diff --git a/Project.toml b/Project.toml
index 1065fe0451fa0df87b736929708f1fe57df28e07..1b5dd3db1655b9b9c4b897d22d63728e669243f6 100644
--- a/Project.toml
+++ b/Project.toml
@@ -8,7 +8,6 @@ Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
DocOpt = "968ba79b-81e4-546f-ab3a-2eecfa62a9db"
Formatting = "59287772-0a20-5a39-b81b-1366585eb4c0"
-JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
JSServe = "824d6782-a2ef-11e9-3a09-e5662e0c26f9"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
diff --git a/recipes/Dockerfile b/recipes/Dockerfile
index 86a4d58c2d737ad5b3c3f9e9e35ca70587e2b236..e4f2cdffd4d3bc1a801a57fb7b30620b28480023 100644
--- a/recipes/Dockerfile
+++ b/recipes/Dockerfile
@@ -1,33 +1,36 @@
-FROM ubuntu:focal
-
-RUN apt-get update &&\
- apt-get install -y wget git &&\
- wget https://raw.githubusercontent.com/abelsiqueira/jill/main/jill.sh &&\
- bash jill.sh -y &&\
- rm jill.sh
+FROM julia:1.7.3-bullseye
ENV DIRNAME app
-
ARG BRANCH=main
-RUN git clone --depth 1 --single-branch -b $BRANCH https://gitlab.pasteur.fr/nyx/larvatagger.jl $DIRNAME &&\
- cd $DIRNAME &&\
- julia --project=. -e 'using Pkg; Pkg.instantiate()' &&\
- ln -s $(pwd)/scripts/larvatagger.jl /bin
+RUN apt-get update && apt-get install -y \
+ git \
+ && rm -rf /var/lib/apt/lists/* \
+ && git clone --depth 1 --single-branch -b $BRANCH https://gitlab.pasteur.fr/nyx/larvatagger.jl $DIRNAME \
+ && julia --project=$DIRNAME -e 'using Pkg; Pkg.instantiate()' \
+ && ln -s /$DIRNAME/scripts/larvatagger.jl /bin
+
+COPY test/precompile.* test/data_sample* $DIRNAME/test/
-COPY ./extra $DIRNAME/
+ARG TIMEZONE=UTC
+RUN ln -snf /usr/share/zoneinfo/$TIMEZONE /etc/localtime \
+ && echo $TIMEZONE > /etc/timezone \
+ && $DIRNAME/test/precompile.sh --shallow \
+ && rm -f test/data_sample*
+
+COPY external $DIRNAME/
ARG BACKEND
-RUN if [ "$BACKEND" = "MaggotUBA_20220418" ]; then \
- apt-get install -y python3-pip &&\
- python3 -m pip install poetry &&\
- cd $DIRNAME &&\
- git clone --depth 1 --single-branch -b 20220418 https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter MaggotUBA &&\
- cd MaggotUBA &&\
- python3 -m poetry remove structured-temporal-convolution &&\
- python3 -m poetry add ../structured-temporal-convolution &&\
- python3 -m poetry install; \
+RUN if [ "$BACKEND" = "MaggotUBA/20220418" ]; then \
+ apt-get update && apt-get install -y \
+ python3-pip \
+ && python3 -m pip install poetry \
+ && cd $DIRNAME \
+ && git clone --depth 1 --single-branch -b 20220418 https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter MaggotUBA \
+ && cd MaggotUBA \
+ && python3 -m poetry remove structured-temporal-convolution \
+ && python3 -m poetry add ../structured-temporal-convolution \
+ && python3 -m poetry install \
+ && rm -rf /var/lib/apt/lists/*; \
fi
-WORKDIR $DIRNAME
-
ENTRYPOINT ["larvatagger.jl"]
diff --git a/recipes/Dockerfile.local b/recipes/Dockerfile.local
index 62e6538767cba74e7039c767a382a3a94461f619..2e44d254ecec6aba6ff3576bf68662400f7c2e2e 100644
--- a/recipes/Dockerfile.local
+++ b/recipes/Dockerfile.local
@@ -1,17 +1,14 @@
-FROM ubuntu:jammy
-
-RUN apt-get update &&\
- apt-get install -y wget git &&\
- wget https://raw.githubusercontent.com/abelsiqueira/jill/main/jill.sh &&\
- bash jill.sh -y &&\
- rm jill.sh
+FROM julia:1.7.3-bullseye
COPY src /app/src/
COPY scripts /app/scripts/
COPY Project.toml Manifest.toml /app/
-RUN cd /app &&\
- julia --project=. -e 'using Pkg; Pkg.instantiate()' &&\
+RUN apt-get update && apt-get install -y \
+ git \
+ && rm -rf /var/lib/apt/lists/* \
+ && cd /app \
+ && julia --project=. -e 'using Pkg; Pkg.instantiate()' \
ln -s /app/scripts/larvatagger.jl /bin
ENTRYPOINT ["larvatagger.jl"]
diff --git a/scripts/larvatagger.sh b/scripts/larvatagger.sh
index d8a4c38f72d7af42a092f1c65a60d2fb438da279..f7ad15726b0880d508019c1ea29a9aa03441cb78 100755
--- a/scripts/larvatagger.sh
+++ b/scripts/larvatagger.sh
@@ -12,13 +12,13 @@ if ! [ -f recipes/Dockerfile ]; then
echo "the build command can only be run from the project root directory"
exit 1
fi
-mkdir -p ./extra
+mkdir -p ./external
while ! [ -z "$1" ]; do
if [ "$1" == "--dev" -o "$1" == "--stable" ]; then
BUILD=$1; shift
elif [ "$1" == "--get-backend" ]; then
-BACKEND="--build-arg BACKEND=MaggotUBA_20220418"; shift
-cd ./extra
+DOCKER_ARGS="--build-arg BACKEND=MaggotUBA/20220418 "; shift
+cd ./external
if [ -d structured-temporal-convolution ]; then
cd structured-temporal-convolution; git pull; cd ..
else
@@ -27,28 +27,32 @@ fi
cd ..
else
echo "argument not supported: $1"; shift
-#rm -rf ./extra
+#rm -rf ./external
exit 1
fi
done
+DOCKER_ARGS="--build-arg TIMEZONE=$(cat /etc/timezone) $DOCKER_ARGS"
if [ "$BUILD" == "--dev" ]; then
-docker build -t "${LARVATAGGER_IMAGE}:dev" -f recipes/Dockerfile.local $BACKEND .
+docker build -t "${LARVATAGGER_IMAGE}:dev" -f recipes/Dockerfile.local ${DOCKER_ARGS}.
elif [ "$BUILD" == "--stable" ]; then
-docker build -t "$LARVATAGGER_IMAGE:stable" -f recipes/Dockerfile $BACKEND .
+docker build -t "${LARVATAGGER_IMAGE}:stable" -f recipes/Dockerfile ${DOCKER_ARGS}.
else
-docker build -t "$LARVATAGGER_IMAGE:latest" -f recipes/Dockerfile $BACKEND --build-arg BRANCH=dev .
+docker build -t "${LARVATAGGER_IMAGE}:latest" -f recipes/Dockerfile ${DOCKER_ARGS}--build-arg BRANCH=dev .
fi
-#rm -rf ./extra
+#rm -rf ./external
;;
open)
-ARGS="-p 9284:9284"
-if ! [ -z "$LARVATAGGER_PORT" -o "$LARVATAGGER_PORT" == "9284" ]; then
-ARGS="-p $LARVATAGGER_PORT:9284 $ARGS"
+if [ -z "$LARVATAGGER_PORT" -o "$LARVATAGGER_PORT" == "9284" ]; then
+DOCKER_ARGS="-p 9284:9284"
+TAGGER_ARGS=
+else
+DOCKER_ARGS="-p $LARVATAGGER_PORT:$LARVATAGGER_PORT"
+TAGGER_ARGS="--port=$LARVATAGGER_PORT"
fi
file=$1; shift
-exec docker run -iv $(pwd):/data $ARGS "$LARVATAGGER_IMAGE" open "/data/$file" $@
+exec docker run -iv $(pwd):/data $DOCKER_ARGS "$LARVATAGGER_IMAGE" open "/data/$file" $TAGGER_ARGS $@
;;
import)
diff --git a/test/precompile.jl b/test/precompile.jl
new file mode 100644
index 0000000000000000000000000000000000000000..00f22103b040bac3057e735a3243dbeb5e81a5dd
--- /dev/null
+++ b/test/precompile.jl
@@ -0,0 +1,24 @@
+using LarvaTagger
+using JSServe: Server
+
+datafile = joinpath(@__DIR__, "data_sample")
+ispath(datafile) || exit()
+
+app = larvaeditor(datafile)
+srv = Server(app, "0.0.0.0", 9284)
+
+if isempty(ARGS)
+
+ using HTTP
+ HTTP.request(:GET, "http://127.0.0.1:9284")
+
+elseif ARGS == ["--electron"]
+
+ using Blink
+ win = Window(async=false)
+ loadurl(win, "http://127.0.0.1:9284")
+ close(win)
+
+end
+
+close(srv)
diff --git a/test/precompile.sh b/test/precompile.sh
new file mode 100755
index 0000000000000000000000000000000000000000..4bda55d90a36c4c16fc0a0f0333f1ea86ca4f38b
--- /dev/null
+++ b/test/precompile.sh
@@ -0,0 +1,27 @@
+#!/bin/sh
+root=$(dirname $(dirname $0))
+if [ "$1" = "--shallow" ]; then
+shift
+echo "Project root: $root"
+julia --project=$root -e 'using Pkg; Pkg.add("HTTP")'
+echo "[$(date +%T)] Further precompiling..."
+julia --project=$root $root/test/precompile.jl
+echo "[$(date +%T)] Precompilation done"
+julia --project=$root -e 'using Pkg; Pkg.rm("HTTP")'
+else
+packages="unzip xvfb libgtk-3-0 libnss3 libxss1 libasound2"
+apt-get update
+apt-get install -y $packages
+echo "Project root: $root"
+julia --project=$root -e 'using Pkg; Pkg.add("Blink")'
+# to find out missing dependencies:
+# electron=$(julia --project=$root -e 'using Blink; println(Blink.AtomShell.electron())')
+# echo $electron
+# $electron
+echo "[$(date +%T)] Further precompiling..."
+xvfb-run julia --project=$root $root/test/precompile.jl --electron
+echo "[$(date +%T)] Precompilation done"
+julia --project=$root -e 'using Pkg; Pkg.rm("Blink")'
+apt-get autoremove -y $packages
+rm -rf /var/lib/apt/lists/*
+fi