diff --git a/requirements.txt b/.docker/requirements.txt similarity index 51% rename from requirements.txt rename to .docker/requirements.txt index 5f46be82d..285820e6d 100644 --- a/requirements.txt +++ b/.docker/requirements.txt @@ -1,10 +1,13 @@ # This file is just used to get security alerts from GitHub. Make sure the versions match -# in .docker/worker.dockerfile. -numpy==1.22.* +# in worker.dockerfile. +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==10.0.1 +Pillow==10.2.0 Shapely==1.8.1 +torch==2.1.* +torchvision==0.16.* +pandas==1.5.3 diff --git a/.docker/worker.dockerfile b/.docker/worker.dockerfile index 3f22309f5..5339ed683 100644 --- a/.docker/worker.dockerfile +++ b/.docker/worker.dockerfile @@ -1,32 +1,37 @@ -# 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 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="$OPENCV_VERSION" + python3-numpy \ + python3-opencv \ + python3-scipy \ + python3-sklearn \ + python3-matplotlib \ + python3-shapely \ + python3-pandas \ + && apt-get -y autoremove \ + && apt-get clean \ + && rm -r /var/lib/apt/lists/* RUN ln -s "$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$(nproc) \ exif \ pcntl \ @@ -35,15 +40,29 @@ RUN apk add --no-cache \ pgsql \ soap \ zip \ - && apk del --purge .build-deps + && apt-get purge -y \ + libxml2-dev \ + libzip-dev \ + libpq-dev \ + && apt-get -y autoremove \ + && apt-get clean \ + && rm -r /var/lib/apt/lists/* # Configure proxy if there is any. See: https://stackoverflow.com/a/2266500/1796523 RUN [ -z "$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 \ @@ -53,70 +72,38 @@ 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 \ - && apk add --no-cache \ - expat \ - glib \ - libgsf \ - libjpeg-turbo \ - libpng \ - tiff \ - && 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==10.0.1 \ - && apk del --purge .build-deps \ - && rm -rf /var/cache/apk/* + 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.* \ + && apt-get purge -y \ + python3-pip \ + && apt-get -y autoremove \ + && apt-get clean \ + && rm -r /var/lib/apt/lists/* WORKDIR /var/www diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 000000000..62d13e938 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,26 @@ +version: 2 +updates: + - package-ecosystem: pip + directory: "/.docker" + schedule: + interval: "weekly" + # Disable version updates + open-pull-requests-limit: 0 + - package-ecosystem: composer + directory: "/" + schedule: + interval: "weekly" + # Disable version updates + open-pull-requests-limit: 0 + - package-ecosystem: npm + directory: "/" + schedule: + interval: "weekly" + # Disable version updates + open-pull-requests-limit: 0 + - package-ecosystem: github-actions + directory: "/" + schedule: + interval: "weekly" + # Disable version updates + open-pull-requests-limit: 0 diff --git a/.github/workflows/update-schema.yml b/.github/workflows/update-schema.yml index 46ea35c70..c117d1cab 100644 --- a/.github/workflows/update-schema.yml +++ b/.github/workflows/update-schema.yml @@ -16,7 +16,7 @@ jobs: - name: Trigger schema update run: | curl -X POST --fail \ - -H "Authorization: token ${{ secrets.TOKEN }}" \ + -H "Authorization: token ${{ secrets.BIIGLE_SCHEMA_API_TOKEN }}" \ -H "Content-Type: application/json" \ --data '{"event_type": "build_application"}' \ https://api.github.com/repos/biigle/schema/dispatches diff --git a/app/Console/Commands/NewUser.php b/app/Console/Commands/NewUser.php index 1059b6b1e..785d503c2 100644 --- a/app/Console/Commands/NewUser.php +++ b/app/Console/Commands/NewUser.php @@ -39,6 +39,8 @@ public function handle() if ($this->confirm('Should the user be global admin? [y|N]')) { $u->role_id = Role::adminId(); + } else { + $u->role_id = Role::editorId(); } if ($this->confirm('Do you wish to auto-generate a password? [y|N]')) { diff --git a/app/Events/AnnotationLabelAttached.php b/app/Events/AnnotationLabelAttached.php new file mode 100644 index 000000000..c710c9991 --- /dev/null +++ b/app/Events/AnnotationLabelAttached.php @@ -0,0 +1,17 @@ +annotation); + AnnotationLabelAttached::dispatch($annotationLabel); + return response($annotationLabel, 201); } catch (QueryException $e) { // Although we check for existence above, this error happened some time. diff --git a/app/Http/Controllers/Api/VideoAnnotationController.php b/app/Http/Controllers/Api/VideoAnnotationController.php index 8e2972122..ff6a17446 100644 --- a/app/Http/Controllers/Api/VideoAnnotationController.php +++ b/app/Http/Controllers/Api/VideoAnnotationController.php @@ -240,6 +240,7 @@ public function store(StoreVideoAnnotation $request) $queue = config('videos.track_object_queue'); Queue::pushOn($queue, new TrackObject($annotation, $request->user())); Cache::increment(TrackObject::getRateLimitCacheKey($request->user())); + $annotation->trackingJobLimitReached = $currentJobs === ($maxJobs - 1); } $annotation->load('labels.label', 'labels.user'); diff --git a/app/Http/Controllers/Api/VideoAnnotationLabelController.php b/app/Http/Controllers/Api/VideoAnnotationLabelController.php index c949988c7..377e3be1b 100644 --- a/app/Http/Controllers/Api/VideoAnnotationLabelController.php +++ b/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 $e) { // Although we check for existence above, this error happened some time. diff --git a/app/Http/Requests/StoreVolume.php b/app/Http/Requests/StoreVolume.php index 0536b53b0..ae34feb48 100644 --- a/app/Http/Requests/StoreVolume.php +++ b/app/Http/Requests/StoreVolume.php @@ -48,7 +48,7 @@ public function rules() return [ 'name' => 'required|max:512', 'media_type' => ['filled', Rule::in(array_keys(MediaType::INSTANCES))], - 'url' => ['required', 'max:256', new VolumeUrl], + 'url' => ['required', 'string', 'max:256', new VolumeUrl], 'files' => [ 'required', 'array', diff --git a/app/Http/Requests/UpdateVolume.php b/app/Http/Requests/UpdateVolume.php index c9be93624..d1ad2c6b3 100644 --- a/app/Http/Requests/UpdateVolume.php +++ b/app/Http/Requests/UpdateVolume.php @@ -37,7 +37,7 @@ public function rules() { return [ 'name' => 'filled|max:512', - 'url' => ['filled', new VolumeUrl], + 'url' => ['filled', 'string', 'max:256', new VolumeUrl], 'handle' => ['nullable', 'max:256', new Handle], ]; } diff --git a/app/Jobs/CloneImagesOrVideos.php b/app/Jobs/CloneImagesOrVideos.php index f087975d4..8af39fd47 100644 --- a/app/Jobs/CloneImagesOrVideos.php +++ b/app/Jobs/CloneImagesOrVideos.php @@ -8,8 +8,8 @@ use Biigle\ImageAnnotation; use Biigle\ImageAnnotationLabel; use Biigle\ImageLabel; -use Biigle\Modules\Largo\Jobs\GenerateImageAnnotationPatch; -use Biigle\Modules\Largo\Jobs\GenerateVideoAnnotationPatch; +use Biigle\Modules\Largo\Jobs\ProcessAnnotatedImage; +use Biigle\Modules\Largo\Jobs\ProcessAnnotatedVideo; use Biigle\Project; use Biigle\Traits\ChecksMetadataStrings; use Biigle\Video; @@ -144,10 +144,10 @@ public function handle() if ($volume->hasIfdo()) { $this->copyIfdoFile($volume->id, $copy->id); } - $copy->save(); - $copy->creating_async = false; + $copy->save(); + event('volume.cloned', [$copy->id]); }); @@ -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($delay) ->onQueue(config('largo.generate_annotation_patch_queue')); - }, 1000, 'video_annotations.id', 'id'); + }); } } @@ -251,6 +253,7 @@ private function copyImageAnnotation($volume, $copy, $selectedFileIds, $selected } $chunkSize = 100; + $parameterLimit = 10000; $newImageIds = $copy->images()->orderBy('id')->pluck('id'); $volume->images() ->with([ @@ -265,7 +268,7 @@ private function copyImageAnnotation($volume, $copy, $selectedFileIds, $selected $newImageIds, $chunkSize, $usedAnnotationIds, - $selectedLabelIds + $parameterLimit, ) { $insertData = []; $chunkNewImageIds = []; @@ -283,7 +286,8 @@ private function copyImageAnnotation($volume, $copy, $selectedFileIds, $selected } } - ImageAnnotation::insert($insertData); + collect($insertData)->chunk($parameterLimit)->each(fn ($chunk) => ImageAnnotation::insert($chunk->toArray())); + // Get the IDs of all newly inserted annotations. Ordering is essential. $newAnnotationIds = ImageAnnotation::whereIn('image_id', $chunkNewImageIds) ->orderBy('id') @@ -300,7 +304,8 @@ private function copyImageAnnotation($volume, $copy, $selectedFileIds, $selected } } } - ImageAnnotationLabel::insert($insertData); + collect($insertData)->chunk($parameterLimit)->each(fn ($chunk) => ImageAnnotationLabel::insert($chunk->toArray())); + }); } @@ -408,6 +413,7 @@ private function copyVideoAnnotation($volume, $copy, $selectedFileIds, $selected } $chunkSize = 100; + $parameterLimit = 10000; $newVideoIds = $copy->videos()->orderBy('id')->pluck('id'); $volume->videos() ->with([ @@ -422,7 +428,7 @@ private function copyVideoAnnotation($volume, $copy, $selectedFileIds, $selected $newVideoIds, $chunkSize, $usedAnnotationIds, - $selectedLabelIds + $parameterLimit, ) { $insertData = []; $chunkNewVideoIds = []; @@ -440,7 +446,9 @@ private function copyVideoAnnotation($volume, $copy, $selectedFileIds, $selected } } - VideoAnnotation::insert($insertData); + collect($insertData)->chunk($parameterLimit)->each(fn ($chunk) => VideoAnnotation::insert($chunk->toArray())); + + // Get the IDs of all newly inserted annotations. Ordering is essential. $newAnnotationIds = VideoAnnotation::whereIn('video_id', $chunkNewVideoIds) ->orderBy('id') @@ -457,7 +465,8 @@ private function copyVideoAnnotation($volume, $copy, $selectedFileIds, $selected } } } - VideoAnnotationLabel::insert($insertData); + collect($insertData)->chunk($parameterLimit)->each(fn ($chunk) => VideoAnnotationLabel::insert($chunk->toArray())); + }); } diff --git a/app/Jobs/TileSingleImage.php b/app/Jobs/TileSingleImage.php index a6c8cda11..f0f262379 100644 --- a/app/Jobs/TileSingleImage.php +++ b/app/Jobs/TileSingleImage.php @@ -51,6 +51,7 @@ public function __construct(Image $image) { $this->image = $image; $this->tempPath = config('image.tiles.tmp_dir')."/{$image->uuid}"; + $this->queue = config('image.tiles.queue'); } /** diff --git a/app/VideoAnnotation.php b/app/VideoAnnotation.php index f3bde3df5..a8bb6b9c1 100644 --- a/app/VideoAnnotation.php +++ b/app/VideoAnnotation.php @@ -105,7 +105,8 @@ public function validatePoints(array $points = []) throw new Exception('The number of key frames does not match the number of annotation coordinates.'); } - array_map([$this, 'parent::validatePoints'], $this->points); + // Gaps are represented as empty arrays + array_map(function ($point) { if (count($point)) { parent::validatePoints($point); } }, $this->points); } /** diff --git a/composer.lock b/composer.lock index 2f0a46f09..5d38d8d5a 100644 --- a/composer.lock +++ b/composer.lock @@ -62,16 +62,16 @@ }, { "name": "biigle/laravel-file-cache", - "version": "v4.5.0", + "version": "v4.5.2", "source": { "type": "git", "url": "https://github.com/biigle/laravel-file-cache.git", - "reference": "02bef6d4431a748c86d401064b4cd4fada97507d" + "reference": "9881936f67f81b40bc2974d0bbe07577547e57b2" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/biigle/laravel-file-cache/zipball/02bef6d4431a748c86d401064b4cd4fada97507d", - "reference": "02bef6d4431a748c86d401064b4cd4fada97507d", + "url": "https://api.github.com/repos/biigle/laravel-file-cache/zipball/9881936f67f81b40bc2974d0bbe07577547e57b2", + "reference": "9881936f67f81b40bc2974d0bbe07577547e57b2", "shasum": "" }, "require": { @@ -115,9 +115,9 @@ "description": "Fetch and cache files from local filesystem, cloud storage or public webservers in Laravel", "support": { "issues": "https://github.com/biigle/laravel-file-cache/issues", - "source": "https://github.com/biigle/laravel-file-cache/tree/v4.5.0" + "source": "https://github.com/biigle/laravel-file-cache/tree/v4.5.2" }, - "time": "2023-09-27T14:12:32+00:00" + "time": "2024-02-21T14:50:23+00:00" }, { "name": "brick/math", @@ -176,16 +176,16 @@ }, { "name": "carbonphp/carbon-doctrine-types", - "version": "2.0.0", + "version": "2.1.0", "source": { "type": "git", "url": "https://github.com/CarbonPHP/carbon-doctrine-types.git", - "reference": "67a77972b9f398ae7068dabacc39c08aeee170d5" + "reference": "99f76ffa36cce3b70a4a6abce41dba15ca2e84cb" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/CarbonPHP/carbon-doctrine-types/zipball/67a77972b9f398ae7068dabacc39c08aeee170d5", - "reference": "67a77972b9f398ae7068dabacc39c08aeee170d5", + "url": "https://api.github.com/repos/CarbonPHP/carbon-doctrine-types/zipball/99f76ffa36cce3b70a4a6abce41dba15ca2e84cb", + "reference": "99f76ffa36cce3b70a4a6abce41dba15ca2e84cb", "shasum": "" }, "require": { @@ -225,7 +225,7 @@ ], "support": { "issues": "https://github.com/CarbonPHP/carbon-doctrine-types/issues", - "source": "https://github.com/CarbonPHP/carbon-doctrine-types/tree/2.0.0" + "source": "https://github.com/CarbonPHP/carbon-doctrine-types/tree/2.1.0" }, "funding": [ { @@ -241,7 +241,7 @@ "type": "tidelift" } ], - "time": "2023-10-01T14:29:01+00:00" + "time": "2023-12-11T17:09:12+00:00" }, { "name": "dasprid/enum", @@ -463,16 +463,16 @@ }, { "name": "doctrine/dbal", - "version": "3.7.2", + "version": "3.8.2", "source": { "type": "git", "url": "https://github.com/doctrine/dbal.git", - "reference": "0ac3c270590e54910715e9a1a044cc368df282b2" + "reference": "a19a1d05ca211f41089dffcc387733a6875196cb" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/doctrine/dbal/zipball/0ac3c270590e54910715e9a1a044cc368df282b2", - "reference": "0ac3c270590e54910715e9a1a044cc368df282b2", + "url": "https://api.github.com/repos/doctrine/dbal/zipball/a19a1d05ca211f41089dffcc387733a6875196cb", + "reference": "a19a1d05ca211f41089dffcc387733a6875196cb", "shasum": "" }, "require": { @@ -488,14 +488,14 @@ "doctrine/coding-standard": "12.0.0", "fig/log-test": "^1", "jetbrains/phpstorm-stubs": "2023.1", - "phpstan/phpstan": "1.10.42", + "phpstan/phpstan": "1.10.57", "phpstan/phpstan-strict-rules": "^1.5", - "phpunit/phpunit": "9.6.13", + "phpunit/phpunit": "9.6.16", "psalm/plugin-phpunit": "0.18.4", "slevomat/coding-standard": "8.13.1", - "squizlabs/php_codesniffer": "3.7.2", - "symfony/cache": "^5.4|^6.0", - "symfony/console": "^4.4|^5.4|^6.0", + "squizlabs/php_codesniffer": 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]; diff --git a/package-lock.json b/package-lock.json index 3ccdb9948..d2834f4b6 100644 --- a/package-lock.json +++ b/package-lock.json @@ -114,9 +114,9 @@ } }, "node_modules/@babel/core/node_modules/semver": { - "version": "6.3.0", - "resolved": "https://registry.npmjs.org/semver/-/semver-6.3.0.tgz", - "integrity": "sha512-b39TBaTSfV6yBrapU89p5fKekE2m/NwnDocOVruQFS1/veMgdzuPcnOM34M6CwxW8jH/lxEa5rBoDeUwu5HHTw==", + "version": "6.3.1", + "resolved": "https://registry.npmjs.org/semver/-/semver-6.3.1.tgz", + "integrity": "sha512-BR7VvDCVHO+q2xBEWskxS6DJE1qRnb7DxzUrogb71CWoSficBxYsiAGd+Kl0mmq/MprG9yArRkyrQxTO6XjMzA==", "dev": true, "bin": { "semver": "bin/semver.js" @@ -190,9 +190,9 @@ } }, "node_modules/@babel/helper-compilation-targets/node_modules/semver": { - "version": "6.3.0", - "resolved": "https://registry.npmjs.org/semver/-/semver-6.3.0.tgz", - "integrity": "sha512-b39TBaTSfV6yBrapU89p5fKekE2m/NwnDocOVruQFS1/veMgdzuPcnOM34M6CwxW8jH/lxEa5rBoDeUwu5HHTw==", + "version": "6.3.1", + 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"^2.3.2", - "http-proxy-middleware": "^2.0.0", + "http-proxy-middleware": "^2.0.3", "ipaddr.js": "^2.0.1", + "launch-editor": "^2.6.0", "open": "^8.0.9", "p-retry": "^4.5.0", - "portfinder": "^1.0.28", + "rimraf": "^3.0.2", "schema-utils": "^4.0.0", - "selfsigned": "^2.0.0", + "selfsigned": "^2.1.1", "serve-index": "^1.9.1", - "sockjs": "^0.3.21", + "sockjs": "^0.3.24", "spdy": "^4.0.2", - "strip-ansi": "^7.0.0", "webpack-dev-middleware": "^5.3.1", - "ws": "^8.4.2" + "ws": "^8.13.0" }, "dependencies": { "ajv": { @@ -20070,12 +19771,6 @@ "fast-deep-equal": "^3.1.3" } }, - "ansi-regex": { - "version": "6.0.1", - "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.0.1.tgz", - "integrity": "sha512-n5M855fKb2SsfMIiFFoVrABHJC8QtHwVx+mHWP3QcEqBHYienj5dHSgjbxtC0WEZXYt4wcD6zrQElDPhFuZgfA==", - "dev": true - }, "json-schema-traverse": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/json-schema-traverse/-/json-schema-traverse-1.0.0.tgz", @@ -20093,15 +19788,6 @@ "ajv-formats": "^2.1.1", "ajv-keywords": "^5.0.0" } - }, - "strip-ansi": { - "version": "7.0.1", - "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-7.0.1.tgz", - "integrity": "sha512-cXNxvT8dFNRVfhVME3JAe98mkXDYN2O1l7jmcwMnOslDeESg1rF/OZMtK0nRAhiari1unG5cD4jG3rapUAkLbw==", - "dev": true, - "requires": { - "ansi-regex": "^6.0.1" - } } } }, @@ -20204,9 +19890,9 @@ "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8=" }, "ws": { - "version": "8.5.0", - "resolved": "https://registry.npmjs.org/ws/-/ws-8.5.0.tgz", - "integrity": "sha512-BWX0SWVgLPzYwF8lTzEy1egjhS4S4OEAHfsO8o65WOVsrnSRGaSiUaa9e0ggGlkMTtBlmOpEXiie9RUcBO86qg==", + "version": "8.16.0", + "resolved": "https://registry.npmjs.org/ws/-/ws-8.16.0.tgz", + "integrity": "sha512-HS0c//TP7Ina87TfiPUz1rQzMhHrl/SG2guqRcTOIUYD2q8uhUdNHZYJUaQ8aTGPzCh+c6oawMKW35nFl1dxyQ==", "dev": true, "requires": {} }, diff --git a/resources/assets/js/videos/components/videoScreen.vue b/resources/assets/js/videos/components/videoScreen.vue index 60a446f1e..1acb99237 100644 --- a/resources/assets/js/videos/components/videoScreen.vue +++ b/resources/assets/js/videos/components/videoScreen.vue @@ -59,7 +59,8 @@ icon="fa-project-diagram" title="Finish and track the point annotation" v-on:click="finishTrackAnnotation" - :disabled="cantFinishTrackAnnotation" + :disabled="cantFinishTrackAnnotation || disableJobTracking" + :loading="disableJobTracking" > { + if (tmpAnnotation.track) { + this.disableJobTracking = res.body.trackingJobLimitReached; + } + return this.addCreatedAnnotation(res); + }, (res) => { + handleErrorResponse(res); + this.disableJobTracking = res.status === 429; + }) .finally(() => { let index = this.annotations.indexOf(tmpAnnotation); if (index !== -1) { @@ -553,7 +565,11 @@ export default { .then(this.handleVideoInformationResponse) .then(this.fetchVideoContent) .catch(this.handleVideoError) - .finally(this.finishLoading); + .finally(() => { + this.finishLoading(); + // Avoid spinning wheel continuing to be displayed after moving fast through videos + this.seeking = false; + }); return promise; }, @@ -616,12 +632,14 @@ export default { handleSucceededTracking(event) { let annotation = this.annotations.find(a => a.id === event.annotation.id); if (annotation) { + this.disableJobTracking = false; annotation.finishTracking(event.annotation); } }, handleFailedTracking(event) { let annotation = this.annotations.find(a => a.id === event.annotation.id); if (annotation) { + this.disableJobTracking = false; annotation.failTracking(); } }, diff --git a/resources/assets/sass/volumes/components/_volume-image-grid-image.scss b/resources/assets/sass/volumes/components/_volume-image-grid-image.scss index 34a2d430a..1cf6be64f 100644 --- a/resources/assets/sass/volumes/components/_volume-image-grid-image.scss +++ b/resources/assets/sass/volumes/components/_volume-image-grid-image.scss @@ -2,7 +2,7 @@ position: relative; &.image-grid__image--selected { - &:before { + &:after { position: absolute; content: ''; top: $padding-base-horizontal; diff --git a/resources/views/videos/show/content.blade.php b/resources/views/videos/show/content.blade.php index b6cf7a816..9ee8d69d6 100644 --- a/resources/views/videos/show/content.blade.php +++ b/resources/views/videos/show/content.blade.php @@ -43,6 +43,7 @@ :show-prev-next="hasSiblingVideos" :has-error="hasError" :seeking="seeking" + :reached-tracked-annotation-limit="reachedTrackedAnnotationLimit" v-on:create-annotation="createAnnotation" v-on:track-annotation="trackAnnotation" v-on:split-annotation="splitAnnotation" diff --git a/tests/php/Http/Controllers/Api/ImageAnnotationLabelControllerTest.php b/tests/php/Http/Controllers/Api/ImageAnnotationLabelControllerTest.php index 1f40b3137..dba26c170 100644 --- a/tests/php/Http/Controllers/Api/ImageAnnotationLabelControllerTest.php +++ b/tests/php/Http/Controllers/Api/ImageAnnotationLabelControllerTest.php @@ -3,11 +3,13 @@ namespace Biigle\Tests\Http\Controllers\Api; use ApiTestCase; +use Biigle\Events\AnnotationLabelAttached; use Biigle\Tests\AnnotationSessionTest; use Biigle\Tests\ImageAnnotationLabelTest; use Biigle\Tests\ImageAnnotationTest; use Cache; use Carbon\Carbon; +use Illuminate\Support\Facades\Event; use Session; class ImageAnnotationLabelControllerTest extends ApiTestCase @@ -115,6 +117,7 @@ public function testStoreLegacy() public function store($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, diff --git a/tests/php/Http/Controllers/Api/VideoAnnotationControllerTest.php b/tests/php/Http/Controllers/Api/VideoAnnotationControllerTest.php index 5fecf71da..24cf0c561 100644 --- a/tests/php/Http/Controllers/Api/VideoAnnotationControllerTest.php +++ b/tests/php/Http/Controllers/Api/VideoAnnotationControllerTest.php @@ -553,6 +553,36 @@ public function testStoreAndTrackRestrictRateLimit() } + public function testTrackingJobLimit() + { + Queue::fake(); + $this->beEditor(); + $res = $this + ->postJson("/api/v1/videos/{$this->video->id}/annotations", [ + 'shape_id' => Shape::pointId(), + 'label_id' => $this->labelRoot()->id, + 'points' => [[10, 11]], + 'frames' => [0.0], + 'track' => true, + ])->assertSuccessful(); + + $this->assertEquals(1, Cache::get(TrackObject::getRateLimitCacheKey($this->editor()))); + $this->assertFalse($res->json()['trackingJobLimitReached']); + + Cache::set(TrackObject::getRateLimitCacheKey($this->editor()), 9); + $res = $this + ->postJson("/api/v1/videos/{$this->video->id}/annotations", [ + 'shape_id' => Shape::pointId(), + 'label_id' => $this->labelRoot()->id, + 'points' => [[10, 11]], + 'frames' => [0.0], + 'track' => true, + ])->assertSuccessful(); + + $this->assertEquals(10, Cache::get(TrackObject::getRateLimitCacheKey($this->editor()))); + $this->assertTrue($res->json()['trackingJobLimitReached']); + } + public function testStoreWholeFrameAnnotation() { $this->beEditor(); diff --git a/tests/php/Http/Controllers/Api/VideoAnnotationLabelControllerTest.php b/tests/php/Http/Controllers/Api/VideoAnnotationLabelControllerTest.php index 055e8f1b9..353d7e04d 100644 --- a/tests/php/Http/Controllers/Api/VideoAnnotationLabelControllerTest.php +++ b/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", [ diff --git a/tests/php/Http/Controllers/Api/VolumeControllerTest.php b/tests/php/Http/Controllers/Api/VolumeControllerTest.php index e3c59b237..44c8cdc43 100644 --- a/tests/php/Http/Controllers/Api/VolumeControllerTest.php +++ b/tests/php/Http/Controllers/Api/VolumeControllerTest.php @@ -186,6 +186,25 @@ public function testUpdateUrl() Queue::assertPushed(ProcessNewVolumeFiles::class); } + public function testUpdateInvalidUrl() + { + $volume = $this->volume(); + + config(['volumes.admin_storage_disks' => ['admin-test']]); + $disk = Storage::fake('admin-test'); + $disk->put('aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/file.txt', 'abc'); + + $this->beGlobalAdmin(); + + // invalid url (>256 characters) + $response = $this->json('PUT', '/api/v1/volumes/'.$volume->id, [ + 'url' => 'admin-test://aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa', + ])->assertStatus(422); + + $this->assertEquals('The url must not be greater than 256 characters.', $response->exception->getMessage()); + Queue::assertNothingPushed(); + } + public function testUpdateUrlProviderDenylist() { $this->beAdmin(); diff --git a/tests/php/Jobs/CloneImagesOrVideosTest.php b/tests/php/Jobs/CloneImagesOrVideosTest.php index 8da61a120..568bdd8f0 100644 --- a/tests/php/Jobs/CloneImagesOrVideosTest.php +++ b/tests/php/Jobs/CloneImagesOrVideosTest.php @@ -5,8 +5,8 @@ use Biigle\Jobs\CloneImagesOrVideos; use Biigle\Jobs\ProcessNewVolumeFiles; use Biigle\MediaType; -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\Tests\ImageAnnotationLabelTest; use Biigle\Tests\ImageAnnotationTest; use Biigle\Tests\ImageLabelTest; @@ -32,6 +32,9 @@ public function testCloneImageVolume() $volume = $this->volume([ 'created_at' => '2022-11-09 14:37:00', 'updated_at' => '2022-11-09 14:37:00', + 'attrs' => [ + 'creating_async' => true, + ], ])->fresh(); // Use fresh() to load even the null fields. $copy = $volume->replicate(); @@ -63,6 +66,7 @@ public function testCloneImageVolume() $this->assertNotEquals($volume->created_at, $copy->created_at); $this->assertNotEquals($volume->updated_at, $copy->updated_at); $this->assertEmpty($copy->images()->first()->labels()->get()); + $this->assertFalse($copy->creating_async); $ignore = ['id', 'created_at', 'updated_at']; $this->assertEquals( @@ -78,6 +82,9 @@ public function testCloneVideoVolume() 'created_at' => '2022-01-09 14:37:00', 'updated_at' => '2022-01-09 14:37:00', 'media_type_id' => MediaType::videoId(), + 'attrs' => [ + 'creating_async' => true, + ], ])->fresh(); // Use fresh() to load even the null fields. $copy = $volume->replicate(); $copy->save(); @@ -104,6 +111,7 @@ public function testCloneVideoVolume() $copy = $project->volumes()->first(); $this->assertEmpty($copy->videos()->first()->labels()->get()); + $this->assertFalse($copy->creating_async); } public function testCloneVolumeImages() @@ -616,13 +624,13 @@ public function testHandleVolumeImages() (new CloneImagesOrVideos($request, $copy))->handle(); Queue::assertPushed(ProcessNewVolumeFiles::class); - Queue::assertNotPushed(GenerateImageAnnotationPatch::class); + Queue::assertNotPushed(ProcessAnnotatedImage::class); } public function testHandleImageAnnotationPatches() { - if (!class_exists(GenerateImageAnnotationPatch::class)) { - $this->markTestSkipped('Requires '.GenerateImageAnnotationPatch::class); + if (!class_exists(ProcessAnnotatedImage::class)) { + $this->markTestSkipped('Requires '.ProcessAnnotatedImage::class); } // The target project. @@ -647,15 +655,15 @@ public function testHandleImageAnnotationPatches() ]); (new CloneImagesOrVideos($request, $copy))->handle(); - // One job for the creation of the annotation and one job for GenerateImageAnnotationPatch + // One job for the creation of the annotation and one job for ProcessAnnotatedImage Queue::assertPushed(ProcessNewVolumeFiles::class); - Queue::assertPushed(GenerateImageAnnotationPatch::class); + Queue::assertPushed(ProcessAnnotatedImage::class); } public function testHandleVideoAnnotationPatches() { - if (!class_exists(GenerateVideoAnnotationPatch::class)) { - $this->markTestSkipped('Requires '.GenerateVideoAnnotationPatch::class); + if (!class_exists(ProcessAnnotatedVideo::class)) { + $this->markTestSkipped('Requires '.ProcessAnnotatedVideo::class); } // The target project. @@ -680,8 +688,8 @@ public function testHandleVideoAnnotationPatches() ]); (new CloneImagesOrVideos($request, $copy))->handle(); - // One job for the creation of the annotation and one job for GenerateVideoAnnotationPatch + // One job for the creation of the annotation and one job for ProcessAnnotatedVideo Queue::assertPushed(ProcessNewVolumeFiles::class); - Queue::assertPushed(GenerateVideoAnnotationPatch::class); + Queue::assertPushed(ProcessAnnotatedVideo::class); } } diff --git a/tests/php/Jobs/TileSingleImageTest.php b/tests/php/Jobs/TileSingleImageTest.php index 54512cc07..7eed98310 100644 --- a/tests/php/Jobs/TileSingleImageTest.php +++ b/tests/php/Jobs/TileSingleImageTest.php @@ -49,6 +49,14 @@ public function testUploadToStorage() File::deleteDirectory($job->tempPath); } } + + public function testQueue() + { + config(['image.tiles.queue' => 'myqueue']); + $image = ImageTest::create(); + $job = new TileSingleImageStub($image); + $this->assertEquals('myqueue', $job->queue); + } } class TileSingleImageStub extends TileSingleImage diff --git a/tests/php/VideoAnnotationTest.php b/tests/php/VideoAnnotationTest.php index 2c2aac66e..d2339cb3a 100644 --- a/tests/php/VideoAnnotationTest.php +++ b/tests/php/VideoAnnotationTest.php @@ -49,6 +49,14 @@ public function testValidatePointsFramesMismatch() $this->model->validatePoints(); } + public function testValidatePointsWithGap() + { + $this->expectNotToPerformAssertions(); + $this->model->points = [[10, 10], [], [20, 20]]; + $this->model->frames = [0.0, null, 1.0]; + $this->model->validatePoints(); + } + public function testValidatePointsPoint() { $this->model->shape_id = Shape::pointId();