Merge pull request #529 from NFDI4Chem/development

Development

app/Console/Commands/UnpublishProjects.php

@@ -3,9 +3,13 @@
 namespace App\Console\Commands;
 
 use App\Actions\Project\UnPublishProject;
+use App\Models\Draft;
+use App\Models\FileSystemObject;
 use App\Models\Project;
 use Illuminate\Console\Command;
 use Illuminate\Support\Facades\DB;
+use Illuminate\Support\Facades\Storage;
+use Illuminate\Support\Str;
 
 class UnpublishProjects extends Command
 {
@@ -36,7 +40,78 @@ public function handle(UnPublishProject $unpublisher)
             $projects = Project::whereIn('identifier', $ids)->get();
             foreach ($projects as $project) {
                 $unpublisher->unPublish($project);
+                $user_id = $project->owner->id;
+                $team_id = $project->team_id;
+                $id = Str::uuid();
+                $environment = env('APP_ENV', 'local');
+                $path = preg_replace(
+                    '~//+~',
+                    '/',
+                    $environment.'/'.$user_id.'/drafts/'.$id
+                );
+
+                $draft = Draft::create([
+                    'name' => $project->name,
+                    'slug' => Str::slug('$project->name'),
+                    'description' => $project->description,
+                    'relative_url' => rtrim(
+                        preg_replace('~//+~', '/', '/'.$id),
+                        '/'
+                    ),
+                    'path' => $path,
+                    'owner_id' => $user_id,
+                    'team_id' => $team_id ? $team_id : null,
+                    'key' => $id,
+                ]);
+
+                $projectFSObjects = FileSystemObject::with('children')
+                        ->where([
+                            ['project_id', $project->id],
+                            ['level', 0],
+                        ])
+                        ->get();
+
+                foreach ($projectFSObjects as $FSObject) {
+                    $this->moveFolder($FSObject, $project, $draft);
+                }
+
+                $project->status = null;
+                $project->process_logs = null;
+                $project->draft_id = $draft->id;
+                $project->save();
+
+                foreach ($project->studies as $study) {
+                    $study->draft_id = $draft->id;
+                    $study->save();
+                    foreach ($study->datasets as $dataset) {
+                        $dataset->draft_id = $draft->id;
+                        $dataset->save();
+                    }
+                }
             }
         });
     }
+
+    public function moveFolder($fsObject, $project, $draft)
+    {
+        $newPath = '/'.$draft->path.$fsObject->relative_url;
+        $fsObject->path = $newPath;
+        $fsObject->draft_id = $draft->id;
+        $fsObject->save();
+
+        $fsObjectChildren = $fsObject->children;
+        foreach ($fsObjectChildren as $fsObjectChild) {
+            if ($fsObjectChild->type == 'file') {
+                $newFilePath = '/'.$draft->path.$fsObjectChild->relative_url;
+                if ($fsObjectChild->path && $newFilePath && $fsObjectChild->path != $newFilePath) {
+                    Storage::disk(env('FILESYSTEM_DRIVER'))->move($fsObjectChild->path, $newFilePath);
+                    $fsObjectChild->path = $newFilePath;
+                    $fsObjectChild->draft_id = $draft->id;
+                    $fsObjectChild->save();
+                }
+            } else {
+                $this->moveFolder($fsObjectChild, $project, $draft);
+            }
+        }
+    }
 }

app/Models/HasDOI.php

@@ -16,60 +16,98 @@ public function generateDOI($doiService)
                 $users = [];
                 $suffix = null;
                 $url = 'https://www.nmrxiv.org/';
+                $releaseDate = null;
+                $citation = null;
+
                 if ($this instanceof Project) {
                     $users = $this->allUsers();
                     $authors = $this->authors ? $this->authors : [];
                     $suffix = 'P'.$identifier;
                     $url = $url.'P'.$identifier;
+                    $releaseDate = $this->release_date;
+                    $resourceType = 'Project';
+                    $citationDoi = $this->citation->doi;
                 } elseif ($this instanceof Study) {
                     $users = $this->allUsers();
                     $authors = $this->project->authors ? $this->project->authors : [];
                     $projectIdentifier = $this->getIdentifier($this->project, 'identifier');
                     $suffix = 'P'.$projectIdentifier.'.'.'S'.$identifier;
                     $url = $url.'S'.$identifier;
+                    $releaseDate = $this->release_date;
+                    $resourceType = 'Study';
+                    $citationDoi = $this->project->citation->doi;
                 } elseif ($this instanceof Dataset) {
                     $users = $this->study->allUsers();
                     $authors = $this->project->authors ? $this->project->authors : [];
                     $projectIdentifier = $this->getIdentifier($this->project, 'identifier');
                     $studyIdentifier = $this->getIdentifier($this->study, 'identifier');
                     $suffix = 'P'.$projectIdentifier.'.'.'S'.$studyIdentifier.'.'.'D'.$identifier;
                     $url = $url.'D'.$identifier;
+                    $releaseDate = $this->study->release_date;
+                    $resourceType = 'Dataset';
+                    $citationDoi = $this->project->citation->doi;
                 }
 
                 $creators = [];
-                foreach ($users as $user) {
-                    array_push($creators, [
-                        'name' => $user->last_name.' '.$user->first_name,
+                foreach ($authors as $user) {
+                    array_push($contributors, [
+                        'name' => $user->family_name.', '.$user->given_name,
                         'nameType' => 'Personal',
-                        'givenName' => $user->first_name,
-                        'familyName' => $user->last_name,
-                        'affiliation' => [],
-                        'nameIdentifiers' => [],
+                        'givenName' => $user->given_name,
+                        'familyName' => $user->family_name,
+                        'nameIdentifiers' => $user->orcid_id,
+                        'nameIdentifierScheme' => 'ORCID',
+                        'schemeURI' => 'https://orcid.org',
+                        'affiliation' => $user->affiliation,
                     ]);
                 }
 
                 $contributors = [];
-                foreach ($authors as $user) {
-                    array_push($contributors, [
-                        'name' => $user->family_name.' '.$user->given_name,
+                foreach ($users as $user) {
+                    array_push($creators, [
+                        'contributorType' => 'Other',
+                        'name' => $user->last_name.', '.$user->first_name,
                         'nameType' => 'Personal',
-                        'contributorType' => 'RightsHolder',
-                        'givenName' => $user->given_name,
-                        'familyName' => $user->family_name,
-                        'affiliation' => [],
-                        'nameIdentifiers' => [],
+                        'givenName' => $user->first_name,
+                        'familyName' => $user->last_name,
                     ]);
                 }
 
+                $citations = [
+                    'relatedIdentifier' => $this->citationDoi,
+                    'relatedIdentifierType' => 'DOI',
+                    'relationType' => 'IsSupplementTo',
+                ];
+
+                $rights = [
+                    'rights' => $this->license,
+                    'rightsURI' => $license->url,
+                    'rightsIdentifier' => $license->spdx_id,
+                    'rightsIdentifierScheme' => 'SPDX',
+                    'schemeURI' => 'https://spdx.org/licenses/',
+                ];
+
+                $description = [
+                    'description' => $this->description,
+                    'descriptionType' => 'Other',
+                ];
+
                 $attributes = [
+                    'creators' => $creators,
                     'titles' => [
                         [
                             'title' => $this->name,
                         ],
                     ],
-                    'url' => $url,
-                    'creators' => $creators,
+                    'publisher' => 'nmrXiv',
                     'contributors' => $contributors,
+                    'publicationYear' => $releaseDate,
+                    'language' => 'en',
+                    'resourceType' => $this->resourceType,
+                    'resourceTypeGeneral' => 'Dataset',
+                    'rights' => $rights,
+                    'description' => $description,
+                    'url' => $url,
                     'isActive' => true,
                     'event' => 'publish',
                     'state' => 'findable',

app/Models/HasProjects.php

@@ -42,6 +42,7 @@ public function sharedProjects()
     public function sharedDrafts()
     {
         $sharedProjects = $this->projects()->wherePivot('role', '!=', 'creator');
+
         return Draft::whereIn('id', $sharedProjects->pluck('draft_id'))->get();
     }
 

resources/js/Jetstream/ApplicationLogo.vue

@@ -27,7 +27,7 @@
         <a
             style="font-size: 0.7em"
             class="float-left font-bold border-red-900 text-red-900 absolute top-0 left-0 mx-1 my-1 text-xs border px-1 rounded-md"
-            >Beta</a
+            >v1.0-rc</a
         >
     </div>
 </template>

resources/js/Shared/AddAuthor.vue

@@ -503,7 +503,7 @@ export default {
                     "Please enter a DOI or ORCID id to proceed.";
             } else {
                 this.queryParam = this.importAuthorsForm.input;
-                if(this.checkDOI(this.importAuthorsForm.input)){
+                if (this.checkDOI(this.importAuthorsForm.input)) {
                     this.queryParam = "DOI:" + this.queryParam;
                     this.isDoi = true;
                 }
@@ -519,7 +519,8 @@ export default {
                     })
                     .then((res) => {
                         this.authorsListDOI = this.formatAuthorResponse(
-                            res.data.resultList.result[0], this.importAuthorsForm.input
+                            res.data.resultList.result[0],
+                            this.importAuthorsForm.input
                         );
                     })
                     .catch((error) => {
@@ -615,22 +616,22 @@ export default {
             });
         },
         /*Format the response*/
-        formatAuthorResponse(response,input) {
+        formatAuthorResponse(response, input) {
             var authorsList = [];
             var author = {};
             var authors = [];
             var tempList = [];
-            if(response){
-                if(!this.checkDOI(input)){
+            if (response) {
+                if (!this.checkDOI(input)) {
                     tempList = response.authorList.author;
                     var orcidId = "";
                     tempList.forEach((item) => {
-                        if(item.hasOwnProperty("authorId")) {
+                        if (item.hasOwnProperty("authorId")) {
                             var idType = item["authorId"].type;
-                            if(idType.toLowerCase() == "orcid"){
+                            if (idType.toLowerCase() == "orcid") {
                                 orcidId = item["authorId"].value;
                             }
-                            if(orcidId == input){
+                            if (orcidId == input) {
                                 authors.push(item);
                             }
                         }
@@ -640,30 +641,29 @@ export default {
                 }
             }
             authors.forEach((item) => {
-            author["given_name"] = item.hasOwnProperty("firstName")
-                ? item["firstName"]
-                : null;
-            author["family_name"] = item.hasOwnProperty("lastName")
-                ? item["lastName"]
-                : null;
-            if (item.hasOwnProperty("authorAffiliationDetailsList")) {
-                var affiliationList =
-                    item["authorAffiliationDetailsList"]
-                        .authorAffiliation;
-                affiliationList.forEach((item) => {
-                    author["affiliation"] = item["affiliation"];
-                });
-            }
-            if (item.hasOwnProperty("authorId")) {
-                var idType = item["authorId"].type;
-                if (idType.toLowerCase() == "orcid") {
-                    author["orcid_id"] = item["authorId"].value;
+                author["given_name"] = item.hasOwnProperty("firstName")
+                    ? item["firstName"]
+                    : null;
+                author["family_name"] = item.hasOwnProperty("lastName")
+                    ? item["lastName"]
+                    : null;
+                if (item.hasOwnProperty("authorAffiliationDetailsList")) {
+                    var affiliationList =
+                        item["authorAffiliationDetailsList"].authorAffiliation;
+                    affiliationList.forEach((item) => {
+                        author["affiliation"] = item["affiliation"];
+                    });
                 }
-            }
-            authorsList.push(author);
-            author = {};
-        });
-        return authorsList;
+                if (item.hasOwnProperty("authorId")) {
+                    var idType = item["authorId"].type;
+                    if (idType.toLowerCase() == "orcid") {
+                        author["orcid_id"] = item["authorId"].value;
+                    }
+                }
+                authorsList.push(author);
+                author = {};
+            });
+            return authorsList;
         },
         /*Validating form*/
         validateForm() {
@@ -715,7 +715,7 @@ export default {
             return link;
         },
         /*Checking if the input is DOI*/
-        checkDOI(input){
+        checkDOI(input) {
             var testKey = String(input);
             var DOIpattern = new RegExp(/\b(10[.][0-9]{4,}(?:[.][0-9]+)*)\b/g);
             var isDOI = DOIpattern.test(testKey);

resources/js/Shared/Submission.vue

@@ -1638,7 +1638,7 @@ export default {
                     let selectedDraft = this.drafts.find(
                         (d) => d.id == data.draft_id
                     );
-                    if(!selectedDraft){
+                    if (!selectedDraft) {
                         selectedDraft = this.sharedDrafts.find(
                             (d) => d.id == data.draft_id
                         );