From 6a518b9692521c49aaf70f7c971c29c6a6ca54b2 Mon Sep 17 00:00:00 2001
From: Venkata Chandra Sekhar Nainala <mailcs76@gmail.com>
Date: Fri, 2 Aug 2024 10:18:23 +0200
Subject: [PATCH 1/2] fix: switched to cheminf studio ws API

---
 .env.example                               | 2 +-
 app/Console/Commands/SanitizeMolecules.php | 2 +-
 app/Jobs/ArchiveStudy.php                  | 2 +-
 resources/js/Pages/Study/About.vue         | 2 +-
 resources/js/Pages/Upload.vue              | 4 ++--
 resources/js/Shared/SpectraEditor.vue      | 2 +-
 6 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/.env.example b/.env.example
index e9a71787..3024f02f 100644
--- a/.env.example
+++ b/.env.example
@@ -14,7 +14,7 @@ EUROPEMC_WS_API=https://www.ebi.ac.uk/europepmc/webservices/rest/search
 ORCID_ID_SEARCH_API=https://pub.orcid.org/v2.1/search
 ORCID_ID_EMPLOYMENT_API=https://pub.orcid.org/v3.0/{orcid_id}/employments
 ORCID_ID_PERSON_API=https://pub.orcid.org/v3.0/{orcid_id}/person
-CM_API=https://api.naturalproducts.net/latest/
+CM_API=https://api.cheminf.studio/latest/
 CROSSREF_API=https://api.crossref.org/works/
 DATACITE_API=https://api.datacite.org/
 
diff --git a/app/Console/Commands/SanitizeMolecules.php b/app/Console/Commands/SanitizeMolecules.php
index 45e576ed..ed6f4b7c 100644
--- a/app/Console/Commands/SanitizeMolecules.php
+++ b/app/Console/Commands/SanitizeMolecules.php
@@ -111,7 +111,7 @@ protected function fetchCAS($smiles)
     protected function standardizeMolecule($mol)
     {
         try {
-            $response = Http::post('https://api.naturalproducts.net/latest/chem/standardize', $mol);
+            $response = Http::post('https://api.cheminf.studio/latest/chem/standardize', $mol);
 
             return $response->json();
         } catch (\Illuminate\Http\Client\ConnectionException $e) {
diff --git a/app/Jobs/ArchiveStudy.php b/app/Jobs/ArchiveStudy.php
index 8f47accd..fb5b8496 100644
--- a/app/Jobs/ArchiveStudy.php
+++ b/app/Jobs/ArchiveStudy.php
@@ -196,7 +196,7 @@ public function handle(): void
 
     // protected function standardizeMolecule($mol)
     // {
-    //     $response = Http::post('https://dev.api.naturalproducts.net/latest/chem/standardize', $mol);
+    //     $response = Http::post('https://api.cheminf.studio/latest/chem/standardize', $mol);
     //     return $response->json();
     // }
 
diff --git a/resources/js/Pages/Study/About.vue b/resources/js/Pages/Study/About.vue
index 33713145..9042bab8 100644
--- a/resources/js/Pages/Study/About.vue
+++ b/resources/js/Pages/Study/About.vue
@@ -735,7 +735,7 @@ export default {
         },
         standardizeMolecules(mol) {
             return axios.post(
-                "https://api.naturalproducts.net/latest/chem/standardize",
+                "https://api.cheminf.studio/latest/chem/standardize",
                 mol
             );
         },
diff --git a/resources/js/Pages/Upload.vue b/resources/js/Pages/Upload.vue
index 9a3cfc2d..1db89b4e 100644
--- a/resources/js/Pages/Upload.vue
+++ b/resources/js/Pages/Upload.vue
@@ -2519,7 +2519,7 @@ export default {
         },
         standardizeMolecules(mol) {
             return axios.post(
-                "https://api.naturalproducts.net/latest/chem/standardize",
+                "https://api.cheminf.studio/latest/chem/standardize",
                 mol
             );
         },
@@ -2547,7 +2547,7 @@ export default {
                             // convert to smiles
                             axios
                                 .post(
-                                    "https://dev.api.naturalproducts.net/latest/chem/standardize",
+                                    "https://api.cheminf.studio/latest/latest/chem/standardize",
                                     response.data
                                 )
                                 .then((res) => {
diff --git a/resources/js/Shared/SpectraEditor.vue b/resources/js/Shared/SpectraEditor.vue
index 75fbcd94..f421a6a0 100644
--- a/resources/js/Shared/SpectraEditor.vue
+++ b/resources/js/Shared/SpectraEditor.vue
@@ -385,7 +385,7 @@ export default {
                     mol = this.fixLineError(mol);
                     axios
                         .post(
-                            "https://api.naturalproducts.net/latest/chem/standardize",
+                            "https://api.cheminf.studio/latest/chem/standardize",
                             mol.molfile
                         )
                         .then((res) => {

From 1e2f8e2ef9228ade5939cd9882b1ace4a4e0a282 Mon Sep 17 00:00:00 2001
From: Venkata Chandra Sekhar Nainala <mailcs76@gmail.com>
Date: Fri, 2 Aug 2024 10:54:17 +0200
Subject: [PATCH 2/2] fix: switched to cdk for 2d rendering

---
 resources/js/Shared/Depictor2D.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/resources/js/Shared/Depictor2D.vue b/resources/js/Shared/Depictor2D.vue
index ae37203e..42cc246f 100644
--- a/resources/js/Shared/Depictor2D.vue
+++ b/resources/js/Shared/Depictor2D.vue
@@ -18,7 +18,7 @@
                     width +
                     '&CIP=' +
                     CIP +
-                    '&toolkit=rdkit'
+                    '&toolkit=cdk'
                 "
                 alt=""
             />