Merge branch 'master' into geo-dependency

.docker/app.dockerfile

@@ -1,11 +1,10 @@
-# PHP 8.1.13
-#FROM php:8.1-fpm-alpine
-FROM php@sha256:88407bcb4821e7a9da273d9dad746e1f795e9a6480d9cba5ba502d7836e23718
-MAINTAINER Martin Zurowietz <martin@cebitec.uni-bielefeld.de>
-LABEL org.opencontainers.image.source https://github.com/biigle/core
+# PHP 8.2.21
+#FROM php:8.2-fpm-alpine
+FROM php@sha256:95c34aeeef07aa9774e0b70d5b70065ab0647ece183ebe007c5f2e6b5db16725
+LABEL org.opencontainers.image.authors="Martin Zurowietz <m.zurowietz@uni-bielefeld.de>"
+LABEL org.opencontainers.image.source="https://github.com/biigle/core"
 
 RUN ln -s "$PHP_INI_DIR/php.ini-production" "$PHP_INI_DIR/php.ini"
-ADD ".docker/all-php.ini" "$PHP_INI_DIR/conf.d/all.ini"
 ADD ".docker/app-php.ini" "$PHP_INI_DIR/conf.d/app.ini"
 
 RUN apk add --no-cache \
@@ -29,17 +28,7 @@ RUN apk add --no-cache \
 
 RUN apk add --no-cache exiftool
 
-# Configure proxy if there is any. See: https://stackoverflow.com/a/2266500/1796523
-RUN [ -z "$HTTP_PROXY" ] || pear config-set http_proxy $HTTP_PROXY
-RUN apk add --no-cache yaml \
-    && apk add --no-cache --virtual .build-deps g++ make autoconf yaml-dev \
-    && pecl install yaml \
-    && docker-php-ext-enable yaml \
-    && apk del --purge .build-deps
-# Unset proxy configuration again.
-RUN [ -z "$HTTP_PROXY" ] || pear config-set http_proxy ""
-
-ARG PHPREDIS_VERSION=5.3.7
+ARG PHPREDIS_VERSION=6.0.2
 RUN curl -L -o /tmp/redis.tar.gz https://github.com/phpredis/phpredis/archive/${PHPREDIS_VERSION}.tar.gz \
     && tar -xzf /tmp/redis.tar.gz \
     && rm /tmp/redis.tar.gz \

.docker/requirements.txt

@@ -1,13 +1,13 @@
 # This file is just used to get security alerts from GitHub. Make sure the versions match
 # in worker.dockerfile.
 numpy==1.24.*
-opencv-contrib-python-headless==4.6.0
+opencv-contrib-python-headless==4.8.1.78
 scipy==1.10.*
 scikit-learn==1.2.*
 matplotlib==3.6.*
 PyExcelerate==0.6.7
 Pillow==10.3.0
 Shapely==1.8.1
-torch==2.1.*
-torchvision==0.16.*
+torch==2.2.*
+torchvision==0.17.*
 pandas==1.5.3

.docker/web.dockerfile

@@ -1,7 +1,7 @@
 # FROM nginx:1.21-alpine
 FROM nginx@sha256:5a0df7fb7c8c03e4158ae9974bfbd6a15da2bdfdeded4fb694367ec812325d31
-MAINTAINER Martin Zurowietz <martin@cebitec.uni-bielefeld.de>
-LABEL org.opencontainers.image.source https://github.com/biigle/core
+LABEL org.opencontainers.image.authors="Martin Zurowietz <m.zurowietz@uni-bielefeld.de>"
+LABEL org.opencontainers.image.source="https://github.com/biigle/core"
 
 ADD .docker/vhost.conf /etc/nginx/conf.d/default.conf
 ADD .docker/ffdhe2048.txt /etc/nginx/conf.d/ffdhe2048.txt

.docker/worker.dockerfile

@@ -1,8 +1,8 @@
-# PHP 8.1.27
-# FROM php:8.1
-FROM php@sha256:9b5dfb7deef3e48d67b2599e4d3967bb3ece19fd5ba09cb8e7ee10f5facf36e0
-MAINTAINER Martin Zurowietz <martin@cebitec.uni-bielefeld.de>
-LABEL org.opencontainers.image.source https://github.com/biigle/core
+# PHP 8.2.21
+# FROM php:8.2
+FROM php@sha256:a61daae986bdf9bbeff9a514e3598a4f72bb2e3d01a0b3d0eff960bbfe85acdf
+LABEL org.opencontainers.image.authors="Martin Zurowietz <m.zurowietz@uni-bielefeld.de>"
+LABEL org.opencontainers.image.source="https://github.com/biigle/core"
 
 RUN LC_ALL=C.UTF-8 apt-get update \
     && apt-get install -y --no-install-recommends \
@@ -21,17 +21,21 @@ RUN LC_ALL=C.UTF-8 apt-get update \
     && rm -r /var/lib/apt/lists/*
 
 RUN ln -s "$PHP_INI_DIR/php.ini-production" "$PHP_INI_DIR/php.ini"
-ADD ".docker/all-php.ini" "$PHP_INI_DIR/conf.d/all.ini"
+# Enable FFI for jcupitt/vips.
+# See: https://github.com/libvips/php-vips?tab=readme-ov-file#install
+RUN echo "ffi.enable = true" > "$PHP_INI_DIR/conf.d/vips.ini"
 
 RUN LC_ALL=C.UTF-8 apt-get update \
     && apt-get install -y --no-install-recommends \
         libxml2-dev \
         libzip-dev \
         libpq-dev \
+        libffi-dev \
     && apt-get install -y --no-install-recommends \
         libxml2 \
         libzip4 \
         postgresql-client \
+        libffi8 \
     && docker-php-ext-configure pgsql -with-pgsql=/usr/bin/pgsql \
     && docker-php-ext-install -j$(nproc) \
         exif \
@@ -41,50 +45,29 @@ RUN LC_ALL=C.UTF-8 apt-get update \
         pgsql \
         soap \
         zip \
+        ffi \
     && apt-get purge -y \
         libxml2-dev \
         libzip-dev \
         libpq-dev \
+        libffi-dev \
     && apt-get -y autoremove \
     && apt-get clean \
     && rm -r /var/lib/apt/lists/*
 
 # Configure proxy if there is any. See: https://stackoverflow.com/a/2266500/1796523
 RUN [ -z "$HTTP_PROXY" ] || pear config-set http_proxy $HTTP_PROXY
 
-RUN LC_ALL=C.UTF-8 apt-get update \
-    && apt-get install -y --no-install-recommends \
-        libyaml-dev \
-    && apt-get install -y --no-install-recommends \
-        libyaml-0-2 \
-    && pecl install yaml \
-    && printf "\n" | docker-php-ext-enable yaml \
-    && apt-get purge -y \
-        libyaml-dev \
-    && apt-get -y autoremove \
-    && apt-get clean \
-    && rm -r /var/lib/apt/lists/*
-
-ARG PHPREDIS_VERSION=5.3.7
+ARG PHPREDIS_VERSION=6.0.2
 RUN curl -L -o /tmp/redis.tar.gz https://github.com/phpredis/phpredis/archive/${PHPREDIS_VERSION}.tar.gz \
     && tar -xzf /tmp/redis.tar.gz \
     && rm /tmp/redis.tar.gz \
     && mkdir -p /usr/src/php/ext \
     && mv phpredis-${PHPREDIS_VERSION} /usr/src/php/ext/redis \
     && docker-php-ext-install -j$(nproc) redis
 
-# ENV PKG_CONFIG_PATH="/usr/local/lib/pkgconfig:${PKG_CONFIG_PATH}"
-
 RUN LC_ALL=C.UTF-8 apt-get update \
-    && apt-get install -y --no-install-recommends \
-        libvips-dev \
-    && apt-get install -y --no-install-recommends \
-        libvips42 \
-    && pecl install vips \
-    && docker-php-ext-enable vips \
-    && apt-get purge -y \
-        libvips-dev \
-    && apt-get -y autoremove \
+    && apt-get install -y --no-install-recommends libvips42 \
     && apt-get clean \
     && rm -r /var/lib/apt/lists/*
 
@@ -98,8 +81,8 @@ RUN LC_ALL=C.UTF-8 apt-get update \
         PyExcelerate==0.6.7 \
         Pillow==10.2.0 \
     && pip3 install --no-cache-dir --break-system-packages --index-url https://download.pytorch.org/whl/cpu \
-        torch==2.1.* \
-        torchvision==0.16.* \
+        torch==2.2.* \
+        torchvision==0.17.* \
     && apt-get purge -y \
         python3-pip \
     && apt-get -y autoremove \

.env.example

@@ -8,7 +8,17 @@ APP_DEBUG=true
 APP_URL="http://localhost:8000"
 APP_TIMEZONE="Europe/Berlin"
 
+APP_LOCALE=en
+APP_FALLBACK_LOCALE=en
+APP_FAKER_LOCALE=en_US
+
+APP_MAINTENANCE_DRIVER=file
+# APP_MAINTENANCE_STORE=database
+
+BCRYPT_ROUNDS=12
+
 LOG_CHANNEL=single
+LOG_STACK=single
 LOG_DEPRECATIONS_CHANNEL=null
 LOG_LEVEL=debug
 
@@ -40,23 +50,29 @@ MIX_PUSHER_APP_KEY="${PUSHER_APP_KEY}"
 #HTTP_PROXY=host:port
 
 # normally you don't have to edit these
-CACHE_DRIVER="file"
-FILESYSTEM_DISK=local
 SESSION_DRIVER="file"
 SESSION_LIFETIME=120
 SESSION_SECURE_COOKIE=false
-QUEUE_CONNECTION="database"
+SESSION_ENCRYPT=false
+SESSION_PATH=/
+SESSION_DOMAIN=null
+
+BROADCAST_CONNECTION=log
+FILESYSTEM_DISK=local
+QUEUE_CONNECTION=database
+
+CACHE_STORE=file
+CACHE_PREFIX=
 
 MEMCACHED_HOST=127.0.0.1
 
+REDIS_CLIENT=phpredis
 REDIS_HOST="127.0.0.1"
 REDIS_PASSWORD=null
 REDIS_PORT=6379
 
-# see config/mail.php for what drivers are available
-# default is the PHP mail function which doesn't require any credentials
-MAIL_MAILER="log"
-MAIL_HOST="smtp.mailtrap.io"
+MAIL_MAILER=log
+MAIL_HOST=127.0.0.1
 MAIL_PORT=2525
 MAIL_USERNAME=null
 MAIL_PASSWORD=null

.github/workflows/lint.yml

@@ -35,7 +35,7 @@ jobs:
     - name: Setup PHP
       uses: shivammathur/setup-php@v2
       with:
-        php-version: '8.1'
+        php-version: '8.2'
 
     - uses: actions/checkout@v1
       with:
@@ -50,8 +50,8 @@ jobs:
     - name: Set testing key
       run: echo "APP_KEY=base64:STZFA4bQKDjE2mlpRPmsJ/okG0eCh4RHd9BghtZeYmQ=" >> .env
 
-    - name: Run Psalm
-      run: composer lint
+    - name: Run Linter
+      run: composer lint -- --error-format=github
 
   cs-php:
 
@@ -61,7 +61,7 @@ jobs:
     - name: Setup PHP
       uses: shivammathur/setup-php@v2
       with:
-        php-version: '8.1'
+        php-version: '8.2'
         tools: cs2pr
 
     - uses: actions/checkout@v1

.gitignore

@@ -8,6 +8,8 @@
 /public/vendor
 /storage/*.key
 /storage/largo_patches
+/storage/metadata
+/storage/pending-metadata
 /vendor
 .env
 .env.backup

.php-cs-fixer.php

@@ -14,6 +14,7 @@
     ->ignoreVCS(true);
 
 return (new PhpCsFixer\Config())
+    ->setParallelConfig(PhpCsFixer\Runner\Parallel\ParallelConfigFactory::detect())
     ->setRules([
         '@PSR2' => true,
         'ordered_imports' => true,

DEVELOPING.md

@@ -7,14 +7,15 @@ To develop BIIGLE on your local machine you can use Docker containers. This way
 First, install the following software:
 
 - PHP >= 8.0
-- [Docker](https://docs.docker.com/install/)
+- [Docker Engine](https://docs.docker.com/engine/install/)
 - [Docker Compose](https://docs.docker.com/compose/install/)
 - [Composer](https://getcomposer.org/doc/00-intro.md#installation-linux-unix-macos)
 - Recommended: The `unzip` tool
 
-On Linux: Make sure to add your user to the new `docker` group with `sudo usermod -aG docker $(whoami)`, then log out and back in. Otherwise you have to call all `docker` or `docker compose` commands with `sudo`.
+> [!IMPORTANT]  
+> The link above points to Docker Engine on purpose. Docker Desktop (on Linux) may have problems mounting the filesystem with the correct permissions.
 
-**Note:** Older versions of Docker Compose used the `docker-compose` command. Newer versions use `docker compose`.
+On Linux: Make sure to add your user to the new `docker` group with `sudo usermod -aG docker $(whoami)`, then log out and back in. Otherwise you have to call all `docker` or `docker compose` commands with `sudo`.
 
 Now you can proceed with the development setup:
 

app/Annotation.php

@@ -11,6 +11,11 @@
 /**
  * An image annotation is a region of an image that can be labeled by the users.
  * It consists of one or many points and has a specific shape.
+ *
+ * @property int $id
+ * @property array $points
+ * @property string $created_at
+ * @property int $shape_id
  */
 abstract class Annotation extends Model implements AnnotationContract
 {
@@ -19,7 +24,7 @@ abstract class Annotation extends Model implements AnnotationContract
     /**
      * The attributes excluded from the model's JSON form.
      *
-     * @var array
+     * @var array<int, string>
      */
     protected $hidden = [
         'pivot',
@@ -28,7 +33,7 @@ abstract class Annotation extends Model implements AnnotationContract
     /**
      * The attributes that should be casted to native types.
      *
-     * @var array
+     * @var array<string, string>
      */
     protected $casts = [
         'points' => 'array',
@@ -40,7 +45,7 @@ abstract class Annotation extends Model implements AnnotationContract
      * @param \Illuminate\Database\Query\Builder $query
      * @param User $user The user to whom the restrictions should apply ('own' user)
      *
-     * @return \Illuminate\Database\Eloquent\Builder
+     * @return \Illuminate\Database\Query\Builder
      */
     public function scopeVisibleFor($query, User $user)
     {
@@ -73,7 +78,7 @@ public function scopeVisibleFor($query, User $user)
      * @param \Illuminate\Database\Query\Builder $query
      * @param Label $label
      *
-     * @return \Illuminate\Database\Eloquent\Builder
+     * @return \Illuminate\Database\Query\Builder
      */
     public function scopeWithLabel($query, Label $label)
     {
@@ -93,7 +98,7 @@ public function scopeWithLabel($query, Label $label)
      * @param \Illuminate\Database\Query\Builder $query
      * @param AnnotationSession $session
      * @param User $user The user to whom the restrictions should apply ('own' user)
-     * @return \Illuminate\Database\Eloquent\Builder
+     * @return \Illuminate\Database\Query\Builder
      */
     public function scopeAllowedBySession($query, AnnotationSession $session, User $user)
     {
@@ -153,14 +158,14 @@ public function scopeAllowedBySession($query, AnnotationSession $session, User $
     /**
      * The file, this annotation belongs to.
      *
-     * @return \Illuminate\Database\Eloquent\Relations\BelongsTo
+     * @return \Illuminate\Database\Eloquent\Relations\BelongsTo<covariant VolumeFile, covariant Annotation>
      */
     abstract public function file();
 
     /**
      * The labels, this annotation got assigned by the users.
      *
-     * @return \Illuminate\Database\Eloquent\Relations\HasMany
+     * @return \Illuminate\Database\Eloquent\Relations\HasMany<covariant AnnotationLabel>
      */
     abstract public function labels();
 
@@ -174,7 +179,7 @@ abstract public function getFileIdAttribute();
     /**
      * The shape of this annotation.
      *
-     * @return \Illuminate\Database\Eloquent\Relations\BelongsTo
+     * @return \Illuminate\Database\Eloquent\Relations\BelongsTo<Shape, Annotation>
      */
     public function shape()
     {