Development

app/Http/Controllers/ApplicationController.php

@@ -372,6 +372,8 @@ private function renderPublicProject(
         $mergedProps = $props;
 
         if ($reviewerPreview && $project) {
+            PublicEntityAccess::rememberReviewerPreview($request, $project);
+
             $mergedProps['reviewerPreview'] = [
                 'obfuscationcode' => $project->obfuscationcode,
                 'samples_count' => $project->studies()->count(),

app/Http/Controllers/UserPreferencesController.php

@@ -23,6 +23,6 @@ public function update(UpdateUserPreferencesRequest $request): RedirectResponse
             'preferences' => $preferences === [] ? null : $preferences,
         ])->save();
 
-        return back();
+        return to_route('profile.show');
     }
 }

app/Jobs/DataBackupJob.php

@@ -17,6 +17,19 @@ class DataBackupJob implements ShouldQueue
 {
     use Dispatchable, InteractsWithQueue, Queueable, SerializesModels;
 
+    /**
+     * Number of times the job may be attempted.
+     */
+    public int $tries = 3;
+
+    /**
+     * Delay (in seconds) between retry attempts, to ride out transient
+     * pg_dump failures caused by concurrent schema changes (e.g. deployments).
+     *
+     * @var array<int, int>
+     */
+    public array $backoff = [60, 300];
+
     /**
      * Execute the job.
      */

app/Support/Public/PublicEntityAccess.php

@@ -3,6 +3,7 @@
 namespace App\Support\Public;
 
 use App\Models\Dataset;
+use App\Models\Project;
 use App\Models\Study;
 use App\Models\User;
 use Illuminate\Auth\Access\AuthorizationException;
@@ -11,12 +12,19 @@
 
 class PublicEntityAccess
 {
+    public const REVIEWER_PREVIEW_SESSION_KEY = 'reviewer_preview_obfuscationcode';
+
     public static function authorizeStudyAccess(Request $request, Study $study, bool $reviewerPreview = false): void
     {
         if ($reviewerPreview) {
             return;
         }
 
+        if (self::requestIncludesReviewerObfuscation($request)
+            && self::hasValidReviewerObfuscation($request, $study->project)) {
+            return;
+        }
+
         if (! Gate::forUser($request->user())->check('viewStudy', $study)) {
             throw new AuthorizationException;
         }
@@ -32,6 +40,13 @@ public static function authorizeDatasetAccess(Request $request, Dataset $dataset
             ? $dataset->study
             : $dataset->study()->first();
 
+        if (self::requestIncludesReviewerObfuscation($request)) {
+            $project = $study?->project ?? $dataset->project;
+            if (self::hasValidReviewerObfuscation($request, $project)) {
+                return;
+            }
+        }
+
         if ($study === null) {
             throw new AuthorizationException;
         }
@@ -50,4 +65,57 @@ public static function authorizeDatasetAccess(Request $request, Dataset $dataset
 
         throw new AuthorizationException;
     }
+
+    public static function rememberReviewerPreview(Request $request, Project $project): void
+    {
+        if (! $request->hasSession() || $project->is_archived) {
+            return;
+        }
+
+        $code = $project->obfuscationcode;
+        if (! is_string($code) || $code === '') {
+            return;
+        }
+
+        $request->session()->put(self::REVIEWER_PREVIEW_SESSION_KEY, $code);
+    }
+
+    protected static function requestIncludesReviewerObfuscation(Request $request): bool
+    {
+        return $request->filled('obfuscationcode')
+            || self::reviewerObfuscationFromSession($request) !== null;
+    }
+
+    protected static function hasValidReviewerObfuscation(Request $request, ?Project $project): bool
+    {
+        if ($project === null || $project->is_archived) {
+            return false;
+        }
+
+        $expected = $project->obfuscationcode;
+        if (! is_string($expected) || $expected === '') {
+            return false;
+        }
+
+        $provided = $request->filled('obfuscationcode')
+            ? (string) $request->query('obfuscationcode')
+            : self::reviewerObfuscationFromSession($request);
+
+        if (! is_string($provided) || $provided === '') {
+            return false;
+        }
+
+        return hash_equals($expected, $provided);
+    }
+
+    protected static function reviewerObfuscationFromSession(Request $request): ?string
+    {
+        if (! $request->hasSession()) {
+            return null;
+        }
+
+        $code = $request->session()->get(self::REVIEWER_PREVIEW_SESSION_KEY);
+
+        return is_string($code) && $code !== '' ? $code : null;
+    }
 }

config/database.php

@@ -19,7 +19,8 @@
             'dump' => [
                 'use_single_transaction',
                 'timeout' => 620 * 100, // 51 minute timeout
-                'exclude_tables' => ['versions'],
+                // mols/fps are ephemeral RDKit search caches dropped & rebuilt daily by nmrxiv:index-molecules, excluded to avoid pg_dump racing that DDL
+                'exclude_tables' => ['versions', 'mols', 'fps'],
             ],
             'search_path' => 'public',
         ],

deployment/docker-compose.dev.yml

@@ -128,6 +128,9 @@ services:
     entrypoint: /bin/sh
     stdin_open: true
     tty: true
+    environment:
+      NODE_OPTIONS: "--max-old-space-size=12288"
+    mem_limit: 16g
     networks:
     - nmrxiv_net
     volumes:

resources/js/Pages/Public/Project/Dataset.vue

@@ -38,11 +38,13 @@ export default {
         };
     },
     mounted() {
-        axios
-            .get(route("bioschemas.id", this.dataset.data.identifier))
-            .then((response) => {
-                this.schema = response.data;
-            });
+        if (this.dataset?.data?.identifier) {
+            axios
+                .get(route("bioschemas.id", this.dataset.data.identifier))
+                .then((response) => {
+                    this.schema = response.data;
+                });
+        }
     },
 };
 </script>

resources/js/Pages/Public/Project/Show.vue

@@ -628,11 +628,13 @@ export default {
     },
 
     mounted() {
-        axios
-            .get(route("bioschemas.id", this.project.data.identifier))
-            .then((response) => {
-                this.schema = response.data;
-            });
+        if (this.project?.data?.identifier) {
+            axios
+                .get(route("bioschemas.id", this.project.data.identifier))
+                .then((response) => {
+                    this.schema = response.data;
+                });
+        }
 
         this.handleEditQueryParam();
     },

resources/js/Pages/Public/Sample/Dataset.vue

@@ -32,11 +32,13 @@ export default {
         };
     },
     mounted() {
-        axios
-            .get(route("bioschemas.id", this.dataset.data.identifier))
-            .then((response) => {
-                this.schema = response.data;
-            });
+        if (this.dataset?.data?.identifier) {
+            axios
+                .get(route("bioschemas.id", this.dataset.data.identifier))
+                .then((response) => {
+                    this.schema = response.data;
+                });
+        }
     },
 };
 </script>

resources/js/Pages/Public/Sample/Show.vue

@@ -723,11 +723,13 @@ export default {
         },
     },
     mounted() {
-        axios
-            .get(route("bioschemas.id", this.study.data.identifier))
-            .then((response) => {
-                this.schema = response.data;
-            });
+        if (this.study?.data?.identifier) {
+            axios
+                .get(route("bioschemas.id", this.study.data.identifier))
+                .then((response) => {
+                    this.schema = response.data;
+                });
+        }
     },
     methods: {
         datasetHref(dataset) {

resources/js/Shared/SpectraViewer.vue

@@ -346,6 +346,9 @@ export default {
         url() {
             return String(this.$page.props.url);
         },
+        reviewerObfuscationCode() {
+            return this.$page.props.reviewerPreview?.obfuscationcode ?? null;
+        },
         nmriumURL() {
             const raw = this.$page.props.nmriumURL;
             if (!raw) {
@@ -457,6 +460,45 @@ export default {
                 getDefaultSpectrumTab(this.$page)
             );
         },
+        nmriumInfoUrl(path) {
+            if (!this.reviewerObfuscationCode) {
+                return path;
+            }
+
+            const separator = path.includes("?") ? "&" : "?";
+
+            return (
+                path +
+                separator +
+                "obfuscationcode=" +
+                encodeURIComponent(this.reviewerObfuscationCode)
+            );
+        },
+        loadNmriumInfo(iframe, path) {
+            this.infoLog("Loading Spectra from NMRium JSON..");
+            axios
+                .get(this.nmriumInfoUrl(path))
+                .then((response) => {
+                    let nmrium_info = response.data;
+                    if (nmrium_info) {
+                        this.postLoadToIframe(iframe, {
+                            data: nmrium_info,
+                            type: "nmrium",
+                        });
+                    } else if (this.study.download_url) {
+                        this.loadFromURL([this.study.download_url]);
+                    } else {
+                        this.updateLoadingStatus(false);
+                    }
+                })
+                .catch((error) => {
+                    this.updateLoadingStatus(false);
+                    this.spectraError =
+                        error?.response?.status === 403
+                            ? "You do not have permission to view these spectra."
+                            : "Unable to load spectra.";
+                });
+        },
         loadSpectra() {
             if (this.study) {
                 const iframe = window.frames.NMRiumIframe;
@@ -467,42 +509,16 @@ export default {
 
                 if (iframe) {
                     if (this.dataset && this.dataset.has_nmrium) {
-                        this.infoLog("Loading Spectra from NMRium JSON..");
-                        axios
-                            .get("/datasets/" + this.dataset.id + "/nmriumInfo")
-                            .then((response) => {
-                                let nmrium_info = response.data;
-                                if (nmrium_info) {
-                                    this.postLoadToIframe(iframe, {
-                                        data: nmrium_info,
-                                        type: "nmrium",
-                                    });
-                                } else {
-                                    let urls = [];
-                                    urls.push(this.study.download_url);
-                                    this.loadFromURL(urls);
-                                }
-                            });
+                        this.loadNmriumInfo(
+                            iframe,
+                            "/datasets/" + this.dataset.id + "/nmriumInfo"
+                        );
                     } else {
                         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) {
-                                        this.postLoadToIframe(iframe, {
-                                            data: nmrium_info,
-                                            type: "nmrium",
-                                        });
-                                    } else {
-                                        let urls = [];
-                                        urls.push(this.study.download_url);
-                                        this.loadFromURL(urls);
-                                    }
-                                });
+                            this.loadNmriumInfo(
+                                iframe,
+                                "/studies/" + this.study.id + "/nmriumInfo"
+                            );
                         } else {
                             if (this.study.download_url) {
                                 let urls = [];

routes/console.php

@@ -20,13 +20,14 @@
 
 Schedule::command('nmrxiv:publish-embargo-projects')->daily();
 Schedule::command('nmrxiv:delete-projects')->daily();
-Schedule::command('nmrxiv:index-molecules')->daily();
+// Staggered away from the backup dump (both defaulted to ->daily(), i.e. midnight) since this rebuilds the mols/fps RDKit tables via DROP/CREATE DDL
+Schedule::command('nmrxiv:index-molecules')->dailyAt('02:00');
 Schedule::command('nmrxiv:index-spectra-metadata-stats')->daily();
 Schedule::command('nmrxiv:delete-citations')->weekly();
 Schedule::command('nmrxiv:delete-authors')->weekly();
 if (App::environment('production')) {
     Schedule::command('nmrxiv:backup-postgres-dump')
-        ->daily()
+        ->dailyAt('04:00')
         ->onOneServer()
         ->withoutOverlapping();
 }