Merge pull request #120 from fractal-analytics-platform/new-example-for-testing

New example for testing

Author: tcompa

examples/staging-full-stack/docker-compose.yml

@@ -1,4 +1,5 @@
 services:
+
   db:
     cpus: 1.0
     mem_limit: "1G"
@@ -28,16 +29,16 @@ services:
     networks:
       - fractal
 
-  server:
-    hostname: server
-    container_name: server
+  fractal-server:
+    hostname: fractal-server
+    container_name: fractal-server
     cpus: 3.0
     mem_limit: 5g
     build:
-      context: server
+      context: ./fractal-server
       dockerfile: Dockerfile
       args:
-        - FRACTAL_SERVER_VERSION=2.14.0a0
+        - FRACTAL_SERVER_VERSION=2.14.0a1
     depends_on:
       db:
         condition: service_healthy
@@ -46,22 +47,22 @@ services:
     ports:
       - 8000:8000
     healthcheck:
-      test: wget http://server:8000/api/alive/ > /dev/null 2>&1
+      test: wget http://fractal-server:8000/api/alive/ > /dev/null 2>&1
       interval: 5s
       timeout: 2s
       retries: 5
     networks:
       - fractal
 
-  web:
+  fractal-web:
     container_name: fractal-web
     build:
-      context: ./web
+      context: ./fractal-web
       dockerfile: Dockerfile
       args:
-        - FRACTAL_WEB_VERSION=1.17.0-a0
+        - FRACTAL_WEB_VERSION=1.17.0-a1
     depends_on:
-      server:
+      fractal-server:
         condition: service_healthy
     ports:
       - 5173:5173
@@ -75,7 +76,7 @@ services:
       args:
         - FRACTAL_CLIENT_VERSION=2.7.1
     depends_on:
-      server:
+      fractal-server:
         condition: service_healthy
     volumes:
       - data:/data
@@ -97,7 +98,7 @@ services:
     container_name: vizarr
     image: ghcr.io/fractal-analytics-platform/fractal-vizarr-viewer:stable
     environment:
-      - FRACTAL_SERVER_URL=http://server:8000
+      - FRACTAL_SERVER_URL=http://fractal-server:8000
       - AUTHORIZATION_SCHEME=fractal-server
     ports:
       - 3000:3000

examples/staging-full-stack/server/.fractal_server.env examples/staging-full-stack/fractal-server/.fractal_server.env

@@ -5,13 +5,11 @@ FRACTAL_RUNNER_BACKEND=local
 FRACTAL_TASKS_DIR=/data/app/Tasks
 FRACTAL_RUNNER_WORKING_BASE_DIR=/data/app/Artifacts
 
-
 FRACTAL_TASKS_PYTHON_DEFAULT_VERSION="3.10"
 FRACTAL_TASKS_PYTHON_3_10=/usr/bin/python3
 
 FRACTAL_VIEWER_AUTHORIZATION_SCHEME=viewer-paths
 
-
 JWT_EXPIRE_SECONDS=84600
 
 POSTGRES_HOST=fractal-db

examples/staging-full-stack/server/Dockerfile examples/staging-full-stack/fractal-server/Dockerfile

@@ -1,8 +1,9 @@
-FROM ghcr.io/fractal-analytics-platform/ubuntu22-slurm:0.1
+FROM ubuntu:22.04
 
-ARG FRACTAL_SERVER_VERSION
+RUN apt update -y
+RUN apt install -y wget vim less python3 python3-pip python3-venv
 
-RUN echo "Install fractal-server ${FRACTAL_SERVER_VERSION}"
+ARG FRACTAL_SERVER_VERSION
 RUN pip3 install fractal-server==${FRACTAL_SERVER_VERSION}
 
 COPY run_server.sh ./

examples/staging-full-stack/server/run_server.sh examples/staging-full-stack/fractal-server/run_server.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+set -e
 
 fractalctl set-db
 

examples/staging-full-stack/web/Dockerfile examples/staging-full-stack/fractal-web/Dockerfile

@@ -7,7 +7,7 @@ ENV NODE_MAJOR_VERSION=20
 
 RUN wget -qO- "https://github.com/fractal-analytics-platform/fractal-web/releases/download/v${FRACTAL_WEB_VERSION}/node-${NODE_MAJOR_VERSION}-fractal-web-v${FRACTAL_WEB_VERSION}.tar.gz" | tar -xz
 
-ENV FRACTAL_SERVER_HOST=http://server:8000
+ENV FRACTAL_SERVER_HOST=http://fractal-server:8000
 ENV PUBLIC_FRACTAL_VIZARR_VIEWER_URL=http://localhost:3000/vizarr
 ENV PUBLIC_FRACTAL_ADMIN_SUPPORT_EMAIL=
 ENV PUBLIC_OAUTH_CLIENT_NAME=

examples/staging-full-stack/makefile

@@ -1,16 +1,18 @@
-# Auxiliary targets
-
 up:
 	docker compose up
 
 build:
-	docker compose build --progress=plain
+	docker compose --progress=plain build
 
 build-no-cache:
-	docker compose build --no-cache --progress=plain
+	docker compose --progress=plain build --no-cache
 
 clean:
 	docker compose down -v --timeout 1
 
 clean-with-volumes:
 	docker compose down --volumes -v --timeout 1
+
+
+all-from-scratch: clean-with-volumes build-no-cache
+	docker compose up

examples/staging-full-stack/scripts/.fractal.env

@@ -1,12 +1,12 @@
 FROM python:3.11-slim
 
-RUN apt update
+RUN apt update -y
 RUN apt install -y unzip wget
 
 ARG FRACTAL_CLIENT_VERSION
 RUN pip install fractal-client==${FRACTAL_CLIENT_VERSION}
 
-ENV FRACTAL_SERVER=http://server:8000
+ENV FRACTAL_SERVER=http://fractal-server:8000
 ENV [email protected]
 ENV FRACTAL_PASSWORD=1234
 

examples/staging-full-stack/scripts/.gitignore

@@ -1,11 +1,14 @@
 #!/bin/bash
 
+set -e
+
 # Update user
 FRACTAL_USER_ID=$(fractal --batch user whoami)
 fractal user edit "$FRACTAL_USER_ID" --new-project-dir /data/zarrs/test01
 
 # Assuming that group 1 is the ALL
 ALL_GROUP_ID=1
+# shellcheck disable=SC2046
 if [ $(fractal group get "$ALL_GROUP_ID" | grep name | grep All) != "0" ]; then
     echo "User group with id $ALL_GROUP_ID is not the 'All' group. Exit."
     exit 1
@@ -14,6 +17,7 @@ fractal group update "$ALL_GROUP_ID" --new-viewer-paths /data
 
 # Download test zarr data
 mkdir -p /data/zarrs
+# shellcheck disable=SC2164
 cd /data/zarrs/
 wget --quiet https://zenodo.org/records/10424292/files/20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr.zip
 unzip -q 20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr.zip
@@ -22,6 +26,7 @@ rm -r 20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr.zip __MACOSX
 # Download test image data
 mkdir -p /data/images
 mkdir /data/images/10.5281_zenodo.8287221
+# shellcheck disable=SC2164
 cd /data/images/10.5281_zenodo.8287221
 wget --quiet https://zenodo.org/api/records/8287221/files-archive
 mv files-archive files-archive.zip