From ca36ea63dd99cd53b875ef2d43ffd2e528438670 Mon Sep 17 00:00:00 2001
From: Venkata Chandra Sekhar Nainala <mailcs76@gmail.com>
Date: Sun, 12 Nov 2023 12:43:50 +0100
Subject: [PATCH 1/4] fix: updated DOIBadge component and various other
 fixes/updates

---
 app/Providers/AppServiceProvider.php          |  6 +-
 resources/js/Mixins/Global.js                 | 12 ++--
 resources/js/Pages/Project/Show.vue           |  4 +-
 resources/js/Pages/Public/Project/Dataset.vue | 20 ++++---
 resources/js/Pages/Public/Project/Files.vue   |  4 +-
 resources/js/Pages/Public/Project/Layout.vue  | 13 ++---
 resources/js/Pages/Public/Project/Samples.vue |  6 +-
 resources/js/Pages/Public/Project/Show.vue    | 15 ++++-
 resources/js/Pages/Public/Project/Study.vue   | 50 +++++-----------
 resources/js/Shared/Citation.vue              |  2 +-
 resources/js/Shared/DOIBadge.vue              | 57 +++++++++++++++++++
 11 files changed, 122 insertions(+), 67 deletions(-)
 create mode 100644 resources/js/Shared/DOIBadge.vue

diff --git a/app/Providers/AppServiceProvider.php b/app/Providers/AppServiceProvider.php
index 5eab1ffb..a83c403d 100644
--- a/app/Providers/AppServiceProvider.php
+++ b/app/Providers/AppServiceProvider.php
@@ -26,8 +26,8 @@ public function register()
      */
     public function boot()
     {
-        // if ($this->app->environment('production')) {
-        //     \URL::forceScheme('https');
-        // }
+        if ($this->app->environment('production')) {
+            \URL::forceScheme('https');
+        }
     }
 }
diff --git a/resources/js/Mixins/Global.js b/resources/js/Mixins/Global.js
index bcf2084f..09a896dc 100644
--- a/resources/js/Mixins/Global.js
+++ b/resources/js/Mixins/Global.js
@@ -74,13 +74,15 @@ export default {
 
             return str;
         },
-        copyToClipboard(text, id) {
-            document.getElementById(id).select();
-            copyText(text, undefined, (error, event) => {
+        copyToClipboard(text, element) {
+            if (typeof element == "string") {
+                document.getElementById(id).select();
+            } else {
+                element.select();
+            }
+            copyText(text, undefined, (error) => {
                 if (error) {
                     console.log(error);
-                } else {
-                    // console.log(event)
                 }
             });
         },
diff --git a/resources/js/Pages/Project/Show.vue b/resources/js/Pages/Project/Show.vue
index 3a90d71c..4f0426ac 100644
--- a/resources/js/Pages/Project/Show.vue
+++ b/resources/js/Pages/Project/Show.vue
@@ -306,7 +306,7 @@
                             v-if="project.identifier"
                             class="text-gray-400 mt-2"
                         >
-                            <img :src="'/badge/doi/' + project.identifier" />
+                            <DOIBadge :doi="project.doi"></DOIBadge>
                         </div>
                         <div
                             class="mt-2 flex items-center text-xs text-gray-400"
@@ -567,6 +567,7 @@ import Citation from "@/Shared/Citation.vue";
 import Publish from "@/Shared/Publish.vue";
 import AuthorCard from "@/Shared/AuthorCard.vue";
 import CitationCard from "@/Shared/CitationCard.vue";
+import DOIBadge from "@/Shared/DOIBadge.vue";
 
 export default {
     components: {
@@ -585,6 +586,7 @@ export default {
         Publish,
         AuthorCard,
         CitationCard,
+        DOIBadge,
     },
     props: [
         "project",
diff --git a/resources/js/Pages/Public/Project/Dataset.vue b/resources/js/Pages/Public/Project/Dataset.vue
index 108f3c96..f70c4f32 100644
--- a/resources/js/Pages/Public/Project/Dataset.vue
+++ b/resources/js/Pages/Public/Project/Dataset.vue
@@ -10,7 +10,10 @@
                     </span>
                     <div class="text-sm">
                         <span class="text-gray-400 pt-2">
-                            <img :src="'badge/doi/' + study.data.identifier" />
+                            <DOIBadge
+                                :doi="study.data.doi"
+                                color="bg-yellow-300"
+                            ></DOIBadge>
                         </span>
                     </div>
                     <div class="float-right">
@@ -97,7 +100,7 @@
                         </div>
                     </div>
                 </h1>
-                <div class="mt-4">
+                <!-- <div class="mt-4">
                     <div class="relative">
                         <div
                             class="absolute inset-0 flex items-center"
@@ -118,7 +121,7 @@
                         class="prose mt-1 text-sm text-blue-gray-500"
                         v-html="md(study.data.description)"
                     ></p>
-                </div>
+                </div> -->
                 <div v-if="study.data.tags.length > 0" class="mt-4">
                     <div class="relative">
                         <div
@@ -309,11 +312,10 @@
                         ><br />
                         <div class="text-sm">
                             <span class="text-gray-400 pt-2">
-                                <img
-                                    :src="
-                                        'badge/doi/' + dataset.data.identifier
-                                    "
-                                />
+                                <DOIBadge
+                                    :doi="dataset.data.doi"
+                                    color="bg-green-100"
+                                ></DOIBadge>
                             </span>
                         </div>
                     </h1>
@@ -338,6 +340,7 @@ import ProjectLayout from "@/Pages/Public/Project/Layout.vue";
 import { ShareIcon, ClipboardDocumentIcon } from "@heroicons/vue/24/solid";
 import { Menu, MenuButton, MenuItem, MenuItems } from "@headlessui/vue";
 import SpectraViewer from "@/Shared/SpectraViewer.vue";
+import DOIBadge from "@/Shared/DOIBadge.vue";
 
 export default {
     components: {
@@ -349,6 +352,7 @@ export default {
         MenuItem,
         MenuItems,
         SpectraViewer,
+        DOIBadge,
     },
     props: ["project", "tab", "study", "dataset"],
     data() {
diff --git a/resources/js/Pages/Public/Project/Files.vue b/resources/js/Pages/Public/Project/Files.vue
index 8d248053..e94d0af1 100644
--- a/resources/js/Pages/Public/Project/Files.vue
+++ b/resources/js/Pages/Public/Project/Files.vue
@@ -1,7 +1,9 @@
 <template>
     <project-layout :project="project" :selected-tab="tab">
         <template #project-content>
-            <div class="pb-10 mb-10 max-w-7xl mx-auto py-4">
+            <div
+                class="pb-10 mb-10 max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 pt-4 pb-6"
+            >
                 <div v-if="project.data.files">
                     <nav
                         v-if="$page.props.selectedFolder"
diff --git a/resources/js/Pages/Public/Project/Layout.vue b/resources/js/Pages/Public/Project/Layout.vue
index b591e26b..ebfe08d6 100644
--- a/resources/js/Pages/Public/Project/Layout.vue
+++ b/resources/js/Pages/Public/Project/Layout.vue
@@ -108,18 +108,15 @@
                                         >
                                     </h1>
                                     <p class="text-gray-700 pl-1 pt-2">
-                                        <img
-                                            :src="
-                                                'badge/doi/' +
-                                                project.data.identifier
-                                            "
-                                        />
+                                        <DOIBadge
+                                            :doi="project.data.doi"
+                                        ></DOIBadge>
                                     </p>
                                     <div class="sm:col-span-12 pt-4">
                                         <span
                                             v-for="tag in project.data.tags"
                                             :key="tag.id"
-                                            class="mt-1 inline-flex items-center rounded-full bg-gray-50 px-2 py-1 text-xs font-medium text-gray-600 ring-1 ring-inset ring-gray-500/10"
+                                            class="mt-1 mr-1 inline-flex items-center rounded-full bg-gray-50 px-2 py-1 text-sm font-medium text-gray-600 ring-1 ring-inset ring-gray-500/10"
                                             target="_blank"
                                             :href="
                                                 '/projects?tag=' + tag.name.en
@@ -179,11 +176,13 @@
 import AppLayout from "@/Layouts/AppLayout.vue";
 import { Link, router } from "@inertiajs/vue3";
 import { ArrowDownTrayIcon } from "@heroicons/vue/24/solid";
+import DOIBadge from "@/Shared/DOIBadge.vue";
 export default {
     components: {
         AppLayout,
         Link,
         ArrowDownTrayIcon,
+        DOIBadge,
     },
     props: ["project", "selectedTab"],
     data() {
diff --git a/resources/js/Pages/Public/Project/Samples.vue b/resources/js/Pages/Public/Project/Samples.vue
index 1be08863..dd623430 100644
--- a/resources/js/Pages/Public/Project/Samples.vue
+++ b/resources/js/Pages/Public/Project/Samples.vue
@@ -1,7 +1,9 @@
 <template>
     <project-layout :project="project" :selected-tab="tab">
         <template #project-content>
-            <div class="p-8">
+            <div
+                class="pb-10 mb-10 max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 pt-4 pb-6"
+            >
                 <div class="flex items-baseline justify-between">
                     <div>
                         <h2 class="text-lg mb-3 font-bold">Studies</h2>
@@ -70,7 +72,7 @@
                     </div>
                     <div v-else>
                         <div
-                            class="mt-8 mx-auto max-w-md grid gap-8 sm:max-w-lg lg:grid-cols-3 lg:max-w-7xl"
+                            class="mt-8 mx-auto max-w-md grid gap-8 sm:max-w-lg lg:grid-cols-4 lg:max-w-7xl"
                         >
                             <div
                                 v-for="study in studies.data"
diff --git a/resources/js/Pages/Public/Project/Show.vue b/resources/js/Pages/Public/Project/Show.vue
index f8cc6192..cd89e4ee 100644
--- a/resources/js/Pages/Public/Project/Show.vue
+++ b/resources/js/Pages/Public/Project/Show.vue
@@ -2,8 +2,17 @@
     <project-layout :project="project" :selected-tab="tab">
         <template #project-content>
             <div
-                class="pb-10 mb-10 max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 py-6"
+                class="pb-10 mb-10 max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 pt-4 pb-6"
             >
+                <div
+                    class="-mx-4"
+                    v-if="project.data.is_public && project.data.doi != null"
+                >
+                    <Citation
+                        :model="'project'"
+                        :doi="project.data.doi"
+                    ></Citation>
+                </div>
                 <div class="mt-2 space-y-4 divide-y divide-y-blue-gray-200">
                     <div>
                         <h3 class="text-xl font-extrabold text-blue-gray-900">
@@ -22,7 +31,7 @@
                         </div>
                     </div>
 
-                    <div class="pt-2">
+                    <div v-if="project.data.species" class="pt-2">
                         <h3 class="text-xl font-extrabold text-blue-gray-900">
                             Organism
                         </h3>
@@ -146,12 +155,14 @@ import ProjectLayout from "@/Pages/Public/Project/Layout.vue";
 import AuthorCard from "@/Shared/AuthorCard.vue";
 import CitationCard from "@/Shared/CitationCard.vue";
 import "ontology-elements/dist/index.js";
+import Citation from "@/Shared/Citation.vue";
 
 export default {
     components: {
         ProjectLayout,
         AuthorCard,
         CitationCard,
+        Citation,
     },
     props: ["project", "tab"],
     data() {
diff --git a/resources/js/Pages/Public/Project/Study.vue b/resources/js/Pages/Public/Project/Study.vue
index 97dc2921..f27f914a 100644
--- a/resources/js/Pages/Public/Project/Study.vue
+++ b/resources/js/Pages/Public/Project/Study.vue
@@ -8,10 +8,11 @@
                     <div class="text-blue-500">
                         {{ study.data.name }}
                     </div>
-                    <div class="text-sm float-left">
-                        <span class="text-gray-400 pt-2">
-                            <img :src="'badge/doi/' + study.data.identifier" />
-                        </span>
+                    <div class="text-sm float-left my-3">
+                        <DOIBadge
+                            :doi="study.data.doi"
+                            color="bg-yellow-300"
+                        ></DOIBadge>
                     </div>
                     <div class="float-right">
                         <span class="flex-0.5 self-center">
@@ -98,6 +99,7 @@
                     </div>
                 </h1>
                 <br />
+                <br />
                 <div
                     v-if="
                         study.data.description &&
@@ -331,17 +333,6 @@
                                 >
                             </option>
                         </select> -->
-                    <!-- <div v-if="selectedDataset" class="text-sm my-2">
-                            <span class="text-gray-400 pt-2">
-                                <img
-                                    :src="
-                                        'badge/doi/' +
-                                        selectedDataset.identifier
-                                    "
-                                />
-                            </span>
-                        </div>
-                    </div> -->
                     <div class="mt-3">
                         <SpectraViewer
                             ref="spectraViewerREF"
@@ -403,16 +394,13 @@
                                                     ></a
                                                 >
                                                 <p class="text-gray-500">
-                                                    <img
-                                                        :src="
-                                                            'badge/doi/' +
-                                                            dataset.identifier
-                                                        "
-                                                    />
+                                                    <DOIBadge
+                                                        color="bg-green-100"
+                                                        :doi="dataset.doi"
+                                                    ></DOIBadge>
                                                 </p>
                                             </div>
                                             <div class="flex-shrink-0 pr-2">
-                                                <!-- {{ dataset.identifier }} -->
                                                 <svg
                                                     xmlns="http://www.w3.org/2000/svg"
                                                     fill="none"
@@ -433,21 +421,6 @@
                                 </li>
                             </ul>
                         </div>
-                        <!-- 
-                        <span
-                               
-                                :value="dataset"
-                            >
-                            <span class="text-gray-400 float-left mr-1 pt-2">
-                                
-                                <img
-                                    :src="
-                                        'badge/doi/' +
-                                        dataset.identifier
-                                    "
-                                />
-                            </span>
-                        </span> -->
                     </div>
                     <div>&emsp;</div>
                 </div>
@@ -465,6 +438,8 @@ import { ShareIcon, ClipboardDocumentIcon } from "@heroicons/vue/24/solid";
 import { Menu, MenuButton, MenuItem, MenuItems } from "@headlessui/vue";
 import SpectraViewer from "@/Shared/SpectraViewer.vue";
 import Depictor2D from "@/Shared/Depictor2D.vue";
+import DOIBadge from "@/Shared/DOIBadge.vue";
+
 export default {
     components: {
         ProjectLayout,
@@ -476,6 +451,7 @@ export default {
         MenuItems,
         SpectraViewer,
         Depictor2D,
+        DOIBadge,
     },
     props: ["project", "tab", "study"],
     data() {
diff --git a/resources/js/Shared/Citation.vue b/resources/js/Shared/Citation.vue
index 457cf82a..163de046 100644
--- a/resources/js/Shared/Citation.vue
+++ b/resources/js/Shared/Citation.vue
@@ -72,7 +72,7 @@ export default {
         dataciteURL() {
             return this.$page.props.dataciteURL
                 ? String(this.$page.props.dataciteURL) + "/dois/"
-                : "https://api.test.datacite.org/dois/";
+                : "https://api.datacite.org/dois/";
         },
     },
     watch: {
diff --git a/resources/js/Shared/DOIBadge.vue b/resources/js/Shared/DOIBadge.vue
new file mode 100644
index 00000000..10e84826
--- /dev/null
+++ b/resources/js/Shared/DOIBadge.vue
@@ -0,0 +1,57 @@
+<template>
+    <div>
+        <div v-if="doi">
+            <div
+                class="inline-flex items-center cursor-pointer"
+                @click.prevent="copyDOIToClipboard"
+            >
+                <span
+                    class="inline-flex items-center rounded-l-md border-r bg-gray-800 px-2 py-1 text-sm font-medium text-white"
+                    >DOI:</span
+                >
+                <span
+                    :class="[
+                        color ? color : 'bg-blue-100',
+                        'inline-flex items-center rounded-r-md px-2 py-1 text-sm font-medium text-gray-900',
+                    ]"
+                    >{{ doi }}</span
+                >
+                <input
+                    readonly
+                    type="hidden"
+                    :value="doi"
+                    class="rounded-l-md focus:ring-gray-500 focus:border-gray-500 block w-full rounded-none rounded-l-md sm:text-sm border-gray-300"
+                    @focus="$event.target.select()"
+                />
+                <span v-if="isVisible" class="text-gray-500 text-xs ml-2"
+                    >Copied to clipboard!</span
+                >
+            </div>
+        </div>
+    </div>
+</template>
+
+<script>
+export default {
+    components: {},
+    props: ["doi", "color"],
+    data() {
+        return {
+            isVisible: false,
+        };
+    },
+    methods: {
+        copyDOIToClipboard(event) {
+            let targetInput =
+                event.target.parentElement.getElementsByTagName("input")[0];
+            if (targetInput) {
+                this.isVisible = true;
+                setTimeout(() => {
+                    this.isVisible = false;
+                }, 2500);
+                this.copyToClipboard(this.doi, targetInput);
+            }
+        },
+    },
+};
+</script>

From e854cbbd1c4c1681c79f128d8bd4f43b1f2524a1 Mon Sep 17 00:00:00 2001
From: Venkata Chandra Sekhar Nainala <mailcs76@gmail.com>
Date: Mon, 13 Nov 2023 00:52:42 +0100
Subject: [PATCH 2/4] fix: updated dataset spectra loading logic and other
 minor updates

---
 app/Console/Commands/ArchiveData.php        |  4 +-
 app/Console/Commands/ExtractSpectra.php     | 85 +++++++++++----------
 app/Http/Controllers/DatasetController.php  |  2 +-
 resources/js/Pages/Public/Project/Study.vue |  1 -
 resources/js/Shared/SpectraViewer.vue       | 37 +++++++--
 5 files changed, 78 insertions(+), 51 deletions(-)

diff --git a/app/Console/Commands/ArchiveData.php b/app/Console/Commands/ArchiveData.php
index 7f6bf796..1c0e5986 100644
--- a/app/Console/Commands/ArchiveData.php
+++ b/app/Console/Commands/ArchiveData.php
@@ -36,8 +36,8 @@ public function handle()
             ])->get();
 
             foreach ($projects as $project) {
-                echo($project->identifier);
-                echo("\r\n");
+                echo $project->identifier;
+                echo "\r\n";
                 ArchiveProject::dispatch($project);
                 ArchiveStudy::dispatch($project);
             }
diff --git a/app/Console/Commands/ExtractSpectra.php b/app/Console/Commands/ExtractSpectra.php
index d471e39c..ae6e55ec 100644
--- a/app/Console/Commands/ExtractSpectra.php
+++ b/app/Console/Commands/ExtractSpectra.php
@@ -35,6 +35,7 @@ public function handle()
         ])->get();
 
         foreach ($projects as $project) {
+            echo "\r\n";
             echo $project->identifier;
             echo "\r\n";
             $studies = $project->studies;
@@ -90,61 +91,63 @@ public function handle()
                 }
                 $study = $study->fresh();
                 foreach ($study->datasets as $dataset) {
-                    echo $dataset->identifier;
-                    echo "\r\n";
+                    // 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;
+
+                    $studyFSObject = $study->fsObject;
+                    $datasetFSObject = $dataset->fsObject;
+                    $path = '/'.$studyFSObject->name.'/'.$datasetFSObject->name;
+                    // echo($path);
+                    // echo "\r\n";
+                    $pathsMatch = false;
                     foreach ($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)) {
-                                    $pathsMatch = false;
+                                if (str_contains($file, $path)) {
+                                    $pathsMatch = true;
                                 }
                             }
                         }
-                        // echo($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;
+                            break;
+                        }
+                    }
+                    if (! $pathsMatch) {
+                        echo $project->identifier;
+                        echo "\r\n";
+
+                        echo '===========> no match';
+                        echo "\r\n";
+                    } else {
+                        $_nmriumJSON['data']['spectra'] = [$spectra];
+                        $_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->save();
+                            $dataset->type = $experiment.','.$nucleus;
                         }
+                        $dataset->save();
                     }
                     // }
                 }
@@ -154,7 +157,7 @@ public function handle()
 
     public function processSpectra($url)
     {
-        $response = Http::timeout(300)->post('https://nodejsdev.nmrxiv.org/spectra-parser', [
+        $response = Http::timeout(300)->post('https://nodejs.nmrxiv.org/spectra-parser', [
             'urls' => [$url],
             'snapshot' => false,
         ]);
diff --git a/app/Http/Controllers/DatasetController.php b/app/Http/Controllers/DatasetController.php
index 1254d5c7..f1bcbf5b 100644
--- a/app/Http/Controllers/DatasetController.php
+++ b/app/Http/Controllers/DatasetController.php
@@ -31,7 +31,7 @@ public function fetchNMRium(Request $request, Dataset $dataset)
         if ($dataset) {
             $nmrium = $dataset->nmrium;
             if ($nmrium) {
-                return $nmrium;
+                return json_decode($nmrium->nmrium_info);
             } else {
                 return null;
             }
diff --git a/resources/js/Pages/Public/Project/Study.vue b/resources/js/Pages/Public/Project/Study.vue
index f27f914a..d5fb6adc 100644
--- a/resources/js/Pages/Public/Project/Study.vue
+++ b/resources/js/Pages/Public/Project/Study.vue
@@ -336,7 +336,6 @@
                     <div class="mt-3">
                         <SpectraViewer
                             ref="spectraViewerREF"
-                            :dataset="selectedDataset"
                             :project="project.data"
                             :study="study.data"
                         ></SpectraViewer>
diff --git a/resources/js/Shared/SpectraViewer.vue b/resources/js/Shared/SpectraViewer.vue
index 75feef26..4990be4a 100644
--- a/resources/js/Shared/SpectraViewer.vue
+++ b/resources/js/Shared/SpectraViewer.vue
@@ -331,10 +331,10 @@ export default {
                 this.currentMolecules = [];
                 this.updateLoadingStatus(true);
                 if (iframe) {
-                    if (this.study.has_nmrium) {
+                    if (this.dataset && this.dataset.has_nmrium) {
                         this.infoLog("Loading Spectra from NMRium JSON..");
                         axios
-                            .get("/studies/" + this.study.id + "/nmriumInfo")
+                            .get("/datasets/" + this.dataset.id + "/nmriumInfo")
                             .then((response) => {
                                 let nmrium_info = response.data;
                                 if (nmrium_info) {
@@ -353,10 +353,35 @@ export default {
                                 }
                             });
                     } else {
-                        if (this.study.download_url) {
-                            let urls = [];
-                            urls.push(this.study.download_url);
-                            this.loadFromURL(urls);
+                        if (this.study.has_nmrium) {
+                            this.infoLog("Loading Spectra from NMRium JSON..");
+                            axios
+                                .get(
+                                    "/studies/" + this.study.id + "/nmriumInfo"
+                                )
+                                .then((response) => {
+                                    let nmrium_info = response.data;
+                                    if (nmrium_info) {
+                                        let data = {
+                                            data: nmrium_info,
+                                            type: "nmrium",
+                                        };
+                                        iframe.postMessage(
+                                            { type: `nmr-wrapper:load`, data },
+                                            "*"
+                                        );
+                                    } else {
+                                        let urls = [];
+                                        urls.push(this.study.download_url);
+                                        this.loadFromURL(urls);
+                                    }
+                                });
+                        } else {
+                            if (this.study.download_url) {
+                                let urls = [];
+                                urls.push(this.study.download_url);
+                                this.loadFromURL(urls);
+                            }
                         }
                     }
                 }

From 5f225518eb7df42aaec30ff67b7f72df298c2742 Mon Sep 17 00:00:00 2001
From: Venkata Chandra Sekhar Nainala <mailcs76@gmail.com>
Date: Mon, 13 Nov 2023 09:07:57 +0100
Subject: [PATCH 3/4] fix: updated nmrium info save routine

---
 app/Http/Controllers/StudyController.php | 61 +++++++++++++-----------
 1 file changed, 33 insertions(+), 28 deletions(-)

diff --git a/app/Http/Controllers/StudyController.php b/app/Http/Controllers/StudyController.php
index 8253e010..787b71a0 100644
--- a/app/Http/Controllers/StudyController.php
+++ b/app/Http/Controllers/StudyController.php
@@ -209,45 +209,50 @@ public function nmriumInfo(Request $request, Study $study)
             $_nmriumJSON = $nmriumInfo;
             foreach ($study->datasets as $dataset) {
                 $fsObject = $dataset->fsObject;
-                $level = -($fsObject->level + 1);
-                // echo $fsObject->path;
-                $path = implode('/', array_slice(explode('/', $fsObject->path), $level));
+
+                $studyFSObject = $study->fsObject;
+                $datasetFSObject = $dataset->fsObject;
+                $path = '/'.$studyFSObject->name.'/'.$datasetFSObject->name;
+                    
+                $pathsMatch = false;
                 foreach ($nmriumInfo['data']['spectra'] as $spectra) {
                     unset($_nmriumJSON['data']['spectra']);
                     $files = $spectra['sourceSelector']['files'];
-                    $pathsMatch = true;
                     if ($files) {
                         foreach ($files as $file) {
-                            if (! str_contains($file, $path)) {
-                                $pathsMatch = false;
+                            if (str_contains($file, $path)) {
+                                $pathsMatch = true;
                             }
                         }
                     }
                     if ($pathsMatch) {
-                        $_nmriumJSON['data']['spectra'] = [$spectra];
-                        $_nmrium = $dataset->nmrium;
-                        if ($_nmrium) {
-                            $_nmrium->nmrium_info = $_nmriumJSON;
-                            $dataset->has_nmrium = true;
-                            $_nmrium->save();
-                        } else {
-                            $_nmrium = NMRium::create([
-                                'nmrium_info' => json_encode($_nmriumJSON),
-                            ]);
-                            $dataset->nmrium()->save($_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;
+                        break;
+                    }
+                }
+                if ($pathsMatch){
+                    $_nmriumJSON['data']['spectra'] = [$spectra];
+                    $_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->save();
+                        $dataset->type = $experiment.','.$nucleus;
                     }
+                    $dataset->save();
                 }
             }
 

From bb6da86da78d2e7f451abb56c2187e18043e6847 Mon Sep 17 00:00:00 2001
From: Venkata Chandra Sekhar Nainala <mailcs76@gmail.com>
Date: Mon, 13 Nov 2023 10:20:37 +0100
Subject: [PATCH 4/4] fix: resolved #888

---
 app/Console/Kernel.php | 1 +
 1 file changed, 1 insertion(+)

diff --git a/app/Console/Kernel.php b/app/Console/Kernel.php
index 5ad1b15a..a4b62bca 100644
--- a/app/Console/Kernel.php
+++ b/app/Console/Kernel.php
@@ -4,6 +4,7 @@
 
 use Illuminate\Console\Scheduling\Schedule;
 use Illuminate\Foundation\Console\Kernel as ConsoleKernel;
+use Illuminate\Support\Facades\App;
 
 class Kernel extends ConsoleKernel
 {