Merge pull request #878 from NFDI4Chem/development

Development
NFDI4Chem · Oct 17, 2023 · 6d1e59c · 6d1e59c
2 parents 1ba3618 + b126b79
commit 6d1e59c
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diff --git a/.env.ci.dev b/.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
+
diff --git a/.env.example b/.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=
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -9,17 +9,66 @@ env:
   GKE_CLUSTER: nmrxiv-dev
   GKE_ZONE: europe-west3-a
   DEPLOYMENT_NAME: nmrxiv-nmrxiv-app
+  SCHEDULER_DEPLOYMENT_NAME: nmrxiv-scheduler
   WORKER_DEPLOYMENT_NAME: nmrxiv-worker
   REPOSITORY_NAME: nmrxiv-dev
   APP_IMAGE: nmrxiv-app
   NGINX_IMAGE: nmrxiv-nginx
 
 jobs:
+  php-unit-test:
+    name: Run test
+    runs-on: ubuntu-latest
+    container:
+      image: kirschbaumdevelopment/laravel-test-runner:8.2
+
+    services:
+      postgres:
+        image: postgres:13
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: nmrxiv
+        ports:
+        - 5432:5432
+        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
+
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        fetch-depth: 1
+
+    - name: Install composer dependencies
+      run: |
+        composer install --ignore-platform-reqs
+    - name: Prepare Laravel Application
+      run: |
+        php -r "file_exists('.env') || copy('.env.ci.dev', '.env');"
+
+        echo AWS_ACCESS_KEY_ID=${{ secrets.AWS_ACCESS_KEY_ID_DEV }} >> .env
+        echo AWS_SECRET_ACCESS_KEY=${{ secrets.AWS_SECRET_ACCESS_KEY_DEV }} >> .env
+        echo MEILISEARCH_KEY=${{ secrets.MEILISEARCH_KEY_DEV }} >> .env
+        echo MEILISEARCH_PUBLICKEY=${{ secrets.MEILISEARCH_PUBLICKEY_DEV }} >> .env
+        echo TWITTER_CLIENT_ID=${{ secrets.TWITTER_CLIENT_ID_DEV }} >> .env
+        echo TWITTER_CLIENT_SECRET=${{ secrets.TWITTER_CLIENT_SECRET_DEV }} >> .env
+        echo GITHUB_CLIENT_ID=${{ secrets.CLIENT_ID_GITHUB_DEV }} >> .env
+        echo GITHUB_CLIENT_SECRET=${{ secrets.CLIENT_SECRET_GITHUB_DEV }} >> .env
+
+        php artisan key:generate
+        php artisan migrate --seed
+    - name: Install front-end dependencies
+      run: |
+        npm install
+        npm run build
+    - name: Run Test
+      run: php artisan test --parallel
+
+
   setup-build-publish-deploy:
-    name: Deploy to Dev
+    name: Build & deploy to development
     if: github.ref == 'refs/heads/development'
     runs-on: ubuntu-latest
-    #needs: build
+    needs: php-unit-test
     steps:
     - name: Checkout
       uses: actions/checkout@v2
@@ -68,5 +117,6 @@ jobs:
       run: |-
         kubectl rollout restart deployment/$DEPLOYMENT_NAME
         kubectl rollout restart deployment/$WORKER_DEPLOYMENT_NAME
+        kubectl rollout restart deployment/$SCHEDULER_DEPLOYMENT_NAME
         kubectl rollout status deployment/$DEPLOYMENT_NAME --timeout=300s
         kubectl get services -o wide
diff --git a/app/Actions/Fortify/CreateNewUser.php b/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)

diff --git a/app/Actions/Fortify/ResetUserPassword.php b/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)

diff --git a/app/Actions/Fortify/UpdateUserPassword.php b/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)

diff --git a/app/Actions/Fortify/UpdateUserProfileInformation.php b/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();

diff --git a/app/Actions/Jetstream/AddTeamMember.php b/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)

diff --git a/app/Actions/Jetstream/CreateTeam.php b/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)

diff --git a/app/Actions/Jetstream/DeleteUser.php b/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)