fix: updated cm public api key and other minor updates

Steinbeck-Lab · Dec 11, 2024 · a63931c · a63931c
1 parent cb6411e
commit a63931c
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Showing 15 changed files with 114 additions and 207 deletions.
diff --git a/app/Console/Kernel.php b/app/Console/Kernel.php
@@ -12,10 +12,9 @@ class Kernel extends ConsoleKernel
      */
     protected function schedule(Schedule $schedule): void
     {
-        // $schedule->command('inspire')->hourly();
         $schedule->command('coconut:entries-process')->everyMinute()->withoutOverlapping();
         $schedule->command('coconut:entries-import')->everyMinute()->withoutOverlapping();
-        $schedule->command('app:dash-widgets-refresh')->everyFifteenMinutes()->withoutOverlapping();
+        $schedule->command('coconut:cache')->everyFifteenMinutes()->withoutOverlapping();
     }
 
     /**

diff --git a/...lament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php b/...lament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php
@@ -99,21 +99,21 @@ public function infolist(Infolist $infolist): Infolist
                     ])
                     ->schema([
                         ImageEntry::make('parent_canonical_smiles')->state(function ($record) {
-                            return env('CM_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->parent_canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
+                            return env('CM_PUBLIC_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->parent_canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
                         })
                             ->width(200)
                             ->height(200)
                             ->ring(5)
                             ->defaultImageUrl(url('/images/placeholder.png')),
                         ImageEntry::make('canonical_smiles')->state(function ($record) {
-                            return env('CM_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
+                            return env('CM_PUBLIC_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
                         })
                             ->width(200)
                             ->height(200)
                             ->ring(5)
                             ->defaultImageUrl(url('/images/placeholder.png')),
                         ImageEntry::make('standardized_canonical_smiles')->state(function ($record) {
-                            return env('CM_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->standardized_canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
+                            return env('CM_PUBLIC_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->standardized_canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
                         })
                             ->width(200)
                             ->height(200)
@@ -133,7 +133,7 @@ public function table(Table $table): Table
                 ImageColumn::make('structure')->square()
                     ->label('Structure')
                     ->state(function ($record) {
-                        return env('CM_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
+                        return env('CM_PUBLIC_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
                     })
                     ->width(200)
                     ->height(200)

diff --git a/app/Filament/Dashboard/Resources/MoleculeResource.php b/app/Filament/Dashboard/Resources/MoleculeResource.php
@@ -78,7 +78,7 @@ public static function table(Table $table): Table
                 ImageColumn::make('structure')->square()
                     ->label('Structure')
                     ->state(function ($record) {
-                        return env('CM_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
+                        return env('CM_PUBLIC_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
                     })
                     ->width(200)
                     ->height(200)

diff --git a/...lament/Dashboard/Resources/MoleculeResource/RelationManagers/MoleculesRelationManager.php b/...lament/Dashboard/Resources/MoleculeResource/RelationManagers/MoleculesRelationManager.php
@@ -26,7 +26,7 @@ public function table(Table $table): Table
                 ImageColumn::make('structure')->square()
                     ->label('Structure')
                     ->state(function ($record) {
-                        return env('CM_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
+                        return env('CM_PUBLIC_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
                     })
                     ->width(200)
                     ->height(200)

diff --git a/...Filament/Dashboard/Resources/MoleculeResource/RelationManagers/RelatedRelationManager.php b/...Filament/Dashboard/Resources/MoleculeResource/RelationManagers/RelatedRelationManager.php
@@ -26,7 +26,7 @@ public function table(Table $table): Table
                 ImageColumn::make('structure')->square()
                     ->label('Structure')
                     ->state(function ($record) {
-                        return env('CM_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
+                        return env('CM_PUBLIC_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
                     })
                     ->width(200)
                     ->height(200)

diff --git a/...lament/Dashboard/Resources/OrganismResource/RelationManagers/MoleculesRelationManager.php b/...lament/Dashboard/Resources/OrganismResource/RelationManagers/MoleculesRelationManager.php
@@ -40,7 +40,7 @@ public function table(Table $table): Table
                 ImageColumn::make('structure')->square()
                     ->label('Structure')
                     ->state(function ($record) {
-                        return env('CM_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
+                        return env('CM_PUBLIC_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
                     })
                     ->width(200)
                     ->height(200)

diff --git a/...Filament/Dashboard/Resources/ReportResource/RelationManagers/MoleculesRelationManager.php b/...Filament/Dashboard/Resources/ReportResource/RelationManagers/MoleculesRelationManager.php
@@ -35,7 +35,7 @@ public function table(Table $table): Table
                 ImageColumn::make('structure')->square()
                     ->label('Structure')
                     ->state(function ($record) {
-                        return env('CM_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
+                        return env('CM_PUBLIC_API', 'https://api.cheminf.studio/latest/').'depict/2D?smiles='.urlencode($record->canonical_smiles).'&height=300&width=300&CIP=true&toolkit=cdk';
                     })
                     ->width(200)
                     ->height(200)

diff --git a/app/Livewire/MoleculeDepict2d.php b/app/Livewire/MoleculeDepict2d.php
@@ -28,13 +28,13 @@ class MoleculeDepict2d extends Component
     #[Computed]
     public function source()
     {
-        return env('CM_API').'depict/2D?smiles='.urlencode($this->smiles).'&height='.$this->height.'&width='.$this->width;
+        return env('CM_PUBLIC_API').'depict/2D?smiles='.urlencode($this->smiles).'&height='.$this->height.'&width='.$this->width;
     }
 
     #[Computed]
     public function preview()
     {
-        return env('CM_API').'depict/2D?smiles='.urlencode($this->smiles);
+        return env('CM_PUBLIC_API').'depict/2D?smiles='.urlencode($this->smiles);
     }
 
     public function downloadMolFile($toolkit)

diff --git a/app/Livewire/MoleculeDepict3d.php b/app/Livewire/MoleculeDepict3d.php
@@ -20,7 +20,7 @@ class MoleculeDepict3d extends Component
     #[Computed]
     public function source()
     {
-        return env('CM_API').'depict/3D?smiles='.urlencode($this->smiles).'&height='.$this->height.'&width='.$this->width.'&CIP='.$this->CIP.'&toolkit=rdkit';
+        return env('CM_PUBLIC_API').'depict/3D?smiles='.urlencode($this->smiles).'&height='.$this->height.'&width='.$this->width.'&CIP='.$this->CIP.'&toolkit=rdkit';
     }
 
     public function downloadSDFFile()

diff --git a/docker-compose.dev.yml b/docker-compose.dev.yml
@@ -0,0 +1,97 @@
+services:
+    app:
+        build:
+            context: .
+            dockerfile: ./FrankenPHP.Dockerfile
+        image: coconut-8.3/app
+        container_name: coconut_app
+        env_file:
+            - .env
+        networks:
+            - coconut
+        ports:
+            - '${APP_PORT:-8000}:8000'
+        depends_on:
+            - pgsql
+            - redis
+            - cm
+    worker:
+        build:
+            context: .
+            dockerfile: ./FrankenPHP.Dockerfile
+        image: coconut-8.3/app
+        container_name: coconut_worker
+        env_file:
+            - .env
+        networks:
+            - coconut
+        depends_on:
+            - app
+            - pgsql
+            - redis
+            - cm
+        environment:
+            WITH_SCHEDULER: true
+            WITH_HORIZON: true
+    pgsql:
+        image: "informaticsmatters/rdkit-cartridge-debian:latest"
+        ports:
+            - '${FORWARD_DB_PORT:-5432}:5432'
+        environment:
+            PGPASSWORD: '${DB_PASSWORD:-secret}'
+            POSTGRES_DB: '${DB_DATABASE}'
+            POSTGRES_USER: '${DB_USERNAME}'
+            POSTGRES_PASSWORD: '${DB_PASSWORD:-secret}'
+        volumes:
+            - 'coconut-pgsql:/var/lib/postgresql/data'
+            - './docker/pgsql/create-testing-database.sql:/docker-entrypoint-initdb.d/10-create-testing-database.sql'
+        networks:
+            - coconut
+        healthcheck:
+            test:
+                - CMD
+                - pg_isready
+                - '-q'
+                - '-d'
+                - '${DB_DATABASE}'
+                - '-U'
+                - '${DB_USERNAME}'
+            retries: 3
+            timeout: 5s
+    redis:
+        image: 'redis:alpine'
+        ports:
+            - '${FORWARD_REDIS_PORT:-6379}:6379'
+        volumes:
+            - 'coconut-redis:/data'
+        networks:
+            - coconut
+        healthcheck:
+            test:
+                - CMD
+                - redis-cli
+                - ping
+            retries: 3
+            timeout: 5s
+    cm:
+        image: "nfdi4chem/cheminformatics-microservice:latest-lite"
+        environment:
+            HOMEPAGE_URL:  "https://docs.api.naturalproducts.net"
+        ports:
+            - '${APP_PORT:-8001}:80'
+        healthcheck:
+            test: ["CMD", "curl", "-f", "http://cm:80/latest/chem/health"]
+            interval: 1m30s
+            timeout: 10s
+            retries: 20
+            start_period: 60s
+        networks:
+            - coconut
+networks:
+    coconut:
+        driver: bridge
+volumes:
+    coconut-pgsql:
+        driver: local
+    coconut-redis:
+        driver: local
diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml
@@ -1,9 +1,6 @@
 services:
     app:
-        build:
-            context: .
-            dockerfile: ./FrankenPHP.Dockerfile
-        image: coconut-8.3/app
+        image: nfdi4chem/coconut:latest
         container_name: coconut_app
         env_file:
             - .env
@@ -16,10 +13,7 @@ services:
             - redis
             - cm
     worker:
-        build:
-            context: .
-            dockerfile: ./FrankenPHP.Dockerfile
-        image: coconut-8.3/app
+        image: nfdi4chem/coconut:latest
         container_name: coconut_worker
         env_file:
             - .env

diff --git a/resources/ops/docker/app/app.dockerfile b/resources/ops/docker/app/app.dockerfile
diff --git a/resources/ops/docker/nginx/nginx.dockerfile b/resources/ops/docker/nginx/nginx.dockerfile