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

…helm-deploy

.env.ci.dev

@@ -0,0 +1,90 @@
+APP_NAME=Laravel
+APP_ENV=development
+APP_KEY=
+APP_DEBUG=true
+APP_URL=http://localhost:80
+APP_DESCRIPTION='nmrXiv is currently developed as the FAIR, consensus-driven NMR data repository and computational platform. The ultimate goal is to accelerate broader coordination and data sharing among natural product (NP) researchers by enabling the storage, management, sharing and analysis of NMR data.'
+COOL_OFF_PERIOD=10
+SCHEMA_VERSION=beta
+
+SHOW_BANNER=true
+
+GITHUB_LICENSE_URL=https://api.github.com/licenses
+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
+
+LOG_CHANNEL=stack
+LOG_LEVEL=debug
+
+DB_CONNECTION=pgsql
+DB_HOST=postgres
+DB_PORT=5432
+DB_DATABASE=nmrxiv
+DB_USERNAME=postgres
+DB_PASSWORD=postgres
+
+BROADCAST_DRIVER=log
+CACHE_DRIVER=file
+FILESYSTEM_DRIVER=local
+QUEUE_CONNECTION=redis
+SESSION_DRIVER=redis
+SESSION_LIFETIME=120
+
+MEMCACHED_HOST=memcached
+
+REDIS_CLIENT=predis
+REDIS_HOST=redis
+REDIS_PASSWORD=null
+REDIS_PORT=6379
+
+MAIL_MAILER=smtp
+MAIL_HOST=mailhog
+MAIL_PORT=1025
+MAIL_USERNAME=null
+MAIL_PASSWORD=null
+MAIL_ENCRYPTION=null
+MAIL_FROM_ADDRESS=info@nmrxiv.org
+MAIL_FROM_NAME="${APP_NAME}"
+
+FILESYSTEM_DRIVER=ceph
+FILESYSTEM_DRIVER_PUBLIC=ceph_public
+
+AWS_ACCESS_KEY_ID=
+AWS_SECRET_ACCESS_KEY=
+AWS_DEFAULT_REGION=us-east-1
+AWS_BUCKET=nmrxiv
+AWS_BUCKET_PUBLIC=nmrxiv-public
+AWS_ENDPOINT=https://s3.uni-jena.de
+AWS_URL=https://s3.uni-jena.de
+
+PUSHER_APP_ID=
+PUSHER_APP_KEY=
+PUSHER_APP_SECRET=
+PUSHER_APP_CLUSTER=mt1
+
+MIX_PUSHER_APP_KEY="${PUSHER_APP_KEY}"
+MIX_PUSHER_APP_CLUSTER="${PUSHER_APP_CLUSTER}"
+
+SCOUT_DRIVER=meilisearch
+SCOUT_PREFIX=dev_
+MEILISEARCH_HOST=https://msdev.nmrxiv.org
+MEILISEARCH_KEY=
+MEILISEARCH_PUBLICKEY=
+
+GITHUB_CLIENT_ID=
+GITHUB_CLIENT_SECRET=
+GITHUB_REDIRECT_URL=http://localhost:80/auth/login/github/callback
+
+TWITTER_CLIENT_ID=
+TWITTER_CLIENT_SECRET=
+TWITTER_REDIRECT_URL=http://localhost:80/auth/login/twitter/callback
+
+TELESCOPE_ENABLED=false
+
+#Bioschema Properties.
+NMRXIV_PROVIDER=NFDI4Chem
+NMRXIV_PROVIDER_URL=https://www.nfdi4chem.de/
+MEASUREMENT_TECHNIQUE=http://purl.obolibrary.org/obo/CHMO_0000613
+

.env.example

@@ -1,8 +1,19 @@
-APP_NAME=nmrXiv
+APP_NAME=Laravel
 APP_ENV=local
 APP_KEY=
 APP_DEBUG=true
-APP_URL=0.0.0.0:80
+APP_URL=http://localhost:80
+APP_DESCRIPTION='nmrXiv is currently developed as the FAIR, consensus-driven NMR data repository and computational platform. The ultimate goal is to accelerate broader coordination and data sharing among natural product (NP) researchers by enabling the storage, management, sharing and analysis of NMR data.'
+COOL_OFF_PERIOD=10
+SCHEMA_VERSION=beta
+
+SHOW_BANNER=true
+
+GITHUB_LICENSE_URL=https://api.github.com/licenses
+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
 
 LOG_CHANNEL=stack
 LOG_LEVEL=debug
@@ -17,12 +28,13 @@ DB_PASSWORD=password
 BROADCAST_DRIVER=log
 CACHE_DRIVER=file
 FILESYSTEM_DRIVER=local
-QUEUE_CONNECTION=sync
-SESSION_DRIVER=database
+QUEUE_CONNECTION=redis
+SESSION_DRIVER=redis
 SESSION_LIFETIME=120
 
 MEMCACHED_HOST=memcached
 
+REDIS_CLIENT=predis
 REDIS_HOST=redis
 REDIS_PASSWORD=null
 REDIS_PORT=6379
@@ -36,31 +48,49 @@ MAIL_ENCRYPTION=null
 MAIL_FROM_ADDRESS=info@nmrxiv.org
 MAIL_FROM_NAME="${APP_NAME}"
 
+FILESYSTEM_DRIVER=minio
+FILESYSTEM_DRIVER_PUBLIC=minio_public
+
 AWS_ACCESS_KEY_ID=
 AWS_SECRET_ACCESS_KEY=
 AWS_DEFAULT_REGION=us-east-1
-AWS_BUCKET=
+AWS_BUCKET=nmrxiv
+AWS_ENDPOINT=http://localhost:9000/
+AWS_URL=http://localhost:9000/
 AWS_USE_PATH_STYLE_ENDPOINT=false
+AWS_BUCKET_PUBLIC=nmrxiv-public
 
 PUSHER_APP_ID=
 PUSHER_APP_KEY=
 PUSHER_APP_SECRET=
 PUSHER_APP_CLUSTER=mt1
 
-VITE_PUSHER_APP_KEY="${PUSHER_APP_KEY}"
-VITE_PUSHER_APP_CLUSTER="${PUSHER_APP_CLUSTER}"
+MIX_PUSHER_APP_KEY="${PUSHER_APP_KEY}"
+MIX_PUSHER_APP_CLUSTER="${PUSHER_APP_CLUSTER}"
 
 SCOUT_DRIVER=meilisearch
-MEILISEARCH_HOST=http://meilisearch:7700
+SCOUT_PREFIX=dev_
+MEILISEARCH_HOST=http://localhost:7700/
+MEILISEARCH_KEY=
+MEILISEARCH_PUBLICKEY=
 
 GITHUB_CLIENT_ID=
 GITHUB_CLIENT_SECRET=
-GITHUB_REDIRECT_URL=
+GITHUB_REDIRECT_URL=http://localhost:80/auth/login/github/callback
+
+TWITTER_CLIENT_ID=
+TWITTER_CLIENT_SECRET=
+TWITTER_REDIRECT_URL=http://localhost:80/auth/login/twitter/callback
 
 ORCID_CLIENT_ID=
 ORCID_CLIENT_SECRET=
-ORCID_REDIRECT_URL=
+ORCID_REDIRECT_URL=http://localhost/auth/login/orcid/callback
+ORCID_ENVIRONMENT=sandbox
+
+TELESCOPE_ENABLED=false
+
+#Bioschema Properties.
+NMRXIV_PROVIDER=NFDI4Chem
+NMRXIV_PROVIDER_URL=https://www.nfdi4chem.de/
+MEASUREMENT_TECHNIQUE=http://purl.obolibrary.org/obo/CHMO_0000613
 
-TWITTER_CLIENT_ID=
-TWITTER_CLIENT_SECRET=
-TWITTER_REDIRECT_URL=

.github/workflows/build.yml → .github/workflows/prod-build.yml

@@ -122,4 +122,5 @@ jobs:
         kubectl rollout restart deployment/$DEPLOYMENT_NAME
         kubectl rollout status deployment/$DEPLOYMENT_NAME --timeout=300s
         kubectl rollout restart deployment/$WORKER_DEPLOYMENT_NAME
+        kubectl rollout restart deployment/$SCHEDULER_DEPLOYMENT_NAME
         kubectl get services -o wide

README.md

@@ -1,16 +1,25 @@
 <p align="center"><a href="https://dev.nmrxiv.org" target="_blank"><img src="/public/img/logo.svg" width="400"></a></p>
 
+[![License](https://img.shields.io/badge/License-MIT%202.0-blue.svg)](https://opensource.org/licenses/MIT)
+[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-blue.svg)](https://GitHub.com/NFDI4Chem/nmrxiv/graphs/commit-activity)
+[![GitHub issues](https://img.shields.io/github/issues/NFDI4Chem/nmrxiv.svg)](https://GitHub.com/NFDI4Chem/nmrxiv/issues/)
+[![GitHub contributors](https://img.shields.io/github/contributors/NFDI4Chem/nmrxiv.svg)](https://GitHub.com/NFDI4Chem/nmrxiv/graphs/contributors/)
+![Workflow](https://github.com/NFDI4Chem/nmrxiv/actions/workflows/build.yml/badge.svg)
+![Workflow](https://github.com/NFDI4Chem/nmrxiv/actions/workflows/release-please.yml/badge.svg)
+[![Powered by Laravel](https://img.shields.io/badge/Powered%20by-Laravel-red.svg?style=flat&logo=Laravel)](https://laravel.com)
+
 ## About nmrXiv
 
-New, Open & FAIR, and consensus-driven NMR data repository and computational platform. The ultimate goal is to accelerate broader coordination and data sharing among natural product (NP) researchers by enabling storage, management, sharing and analysis of NMR data.
+Open, FAIR and Consensus-Driven NMR data repository and analysis platform.. The ultimate goal is to accelerate broader coordination and data sharing among natural product (NP) researchers by enabling storage, management, sharing and analysis of NMR data.
 
 ## User Documentation
 
 To get more details about nmrXiv, visit our [documentation site](https://docs.nmrxiv.org/).
 
 ## Help Desk
 
-If you discover any issue or need any support please raise a ticket at our [Help Desk](https://helpdesk.nfdi4chem.de/).
+If you discover any issue or need any support please raise a ticket at our [Help Desk](https://helpdesk.nfdi4chem.de/) or write to us at info.nmrxiv@uni-jena.de.
+
 
 ## Features and Bugs
 
@@ -20,4 +29,19 @@ To raise request for any new feature or report any bug please add it to our [Git
 
 Licensed under the [MIT license](https://opensource.org/licenses/MIT).
 
-![Alt](https://repobeats.axiom.co/api/embed/5c87933e128e7f9b2a73abba45104de51b4c7b4c.svg "Repobeats analytics image")
+![Alt](https://repobeats.axiom.co/api/embed/5c87933e128e7f9b2a73abba45104de51b4c7b4c.svg "Repobeats analytics image")
+
+## Maintained by
+[nmrXiv](https://nmrxiv.org/) is developed and maintained by the [NFDI4Chem partners](https://www.nfdi4chem.de/) at the [Friedrich Schiller University](https://www.uni-jena.de/en/) Jena, Germany. 
+The code for this web application is released under the [MIT license](https://opensource.org/licenses/MIT).
+
+
+<p align="left"><a href="https://nfdi4chem.de/" target="_blank"><img src="https://www.nfdi4chem.de/wp-content/themes/wptheme/assets/img/logo.svg" width="50%" alt="NFDI4Chem Logo"></a></p>
+
+## Acknowledgments
+
+Funded by the [Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)](https://www.dfg.de/) under the [National Research Data Infrastructure – NFDI4Chem](https://nfdi4chem.de/) – Projektnummer **441958208**.
+
+<p align="left"><a href="https://www.dfg.de/" target="_blank"><img src="./public/img/dfg_logo_schriftzug_blau_foerderung_en.gif" width="50%" alt="DFG Logo"></a></p>
+
+

app/Actions/Fortify/CreateNewUser.php

@@ -17,7 +17,6 @@ class CreateNewUser implements CreatesNewUsers
     /**
      * Create a newly registered user.
      *
-     * @param  array  $input
      * @return \App\Models\User
      */
     public function create(array $input)
@@ -38,7 +37,10 @@ public function create(array $input)
                 'last_name' => $input['last_name'],
                 'email' => $input['email'],
                 'username' => $input['username'],
+                'orcid_id' => $input['orcid_id'],
+                'affiliation' => $input['affiliation'],
                 'password' => Hash::make($input['password']),
+
             ]), function (User $user) {
                 $this->createTeam($user);
             });
@@ -48,7 +50,6 @@ public function create(array $input)
     /**
      * Create a personal team for the user.
      *
-     * @param  \App\Models\User  $user
      * @return void
      */
     protected function createTeam(User $user)

app/Actions/Fortify/ResetUserPassword.php

@@ -14,7 +14,6 @@ class ResetUserPassword implements ResetsUserPasswords
      * Validate and reset the user's forgotten password.
      *
      * @param  mixed  $user
-     * @param  array  $input
      * @return void
      */
     public function reset($user, array $input)

app/Actions/Fortify/UpdateUserPassword.php

@@ -14,7 +14,6 @@ class UpdateUserPassword implements UpdatesUserPasswords
      * Validate and update the user's password.
      *
      * @param  mixed  $user
-     * @param  array  $input
      * @return void
      */
     public function update($user, array $input)

app/Actions/Fortify/UpdateUserProfileInformation.php

@@ -13,7 +13,6 @@ class UpdateUserProfileInformation implements UpdatesUserProfileInformation
      * Validate and update the given user's profile information.
      *
      * @param  mixed  $user
-     * @param  array  $input
      * @return void
      */
     public function update($user, array $input)
@@ -25,6 +24,8 @@ public function update($user, array $input)
             'email' => ['required', 'email', 'max:255', Rule::unique('users')->ignore($user->id)],
             'username' => ['required', 'string', 'max:255', Rule::unique('users')->ignore($user->id)],
             'photo' => ['nullable', 'mimes:jpg,jpeg,png', 'max:1024'],
+            'orcid_id' => ['nullable', 'string', 'max:255'],
+            'affiliation' => ['nullable', 'string', 'max:255'],
         ])->validateWithBag('updateProfileInformation');
 
         if (isset($input['photo'])) {
@@ -41,6 +42,8 @@ public function update($user, array $input)
                 'username' => $input['username'],
                 'name' => $input['username'] ? $input['username'] : $user->name,
                 'email' => $input['email'],
+                'orcid_id' => $input['orcid_id'],
+                'affiliation' => $input['affiliation'],
             ])->save();
         }
     }
@@ -49,18 +52,18 @@ public function update($user, array $input)
      * Update the given verified user's profile information.
      *
      * @param  mixed  $user
-     * @param  array  $input
      * @return void
      */
     protected function updateVerifiedUser($user, array $input)
     {
         $user->forceFill([
             'first_name' => $input['first_name'],
             'last_name' => $input['last_name'],
-            'name' => $input['name'] ? $input['name'] : $user->name,
             'username' => $input['username'],
+            'name' => $input['username'] ? $input['username'] : $user->name,
             'email' => $input['email'],
-            'email_verified_at' => null,
+            'orcid_id' => $input['orcid_id'],
+            'affiliation' => $input['affiliation'],
         ])->save();
 
         $user->sendEmailVerificationNotification();

app/Actions/Jetstream/AddTeamMember.php

@@ -17,8 +17,6 @@ class AddTeamMember implements AddsTeamMembers
      *
      * @param  mixed  $user
      * @param  mixed  $team
-     * @param  string  $email
-     * @param  string|null  $role
      * @return void
      */
     public function add($user, $team, string $email, string $role = null)
@@ -42,8 +40,6 @@ public function add($user, $team, string $email, string $role = null)
      * Validate the add member operation.
      *
      * @param  mixed  $team
-     * @param  string  $email
-     * @param  string|null  $role
      * @return void
      */
     protected function validate($team, string $email, ?string $role)
@@ -77,7 +73,6 @@ protected function rules()
      * Ensure that the user is not already on the team.
      *
      * @param  mixed  $team
-     * @param  string  $email
      * @return \Closure
      */
     protected function ensureUserIsNotAlreadyOnTeam($team, string $email)

app/Actions/Jetstream/CreateTeam.php

@@ -14,7 +14,6 @@ class CreateTeam implements CreatesTeams
      * Validate and create a new team for the given user.
      *
      * @param  mixed  $user
-     * @param  array  $input
      * @return mixed
      */
     public function create($user, array $input)

app/Actions/Jetstream/DeleteUser.php

@@ -18,7 +18,6 @@ class DeleteUser implements DeletesUsers
     /**
      * Create a new action instance.
      *
-     * @param  \Laravel\Jetstream\Contracts\DeletesTeams  $deletesTeams
      * @return void
      */
     public function __construct(DeletesTeams $deletesTeams)