Steinbeck-Lab · vcnainala · Jun 1, 2026 · Jun 1, 2026 · Jun 1, 2026 · Jun 1, 2026
diff --git a/.env.ci b/.env.ci
@@ -40,8 +40,24 @@ MAIL_FROM_NAME="${APP_NAME}"
 AWS_ACCESS_KEY_ID=test-key
 AWS_SECRET_ACCESS_KEY=test-secret
 AWS_DEFAULT_REGION=us-east-1
+AWS_URL=https://s3.uni-jena.de
+AWS_ENDPOINT=https://s3.uni-jena.de
 AWS_BUCKET=test-bucket
-AWS_USE_PATH_STYLE_ENDPOINT=false
+AWS_USE_PATH_STYLE_ENDPOINT=true
+AWS_DOWNLOADS_URL=https://coconut.s3.uni-jena.de/prod/downloads
+
+COCONUT_PUBLIC_URL=https://coconut.naturalproducts.net
+CM_PUBLIC_API=https://api.cheminf.studio/latest/
+API_URL=https://api.cheminf.studio/latest/
+EUROPEPMC_WS_API=https://www.ebi.ac.uk/europepmc/webservices/rest/search
+CROSSREF_WS_API=https://api.crossref.org/works/
+DATACITE_WS_API=https://api.datacite.org/dois/
+PUBCHEM_API_BASE=https://pubchem.ncbi.nlm.nih.gov/rest/pug
+NP_CLASSIFIER_URL=https://npclassifier.gnps2.org/classify
+NFDI_OIDC_BASE_URL=https://regapp.nfdi-aai.de/oidc/realms/nfdi/protocol/openid-connect
+GLOBALNAMES_API_URL=https://finder.globalnames.org/api/v1/find
+OLS4_API_BASE=https://www.ebi.ac.uk/ols4/api
+UI_AVATARS_URL=https://ui-avatars.com/api
 
 PUSHER_APP_ID=
 PUSHER_APP_KEY=

diff --git a/.env.example b/.env.example
@@ -40,8 +40,27 @@ MAIL_FROM_NAME="${APP_NAME}"
 AWS_ACCESS_KEY_ID=
 AWS_SECRET_ACCESS_KEY=
 AWS_DEFAULT_REGION=us-east-1
-AWS_BUCKET=
-AWS_USE_PATH_STYLE_ENDPOINT=false
+AWS_URL=https://s3.uni-jena.de
+AWS_ENDPOINT=https://s3.uni-jena.de
+AWS_BUCKET=coconut
+AWS_USE_PATH_STYLE_ENDPOINT=true
+AWS_DOWNLOADS_URL=https://coconut.s3.uni-jena.de/prod/downloads
+
+COCONUT_PUBLIC_URL=https://coconut.naturalproducts.net
+
+CM_PUBLIC_API=https://api.cheminf.studio/latest/
+API_URL=https://api.cheminf.studio/latest/
+
+EUROPEPMC_WS_API=https://www.ebi.ac.uk/europepmc/webservices/rest/search
+CROSSREF_WS_API=https://api.crossref.org/works/
+DATACITE_WS_API=https://api.datacite.org/dois/
+
+PUBCHEM_API_BASE=https://pubchem.ncbi.nlm.nih.gov/rest/pug
+NP_CLASSIFIER_URL=https://npclassifier.gnps2.org/classify
+NFDI_OIDC_BASE_URL=https://regapp.nfdi-aai.de/oidc/realms/nfdi/protocol/openid-connect
+GLOBALNAMES_API_URL=https://finder.globalnames.org/api/v1/find
+OLS4_API_BASE=https://www.ebi.ac.uk/ols4/api
+UI_AVATARS_URL=https://ui-avatars.com/api
 
 PUSHER_APP_ID=
 PUSHER_APP_KEY=

diff --git a/SocialiteProviders/src/NFDIAAI/Provider.php b/SocialiteProviders/src/NFDIAAI/Provider.php
@@ -21,23 +21,23 @@ class Provider extends AbstractProvider
      */
     protected function getAuthUrl($state)
     {
-        return $this->buildAuthUrlFromBase('https://regapp.nfdi-aai.de/oidc/realms/nfdi/protocol/openid-connect/auth', $state);
+        return $this->buildAuthUrlFromBase(config('services.regapp.oidc_base_url').'/auth', $state);
     }
 
     /**
      * {@inheritdoc}
      */
     protected function getTokenUrl()
     {
-        return 'https://regapp.nfdi-aai.de/oidc/realms/nfdi/protocol/openid-connect/token';
+        return config('services.regapp.oidc_base_url').'/token';
     }
 
     /**
      * {@inheritdoc}
      */
     protected function getUserByToken($token)
     {
-        $response = $this->getHttpClient()->get('https://regapp.nfdi-aai.de/oidc/realms/nfdi/protocol/openid-connect/userinfo', [
+        $response = $this->getHttpClient()->get(config('services.regapp.oidc_base_url').'/userinfo', [
             RequestOptions::HEADERS => [
                 'Authorization' => 'Bearer '.$token,
             ],

diff --git a/app/Console/Commands/Classify.php b/app/Console/Commands/Classify.php
@@ -70,7 +70,7 @@ public function handle()
                     $canonical_smiles = $mol->canonical_smiles;
 
                     // Build endpoints.
-                    $apiUrl = 'https://npclassifier.gnps2.org/classify?smiles=';
+                    $apiUrl = config('services.npclassifier.url').'?smiles=';
                     $endpoint = $apiUrl.urlencode($canonical_smiles);
 
                     // Log the start of processing for this molecule.

diff --git a/app/Console/Commands/MapOrganismNamesToOGG.php b/app/Console/Commands/MapOrganismNamesToOGG.php
@@ -19,7 +19,7 @@ public function __construct()
     {
         parent::__construct();
         $this->client = new Client([
-            'base_uri' => 'https://www.ebi.ac.uk/ols4/api/v2/',
+            'base_uri' => config('services.ols.base_url').'/v2/',
         ]);
     }
 
@@ -84,7 +84,7 @@ protected function getGNFMatches($name, $organism)
         ];
 
         $client = new Client;
-        $url = 'https://finder.globalnames.org/api/v1/find';
+        $url = config('services.globalnames.url');
 
         $response = $client->post($url, [
             'json' => $data,

diff --git a/app/Filament/Dashboard/Resources/CollectionResource.php b/app/Filament/Dashboard/Resources/CollectionResource.php
@@ -174,7 +174,7 @@ public static function infolist(Schema $schema): Schema
                             ->label('Collection Image')
                             ->visibility('public')
                             ->size(200)
-                            ->state(fn ($record) => $record->image ? 'https://s3.uni-jena.de/coconut/'.$record->image : null),
+                            ->state(fn ($record) => $record->image ? public_storage_url($record->image) : null),
                     ]),
                 Section::make('Distribution')
                     ->schema([

diff --git a/app/Filament/Dashboard/Resources/OrganismResource.php b/app/Filament/Dashboard/Resources/OrganismResource.php
@@ -164,7 +164,7 @@ protected static function getGNFMatches($name, $organism)
         ];
 
         $client = new Client;
-        $url = 'https://finder.globalnames.org/api/v1/find';
+        $url = config('services.globalnames.url');
 
         $response = $client->post($url, [
             'json' => $data,
@@ -228,7 +228,7 @@ protected static function updateOrganismModel($name, $iri, $organism = null, $ra
     protected static function getOLSIRI($name, $rank)
     {
         $client = new Client([
-            'base_uri' => 'https://www.ebi.ac.uk/ols4/api/',
+            'base_uri' => config('services.ols.base_url').'/',
         ]);
 
         try {

diff --git a/app/Filament/Dashboard/Widgets/TopContributors.php b/app/Filament/Dashboard/Widgets/TopContributors.php
@@ -35,7 +35,7 @@ public function getTopContributors(): array
                     $contributorData[] = [
                         'user' => $user,
                         'contribution_count' => $contributor->contribution_count,
-                        'avatar_url' => $user->profile_photo_url ?? 'https://ui-avatars.com/api/?name='.urlencode($user->name).'&color=7F9CF5&background=EBF4FF',
+                        'avatar_url' => $user->profile_photo_url ?? config('services.avatars.url').'?name='.urlencode($user->name).'&color=7F9CF5&background=EBF4FF',
                     ];
                 }
             }

diff --git a/app/Helper.php b/app/Helper.php
@@ -23,6 +23,30 @@ function csp_nonce(): string
     return app('csp-nonce');
 }
 
+/**
+ * Public base URL for objects on the configured S3/Ceph disk.
+ */
+function public_storage_url(?string $path = null): string
+{
+    $base = rtrim((string) config('filesystems.disks.s3.url'), '/');
+
+    if ($path === null || $path === '') {
+        return $base;
+    }
+
+    return $base.'/'.ltrim($path, '/');
+}
+
+/**
+ * Public base URL for COCONUT release downloads on object storage.
+ */
+function public_downloads_url(string $path): string
+{
+    $base = rtrim((string) config('filesystems.disks.s3.downloads_url'), '/');
+
+    return $base.'/'.ltrim($path, '/');
+}
+
 /**
  * Get all curator users.
  * This centralizes curator fetching logic that may change in the future.

diff --git a/app/Jobs/ClassifyMoleculeAuto.php b/app/Jobs/ClassifyMoleculeAuto.php
@@ -60,7 +60,7 @@ public function handle(): void
             $canonical_smiles = $this->molecule->canonical_smiles;
 
             // Build endpoint
-            $apiUrl = 'https://npclassifier.gnps2.org/classify?smiles=';
+            $apiUrl = config('services.npclassifier.url').'?smiles=';
             $endpoint = $apiUrl.urlencode($canonical_smiles);
 
             // Fetch classification data from API

diff --git a/app/Jobs/ImportPubChem.php b/app/Jobs/ImportPubChem.php
@@ -59,7 +59,7 @@ private function throttledGet(string $url)
 
     public function fetchIUPACNameFromPubChem()
     {
-        $smilesURL = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/cids/TXT?smiles='
+        $smilesURL = config('services.pubchem.base_url').'/compound/smiles/cids/TXT?smiles='
             .urlencode($this->molecule->canonical_smiles);
         $cidResponse = $this->throttledGet($smilesURL);
 
@@ -71,7 +71,7 @@ public function fetchIUPACNameFromPubChem()
 
         if ($cid && trim($cid) != '0') {
             $cid = trim(preg_replace('/\s+/', ' ', $cid));
-            $cidPropsURL = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/'.$cid.'/json';
+            $cidPropsURL = config('services.pubchem.base_url').'/compound/cid/'.$cid.'/json';
             $dataResponse = $this->throttledGet($cidPropsURL);
 
             if (! $dataResponse->successful()) {
@@ -112,7 +112,7 @@ public function fetchSynonymsCASFromPubChem($cid)
     {
         if ($cid && trim($cid) != '0') {
             $cid = trim(preg_replace('/\s+/', ' ', $cid));
-            $synonymsURL = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/'.$cid.'/synonyms/txt';
+            $synonymsURL = config('services.pubchem.base_url').'/compound/cid/'.$cid.'/synonyms/txt';
 
             $maxRetries = 3;
             $backoffSeconds = 2;

diff --git a/app/Jobs/ImportPubChemAuto.php b/app/Jobs/ImportPubChemAuto.php
@@ -168,7 +168,7 @@ private function throttledGet(string $url)
 
     public function fetchIUPACNameFromPubChem()
     {
-        $smilesURL = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/cids/TXT?smiles='.urlencode($this->molecule->canonical_smiles);
+        $smilesURL = config('services.pubchem.base_url').'/compound/smiles/cids/TXT?smiles='.urlencode($this->molecule->canonical_smiles);
         $cidResponse = $this->throttledGet($smilesURL);
 
         if (! $cidResponse->successful()) {
@@ -180,7 +180,7 @@ public function fetchIUPACNameFromPubChem()
         $cid = $cidResponse->body();
         if ($cid && trim($cid) != '0') {
             $cid = trim(preg_replace('/\s+/', ' ', $cid));
-            $cidPropsURL = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/'.$cid.'/json';
+            $cidPropsURL = config('services.pubchem.base_url').'/compound/cid/'.$cid.'/json';
             $dataResponse = $this->throttledGet($cidPropsURL);
 
             if (! $dataResponse->successful()) {
@@ -229,7 +229,7 @@ public function fetchSynonymsCASFromPubChem($cid)
     {
         if ($cid && trim($cid) != '0') {
             $cid = trim(preg_replace('/\s+/', ' ', $cid));
-            $synonymsURL = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/'.$cid.'/synonyms/txt';
+            $synonymsURL = config('services.pubchem.base_url').'/compound/cid/'.$cid.'/synonyms/txt';
 
             $maxRetries = 3;
             $backoffSeconds = 2;

diff --git a/app/Models/HasDOI.php b/app/Models/HasDOI.php
@@ -10,7 +10,7 @@ public function generateDOI($doiService)
         if (! is_null($doi_host)) {
             $identifier = $this->getIdentifier($this, 'identifier');
             if ($this->doi == null) {
-                $url = 'https://coconut.naturalproducts.net/collections/'.$identifier;
+                $url = url('/collections/'.$identifier);
                 $attributes = $this->getMetadata();
                 $attributes['url'] = $url;
                 $doiResponse = $doiService->createDOI($identifier, $attributes);

diff --git a/app/Models/Molecule.php b/app/Models/Molecule.php
@@ -318,7 +318,7 @@ public function getSchema($type = 'bioschemas')
                 ->email('info.coconut@uni-jena.de');
 
             $coconut = Schema::Organization();
-            $coconut->url('https://coconut.naturalproducts.net/')
+            $coconut->url(url('/'))
                 ->name('COCONUT - COlleCtion of Open Natural prodUcTs')
                 ->contactPoint($contactPoint);
 

diff --git a/app/Services/DOI/DataCite.php b/app/Services/DOI/DataCite.php
@@ -41,7 +41,7 @@ public function getDOI($doi)
     public function createDOI($identifier, $metadata = [])
     {
         $doi = $this->prefix.'/'.Config::get('app.name').'.'.$identifier;
-        $url = 'https://coconut.naturalproducts.net/collections/'.$identifier;
+        $url = url('/collections/'.$identifier);
         $suffix = Config::get('app.name').'.'.$identifier;
         $attributes = [
             'doi' => $this->prefix.'/'.Config::get('app.name').'.'.$identifier,