Merge pull request #898 from NFDI4Chem/development

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NFDI4Chem · Nov 15, 2023 · d61e788 · d61e788
2 parents acf920b + 345da39
commit d61e788
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Showing 28 changed files with 449 additions and 269 deletions.
diff --git a/app/Console/Commands/ExtractSpectra.php b/app/Console/Commands/ExtractSpectra.php
@@ -79,78 +79,87 @@ public function handle()
  }
  }
  });
- } else {
+ }
+ $study = $study->fresh();
+ if ($study->has_nmrium) {
  $nmriumInfo = json_decode($study->nmrium['nmrium_info'], true);
  if (count($nmriumInfo['data']['spectra']) == 0) {
  echo '--MISSING SPECTRA INFO (NMRIUM JSON)--';
  echo "\r\n";
- }
- }
- } catch (Exception $e) {
- echo 'Caught exception: ', $e->getMessage(), "\n";
- }
- $study = $study->fresh();
- foreach ($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 = $dataset->fsObject;
+ } else {
+ foreach ($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 "\r\n";
- $pathsMatch = false;
- foreach ($nmriumInfo['data']['spectra'] as $spectra) {
- unset($_nmriumJSON['data']['spectra']);
- $files = $spectra['sourceSelector']['files'];
- if ($files) {
- foreach ($files as $file) {
- if (str_contains($file, $path)) {
- $pathsMatch = true;
- }
- }
- }
- if ($pathsMatch) {
- break;
- }
- }
- if (! $pathsMatch) {
- echo $project->identifier;
- echo "\r\n";
+ $studyFSObject = $study->fsObject;
+ $datasetFSObject = $dataset->fsObject;
+ $path = '/'.$studyFSObject->name.'/'.$datasetFSObject->name;
+ // echo($path);
+ // echo "\r\n";
+ $fsObject = $dataset->fsObject;
+ $studyFSObject = $study->fsObject;
+ $datasetFSObject = $dataset->fsObject;
+ $path = '/'.$studyFSObject->name.'/'.$datasetFSObject->name;
 
- echo '===========> no match';
- echo "\r\n";
- } else {
- $_nmriumJSON['data']['spectra'] = [$spectra];
- $_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;
- }
- $experimentDetailsExists = array_key_exists('experiment', $spectra['info']);
- if ($experimentDetailsExists) {
- $experiment = $spectra['info']['experiment'];
- $nucleus = $spectra['info']['nucleus'];
- if (is_array($nucleus)) {
- $nucleus = implode('-', $nucleus);
+ $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)) {
+ $pathsMatch = true;
+ }
+ }
+ }
+ if ($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);
+ }
+ $pathsMatch = false;
+ }
+ }
+ if (count($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;
+ }
+ }
+ $uType = array_unique($type);
+ if (count($uType) == 1) {
+ $dataset->type = $uType[0];
+ }
+ $dataset->save();
+ // }
  }
- $dataset->type = $experiment.','.$nucleus;
  }
- $dataset->save();
  }
- // }
+ } catch (Exception $e) {
+ echo 'Caught exception: ', $e->getMessage(), "\n";
  }
+
  }
  }
  }

diff --git a/app/Http/Controllers/DownloadController.php b/app/Http/Controllers/DownloadController.php
@@ -102,17 +102,22 @@ public function downloadFromProject(Request $request, $username, $project, $key
  array_push($s3keys, substr($fsObj->path, 1));
  }
  } else {
- $command = $s3Client->getCommand('ListObjects');
- $command['Bucket'] = $bucket;
+
+ $command = [
+ 'Bucket' => $bucket,
+ ];
  if ($path[0] == '/') {
  $command['Prefix'] = ltrim($path, $path[0]).'/';
  } else {
  $command['Prefix'] = $path.'/';
  }
- $result = $s3Client->execute($command);
- if ($result['Contents']) {
- foreach ($result['Contents'] as $file) {
- array_push($s3keys, $file['Key']);
+ $results = $s3Client->getPaginator('ListObjects', $command);
+ foreach ($results as $result) {
+ $contents = $result->get('Contents');
+ if ($contents) {
+ foreach ($contents as $file) {
+ array_push($s3keys, $file['Key']);
+ }
  }
  }
  }

diff --git a/app/Http/Controllers/DraftController.php b/app/Http/Controllers/DraftController.php
@@ -548,7 +548,13 @@ public function isJcampDX($folder)
  $isDX = true;
  }
 
- if ($isJDX || $isDX) {
+ $fileTypes = ['jcamp'];
+ $isJCAMP = false;
+ if (array_intersect($fileTypes, $extensions) == $fileTypes) {
+ $isJCAMP = true;
+ }
+
+ if ($isJDX || $isDX || $isJCAMP) {
  return true;
  }
 

diff --git a/app/Http/Controllers/StudyController.php b/app/Http/Controllers/StudyController.php
@@ -213,8 +213,10 @@ public function nmriumInfo(Request $request, Study $study)
  $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'];
@@ -226,11 +228,21 @@ public function nmriumInfo(Request $request, Study $study)
  }
  }
  if ($pathsMatch) {
- break;
+ 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);
+ }
+ $pathsMatch = false;
  }
  }
- if ($pathsMatch){
- $_nmriumJSON['data']['spectra'] = [$spectra];
+ if (count($spectrum) > 0) {
+ $_nmriumJSON['data']['spectra'] = $spectrum;
  $_nmrium = $dataset->nmrium;
  if ($_nmrium) {
  $_nmrium->nmrium_info = json_encode($_nmriumJSON, JSON_UNESCAPED_UNICODE);
@@ -243,17 +255,13 @@ public function nmriumInfo(Request $request, Study $study)
  $dataset->nmrium()->save($_nmrium);
  $dataset->has_nmrium = true;
  }
- $experimentDetailsExists = array_key_exists('experiment', $spectra['info']);
- if ($experimentDetailsExists) {
- $experiment = $spectra['info']['experiment'];
- $nucleus = $spectra['info']['nucleus'];
- if (is_array($nucleus)) {
- $nucleus = implode('-', $nucleus);
- }
- $dataset->type = $experiment.','.$nucleus;
- }
- $dataset->save();
  }
+ $uType = array_unique($type);
+ if (count($uType) == 1) {
+ $dataset->type = $uType[0];
+ }
+ $dataset->save();
+
  }
 
  return $study->fresh();

diff --git a/app/Jobs/ArchiveProject.php b/app/Jobs/ArchiveProject.php
@@ -72,17 +72,21 @@ public function handle(): void
  array_push($s3keys, substr($fsObject->path, 1));
  }
  } else {
- $command = $s3Client->getCommand('ListObjects');
- $command['Bucket'] = $bucket;
+ $command = [
+ 'Bucket' => $bucket,
+ ];
  if ($path[0] == '/') {
  $command['Prefix'] = ltrim($path, $path[0]).'/';
  } else {
  $command['Prefix'] = $path.'/';
  }
- $result = $s3Client->execute($command);
- if ($result['Contents']) {
- foreach ($result['Contents'] as $file) {
- array_push($s3keys, $file['Key']);
+ $results = $s3Client->getPaginator('ListObjects', $command);
+ foreach ($results as $result) {
+ $contents = $result->get('Contents');
+ if ($contents) {
+ foreach ($contents as $file) {
+ array_push($s3keys, $file['Key']);
+ }
  }
  }
  }

diff --git a/app/Jobs/ArchiveStudy.php b/app/Jobs/ArchiveStudy.php
@@ -59,17 +59,22 @@ public function handle(): void
  array_push($s3keys, substr($fsObject->path, 1));
  }
  } else {
- $command = $s3Client->getCommand('ListObjects');
- $command['Bucket'] = $bucket;
+
+ $command = [
+ 'Bucket' => $bucket,
+ ];
  if ($path[0] == '/') {
  $command['Prefix'] = ltrim($path, $path[0]).'/';
  } else {
  $command['Prefix'] = $path.'/';
  }
- $result = $s3Client->execute($command);
- if ($result['Contents']) {
- foreach ($result['Contents'] as $file) {
- array_push($s3keys, $file['Key']);
+ $results = $s3Client->getPaginator('ListObjects', $command);
+ foreach ($results as $result) {
+ $contents = $result->get('Contents');
+ if ($contents) {
+ foreach ($contents as $file) {
+ array_push($s3keys, $file['Key']);
+ }
  }
  }
  }

diff --git a/app/Providers/AppServiceProvider.php b/app/Providers/AppServiceProvider.php
@@ -2,6 +2,7 @@
 
 namespace App\Providers;
 
+use Illuminate\Support\Facades\App;
 use Illuminate\Support\ServiceProvider;
 
 class AppServiceProvider extends ServiceProvider
@@ -26,7 +27,7 @@ public function register()
  */
  public function boot()
  {
- if ($this->app->environment('production')) {
+ if (App::environment() == 'production') {
  \URL::forceScheme('https');
  }
  }

diff --git a/database/scripts/sync_index.sql b/database/scripts/sync_index.sql
@@ -0,0 +1,50 @@
+SELECT setval('announcements_id_seq', max(id)) FROM announcements;
+SELECT setval('assays_id_seq', max(id)) FROM assays;
+SELECT setval('audits_id_seq', max(id)) FROM audits;
+SELECT setval('author_project_id_seq', max(id)) FROM author_project;
+SELECT setval('authors_id_seq', max(id)) FROM authors;
+SELECT setval('citation_project_id_seq', max(id)) FROM citation_project;
+SELECT setval('citations_id_seq', max(id)) FROM citations;
+SELECT setval('dataset_invitations_id_seq', max(id)) FROM dataset_invitations;
+SELECT setval('dataset_molecule_id_seq', max(id)) FROM dataset_molecule;
+SELECT setval('dataset_user_id_seq', max(id)) FROM dataset_user;
+SELECT setval('datasets_id_seq', max(id)) FROM datasets;
+SELECT setval('drafts_id_seq', max(id)) FROM drafts;
+SELECT setval('failed_jobs_id_seq', max(id)) FROM failed_jobs;
+SELECT setval('file_system_objects_id_seq', max(id)) FROM file_system_objects;
+SELECT setval('licenses_id_seq', max(id)) FROM licenses;
+SELECT setval('linked_social_accounts_id_seq', max(id)) FROM linked_social_accounts;
+SELECT setval('markable_reactions_id_seq', max(id)) FROM markable_reactions;
+SELECT setval('markable_likes_id_seq', max(id)) FROM markable_likes;
+SELECT setval('markable_favorites_id_seq', max(id)) FROM markable_favorites;
+SELECT setval('markable_bookmarks_id_seq', max(id)) FROM markable_bookmarks;
+SELECT setval('migrations_id_seq', max(id)) FROM migrations;
+-- model_has_permissions -- combi
+-- model_has_roles SELECT setval('molecule_sample_id_seq', max(id)) FROM molecule_sample; -- combi
+SELECT setval('molecule_sample_id_seq', max(id)) FROM molecule_sample;
+SELECT setval('molecules_id_seq', max(id)) FROM molecules;
+SELECT setval('nmrium_id_seq', max(id)) FROM nmrium;
+-- SELECT setval('notifications_id_seq', max(id)) FROM notifications; UUID
+-- SELECT setval('password_resets_id_seq', max(id)) FROM password_resets; no pkey
+SELECT setval('permissions_id_seq', max(id)) FROM permissions;
+SELECT setval('personal_access_tokens_id_seq', max(id)) FROM personal_access_tokens;
+SELECT setval('project_invitations_id_seq', max(id)) FROM project_invitations;
+SELECT setval('project_user_id_seq', max(id)) FROM project_user;
+SELECT setval('projects_id_seq', max(id)) FROM projects;
+-- role_has_permissions SELECT setval('role_has_permissions_id_seq', max(id)) FROM role_has_permissions; -- combi
+SELECT setval('roles_id_seq', max(id)) FROM roles;
+SELECT setval('samples_id_seq', max(id)) FROM samples;
+-- SELECT setval('sessions_id_seq', max(id)) FROM sessions; UUID
+SELECT setval('studies_id_seq', max(id)) FROM studies;
+SELECT setval('study_invitations_id_seq', max(id)) FROM study_invitations;
+SELECT setval('study_user_id_seq', max(id)) FROM study_user;
+-- SELECT setval('taggables_id_seq', max(id)) FROM taggables; no pkey
+SELECT setval('tags_id_seq', max(id)) FROM tags;
+SELECT setval('team_invitations_id_seq', max(id)) FROM team_invitations;
+SELECT setval('team_user_id_seq', max(id)) FROM team_user;
+SELECT setval('teams_id_seq', max(id)) FROM teams;
+SELECT setval('templates_id_seq', max(id)) FROM templates;
+SELECT setval('tickers_id_seq', max(id)) FROM tickers;
+SELECT setval('users_id_seq', max(id)) FROM users;
+SELECT setval('validations_id_seq', max(id)) FROM validations;
+SELECT setval('versions_version_id_seq', max(version_id)) FROM versions;