feat: various bug fixes, ui improvements, updated commands, php 8.2 m…

…igration and rdkit cartridge based postgresql
NFDI4Chem · Nov 9, 2023 · 2eed0ed · 2eed0ed
1 parent 3c0639b
commit 2eed0ed
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Showing 67 changed files with 1,160 additions and 653 deletions.
diff --git a/app/Console/Commands/ArchiveData.php b/app/Console/Commands/ArchiveData.php
@@ -3,6 +3,7 @@
 namespace App\Console\Commands;
 
 use App\Jobs\ArchiveProject;
+use App\Jobs\ArchiveStudy;
 use App\Models\Project;
 use Illuminate\Console\Command;
 use Illuminate\Support\Facades\DB;
@@ -35,7 +36,9 @@ public function handle()
             ])->get();
 
             foreach ($projects as $project) {
+                // echo($project->identifier);
                 ArchiveProject::dispatch($project);
+                ArchiveStudy::dispatch($project);
             }
         });
     }

diff --git a/app/Console/Commands/ExtractSpectra.php b/app/Console/Commands/ExtractSpectra.php
@@ -0,0 +1,164 @@
+<?php
+
+namespace App\Console\Commands;
+
+use App\Models\NMRium;
+use App\Models\Project;
+use Exception;
+use Illuminate\Console\Command;
+use Illuminate\Support\Facades\DB;
+use Illuminate\Support\Facades\Http;
+
+class ExtractSpectra extends Command
+{
+    /**
+     * The name and signature of the console command.
+     *
+     * @var string
+     */
+    protected $signature = 'nmrxiv:nmrium-import';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'extract nmrium json from spectra';
+
+    /**
+     * Execute the console command.
+     */
+    public function handle()
+    {
+        $projects = Project::where([
+            ['is_public', true],
+        ])->get();
+
+        foreach ($projects as $project) {
+            echo $project->identifier;
+            echo "\r\n";
+            $studies = $project->studies;
+            foreach ($studies as $study) {
+                echo $study->identifier;
+                echo "\r\n";
+                try {
+                    if (! $study->has_nmrium) {
+                        DB::transaction(function () use ($study) {
+                            $download_url = $study->download_url;
+                            if ($download_url) {
+                                $nmrium_ = $this->processSpectra($download_url);
+                                $parsedSpectra = $nmrium_['data'];
+                                foreach ($parsedSpectra['spectra'] as $spectra) {
+                                    unset($spectra['data']);
+                                    unset($spectra['meta']);
+                                    unset($spectra['originalData']);
+                                    unset($spectra['originalInfo']);
+                                }
+
+                                $version = $parsedSpectra['version'];
+                                unset($parsedSpectra['version']);
+
+                                $nmriumJSON = [
+                                    'data' => $parsedSpectra,
+                                    'version' => $version,
+                                ];
+
+                                $nmrium = $study->nmrium;
+
+                                if ($nmrium) {
+                                    $nmrium->nmrium_info = json_encode($nmriumJSON, JSON_UNESCAPED_UNICODE);
+                                    $nmrium->save();
+                                } else {
+                                    $nmrium = NMRium::create([
+                                        'nmrium_info' => json_encode($nmriumJSON, JSON_UNESCAPED_UNICODE),
+                                    ]);
+                                    $study->nmrium()->save($nmrium);
+                                    $study->has_nmrium = true;
+                                    $study->save();
+                                }
+                            }
+                        });
+                    } else {
+                        $nmriumInfo = json_decode($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: ',  $e->getMessage(), "\n";
+                }
+
+                foreach ($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;
+                    $level = -($fsObject->level);
+                    // echo $fsObject->path;
+                    // echo("\r\n");
+                    // echo $study->name;
+                    // echo("\r\n");
+                    $path = $study->name.'/'.$dataset->name;
+                    foreach ($nmriumInfo['data']['spectra'] as $spectra) {
+                        unset($_nmriumJSON['data']['spectra']);
+                        $files = $spectra['sourceSelector']['files'];
+                        // echo($path);
+                        // echo("\r\n");
+                        $pathsMatch = true;
+                        if ($files) {
+                            foreach ($files as $file) {
+                                echo $file;
+                                echo "\r\n";
+                                if (! str_contains($file, $path)) {
+                                    $pathsMatch = false;
+                                }
+                            }
+                        }
+                        // echo($pathsMatch);
+                        // echo("\r\n");
+                        if ($pathsMatch) {
+                            $_nmriumJSON['data']['spectra'] = [$spectra];
+                            // dd($_nmriumJSON);
+                            $_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);
+                                }
+                                $dataset->type = $experiment.','.$nucleus;
+                            }
+                            $dataset->save();
+                        }
+                    }
+                    // }
+                }
+            }
+        }
+    }
+
+    public function processSpectra($url)
+    {
+        $response = Http::timeout(300)->post('https://nodejsdev.nmrxiv.org/spectra-parser', [
+            'urls' => [$url],
+            'snapshot' => false,
+        ]);
+
+        return $response->json();
+    }
+}
diff --git a/app/Console/Commands/ManageFiles.php b/app/Console/Commands/ManageFiles.php
@@ -58,7 +58,7 @@ public function processFiles($path)
                     $fsObject->save();
                 }
             } elseif ($item instanceof \League\Flysystem\DirectoryAttributes) {
-                echo $item->study_id;
+                // echo $item->study_id;
             }
         }
     }

diff --git a/app/Console/Commands/SanitizeMolecules.php b/app/Console/Commands/SanitizeMolecules.php
@@ -0,0 +1,51 @@
+<?php
+
+namespace App\Console\Commands;
+
+use App\Models\Molecule;
+use Illuminate\Console\Command;
+use Illuminate\Support\Facades\Http;
+
+class SanitizeMolecules extends Command
+{
+    /**
+     * The name and signature of the console command.
+     *
+     * @var string
+     */
+    protected $signature = 'nmrxiv:molecules-clean';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'Sanitize molecules';
+
+    /**
+     * Execute the console command.
+     */
+    public function handle()
+    {
+        $molecules = Molecule::whereNull('CANONICAL_SMILES')->get();
+
+        foreach ($molecules as $molecule) {
+            echo $molecule->id;
+            echo "\r\n";
+            $molecule->MOL = '
+            '.$molecule->MOL;
+            $standardisedMOL = $this->standardizeMolecule($molecule->MOL);
+            $molecule->CANONICAL_SMILES = $standardisedMOL['canonical_smiles'];
+            $molecule->STANDARD_INCHI = $standardisedMOL['inchi'];
+            $molecule->INCHI_KEY = $standardisedMOL['inchikey'];
+            $molecule->save();
+        }
+    }
+
+    protected function standardizeMolecule($mol)
+    {
+        $response = Http::post('https://dev.api.naturalproducts.net/latest/chem/standardize', $mol);
+
+        return $response->json();
+    }
+}
diff --git a/app/Console/Commands/SanitizeProjects.php b/app/Console/Commands/SanitizeProjects.php
@@ -57,8 +57,9 @@ public function cleanProjects()
             ['draft_id', null],
         ])->get();
 
-        return DB::transaction(function () use ($projects) {
-            foreach ($projects as $project) {
+        foreach ($projects as $project) {
+            return DB::transaction(function () use ($project) {
+
                 $user_id = $project->owner->id;
                 $team_id = $project->team_id;
                 $id = Str::uuid();
@@ -107,8 +108,9 @@ public function cleanProjects()
                         $dataset->save();
                     }
                 }
-            }
-        });
+            });
+
+        }
     }
 
     public function cleanDrafts()
@@ -307,10 +309,20 @@ public function localise()
 
     public function updateFilesStatus()
     {
-        return DB::transaction(function () {
-            $fsObjects = FileSystemObject::all();
+        $drafts = Draft::where('is_deleted', true)->get();
+        foreach ($drafts as $draft) {
+            echo $draft->id;
+            echo "\r\n";
+            echo 'Deleting associated files';
+            FileSystemObject::where('draft_id', $draft->id)->delete();
+            echo 'Deleting draft';
+            echo "\r\n";
+            Draft::where('id', $draft->id)->delete();
+        }
 
-            foreach ($fsObjects as $fsObject) {
+        $fsObjects = FileSystemObject::whereNull('status')->get();
+        foreach ($fsObjects as $fsObject) {
+            DB::transaction(function () use ($fsObject) {
                 if ($fsObject->path) {
                     $exists = Storage::disk(env('FILESYSTEM_DRIVER'))->exists($fsObject->path);
                     if (! $exists) {
@@ -320,8 +332,8 @@ public function updateFilesStatus()
                     }
                     $fsObject->save();
                 }
-            }
-        });
+            });
+        }
     }
 
     public function updateFilePaths()