CodecheckRegister/CodecheckGithubRegisterIssue.php

@@ -4,6 +4,11 @@
 
 use APP\plugins\generic\codecheck\classes\CodecheckRegister\CertificateIdentifier;
 use APP\plugins\generic\codecheck\classes\CodecheckRegister\CodecheckIssueLabels;
+use APP\plugins\generic\codecheck\classes\Workflow\CodecheckStatusHandler;
+use APP\plugins\generic\codecheck\classes\Constants;
+use PKP\plugins\PluginRegistry;
+use APP\core\Application;
+use APP\plugins\generic\codecheck\classes\Log\CodecheckLogger;
 
 class CodecheckGithubRegisterIssue {
     private string $repositoryOwner;
@@ -13,6 +18,8 @@ class CodecheckGithubRegisterIssue {
     private string $submissionID;
     private array $labels;
     private string $jsonEncodedCodecheckMetadata;
+    private string $codecheckStatus;
+    private bool $updateStatus;
 
     public function __construct(
         string $repositoryOwner,
@@ -24,11 +31,20 @@ public function __construct(
         string $authorString,
         string $submissionID,
         array $codecheckers,
-        array $repositories
+        array $repositories,
+        array $updateInformation
     ){
         $this->repositoryOwner = $repositoryOwner;
         $this->repository = $repository;
         $this->submissionID = $submissionID;
+        $this->codecheckStatus = '';
+        $this->updateStatus = false;
+        if(in_array(Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_STATUS, $updateInformation)) {
+            $this->updateStatus = true;
+            $this->codecheckStatus = CodecheckStatusHandler::getCurrentStatusData($this->submissionID)->status;
+        }
+        $updateCodecheckStatus = $this->updateStatus ? 'true' : 'false';
+        CodecheckLogger::debug("Record / Update Status: " . $updateCodecheckStatus);
         $authorString = empty($authorString) ? 'New CODECHECK' : $authorString;
         $this->title = $this->createTitleMarkdown($authorString, $certificateIdentifier);
         $this->jsonEncodedCodecheckMetadata = $this->createJsonEncodedCodecheckMetadataMarkdown($authorString, $certificateIdentifier, $journalName, $submissionID, $codecheckers, $repositories);
@@ -73,10 +89,12 @@ private function createJsonEncodedCodecheckMetadataMarkdown(
         array $repositories
     ): string
     {
+        $statusInformation = $this->updateStatus ? "\n\t\"status\": \"" . $this->codecheckStatus . "\"," : "";
         return "<details>\n<summary><h3>JSON encoded CODECHECK metadata</h3></summary>\n\n"
         . "```json\n"
         . "{"
         . "\n\t\"identifier\": \"" . $certificateIdentifier->toStr() . "\","
+        . $statusInformation
         . "\n\t\"repositories\": " . json_encode($repositories) . ","
         . "\n\t\"codecheckers\": " . json_encode($codecheckers) . ","
         . "\n\t\"links\": [],"
@@ -96,11 +114,13 @@ private function createBodyMarkdown(
         foreach ($repositories as $repo) {
             $repoStr .= "\t- " . $repo . "\n";
         }
+        $statusInformation = $this->updateStatus ? "<!-- The current status of the CODECHECK -->\n**CODECHECK Status:** " . __($this->codecheckStatus) . "\n\n" : "";
+
         return "<!-- Provide the title of your published paper or preprint -->\n## " . $paperTitle . "\n\n"
         . "<!-- Provide a link to your published paper or preprint, ideally with a DOI -->\n**Article:**\n\n"
         . "<!-- Information about the Journal in which the paper/ preprint is published -->\n**Journal:** " . $journalName . " *(Submission ID: " . $this->submissionID . ")*\n\n"
-        . "<!-- Provide a link to your code (and data) repository(s) (GitHub, GitLab, etc.) -->\n**Repositories:**\n"
-        . $repoStr;
+        . "<!-- Provide a link to your code (and data) repository(s) (GitHub, GitLab, etc.) -->\n**Repositories:**\n" . $repoStr . "\n\n"
+        . $statusInformation;
     }
 
     private function fillLabels(

classes/Constants.php

@@ -26,6 +26,7 @@ class Constants
     /**
      * The possible Codecheck Statuses
      */
+    public const CODECHECK_STATUS_PENDING = 'plugins.generic.codecheck.status.pending';
     public const CODECHECK_STATUS_NEEDS_CODECHECKER = 'plugins.generic.codecheck.status.needsCodechecker';
     public const CODECHECK_STATUS_ASSIGNED_CODECHECKER = 'plugins.generic.codecheck.status.assignedCodechecker';
     public const CODECHECK_STATUS_STALLED_AUTHOR = 'plugins.generic.codecheck.status.stalled.author';
@@ -65,6 +66,7 @@ class Constants
     public const CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_FIELDS = 'codecheckGithubUpdateFields';
     public const CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_TITLE = 'updateTitle';
     public const CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_BODY = 'updateBody';
+    public const CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_STATUS = 'updateStatus';
     # Codecheck Publication Validation
     # Codecheck Status
     public const CODECHECK_STATUS = 'codecheckStatus';

classes/Settings/SettingsForm.php

@@ -151,6 +151,7 @@ public function initData(): void
         // Unpack so each checkbox gets its own template variable
         $this->setData(Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_TITLE, in_array(Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_TITLE, $updateFields));
         $this->setData(Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_BODY, in_array(Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_BODY, $updateFields));
+        $this->setData(Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_STATUS, in_array(Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_STATUS, $updateFields));
 
         $this->setData(
             Constants::CODECHECK_PUBLICATION_VALIDATION_EXTENDED,
@@ -181,6 +182,7 @@ public function readInputData(): void
             Constants::CODECHECK_SHOW_DASHBOARD_COLUMN,
             Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_TITLE,
             Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_BODY,
+            Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_STATUS,
             Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_FIELDS,
             Constants::CODECHECK_STATUS,
             Constants::CODECHECK_STATUSES_SELECTED,
@@ -308,6 +310,7 @@ public function execute(...$functionArgs): mixed
         $updateFields = array_values(array_filter([
             $this->getData(Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_TITLE) ? Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_TITLE : null,
             $this->getData(Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_BODY) ? Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_BODY : null,
+            $this->getData(Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_STATUS) ? Constants::CODECHECK_GITHUB_REGISTER_ISSUE_UPDATE_STATUS : null,
         ]));
 
         $this->plugin->updateSetting(

classes/Workflow/CodecheckStatusHandler.php

@@ -4,22 +4,27 @@
 
 use Illuminate\Support\Facades\DB;
 use APP\plugins\generic\codecheck\classes\Constants;
+use APP\plugins\generic\codecheck\classes\Log\CodecheckLogger;
 
 class CodecheckStatusHandler {
-    public static function getCurrentStatusData(int $submissionId): object|null {
-        return DB::table('codecheck_status')
+    public static function getCurrentStatusData(int $submissionId): object {
+        $codecheckStatus = DB::table('codecheck_status')
             ->where('submission_id', $submissionId)
             ->orderBy('timestamp', 'desc')
             ->orderBy('status_id', 'desc')
             ->first();
+
+        return $codecheckStatus ?? (object) ['status' => 'plugins.generic.codecheck.status.pending'];
     }
 
     public static function getStatusDataHistory(int $submissionId): object|null {
-        return DB::table('codecheck_status')
+        $statusHistory = DB::table('codecheck_status')
             ->where('submission_id', $submissionId)
             ->orderBy('timestamp', 'desc')
             ->orderBy('status_id', 'desc')
             ->get();
+
+        return $statusHistory->isEmpty() ? null : $statusHistory;
     }
 
     public static function updateStatus(int $submissionId, string $status, int $userId): object|false {
@@ -43,11 +48,9 @@ public static function automaticStatusUpdate(array $submissionMetadata): object|
         $submissionId = $submissionMetadata['submissionId'];
         $statusHistory = CodecheckStatusHandler::getStatusDataHistory($submissionId);
 
-        error_log("Status History: " . json_encode($statusHistory));
-        error_log("Status History count: " . $statusHistory->count());
-        error_log("Is null: " . ($statusHistory === null ? 'true' : 'false'));
+        CodecheckLogger::debug("Status History: " . json_encode($statusHistory));
 
-        if($statusHistory == null || $statusHistory->count() < 2) {
+        if(empty($statusHistory) || $statusHistory->count() < 2) {
             $status = Constants::CODECHECK_STATUS_NEEDS_CODECHECKER;
             if(!empty($submissionMetadata['codecheck']['codecheckers'])) {
                 $status = Constants::CODECHECK_STATUS_ASSIGNED_CODECHECKER;

cypress/tests/component/CodecheckMetadataForm.cy.js

@@ -26,7 +26,7 @@ describe('CodecheckMetadataForm Component', () => {
           version: 'latest',
           publicationType: 'doi',
           manifest: [],
-          repository: '',
+          repository: JSON.stringify({ repositories: null, repoWithCodecheckYaml: null }),
           source: '',
           codecheckers: [],
           certificate: '',

locale/en/locale.po

@@ -119,6 +119,9 @@ msgstr "Update the Issue Title (containing the article's authors)"
 msgid "plugins.generic.codecheck.settings.updateIssue.body"
 msgstr "Update the Issue Description (containing the article, codechecker and repository information)"
 
+msgid "plugins.generic.codecheck.settings.updateIssue.status"
+msgstr "Record & update the CODECHECK Status in the GitHub Register Issue"
+
 msgid "plugins.generic.codecheck.settings.status"
 msgstr "What status must a check have for a submission to proceed with the publication?"
 

resources/js/Components/CodecheckMetadataForm.vue

@@ -564,13 +564,13 @@ export default {
           manifestFiles: data.submission?.manifestFiles || '',
           dataAvailabilityStatement: data.submission?.dataAvailabilityStatement || ''
         };
-
-        let repositoryData = typeof data.codecheck.repository === 'string' ? JSON.parse(data.codecheck.repository) :  {
-          repositories: null,
-          repoWithCodecheckYaml: null,
-        };
 
         if (data.codecheck && typeof data.codecheck === 'object') {
+          let repositoryData = typeof data.codecheck.repository === 'string' ? JSON.parse(data.codecheck.repository) :  {
+            repositories: null,
+            repoWithCodecheckYaml: null,
+          };
+
           this.metadata = {
             version: data.codecheck.version || data.codecheck.version || 'latest',
             publicationType: data.codecheck.publicationType || data.codecheck.publication_type || 'doi',