Merge pull request #730 from biigle/largo-sim-sort

Largo sort

.docker/requirements.txt

@@ -1,10 +1,12 @@
 # This file is just used to get security alerts from GitHub. Make sure the versions match
 # in worker.dockerfile.
-numpy==1.22.*
+numpy==1.24.*
 opencv-contrib-python-headless==4.6.0
-scipy==1.10.0
-scikit-learn
-matplotlib==3.5.2
+scipy==1.10.*
+scikit-learn==1.2.*
+matplotlib==3.6.*
 PyExcelerate==0.6.7
 Pillow==10.2.0
 Shapely==1.8.1
+torch==2.1.*
+torchvision==0.16.*

.docker/worker.dockerfile

@@ -1,32 +1,36 @@
-# PHP 8.1.13
-#FROM php:8.1-alpine
-FROM php@sha256:f9e31f22bdd89c1334a03db5c8800a5f3b1e1fe042d470adccf58a29672c6202
+# PHP 8.1.27
+# FROM php:8.1
+FROM php@sha256:9b5dfb7deef3e48d67b2599e4d3967bb3ece19fd5ba09cb8e7ee10f5facf36e0
 MAINTAINER Martin Zurowietz <[email protected]>
 LABEL org.opencontainers.image.source https://github.com/biigle/core
 
-ARG OPENCV_VERSION=4.6.0-r3
-RUN apk add --no-cache \
-        eigen \
+RUN LC_ALL=C.UTF-8 apt-get update \
+    && apt-get install -y --no-install-recommends \
         ffmpeg \
-        lapack \
-        openblas \
-        py3-numpy \
         python3 \
-        py3-opencv="$OPENCV_VERSION"
+        python3-numpy \
+        python3-opencv \
+        python3-scipy \
+        python3-sklearn \
+        python3-matplotlib \
+        python3-shapely \
+    && apt-get -y autoremove \
+    && apt-get clean \
+    && 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"
 
-RUN apk add --no-cache \
-        libxml2 \
-        libzip \
-        openssl \
-        postgresql \
-    && apk add --no-cache --virtual .build-deps \
+RUN LC_ALL=C.UTF-8 apt-get update \
+    && apt-get install -y --no-install-recommends \
         libxml2-dev \
         libzip-dev \
-        postgresql-dev \
-    && docker-php-ext-configure pgsql -with-pgsql=/usr/local/pgsql \
+        libpq-dev \
+    && apt-get install -y --no-install-recommends \
+        libxml2 \
+        libzip4 \
+        postgresql-client \
+    && docker-php-ext-configure pgsql -with-pgsql=/usr/bin/pgsql \
     && docker-php-ext-install -j$(nproc) \
         exif \
         pcntl \
@@ -35,15 +39,29 @@ RUN apk add --no-cache \
         pgsql \
         soap \
         zip \
-    && apk del --purge .build-deps
+    && apt-get purge -y \
+        libxml2-dev \
+        libzip-dev \
+        libpq-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 apk add --no-cache yaml \
-    && apk add --no-cache --virtual .build-deps g++ make autoconf yaml-dev \
+
+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 \
-    && docker-php-ext-enable yaml \
-    && apk del --purge .build-deps
+    && 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
 RUN curl -L -o /tmp/redis.tar.gz https://github.com/phpredis/phpredis/archive/${PHPREDIS_VERSION}.tar.gz \
@@ -53,72 +71,38 @@ RUN curl -L -o /tmp/redis.tar.gz https://github.com/phpredis/phpredis/archive/${
     && mv phpredis-${PHPREDIS_VERSION} /usr/src/php/ext/redis \
     && docker-php-ext-install -j$(nproc) redis
 
-ENV PKG_CONFIG_PATH="/usr/local/lib/pkgconfig:${PKG_CONFIG_PATH}"
-# Install vips from source because the apk package does not have dzsave support! Install
-# libvips and the vips PHP extension in one go so the *-dev dependencies are reused.
-ARG LIBVIPS_VERSION=8.12.2
-ARG PHP_VIPS_EXT_VERSION=1.0.13
-RUN apk add --no-cache --virtual .build-deps \
-        autoconf \
-        automake \
-        build-base \
-        expat-dev \
-        glib-dev \
-        libgsf-dev \
-        libjpeg-turbo-dev \
-        libpng-dev \
-        tiff-dev \
-        librsvg-dev \
-    && apk add --no-cache \
-        expat \
-        glib \
-        libgsf \
-        libjpeg-turbo \
-        libpng \
-        tiff \
-        librsvg \
-    && cd /tmp \
-    && curl -L https://github.com/libvips/libvips/releases/download/v${LIBVIPS_VERSION}/vips-${LIBVIPS_VERSION}.tar.gz -o vips-${LIBVIPS_VERSION}.tar.gz \
-    && tar -xzf vips-${LIBVIPS_VERSION}.tar.gz \
-    && cd vips-${LIBVIPS_VERSION} \
-    && ./configure \
-        --without-python \
-        --enable-debug=no \
-        --disable-dependency-tracking \
-        --disable-static \
-    && make -j $(nproc) \
-    && make -s install-strip \
-    && cd /tmp \
-    && curl -L https://github.com/libvips/php-vips-ext/raw/master/vips-${PHP_VIPS_EXT_VERSION}.tgz -o  vips-${PHP_VIPS_EXT_VERSION}.tgz \
-    && echo '' | pecl install vips-${PHP_VIPS_EXT_VERSION}.tgz \
+# 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 \
-    && rm -r /tmp/* \
-    && apk del --purge .build-deps \
-    && rm -rf /var/cache/apk/*
+    && apt-get purge -y \
+        libvips-dev \
+    && apt-get -y autoremove \
+    && apt-get clean \
+    && rm -r /var/lib/apt/lists/*
 
 # Unset proxy configuration again.
 RUN [ -z "$HTTP_PROXY" ] || pear config-set http_proxy ""
 
-# Other Python dependencies are added with the OpenCV build above.
-RUN apk add --no-cache py3-scipy py3-scikit-learn py3-matplotlib py3-shapely
-
-# Set this library path so the Python modules are linked correctly.
-# See: https://github.com/python-pillow/Pillow/issues/1763#issuecomment-204252397
-ENV LIBRARY_PATH=/lib:/usr/lib
-# Install Python dependencies. Note that these also depend on some image processing libs
-# that were installed along with vips.
-RUN apk add --no-cache --virtual .build-deps \
-        python3-dev \
-        py3-pip \
-        py3-wheel \
-        build-base \
-        libjpeg-turbo-dev \
-        libpng-dev \
-    && pip3 install --no-cache-dir \
+RUN LC_ALL=C.UTF-8 apt-get update \
+    && apt-get install -y --no-install-recommends \
+        python3-pip \
+    && pip3 install --no-cache-dir --break-system-packages \
         PyExcelerate==0.6.7 \
         Pillow==10.2.0 \
-    && apk del --purge .build-deps \
-    && rm -rf /var/cache/apk/*
+    && pip3 install --no-cache-dir --break-system-packages --index-url https://download.pytorch.org/whl/cpu \
+        torch==2.1.* \
+        torchvision==0.16.* \
+    && apt-get purge -y \
+        python3-pip \
+    && apt-get -y autoremove \
+    && apt-get clean \
+    && rm -r /var/lib/apt/lists/*
 
 WORKDIR /var/www
 

app/Events/AnnotationLabelAttached.php

@@ -0,0 +1,17 @@
+<?php
+
+namespace Biigle\Events;
+
+use Biigle\AnnotationLabel;
+use Illuminate\Contracts\Events\ShouldDispatchAfterCommit;
+use Illuminate\Foundation\Events\Dispatchable;
+
+class AnnotationLabelAttached implements ShouldDispatchAfterCommit
+{
+    use Dispatchable;
+
+    public function __construct(public AnnotationLabel $annotationLabel)
+    {
+        //
+    }
+}

app/Http/Controllers/Api/ImageAnnotationLabelController.php

@@ -2,6 +2,7 @@
 
 namespace Biigle\Http\Controllers\Api;
 
+use Biigle\Events\AnnotationLabelAttached;
 use Biigle\Http\Requests\StoreImageAnnotationLabel;
 use Biigle\ImageAnnotation;
 use Biigle\ImageAnnotationLabel;
@@ -184,6 +185,8 @@ public function store(StoreImageAnnotationLabel $request)
             // should not be returned
             unset($annotationLabel->annotation);
 
+            AnnotationLabelAttached::dispatch($annotationLabel);
+
             return response($annotationLabel, 201);
         } catch (QueryException $e) {
             // Although we check for existence above, this error happened some time.

app/Http/Controllers/Api/VideoAnnotationLabelController.php

@@ -2,6 +2,7 @@
 
 namespace Biigle\Http\Controllers\Api;
 
+use Biigle\Events\AnnotationLabelAttached;
 use Biigle\Http\Requests\DestroyVideoAnnotationLabel;
 use Biigle\Http\Requests\StoreVideoAnnotationLabel;
 use Biigle\VideoAnnotationLabel;
@@ -65,6 +66,8 @@ public function store(StoreVideoAnnotationLabel $request)
             // should not be returned
             unset($annotationLabel->annotation);
 
+            AnnotationLabelAttached::dispatch($annotationLabel);
+
             return response($annotationLabel, 201);
         } catch (QueryException $e) {
             // Although we check for existence above, this error happened some time.

app/Jobs/CloneImagesOrVideos.php

@@ -8,8 +8,8 @@
 use Biigle\ImageAnnotation;
 use Biigle\ImageAnnotationLabel;
 use Biigle\ImageLabel;
-use Biigle\Modules\Largo\Jobs\GenerateImageAnnotationPatch;
-use Biigle\Modules\Largo\Jobs\GenerateVideoAnnotationPatch;
+use Biigle\Modules\Largo\Jobs\ProcessAnnotatedImage;
+use Biigle\Modules\Largo\Jobs\ProcessAnnotatedVideo;
 use Biigle\Project;
 use Biigle\Traits\ChecksMetadataStrings;
 use Biigle\Video;
@@ -162,24 +162,26 @@ public function postProcessCloning($volume)
     {
         ProcessNewVolumeFiles::dispatch($volume);
 
-        if (class_exists(GenerateImageAnnotationPatch::class)) {
-            ImageAnnotation::join('images', 'images.id', '=', 'image_annotations.image_id')
-                ->where('images.volume_id', "=", $volume->id)
-                ->select('image_annotations.id')
-                ->eachById(function ($annotation) {
-                    GenerateImageAnnotationPatch::dispatch($annotation)
+        // Give the ProcessNewVolumeFiles job a head start so the file thumbnails are
+        // generated (mostly) before the annotation thumbnails.
+        $delay = now()->addSeconds(30);
+
+        if (class_exists(ProcessAnnotatedImage::class)) {
+            $volume->images()->whereHas('annotations')
+                ->eachById(function ($image) use ($delay) {
+                    ProcessAnnotatedImage::dispatch($image)
+                        ->delay($delay)
                         ->onQueue(config('largo.generate_annotation_patch_queue'));
-                }, 1000, 'image_annotations.id', 'id');
+                });
         }
 
-        if (class_exists(GenerateVideoAnnotationPatch::class)) {
-            VideoAnnotation::join('videos', 'videos.id', '=', 'video_annotations.video_id')
-                ->where('videos.volume_id', "=", $volume->id)
-                ->select('video_annotations.id')
-                ->eachById(function ($annotation) {
-                    GenerateVideoAnnotationPatch::dispatch($annotation)
+        if (class_exists(ProcessAnnotatedVideo::class)) {
+            $volume->videos()
+                ->whereHas('annotations')->eachById(function ($video) use ($delay) {
+                    ProcessAnnotatedVideo::dispatch($video)
+                        ->delay($delay)
                         ->onQueue(config('largo.generate_annotation_patch_queue'));
-                }, 1000, 'video_annotations.id', 'id');
+                });
         }
     }
 

tests/php/Http/Controllers/Api/ImageAnnotationLabelControllerTest.php

@@ -3,11 +3,13 @@
 namespace Biigle\Tests\Http\Controllers\Api;
 
 use ApiTestCase;
+use Biigle\Events\AnnotationLabelAttached;
 use Biigle\Tests\AnnotationSessionTest;
 use Biigle\Tests\ImageAnnotationLabelTest;
 use Biigle\Tests\ImageAnnotationTest;
 use Cache;
 use Carbon\Carbon;
+use Illuminate\Support\Facades\Event;
 use Session;
 
 class ImageAnnotationLabelControllerTest extends ApiTestCase
@@ -115,6 +117,7 @@ public function testStoreLegacy()
 
     public function store($url)
     {
+        Event::fake();
         $id = $this->annotation->id;
         $this->doTestApiRoute('POST', "{$url}/{$id}/labels");
 
@@ -150,12 +153,16 @@ public function store($url)
         $response->assertStatus(201);
         $this->assertEquals(1, $this->annotation->labels()->count());
 
+        Event::assertDispatched(AnnotationLabelAttached::class);
+
         $this->beAdmin();
         $response = $this->json('POST', "{$url}/{$id}/labels", [
             'label_id' => $this->labelRoot()->id,
             'confidence' => 0.1,
         ]);
         $response->assertStatus(201);
+
+        Event::assertDispatched(AnnotationLabelAttached::class);
         $this->assertEquals(2, $this->annotation->labels()->count());
         $response->assertJsonFragment([
             'id' => $this->labelRoot()->id,

tests/php/Http/Controllers/Api/VideoAnnotationLabelControllerTest.php

@@ -3,11 +3,13 @@
 namespace Biigle\Tests\Http\Controllers\Api;
 
 use ApiTestCase;
+use Biigle\Events\AnnotationLabelAttached;
 use Biigle\MediaType;
 use Biigle\Tests\LabelTest;
 use Biigle\Tests\VideoAnnotationLabelTest;
 use Biigle\Tests\VideoAnnotationTest;
 use Biigle\Tests\VideoTest;
+use Illuminate\Support\Facades\Event;
 
 class VideoAnnotationLabelControllerTest extends ApiTestCase
 {
@@ -20,6 +22,7 @@ public function setUp(): void
 
     public function testStore()
     {
+        Event::fake();
         $annotation = VideoAnnotationTest::create(['video_id' => $this->video->id]);
         $id = $annotation->id;
 
@@ -51,6 +54,7 @@ public function testStore()
         $this->assertNotNull($label);
         $this->assertEquals($this->labelRoot()->id, $label->label_id);
         $this->assertEquals($this->editor()->id, $label->user_id);
+        Event::assertDispatched(AnnotationLabelAttached::class);
 
         $this
             ->postJson("api/v1/video-annotations/{$id}/labels", [