Development

.github/workflows/dev-build.yml

@@ -72,6 +72,7 @@ jobs:
         push: true
         build-args: |
           RELEASE_VERSION=dev-app-latest
+          COMPOSER_AUTH=${{ secrets.COMPOSER_AUTH }}
         tags: ${{ env.REPOSITORY_NAMESPACE }}/${{ env.REPOSITORY_NAME }}:dev-app-latest
 
     # Build and push the nginx Docker image
@@ -83,6 +84,7 @@ jobs:
         push: true
         build-args: |
           RELEASE_VERSION=dev-nginx-latest
+          COMPOSER_AUTH=${{ secrets.COMPOSER_AUTH }}
         tags: ${{ env.REPOSITORY_NAMESPACE }}/${{ env.REPOSITORY_NAME }}:dev-nginx-latest
 
     # Deploy the latest Docker image to the GKE cluster
@@ -92,4 +94,4 @@ jobs:
         kubectl rollout restart deployment/$WORKER_DEPLOYMENT_NAME
         kubectl rollout restart deployment/$SCHEDULER_DEPLOYMENT_NAME
         kubectl rollout status deployment/$DEPLOYMENT_NAME --timeout=300s
-        kubectl get services -o wide
+        kubectl get services -o wide

.gitignore

@@ -17,3 +17,5 @@ yarn-error.log
 /.fleet
 /.idea
 /.vscode
+storage/*.tsv
+storage/*.csv

app/Console/Commands/AssignIdentifiers.php

@@ -0,0 +1,104 @@
+<?php
+
+namespace App\Console\Commands;
+
+use App\Models\Molecule;
+use App\Models\Ticker;
+use DB;
+use Illuminate\Console\Command;
+
+class AssignIdentifiers extends Command
+{
+    /**
+     * The name and signature of the console command.
+     *
+     * @var string
+     */
+    protected $signature = 'molecules:assign-identifiers';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'Command description';
+
+    /**
+     * Execute the console command.
+     */
+    public function handle()
+    {
+        $batchSize = 1000;
+        $currentIndex = $this->fetchLastIndex() + 1;
+        $data = [];
+        $this->info('Mapping parents');
+        Molecule::select('identifier', 'id', 'has_variants')->where([
+            ['has_stereo', '=', false],
+            ['identifier', '=', null],
+        ])->chunk($batchSize, function ($molecules) use (&$currentIndex) {
+            $data = [];
+            $header = ['id', 'identifier'];
+            foreach ($molecules as $molecule) {
+                if (! $molecule->identifier) {
+                    $data[] = array_combine($header, [$molecule->id, $this->generateIdentifier($currentIndex)]);
+                    $currentIndex++;
+                }
+            }
+            $this->insertBatch($data);
+        });
+        $this->info('Mapping parents: Done');
+
+        $this->info('Mapping variants');
+        Molecule::select('identifier', 'id', 'has_variants')->where(
+            [
+                ['is_parent', '=', true],
+                ['identifier', '!=', null],
+            ])->chunk($batchSize, function ($molecules) {
+                $data = [];
+                $header = ['id', 'identifier'];
+                foreach ($molecules as $molecule) {
+                    $i = 1;
+                    $variants = $molecule->variants;
+                    foreach ($variants as $variant) {
+                        $data[] = array_combine($header, [$variant->id, $molecule->identifier.'.'.$i]);
+                        $i++;
+                    }
+                }
+                $this->insertBatch($data);
+            });
+        $this->info('Mapping variants: Done');
+    }
+
+    public function generateIdentifier($index)
+    {
+        return 'CNP'.str_pad($index, 7, '0', STR_PAD_LEFT);
+    }
+
+    public function fetchLastIndex()
+    {
+        $ticker = Ticker::where('type', 'molecule')->first();
+
+        return (int) $ticker->index;
+    }
+
+    /**
+     * Insert a batch of data into the database.
+     *
+     * @return void
+     */
+    private function insertBatch(array $data)
+    {
+        DB::transaction(function () use ($data) {
+            foreach ($data as $row) {
+                Molecule::updateorCreate(
+                    [
+                        'id' => $row['id'],
+                    ],
+                    [
+                        'identifier' => $row['identifier'],
+                    ]
+                );
+            }
+        });
+    }
+}

app/Console/Commands/DashWidgetsRefresh.php

@@ -0,0 +1,189 @@
+<?php
+
+namespace App\Console\Commands;
+
+use App\Models\Collection;
+use App\Models\GeoLocation;
+use App\Models\Molecule;
+use App\Models\Organism;
+use Illuminate\Console\Command;
+use Illuminate\Support\Facades\Cache;
+use Illuminate\Support\Facades\DB;
+
+class DashWidgetsRefresh extends Command
+{
+    /**
+     * The name and signature of the console command.
+     *
+     * @var string
+     */
+    protected $signature = 'app:cache';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'This refreshes the dashboard widgets.';
+
+    /**
+     * Execute the console command.
+     */
+    public function handle()
+    {
+        // Clear the cache for all widgets
+        Cache::forget('stats');
+
+        // Create the cache for all DashboardStats widgets
+        Cache::rememberForever('stats.collections', function () {
+            return DB::table('collections')->selectRaw('count(*)')->get()[0]->count;
+        });
+        Cache::rememberForever('stats.citations', function () {
+            return DB::table('citations')->selectRaw('count(*)')->get()[0]->count;
+        });
+        Cache::rememberForever('stats.organisms', function () {
+            return DB::table('organisms')->selectRaw('count(*)')->get()[0]->count;
+        });
+        Cache::rememberForever('stats.geo_locations', function () {
+            return DB::table('geo_locations')->selectRaw('count(*)')->get()[0]->count;
+        });
+        Cache::rememberForever('stats.reports', function () {
+            return DB::table('reports')->selectRaw('count(*)')->get()[0]->count;
+        });
+
+        // Create the cache for all DashboardStatsMid widgets
+        Cache::rememberForever('stats.molecules', function () {
+            return DB::table('molecules')->selectRaw('count(*)')->get()[0]->count;
+        });
+        Cache::rememberForever('stats.molecules.non_stereo', function () {
+            return DB::table('molecules')->selectRaw('count(*)')->whereRaw('has_stereo=false and is_parent=false')->get()[0]->count;
+        });
+        Cache::rememberForever('stats.molecules.stereo', function () {
+            return DB::table('molecules')->selectRaw('count(*)')->whereRaw('has_stereo=true')->get()[0]->count;
+        });
+        Cache::rememberForever('stats.molecules.parent', function () {
+            return DB::table('molecules')->selectRaw('count(*)')->whereRaw('has_stereo=false and is_parent=true')->get()[0]->count;
+        });
+
+        // Create the cache for all Collection widgets
+
+        $collection_ids = Collection::pluck('id')->toArray();
+
+        foreach ($collection_ids as $collection_id) {
+
+            Cache::rememberForever('stats.collections'.$collection_id.'entries.count', function () use ($collection_id) {
+                return DB::table('entries')->selectRaw('count(*)')->whereRaw('collection_id='.$collection_id)->get()[0]->count;
+            });
+
+            Cache::rememberForever('stats.collections'.$collection_id.'passed_entries.count', function () use ($collection_id) {
+                return DB::table('entries')->selectRaw('count(*)')->whereRaw('collection_id='.$collection_id)->whereRaw("status = 'PASSED'")->get()[0]->count;
+            });
+
+            Cache::rememberForever('stats.collections'.$collection_id.'rejected_entries.count', function () use ($collection_id) {
+                return DB::table('entries')->selectRaw('count(*)')->whereRaw('collection_id='.$collection_id)->whereRaw("status = 'REJECTED'")->get()[0]->count;
+            });
+
+            Cache::rememberForever('stats.collections'.$collection_id.'citations.count', function () use ($collection_id) {
+                $entries = DB::table('entries')
+                    ->select('entries.doi')
+                    ->join('collections', 'collections.id', '=', 'entries.collection_id')
+                    ->where('collections.id', $collection_id)
+                    ->pluck('doi');
+
+                $dois = collect();
+
+                foreach ($entries as $entry) {
+                    $dois = $dois->merge(explode('|', $entry));
+                }
+
+                $uniqueDois = $dois->filter(function ($doi) {
+                    return ! empty($doi);
+                })->unique();
+
+                return $uniqueDois->count();
+            });
+
+            Cache::rememberForever('stats.collections'.$collection_id.'molecules.count', function () use ($collection_id) {
+                return DB::table('collection_molecule')->selectRaw('count(*)')->whereRaw('collection_id ='.$collection_id)->get()[0]->count;
+            });
+
+            Cache::rememberForever('stats.collections'.$collection_id.'organisms.count', function () use ($collection_id) {
+                $entries = DB::table('entries')
+                    ->select('entries.organism')
+                    ->join('collections', 'collections.id', '=', 'entries.collection_id')
+                    ->where('collections.id', $collection_id)
+                    ->pluck('organism');
+
+                $organisms = collect();
+
+                foreach ($entries as $entry) {
+                    $organisms = $organisms->merge(explode('|', $entry));
+                }
+
+                $uniqueOrgs = $organisms->filter(function ($organism) {
+                    return ! empty($organism);
+                })->unique();
+
+                return $uniqueOrgs->count();
+            });
+
+            Cache::rememberForever('stats.collections'.$collection_id.'geo_locations.count', function () use ($collection_id) {
+                $entries = DB::table('entries')
+                    ->select('entries.geo_location')
+                    ->join('collections', 'collections.id', '=', 'entries.collection_id')
+                    ->where('collections.id', $collection_id)
+                    ->pluck('geo_location');
+
+                $geo_locations = collect();
+
+                foreach ($entries as $entry) {
+                    $geo_locations = $geo_locations->merge(explode('|', $entry));
+                }
+
+                $uniqueGeos = $geo_locations->filter(function ($geo_location) {
+                    return ! empty($geo_location);
+                })->unique();
+
+                return $uniqueGeos->count();
+            });
+        }
+
+        // Create the cache for all Molecule widgets
+        //     $molecule_ids = Molecule::pluck('id')->toArray();
+        //     foreach ($molecule_ids as $molecule_id) {
+        //         Cache::rememberForever('stats.molecules'.$molecule_id.'organisms.count', function () use ($molecule_id){
+        //             return DB::table('molecule_organism')->selectRaw('count(*)')->whereRaw('molecule_id='.$molecule_id)->get()[0]->count;
+        //         });
+        //         Cache::rememberForever('stats.molecules'.$molecule_id.'geo_locations.count', function () use ($molecule_id){
+        //             return DB::table('geo_location_molecule')->selectRaw('count(*)')->whereRaw('molecule_id='.$molecule_id)->get()[0]->count;
+        //         });
+        //     }
+
+        // // Create the cache for all Organism widgets
+
+        // $organism_ids = Organism::pluck('id')->toArray();
+
+        // foreach ($organism_ids as $organism_id) {
+        //     Cache::rememberForever('stats.organisms'.$organism_id.'molecules.count', function () use ($organism_id){
+        //         return DB::table('molecule_organism')->selectRaw('count(*)')->whereRaw('organism_id='.$organism_id)->get()[0]->count;
+        //     });
+        //     Cache::rememberForever('stats.organisms'.$organism_id.'geo_locations.count', function () use ($organism_id){
+        //         return DB::table('molecule_organism')->selectRaw('count(*)')->whereRaw('organism_id='.$organism_id)->Join('geo_location_molecule', 'molecule_organism.molecule_id', '=', 'geo_location_molecule.molecule_id')->get()[0]->count;
+        //     });
+        // }
+
+        // Create the cache for all Geo Location widgets
+
+        // $geo_location_ids = GeoLocation::pluck('id')->toArray();
+
+        // foreach ($geo_location_ids as $geo_location_id) {
+        //     Cache::rememberForever('stats.geo_locations'.$geo_location_id.'molecules.count', function () use ($geo_location_id) {
+        //         return DB::table('geo_location_molecule')->selectRaw('count(*)')->whereRaw('geo_location_id='.$geo_location_id)->get()[0]->count;
+        //     });
+        //     Cache::rememberForever('stats.geo_locations'.$geo_location_id.'organisms.count', function () use ($geo_location_id) {
+        //         return DB::table('geo_location_molecule')->selectRaw('count(*)')->whereRaw('geo_location_id='.$geo_location_id)->Join('molecule_organism', 'geo_location_molecule.molecule_id', '=', 'molecule_organism.molecule_id')->get()[0]->count;
+        //     });
+        // }
+
+    }
+}