Merge pull request #921 from NFDI4Chem/development

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NFDI4Chem · Nov 28, 2023 · 2b01728 · 2b01728
2 parents efa68d4 + 47c2020
commit 2b01728
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Showing 62 changed files with 1,406 additions and 1,091 deletions.
diff --git a/.env.example b/.env.example
@@ -14,6 +14,9 @@ EUROPEMC_WS_API=https://www.ebi.ac.uk/europepmc/webservices/rest/search
 ORCID_ID_SEARCH_API=https://pub.orcid.org/v2.1/search
 ORCID_ID_EMPLOYMENT_API=https://pub.orcid.org/v3.0/{orcid_id}/employments
 ORCID_ID_PERSON_API=https://pub.orcid.org/v3.0/{orcid_id}/person
+CM_API=https://api.naturalproducts.net/latest/
+CROSSREF_API=https://api.crossref.org/works/
+
 
 LOG_CHANNEL=stack
 LOG_LEVEL=debug
@@ -94,3 +97,10 @@ NMRXIV_PROVIDER=NFDI4Chem
 NMRXIV_PROVIDER_URL=https://www.nfdi4chem.de/
 MEASUREMENT_TECHNIQUE=http://purl.obolibrary.org/obo/CHMO_0000613
 
+#DATACITE Properties
+DOI_HOST=datacite
+DATACITE_USERNAME=
+DATACITE_SECRET=
+DATACITE_PREFIX=
+DATACITE_ENDPOINT=
+
diff --git a/app/Console/Commands/ExtractSpectra.php b/app/Console/Commands/ExtractSpectra.php
@@ -90,69 +90,73 @@ public function handle()
  foreach ($study->datasets as $dataset) {
  echo $dataset->identifier;
  echo "\r\n";
- // if(!$dataset->has_nmrium){
- $nmriumInfo = json_decode($study->nmrium['nmrium_info'], true);
- $_nmriumJSON = $nmriumInfo;
- $fsObject = $dataset->fsObject;
-
- $studyFSObject = $study->fsObject;
- $datasetFSObject = $dataset->fsObject;
- $path = '/'.$studyFSObject->name.'/'.$datasetFSObject->name;
- // echo($path);
+ // echo $dataset->type;
  // echo "\r\n";
- $fsObject = $dataset->fsObject;
- $studyFSObject = $study->fsObject;
- $datasetFSObject = $dataset->fsObject;
- $path = '/'.$studyFSObject->name.'/'.$datasetFSObject->name;
-
- $pathsMatch = false;
- $spectrum = [];
- $type = [];
- foreach ($nmriumInfo['data']['spectra'] as $spectra) {
- unset($_nmriumJSON['data']['spectra']);
- $files = $spectra['sourceSelector']['files'];
- if ($files) {
- foreach ($files as $file) {
- if (str_contains($file, $path)) {
- $pathsMatch = true;
+ if (! $dataset->has_nmrium) {
+ $nmriumInfo = json_decode($study->nmrium['nmrium_info'], true);
+ $_nmriumJSON = $nmriumInfo;
+ $fsObject = $dataset->fsObject;
+
+ $studyFSObject = $study->fsObject;
+ $datasetFSObject = $dataset->fsObject;
+ $path = '/'.$studyFSObject->name.'/'.$datasetFSObject->name;
+ $fType = $studyFSObject->type;
+
+ // echo($path);
+ // echo "\r\n";
+ $fsObject = $dataset->fsObject;
+ $studyFSObject = $study->fsObject;
+ $datasetFSObject = $dataset->fsObject;
+ $path = '/'.$studyFSObject->name.'/'.$datasetFSObject->name;
+
+ $pathsMatch = false;
+ $spectrum = [];
+ $type = [];
+ foreach ($nmriumInfo['data']['spectra'] as $spectra) {
+ unset($_nmriumJSON['data']['spectra']);
+ $files = $spectra['sourceSelector']['files'];
+ if ($files) {
+ foreach ($files as $file) {
+ if (str_contains($file, $fType == 'file' ? $path : $path.'/')) {
+ $pathsMatch = true;
+ }
  }
  }
- }
- if ($pathsMatch) {
- array_push($spectrum, $spectra);
- $experimentDetailsExists = array_key_exists('experiment', $spectra['info']);
- if ($experimentDetailsExists) {
- $experiment = $spectra['info']['experiment'];
- $nucleus = $spectra['info']['nucleus'];
- if (is_array($nucleus)) {
- $nucleus = implode('-', $nucleus);
+ if ($pathsMatch) {
+ array_push($spectrum, $spectra);
+ $experimentDetailsExists = array_key_exists('experiment', $spectra['info']);
+ if ($experimentDetailsExists) {
+ $experiment = $spectra['info']['experiment'];
+ $nucleus = $spectra['info']['nucleus'];
+ if (is_array($nucleus)) {
+ $nucleus = implode('-', $nucleus);
+ }
+ array_push($type, $experiment.' - '.$nucleus);
  }
- array_push($type, $experiment.' - '.$nucleus);
+ $pathsMatch = false;
  }
- $pathsMatch = false;
  }
- }
- if (count($spectrum) > 0) {
- $_nmriumJSON['data']['spectra'] = $spectrum;
- $_nmrium = $dataset->nmrium;
- if ($_nmrium) {
- $_nmrium->nmrium_info = json_encode($_nmriumJSON, JSON_UNESCAPED_UNICODE);
- $dataset->has_nmrium = true;
- $_nmrium->save();
- } else {
- $_nmrium = NMRium::create([
- 'nmrium_info' => json_encode($_nmriumJSON, JSON_UNESCAPED_UNICODE),
- ]);
- $dataset->nmrium()->save($_nmrium);
- $dataset->has_nmrium = true;
+  if (count($spectrum) > 0) {
+  $_nmriumJSON['data']['spectra'] = $spectrum;
+  $_nmrium = $dataset->nmrium;
+  if ($_nmrium) {
+  $_nmrium->nmrium_info = json_encode($_nmriumJSON, JSON_UNESCAPED_UNICODE);
+  $dataset->has_nmrium = true;
+  $_nmrium->save();
+ } else {
+  $_nmrium = NMRium::create([
+  'nmrium_info' => json_encode($_nmriumJSON, JSON_UNESCAPED_UNICODE),
+ ]);
+  $dataset->nmrium()->save($_nmrium);
+  $dataset->has_nmrium = true;
+ }
  }
+ $uType = array_unique($type);
+ if (count($uType) == 1) {
+ $dataset->type = $uType[0];
+ }
+ $dataset->save();
  }
- $uType = array_unique($type);
- if (count($uType) == 1) {
- $dataset->type = $uType[0];
- }
- $dataset->save();
- // }
  }
  }
  }

diff --git a/app/Http/Controllers/Admin/UsersController.php b/app/Http/Controllers/Admin/UsersController.php
@@ -220,4 +220,12 @@ public function markAllNotificationAsRead(Request $request)
 
  return $request->wantsJson() ? new JsonResponse('', 200) : back()->with('status', 'all-notification-markedAsRead');
  }
+
+ /**
+ * Impersonate the user
+ */
+ public function impersonate(User $user)
+ {
+ return redirect()->route('impersonate', $user->id);
+ }
 }
diff --git a/app/Http/Controllers/DraftController.php b/app/Http/Controllers/DraftController.php
@@ -3,6 +3,7 @@
 namespace App\Http\Controllers;
 
 use App\Jobs\ArchiveStudy;
+use App\Jobs\ProcessFiles;
 use App\Models\Dataset;
 use App\Models\Draft;
 use App\Models\FileSystemObject;
@@ -95,6 +96,24 @@ public function files(Request $request, Draft $draft)
  ->orderBy('type')
  ->get(),
  ],
+ 'missing_files' => FileSystemObject::where([
+ ['draft_id', $draft->id],
+ ['status', 'missing'],
+ ])
+ ->count(),
+ ]);
+ }
+
+ public function missingFiles(Request $request, Draft $draft)
+ {
+ return response()->json(
+ [
+ 'missing_files' => FileSystemObject::select('relative_url')
+ ->where([
+ ['draft_id', $draft->id],
+ ['status', 'missing'],
+ ])
+ ->get(),
  ]);
  }
 
@@ -261,7 +280,6 @@ public function process(Request $request, Draft $draft)
  $folders = FileSystemObject::with('children')
  ->where([
  ['draft_id', $draft->id],
- ['status', '<>', 'missing'],
  ['model_type', 'study'],
  ])
  ->orderBy('type')
@@ -443,11 +461,11 @@ public function annotate(Request $request, Draft $draft)
  $draftFolders = FileSystemObject::with('children')
  ->where([
  ['level', 0],
- ['status', '<>', 'missing'],
  ['draft_id', $draft->id],
  ])
  ->orderBy('type')
  ->get();
+ ProcessFiles::dispatch($draft);
  $this->processFolder($draftFolders);
  }
 

diff --git a/app/Http/Controllers/ProjectController.php b/app/Http/Controllers/ProjectController.php
@@ -92,7 +92,7 @@ public function publicProjectsView(Request $request)
 
  public function publicStudies(Request $request, Project $project)
  {
- return StudyResource::collection(Study::where([['project_id', $project->id], ['is_public', true]])->filter($request->only('search', 'sort', 'mode'))->paginate(9)->withQueryString());
+ return StudyResource::collection(Study::where([['project_id', $project->id], ['is_public', true]])->filter($request->only('search', 'sort', 'mode'))->paginate(12)->withQueryString());
  }
 
  public function toggleUpVote(Request $request, Project $project)

diff --git a/app/Http/Controllers/StudyController.php b/app/Http/Controllers/StudyController.php
@@ -30,6 +30,7 @@ class StudyController extends Controller
  public function publicStudiesView(Request $request)
  {
  $moleculeId = $request->get('compound');
+ $molecule = null;
  if ($moleculeId) {
  $molecule = Molecule::where('identifier', $moleculeId)->first();
  if ($molecule) {
@@ -46,6 +47,7 @@ public function publicStudiesView(Request $request)
  return Inertia::render('Public/Studies', [
  'filters' => $request->all('search', 'sort', 'mode'),
  'studies' => $studiesResource,
+ 'molecule' => $molecule,
  ]);
  }
 
@@ -223,7 +225,7 @@ public function nmriumInfo(Request $request, Study $study)
  $studyFSObject = $study->fsObject;
  $datasetFSObject = $dataset->fsObject;
  $path = '/'.$studyFSObject->name.'/'.$datasetFSObject->name;
-
+ $fType = $studyFSObject->type;
  $pathsMatch = false;
  $spectrum = [];
  $type = [];
@@ -232,7 +234,7 @@ public function nmriumInfo(Request $request, Study $study)
  $files = $spectra['sourceSelector']['files'];
  if ($files) {
  foreach ($files as $file) {
- if (str_contains($file, $path)) {
+ if (str_contains($file, $fType == 'file' ? $path : $path.'/')) {
  $pathsMatch = true;
  }
  }

diff --git a/app/Http/Middleware/HandleInertiaRequests.php b/app/Http/Middleware/HandleInertiaRequests.php
@@ -79,6 +79,7 @@ public function share(Request $request)
  'orcidPersonApi' => env('ORCID_ID_PERSON_API'),
  'orcidEmploymentApi' => env('ORCID_ID_EMPLOYMENT_API'),
  'CM_API' => env('CM_API'),
+ 'CROSSREF_API' => env('CROSSREF_API'),
  ]);
  }
 }
diff --git a/app/Jobs/ArchiveStudy.php b/app/Jobs/ArchiveStudy.php
@@ -35,6 +35,14 @@ public function __construct(Project $project)
  $this->project = $project;
  }
 
+ /**
+ * Get the unique ID for the job.
+ */
+ public function uniqueId(): string
+ {
+ return $this->project->id;
+ }
+
  /**
  * Execute the job.
  */
@@ -48,7 +56,7 @@ public function handle(): void
  $archiveDownloadURL = $study->download_url;
  if (! $archiveDownloadURL) {
  $fsObject = $study->fsObject;
- if ($fsObject && $fsObject->status != 'missing') {
+ if ($fsObject) {
  $path = $fsObject->path;
  $s3Client = $this->storageClient();
  $bucket = config('filesystems.disks.'.env('FILESYSTEM_DRIVER').'.bucket');