Merge branch 'main' of https://github.com/NFDI4Chem/nmrxiv into prod-…

…helm-deploy
NFDI4Chem · Nov 13, 2023 · cf245dc · cf245dc
2 parents 8aed0de + acf920b
commit cf245dc
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,15 @@
 # Changelog
 
+## [1.0.1-rc.8](https://github.com/NFDI4Chem/nmrxiv/compare/v1.0.0-rc.8...v1.0.1-rc.8) (2023-11-13)
+
+
+### Bug Fixes
+
+* resolved [#888](https://github.com/NFDI4Chem/nmrxiv/issues/888) ([bb6da86](https://github.com/NFDI4Chem/nmrxiv/commit/bb6da86da78d2e7f451abb56c2187e18043e6847))
+* updated dataset spectra loading logic and other minor updates ([e854cbb](https://github.com/NFDI4Chem/nmrxiv/commit/e854cbbd1c4c1681c79f128d8bd4f43b1f2524a1))
+* updated DOIBadge component and various other fixes/updates ([ca36ea6](https://github.com/NFDI4Chem/nmrxiv/commit/ca36ea63dd99cd53b875ef2d43ffd2e528438670))
+* updated nmrium info save routine ([5f22551](https://github.com/NFDI4Chem/nmrxiv/commit/5f225518eb7df42aaec30ff67b7f72df298c2742))
+
 ## 1.0.0 (2023-11-10)
 
 

diff --git 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
@@ -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/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
 {

diff --git 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/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();
                 }
             }
 

diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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"