Merge pull request #887 from NFDI4Chem/development

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NFDI4Chem · Nov 13, 2023 · 89eddbc · 89eddbc
2 parents 4236d59 + bb6da86
commit 89eddbc
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Showing 17 changed files with 234 additions and 146 deletions.
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"

diff --git 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() {